Repository: aidenlab/Juicebox Branch: master Commit: 9697464526f6 Files: 472 Total size: 91.9 MB Directory structure: gitextract_y7dv046v/ ├── .github/ │ └── ISSUE_TEMPLATE/ │ ├── bug_report.md │ ├── custom.md │ └── feature_request.md ├── .gitignore ├── .idea/ │ ├── artifacts/ │ │ ├── Juicebox.xml │ │ └── JuicerTools.xml │ ├── compiler.xml │ ├── copyright/ │ │ ├── Juicebox.xml │ │ └── profiles_settings.xml │ ├── encodings.xml │ ├── jarRepositories.xml │ ├── kotlinc.xml │ ├── libraries/ │ │ ├── KotlinJavaRuntime.xml │ │ ├── broadinstitute.xml │ │ ├── general.xml │ │ ├── jargs.xml │ │ ├── jcuda.xml │ │ ├── jfreechart_1_0_19.xml │ │ ├── log4j_core_2_11_0.xml │ │ └── npy.xml │ ├── misc.xml │ ├── modules.xml │ ├── scopes/ │ │ ├── Juicebox_Source.xml │ │ └── scope_settings.xml │ ├── uiDesigner.xml │ └── vcs.xml ├── CODE_OF_CONDUCT.md ├── CONTRIBUTING.md ├── HiCFormatV8.md ├── HiC_format_v7.docx ├── JuiceboxIcon.icns ├── Juicer.README ├── LICENSE ├── README.md ├── benchmark.sh ├── build.xml ├── data/ │ └── inter.hic ├── internalREADME.md ├── juicebox.properties ├── l4j/ │ ├── config.xml │ ├── config_bcm.xml │ ├── config_broad.xml │ ├── config_fix_for_Erez.xml │ └── config_nosplash.xml ├── lib/ │ ├── appbundler-1.0.jar │ ├── broadinstitute/ │ │ ├── htsjdk-1.139.jar │ │ ├── igv.jar │ │ └── log4j-core-2.11.0.jar │ ├── general/ │ │ ├── VectorGraphics2D-0.11.jar │ │ ├── VectorGraphics2D.LGPL.LICENSE │ │ ├── commons-math3-3.6.1.jar │ │ ├── guava-18.0.jar │ │ ├── hic_tools.3.30.00.jar │ │ ├── jahmm-0.6.1.jar │ │ ├── jargs.jar │ │ ├── jfreechart-1.0.19.jar │ │ ├── jsi1.1.jar │ │ └── npy.jar │ ├── jarbundler-core-3.3.0.jar │ ├── jcuda/ │ │ ├── jcuda-0.7.0.jar │ │ ├── jcuda-0.8.0.jar │ │ ├── jcuda-natives-0.8.0-apple-x86_64.jar │ │ ├── jcuda-natives-0.8.0-linux-ppc_64.jar │ │ ├── jcuda-natives-0.8.0-linux-x86_64.jar │ │ └── jcudaUtils-0.0.4.jar │ ├── kotlin/ │ │ ├── kotlin-reflect-sources.jar │ │ ├── kotlin-reflect.jar │ │ ├── kotlin-stdlib-jdk7-sources.jar │ │ ├── kotlin-stdlib-jdk7.jar │ │ ├── kotlin-stdlib-jdk8-sources.jar │ │ ├── kotlin-stdlib-jdk8.jar │ │ ├── kotlin-stdlib-sources.jar │ │ ├── kotlin-stdlib.jar │ │ ├── kotlin-test-sources.jar │ │ └── kotlin-test.jar │ └── universalJavaApplicationStub ├── package.sh └── src/ ├── images/ │ └── manifest.mf ├── juicebox/ │ ├── CommandBroadcaster.java │ ├── CommandExecutor.java │ ├── CommandListener.java │ ├── Context.java │ ├── DirectoryManager.java │ ├── HiC.java │ ├── HiCGlobals.java │ ├── IGVUtils.java │ ├── MainWindow.java │ ├── ProcessHelper.java │ ├── Unused.java │ ├── assembly/ │ │ ├── AssemblyFileExporter.java │ │ ├── AssemblyFileImporter.java │ │ ├── AssemblyHeatmapHandler.java │ │ ├── AssemblyOperationExecutor.java │ │ ├── AssemblyScaffoldHandler.java │ │ ├── AssemblyStateTracker.java │ │ ├── IGVFeatureCopy.java │ │ ├── OneDimAssemblyTrackLifter.java │ │ ├── PsfFileExporter.java │ │ ├── PsfFileImporter.java │ │ └── Scaffold.java │ ├── data/ │ │ ├── AbstractDatasetReader.java │ │ ├── BinReader.java │ │ ├── Block.java │ │ ├── BlockIndex.java │ │ ├── ChromosomeHandler.java │ │ ├── CombinedDatasetReader.java │ │ ├── CombinedExpectedValueFunction.java │ │ ├── ContactRecord.java │ │ ├── CustomMatrixZoomData.java │ │ ├── Dataset.java │ │ ├── DatasetReader.java │ │ ├── DatasetReaderFactory.java │ │ ├── DatasetReaderV2.java │ │ ├── DynamicBlock.java │ │ ├── DynamicBlockIndex.java │ │ ├── DynamicMatrixZoomData.java │ │ ├── ExpectedValueFunction.java │ │ ├── ExpectedValueFunctionImpl.java │ │ ├── GeneLocation.java │ │ ├── HiCFileLoader.java │ │ ├── HiCFileTools.java │ │ ├── Matrix.java │ │ ├── MatrixZoomData.java │ │ ├── NormFactorMapReader.java │ │ ├── NormalizationVector.java │ │ ├── ZoomAction.java │ │ ├── ZoomActionTracker.java │ │ ├── anchor/ │ │ │ ├── BEDTools.java │ │ │ ├── GenericLocus.java │ │ │ ├── GenericLocusParser.java │ │ │ ├── GenericLocusTools.java │ │ │ ├── MotifAnchor.java │ │ │ ├── MotifAnchorParser.java │ │ │ └── MotifAnchorTools.java │ │ ├── basics/ │ │ │ ├── Chromosome.java │ │ │ ├── ListOfDoubleArrays.java │ │ │ ├── ListOfFloatArrays.java │ │ │ └── ListOfIntArrays.java │ │ ├── binary_file_layout.txt │ │ ├── censoring/ │ │ │ ├── CustomMZDRegionHandler.java │ │ │ ├── OneDimSearchUtils.java │ │ │ ├── OneDimTrackCensoring.java │ │ │ └── RegionPair.java │ │ ├── feature/ │ │ │ ├── Feature.java │ │ │ ├── FeatureFilter.java │ │ │ ├── FeatureFunction.java │ │ │ └── GenomeWideList.java │ │ ├── iterator/ │ │ │ ├── BigContactRecordList.java │ │ │ ├── ContactRecordIterator.java │ │ │ ├── CoupledIteratorAndOffset.java │ │ │ ├── GWIteratorContainer.java │ │ │ ├── GenomeWideIterator.java │ │ │ ├── IteratorContainer.java │ │ │ ├── ListIteratorContainer.java │ │ │ ├── ListOfListGenerator.java │ │ │ ├── ListOfListIterator.java │ │ │ ├── ListOfListIteratorContainer.java │ │ │ ├── ParallelizedListOperations.java │ │ │ └── ZDIteratorContainer.java │ │ └── v9depth/ │ │ ├── ConstantDepth.java │ │ ├── LogDepth.java │ │ └── V9Depth.java │ ├── encode/ │ │ ├── EncodeFileBrowser.java │ │ ├── EncodeFileRecord.java │ │ ├── EncodeTableModel.java │ │ ├── UCSCEncodeUtils.java │ │ ├── encode.hg18.txt │ │ ├── encode.hg19.txt │ │ ├── encode.hic.txt │ │ ├── encode.mm9.txt │ │ └── rnaChip.txt │ ├── gui/ │ │ ├── BoundsPopupMenuListener.java │ │ ├── MainMenuBar.java │ │ ├── MainViewPanel.java │ │ ├── PseudoCountEditor.java │ │ └── SuperAdapter.java │ ├── mapcolorui/ │ │ ├── BoundingBoxRenderer.java │ │ ├── ColorRangeDialog.java │ │ ├── ColorScaleHandler.java │ │ ├── CursorRenderer.java │ │ ├── Feature2DHandler.java │ │ ├── FeatureRenderer.java │ │ ├── GeneralTileManager.java │ │ ├── HeatmapClickListener.java │ │ ├── HeatmapMouseHandler.java │ │ ├── HeatmapPanel.java │ │ ├── HeatmapRenderer.java │ │ ├── HiCMapTileManager.java │ │ ├── JColorRangePanel.java │ │ ├── OEColorScale.java │ │ ├── PearsonColorScale.java │ │ ├── PearsonColorScaleEditor.java │ │ ├── RangeSlider.java │ │ ├── RangeSliderUI.java │ │ ├── ResolutionControl.java │ │ └── ThumbnailPanel.java │ ├── matrix/ │ │ ├── BasicMatrix.java │ │ ├── DiskResidentBlockMatrix.java │ │ ├── InMemoryMatrix.java │ │ ├── RealMatrixWrapper.java │ │ ├── SparseSymmetricMatrix.java │ │ ├── SparseVector.java │ │ └── SymmetricMatrix.java │ ├── state/ │ │ ├── ImportStateFileDialog.java │ │ ├── LoadStateFromXMLFile.java │ │ ├── SaveFileDialog.java │ │ ├── Slideshow.java │ │ ├── State.java │ │ ├── XMLFileHandling.java │ │ ├── XMLFileParser.java │ │ └── XMLFileWriter.java │ ├── tools/ │ │ ├── HiCTools.java │ │ ├── chrom/ │ │ │ └── sizes/ │ │ │ ├── ChromosomeSizes.java │ │ │ ├── EBV.chrom.sizes │ │ │ ├── GRCm38.chrom.sizes │ │ │ ├── Pf3D7.chrom.sizes │ │ │ ├── TAIR10.chrom.sizes │ │ │ ├── aedAeg1.chrom.sizes │ │ │ ├── anasPlat1.chrom.sizes │ │ │ ├── assembly.chrom.sizes │ │ │ ├── b37.chrom.sizes │ │ │ ├── bTaurus3.chrom.sizes │ │ │ ├── calJac3.chrom.sizes │ │ │ ├── canFam3.chrom.sizes │ │ │ ├── capHir1.chrom.sizes │ │ │ ├── ce10.chrom.sizes │ │ │ ├── dMel.chrom.sizes │ │ │ ├── dm3.chrom.sizes │ │ │ ├── dm6.chrom.sizes │ │ │ ├── equCab2.chrom.sizes │ │ │ ├── felCat8.chrom.sizes │ │ │ ├── galGal4.chrom.sizes │ │ │ ├── hg18.chrom.sizes │ │ │ ├── hg19.chrom.sizes │ │ │ ├── hg19_contig.chrom.sizes │ │ │ ├── hg38.chrom.sizes │ │ │ ├── loxAfr3.chrom.sizes │ │ │ ├── macMul1.chrom.sizes │ │ │ ├── macMulBaylor.chrom.sizes │ │ │ ├── mm10.chrom.sizes │ │ │ ├── mm9.chrom.sizes │ │ │ ├── oryCun2.chrom.sizes │ │ │ ├── oryLat2.chrom.sizes │ │ │ ├── panTro4.chrom.sizes │ │ │ ├── ratNor5.chrom.sizes │ │ │ ├── ratNor6.chrom.sizes │ │ │ ├── sCerS288c.chrom.sizes │ │ │ ├── sacCer3.chrom.sizes │ │ │ ├── spretus.chrom.sizes │ │ │ └── susScr3.chrom.sizes │ │ ├── clt/ │ │ │ ├── AggregateProcessing.java │ │ │ ├── CLTFactory.java │ │ │ ├── CommandLineParser.java │ │ │ ├── CommandLineParserForJuicer.java │ │ │ ├── JuiceboxCLT.java │ │ │ ├── JuicerCLT.java │ │ │ ├── UnitTests.java │ │ │ ├── juicer/ │ │ │ │ ├── ABCompartmentsDiff.java │ │ │ │ ├── APA.java │ │ │ │ ├── Arrowhead.java │ │ │ │ ├── CompareLists.java │ │ │ │ ├── HiCCUPS.java │ │ │ │ ├── HiCCUPS2.java │ │ │ │ ├── HiCCUPSDiff.java │ │ │ │ ├── HiCCUPSRegionHandler.java │ │ │ │ ├── HiCCUPSscores.java │ │ │ │ ├── Localizer.java │ │ │ │ ├── LoopDomains.java │ │ │ │ └── MotifFinder.java │ │ │ └── old/ │ │ │ ├── AddNorm.java │ │ │ ├── BPToFragment.java │ │ │ ├── BigWig.java │ │ │ ├── BinToPairs.java │ │ │ ├── CalcKR.java │ │ │ ├── CalcMatrixSum.java │ │ │ ├── Dump.java │ │ │ ├── Eigenvector.java │ │ │ ├── FragmentToBed.java │ │ │ ├── LibraryComplexity.java │ │ │ ├── PairsToBin.java │ │ │ ├── Pearsons.java │ │ │ ├── PreProcessing.java │ │ │ ├── SQLDatabase.java │ │ │ ├── Statistics.java │ │ │ ├── Summation.java │ │ │ └── ValidateFile.java │ │ ├── dev/ │ │ │ ├── APAvsDistance.java │ │ │ ├── ChromosomeCalculation.java │ │ │ ├── CompareVectors.java │ │ │ ├── GeneFinder.java │ │ │ ├── HiCArtMNDWriter.java │ │ │ ├── IntraChromTriple.java │ │ │ ├── MapSelectionPanel.java │ │ │ ├── ParallelizedJuicerTools.java │ │ │ ├── Private.java │ │ │ ├── RandomUtils.java │ │ │ ├── TripleCentroid.java │ │ │ └── TriplesAPA.java │ │ └── utils/ │ │ ├── Benchmark.java │ │ ├── common/ │ │ │ ├── ArrayTools.java │ │ │ ├── HiCFileUtils.java │ │ │ ├── MatrixTools.java │ │ │ ├── ShellCommandRunner.java │ │ │ ├── StatPercentile.java │ │ │ └── UNIXTools.java │ │ ├── dev/ │ │ │ ├── AFAUtils.java │ │ │ ├── LocalGenomeRegion.java │ │ │ ├── LocationType.java │ │ │ └── PearsonCorrelationMetric.java │ │ ├── juicer/ │ │ │ ├── GeneTools.java │ │ │ ├── apa/ │ │ │ │ ├── APADataStack.java │ │ │ │ ├── APAPlotter.java │ │ │ │ ├── APARegionStatistics.java │ │ │ │ └── APAUtils.java │ │ │ ├── arrowhead/ │ │ │ │ ├── ArrowheadScore.java │ │ │ │ ├── ArrowheadScoreList.java │ │ │ │ ├── BinnedScore.java │ │ │ │ ├── BlockBuster.java │ │ │ │ ├── BlockResults.java │ │ │ │ ├── CumulativeBlockResults.java │ │ │ │ ├── DynamicProgrammingUtils.java │ │ │ │ ├── HighScore.java │ │ │ │ ├── MatrixTriangles.java │ │ │ │ └── connectedcomponents/ │ │ │ │ ├── BinaryConnectedComponents.java │ │ │ │ └── IndexNode.java │ │ │ ├── hiccups/ │ │ │ │ ├── GPUController.java │ │ │ │ ├── GPUController2.java │ │ │ │ ├── GPUHelper.java │ │ │ │ ├── GPUOutputContainer.java │ │ │ │ ├── GPUOutputContainer2.java │ │ │ │ ├── GPUTesting.java │ │ │ │ ├── HiCCUPS2Kernel_1kb.cu │ │ │ │ ├── HiCCUPSConfiguration.java │ │ │ │ ├── HiCCUPSKernel.cu │ │ │ │ ├── HiCCUPSRegionContainer.java │ │ │ │ └── HiCCUPSUtils.java │ │ │ └── localizer/ │ │ │ └── LocalizerUtils.java │ │ ├── norm/ │ │ │ ├── CustomNormVectorFileHandler.java │ │ │ ├── ExternalNormalizationVectorLoader.java │ │ │ ├── GenomeWideNormalizationVectorUpdater.java │ │ │ ├── MultithreadedNormalizationVectorUpdater.java │ │ │ ├── NormVectorInfo.java │ │ │ ├── NormVectorUpdater.java │ │ │ ├── NormalizationCalculations.java │ │ │ ├── NormalizationTools.java │ │ │ ├── NormalizationVectorIndexEntry.java │ │ │ ├── NormalizationVectorUpdater.java │ │ │ ├── NormalizedSum.java │ │ │ ├── UnusedFunctions.java │ │ │ ├── ZeroScale.java │ │ │ └── final2/ │ │ │ ├── FinalScale.java │ │ │ └── ScaleThreadObject.java │ │ └── original/ │ │ ├── BigWigUtils.java │ │ ├── BlockPP.java │ │ ├── BlockQueue.java │ │ ├── BlockQueueFB.java │ │ ├── BlockQueueMem.java │ │ ├── Chunk.java │ │ ├── ContactCount.java │ │ ├── ExpectedValueCalculation.java │ │ ├── FragmentCalculation.java │ │ ├── HiCDBUtils.java │ │ ├── IndexEntry.java │ │ ├── LargeIndexEntry.java │ │ ├── MTIndexHandler.java │ │ ├── MatrixPP.java │ │ ├── MatrixZoomDataPP.java │ │ ├── MultithreadedPreprocessor.java │ │ ├── MultithreadedPreprocessorHic.java │ │ ├── Preprocessor.java │ │ ├── merge/ │ │ │ ├── HiCMergeTools.java │ │ │ ├── StatsUtils.java │ │ │ └── merger/ │ │ │ ├── GraphsMerger.java │ │ │ ├── Merger.java │ │ │ ├── PairedAlignmentStatsMerger.java │ │ │ ├── SingleAlignmentStatsMerger.java │ │ │ └── StatsMerger.java │ │ ├── mnditerator/ │ │ │ ├── AlignmentPair.java │ │ │ ├── AlignmentPairLong.java │ │ │ ├── AsciiPairIterator.java │ │ │ ├── AsciiToBinConverter.java │ │ │ ├── BAMPairIterator.java │ │ │ ├── BinPairIterator.java │ │ │ ├── ComplexLineParser.java │ │ │ ├── GenericPairIterator.java │ │ │ ├── MNDFileParser.java │ │ │ ├── MNDLineParser.java │ │ │ ├── PairIterator.java │ │ │ ├── RandomAccessAsciiPairIterator.java │ │ │ ├── ShortBinPairIterator.java │ │ │ ├── SimpleAsciiPairIterator.java │ │ │ └── SimpleLineParser.java │ │ └── stats/ │ │ ├── LoneStatisticsWorker.java │ │ ├── ParallelStatistics.java │ │ ├── ParallelStatisticsWorker.java │ │ ├── StatisticsContainer.java │ │ └── StatisticsWorker.java │ ├── track/ │ │ ├── CategoryPanel.java │ │ ├── EigenvectorTrack.java │ │ ├── HiCCoverageDataSource.java │ │ ├── HiCDataAdapter.java │ │ ├── HiCDataPoint.java │ │ ├── HiCDataSource.java │ │ ├── HiCDataTrack.java │ │ ├── HiCFeatureTrack.java │ │ ├── HiCFixedGridAxis.java │ │ ├── HiCFragmentAxis.java │ │ ├── HiCGridAxis.java │ │ ├── HiCIGVDataAdapter.java │ │ ├── HiCLoadDialog.java │ │ ├── HiCTrack.java │ │ ├── HiCTrackManager.java │ │ ├── HiCWigAdapter.java │ │ ├── LoadAction.java │ │ ├── LoadEncodeAction.java │ │ ├── ResourceTree.java │ │ ├── TrackConfigDialog.java │ │ ├── TrackConfigDialog.jfd │ │ ├── TrackConfigPanel.java │ │ ├── TrackLabelPanel.java │ │ ├── TrackPanel.java │ │ ├── feature/ │ │ │ ├── AnnotationLayer.java │ │ │ ├── AnnotationLayerHandler.java │ │ │ ├── CustomAnnotationRTree2DHandler.java │ │ │ ├── Feature2D.java │ │ │ ├── Feature2DGuiContainer.java │ │ │ ├── Feature2DList.java │ │ │ ├── Feature2DParser.java │ │ │ ├── Feature2DTools.java │ │ │ ├── Feature2DWithMotif.java │ │ │ ├── FeatureFilter.java │ │ │ └── FeatureFunction.java │ │ ├── tracksMenu_GalGal5.xml │ │ ├── tracksMenu_hg19.xml │ │ ├── tracksMenu_hg38.xml │ │ ├── tracksMenu_mm10.xml │ │ └── tracksMenu_mm9.xml │ └── windowui/ │ ├── DisabledGlassPane.java │ ├── DumpDialog.java │ ├── EditFeatureAttributesDialog.java │ ├── FileDropTargetListener.java │ ├── GoToPanel.java │ ├── HiCChromosomeFigPanel.java │ ├── HiCKeyDispatcher.java │ ├── HiCLayout.java │ ├── HiCRulerPanel.java │ ├── HiCZoom.java │ ├── JBTreeCellRenderer.java │ ├── JSplitButton.java │ ├── LoadAssemblyAnnotationsDialog.java │ ├── LoadDialog.java │ ├── LoadModifiedAssemblyAnnotationsDialog.java │ ├── MatrixType.java │ ├── NormalizationHandler.java │ ├── NormalizationType.java │ ├── QCDialog.java │ ├── RecentMenu.java │ ├── SaveAssemblyDialog.java │ ├── SaveImageDialog.java │ └── layers/ │ ├── LayerPanelButtons.java │ ├── LayersPanel.java │ ├── Load2DAnnotationsDialog.java │ ├── MiniAnnotationsLayerPanel.java │ ├── PlottingStyleButton.java │ ├── SaveAnnotationsDialog.java │ ├── UnsavedAnnotationWarning.java │ └── annotations2d.txt ├── org/ │ └── tc33/ │ └── jheatchart/ │ ├── HeatChart.java │ ├── LICENSE.MD │ └── README.MD └── resources/ └── manifests/ ├── juicebox_jar/ │ └── META-INF/ │ └── MANIFEST.MF └── juicer_tools_jar/ └── META-INF/ └── MANIFEST.MF ================================================ FILE CONTENTS ================================================ ================================================ FILE: .github/ISSUE_TEMPLATE/bug_report.md ================================================ --- name: Bug report about: Create a report to help us improve title: "[BUG]" labels: bug assignees: '' --- **Describe the bug** A clear and concise description of what the bug is. **To Reproduce** Steps to reproduce the behavior: 1. 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I'm always frustrated when [...] **Describe the solution you'd like** A clear and concise description of what you want to happen. **Describe alternatives you've considered** A clear and concise description of any alternative solutions or features you've considered. **Additional context** Add any other context or screenshots about the feature request here. ================================================ FILE: .gitignore ================================================ # Created by .gitignore support plugin (hsz.mobi) *.iml .idea/workspace.xml *.DS_Store out/ .vscode ================================================ FILE: .idea/artifacts/Juicebox.xml ================================================ $PROJECT_DIR$/out/artifacts/Juicebox ================================================ FILE: .idea/artifacts/JuicerTools.xml ================================================ $PROJECT_DIR$/out/artifacts/JuicerTools ================================================ FILE: .idea/compiler.xml ================================================ ================================================ FILE: .idea/copyright/Juicebox.xml ================================================ ================================================ FILE: .idea/copyright/profiles_settings.xml ================================================ ================================================ FILE: .idea/encodings.xml ================================================ ================================================ FILE: .idea/jarRepositories.xml ================================================ ================================================ FILE: .idea/kotlinc.xml ================================================ ================================================ FILE: .idea/libraries/KotlinJavaRuntime.xml ================================================ ================================================ FILE: .idea/libraries/broadinstitute.xml ================================================ ================================================ FILE: .idea/libraries/general.xml ================================================ ================================================ FILE: .idea/libraries/jargs.xml ================================================ ================================================ FILE: .idea/libraries/jcuda.xml ================================================ ================================================ FILE: .idea/libraries/jfreechart_1_0_19.xml ================================================ ================================================ FILE: .idea/libraries/log4j_core_2_11_0.xml ================================================ ================================================ FILE: .idea/libraries/npy.xml ================================================ ================================================ FILE: .idea/misc.xml ================================================ ================================================ FILE: .idea/modules.xml ================================================ ================================================ FILE: .idea/scopes/Juicebox_Source.xml ================================================ ================================================ FILE: .idea/scopes/scope_settings.xml ================================================ ================================================ FILE: .idea/uiDesigner.xml ================================================ ================================================ FILE: .idea/vcs.xml ================================================ ================================================ FILE: CODE_OF_CONDUCT.md ================================================ # Contributor Covenant Code of Conduct ## Our Pledge In the interest of fostering an open and welcoming environment, we as contributors and maintainers pledge to making participation in our project and our community a harassment-free experience for everyone, regardless of age, body size, disability, ethnicity, sex characteristics, gender identity and expression, level of experience, education, socio-economic status, nationality, personal appearance, race, religion, or sexual identity and orientation. ## Our Standards Examples of behavior that contributes to creating a positive environment include: * Using welcoming and inclusive language * Being respectful of differing viewpoints and experiences * Gracefully accepting constructive criticism * Focusing on what is best for the community * Showing empathy towards other community members Examples of unacceptable behavior by participants include: * The use of sexualized language or imagery and unwelcome sexual attention or advances * Trolling, insulting/derogatory comments, and personal or political attacks * Public or private harassment * Publishing others' private information, such as a physical or electronic address, without explicit permission * Other conduct which could reasonably be considered inappropriate in a professional setting ## Our Responsibilities Project maintainers are responsible for clarifying the standards of acceptable behavior and are expected to take appropriate and fair corrective action in response to any instances of unacceptable behavior. Project maintainers have the right and responsibility to remove, edit, or reject comments, commits, code, wiki edits, issues, and other contributions that are not aligned to this Code of Conduct, or to ban temporarily or permanently any contributor for other behaviors that they deem inappropriate, threatening, offensive, or harmful. ## Scope This Code of Conduct applies both within project spaces and in public spaces when an individual is representing the project or its community. Examples of representing a project or community include using an official project e-mail address, posting via an official social media account, or acting as an appointed representative at an online or offline event. Representation of a project may be further defined and clarified by project maintainers. ## Enforcement Instances of abusive, harassing, or otherwise unacceptable behavior may be reported by contacting the project team at aidenlab@bcm.edu. All complaints will be reviewed and investigated and will result in a response that is deemed necessary and appropriate to the circumstances. The project team is obligated to maintain confidentiality with regard to the reporter of an incident. Further details of specific enforcement policies may be posted separately. Project maintainers who do not follow or enforce the Code of Conduct in good faith may face temporary or permanent repercussions as determined by other members of the project's leadership. ## Attribution This Code of Conduct is adapted from the [Contributor Covenant][homepage], version 1.4, available at https://www.contributor-covenant.org/version/1/4/code-of-conduct.html [homepage]: https://www.contributor-covenant.org For answers to common questions about this code of conduct, see https://www.contributor-covenant.org/faq ================================================ FILE: CONTRIBUTING.md ================================================ # Contributing to Juicebox and/or Juicebox Assembly Tools :+1::tada: First off, thanks for taking the time to contribute! :tada::+1: The following is a set of guidelines for contributing to Juicebox and its modules, which are hosted in the [Aiden Lab Repositories](https://github.com/aidenlab) on GitHub. These are mostly guidelines, not rules. Use your best judgment, and feel free to propose changes to this document in a pull request. ## Code of Conduct This project and everyone participating in it is governed by the [Juicebox Code of Conduct](CODE_OF_CONDUCT.md). By participating, you are expected to uphold this code. Please report unacceptable behavior to [aidenlab@bcm.edu](mailto:aidenlab@bcm.edu). ## I don't want to read this whole thing I just have a question!!! > **Note:** Please don't file an issue to ask a question. You'll get faster results by using our [3D-Genomics Official Forum](https://aidenlab.org/forum.html). We have an official message board where the community chimes in with helpful advice if you have questions. While we strongly suggest using the public forum so that the community at large benefits from the discussion, you can also send us an email at [aidenlab@bcm.edu](mailto:aidenlab@bcm.edu) for questions related to sensitive datasets. ## **Did you find a bug?** * **Ensure the bug was not already reported** by searching on GitHub under [Issues](https://github.com/aidenlab/Juicebox/issues). * If you're unable to find an open issue addressing the problem, [open a new one](https://github.com/aidenlab/juicebox/issues/new). Be sure to include a **title and clear description**, as much relevant information as possible, and a **code sample, executable test case, or clear set of instructions** demonstrating the expected behavior that is not occurring. ## **Did you write a patch that fixes a bug?** * Open a new GitHub pull request with the patch. * Ensure the Pull Request description clearly describes the problem and solution. Include the relevant issue number if applicable. ## **Did you fix whitespace, format code, or make a purely cosmetic patch?** We welcome changes that are cosmetic in nature and do not necessarily add anything to the stability, functionality, or testability of Juicebox. Please follow commonly practiced Java Style Guides when doing so. ## **Do you intend to add a new feature or change an existing one?** * Suggest your change by creating a Github issue! Reach out to us at [aidenlab@bcm.edu](mailto:aidenlab@bcm.edu) for advice and start writing code! ## **Do you have questions about the source code?** * Ask any question about how to use Juicebox and Juicebox Assembly Tools in the [3D Genomics Official Forum](https://aidenlab.org/forum.html). ## **Do you want to contribute to the Juicebox documentation?** * Reach out to us at [aidenlab@bcm.edu](mailto:aidenlab@bcm.edu). Juicebox and Juicebox Assembly Tools is a volunteer effort. We encourage you to pitch in and join the team! Thanks! :heart: :heart: :heart: The Center for Genome Architecture Baylor College of Medicine & Rice University ================================================ FILE: HiCFormatV8.md ================================================ # hic file format ## Structure * Header * Body * Matrix * Block * Footer * Master index * Expected value vectors ## Header |Field | Description | Type | Value | |------|------------|------|-------| |Magic|HiC magic string|String|HIC| |Version|Version number|int|8| |footerPosition|File position of the Footer section, containing the master index, expected values, and normalization vectors. |long|| |genomeId| Genome identifier (e.g. hg19, mm9, etc)| String|| |||| |nAttributes |Number of key-value pair attributes| int|| ||*List of key-value pair attributes (n = nAttributes). See notes on common attributes below.*|| |key |Attribute key| String || |value|Attribute value| String|| ||||| |nChrs| Number of chromosomes|int|| ||*List of chromosome lengths (n = nChrs)*|| |chrName |Chromosome name |String|| |chrLength| Chromosome length | int || ||||| |nBpResolutions |Number of base pair resolutions| int|| ||*List of bin sizes for bp resolution levels (n = nBpResolutions)*|| |resBP |Bin size in base pairs |int|| ||||| |nFragResolutions |Number of fragment resolutions |int|| ||*List of bin sizes for frag resolution levels (n = nFragResolutions)*|| |resFrag |Bin size in fragment units (1, 2, 5, etc)| int|| ||||| ||*List of fragment site positions per chromosome, in same order as chromosome list above (n = nChrs). This section absent if nFragResolutions = 0.*|| |nSites| Number of sites for this chromosome| int|| ||*List of sites (n = nSites)*|| |sitePosition| Site position in base pairs| int|| ## Body The **Header** section is followed immediatly by the **Body**, which containe the contact map data for each chromosome-chromosome pairing and each resolution. ### Matrix metadata This section contains metadata for the contact matrices. It is repeated for all each chromosome-chromosome pair. The master index contains an entry for each combination and is used to randomly access a specific matrix as needed. The metadata in this section includes an index for data blocks which contain the actual contact data. |Field |Description| Type| Value| |------|------------|------|-------| |chr1Idx| Index for chromosome 1. This is the index into the array of chromosomes defined in the header above. The first chromosome has index **0**.| int|| |chr2Idx| Index for chromosome 2. | int || |nResolutions |Total number of resolutions for this chromosome-chromosome pair, including base pair and fragment resolutions. |int|| ||*Resolution metadata. Repeat for each resolution. (n = nResolutions)*|| |unit| Distance unit, base-pairs or fragments |String |BP or FRAG| |resIdx |Index number for this resolution level, an Array index into the bin size list of the header, first element is **0**. | int|| |sumCounts| Sum of all counts (or scores) across all bins at current resolution.| float|| |occupiedCellCount| Total count of cells that are occupied. **Not currently used**|int|0| |percent5| Estimate of 5th percentile of counts among occupied bins. **Not currently used**|float|0| |percent95| Estimate of 95th percentile of counts among occupied bins **Not currently used**|float|0| |binSize| The bin size in base-pairs or fragments |int|| |blockSize |Dimension of each block in bins. Blocks are square, so the total number of bins is ```blockSize^2```. See description of grid strcture below|int|| |blockColumnCount|The number of columns in the grid of blocks. |int|| |blockCount|The number of blocks stored in the file. Note empty blocks are not stored.||| ||||| |*Block index. Repeat for each resolution (n = nResolutions)*|| |blockNumber |Numeric id for block. This is the linear position of the block in the grid when counted in row-major order. ```blockNumber = column * blockColumnCount + row``` where first row and column **0** |int| |blockPosition| File position of block| long| |blockSizeBytes |Size of block in bytes| int| |||| ||*Block data*|| | blocks | Compressed blocks for all matrices and resolutions. See description below. ||| #### Block A block represents a square sub-matrix of a contact map. ***Note: Blocks are indivdually compressed with ZLib*** |Field |Description| Type| Value| |------|------------|------|-------| |nRecords |Number or contact records in this block| int | |binXOffset | X offset for the contact records in this block. The binX value below is relative to this offset.|| |binYOffset | Y offset for the contact records in this block. The binX value below is relative to this offset. |useFloat | Flag indicating the ```value``` field in contact records for this block are recorded with data type ```float```. If == 1 a ```float``` is used, otherwise type is ```short```| byte | |matrixRepresentation | Representation of matrix used for the contact records. If == 1 the representation is a ```list of rows```, if == 2 ```dense```. | byte | |blockData| The block matrix data. See descriptions below, also in the notes section. ##### Block data - list of rows |Field |Description| Type| Value| |------|------------|------|-------| |rowCount | Number or rows | short || || |*rows (n = rowCount)* |rowNumber | Matrix row number, first row is ```0``` | short || |recordCount | Number of records for this row. Row is sparse, zeroes are not recorded. | short || || |*contact records (n = cellCount)*|| |binX |X axis index| short|| |value |Value (counts or score). The data type is determined by the ```useFloat``` flag above.| float : short|| ##### Block data - dense |Field |Description| Type| Value| |------|------------|------|-------| |nRecords | Number of contact records in this block. | int || |w | Width of the dense block. This can be < the blockSize if the edge columns on either side are zeroes. See discussion on block representation below | short || || |*contact records (n = nRecords)*|| |value |Value (counts or score). The data type is determined by the ```useFloat``` flag above.| float : short|| ### Footer | Field | Description| Type | Value | |------|------------|------|-------| |nBytesV5| Number of bytes for the “version 5” footer, that is everything up to the normalized expected vectors. This field (*nBytesV5*) is not included, so the total number of bytes between ```footerPosition``` and ```nNormVectors``` is ```nBytesV5 + 4```. |int|| #### Master index | Field | Description| Type | Value | |------|------------|------|-------| |nEntries| Number of index entries| int|| || ||*List of index entries (n = nEntries)*|| |key| A key constructed from the indeces of the two chromosomes for this matrix. The indeces are defined by the list of chromosomes in the header section with the first chromosome occupying index **0**|String|| |position |Position of the start of the chromosome-chromosome matrix record in bytes |long|| |size |Size of the chromosome-chromsome matrix record in bytes. This does not include the **Block** data.| int|| #### Expected value vectors | Field | Description| Type | Value | |------|------------|------|-------| |nExpectedValueVectors| Number of expected value vectors to follow. These are expected values from the non-normalized observed matrix.| int| || ||*List of expected value vectors (n = nExpectedValueVectors)*|| |unit| Bin units either FRAG or BP. |String |FRAG : BP| |binSize |Bin (grid) size for this calculation |int|| |nValues |Size of the vector| int|| || |*List of expected values (n = nValues)*| |value |Expected value| double|| |nChrScaleFactors| Number of chromosome normalization factors| int|| || ||*List of normalization factors (n = nChrScaleFactors)*|| |chrIndex| Chromosome index| int|| |chrScaleFactor| Chromosome scale factor |double|| #### Normalized expected value vectors | Field | Description| Type | Value | |------|------------|------|-------| |nNormExpectedValueVectors| Number of normalized expected value vectors to follow |int|| || |*List of normalized vectors (n = nNormExpectedValueVectors)*|| |type| Indicates type of normalization |String| VC:KR:INTER_KR:INTER_VC:GW_KR:GW_VC| |unit |Bin units either FRAG or BP. |String| FRAG : BP| |binSize| Bin (grid) size for this calculation |int|| |nValues| Size of the vector |int || || ||*List of expected values (n = nValues)*|| |value |Expected value |double|| || |nChrScaleFactors|Number of normalizatoin factos for this vector||| ||*List of normalization factors (n = nChrScaleFactors)*|| |chrIndex| Chromosome index |int || |chrScaleFactor| Chromosome scale factor |double|| #### Normalization vectors | Field | Description| Type | Value | |------|------------|------|-------| |nNormVectors| Number of normalization vectors | int|| ||*List of normalization vectors (n= nNormalizationVectors)*|| |type |Indicates type of normalization |String| VC:KR:INTER_KR:INTER_VC:GW_KR:GW_VC| |chrIdx| Chromosome index |int| | |unit| Bin units either FRAG or BP.| String| FRAG : BP| |binSize |Resolution |int|| |position| File position of value array| long || |nBytes| Size in bytes of value array |int || ||*Normalization vector arrays (repeat for each entry above)*|| |nValues| Number of values in array| int|| ||*Normalization vector values (n= nValues)*|| #### Notes ##### Data types * Strings are null (0) terminated. So for example the string "HIC" is represented by 4 bytes [48 49 43 0] * Other data types are Java * short - 16 bit integer * int - 32 bit integer * long - 64 bit integer * float - 32 bit floating point * double - 64 bit floating point ##### Attributes The attributes table in the header can contain an arbitrary number of key-value string pairs. The **Juicer** tool inserts one or more of the following attributes. * "statistics": * "graphs": * "software": * "nviIndex": reserved for future use * "nviLength": reserved for future use #### Grid structure Each chr-chr matrix at a given resolution is subdivided into a grid structure of square **blocks**. Each block consists of NxN bins, where N is referred to as **blockSize**. In older versions of the spec, and in code, this parameter is referred to as **blockBinCount**. For intra chromosome matrices (chr1 == chr2) only the lower diagonal is stored (row >= column). The upper diagonal can be inferred upon reading by tansposition. #### Block matrix representation The spatial unit for a block is a ```bin```, which can be computed from a genomic position with the formulat ```bin = floor(position / binSize)```. The origin of a block is then ```floor(x / binsSize), floor(y / binSize)``` where x and y are genomic positions in either base pairs or fragment number, depending on the * List of rows The list of rows is a sparse matrix format. Each row is represented as follows ```rowNumber rowSize [binX1 value1, binX2 value2, ...]``` The first row in the matrix has ```rowNumber = 0```. The highest row number possible is ```blockSize - 1``` * Dense In dense matrix format all values including zero are output in row major order. Allowance is made however for the possibility that only a sub-matrix of the block is populated, specifically that leading or trailing columns of the block might have no contacts (value = 0). To account for this possibility the maximum column number within the block which has at least 1 non-zero value is determined, which we will call ```binXMax```. The width of the block can then be determined and used to obtain the x and y coordinates in bin units for each value as follows. w = (binXMax - binXOffset + 1); row = floor(i / w); col = i - row * w; binX = binXOffset + col; binY = binYOffset + row; ================================================ FILE: Juicer.README ================================================ # Juicer Juicer is a platform for analyzing kilobase resolution Hi-C data. In this distribution, we include the pipeline for generating Hi-C maps from fastq raw data files and command line tools for feature annotation on the Hi-C maps. ---------------------- Example for Reviewers ---------------------- We've provided a step-by-step guide to showcase some of the features of Juicer. If you run into problems, see below for more detailed documentation. This example runs on Amazon Web Services, but you can install the pipeline on any LSF, Univa Grid Engine, or SLURM cluster. 1. Make sure you're in the top-level directory, with this README and the Juicer_AWS.pem file. (NOTE: please do not share this .pem file with anyone) 2. You were given an anonymous IP address. At a command line prompt, type: ssh -i Juicer_AWS.pem ubuntu@ 3. This will log you into an AWS instance that contains all the software needed to run the pipeline. Type cd /opt/juicer/work/ 4. We will run the pipeline on a test dataset of a single chromosome of the primary+ replicate map from (Rao+Huntley et al., 2014). Type: cd MBR19 5. Run the Juicer pipeline on the raw data, which is stored in the fastq directory: /opt/juicer/scripts/juicer.sh -g hg19 -s MboI 6. You will see a series of messages sending jobs to the cluster. Do not kill the script or close the server connection until you see: “(-: Finished adding all jobs... please wait while processing.” 7. At this point you can close the connection and come back later. To see the progress of the pipeline as it works, type: bjobs -w 7. Eventually the bjobs command will report “No unfinished job found”. Type: tail lsf.out You should see “(-: Pipeline successfully completed (-:” 8. Results are available in the aligned directory. The Hi-C maps are in inter.hic (for MAPQ > 0) and inter_30.hic (for MAPQ >= 30). The Hi-C maps can be loaded in Juicebox and explored. They can also be used for automatic feature annotation and to extract matrices at specific resolutions. These results also include automatic feature annotation. The output files include a genome-wide annotation of loops and, whenever possible, the CTCF motifs that anchor them (identified using the HiCCUPS algorithm). The files also include a genome-wide annotation of contact domains (identified using the Arrowhead algorithm). The formats of these files are described in the Juicebox tutorial online; both files can be loaded into Juicebox as a 2D annotation. 9. To download a file (e.g. inter.hic) from AWS to load into Juicebox, type: sftp -i Juicer_AWS.pem ubuntu@ cd /opt/juicer/work/MBR19/aligned get inter.hic get inter_30.hic get ... (each of hiccups, apa, motifs, and arrowhead output files) 10. You can also run the pipeline on genome-wide dataset that is lower resolution. Type cd /opt/juicer/work/HIC003 Then /opt/juicer/scripts/juicer.sh -g hg19 -s MboI Again the pipeline will run. The results will be available in the aligned directory. Because this is not a deeply sequenced map, loop lists and domain lists will not be produced. See below for more documentation. ------------ Distribution ------------ The files included on the AWS distribution are in /opt/juicer and are: *references - Genome references *restriction_sites - Restriction positions for combinations of reference genome and restriction enzymes *scripts - Juicer main scripts *work - Data samples *hic_files - Internal property file In this zip file, we include the scripts for running Juicer on LSF, Univa Grid Engine, and SLURM /AWS - scripts for running pipeline and postprocessing on AWS /UGER - scripts for running pipeline and postprocessing on UGER /SLURM - scripts for running pipeline and postprocessing on SLURM /juicebox_tools - source files for postprocessing algorithms /Juicer_AWS.pem - ssh key to access anonymous AWS server ---------------------------------- Hardware and Software Requirements ---------------------------------- Juicer is a pipeline optimized for parallel computation on a cluster. Juicer consists of two parts: the pipeline that creates Hi-C files from raw data, and the post-processing command line tools. * * Cluster requirements: * Juicer requires the use of a cluster, with ideally >= 4 cores (min 1 core) and >= 64 GB RAM (min 16 GB RAM) Juicer currently works with the following resource management software: - OpenLava (http://www.openlava.org/) - LSF (http://www-03.ibm.com/systems/services/platformcomputing/lsf.html) - SLURM (http://slurm.schedmd.com/download.html) - GridEngine (Univa, etc. any flavor) * * Command line tool requirements: * The minimum software requirement to run Juicer is a working Java installation (version >= 1.7) on Windows, Linux, and Mac OSX. We recommend using the latest Java version available, but please do not use the Java Beta Version. Minimum system requirements for running Java can be found at http://java.com/en/download/help/sysreq.xml To download and install the latest Java Runtime Environment (JRE), please go to http://www.java.com/download * * GNU CoreUtils * The latest version of GNU coreutils can be downloaded from https://www.gnu.org/software/coreutils/manual/ * * Burrows-Wheeler Aligner (BWA) * The latest version of BWA should be installed from http://bio-bwa.sourceforge.net/ * * CUDA (for HiCCUPS peak calling) * You must have an NVIDIA GPU to install CUDA Instructions for installing the latest version of CUDA can be found on the NVIDIA Developer site: https://developer.nvidia.com/cuda-downloads The native libraries included with Juicer are compiled for CUDA 7. Other versions of CUDA can be used, but you will need to download the respective native libraries from http://www.jcuda.org/downloads/downloads.html For best performance, use a dedicated GPU. You may also be able to obtain access to GPU clusters through Amazon Web Services or a local research institution. * * Java 1.7 or 1.8 JDK (for compiling from source files) * The instructions here are for the Java 1.8 JDK. For Windows/Mac/Linux, the Java 1.8 JDK can be installed from here: http://www.oracle.com/technetwork/java/javase/downloads/jdk8-downloads-2133151.html (Alternative) For Ubuntu/LinuxMint http://tecadmin.net/install-oracle-java-8-jdk-8-ubuntu-via-ppa/ * * Apache Ant (for compiling from source files) * Mac Ant should be installed on most Macs. To verify installation via the command prompt, type ant -version If Ant is not on your Mac, install it via homebrew. At the command prompt, type brew update brew install ant You may need to install Homebrew (http://brew.sh/) on your machine See the following Stackoverflow post for more details: http://stackoverflow.com/questions/3222804/how-can-i-install-apache-ant-on-mac-os-x Windows Installing Ant requires some minor changes to your system environment. Follow the instructions in this article: http://www.nczonline.net/blog/2012/04/12/how-to-install-apache-ant-on-windows/ Linux In the command prompt, type sudo apt-get install ant or sudo yum install ant depending on your package installer -------------------------------- Compiling Jars from Source Files -------------------------------- 1. You should have Java 1.7 (or 1.8) JDK and Apache Ant installed on your system. See below for more information. 2. Go to the folder containing the Juicebox source files and edit the juicebox.properties file with the proper Java JDK Address. 3. Open the command line, navigate to the folder containing the build.xml file and type ant The process should take no more than a minute to build on most machines. 4. The jars are written to the directory out/. You can change this by editing the build.xml file. ------------- Documentation ------------- We have extensive documentation below for how to use Juicer. ------------------------ Command Line Tools Usage ------------------------ To launch the command line tools, use the shell script “juicebox.sh” on Unix/MacOS or type java -jar juicebox_tools.jar (command...) [flags...] For HiCCUPS loop calling without the shell or bat script, you will need to call: java -Xms512m -Xmx2048m -Djava.library.path=path/to/natives/ -jar Juicebox_CLT.jar hiccups [flags...] where path/to/natives is the path to the native libraries used for Jcuda By default, these are located in the lib/jcuda folder. In the command line tools, there are 4 functions: > "apa" for conducting aggregate peak analysis > "hiccups" for annotating loops > "motifs" for finding CTCF motifs > "arrowhead" for annotating contact domains The "juicebox.sh” (Unix/MacOS) script can be used in place of the unwieldy "java -Djava.library.path=path/to/natives/ -jar juicebox_tools.jar" --- APA --- The "apa" command takes three required arguments and a number of optional arguments. apa [-n minval] [-x maxval] [-w window] [-r resolution(s)] [-c chromosome(s)] [-k NONE/VC/VC_SQRT/KR] The required arguments are: : Address of hic file(s) which should end with ".hic". This is the file you will load into Juicebox. URLs or local addresses may be used. To sum multiple hic Files together, use the '+' symbol between the addresses (no whitespace between addresses) : List of peaks in standard 2D feature format (chr1 x1 x2 chr2 y1 y2 color ...) : Working directory where outputs will be saved The optional arguments are: -n minimum distance away from the diagonal. Used to filter peaks too close to the diagonal. Units are in terms of the provided resolution. (e.g. -n 30 @ resolution 5kB will filter loops within 30*(5000/sqrt(2)) units of the diagonal) -x maximum distance away from the diagonal. Used to filter peaks too far from the diagonal. Units are in terms of the provided resolution. (e.g. -n 30 @ resolution 5kB will filter loops further than 30*(5000/sqrt(2)) units of the diagonal) -w width of region to be aggregated around the specified loops (units of resolution) -r resolution for APA; multiple resolutions can be specified using commas (e.g. 5000,10000) -c Chromosome(s) on which APA will be run. The number/letter for the chromosome can be used with or without appending the "chr" string. Multiple chromosomes can be specified using commas (e.g. 1,chr2,X,chrY) -k Normalizations (case sensitive) that can be selected. Generally, KR (Knight-Ruiz) balancing should be used when available. Default settings of optional arguments: -n 30 -x (infinity) -w 10 -r 25000,10000 -c (all chromosomes) -k KR ------------ APA Examples ------------ apa HIC006.hic all_loops.txt results1 > This command will run APA on HIC006 using loops from the all_loops files > and save them under the results1 folder. apa https://hicfiles.s3.amazonaws.com/hiseq/gm12878/in-situ/combined.hic all_loops.txt results1 > This command will run APA on the GM12878 mega map using loops from the all_loops > files and save them under the results1 folder. apa -r 10000,5000 -c 17,18 HIC006.hic+HIC007.hic all_loops.txt results > This command will run APA at 50 kB resolution on chromosomes 17 and 18 for the > summed HiC maps (HIC006 and HIC007) using loops from the all_loops files > and save them under the results folder ------- HiCCUPS ------- hiccups [-m matrixSize] [-c chromosome(s)] [-r resolution(s)] [-k normalization (NONE/VC/VC_SQRT/KR)] [-f fdr] [-p peak width] [-i window] [-t thresholds] [-d centroid distances] The required arguments are: : Address of hic file which should end with ".hic". This is the file you will load into Juicebox. URLs or local addresses may be used. : Final list of all loops found by HiCCUPS. Can be visualized directly in Juicebox as a 2D annotation. By default, various values critical to the HICCUPS algorithm are saved as attributes for each loop found. These can be disabled using the suppress flag below. The optional arguments are: -m Maximum size of the submatrix within the chromosome passed on to GPU (Must be an even number greater than 40 to prevent issues from running the CUDA kernel). The upper limit will depend on your GPU. Dedicated GPUs should be able to use values such as 500, 1000, or 2048 without trouble. Integrated GPUs are unlikely to run sizes larger than 90 or 100. Matrix size will not effect the result, merely the time it takes for hiccups. Larger values (with a dedicated GPU) will run fastest. -c Chromosome(s) on which HiCCUPS will be run. The number/letter for the chromosome can be used with or without appending the "chr" string. Multiple chromosomes can be specified using commas (e.g. 1,chr2,X,chrY) -r Resolution(s) for which HiCCUPS will be run. Multiple resolutions can be specified using commas (e.g. 25000,10000,5000). Due to the nature of DNA looping, it is unlikely that loops will be found at lower resolutions (i.e. 50kB or 100kB) IMPORTANT: if multiple resolutions are used, the flags below can be configured so that different parameters are used for the different resolutions. -k Normalizations (case sensitive) that can be selected. Generally, KR (Knight-Ruiz) balancing should be used when available. -f FDR values actually corresponding to max_q_val (i.e. for 1% FDR use 0.01, for 10%FDR use 0.1). Different FDR values can be used for each resolution using commas. (e.g "-r 5000,10000 -f 0.1,0.15" would run HiCCUPS at 10% FDR for resolution 5000 and 15% FDR for resolution 10000) -p Peak width used for finding enriched pixels in HiCCUPS. Different peak widths can be used for each resolution using commas. (e.g "-r 5000,10000 -p 4,2" would run at peak width 4 for resolution 5000 and peak width 2 for resolution 10000) -i Window width used for finding enriched pixels in HiCCUPS. Different window widths can be used for each resolution using commas. (e.g "-r 5000,10000 -p 10,6" would run at window width 10 for resolution 5000 and window width 6 for resolution 10000) -t Thresholds for merging loop lists of different resolutions. Four values must be given, separated by commas (e.g. 0.02,1.5,1.75,2). These thresholds (in order) represent: > threshold allowed for sum of FDR values of the horizontal, vertical, donut, and bottom left filters (an accepted loop must stay below this threshold) > threshold ratio that both the horizontal and vertical filters must exceed > threshold ratio that both the donut and bottom left filters must exceed > threshold ratio that at least one of the donut and bottom left filters must exceed -d Distances used for merging nearby pixels to a centroid. Different distances can be used for each resolution using commas. (e.g "-r 5000,10000 -d 20000,21000” would merge pixels within 20kB of each other at 5kB resolution and within 21kB at 10kB resolution. Defaults: Medium resolution maps: -m 512 -c (all chromosomes) -r 10000 -k KR -f .1 -p 2 -i 5 -t 0.02,1.5,1.75,2 -d 20000,20000,50000 High resolution maps: -m 512 -c (all chromosomes) -r 5000,10000 -k KR -f .1,.1 -p 4,2 -i 7,5 -t 0.02,1.5,1.75,2 -d 20000,20000,50000 ---------------- HiCCUPS Examples ---------------- hiccups HIC006.hic all_hiccups_loops > This command will run HiCCUPS on HIC006 and save all found loops to the all_hiccups_loops files hiccups -m 500 -r 5000,10000 -f 0.1,0.1 -p 4,2 -i 7,5 -d 20000,20000,0 -c 22 HIC006.hic all_hiccups_loops > This command will run HiCCUPS on chromosome 22 of HIC006 at 5kB and 10kB resolution using the following values: >> 5kB: fdr 10%, peak width 4, window width 7, and centroid distance 20kB >> 10kB: fdr 10%, peak width 2, window width 5, and centroid distance 20kB > The resulting loop list will be merged and saved as all_hiccups_loops > Note that these are values used for generating the GM12878 loop list ------- Arrowhead ------- arrowhead [-c chromosome(s)] [-m matrix size] [-r resolution] [-k normalization (NONE/VC/VC_SQRT/KR)] " + " [feature_list] [control_list] The required arguments are: : Address of hic file(s) which should end with ".hic". This is the file you will load into Juicebox. URLs or local addresses may be used. To sum multiple hic Files together, use the '+' symbol between the addresses (no whitespace between addresses) : Final list of all contact domains found by Arrowhead. Can be visualized directly in Juicebox as a 2D annotation. -- NOTE -- If you want to find scores for a feature and control list, both must be provided: [feature_list]: Feature list of loops/domains for which block scores are to be calculated [control_list]: Control list of loops/domains for which block scores are to be calculated The optional arguments are: -c Chromosome(s) on which Arrowhead will be run. The number/letter for the chromosome can be used with or without appending the "chr" string. Multiple chromosomes can be specified using commas (e.g. 1,chr2,X,chrY) -m Size of the sliding window along the diagonal in which contact domains will be found. Must be an even number as (m/2) is used as the increment for the sliding window. (Default 2000) -r resolution for which Arrowhead will be run. Generally, 5kB (5000) or 10kB (10000) resolution is used depending on the depth of sequencing in the hic file(s). -k Normalizations (case sensitive) that can be selected. Generally, KR (Knight-Ruiz) balancing should be used when available. Default settings of optional arguments: Medium resolution maps: -c (all chromosomes) -m 2000 -r 10000 -k KR High resolution maps: -c (all chromosomes) -m 2000 -r 5000 -k KR ---------------- Arrowhead Examples ---------------- NOTE: Arrowhead will choose appropriate defaults for hic files if no specifications are given arrowhead https://hicfiles.s3.amazonaws.com/hiseq/ch12-lx-b-lymphoblasts/in-situ/combined_30.hic contact_domains_list This command will run Arrowhead on a mouse cell line HiC map (medium resolution) at resolution 10 kB and save all contact domains to the contact_domains_list file. These are the settings used to generate the official contact domain list on the ch12-lx-b-lymphoblast cell line. arrowhead https://hicfiles.s3.amazonaws.com/hiseq/gm12878/in-situ/combined_30.hic contact_domains_list This command will run Arrowhead at resolution 5kB on the GM12878 HiC map (high resolution) and save all contact domains to the contact_domains_list file. These are the settings used to generate the official GM12878 contact domain list. ----------------------- Motif Finder ----------------------- motifs [custom_global_motif_list] The required arguments are: : hg19 supported by default. For other genome assemblies, provide a custom_global_motif_list in FIMO format. File path to a directory (e.g. ) which contains two folders: "unique" and "inferred". These folders should contain a combination of RAD21, SMC3, and CTCF BED files. By intersecting these 1D tracks, the strongest peaks will be identified. Unique motifs generally use a more stringent combination of BED files than inferred motifs. : List of peaks in standard 2D feature format (chr1 x1 x2 chr2 y1 y2 color ...) -- NOTE -- If you want to use a custom list of potential motifs: [custom_global_motif_list]: Motif list output using FIMO format can be used as an alternative to the internal motif list ------------------- Motif Finder Examples ------------------- Assuming the following file structure is present: /path/to/local/bed/files/unique/CTCF.bed /path/to/local/bed/files/unique/RAD21.bed /path/to/local/bed/files/unique/SMC3.bed /path/to/local/bed/files/inferred/CTCF.bed motifs hg19 /path/to/local/bed/files /gm12878_hiccups_loops.txt This command will find motifs from the internal hg19 motif list for the loops in gm12878_hiccups_loops.txt and save them to gm12878_hiccups_loops_with_motifs.txt. The CTCF, RAD21, and SMC3 BED files will be used together (i.e. intersected) to find unique motifs. Just the CTCF track will be used to infer best motifs. motifs hg19 /path/to/local/bed/files gm12878_hiccups_loops.txt hg_19_custom_motif_list.txt This command will find motifs from hg_19_custom_motif_list.txt for the loops in gm12878_hiccups_loops.txt and save them to gm12878_hiccups_loops_with_motifs.txt. The CTCF, RAD21, and SMC3 BED files will be used together (i.e. intersected) to find unique motifs. Just the CTCF track will be used to infer best motifs. ================================================ FILE: LICENSE ================================================ The MIT License (MIT) Copyright (c) 2016 Aiden Lab Permission is hereby granted, free of charge, to any person obtaining a copy of this software and associated documentation files (the "Software"), to deal in the Software without restriction, including without limitation the rights to use, copy, modify, merge, publish, distribute, sublicense, and/or sell copies of the Software, and to permit persons to whom the Software is furnished to do so, subject to the following conditions: The above copyright notice and this permission notice shall be included in all copies or substantial portions of the Software. THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE. ================================================ FILE: README.md ================================================ -------------- Breaking News! -------------- This codebase is in the process of being split up to better support long-term maintenance and modular aspects of different tools available. The new repositories will be: - [JuiceboxGUI](https://github.com/aidenlab/juiceboxgui) for visualization of Hi-C maps with Juicebox Desktop and genome assembly correction with Assembly Tools. - [HiCTools](https://github.com/aidenlab/hictools) for building and writing .hic files (Pre, Addnorm, and Statistics) - [JuicerTools](https://github.com/aidenlab/juicertools) for downstream analysis of .hic files (HiCCUPS, Arrowhead, APA, etc.) - [Java Straw](https://github.com/aidenlab/java-straw) to quickly read and stream data from .hic files into Java, and is used by the above repositories. We also have new tools: - [Straw](https://github.com/aidenlab/straw) to quickly read and stream data from .hic files into C++, python, R, and MATLAB. - [POSSUMM](https://github.com/sa501428/EigenVector) for new C++ code to rapidly calculate A-B compartments (i.e. eigenvectors) for higher resolutions - [EMT](https://github.com/sa501428/hic-emt) for upgrading older .hic files or making smaller .hic files for regions of interest. -------------- About Juicebox -------------- Juicebox is visualization software for Hi-C data. This distribution includes the source code for Juicebox, Juicer Tools, and Assembly Tools . Download Juicebox here, or use Juicebox on the web. Detailed documentation is available on the wiki. Instructions below pertain primarily to usage of command line tools and the Juicebox jar files. Juicebox can now be used to visualize and interactively (re)assemble genomes. Check out the Juicebox Assembly Tools Module website https://aidenlab.org/assembly for more details on how to use Juicebox for assembly. Juicebox was created by Jim Robinson, Neva C. Durand, and Erez Lieberman Aiden. Past contributors include Ido Machol, Zulkifl Gire, Marie Hoeger, Fanny Huang, Nam Hee Kim, Vi Nguyen, Jay Ryu, Nathaniel T. Musial, and Ragib Mostofa. Ongoing development work is carried out by Muhammad Saad Shamim, Neva C. Durand, and Olga Dudchenko. -------------- Questions? -------------- For FAQs, or for asking new questions, please see our forum: aidenlab.org/forum.html. -------------- IntelliJ Setup -------------- Use IntelliJ IDEA (Community edition - free) To set up in IDEA, have the Java SDK installed then you'll point to it (IntelliJ has lots of documentation on this sort of thing). * Then go to `VCS` -> `checkout from version control`. * You'll need to do is be sure `*.sizes` is included as a file to be copied over to the class files. Set this up via IntelliJ `Preferences` -> `Compiler`. Add `?*.sizes` to the list of `Resource Patterns`. * While there, also go to `Java Compiler` and put this into additional command line options: `-Xlint:all -target 1.7` The former turns on all warnings, the latter gives some flexibility since some people haven't updated Java to 1.8 yet. * Then go to `Run` -> `Edit Configurations`. * With the `+` sign, add `Application`. * You'll create two of these, one for the GUI (call it Juicebox GUI or whatever you want, really) and one for the CLT. * Set the main class by clicking the little `...` button next to the text box for main class MainWindow.java is the main method class for the visualization/GUI portion of the software. HiCTools.java is the main method class for the analysis/CLT portion. * For the GUI under VM Options: -Xmx2000m -Djnlp.loadMenu="https://hicfiles.tc4ga.com/juicebox.properties" * For the CLT use -Xmx2000m * Note that the `Xmx2000m` flag sets the maximum memory heap size to 2GB. Depending on your computer you might want more or less. Some tools will break if there's not enough memory and the file is too large, but don't worry about that for development; 2GB should be fine. * One last note: be sure to `Commit and Push` when you commit files, it's hidden in the dropdown menu button in the commit window. ---------------------------------- Hardware and Software Requirements ---------------------------------- The minimum software requirement to run Juicebox is a working Java installation (version > 1.6) on Windows, Linux, and Mac OSX. We recommend using the latest Java version available, but please do not use the Java Beta Version. Minimum system requirements for running Java can be found at https://java.com/en/download/help/sysreq.xml. To download and install the latest Java Runtime Environment (JRE), please go to https://www.java.com/download. We recommend having at least 2GB free RAM for the best user experience with Juicebox. To launch the Juicebox application from command line, type java -Xms512m -Xmx2048m -jar Juicebox.jar Note: the -Xms512m flag sets the minimum memory heap size at 512 megabytes, and the -Xmx2048m flag sets the maximum size at 2048 megabytes (2 gigabytes). These values may be adjusted as appropriate for your machine. ------------- Documentation ------------- We have extensive documentation for how to use Juicebox at https://github.com/theaidenlab/juicebox/wiki including a video, a Quick Start Guide, and a detailed tutorial. For using Juicebox to assemble genomes see https://www.aidenlab.org/assembly/. ------------------------ Command Line Tools Usage ------------------------ See the documentation at https://github.com/theaidenlab/juicer/wiki for information on how to use the Juicer tools. -------------------------------- Compiling Jars from Source Files -------------------------------- 1. You should have Java 1.8 JDK and Apache Ant installed on your system. See below for more information. 2. Go to the folder containing the Juicebox source files and edit the juicebox.properties file with the proper Java JDK Address. 3. Open the command line, navigate to the folder containing the build.xml file and type ant The process should take no more than a minute to build on most machines. 4. The jars are written to the directory out/. You can change this by editing the build.xml file. * Installing Java 1.8 JDK For Windows/Mac/Linux, the Java 1.8 JDK can be installed from here: https://www.oracle.com/technetwork/java/javase/downloads/jdk8-downloads-2133151.html (Alternative) For Ubuntu/LinuxMint https://tecadmin.net/install-oracle-java-8-jdk-8-ubuntu-via-ppa/ * Installing Apache Ant Mac Ant should be installed on most Macs. To verify installation via the command prompt, type ant -version If Ant is not on your Mac, install it via homebrew. At the command prompt, type brew update brew install ant You may need to install Homebrew (https://brew.sh/) on your machine See the following Stackoverflow post for more details: https://stackoverflow.com/questions/3222804/how-can-i-install-apache-ant-on-mac-os-x Windows Installing Ant requires some minor changes to your system environment. Follow the instructions in this article: https://www.nczonline.net/blog/2012/04/12/how-to-install-apache-ant-on-windows/ Linux In the command prompt, type sudo apt-get install ant or sudo yum install ant depending on your package installer ================================================ FILE: benchmark.sh ================================================ #!/bin/bash ### Benchmarks for DCIC ### To run, get juicebox_tools.jar and the test data files: ### wget http://hicfiles.s3.amazonaws.com/internal/juicebox_tools/8.5.16/juicebox_tools.jar ### wget ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1551nnn/GSM1551552/suppl/GSM1551552_HIC003_merged_nodups.txt.gz ### wget https://s3.amazonaws.com/pkerp/data/matrix_test/chrX_5KB_bins.tsv.gz ### First benchmark echo "Create index for data at 1MB resolution, all chromosomes" time java -Xmx8g -jar juicebox_tools.jar pre -r 1000000 -v -q 1 GSM1551552_HIC003_merged_nodups.txt.gz HIC003_1MB.hic hg19 echo "Create index for data at all resolutions, all chromosomes" time java -Xmx8g -jar juicebox_tools.jar pre -v -q 1 GSM1551552_HIC003_merged_nodups.txt.gz HIC003.hic hg19 echo "Querying: 256x256 / 2048x2048 / slices / single resolution no norm" java -Xmx8g -jar juicebox_tools.jar benchmark HIC003_1MB.hic NONE echo "Querying: 256x256 / 2048x2048 / slices / single resolution balanced norm" java -Xmx8g -jar juicebox_tools.jar benchmark HIC003_1MB.hic KR echo "Querying: 256x256 / 2048x2048 / slices / multiple resolution no norm" java -Xmx8g -jar juicebox_tools.jar benchmark HIC003.hic NONE echo "Querying: 256x256 / 2048x2048 / slices / multiple resolution balanced norm" java -Xmx8g -jar juicebox_tools.jar benchmark HIC003.hic KR # repeated query without loading index of 2048x2048 echo "Query without loading index 2048x2048....ten times" time ./straw KR HIC003.hic 1:20480000:40960000 1:20480000:40960000 BP 10000 > tmp.txt time ./straw KR HIC003.hic 2:20480000:40960000 2:20480000:40960000 BP 10000 > tmp.txt time ./straw KR HIC003.hic 3:20480000:40960000 3:20480000:40960000 BP 10000 > tmp.txt time ./straw KR HIC003.hic 4:20480000:40960000 4:20480000:40960000 BP 10000 > tmp.txt time ./straw KR HIC003.hic 5:20480000:40960000 5:20480000:40960000 BP 10000 > tmp.txt time ./straw KR HIC003.hic 6:20480000:40960000 6:20480000:40960000 BP 10000 > tmp.txt time ./straw KR HIC003.hic 7:20480000:40960000 7:20480000:40960000 BP 10000 > tmp.txt time ./straw KR HIC003.hic 8:20480000:40960000 8:20480000:40960000 BP 10000 > tmp.txt time ./straw KR HIC003.hic 9:20480000:40960000 9:20480000:40960000 BP 10000 > tmp.txt time ./straw KR HIC003.hic 10:20480000:40960000 10:20480000:40960000 BP 10000 > tmp.txt ### Second benchmark #transform to valid-pairs format with scores #gunzip -c chrX_5KB_bins.tsv.gz | awk '{print 0,"X",$1*5000,0,0,"X",$2*5000,1,$3}' | gzip > chrX_5KB.txt.gz echo "Create index for binned data" time java -Xmx8g -jar juicebox_tools.jar pre -r 5000 -c X -v -d chrX_5KB.txt.gz chrX_5KB.hic hg19 echo "Querying: 256x256 / 2048x2048 / slices / no norm" java -Xmx8g -jar juicebox_tools.jar -v benchmark chrX_5KB.hic NONE X echo "Querying: 256x256 / 2048x2048 / slices / balanced norm" java -Xmx8g -jar juicebox_tools.jar -v benchmark chrX_5KB.hic KR X echo "Binary index to text" time java -Xmx8g -jar juicebox_tools.jar dump observed NONE chrX_5KB.hic X X BP 5000 chrX_5KB_out.txt ================================================ FILE: build.xml ================================================ ================================================ FILE: data/inter.hic ================================================ [File too large to display: 40.0 MB] ================================================ FILE: internalREADME.md ================================================ -------------------- Quick Start -------------------- 1. Run `package.sh ` versionNum lives in src/juicebox/HiCGlobals. This will compile, sign, bundle, and create the DMG and EXE. You will be prompted to change the EXE with a HEX editor, just follow the instructions. 2. The new executables will be in out/artifacts/Juicebox_jar 3. move old jars, EXEs, and DMGs, update CHANGES in important_jars ------------------ Previous version ------------------ ``` rm -r out ant ant sign ant bundle cd l4j ~/Downloads/launch4j/launch4j config_bcm.xml cd ../out/artifacts/Juicebox_jar/ codesign -s "Erez Aiden" Juicebox.app --deep hdiutil create -srcfolder Juicebox.app Juicebox.dmg cd ~/Dropbox\ \(Lab\ at\ Large\)/important_jars/ # move old jars, EXEs, and DMGs, update CHANGES emacs -nw CHANGES # XXXXXX should be date when file written i.e. 20170103 mv Juicebox_BCM.dmg Juicebox_BCMXXXXXXXX.dmg mv Juicebox_BCM.exe Juicebox_BCMXXXXXXXX.exe mv Juicebox.jar JuiceboxXXXXXXXX.jar mv ~/Dropbox/Research/JuiceboxDev/l4j/Juicebox.exe Juicebox_BCM.exe mv ~/Dropbox/Research/JuiceboxDev/out/artifacts/Juicebox_jar/Juicebox.dmg Juicebox_BCM.dmg mv ~/Dropbox/Research/JuiceboxDev/out/artifacts/Juicebox_jar/Juicebox.jar Juicebox.jar mv ~/Dropbox/Research/JuiceboxDev/out/artifacts/Juicebox_clt_jar/Juicebox.jar juicebox_tools.8.0.jar ``` -------------------- Creating Executables -------------------- 0. Compile Jars from Source Files as described in Juicebox README. * EXE Build (Windows) 1. Download the launch4j tarball and unzip it. 2. Run > ./launch4j/launch4j config.xml Modify the config.xml file to set the properties file and other parameters. 3. Signing is complicated. You'll need openssl and osslsigncode and will need to do a two step procedure. - openssl pkcs12 -in ~/Dropbox\ \(Lab\ at\ Large\)/important_jars/ErezSLieberman.p12 -nocerts -nodes -out certificate.pem (You can save this certificate and use it later, just don't forget your password) - Sign for the first time osslsigncode sign -certs ~/Dropbox\ \(Lab\ at\ Large\)/important_jars/erez_s_lieberman.pem -key certificate.pem \ -askpass -n "Juicebox" -i http://aidenlab.org/ -in ~/Dropbox\ \(Lab\ at\ Large\)/important_jars/Juicebox.exe \ -out signed.exe - Find the size of the signature in bytes i.e. sizeInBytesOf(signed.exe) - sizeInBytesOf(Juicebox.exe) You can use ls -l for this - Edit Juicebox.exe with favorite HEX editor to change last two bytes of exe i.e. the jar i.e. the zip end of central directory to the size using littleendian byte order and save. File size should remain the same. For example, if the size difference is 4384, the hex number is 0x1120; in Little Endian, this will be 20 11 - Sign the modified Juicebox.exe using above osslsigncode again * .app Build (Mac) 1. After making jars as described above, type > ant bundle to make the Juicebox.app executable. 2. Sign the app with codesign -s "Erez Aiden" Juicebox.app --deep You must have things appropriately installed in your keychain. Follow the instructions on the Apple Developer website. Our csr and cer are in the Dropbox under important_jars but I'm not sure exactly how you would add both the csr and the cer to KeyChain so you might just have to do it from scratch (this is what I did, eventually). Look for the ones created Wed Dec 23 2015 3. hdiutil create -size 210m -srcfolder Juicebox.app Juicebox.dmg Size depends on what the size of your .app file is, make it big enough so this command doesn't fail. You can also do Disk Utility -> New Image From Folder and choose Juicebox.app. 4. Modify the code under the bundle taskdef in the build.xml file to change properties and other parameters. -------------------- Steps for creating Public Friendly Version -------------------- 1. Create a new branch 2. Remove sensitive chrom.sizes. First, delete all contents of the chrom.sizes folder (/src/juicebox/tools/chrom.sizes). Next, go to the top level directory. You will see a compressed folder called PublicFriendlyChromSizes.zip. Extract its contents and copy them into the chrom.sizes folder which was just emptied. Recompile the project in IntelliJ. 3. Delete anything under development (e.g. clustering, APAvsDistance, etc.). These should all be in the dev folder, so it should usually be sufficient to just delete it and all its contents (src/juicebox/tools/dev). After deleting the folder, compile in IntelliJ and fix all the bugs/warnings (i.e. remove any calls to the dev/private folder). This may be tricky for some parts (especially the restriction enzymes section) See https://github.com/theaidenlab/JuiceboxDev/commit/fd930f5fac9af3df9f44cd87d4fc31e8df5d3ac3 for an example of what was deleted. (Aside: Any new sensitive project should be created in this dev directory to simplify this entire process for us.) 4. Remove any mention of assembly/sensitive projects (should have technically been taken care on in step 3, but a quick search for the word assembly in the whole project is easy to do) 5. Change version number as appropriate - HiCGlobals, for display purposes only. Note this is only in terms of jars/executables. For actual code release / open-sourcing, we need to wipe other private files, especially the .git histories, hidden files, internalREADME (i.e. me!), etc. -------------------- Building a new IGV jar for use in Juicebox ------------------- Two problems with IGV jar: signatures and classpaths in the MANIFEST. If it was just the first, it would be a one-liner. Instead: 1 - Unzip IGV jar (be sure to get the "snapshot" build, currently at https://data.broadinstitute.org/igv/projects/snapshot/igv.jar ) ``` mkdir tmp mv igv.jar tmp cd tmp unzip igv.jar ``` 2 - Remove META-INF/*.SF META-INF/*.DSA META-INF/*.RSA ``` rm META-INF/*.SF META-INF/*.DSA META-INF/*.RSA ``` 3 - Go into the META-INF/MANIFEST file with your favorite editor and remove the Class-Path lines. 4 - Rezip the jar ``` rm igv.jar jar cvf igv.jar ./* ``` -------------------- Building Different CUDA versions -------------------- ​​Right now JuiceboxDev (assuming what's in the repo now) is defaulting to 7.0 CUDA 7.0 is used on AWS CUDA 7.5 is on most of our internal machines (Hailmary) CUDA 8.0 is used on Adam; linux-x64 CUDA 8.0 is used on Rice; linux-ppc CUDA 8.0 for Mac; apple-x86 To change from 7.0 to 7.5, the build.xml and libraries for compilation need to be changed ---build.xml changes Change the following line (has x2 occurrences, one for each jar build) `` to `` or `` and for Power (Rice) will need `` and otherwise `` ---jcuda lib changes - Go to ~/lib/jcuda - Delete all the non .zip files - Unzip Archive.JCuda.0.7.5.zip this creates a new folder - Move everything in this newly made folder to the folder above it (e.g. path should be ~/lib/jcuda/jcuda-0.7.5.jar, NOT ~/lib/jcuda/Archive.JCuda.0.7.5/jcuda-0.7.0.jar) - For JCuda 0.8, you should define if this is for x86 or ppc (Power8) architecture and add those natives: jcuda-natives-0.8.0-linux-ppc_64.jar or jcuda-natives-0.8.0-linux-x86_64.jar The jars are really the ones that matter, but I think it's easier to update everything here (especially if testing GPU stuff from within IntelliJ) ​And now it should be fine to build via ant​ ================================================ FILE: juicebox.properties ================================================ # # The MIT License (MIT) # # Copyright (c) 2011-2020 Broad Institute, Aiden Lab, Rice University, Baylor College of Medicine # # Permission is hereby granted, free of charge, to any person obtaining a copy # of this software and associated documentation files (the "Software"), to deal # in the Software without restriction, including without limitation the rights # to use, copy, modify, merge, publish, distribute, sublicense, and/or sell # copies of the Software, and to permit persons to whom the Software is # furnished to do so, subject to the following conditions: # # The above copyright notice and this permission notice shall be included in # all copies or substantial portions of the Software. # # THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR # IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, # FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE # AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER # LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, # OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN # THE SOFTWARE. # jdk.home.1.8=/Library/Java/JavaVirtualMachines/jdk-13.0.2.jdk/Contents/Home/ sign.keystore=/Users/nchernia/Dropbox\ \(Lab\ at\ Large\)/important_jars//ErezSLieberman.jks sign.storepass=juicebox sign.alias=server ================================================ FILE: l4j/config.xml ================================================ gui ../out/artifacts/Juicebox_jar/Juicebox.jar Juicebox.exe Juicebox . Juicebox.ico true 1.7.0 64 5000 10000 juicebox.bmp true 60 true ================================================ FILE: l4j/config_bcm.xml ================================================ gui ../out/artifacts/Juicebox_jar/Juicebox.jar Juicebox.exe Juicebox . Juicebox.ico true 1.7.0 64 5000 10000 -Djnlp.loadMenu="http://hicfiles.s3.amazonaws.com/internal/hiculfite.properties" juicebox.bmp true 60 true ================================================ FILE: l4j/config_broad.xml ================================================ gui ../out/artifacts/Juicebox_jar/juicebox_64.jar ../Juicebox.exe Juicebox . Juicebox.ico true 1.7.0 64 5000 10000 -Djnlp.loadMenu="http://iwww.broadinstitute.org/igvdata/hic/files/hicInternalMenu.properties" juicebox.bmp true 60 true ================================================ FILE: l4j/config_fix_for_Erez.xml ================================================ gui ../out/artifacts/Juicebox_jar/Juicebox.jar ../Juicebox.exe Juicebox . Juicebox.ico true 1.7.0 64 5000 10000 -Dswing.aatext=true -Dswing.plaf.metal.controlFont=Tahoma -Dswing.plaf.metal.userFont=Tahoma juicebox.bmp true 60 true ================================================ FILE: l4j/config_nosplash.xml ================================================ gui ../out/artifacts/Juicebox_jar/Juicebox.jar ../out/artifacts/Juicebox_jar/Juicebox.exe Juicebox . Juicebox.ico true 1.7.0 64 5000 10000 ================================================ FILE: lib/broadinstitute/igv.jar ================================================ [File too large to display: 19.3 MB] ================================================ FILE: lib/general/VectorGraphics2D.LGPL.LICENSE ================================================ GNU LESSER GENERAL PUBLIC LICENSE Version 3, 29 June 2007 Copyright (C) 2007 Free Software Foundation, Inc. Everyone is permitted to copy and distribute verbatim copies of this license document, but changing it is not allowed. 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If you modify a copy of the Library, and, in your modifications, a facility refers to a function or data to be supplied by an Application that uses the facility (other than as an argument passed when the facility is invoked), then you may convey a copy of the modified version: a) under this License, provided that you make a good faith effort to ensure that, in the event an Application does not supply the function or data, the facility still operates, and performs whatever part of its purpose remains meaningful, or b) under the GNU GPL, with none of the additional permissions of this License applicable to that copy. 3. Object Code Incorporating Material from Library Header Files. The object code form of an Application may incorporate material from a header file that is part of the Library. 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You may place library facilities that are a work based on the Library side by side in a single library together with other library facilities that are not Applications and are not covered by this License, and convey such a combined library under terms of your choice, if you do both of the following: a) Accompany the combined library with a copy of the same work based on the Library, uncombined with any other library facilities, conveyed under the terms of this License. b) Give prominent notice with the combined library that part of it is a work based on the Library, and explaining where to find the accompanying uncombined form of the same work. 6. Revised Versions of the GNU Lesser General Public License. The Free Software Foundation may publish revised and/or new versions of the GNU Lesser General Public License from time to time. Such new versions will be similar in spirit to the present version, but may differ in detail to address new problems or concerns. Each version is given a distinguishing version number. If the Library as you received it specifies that a certain numbered version of the GNU Lesser General Public License "or any later version" applies to it, you have the option of following the terms and conditions either of that published version or of any later version published by the Free Software Foundation. If the Library as you received it does not specify a version number of the GNU Lesser General Public License, you may choose any version of the GNU Lesser General Public License ever published by the Free Software Foundation. If the Library as you received it specifies that a proxy can decide whether future versions of the GNU Lesser General Public License shall apply, that proxy's public statement of acceptance of any version is permanent authorization for you to choose that version for the Library. ================================================ FILE: lib/general/hic_tools.3.30.00.jar ================================================ [File too large to display: 24.7 MB] ================================================ FILE: lib/universalJavaApplicationStub ================================================ #!/bin/bash ################################################################################## # # # universalJavaApplicationStub # # # # A BASH based JavaApplicationStub for Java Apps on Mac OS X # # that works with both Apple's and Oracle's plist format. # # # # Inspired by Ian Roberts stackoverflow answer # # at http://stackoverflow.com/a/17546508/1128689 # # # # @author Tobias Fischer # # @url https://github.com/tofi86/universalJavaApplicationStub # # @date 2018-03-10 # # @version 3.0.1 # # # ################################################################################## # # # The MIT License (MIT) # # # # Copyright (c) 2014-2018 Tobias Fischer # # # # Permission is hereby granted, free of charge, to any person obtaining a copy # # of this software and associated documentation files (the "Software"), to deal # # in the Software without restriction, including without limitation the rights # # to use, copy, modify, merge, publish, distribute, sublicense, and/or sell # # copies of the Software, and to permit persons to whom the Software is # # furnished to do so, subject to the following conditions: # # # # The above copyright notice and this permission notice shall be included in all # # copies or substantial portions of the Software. # # # # THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR # # IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, # # FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE # # AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER # # LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, # # OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE # # SOFTWARE. # # # ################################################################################## # function 'stub_logger()' # # A logger which logs to the macOS Console.app using the 'syslog' command # # @param1 the log message # @return void ################################################################################ function stub_logger() { syslog -s -k \ Facility com.apple.console \ Level Notice \ Sender "$(basename "$0")" \ Message "[$$][${CFBundleName:-$(basename "$0")}] $1" } # set the directory abspath of the current # shell script with symlinks being resolved ############################################ PRG=$0 while [ -h "$PRG" ]; do ls=$(ls -ld "$PRG") link=$(expr "$ls" : '^.*-> \(.*\)$' 2>/dev/null) if expr "$link" : '^/' 2> /dev/null >/dev/null; then PRG="$link" else PRG="$(dirname "$PRG")/$link" fi done PROGDIR=$(dirname "$PRG") stub_logger "[StubDir] $PROGDIR" # set files and folders ############################################ # the absolute path of the app package cd "$PROGDIR"/../../ || exit 11 AppPackageFolder=$(pwd) # the base path of the app package cd .. || exit 12 AppPackageRoot=$(pwd) # set Apple's Java folder AppleJavaFolder="${AppPackageFolder}"/Contents/Resources/Java # set Apple's Resources folder AppleResourcesFolder="${AppPackageFolder}"/Contents/Resources # set Oracle's Java folder OracleJavaFolder="${AppPackageFolder}"/Contents/Java # set Oracle's Resources folder OracleResourcesFolder="${AppPackageFolder}"/Contents/Resources # set path to Info.plist in bundle InfoPlistFile="${AppPackageFolder}"/Contents/Info.plist # set the default JVM Version to a null string JVMVersion="" JVMMaxVersion="" # function 'plist_get()' # # read a specific Plist key with 'PlistBuddy' utility # # @param1 the Plist key with leading colon ':' # @return the value as String or Array ################################################################################ plist_get(){ /usr/libexec/PlistBuddy -c "print $1" "${InfoPlistFile}" 2> /dev/null } # function 'plist_get_java()' # # read a specific Plist key with 'PlistBuddy' utility # in the 'Java' or 'JavaX' dictionary () # # @param1 the Plist :Java(X):Key with leading colon ':' # @return the value as String or Array ################################################################################ plist_get_java(){ plist_get ${JavaKey:-":Java"}$1 } # read Info.plist and extract JVM options ############################################ # read the program name from CFBundleName CFBundleName=$(plist_get ':CFBundleName') # read the icon file name CFBundleIconFile=$(plist_get ':CFBundleIconFile') # check Info.plist for Apple style Java keys -> if key :Java is present, parse in apple mode /usr/libexec/PlistBuddy -c "print :Java" "${InfoPlistFile}" > /dev/null 2>&1 exitcode=$? JavaKey=":Java" # if no :Java key is present, check Info.plist for universalJavaApplication style JavaX keys -> if key :JavaX is present, parse in apple mode if [ $exitcode -ne 0 ]; then /usr/libexec/PlistBuddy -c "print :JavaX" "${InfoPlistFile}" > /dev/null 2>&1 exitcode=$? JavaKey=":JavaX" fi # read 'Info.plist' file in Apple style if exit code returns 0 (true, ':Java' key is present) if [ $exitcode -eq 0 ]; then stub_logger "[PlistStyle] Apple" # set Java and Resources folder JavaFolder="${AppleJavaFolder}" ResourcesFolder="${AppleResourcesFolder}" APP_PACKAGE="${AppPackageFolder}" JAVAROOT="${AppleJavaFolder}" USER_HOME="$HOME" # read the Java WorkingDirectory JVMWorkDir=$(plist_get_java ':WorkingDirectory' | xargs) # set Working Directory based upon PList value if [[ ! -z ${JVMWorkDir} ]]; then WorkingDirectory="${JVMWorkDir}" else # AppPackageRoot is the standard WorkingDirectory when the script is started WorkingDirectory="${AppPackageRoot}" fi # expand variables $APP_PACKAGE, $JAVAROOT, $USER_HOME WorkingDirectory=$(eval echo "${WorkingDirectory}") # read the MainClass name JVMMainClass="$(plist_get_java ':MainClass')" # read the SplashFile name JVMSplashFile=$(plist_get_java ':SplashFile') # read the JVM Properties as an array and retain spaces IFS=$'\t\n' JVMOptions=($(xargs -n1 <<<$(plist_get_java ':Properties' | grep " =" | sed 's/^ */-D/g' | sed -E 's/ = (.*)$/="\1"/g'))) unset IFS # post processing of the array follows further below... # read the ClassPath in either Array or String style JVMClassPath_RAW=$(plist_get_java ':ClassPath' | xargs) if [[ $JVMClassPath_RAW == *Array* ]] ; then JVMClassPath=.$(plist_get_java ':ClassPath' | grep " " | sed 's/^ */:/g' | tr -d '\n' | xargs) else JVMClassPath=${JVMClassPath_RAW} fi # expand variables $APP_PACKAGE, $JAVAROOT, $USER_HOME JVMClassPath=$(eval echo "${JVMClassPath}") # read the JVM Options in either Array or String style JVMDefaultOptions_RAW=$(plist_get_java ':VMOptions' | xargs) if [[ $JVMDefaultOptions_RAW == *Array* ]] ; then JVMDefaultOptions=$(plist_get_java ':VMOptions' | grep " " | sed 's/^ */ /g' | tr -d '\n' | xargs) else JVMDefaultOptions=${JVMDefaultOptions_RAW} fi # read StartOnMainThread and add as -XstartOnFirstThread JVMStartOnMainThread=$(plist_get_java ':StartOnMainThread') if [ "${JVMStartOnMainThread}" == "true" ]; then JVMDefaultOptions+=" -XstartOnFirstThread" fi # read the JVM Arguments as an array and retain spaces IFS=$'\t\n' MainArgs=($(xargs -n1 <<<$(plist_get_java ':Arguments'))) unset IFS # post processing of the array follows further below... # read the Java version we want to find JVMVersion=$(plist_get_java ':JVMVersion' | xargs) # post processing of the version string follows below... # read 'Info.plist' file in Oracle style else stub_logger "[PlistStyle] Oracle" # set Working Directory and Java and Resources folder JavaFolder="${OracleJavaFolder}" ResourcesFolder="${OracleResourcesFolder}" WorkingDirectory="${OracleJavaFolder}" APP_ROOT="${AppPackageFolder}" # read the MainClass name JVMMainClass="$(plist_get ':JVMMainClassName')" # read the SplashFile name JVMSplashFile=$(plist_get ':JVMSplashFile') # read the JVM Options as an array and retain spaces IFS=$'\t\n' JVMOptions=($(plist_get ':JVMOptions' | grep " " | sed 's/^ *//g')) unset IFS # post processing of the array follows further below... # read the ClassPath in either Array or String style JVMClassPath_RAW=$(plist_get ':JVMClassPath') if [[ $JVMClassPath_RAW == *Array* ]] ; then JVMClassPath=.$(plist_get ':JVMClassPath' | grep " " | sed 's/^ */:/g' | tr -d '\n' | xargs) # expand variables $APP_PACKAGE, $JAVAROOT, $USER_HOME JVMClassPath=$(eval echo "${JVMClassPath}") elif [[ ! -z ${JVMClassPath_RAW} ]] ; then JVMClassPath=${JVMClassPath_RAW} # expand variables $APP_PACKAGE, $JAVAROOT, $USER_HOME JVMClassPath=$(eval echo "${JVMClassPath}") else #default: fallback to OracleJavaFolder JVMClassPath="${JavaFolder}/*" # Do NOT expand the default 'AppName.app/Contents/Java/*' classpath (#42) fi # read the JVM Default Options JVMDefaultOptions=$(plist_get ':JVMDefaultOptions' | grep -o " \-.*" | tr -d '\n' | xargs) # read the Main Arguments from JVMArguments key as an array and retain spaces (see #46 for naming details) IFS=$'\t\n' MainArgs=($(xargs -n1 <<<$(plist_get ':JVMArguments' | tr -d '\n' | sed -E 's/Array \{ *(.*) *\}/\1/g' | sed 's/ */ /g'))) unset IFS # post processing of the array follows further below... # read the Java version we want to find JVMVersion=$(plist_get ':JVMVersion' | xargs) # post processing of the version string follows below... fi # JVMVersion: post processing and optional splitting if [[ ${JVMVersion} == *";"* ]]; then minMaxArray=(${JVMVersion//;/ }) JVMVersion=${minMaxArray[0]//+} JVMMaxVersion=${minMaxArray[1]//+} fi stub_logger "[JavaRequirement] JVM minimum version: ${JVMVersion}" stub_logger "[JavaRequirement] JVM maximum version: ${JVMMaxVersion}" # MainArgs: replace occurences of $APP_ROOT with its content MainArgsArr=() for i in "${MainArgs[@]}" do MainArgsArr+=("$(eval echo "$i")") done # JVMOptions: replace occurences of $APP_ROOT with its content JVMOptionsArr=() for i in "${JVMOptions[@]}" do JVMOptionsArr+=("$(eval echo "$i")") done # internationalized messages ############################################ LANG=$(defaults read -g AppleLocale) stub_logger "[Language] $LANG" # French localization if [[ $LANG == fr* ]] ; then MSG_ERROR_LAUNCHING="ERREUR au lancement de '${CFBundleName}'." MSG_MISSING_MAINCLASS="'MainClass' n'est pas spécifié.\nL'application Java ne peut pas être lancée." MSG_JVMVERSION_REQ_INVALID="La syntaxe de la version Java demandée est invalide: %s\nVeuillez contacter le développeur de l'application." MSG_NO_SUITABLE_JAVA="La version de Java installée sur votre système ne convient pas.\nCe programme nécessite Java %s" MSG_JAVA_VERSION_OR_LATER="ou ultérieur" MSG_JAVA_VERSION_LATEST="(dernière mise à jour)" MSG_JAVA_VERSION_MAX="à %s" MSG_NO_SUITABLE_JAVA_CHECK="Merci de bien vouloir installer la version de Java requise." MSG_INSTALL_JAVA="Java doit être installé sur votre système.\nRendez-vous sur java.com et suivez les instructions d'installation..." MSG_LATER="Plus tard" MSG_VISIT_JAVA_DOT_COM="Visiter java.com" # German localization elif [[ $LANG == de* ]] ; then MSG_ERROR_LAUNCHING="FEHLER beim Starten von '${CFBundleName}'." MSG_MISSING_MAINCLASS="Die 'MainClass' ist nicht spezifiziert!\nDie Java-Anwendung kann nicht gestartet werden!" MSG_JVMVERSION_REQ_INVALID="Die Syntax der angeforderten Java-Version ist ungültig: %s\nBitte kontaktieren Sie den Entwickler der App." MSG_NO_SUITABLE_JAVA="Es wurde keine passende Java-Version auf Ihrem System gefunden!\nDieses Programm benötigt Java %s" MSG_JAVA_VERSION_OR_LATER="oder neuer" MSG_JAVA_VERSION_LATEST="(neuste Unterversion)" MSG_JAVA_VERSION_MAX="bis %s" MSG_NO_SUITABLE_JAVA_CHECK="Stellen Sie sicher, dass die angeforderte Java-Version installiert ist." MSG_INSTALL_JAVA="Auf Ihrem System muss die 'Java'-Software installiert sein.\nBesuchen Sie java.com für weitere Installationshinweise." MSG_LATER="Später" MSG_VISIT_JAVA_DOT_COM="java.com öffnen" # Simplifyed Chinese localization elif [[ $LANG == zh* ]] ; then MSG_ERROR_LAUNCHING="无法启动 '${CFBundleName}'." MSG_MISSING_MAINCLASS="没有指定 'MainClass'！\nJava程序无法启动!" MSG_JVMVERSION_REQ_INVALID="Java版本参数语法错误: %s\n请联系该应用的开发者。" MSG_NO_SUITABLE_JAVA="没有在系统中找到合适的Java版本！\n必须安装Java %s才能够使用该程序！" MSG_JAVA_VERSION_OR_LATER="及以上版本" MSG_JAVA_VERSION_LATEST="（最新版本）" MSG_JAVA_VERSION_MAX="最高为 %s" MSG_NO_SUITABLE_JAVA_CHECK="请确保系统中安装了所需的Java版本" MSG_INSTALL_JAVA="你需要在Mac中安装Java运行环境！\n访问 java.com 了解如何安装。" MSG_LATER="稍后" MSG_VISIT_JAVA_DOT_COM="访问 java.com" # English default localization else MSG_ERROR_LAUNCHING="ERROR launching '${CFBundleName}'." MSG_MISSING_MAINCLASS="'MainClass' isn't specified!\nJava application cannot be started!" MSG_JVMVERSION_REQ_INVALID="The syntax of the required Java version is invalid: %s\nPlease contact the App developer." MSG_NO_SUITABLE_JAVA="No suitable Java version found on your system!\nThis program requires Java %s" MSG_JAVA_VERSION_OR_LATER="or later" MSG_JAVA_VERSION_LATEST="(latest update)" MSG_JAVA_VERSION_MAX="up to %s" MSG_NO_SUITABLE_JAVA_CHECK="Make sure you install the required Java version." MSG_INSTALL_JAVA="You need to have JAVA installed on your Mac!\nVisit java.com for installation instructions..." MSG_LATER="Later" MSG_VISIT_JAVA_DOT_COM="Visit java.com" fi # function 'get_java_version_from_cmd()' # # returns Java version string from 'java -version' command # works for both old (1.8) and new (9) version schema # # @param1 path to a java JVM executable # @return the Java version number as displayed in 'java -version' command ################################################################################ function get_java_version_from_cmd() { # second sed command strips " and -ea from the version string echo $("$1" -version 2>&1 | awk '/version/{print $NF}' | sed -E 's/"//g;s/-ea//g') } # function 'extract_java_major_version()' # # extract Java major version from a version string # # @param1 a Java version number ('1.8.0_45') or requirement string ('1.8+') # @return the major version (e.g. '7', '8' or '9', etc.) ################################################################################ function extract_java_major_version() { echo $(echo "$1" | sed -E 's/^1\.//;s/^([0-9]+)(-ea|(\.[0-9_.]{1,7})?)(-b[0-9]+-[0-9]+)?[+*]?$/\1/') } # function 'get_comparable_java_version()' # # return comparable version for a Java version number or requirement string # # @param1 a Java version number ('1.8.0_45') or requirement string ('1.8+') # @return an 8 digit numeral ('1.8.0_45'->'08000045'; '9.1.13'->'09001013') ################################################################################ function get_comparable_java_version() { # cleaning: 1) remove leading '1.'; 2) remove build string (e.g. '-b14-468'); 3) remove 'a-Z' and '-*+' (e.g. '-ea'); 4) replace '_' with '.' local cleaned=$(echo "$1" | sed -E 's/^1\.//g;s/-b[0-9]+-[0-9]+$//g;s/[a-zA-Z+*\-]//g;s/_/./g') # splitting at '.' into an array local arr=( ${cleaned//./ } ) # echo a string with left padded version numbers echo "$(printf '%02s' ${arr[0]})$(printf '%03s' ${arr[1]})$(printf '%03s' ${arr[2]})" } # function 'is_valid_requirement_pattern()' # # check whether the Java requirement is a valid requirement pattern # # supported requirements are for example: # - 1.6 requires Java 6 (any update) [1.6, 1.6.0_45, 1.6.0_88] # - 1.6* requires Java 6 (any update) [1.6, 1.6.0_45, 1.6.0_88] # - 1.6+ requires Java 6 or higher [1.6, 1.6.0_45, 1.8, 9, etc.] # - 1.6.0 requires Java 6 (any update) [1.6, 1.6.0_45, 1.6.0_88] # - 1.6.0_45 requires Java 6u45 [1.6.0_45] # - 1.6.0_45+ requires Java 6u45 or higher [1.6.0_45, 1.6.0_88, 1.8, etc.] # - 9 requires Java 9 (any update) [9.0.*, 9.1, 9.3, etc.] # - 9* requires Java 9 (any update) [9.0.*, 9.1, 9.3, etc.] # - 9+ requires Java 9 or higher [9.0, 9.1, 10, etc.] # - 9.1 requires Java 9.1 (any update) [9.1.*, 9.1.2, 9.1.13, etc.] # - 9.1* requires Java 9.1 (any update) [9.1.*, 9.1.2, 9.1.13, etc.] # - 9.1+ requires Java 9.1 or higher [9.1, 9.2, 10, etc.] # - 9.1.3 requires Java 9.1.3 [9.1.3] # - 9.1.3* requires Java 9.1.3 (any update) [9.1.3] # - 9.1.3+ requires Java 9.1.3 or higher [9.1.3, 9.1.4, 9.2.*, 10, etc.] # - 10-ea requires Java 10 (early access release) # # unsupported requirement patterns are for example: # - 1.2, 1.3, 1.9 Java 2, 3 are not supported # - 1.9 Java 9 introduced a new versioning scheme # - 6u45 known versioning syntax, but unsupported # - 9-ea*, 9-ea+ early access releases paired with */+ # - 9., 9.*, 9.+ version ending with a . # - 9.1., 9.1.*, 9.1.+ version ending with a . # - 9.3.5.6 4 part version number is unsupported # # @param1 a Java requirement string ('1.8+') # @return boolean exit code: 0 (is valid), 1 (is not valid) ################################################################################ function is_valid_requirement_pattern() { local java_req=$1 java8pattern='1\.[4-8](\.0)?(\.0_[0-9]+)?[*+]?' java9pattern='(9|1[0-9])(-ea|[*+]|(\.[0-9]+){1,2}[*+]?)?' # test matches either old Java versioning scheme (up to 1.8) or new scheme (starting with 9) if [[ ${java_req} =~ ^(${java8pattern}|${java9pattern})$ ]]; then return 0 else return 1 fi } # determine which JVM to use ############################################ # default Apple JRE plugin path (< 1.6) apple_jre_plugin="/Library/Java/Home/bin/java" apple_jre_version=$(get_java_version_from_cmd "${apple_jre_plugin}") # default Oracle JRE plugin path (>= 1.7) oracle_jre_plugin="/Library/Internet Plug-Ins/JavaAppletPlugin.plugin/Contents/Home/bin/java" oracle_jre_version=$(get_java_version_from_cmd "${oracle_jre_plugin}") # first check system variable "$JAVA_HOME" -> has precedence over any other System JVM stub_logger '[JavaSearch] Checking for $JAVA_HOME ...' if [ -n "$JAVA_HOME" ] ; then stub_logger "[JavaSearch] ... found JAVA_HOME with value $JAVA_HOME" # PR 26: Allow specifying "$JAVA_HOME" relative to "$AppPackageFolder" # which allows for bundling a custom version of Java inside your app! if [[ $JAVA_HOME == /* ]] ; then # if "$JAVA_HOME" starts with a Slash it's an absolute path JAVACMD="$JAVA_HOME/bin/java" else # otherwise it's a relative path to "$AppPackageFolder" JAVACMD="$AppPackageFolder/$JAVA_HOME/bin/java" fi JAVACMD_version=$(get_comparable_java_version $(get_java_version_from_cmd "${JAVACMD}")) else stub_logger "[JavaSearch] ... didn't found JAVA_HOME" fi # check for any other or a specific Java version # also if $JAVA_HOME exists but isn't executable if [ -z "${JAVACMD}" ] || [ ! -x "${JAVACMD}" ] ; then stub_logger "[JavaSearch] Checking for JavaVirtualMachines on the system ..." # reset variables JAVACMD="" JAVACMD_version="" # first check whether JVMVersion string is a valid requirement string if [ ! -z "${JVMVersion}" ] && ! is_valid_requirement_pattern ${JVMVersion} ; then MSG_JVMVERSION_REQ_INVALID_EXPANDED=$(printf "${MSG_JVMVERSION_REQ_INVALID}" "${JVMVersion}") # log exit cause stub_logger "[EXIT 4] ${MSG_JVMVERSION_REQ_INVALID_EXPANDED}" # display error message with AppleScript osascript -e "tell application \"System Events\" to display dialog \"${MSG_ERROR_LAUNCHING}\n\n${MSG_JVMVERSION_REQ_INVALID_EXPANDED}\" with title \"${CFBundleName}\" buttons {\" OK \"} default button 1 with icon path to resource \"${CFBundleIconFile}\" in bundle (path to me)" # exit with error exit 4 fi # then check whether JVMMaxVersion string is a valid requirement string if [ ! -z "${JVMMaxVersion}" ] && ! is_valid_requirement_pattern ${JVMMaxVersion} ; then MSG_JVMVERSION_REQ_INVALID_EXPANDED=$(printf "${MSG_JVMVERSION_REQ_INVALID}" "${JVMMaxVersion}") # log exit cause stub_logger "[EXIT 5] ${MSG_JVMVERSION_REQ_INVALID_EXPANDED}" # display error message with AppleScript osascript -e "tell application \"System Events\" to display dialog \"${MSG_ERROR_LAUNCHING}\n\n${MSG_JVMVERSION_REQ_INVALID_EXPANDED}\" with title \"${CFBundleName}\" buttons {\" OK \"} default button 1 with icon path to resource \"${CFBundleIconFile}\" in bundle (path to me)" # exit with error exit 5 fi # find installed JavaVirtualMachines (JDK + JRE) allJVMs=() # read JDK's from '/usr/libexec/java_home -V' command while read -r line; do version=$(echo $line | awk -F $',' '{print $1;}') path=$(echo $line | awk -F $'" ' '{print $2;}') path+="/bin/java" allJVMs+=("$version:$path") done < <(/usr/libexec/java_home -V 2>&1 | grep '^[[:space:]]') # unset while loop variables unset version path # add Apple JRE if available if [ -x "${apple_jre_plugin}" ] ; then allJVMs+=("$apple_jre_version:$apple_jre_plugin") fi # add Oracle JRE if available if [ -x "${oracle_jre_plugin}" ] ; then allJVMs+=("$oracle_jre_version:$oracle_jre_plugin") fi # debug output for i in "${allJVMs[@]}" do stub_logger "[JavaSearch] ... found JVM: $i" done # determine JVMs matching the min/max version requirement minC=$(get_comparable_java_version ${JVMVersion}) maxC=$(get_comparable_java_version ${JVMMaxVersion}) matchingJVMs=() for i in "${allJVMs[@]}" do # split JVM string at ':' delimiter to retain spaces in $path substring IFS=: arr=($i) ; unset IFS # [0] JVM version number ver=${arr[0]} # comparable JVM version number comp=$(get_comparable_java_version $ver) # [1] JVM path path="${arr[1]}" # construct string item for adding to the "matchingJVMs" array item="$comp:$ver:$path" # pre-requisite: current version number needs to be greater than min version number if [ "$comp" -ge "$minC" ] ; then # perform max version checks if max version requirement is present if [ ! -z ${JVMMaxVersion} ] ; then # max version requirement ends with '*' modifier if [[ ${JVMMaxVersion} == *\* ]] ; then # use the '*' modifier from the max version string as wildcard for a 'starts with' comparison # and check whether the current version number starts with the max version wildcard string if [[ ${ver} == ${JVMMaxVersion} ]]; then matchingJVMs+=("$item") # or whether the current comparable version is lower than the comparable max version elif [ "$comp" -le "$maxC" ] ; then matchingJVMs+=("$item") fi # max version requirement ends with '+' modifier -> always add this version if it's greater than $min # because a max requirement with + modifier doesn't make sense elif [[ ${JVMMaxVersion} == *+ ]] ; then matchingJVMs+=("$item") # matches 6 zeros at the end of the max version string (e.g. for 1.8, 9) # -> then the max version string should be treated like with a '*' modifier at the end #elif [[ ${maxC} =~ ^[0-9]{2}0{6}$ ]] && [ "$comp" -le $(( ${maxC#0} + 999 )) ] ; then # matchingJVMs+=("$item") # matches 3 zeros at the end of the max version string (e.g. for 9.1, 10.3) # -> then the max version string should be treated like with a '*' modifier at the end #elif [[ ${maxC} =~ ^[0-9]{5}0{3}$ ]] && [ "$comp" -le "${maxC}" ] ; then # matchingJVMs+=("$item") # matches standard requirements without modifier elif [ "$comp" -le "$maxC" ]; then matchingJVMs+=("$item") fi # no max version requirement: # min version requirement ends with '+' modifier # -> always add the current version because it's greater than $min elif [[ ${JVMVersion} == *+ ]] ; then matchingJVMs+=("$item") # min version requirement ends with '*' modifier # -> use the '*' modifier from the min version string as wildcard for a 'starts with' comparison # and check whether the current version number starts with the min version wildcard string elif [[ ${JVMVersion} == *\* ]] ; then if [[ ${ver} == ${JVMVersion} ]] ; then matchingJVMs+=("$item") fi # compare the min version against the current version with an additional * wildcard for a 'starts with' comparison # -> e.g. add 1.8.0_44 when the requirement is 1.8 elif [[ ${ver} == ${JVMVersion}* ]] ; then matchingJVMs+=("$item") fi fi done # unset for loop variables unset arr ver comp path item # debug output for i in "${matchingJVMs[@]}" do stub_logger "[JavaSearch] ... ... matches all requirements: $i" done # sort the matching JavaVirtualMachines by version number # https://stackoverflow.com/a/11789688/1128689 IFS=$'\n' matchingJVMs=($(sort -nr <<<"${matchingJVMs[*]}")) unset IFS # get the highest matching JVM for ((i = 0; i < ${#matchingJVMs[@]}; i++)); do # split JVM string at ':' delimiter to retain spaces in $path substring IFS=: arr=(${matchingJVMs[$i]}) ; unset IFS # [0] comparable JVM version number comp=${arr[0]} # [1] JVM version number ver=${arr[1]} # [2] JVM path path="${arr[2]}" # use current value as JAVACMD if it's executable if [ -x "$path" ] ; then JAVACMD="$path" JAVACMD_version=$comp break fi done # unset for loop variables unset arr comp ver path fi # log the Java Command and the extracted version number stub_logger "[JavaCommand] '$JAVACMD'" stub_logger "[JavaVersion] $(get_java_version_from_cmd "${JAVACMD}")${JAVACMD_version:+ / $JAVACMD_version}" if [ -z "${JAVACMD}" ] || [ ! -x "${JAVACMD}" ] ; then # different error messages when a specific JVM was required if [ ! -z "${JVMVersion}" ] ; then # display human readable java version (#28) java_version_hr=$(echo ${JVMVersion} | sed -E 's/^1\.([0-9+*]+)$/ \1/g' | sed "s/+/ ${MSG_JAVA_VERSION_OR_LATER}/;s/*/ ${MSG_JAVA_VERSION_LATEST}/") MSG_NO_SUITABLE_JAVA_EXPANDED=$(printf "${MSG_NO_SUITABLE_JAVA}" "${java_version_hr}"). if [ ! -z "${JVMMaxVersion}" ] ; then java_version_hr=$(extract_java_major_version ${JVMVersion}) java_version_max_hr=$(echo ${JVMMaxVersion} | sed -E 's/^1\.([0-9+*]+)$/ \1/g' | sed "s/+//;s/*/ ${MSG_JAVA_VERSION_LATEST}/") MSG_NO_SUITABLE_JAVA_EXPANDED="$(printf "${MSG_NO_SUITABLE_JAVA}" "${java_version_hr}") $(printf "${MSG_JAVA_VERSION_MAX}" "${java_version_max_hr}")" fi # log exit cause stub_logger "[EXIT 3] ${MSG_NO_SUITABLE_JAVA_EXPANDED}" # display error message with AppleScript osascript -e "tell application \"System Events\" to display dialog \"${MSG_ERROR_LAUNCHING}\n\n${MSG_NO_SUITABLE_JAVA_EXPANDED}\n${MSG_NO_SUITABLE_JAVA_CHECK}\" with title \"${CFBundleName}\" buttons {\" OK \", \"${MSG_VISIT_JAVA_DOT_COM}\"} default button \"${MSG_VISIT_JAVA_DOT_COM}\" with icon path to resource \"${CFBundleIconFile}\" in bundle (path to me)" \ -e "set response to button returned of the result" \ -e "if response is \"${MSG_VISIT_JAVA_DOT_COM}\" then open location \"http://java.com\"" # exit with error exit 3 else # log exit cause stub_logger "[EXIT 1] ${MSG_ERROR_LAUNCHING}" # display error message with AppleScript osascript -e "tell application \"System Events\" to display dialog \"${MSG_ERROR_LAUNCHING}\n\n${MSG_INSTALL_JAVA}\" with title \"${CFBundleName}\" buttons {\"${MSG_LATER}\", \"${MSG_VISIT_JAVA_DOT_COM}\"} default button \"${MSG_VISIT_JAVA_DOT_COM}\" with icon path to resource \"${CFBundleIconFile}\" in bundle (path to me)" \ -e "set response to button returned of the result" \ -e "if response is \"${MSG_VISIT_JAVA_DOT_COM}\" then open location \"http://java.com\"" # exit with error exit 1 fi fi # MainClass check ############################################ if [ -z "${JVMMainClass}" ]; then # log exit cause stub_logger "[EXIT 2] ${MSG_MISSING_MAINCLASS}" # display error message with AppleScript osascript -e "tell application \"System Events\" to display dialog \"${MSG_ERROR_LAUNCHING}\n\n${MSG_MISSING_MAINCLASS}\" with title \"${CFBundleName}\" buttons {\" OK \"} default button 1 with icon path to resource \"${CFBundleIconFile}\" in bundle (path to me)" # exit with error exit 2 fi # execute $JAVACMD and do some preparation ############################################ # enable drag&drop to the dock icon export CFProcessPath="$0" # remove Apples ProcessSerialNumber from passthru arguments (#39) if [[ $@ == -psn* ]] ; then ArgsPassthru=() else ArgsPassthru=("$@") fi # change to Working Directory based upon Apple/Oracle Plist info cd "${WorkingDirectory}" || exit 13 stub_logger "[WorkingDirectory] ${WorkingDirectory}" # execute Java and set # - classpath # - splash image # - dock icon # - app name # - JVM options # - JVM default options # - main class # - main arguments # - passthru arguments stub_logger "[Exec] \"$JAVACMD\" -cp \"${JVMClassPath}\" -splash:\"${ResourcesFolder}/${JVMSplashFile}\" -Xdock:icon=\"${ResourcesFolder}/${CFBundleIconFile}\" -Xdock:name=\"${CFBundleName}\" ${JVMOptionsArr:+$(printf "'%s' " "${JVMOptionsArr[@]}") }${JVMDefaultOptions:+$JVMDefaultOptions }${JVMMainClass}${MainArgsArr:+ $(printf "'%s' " "${MainArgsArr[@]}")}${ArgsPassthru:+ $(printf "'%s' " "${ArgsPassthru[@]}")}" exec "${JAVACMD}" \ -cp "${JVMClassPath}" \ -splash:"${ResourcesFolder}/${JVMSplashFile}" \ -Xdock:icon="${ResourcesFolder}/${CFBundleIconFile}" \ -Xdock:name="${CFBundleName}" \ ${JVMOptions:+"$JVMOptions[@]}" }\ ${JVMDefaultOptions:+$JVMDefaultOptions }\ "${JVMMainClass}"\ ${MainArgsArr:+ "${MainArgsArr[@]}"}\ ${ArgsPassthru:+ "${ArgsPassthru[@]}"} ================================================ FILE: package.sh ================================================ ## Internal script for compiling and packaging DMG and EXE ## Compiles with appropriate properties file depending on if ## -b flag is set (if set, compile for BCM) ## Set the two globals at the top for your system #!/bin/bash set -e shopt -s extglob ## GLOBALS: Set for your system # executable for launch4j, which bundles EXE LAUNCH4J_EXE="/Users/nchernia/Downloads/launch4j/launch4j" # Lab At Large location, needed for certificates LAL_DROPBOX="/Users/nchernia/Dropbox (Lab at Large)/" printHelpAndExit() { echo "Usage: ${0##*/} -bh" echo " -v : 1.6.1 e.g. Required" echo " -b: BCM-only version" echo " -h: Print this help and exit" exit "$1" } while getopts "v:bh" opt; do case $opt in v) VERSION=$OPTARG ;; h) printHelpAndExit 0;; b) BCM=1 ;; [?]) printHelpAndExit 1;; esac done if [ -z "$VERSION" ] then printHelpAndExit 1 fi if [ -z "${BCM}" ] then CONFIG_FILE="config.xml" else CONFIG_FILE="config_bcm.xml" fi # these shouldn't need to be changed BASE_DIR=$(pwd) APP_NAME="Juicebox" ARTIFACT_DIR="${BASE_DIR}/out/artifacts/Juicebox_jar" DMG_BACKGROUND_IMG="Juicebox_bg.png" # compile, bundle, sign cd "${BASE_DIR}" rm -r out ant #ant sign -- don't sign for DMG, problem with slowness if [ -z "${BCM}" ] then ant bundle -Dversion="$VERSION" else ant bundlebcm # this is deprecated fi cd "${ARTIFACT_DIR}" APP_EXE="${APP_NAME}.app/Contents/MacOS/JavaAppLauncher" VOL_NAME="${APP_NAME}_${VERSION}" DMG_TMP="${VOL_NAME}-temp.dmg" DMG_FINAL="${VOL_NAME}.dmg" STAGING_DIR="./Install" # clear out any old data rm -rf "${STAGING_DIR}" "${DMG_TMP}" "${DMG_FINAL}" codesign -s "Erez Aiden" "${APP_NAME}".app --deep # copy over the stuff we want in the final disk image to our staging dir mkdir -p "${STAGING_DIR}" cp -rpf "${APP_NAME}.app" "${STAGING_DIR}" # ... cp anything else you want in the DMG - documentation, etc. pushd "${STAGING_DIR}" # strip the executable #echo "Stripping ${APP_EXE}..." #strip -u -r "${APP_EXE}" # compress the executable if we have upx in PATH # UPX: http://upx.sourceforge.net/ #if hash upx 2>/dev/null; then # echo "Compressing (UPX) ${APP_EXE}..." # upx -9 "${APP_EXE}" #fi # ... perform any other stripping/compressing of libs and executables popd # figure out how big our DMG needs to be # assumes our contents are at least 1M! SIZE=`du -sh "${STAGING_DIR}" | sed 's/\([0-9]*\)M\(.*\)/\1/'` SIZE=`echo "${SIZE} + 1.0" | bc | awk '{print int($1+0.5)}'` if [ $? -ne 0 ]; then echo "Error: Cannot compute size of staging dir" exit fi # create the temp DMG file hdiutil create -srcfolder "${STAGING_DIR}" -volname "${VOL_NAME}" -fs HFS+ \ -fsargs "-c c=64,a=16,e=16" -format UDRW -size ${SIZE}M "${DMG_TMP}" echo "Created DMG: ${DMG_TMP}" # mount it and save the device DEVICE=$(hdiutil attach -readwrite -noverify "${DMG_TMP}" | \ egrep '^/dev/' | sed 1q | awk '{print $1}') sleep 2 # add a link to the Applications dir echo "Add link to /Applications" pushd /Volumes/"${VOL_NAME}" ln -s /Applications popd # add a background image mkdir /Volumes/"${VOL_NAME}"/.background cp "${BASE_DIR}/${DMG_BACKGROUND_IMG}" /Volumes/"${VOL_NAME}"/.background/ # tell the Finder to resize the window, set the background, # change the icon size, place the icons in the right position, etc. echo ' tell application "Finder" tell disk "'${VOL_NAME}'" open set current view of container window to icon view set toolbar visible of container window to false set statusbar visible of container window to false set the bounds of container window to {400, 100, 920, 460} set viewOptions to the icon view options of container window set arrangement of viewOptions to not arranged set icon size of viewOptions to 72 set background picture of viewOptions to file ".background:'${DMG_BACKGROUND_IMG}'" set position of item "'${APP_NAME}'.app" of container window to {140, 170} set position of item "Applications" of container window to {380, 170} close open update without registering applications delay 2 end tell end tell ' | osascript sync # unmount it hdiutil detach "${DEVICE}" # now make the final image a compressed disk image echo "Creating compressed image" hdiutil convert "${DMG_TMP}" -format UDZO -imagekey zlib-level=9 -o "${DMG_FINAL}" # clean up rm -rf "${DMG_TMP}" rm -rf "${STAGING_DIR}" echo 'Done creating DMG' ### ### BUNDLE EXE ### cd "${BASE_DIR}" ant sign cd "${BASE_DIR}"/l4j # clean up any old versions if ls *.exe 1> /dev/null 2>&1 then rm *.exe fi # Package exe "${LAUNCH4J_EXE}" "${CONFIG_FILE}" # Sign. Uncomment below to change signature #openssl pkcs12 -in ${LAL_DROPBOX}/important_jars/ErezSLieberman.p12 -nocerts\ # -nodes -out ${LAL_DROPBOX}/important_jars/certificate.pem # Sign for the first time. Password juicebox. To create new password, # uncomment above line, change "-pass" below osslsigncode sign -certs "${LAL_DROPBOX}"/important_jars/erez_s_lieberman.pem \ -key "${LAL_DROPBOX}"/important_jars/certificate.pem -pass juicebox \ -n ${APP_NAME} -i http://aidenlab.org/ -in "${BASE_DIR}"/l4j/Juicebox.exe \ -out "${BASE_DIR}"/l4j/signed.exe # Find the size of the signature in bytes # i.e. sizeInBytesOf(signed.exe) - sizeInBytesOf(Juicebox.exe) sizeInBytesSigned=$(ls -l "${BASE_DIR}"/l4j/signed.exe | awk '{print $5}') sizeInBytesUnsigned=$(ls -l "${BASE_DIR}"/l4j/Juicebox.exe | awk '{print $5}') # Print difference in Little Endian hex echo "Edit ${BASE_DIR}/l4j/Juicebox.exe " echo "with your favorite HEX editor to change last two bytes of the exe." # This tells the zip file that there is a signature and what size. echo "Edit with the following value, save, and press enter to continue:" awk -v s1=$sizeInBytesSigned -v s2=$sizeInBytesUnsigned 'BEGIN{str=sprintf("%x", s1-s2); x=substr(str,3,2); x=x substr(str,1,2); print x}' read line # Sign the modified Juicebox.exe using above osslsigncode again osslsigncode sign -certs "${LAL_DROPBOX}"/important_jars/erez_s_lieberman.pem \ -key "${LAL_DROPBOX}"/important_jars/certificate.pem -pass juicebox \ -n "Juicebox" -i http://aidenlab.org/ -in "${BASE_DIR}"/l4j/Juicebox.exe \ -out "${BASE_DIR}"/l4j/signed.exe mv "${BASE_DIR}"/l4j/signed.exe "${ARTIFACT_DIR}"/Juicebox\ ${VERSION}.exe mv "${ARTIFACT_DIR}"/Juicebox.jar "${ARTIFACT_DIR}"/Juicebox\ ${VERSION}.jar echo "Done. The packaged executables live in ${ARTIFACT_DIR}" ================================================ FILE: src/images/manifest.mf ================================================ Manifest-Version: 1.0 X-COMMENT: Main-Class will be added automatically by build ================================================ FILE: src/juicebox/CommandBroadcaster.java ================================================ /* * The MIT License (MIT) * * Copyright (c) 2011-2020 Broad Institute, Aiden Lab, Rice University, Baylor College of Medicine * * Permission is hereby granted, free of charge, to any person obtaining a copy * of this software and associated documentation files (the "Software"), to deal * in the Software without restriction, including without limitation the rights * to use, copy, modify, merge, publish, distribute, sublicense, and/or sell * copies of the Software, and to permit persons to whom the Software is * furnished to do so, subject to the following conditions: * * The above copyright notice and this permission notice shall be included in * all copies or substantial portions of the Software. * * THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR * IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, * FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE * AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER * LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, * OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN * THE SOFTWARE. */ package juicebox; import java.io.IOException; import java.io.PrintWriter; import java.net.Socket; //import java.io.InputStreamReader; //import java.net.UnknownHostException; //import java.util.ArrayList; //import java.util.List; /** * @author jrobinso * Date: 10/21/13 * Time: 2:59 PM */ class CommandBroadcaster { public static int selfPort; public static final int numPorts = 50; public static void broadcast(String command) { // Broadcast self port to other running instances for (int p = 30000; p <= 30000 + numPorts - 1; p++) { if (p == selfPort) continue; // don't broadcast to self try { CommandBroadcaster.broadcastCommand(command, p); } catch (java.net.ConnectException e) { // Expected } catch (IOException e) { e.printStackTrace(); //To change body of catch statement use File | Settings | File Templates. } } } private static void broadcastCommand(String command, int port) throws IOException { Socket socket = null; PrintWriter out = null; try { socket = new Socket("127.0.0.1", port); out = new PrintWriter(socket.getOutputStream(), true); out.println(command); } finally { try { if (out != null) out.close(); if (socket != null) socket.close(); } catch (IOException e) { e.printStackTrace(); //To change body of catch statement use File | Settings | File Templates. } } } } ================================================ FILE: src/juicebox/CommandExecutor.java ================================================ /* * The MIT License (MIT) * * Copyright (c) 2011-2020 Broad Institute, Aiden Lab, Rice University, Baylor College of Medicine * * Permission is hereby granted, free of charge, to any person obtaining a copy * of this software and associated documentation files (the "Software"), to deal * in the Software without restriction, including without limitation the rights * to use, copy, modify, merge, publish, distribute, sublicense, and/or sell * copies of the Software, and to permit persons to whom the Software is * furnished to do so, subject to the following conditions: * * The above copyright notice and this permission notice shall be included in * all copies or substantial portions of the Software. * * THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR * IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, * FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE * AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER * LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, * OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN * THE SOFTWARE. */ /* * To change this template, choose Tools | Templates * and open the template in the editor. */ package juicebox; import org.broad.igv.util.StringUtils; import java.util.ArrayList; import java.util.List; class CommandExecutor { private final HiC hic; public CommandExecutor(HiC hic) { this.hic = hic; } private List getArgs(String[] tokens) { List args = new ArrayList<>(tokens.length); for (String s : tokens) { if (s.trim().length() > 0) { args.add(s.trim()); } } return args; } public String execute(String command) { List commandString = StringUtils.breakQuotedString(command, ' '); List args = getArgs(commandString.toArray(new String[commandString.size()])); String result = "OK"; System.err.println("Executing: " + command); try { if (args.size() > 0) { String cmd = args.get(0).toLowerCase(); if (cmd.equals("setlocation")) { if (args.size() > 7) { String chrXName = args.get(1); String chrYName = args.get(2); String unitName = args.get(3); HiC.Unit unit = HiC.valueOfUnit(unitName); int binSize = Integer.parseInt(args.get(4)); double xOrigin = Double.parseDouble(args.get(5)); double yOrigin = Double.parseDouble(args.get(6)); double scaleFactor = Double.parseDouble(args.get(7)); hic.setLocation(chrXName, chrYName, unit, binSize, xOrigin, yOrigin, scaleFactor, HiC.ZoomCallType.DIRECT, "Goto Sync", false); } else { result = "Not enough parameters"; } } } else { result = "Unknown command string"; } } catch (Exception e) { System.err.println(e.getLocalizedMessage()); result = "Error: " + e.getMessage(); } return result; } } ================================================ FILE: src/juicebox/CommandListener.java ================================================ /* * The MIT License (MIT) * * Copyright (c) 2011-2021 Broad Institute, Aiden Lab, Rice University, Baylor College of Medicine * * Permission is hereby granted, free of charge, to any person obtaining a copy * of this software and associated documentation files (the "Software"), to deal * in the Software without restriction, including without limitation the rights * to use, copy, modify, merge, publish, distribute, sublicense, and/or sell * copies of the Software, and to permit persons to whom the Software is * furnished to do so, subject to the following conditions: * * The above copyright notice and this permission notice shall be included in * all copies or substantial portions of the Software. * * THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR * IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, * FITNESS FOR A PARTICULAR PURPOSE AND NON-INFRINGEMENT. IN NO EVENT SHALL THE * AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER * LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, * OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN * THE SOFTWARE. */ package juicebox; import java.io.BufferedReader; import java.io.IOException; import java.io.InputStreamReader; import java.net.ServerSocket; import java.net.Socket; class CommandListener implements Runnable { private static CommandListener listener; private final Thread listenerThread; private final HiC hic; private int port = -1; private ServerSocket serverSocket = null; private Socket clientSocket = null; private boolean halt = false; private CommandListener(int port, HiC hic) throws IOException { this.port = port; this.hic = hic; listenerThread = new Thread(this); serverSocket = new ServerSocket(port); } public static synchronized void start(HiC hic) { // Grab the first available port int port = 0; for (int p = 30000; p <= 30000 + CommandBroadcaster.numPorts - 1; p++) { try { listener = new CommandListener(p, hic); listener.listenerThread.start(); port = p; break; } catch (IOException e) { // Expected condition -- port in use } } CommandBroadcaster.selfPort = port; } public static synchronized void halt() { if (listener != null) { listener.halt = true; listener.listenerThread.interrupt(); listener.closeSockets(); listener = null; } } /** * Loop forever, processing client requests synchronously. The server is single threaded. */ public void run() { CommandExecutor cmdExe = new CommandExecutor(hic); System.out.println("Listening on port " + port); try { while (!halt) { clientSocket = serverSocket.accept(); processClientRequest(cmdExe); if (clientSocket != null) { try { clientSocket.close(); clientSocket = null; } catch (IOException e) { System.err.println("Error in client socket loop" + e.getLocalizedMessage()); } } } } catch (IOException e) { e.printStackTrace(); //To change body of catch statement use File | Settings | File Templates. } } /** * Process a client request * * @param cmdExe * @throws IOException */ private void processClientRequest(CommandExecutor cmdExe) throws IOException { BufferedReader in = null; try { in = new BufferedReader(new InputStreamReader(clientSocket.getInputStream()), HiCGlobals.bufferSize); String cmd; while (!halt && (cmd = in.readLine()) != null) { if (cmd.equalsIgnoreCase("halt")) { halt = true; return; } cmdExe.execute(cmd); } } catch (IOException e) { System.err.println("Error processing client session" + e.getLocalizedMessage()); } finally { if (in != null) in.close(); } } private void closeSockets() { if (clientSocket != null) { try { clientSocket.close(); clientSocket = null; } catch (IOException e) { System.err.println("Error closing clientSocket" + e.getLocalizedMessage()); } } if (serverSocket != null) { try { serverSocket.close(); serverSocket = null; } catch (IOException e) { System.err.println("Error closing server socket" + e.getLocalizedMessage()); } } } } ================================================ FILE: src/juicebox/Context.java ================================================ /* * The MIT License (MIT) * * Copyright (c) 2011-2020 Broad Institute, Aiden Lab, Rice University, Baylor College of Medicine * * Permission is hereby granted, free of charge, to any person obtaining a copy * of this software and associated documentation files (the "Software"), to deal * in the Software without restriction, including without limitation the rights * to use, copy, modify, merge, publish, distribute, sublicense, and/or sell * copies of the Software, and to permit persons to whom the Software is * furnished to do so, subject to the following conditions: * * The above copyright notice and this permission notice shall be included in * all copies or substantial portions of the Software. * * THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR * IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, * FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE * AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER * LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, * OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN * THE SOFTWARE. */ package juicebox; import juicebox.data.basics.Chromosome; import juicebox.windowui.HiCZoom; /** * @author jrobinso * @since Aug 11, 2010 */ public class Context { private final Chromosome chromosome; private HiCZoom zoom; private double binOrigin = 0; public Context(Chromosome chromosome) { this.chromosome = chromosome; } public double getBinOrigin() { return binOrigin; } public void setBinOrigin(double binOrigin) { this.binOrigin = binOrigin; } public int getGenomicPositionOrigin() { return (int) (binOrigin * zoom.getBinSize()); } public HiCZoom getZoom() { return zoom; } public void setZoom(HiCZoom zoom) { this.zoom = zoom; } public long getChrLength() { return chromosome.getLength(); } public Chromosome getChromosome() { return chromosome; } } ================================================ FILE: src/juicebox/DirectoryManager.java ================================================ /* * The MIT License (MIT) * * Copyright (c) 2011-2020 Broad Institute, Aiden Lab, Rice University, Baylor College of Medicine * * Permission is hereby granted, free of charge, to any person obtaining a copy * of this software and associated documentation files (the "Software"), to deal * in the Software without restriction, including without limitation the rights * to use, copy, modify, merge, publish, distribute, sublicense, and/or sell * copies of the Software, and to permit persons to whom the Software is * furnished to do so, subject to the following conditions: * * The above copyright notice and this permission notice shall be included in * all copies or substantial portions of the Software. * * THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR * IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, * FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE * AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER * LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, * OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN * THE SOFTWARE. */ package juicebox; import org.broad.igv.Globals; import org.broad.igv.exceptions.DataLoadException; import org.broad.igv.ui.util.FileDialogUtils; import javax.swing.*; import javax.swing.filechooser.FileSystemView; import java.io.File; import java.io.IOException; import java.util.prefs.Preferences; /** * @author Jim Robinson * @since 3/19/12 */ public class DirectoryManager { private final static String HIC_DIR_USERPREF = "hicDir"; private static File USER_HOME; private static File USER_DIRECTORY; // FileSystemView.getFileSystemView().getDefaultDirectory(); private static File HIC_DIRECTORY; // The HIC application directory private static File getUserHome() { if (USER_HOME == null) { String userHomeString = System.getProperty("user.home"); USER_HOME = new File(userHomeString); } return USER_HOME; } /** * The user directory. On Mac and Linux this should be the user home directory. On Windows platforms this * is the "My Documents" directory. */ public static synchronized File getUserDirectory() { if (USER_DIRECTORY == null) { System.out.print("Fetching user directory... "); USER_DIRECTORY = FileSystemView.getFileSystemView().getDefaultDirectory(); //Mostly for testing, in some environments USER_DIRECTORY can be null if (USER_DIRECTORY == null) { USER_DIRECTORY = getUserHome(); } } return USER_DIRECTORY; } public static File getHiCDirectory() { if (HIC_DIRECTORY == null) { // Hack for known Java / Windows bug. Attempt to remove (possible) read-only bit from user directory if (System.getProperty("os.name").startsWith("Windows")) { try { Runtime.getRuntime().exec("attrib -r \"" + getUserDirectory().getAbsolutePath() + "\""); } catch (Exception e) { // We tried } } HIC_DIRECTORY = getHiCDirectoryOverride(); // If still null, try the default place if (HIC_DIRECTORY == null) { File rootDir = getUserHome(); HIC_DIRECTORY = new File(rootDir, "juicebox"); if (!HIC_DIRECTORY.exists()) { try { boolean wasSuccessful = HIC_DIRECTORY.mkdir(); if (!wasSuccessful) { System.err.println("Failed to create user directory!"); HIC_DIRECTORY = null; } } catch (Exception e) { System.err.println("Error creating juicebox directory" + e.getLocalizedMessage()); } } } // The HIC directory either doesn't exist or isn't writeable. This situation can arise with Windows Vista // and Windows 7 due to a Java bug (http://bugs.sun.com/view_bug.do?bug_id=4787931) if (HIC_DIRECTORY == null || !HIC_DIRECTORY.exists() || !canWrite(HIC_DIRECTORY)) { if (Globals.isHeadless() || Globals.isSuppressMessages()) { System.err.println("Cannot write to hic directory: " + HIC_DIRECTORY.getAbsolutePath()); HIC_DIRECTORY = (new File(".")).getParentFile(); } else { int option = JOptionPane.showConfirmDialog(null, "The default Hi-C directory (" + HIC_DIRECTORY + ") " + "cannot be accessed. Click Yes to choose a new folder or No to exit.
" + "This folder will be used to create the 'hic' directory", "Hi-C Directory Error", JOptionPane.YES_NO_OPTION); if (option == JOptionPane.YES_OPTION) { File parentDirectory = FileDialogUtils.chooseDirectory("Select a location for the hic directory", null); if (parentDirectory != null) { HIC_DIRECTORY = new File(parentDirectory, "hic"); HIC_DIRECTORY.mkdir(); Preferences prefs = Preferences.userNodeForPackage(Globals.class); prefs.put(HIC_DIR_USERPREF, HIC_DIRECTORY.getAbsolutePath()); } } } } if (HIC_DIRECTORY == null || !HIC_DIRECTORY.canRead()) { throw new DataLoadException("Cannot read from user directory", HIC_DIRECTORY.getAbsolutePath()); } else if (!canWrite(HIC_DIRECTORY)) { throw new DataLoadException("Cannot write to user directory", HIC_DIRECTORY.getAbsolutePath()); } System.err.println("HiC Directory: " + HIC_DIRECTORY.getAbsolutePath()); } return HIC_DIRECTORY; } private static File getHiCDirectoryOverride() { Preferences userPrefs = null; File override = null; try { // See if an override location has been specified. This is stored with the Java Preferences API userPrefs = Preferences.userNodeForPackage(Globals.class); String userDir = userPrefs.get(HIC_DIR_USERPREF, null); if (userDir != null) { override = new File(userDir); if (!override.exists()) { override = null; userPrefs.remove(HIC_DIR_USERPREF); } } } catch (Exception e) { assert userPrefs != null; userPrefs.remove(HIC_DIR_USERPREF); override = null; System.err.println("Error creating user directory"); e.printStackTrace(); } return override; } private static boolean canWrite(File directory) { // There are bugs in the Windows Java JVM that can cause user directories to be non-writable (target fix is // Java 7). The only way to know if the directory is writable for sure is to try to write something. if (Globals.IS_WINDOWS) { File testFile = null; try { testFile = new File(directory, "hic332415dsfjdsklt.testfile"); if (testFile.exists()) { testFile.delete(); } testFile.deleteOnExit(); testFile.createNewFile(); return testFile.exists(); } catch (IOException e) { return false; } finally { assert testFile != null; if (testFile.exists()) { testFile.delete(); } } } else { return directory.canWrite(); } } } ================================================ FILE: src/juicebox/HiC.java ================================================ /* * The MIT License (MIT) * * Copyright (c) 2011-2021 Broad Institute, Aiden Lab, Rice University, Baylor College of Medicine * * Permission is hereby granted, free of charge, to any person obtaining a copy * of this software and associated documentation files (the "Software"), to deal * in the Software without restriction, including without limitation the rights * to use, copy, modify, merge, publish, distribute, sublicense, and/or sell * copies of the Software, and to permit persons to whom the Software is * furnished to do so, subject to the following conditions: * * The above copyright notice and this permission notice shall be included in * all copies or substantial portions of the Software. * * THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR * IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, * FITNESS FOR A PARTICULAR PURPOSE AND NON-INFRINGEMENT. IN NO EVENT SHALL THE * AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER * LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, * OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN * THE SOFTWARE. */ package juicebox; import juicebox.data.*; import juicebox.data.anchor.GenericLocus; import juicebox.data.anchor.MotifAnchor; import juicebox.data.basics.Chromosome; import juicebox.gui.SuperAdapter; import juicebox.tools.utils.common.MatrixTools; import juicebox.track.*; import juicebox.track.feature.Feature2D; import juicebox.windowui.HiCZoom; import juicebox.windowui.MatrixType; import juicebox.windowui.NormalizationHandler; import juicebox.windowui.NormalizationType; import org.apache.commons.math.linear.RealMatrix; import org.broad.igv.ui.util.MessageUtils; import org.broad.igv.util.Pair; import org.broad.igv.util.ResourceLocator; import javax.swing.*; import java.awt.*; import java.io.File; import java.io.IOException; import java.io.PrintWriter; import java.util.ArrayList; import java.util.List; /** * This is the "model" class for the HiC viewer. */ public class HiC { private final HiCTrackManager trackManager; private final SuperAdapter superAdapter; private final String eigString = "Eigenvector"; private final String ctrlEigString = "Ctrl_Eigenvector"; private final ZoomActionTracker zoomActionTracker = new ZoomActionTracker(); private final List highlightedFeatures = new ArrayList<>(); private double scaleFactor; private String xPosition; private String yPosition; private MatrixType displayOption = MatrixType.OBSERVED; private NormalizationType obsNormalizationType = NormalizationHandler.NONE; private NormalizationType ctrlNormalizationType = NormalizationHandler.NONE; private ChromosomeHandler chromosomeHandler; private Dataset dataset; private Dataset controlDataset; private HiCZoom currentZoom; //private MatrixZoomData matrixForReloadState; private Context xContext; private Context yContext; private EigenvectorTrack eigenvectorTrack, controlEigenvectorTrack; private ResourceTree resourceTree; private LoadEncodeAction encodeAction; private Point cursorPoint, diagonalCursorPoint, gwCursorPoint; private Point selectedBin; private boolean linkedMode; private boolean m_zoomChanged; private boolean m_displayOptionChanged; private boolean m_normalizationTypeChanged; private boolean showFeatureHighlight; public HiC(SuperAdapter superAdapter) { this.superAdapter = superAdapter; trackManager = new HiCTrackManager(superAdapter, this); //feature2DHandler = new Feature2DHandler(); m_zoomChanged = false; m_displayOptionChanged = false; m_normalizationTypeChanged = false; } /** * @param string * @return string with replacements of 000000 with M and 000 with K */ private static String cleanUpNumbersInName(String string) { string = (new StringBuilder(string)).reverse().toString(); string = string.replaceAll("000000", "M").replaceAll("000", "K"); return (new StringBuilder(string)).reverse().toString(); } public static HiC.Unit valueOfUnit(String unit) { if (unit.equalsIgnoreCase(Unit.BP.toString())) { return Unit.BP; } else if (unit.equalsIgnoreCase(Unit.FRAG.toString())) { return Unit.FRAG; } return null; } public Unit getDefaultUnit() { return dataset.getBpZooms().size() > 0 ? Unit.BP : Unit.FRAG; } public void reset() { dataset = null; controlDataset = null; displayOption = MatrixType.OBSERVED; currentZoom = null; resetContexts(); chromosomeHandler = null; eigenvectorTrack = null; controlEigenvectorTrack = null; resourceTree = null; encodeAction = null; obsNormalizationType = NormalizationHandler.NONE; ctrlNormalizationType = NormalizationHandler.NONE; zoomActionTracker.clear(); clearFeatures(); } //Todo why iterate through tracksToRemove if you end up calling clearFeatures() at the end? public void clearTracksForReloadState() { ArrayList tracksToRemove = new ArrayList<>(trackManager.getLoadedTracks()); for (HiCTrack trackToRemove : tracksToRemove) { String name = trackToRemove.getName(); if (name.equalsIgnoreCase(eigString)) { eigenvectorTrack = null; } else if (name.equalsIgnoreCase(ctrlEigString)) { controlEigenvectorTrack = null; } else { trackManager.removeTrack(trackToRemove); } } clearFeatures(); superAdapter.updateTrackPanel(); } private void clearFeatures() { trackManager.clearTracks(); // feature2DHandler.clearLists(); } /** * Use setCursorPoint() to set cursorPoint to the last known mouse click position before calling this method */ public void undoZoomAction() { zoomActionTracker.undoZoom(); ZoomAction currentZoomAction = zoomActionTracker.getCurrentZoomAction(); unsafeActuallySetZoomAndLocation(currentZoomAction.getChromosomeX(), currentZoomAction.getChromosomeY(), currentZoomAction.getHiCZoom(), currentZoomAction.getGenomeX(), currentZoomAction.getGenomeY(), currentZoomAction.getScaleFactor(), currentZoomAction.getResetZoom(), currentZoomAction.getZoomCallType(), true, currentZoomAction.getResolutionLocked(), false); } /** * Use setCursorPoint() to set cursorPoint to the last known mouse click position before calling this method */ public void redoZoomAction() { zoomActionTracker.redoZoom(); ZoomAction currentZoomAction = zoomActionTracker.getCurrentZoomAction(); unsafeActuallySetZoomAndLocation(currentZoomAction.getChromosomeX(), currentZoomAction.getChromosomeY(), currentZoomAction.getHiCZoom(), currentZoomAction.getGenomeX(), currentZoomAction.getGenomeY(), currentZoomAction.getScaleFactor(), currentZoomAction.getResetZoom(), currentZoomAction.getZoomCallType(), true, currentZoomAction.getResolutionLocked(), false); } public double getScaleFactor() { return scaleFactor; } private void setScaleFactor(double scaleFactor) { this.scaleFactor = Math.max(Math.min(50, scaleFactor), 1e-10); } public void loadEigenvectorTrack() { if (eigenvectorTrack == null) { eigenvectorTrack = new EigenvectorTrack(eigString, eigString, this, false); } if (controlEigenvectorTrack == null && isControlLoaded()) { controlEigenvectorTrack = new EigenvectorTrack(ctrlEigString, ctrlEigString, this, true); } trackManager.add(eigenvectorTrack); if (controlEigenvectorTrack != null && isControlLoaded()) { trackManager.add(controlEigenvectorTrack); } } public void refreshEigenvectorTrackIfExists() { if (eigenvectorTrack != null) { eigenvectorTrack.forceRefreshCache(); } if (controlEigenvectorTrack != null) { controlEigenvectorTrack.forceRefreshCache(); } } public ResourceTree getResourceTree() { return resourceTree; } public void setResourceTree(ResourceTree rTree) { resourceTree = rTree; } public void setEncodeAction(LoadEncodeAction eAction) { encodeAction = eAction; } public boolean isLinkedMode() { return linkedMode; } public void setLinkedMode(boolean linkedMode) { this.linkedMode = linkedMode; } public List getLoadedTracks() { return trackManager == null ? new ArrayList<>() : trackManager.getLoadedTracks(); } public void unsafeLoadHostedTracks(List locators) { trackManager.unsafeTrackLoad(locators); } public void unsafeLoadTrack(String path) { trackManager.unsafeLoadTrackDirectPath(path); } public void loadCoverageTrack(String label) { NormalizationType no = dataset.getNormalizationHandler().getNormTypeFromString(label); trackManager.loadCoverageTrack(no, false); if (isControlLoaded()) { trackManager.loadCoverageTrack(no, true); } } public void removeTrack(HiCTrack track) { if (resourceTree != null) resourceTree.remove(track.getLocator()); if (encodeAction != null) encodeAction.remove(track.getLocator()); trackManager.removeTrack(track); } public void removeTrack(ResourceLocator locator) { if (resourceTree != null) resourceTree.remove(locator); if (encodeAction != null) encodeAction.remove(locator); trackManager.removeTrack(locator); } public void moveTrack(HiCTrack track, boolean thisShouldBeMovedUp) { if (thisShouldBeMovedUp) { //move the track up trackManager.moveTrackUp(track); } else { //move the track down trackManager.moveTrackDown(track); } } public Dataset getDataset() { return dataset; } public void setDataset(Dataset dataset) { this.dataset = dataset; } public Dataset getControlDataset() { return controlDataset; } public void setControlDataset(Dataset controlDataset) { this.controlDataset = controlDataset; } public void setSelectedChromosomes(Chromosome chrX, Chromosome chrY) { this.xContext = new Context(chrX); this.yContext = new Context(chrY); refreshEigenvectorTrackIfExists(); } public HiCZoom getZoom() { return currentZoom; } public MatrixZoomData getZd() throws NullPointerException { Matrix matrix = getMatrix(); if (matrix == null) { throw new NullPointerException("Uninitialized matrix"); } else if (currentZoom == null) { throw new NullPointerException("Uninitialized zoom"); } else { return matrix.getZoomData(currentZoom); } } public MatrixZoomData getControlZd() { Matrix matrix = getControlMatrix(); if (matrix == null || currentZoom == null) { return null; } else { return matrix.getZoomData(currentZoom); } } public Matrix getControlMatrix() { if (controlDataset == null || xContext == null || currentZoom == null) return null; return controlDataset.getMatrix(xContext.getChromosome(), yContext.getChromosome()); } public Context getXContext() { return xContext; } public Context getYContext() { return yContext; } public void resetContexts() { this.xContext = null; this.yContext = null; } public Point getCursorPoint() { return cursorPoint; } public void setCursorPoint(Point point) { this.cursorPoint = point; } public Point getDiagonalCursorPoint() { return diagonalCursorPoint; } public void setDiagonalCursorPoint(Point point) { this.diagonalCursorPoint = point; } public Point getGWCursorPoint() { return gwCursorPoint; } public void setGWCursorPoint(Point point) { gwCursorPoint = point; } public long[] getCurrentRegionWindowGenomicPositions() { // address int overflow or exceeding bound issues long xEndEdge = xContext.getGenomicPositionOrigin() + (int) ((double) getZoom().getBinSize() * superAdapter.getHeatmapPanel().getWidth() / getScaleFactor()); if (xEndEdge < 0 || xEndEdge > xContext.getChromosome().getLength()) { xEndEdge = xContext.getChromosome().getLength(); } long yEndEdge = yContext.getGenomicPositionOrigin() + (int) ((double) getZoom().getBinSize() * superAdapter.getHeatmapPanel().getHeight() / getScaleFactor()); if (yEndEdge < 0 || yEndEdge > yContext.getChromosome().getLength()) { yEndEdge = yContext.getChromosome().getLength(); } return new long[]{xContext.getGenomicPositionOrigin(), xEndEdge, yContext.getGenomicPositionOrigin(), yEndEdge}; } public String getXPosition() { return xPosition; } public void setXPosition(String txt) { this.xPosition = txt; } public String getYPosition() { return yPosition; } public void setYPosition(String txt) { this.yPosition = txt; } public Matrix getMatrix() { if (dataset == null) { if (HiCGlobals.printVerboseComments) { System.err.println("Dataset is null"); } return null; } else if (xContext == null) { if (HiCGlobals.printVerboseComments) { System.err.println("xContext is null"); } return null; } else if (yContext == null) { if (HiCGlobals.printVerboseComments) { System.err.println("yContext is null"); } return null; } return dataset.getMatrix(xContext.getChromosome(), yContext.getChromosome()); } public void setSelectedBin(Point point) { if (point.equals(this.selectedBin)) { this.selectedBin = null; } else { this.selectedBin = point; } } public MatrixType getDisplayOption() { return displayOption; } public void setDisplayOption(MatrixType newDisplay) { if (this.displayOption != newDisplay) { this.displayOption = newDisplay; setDisplayOptionChanged(); } } public boolean isControlLoaded() { return controlDataset != null; } public boolean isWholeGenome() { return xContext != null && ChromosomeHandler.isAllByAll(xContext.getChromosome()); } private void setZoomChanged() { m_zoomChanged = true; } //Check zoom change value and reset. public synchronized boolean testZoomChanged() { if (m_zoomChanged) { m_zoomChanged = false; return true; } return false; } public void centerFragment(int fragmentX, int fragmentY) { if (currentZoom != null) { MatrixZoomData zd = getMatrix().getZoomData(currentZoom); HiCGridAxis xAxis = zd.getXGridAxis(); HiCGridAxis yAxis = zd.getYGridAxis(); int binX; int binY; try { binX = xAxis.getBinNumberForFragment(fragmentX); //noinspection SuspiciousNameCombination binY = yAxis.getBinNumberForFragment(fragmentY); center(binX, binY); } catch (RuntimeException error) { superAdapter.launchGenericMessageDialog(error.getMessage(), "Error", JOptionPane.ERROR_MESSAGE); } } } public void centerBP(int bpX, int bpY) { if (currentZoom != null && getMatrix() != null) { MatrixZoomData zd = getMatrix().getZoomData(currentZoom); HiCGridAxis xAxis = zd.getXGridAxis(); HiCGridAxis yAxis = zd.getYGridAxis(); int binX = xAxis.getBinNumberForGenomicPosition(bpX); int binY = yAxis.getBinNumberForGenomicPosition(bpY); center(binX, binY); } } /** * Center the bins in view at the current resolution. * * @param binX center X * @param binY center Y */ public void center(double binX, double binY) { double w = superAdapter.getHeatmapPanel().getWidth() / getScaleFactor(); // view width in bins int newOriginX = (int) (binX - w / 2); double h = superAdapter.getHeatmapPanel().getHeight() / getScaleFactor(); // view height in bins int newOriginY = (int) (binY - h / 2); moveTo(newOriginX, newOriginY); } /** * Move by the specified delta (in bins) * * @param dxBins -- delta x in bins * @param dyBins -- delta y in bins */ public void moveBy(double dxBins, double dyBins) { final double newX = xContext.getBinOrigin() + dxBins; final double newY = yContext.getBinOrigin() + dyBins; moveTo(newX, newY); } /** * Move to the specified origin (in bins) * * @param newBinX new location X * @param newBinY new location Y */ private void moveTo(double newBinX, double newBinY) { try { MatrixZoomData zd = getZd(); final double wBins = (superAdapter.getHeatmapPanel().getWidth() / getScaleFactor()); double maxX = zd.getXGridAxis().getBinCount() - wBins; final double hBins = (superAdapter.getHeatmapPanel().getHeight() / getScaleFactor()); double maxY = zd.getYGridAxis().getBinCount() - hBins; double x = Math.max(0, Math.min(maxX, newBinX)); double y = Math.max(0, Math.min(maxY, newBinY)); xContext.setBinOrigin(x); yContext.setBinOrigin(y); superAdapter.repaint(); } catch (Exception e) { e.printStackTrace(); } if (linkedMode) { broadcastLocation(); } } private void setDisplayOptionChanged() { m_displayOptionChanged = true; } //Check zoom change value and reset. public synchronized boolean testDisplayOptionChanged() { if (m_displayOptionChanged) { m_displayOptionChanged = false; return true; } return false; } private void setNormalizationTypeChanged() { m_normalizationTypeChanged = true; } //Check zoom change value and reset. public synchronized boolean testNormalizationTypeChanged() { if (m_normalizationTypeChanged) { m_normalizationTypeChanged = false; return true; } return false; } public NormalizationType getObsNormalizationType() { return obsNormalizationType; } public void setObsNormalizationType(String label) { NormalizationType option = dataset.getNormalizationHandler().getNormTypeFromString(label); if (this.obsNormalizationType != option) { this.obsNormalizationType = option; setNormalizationTypeChanged(); } } public NormalizationType getControlNormalizationType() { return ctrlNormalizationType; } public void setControlNormalizationType(String label) { NormalizationType option = dataset.getNormalizationHandler().getNormTypeFromString(label); if (this.ctrlNormalizationType != option) { this.ctrlNormalizationType = option; setNormalizationTypeChanged(); } } public double[] getEigenvector(final int chrIdx, final int n, boolean isControl) { if (isControl) { if (controlDataset == null) return null; Chromosome chr = chromosomeHandler.getChromosomeFromIndex(chrIdx); return controlDataset.getEigenvector(chr, currentZoom, n, ctrlNormalizationType); } else { if (dataset == null) return null; Chromosome chr = chromosomeHandler.getChromosomeFromIndex(chrIdx); return dataset.getEigenvector(chr, currentZoom, n, obsNormalizationType); } } public ExpectedValueFunction getExpectedValues() { if (dataset == null) return null; return dataset.getExpectedValues(currentZoom, obsNormalizationType); } public ExpectedValueFunction getExpectedControlValues() { if (controlDataset == null) return null; return controlDataset.getExpectedValues(currentZoom, ctrlNormalizationType); } public NormalizationVector getNormalizationVector(int chrIdx) { if (dataset == null) return null; return dataset.getNormalizationVector(chrIdx, currentZoom, obsNormalizationType); } public NormalizationVector getControlNormalizationVector(int chrIdx) { if (controlDataset == null) return null; return controlDataset.getNormalizationVector(chrIdx, currentZoom, ctrlNormalizationType); } // Note - this is an inefficient method, used to support tooltip text only. public float getNormalizedObservedValue(int binX, int binY) { float val = Float.NaN; try { val = getZd().getObservedValue(binX, binY, obsNormalizationType); } catch (Exception e) { e.printStackTrace(); } return val; } public float getNormalizedControlValue(int binX, int binY) { float val = Float.NaN; try { val = getControlZd().getObservedValue(binX, binY, ctrlNormalizationType); } catch (Exception e) { e.printStackTrace(); } return val; } /** * Called from alt-drag zoom * * @param xBP0 * @param yBP0 * @param targetBinSize */ public void zoomToDrawnBox(final long xBP0, final long yBP0, final double targetBinSize) { HiCZoom newZoom = currentZoom; if (!isResolutionLocked()) { List zoomList = currentZoom.getUnit() == HiC.Unit.BP ? dataset.getBpZooms() : dataset.getFragZooms(); for (int i = zoomList.size() - 1; i >= 0; i--) { if (zoomList.get(i).getBinSize() >= targetBinSize) { newZoom = zoomList.get(i); break; } } // this addresses draw box to zoom when down from low res pearsons // it can't zoom all the way in, but can zoom in a little more up to 500K if (isInPearsonsMode() && newZoom.getBinSize() < HiCGlobals.MAX_PEARSON_ZOOM) { for (int i = zoomList.size() - 1; i >= 0; i--) { if (zoomList.get(i).getBinSize() >= HiCGlobals.MAX_PEARSON_ZOOM) { newZoom = zoomList.get(i); break; } } } } safeActuallySetZoomAndLocation(newZoom, xBP0, yBP0, newZoom.getBinSize() / targetBinSize, false, ZoomCallType.DRAG, "DragZoom", true); } /** * Triggered by syncs, goto, and load state. */ //reloading the previous location public void setLocation(String chrXName, String chrYName, HiC.Unit unit, int binSize, double xOrigin, double yOrigin, double scaleFactor, ZoomCallType zoomCallType, String message, boolean allowLocationBroadcast) { HiCZoom newZoom = currentZoom; if (currentZoom.getBinSize() != binSize) { newZoom = new HiCZoom(unit, binSize); } safeActuallySetZoomAndLocation(chrXName, chrYName, newZoom, (int) xOrigin, (int) yOrigin, scaleFactor, true, zoomCallType, message, allowLocationBroadcast); } public void unsafeSetLocation(String chrXName, String chrYName, String unitName, int binSize, double xOrigin, double yOrigin, double scaleFactor, ZoomCallType zoomCallType, boolean allowLocationBroadcast) { HiCZoom newZoom = currentZoom; if (currentZoom.getBinSize() != binSize) { newZoom = new HiCZoom(HiC.valueOfUnit(unitName), binSize); } unsafeActuallySetZoomAndLocation(chrXName, chrYName, newZoom, (int) xOrigin, (int) yOrigin, scaleFactor, true, zoomCallType, allowLocationBroadcast, isResolutionLocked() ? 1 : 0, true); } private boolean safeActuallySetZoomAndLocation(HiCZoom newZoom, long genomeX, long genomeY, double scaleFactor, boolean resetZoom, ZoomCallType zoomCallType, String message, boolean allowLocationBroadcast) { return safeActuallySetZoomAndLocation(xContext.getChromosome().toString(), yContext.getChromosome().toString(), newZoom, genomeX, genomeY, scaleFactor, resetZoom, zoomCallType, message, allowLocationBroadcast); } private boolean safeActuallySetZoomAndLocation(final String chrXName, final String chrYName, final HiCZoom newZoom, final long genomeX, final long genomeY, final double scaleFactor, final boolean resetZoom, final ZoomCallType zoomCallType, String message, final boolean allowLocationBroadcast) { final boolean[] returnVal = new boolean[1]; superAdapter.executeLongRunningTask(new Runnable() { @Override public void run() { returnVal[0] = unsafeActuallySetZoomAndLocation(chrXName, chrYName, newZoom, genomeX, genomeY, scaleFactor, resetZoom, zoomCallType, allowLocationBroadcast, isResolutionLocked() ? 1 : 0, true); } }, message); return returnVal[0]; } /** * ************************************************************* * Official Method for setting the zoom and location for heatmap * DO NOT IMPLEMENT A NEW FUNCTION * Make the necessary customizations, then call this function * ************************************************************* * * @param newZoom * @param genomeX * @param genomeY * @param scaleFactor (pass -1 if scaleFactor should be calculated) * @param resolutionLocked (pass -1 if status of lock button should not be saved) * @param storeZoomAction (pass false if function is being used to undo/redo zoom, true otherwise) * @return */ public boolean unsafeActuallySetZoomAndLocation(String chrXName, String chrYName, HiCZoom newZoom, long genomeX, long genomeY, double scaleFactor, boolean resetZoom, ZoomCallType zoomCallType, boolean allowLocationBroadcast, int resolutionLocked, boolean storeZoomAction) { if (dataset == null) return false; // No data in view boolean chromosomesChanged = !(xContext.getChromosome().equals(chromosomeHandler.getChromosomeFromName(chrXName)) && yContext.getChromosome().equals(chromosomeHandler.getChromosomeFromName(chrYName))); if (chrXName.length() > 0 && chrYName.length() > 0) { setChromosomesFromBroadcast(chrXName, chrYName); //We might end with All->All view, make sure normalization state is updated accordingly... superAdapter.getMainViewPanel().setNormalizationDisplayState(superAdapter.getHiC()); } if (newZoom == null) { System.err.println("Invalid zoom " + newZoom); } Chromosome chrX = chromosomeHandler.getChromosomeFromName(chrXName); Chromosome chrY = chromosomeHandler.getChromosomeFromName(chrYName); final Matrix matrix = dataset.getMatrix(chrX, chrY); if (matrix == null) { superAdapter.launchGenericMessageDialog("Sorry, this region is not available", "Matrix unavailable", JOptionPane.WARNING_MESSAGE); return false; } MatrixZoomData newZD = matrix.getZoomData(newZoom); if (ChromosomeHandler.isAllByAll(chrX)) { newZD = matrix.getFirstZoomData(Unit.BP); } if (newZD == null) { superAdapter.launchGenericMessageDialog("Sorry, this zoom is not available", "Zoom unavailable", JOptionPane.WARNING_MESSAGE); return false; } Matrix preZoomMatrix = getMatrix(); double preZoomScaleFactor = getScaleFactor(); Context preZoomXContext = xContext; Context preZoomYContext = yContext; HiCZoom preZoomHiCZoom = currentZoom; if (resolutionLocked >= 0) { adjustLockButton(resolutionLocked != 0); } currentZoom = newZoom; xContext.setZoom(currentZoom); yContext.setZoom(currentZoom); if (scaleFactor > 0) { setScaleFactor(scaleFactor); } else { long maxBinCount = Math.max(newZD.getXGridAxis().getBinCount(), newZD.getYGridAxis().getBinCount()); double defaultScaleFactor = Math.max(1.0, (double) superAdapter.getHeatmapPanel().getMinimumDimension() / maxBinCount); setScaleFactor(defaultScaleFactor); } int binX = newZD.getXGridAxis().getBinNumberForGenomicPosition(genomeX); int binY = newZD.getYGridAxis().getBinNumberForGenomicPosition(genomeY); if (zoomCallType == ZoomCallType.INITIAL || zoomCallType == ZoomCallType.STANDARD) { if (storeZoomAction || chromosomesChanged) { center(binX, binY); } else if (preZoomHiCZoom != null && getCursorPoint() != null) { Point standardUnzoomCoordinates = computeStandardUnzoomCoordinates(preZoomMatrix, preZoomXContext, preZoomYContext, newZD, preZoomHiCZoom, preZoomScaleFactor); center(standardUnzoomCoordinates.getX(), standardUnzoomCoordinates.getY()); } } else if (zoomCallType == ZoomCallType.DRAG) { xContext.setBinOrigin(binX); yContext.setBinOrigin(binY); } else if (zoomCallType == ZoomCallType.DIRECT) { xContext.setBinOrigin(genomeX); yContext.setBinOrigin(genomeY); } // Notify HeatmapPanel render that zoom has changed. Render should update zoom slider once with previous range values setZoomChanged(); if (resetZoom) { superAdapter.updateAndResetZoom(newZoom); } else { superAdapter.updateZoom(newZoom); } superAdapter.refresh(); if (linkedMode && allowLocationBroadcast) { broadcastLocation(); } if (storeZoomAction) { ZoomAction newZoomAction = new ZoomAction(chrXName, chrYName, newZoom, genomeX, genomeY, scaleFactor, resetZoom, zoomCallType, resolutionLocked); if (zoomActionTracker.getCurrentZoomAction() == null) { this.zoomActionTracker.addZoomState(newZoomAction); } else if (!zoomActionTracker.getCurrentZoomAction().equals(newZoomAction)) { this.zoomActionTracker.addZoomState(newZoomAction); } } return true; } private Point computeStandardUnzoomCoordinates(Matrix preZoomMatrix, Context preZoomXContext, Context preZoomYContext, MatrixZoomData newZD, HiCZoom preZoomHiCZoom, double preZoomScaleFactor) { double xMousePos = cursorPoint.getX(); double yMousePos = cursorPoint.getY(); double preZoomCenterBinX = preZoomXContext.getBinOrigin() + xMousePos / preZoomScaleFactor; double preZoomCenterBinY = preZoomYContext.getBinOrigin() + yMousePos / preZoomScaleFactor; long preZoomBinCountX = preZoomMatrix.getZoomData(preZoomHiCZoom).getXGridAxis().getBinCount(); long preZoomBinCountY = preZoomMatrix.getZoomData(preZoomHiCZoom).getYGridAxis().getBinCount(); long postZoomBinCountX = newZD.getXGridAxis().getBinCount(); long postZoomBinCountY = newZD.getYGridAxis().getBinCount(); return new Point((int) (preZoomCenterBinX / preZoomBinCountX * postZoomBinCountX), (int) (preZoomCenterBinY / preZoomBinCountY * postZoomBinCountY)); } private void adjustLockButton(boolean savedResolutionLocked) { if (isResolutionLocked() != savedResolutionLocked) { superAdapter.getMainViewPanel().getResolutionSlider().setResolutionLocked(savedResolutionLocked); } } private void setChromosomesFromBroadcast(String chrXName, String chrYName) { if (!chrXName.equals(xContext.getChromosome().getName()) || !chrYName.equals(yContext.getChromosome().getName())) { Chromosome chrX = chromosomeHandler.getChromosomeFromName(chrXName); Chromosome chrY = chromosomeHandler.getChromosomeFromName(chrYName); if (chrX == null || chrY == null) { //System.out.println("Most probably origin is a different species saved location or sync/link between two different species maps."); return; } this.xContext = new Context(chrX); this.yContext = new Context(chrY); superAdapter.setSelectedChromosomesNoRefresh(chrX, chrY); refreshEigenvectorTrackIfExists(); } } public void broadcastLocation() { String command = getLocationDescription(); CommandBroadcaster.broadcast(command); } public String getLocationDescription() { String xChr = xContext.getChromosome().getName(); String yChr = yContext.getChromosome().getName(); // if (!xChr.toLowerCase().equals("assembly") && !(xChr.toLowerCase().contains("chr"))) xChr = "chr" + xChr; // if (!yChr.toLowerCase().equals("assembly") && !(yChr.toLowerCase().contains("chr"))) yChr = "chr" + yChr; return "setlocation " + xChr + " " + yChr + " " + currentZoom.getUnit().toString() + " " + currentZoom.getBinSize() + " " + xContext.getBinOrigin() + " " + yContext.getBinOrigin() + " " + getScaleFactor(); } public String getDefaultLocationDescription() { String xChr = xContext.getChromosome().getName(); String yChr = yContext.getChromosome().getName(); // if (!xChr.toLowerCase().equals("assembly") && !(xChr.toLowerCase().contains("chr"))) xChr = "chr" + xChr; // if (!yChr.toLowerCase().equals("assembly") && !(yChr.toLowerCase().contains("chr"))) yChr = "chr" + yChr; return xChr + "@" + (long) (xContext.getBinOrigin() * currentZoom.getBinSize()) + "_" + yChr + "@" + (long) (yContext.getBinOrigin() * currentZoom.getBinSize()); } public void restoreLocation(String cmd) { CommandExecutor cmdExe = new CommandExecutor(this); cmdExe.execute(cmd); if (linkedMode) { broadcastLocation(); } } public void loadLoopList(String path) { superAdapter.getActiveLayerHandler().loadLoopList(path, chromosomeHandler); } public void generateTrackFromLocation(int mousePos, boolean isHorizontal) { if (!MatrixType.isObservedOrControl(displayOption)) { SuperAdapter.showMessageDialog("This feature is only available for Observed or Control views"); return; } // extract the starting position long binStartPosition = (long) (getXContext().getBinOrigin() + mousePos / getScaleFactor()); if (isHorizontal) binStartPosition = (long) (getYContext().getBinOrigin() + mousePos / getScaleFactor()); // Initialize default file name String filename = displayOption == MatrixType.OBSERVED ? "obs" : "ctrl"; filename += isHorizontal ? "_horz" : "_vert"; filename += "_bin" + binStartPosition + "_res" + currentZoom.getBinSize(); filename = cleanUpNumbersInName(filename); // allow user to customize or change the name filename = MessageUtils.showInputDialog("Enter a name for the resulting .wig file", filename); if (filename == null || filename.equalsIgnoreCase("null")) return; File outputWigFile = new File(DirectoryManager.getHiCDirectory(), filename + ".wig"); SuperAdapter.showMessageDialog("Data will be saved to " + outputWigFile.getAbsolutePath()); Chromosome chromosomeForPosition = getXContext().getChromosome(); if (isHorizontal) chromosomeForPosition = getYContext().getChromosome(); safeSave1DTrackToWigFile(chromosomeForPosition, outputWigFile, binStartPosition); } /* public List getAllVisibleLoops() { return feature2DHandler.getAllVisibleLoops(); } /* public List getVisibleFeatures(int chrIdx1, int chrIdx2) { return feature2DHandler.getVisibleFeatures(chrIdx1, chrIdx2); } public List findNearbyFeatures(MatrixZoomData zd, int chrIdx1, int chrIdx2, int x, int y, int n) { double binOriginX = getXContext().getBinOrigin(); double binOriginY = getYContext().getBinOrigin(); double scale = getScaleFactor(); return feature2DHandler.getNearbyFeatures(zd, chrIdx1, chrIdx2, x, y, n, binOriginX, binOriginY, scale); } public List> findNearbyFeaturePairs(MatrixZoomData zd, int chrIdx1, int chrIdx2, int x, int y, int n) { double binOriginX = getXContext().getBinOrigin(); double binOriginY = getYContext().getBinOrigin(); double scale = getScaleFactor(); return feature2DHandler.getNearbyFeaturePairs(zd, chrIdx1, chrIdx2, x, y, n, binOriginX, binOriginY, scale); } */ /* public void removeLoadedAnnotation(String path) { feature2DHandler.removeFeaturePath(path); } */ private void safeSave1DTrackToWigFile(final Chromosome chromosomeForPosition, final File outputWigFile, final long binStartPosition) { superAdapter.getMainWindow().executeLongRunningTask(new Runnable() { @Override public void run() { try { PrintWriter printWriter = new PrintWriter(outputWigFile); unsafeSave1DTrackToWigFile(chromosomeForPosition, printWriter, binStartPosition); printWriter.close(); if (outputWigFile.exists() && outputWigFile.length() > 0) { // TODO this still doesn't add to the resource tree / load annotation dialog box //superAdapter.getTrackLoadAction(); //getResourceTree().add1DCustomTrack(outputWigFile); HiC.this.unsafeLoadTrack(outputWigFile.getAbsolutePath()); LoadAction loadAction = superAdapter.getTrackLoadAction(); loadAction.checkBoxesForReload(outputWigFile.getName()); } } catch (Exception e) { System.err.println("Unable to generate and save 1D HiC track"); } } }, "Saving_1D_track_as_wig"); } private void unsafeSave1DTrackToWigFile(Chromosome chromosomeForPosition, PrintWriter printWriter, long binStartPosition) { // todo could crash with custom chromosomes - so make sure this doesn't get called on those chromosomes int resolution = getZoom().getBinSize(); for (Chromosome chromosome : chromosomeHandler.getChromosomeArrayWithoutAllByAll()) { Matrix matrix = null; if (displayOption == MatrixType.OBSERVED) { matrix = dataset.getMatrix(chromosomeForPosition, chromosome); } else if (displayOption == MatrixType.CONTROL) { matrix = controlDataset.getMatrix(chromosomeForPosition, chromosome); } if (matrix == null) continue; MatrixZoomData zd = matrix.getZoomData(currentZoom); printWriter.println("fixedStep chrom=chr" + chromosome.getName().replace("chr", "") + " start=1 step=" + resolution + " span=" + resolution); long[] regionIndices; if (chromosomeForPosition.getIndex() < chromosome.getIndex()) { regionIndices = new long[]{binStartPosition, binStartPosition, 0, chromosome.getLength()}; } else { regionIndices = new long[]{0, chromosome.getLength(), binStartPosition, binStartPosition}; } zd.dump1DTrackFromCrossHairAsWig(printWriter, binStartPosition, chromosomeForPosition.getIndex() == chromosome.getIndex(), regionIndices, obsNormalizationType, displayOption); } } public void generateRainbowBed() { // Initialize default file name String filename = "temp.rainbow"; File outputBedFile = new File(DirectoryManager.getHiCDirectory(), filename + ".bed"); // SuperAdapter.showMessageDialog("Data will be saved to " + outputWigFile.getAbsolutePath()); Chromosome chromosome = getXContext().getChromosome(); safeGenerateRainbowBed(chromosome, outputBedFile); } private void safeGenerateRainbowBed(final Chromosome chromosome, final File outputBedFile) { superAdapter.getMainWindow().executeLongRunningTask(new Runnable() { @Override public void run() { try { PrintWriter printWriter = new PrintWriter(outputBedFile); unsafeGenerateRainbowBed(chromosome, printWriter); printWriter.close(); if (outputBedFile.exists() && outputBedFile.length() > 0) { // TODO this still doesn't add to the resource tree / load annotation dialog box //superAdapter.getTrackLoadAction(); //getResourceTree().add1DCustomTrack(outputWigFile); HiC.this.unsafeLoadTrack(outputBedFile.getAbsolutePath()); LoadAction loadAction = superAdapter.getTrackLoadAction(); loadAction.checkBoxesForReload(outputBedFile.getName()); } } catch (Exception e) { System.err.println("Unable to generate rainbow track"); } } }, "Saving rainbow bed file."); } private void unsafeGenerateRainbowBed(Chromosome chromosome, PrintWriter printWriter) { printWriter.println("track name=\"Rainbow track\" description=\"Rainbow track\" visibility=2 itemRgb=\"On\""); int resolution = getZoom().getBinSize(); long size = chromosome.getLength() / resolution + 1; for (int i = 0; i < size; i++) { printWriter.println(chromosome.getName() + "\t" + i * resolution + "\t" + ((i + 1) * resolution) + "\t-\t0\t+\t" + i * resolution + "\t" + ((i + 1) * resolution) + "\t" + getRgb(i, size)); } } private String getRgb(int i, long size) { int red = (int) Math.floor(127 * Math.sin(Math.PI / size * 2 * i + 0 * Math.PI * 2 / 3)) + 128; int blue = (int) Math.floor(127 * Math.sin(Math.PI / size * 2 * i + 1 * Math.PI * 2 / 3)) + 128; int green = (int) Math.floor(127 * Math.sin(Math.PI / size * 2 * i + 2 * Math.PI * 2 / 3)) + 128; return red + "," + green + "," + blue; } public boolean isInPearsonsMode() { return MatrixType.isPearsonType(displayOption); } public boolean isPearsonEdgeCaseEncountered(HiCZoom zoom) { return isInPearsonsMode() && zoom.getBinSize() < HiCGlobals.MAX_PEARSON_ZOOM; } public boolean isResolutionLocked() { return superAdapter.isResolutionLocked() || // pearson can't zoom in // even though it should never be less, I think we should try to catch it // (i.e. <= rather than ==)? (isInPearsonsMode() && currentZoom.getBinSize() <= HiCGlobals.MAX_PEARSON_ZOOM); } public boolean isPearsonsNotAvailableForFile(boolean isControl) { try { if (isControl) { MatrixZoomData cZd = getControlZd(); return cZd.getPearsons(controlDataset.getExpectedValues(cZd.getZoom(), ctrlNormalizationType)) == null; } else { MatrixZoomData zd = getZd(); return zd.getPearsons(dataset.getExpectedValues(zd.getZoom(), obsNormalizationType)) == null; } } catch (Exception e) { return true; } } public boolean isPearsonsNotAvailableAtSpecificZoom(boolean isControl, HiCZoom zoom) { try { if (isControl) { return getControlZd().getPearsons(controlDataset.getExpectedValues(zoom, ctrlNormalizationType)) == null; } else { return getZd().getPearsons(dataset.getExpectedValues(zoom, obsNormalizationType)) == null; } } catch (Exception e) { return true; } } public Color getColorForRuler() { if (MatrixType.isPearsonType(displayOption)) { return Color.WHITE; } else { if (HiCGlobals.isDarkulaModeEnabled) { return HiCGlobals.DARKULA_RULER_LINE_COLOR; } else { return HiCGlobals.RULER_LINE_COLOR; } } } public boolean isVSTypeDisplay() { return MatrixType.isVSTypeDisplay(displayOption); } public boolean isInControlPearsonsMode() { return MatrixType.isControlPearsonType(displayOption); } public String getColorScaleKey() { try { return getZd().getColorScaleKey(displayOption, obsNormalizationType, ctrlNormalizationType); } catch (Exception ignored) { } return null; } public List getHighlightedFeatures() { if (showFeatureHighlight) { return highlightedFeatures; } return new ArrayList<>(); } public void setHighlightedFeatures(List highlightedFeatures) { this.highlightedFeatures.clear(); this.highlightedFeatures.addAll(highlightedFeatures); } public void setShowFeatureHighlight(boolean showFeatureHighlight) { this.showFeatureHighlight = showFeatureHighlight; } public ChromosomeHandler getChromosomeHandler() { return chromosomeHandler; } public void setChromosomeHandler(ChromosomeHandler chromosomeHandler) { this.chromosomeHandler = chromosomeHandler; dataset.setChromosomeHandler(chromosomeHandler); if (controlDataset != null) controlDataset.setChromosomeHandler(chromosomeHandler); } public ZoomActionTracker getZoomActionTracker() { return this.zoomActionTracker; } public void clearAllMatrixZoomDataCache() { clearAllCacheForDataset(dataset); if (isControlLoaded()) { clearAllCacheForDataset(controlDataset); } } private void clearAllCacheForDataset(Dataset ds) { ds.clearCache(false); } public List> getRTreeHandlerIntersectingFeatures(String name, int g1, int g2) { try { return ((CustomMatrixZoomData) getZd()).getRTreeHandlerIntersectingFeatures(name, g1, g2); } catch (Exception ignored) { return new ArrayList<>(); } } public String[] getNormalizationOptions(boolean isControl) { if (isControl) { if (controlDataset == null || controlDataset.getVersion() < HiCGlobals.minVersion) { return new String[]{NormalizationHandler.NONE.getDescription()}; } else { ArrayList tmp = new ArrayList<>(); tmp.add(NormalizationHandler.NONE.getDescription()); for (NormalizationType t : controlDataset.getNormalizationTypes()) { tmp.add(t.getDescription()); } return tmp.toArray(new String[tmp.size()]); } } else { if (dataset.getVersion() < HiCGlobals.minVersion) { return new String[]{NormalizationHandler.NONE.getDescription()}; } else { ArrayList tmp = new ArrayList<>(); tmp.add(NormalizationHandler.NONE.getDescription()); for (NormalizationType t : dataset.getNormalizationTypes()) { tmp.add(t.getDescription()); } return tmp.toArray(new String[tmp.size()]); } } } public void exportDataCenteredAboutRegion(int xBinPos, int yBinPos) throws IOException { int radius = 20; // Initialize default file name String filename = displayOption == MatrixType.OBSERVED ? "obs" : "ctrl"; filename += "_bin_" + xBinPos + "_" + yBinPos + "_res_" + currentZoom.getBinSize(); filename = cleanUpNumbersInName(filename); // allow user to customize or change the name filename = MessageUtils.showInputDialog("Enter a name for the resulting .txt file", filename); if (filename == null || filename.equalsIgnoreCase("null")) return; String radiusSize = MessageUtils.showInputDialog("What radius of pixels around the selected point would you like", "" + radius); try { radius = Integer.parseInt(radiusSize); } catch (Exception ignored) { radius = 20; } File outputMatrixFile = new File(DirectoryManager.getHiCDirectory(), filename + ".txt"); SuperAdapter.showMessageDialog("Data will be saved to " + outputMatrixFile.getAbsolutePath()); // extract the starting position int xbinStartPosition = (int) (getXContext().getBinOrigin() + xBinPos / getScaleFactor()); int ybinStartPosition = (int) (getYContext().getBinOrigin() + yBinPos / getScaleFactor()); int binXStart = xbinStartPosition - radius; int binXEnd = xbinStartPosition + radius; int binYStart = ybinStartPosition - radius; int binYEnd = ybinStartPosition + radius; int matrixWidth = 2 * radius + 1; MatrixZoomData requestedZd = getZd(); NormalizationType requestedNormType = getObsNormalizationType(); if (MatrixType.isSimpleControlType(displayOption)) { requestedZd = getControlZd(); requestedNormType = getControlNormalizationType(); } RealMatrix realMatrix = HiCFileTools.extractLocalBoundedRegion(requestedZd, binXStart, binXEnd, binYStart, binYEnd, matrixWidth, matrixWidth, requestedNormType, true); MatrixTools.saveMatrixTextV2(outputMatrixFile.getAbsolutePath(), realMatrix); } public void createNewDynamicResolutions(int newResolution) { dataset.addDynamicResolution(newResolution); if (controlDataset != null) { controlDataset.addDynamicResolution(newResolution); } } // use REVERSE for only undoing and redoing zoom actions public enum ZoomCallType { STANDARD, DRAG, DIRECT, INITIAL, REVERSE } public enum Unit {BP, FRAG} } ================================================ FILE: src/juicebox/HiCGlobals.java ================================================ /* * The MIT License (MIT) * * Copyright (c) 2011-2024 Broad Institute, Aiden Lab, Rice University, Baylor College of Medicine * * Permission is hereby granted, free of charge, to any person obtaining a copy * of this software and associated documentation files (the "Software"), to deal * in the Software without restriction, including without limitation the rights * to use, copy, modify, merge, publish, distribute, sublicense, and/or sell * copies of the Software, and to permit persons to whom the Software is * furnished to do so, subject to the following conditions: * * The above copyright notice and this permission notice shall be included in * all copies or substantial portions of the Software. * * THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR * IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, * FITNESS FOR A PARTICULAR PURPOSE AND NON-INFRINGEMENT. IN NO EVENT SHALL THE * AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER * LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, * OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN * THE SOFTWARE. */ package juicebox; import java.awt.*; import java.io.File; import java.util.ArrayList; import java.util.concurrent.ExecutorService; import java.util.concurrent.Executors; /** * @author Muhammad Shamim * @since 11/25/14 */ public class HiCGlobals { public static final String versionNum = "2.24.00"; public static final String juiceboxTitle = "[Juicebox " + versionNum + "] Hi-C Map "; // MainWindow variables public static final Color RULER_LINE_COLOR = new Color(0, 0, 230, 100); public static final Color DARKULA_RULER_LINE_COLOR = new Color(200, 200, 250, 100); // for plotting public static final String topChromosomeColor = "#0000FF"; public static final String leftChromosomeColor = "#009900"; public static final Color backgroundColor = new Color(204, 204, 204); public static final String BACKUP_FILE_STEM = "unsaved_hic_annotations_backup_"; // for state saving public static File stateFile; public static File xmlSavedStatesFile; // Feature2D hover text public static final boolean allowSpacingBetweenFeatureText = true; public static final ArrayList savedStatesList = new ArrayList<>(); // min hic file version supported public static final int minVersion = 6; public static final int writingVersion = 9; public static final int bufferSize = 2097152; public static final String defaultPropertiesURL = "http://hicfiles.tc4ga.com/juicebox.properties"; public static final Color diffGrayColor = new Color(238, 238, 238); // for state saving public static int MAX_PEARSON_ZOOM = 50000; public static int MAX_EIGENVECTOR_ZOOM = 250000; // implement Map scaling with this global variable public static double hicMapScale = 1; // whether MatrixZoomData should cache or not public static boolean useCache = true; public static boolean guiIsCurrentlyActive = false; public static boolean allowDynamicBlockIndex = true; public static boolean printVerboseComments = false; public static boolean slideshowEnabled = false; public static boolean splitModeEnabled = false; public static boolean translationInProgress = false; public static boolean displayTiles = false; public static boolean isDarkulaModeEnabled = false; public static boolean isAssemblyMatCheck = false; // whether instance was linked before mouse press or not public static boolean phasing = false; public static boolean noSortInPhasing = false; public static boolean wasLinkedBeforeMousePress = false; public static boolean isLegacyOutputPrintingEnabled = false; public static final boolean isDevAssemblyToolsAllowedPublic = true; public static final boolean isDevCustomChromosomesAllowedPublic = true; public static boolean HACK_COLORSCALE = false; public static boolean HACK_COLORSCALE_EQUAL = false; public static boolean HACK_COLORSCALE_LINEAR = false; // for norm/pre, save contact records into memory public static boolean USE_ITERATOR_NOT_ALL_IN_RAM = false; public static boolean CHECK_RAM_USAGE = false; public static void verifySupportedHiCFileVersion(int version) throws RuntimeException { if (version < minVersion) { throw new RuntimeException("This file is version " + version + ". Only versions " + minVersion + " and greater are supported at this time."); } } public static void verifySupportedHiCFileWritingVersion(int version) throws RuntimeException { if (version < writingVersion) { throw new RuntimeException("This file is version " + version + ". Only versions " + writingVersion + " and greater can be edited using this jar."); } } public static Font font(int size, boolean isBold) { if (isBold) return new Font("Arial", Font.BOLD, size); return new Font("Arial", Font.PLAIN, size); } public static int getIdealThreadCount() { return Math.max(1, Runtime.getRuntime().availableProcessors()); } public static ExecutorService newFixedThreadPool() { return Executors.newFixedThreadPool(getIdealThreadCount()); } public enum menuType {MAP, LOCATION, STATE} } ================================================ FILE: src/juicebox/IGVUtils.java ================================================ /* * The MIT License (MIT) * * Copyright (c) 2011-2020 Broad Institute, Aiden Lab, Rice University, Baylor College of Medicine * * Permission is hereby granted, free of charge, to any person obtaining a copy * of this software and associated documentation files (the "Software"), to deal * in the Software without restriction, including without limitation the rights * to use, copy, modify, merge, publish, distribute, sublicense, and/or sell * copies of the Software, and to permit persons to whom the Software is * furnished to do so, subject to the following conditions: * * The above copyright notice and this permission notice shall be included in * all copies or substantial portions of the Software. * * THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR * IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, * FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE * AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER * LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, * OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN * THE SOFTWARE. */ package juicebox; import juicebox.data.ChromosomeHandler; import org.broad.igv.ui.IGV; import java.io.BufferedReader; import java.io.IOException; import java.io.InputStreamReader; import java.io.PrintWriter; import java.net.Socket; import java.util.Arrays; import java.util.concurrent.ExecutorService; import java.util.concurrent.Executors; //import org.broad.igv.lists.GeneList; //import org.broad.igv.ui.WaitCursorManager; //import org.broad.igv.util.LongRunningTask; //import org.broad.igv.util.NamedRunnable; //import java.net.UnknownHostException; /** * @author Jim Robinson * @since 1/5/12 */ class IGVUtils { private static final ExecutorService threadExecutor = Executors.newFixedThreadPool(1); private static SocketHelper helper = null; private static void createSocketHelper() { if (helper == null) { Socket socket; PrintWriter out; BufferedReader in; try { socket = new Socket("127.0.0.1", 60151); out = new PrintWriter(socket.getOutputStream(), true); in = new BufferedReader(new InputStreamReader(socket.getInputStream()), HiCGlobals.bufferSize); helper = new SocketHelper(in, out, socket); } catch (IOException e) { System.err.println("IOException" + e.getLocalizedMessage()); helper = null; } } } /** * Send instructions to IGV to open or adjust views on the 2 loci. * * @param locus1 * @param locus2 */ public static void sendToIGV(final String locus1, final String locus2) { Runnable runnable = new Runnable() { public void run() { if (ChromosomeHandler.isAllByAll(locus1)) { return; } // Same JVM? if (IGV.hasInstance()) { IGV.getInstance().goToLociList(Arrays.asList(locus1, locus2)); } else { if (helper == null) createSocketHelper(); if (helper != null) { String cmd = "gotoimmediate " + locus1 + " " + locus2; helper.out.println(cmd); String response = null; try { response = helper.in.readLine(); } catch (IOException e) { e.printStackTrace(); //To change body of catch statement use File | Settings | File Templates. } System.out.println(cmd + " " + response); } } } }; threadExecutor.submit(runnable); } static class SocketHelper { Socket socket = null; PrintWriter out = null; BufferedReader in = null; SocketHelper(BufferedReader in, PrintWriter out, Socket socket) { this.in = in; this.out = out; this.socket = socket; } } } ================================================ FILE: src/juicebox/MainWindow.java ================================================ /* * The MIT License (MIT) * * Copyright (c) 2011-2021 Broad Institute, Aiden Lab, Rice University, Baylor College of Medicine * * Permission is hereby granted, free of charge, to any person obtaining a copy * of this software and associated documentation files (the "Software"), to deal * in the Software without restriction, including without limitation the rights * to use, copy, modify, merge, publish, distribute, sublicense, and/or sell * copies of the Software, and to permit persons to whom the Software is * furnished to do so, subject to the following conditions: * * The above copyright notice and this permission notice shall be included in * all copies or substantial portions of the Software. * * THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR * IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, * FITNESS FOR A PARTICULAR PURPOSE AND NON-INFRINGEMENT. IN NO EVENT SHALL THE * AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER * LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, * OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN * THE SOFTWARE. */ package juicebox; import juicebox.gui.MainViewPanel; import juicebox.gui.SuperAdapter; import juicebox.windowui.DisabledGlassPane; import juicebox.windowui.FileDropTargetListener; import juicebox.windowui.layers.LayersPanel; import org.broad.igv.Globals; import org.broad.igv.ui.util.IconFactory; import javax.swing.*; import java.awt.*; import java.awt.dnd.DropTarget; import java.awt.event.MouseAdapter; import java.awt.event.MouseEvent; import java.awt.geom.Rectangle2D; import java.awt.image.BufferedImage; import java.io.BufferedReader; import java.io.File; import java.io.IOException; import java.io.InputStreamReader; import java.net.URI; import java.net.URISyntaxException; import java.net.URL; import java.net.URLConnection; import java.util.concurrent.Callable; import java.util.concurrent.ExecutorService; import java.util.concurrent.Executors; import java.util.concurrent.Future; public class MainWindow extends JFrame { private static final long serialVersionUID = -9000020; private static final DisabledGlassPane disabledGlassPane = new DisabledGlassPane(Cursor.WAIT_CURSOR); private static final SuperAdapter superAdapter = new SuperAdapter(); public static Cursor fistCursor; public static Cursor pasteNECursor; public static Cursor pasteSWCursor; public static Cursor pasteSECursor; public static Cursor pasteNWCursor; public static Cursor invertNECursor; public static Cursor invertSWCursor; public static Cursor scissorCursor; public static Cursor groupNECursor; public static Cursor groupSWCursor; private static MainWindow theInstance; private final ExecutorService threadExecutor = Executors.newFixedThreadPool(3); private final HiC hic; // The "model" object containing the state for this instance. private MainWindow() { setDefaultCloseOperation(WindowConstants.DISPOSE_ON_CLOSE); HiCGlobals.guiIsCurrentlyActive = true; hic = new HiC(superAdapter); MainViewPanel mainViewPanel = new MainViewPanel(); superAdapter.setAdapters(this, hic, mainViewPanel); initComponents(); createCursors(); setExtendedState(JFrame.MAXIMIZED_BOTH); pack(); DropTarget target = new DropTarget(this, new FileDropTargetListener(superAdapter)); setDropTarget(target); // Tooltip settings ToolTipManager.sharedInstance().setDismissDelay(60000); // 60 seconds KeyboardFocusManager.getCurrentKeyboardFocusManager().addKeyEventDispatcher(superAdapter.getNewHiCKeyDispatcher()); } private static MainWindow createMainWindow() { return new MainWindow(); } public static synchronized MainWindow getInstance() { if (theInstance == null) { try { theInstance = createMainWindow(); } catch (Exception e) { System.err.println("Error creating main window " + e.getLocalizedMessage()); } } return theInstance; } public static void main(String[] args) { initApplication(); // Runnable runnable = new Runnable() { // public void run() { theInstance = getInstance(); theInstance.setVisible(true); theInstance.setDefaultCloseOperation(WindowConstants.EXIT_ON_CLOSE); CommandListener.start(theInstance.hic); // } // }; // SwingUtilities.invokeAndWait(runnable); try { URL url = new URL("https://s3.amazonaws.com/hicfiles.tc4ga.com/juicebox.version"); URLConnection next = url.openConnection(); BufferedReader reader = new BufferedReader(new InputStreamReader(next.getInputStream())); String latestVersion = reader.readLine(); String[] latest = latestVersion.split("\\."); String[] current = HiCGlobals.versionNum.split("\\."); boolean isOutdated = false; int iC = Integer.parseInt(current[0]); int iL = Integer.parseInt(latest[0]); if (iC < iL) { isOutdated = true; } else if (iC == iL) { int jC = Integer.parseInt(current[1]); int jL = Integer.parseInt(latest[1]); int kC = Integer.parseInt(current[2]); int kL = Integer.parseInt(latest[2]); if (jC < jL) { isOutdated = true; } else if (jC == jL && kC < kL) { isOutdated = true; } } if (isOutdated) { JPanel textPanel = new JPanel(new GridLayout(0, 1)); JLabel label = new JLabel("

You are using Juicebox " + HiCGlobals.versionNum + "
The lastest version is " + latestVersion + "
To download the lastest version, go to

"); JLabel label2 = new JLabel(" https://github.com/theaidenlab/juicebox/wiki/Download "); textPanel.add(label); textPanel.add(label2); label2.setCursor(new Cursor(Cursor.HAND_CURSOR)); label2.addMouseListener(new MouseAdapter() { @Override public void mouseClicked(MouseEvent e) { try { Desktop.getDesktop().browse(new URI("https://github.com/theaidenlab/juicebox/wiki/Download")); } catch (URISyntaxException | IOException ex) { //It looks like there's a problem } } }); JOptionPane.showMessageDialog(superAdapter.getMainWindow(), textPanel, "Update Information", JOptionPane.PLAIN_MESSAGE); } } catch (Exception e) { System.err.println(e.getLocalizedMessage()); } } private static void initApplication() { System.err.println("Default User Directory: " + DirectoryManager.getUserDirectory()); try { HiCGlobals.stateFile = new File(DirectoryManager.getHiCDirectory(), "CurrentJuiceboxStates"); HiCGlobals.xmlSavedStatesFile = new File(DirectoryManager.getHiCDirectory(), "JuiceboxStatesForExport.xml"); } catch (Exception e) { System.err.println(e.getLocalizedMessage()); if (HiCGlobals.guiIsCurrentlyActive) { SuperAdapter.showMessageDialog("Error with state file\n" + e.getLocalizedMessage()); } } System.setProperty("http.agent", Globals.applicationString()); } private void initComponents() { addWindowListener(new java.awt.event.WindowAdapter() { public void windowClosing(java.awt.event.WindowEvent e) { superAdapter.exitActionPerformed(); } }); if (HiCGlobals.printVerboseComments) { System.out.println("Initializing Components"); } // first annotation layer must get created MainWindow.superAdapter.createNewLayer(null); Dimension screenSize = Toolkit.getDefaultToolkit().getScreenSize(); Insets scnMax = Toolkit.getDefaultToolkit().getScreenInsets(getGraphicsConfiguration()); int taskBarHeight = scnMax.bottom; MainWindow.superAdapter.initializeMainView(getContentPane(), screenSize, taskBarHeight); initializeGlassPaneListening(); ImageIcon icon = new ImageIcon(getClass().getResource("/images/juicebox256.png")); setIconImage(icon.getImage()); } private void createCursors() { boolean isWindows = (System.getProperty("os.name").toLowerCase().contains("win")); // Make background transparent BufferedImage handImage = new BufferedImage(32, 32, BufferedImage.TYPE_INT_ARGB); Graphics2D g = handImage.createGraphics(); g.setComposite(AlphaComposite.getInstance(AlphaComposite.CLEAR, 0.0f)); Rectangle2D.Double rect = new Rectangle2D.Double(0, 0, 32, 32); g.fill(rect); // Draw hand image in middle g = handImage.createGraphics(); g.drawImage(IconFactory.getInstance().getIcon(IconFactory.IconID.FIST).getImage(), 0, 0, null); fistCursor = getToolkit().createCustomCursor(handImage, new Point(8, 6), "Move"); // Additional cursors for assembly ImageIcon imageIcon; // Insert (paste) prompts BufferedImage pasteNEImage = new BufferedImage(32, 32, BufferedImage.TYPE_INT_ARGB); g = pasteNEImage.createGraphics(); g.setComposite(AlphaComposite.getInstance(AlphaComposite.CLEAR, 0.0f)); rect = new Rectangle2D.Double(0, 0, 32, 32); g.fill(rect); g = pasteNEImage.createGraphics(); imageIcon = new ImageIcon(this.getClass().getResource("/images/assembly/small-ne-paste.png"), "paste"); g.drawImage(imageIcon.getImage(), 0, 0, null); if (isWindows) { pasteNEImage = windowsCreateCursor(pasteNEImage, 240); } pasteNECursor = getToolkit().createCustomCursor(pasteNEImage, new Point(8, 6), "PasteNE"); // Insert (paste) prompts BufferedImage pasteSWImage = new BufferedImage(32, 32, BufferedImage.TYPE_INT_ARGB); g = pasteSWImage.createGraphics(); g.setComposite(AlphaComposite.getInstance(AlphaComposite.CLEAR, 0.0f)); rect = new Rectangle2D.Double(0, 0, 32, 32); g.fill(rect); g = pasteSWImage.createGraphics(); imageIcon = new ImageIcon(this.getClass().getResource("/images/assembly/small-sw-paste.png"), "paste"); g.drawImage(imageIcon.getImage(), 0, 0, null); if (isWindows) { pasteSWImage = windowsCreateCursor(pasteSWImage, 240); } pasteSWCursor = getToolkit().createCustomCursor(pasteSWImage, new Point(8, 6), "PasteSW"); // Insert (paste) prompts BufferedImage pasteNWImage = new BufferedImage(32, 32, BufferedImage.TYPE_INT_ARGB); g = pasteNWImage.createGraphics(); g.setComposite(AlphaComposite.getInstance(AlphaComposite.CLEAR, 0.0f)); rect = new Rectangle2D.Double(0, 0, 32, 32); g.fill(rect); g = pasteNWImage.createGraphics(); imageIcon = new ImageIcon(this.getClass().getResource("/images/assembly/small-nw-paste.png"), "paste"); g.drawImage(imageIcon.getImage(), 0, 0, null); if (isWindows) { pasteNWImage = windowsCreateCursor(pasteNWImage, 240); } pasteNWCursor = getToolkit().createCustomCursor(pasteNWImage, new Point(8, 6), "PasteNW"); // Insert (paste) prompts BufferedImage pasteSEImage = new BufferedImage(32, 32, BufferedImage.TYPE_INT_ARGB); g = pasteSEImage.createGraphics(); g.setComposite(AlphaComposite.getInstance(AlphaComposite.CLEAR, 0.0f)); rect = new Rectangle2D.Double(0, 0, 32, 32); g.fill(rect); g = pasteSEImage.createGraphics(); imageIcon = new ImageIcon(this.getClass().getResource("/images/assembly/small-se-paste.png"), "paste"); g.drawImage(imageIcon.getImage(), 0, 0, null); if (isWindows) { pasteSEImage = windowsCreateCursor(pasteSEImage, 240); } pasteSECursor = getToolkit().createCustomCursor(pasteSEImage, new Point(8, 6), "PasteSE"); // Invert prompts BufferedImage invertNEImage = new BufferedImage(32, 32, BufferedImage.TYPE_INT_ARGB); g = invertNEImage.createGraphics(); g.setComposite(AlphaComposite.getInstance(AlphaComposite.CLEAR, 0.0f)); g.addRenderingHints(new RenderingHints(RenderingHints.KEY_RENDERING, RenderingHints.VALUE_RENDER_QUALITY)); rect = new Rectangle2D.Double(0, 0, 32, 32); g.fill(rect); g = invertNEImage.createGraphics(); imageIcon = new ImageIcon(this.getClass().getResource("/images/assembly/small-ne-invert.png"), "invert"); g.drawImage(imageIcon.getImage(), 0, 0, null); if (isWindows) { invertNEImage = windowsCreateCursor(invertNEImage, 240); } invertNECursor = getToolkit().createCustomCursor(invertNEImage, new Point(8, 6), "InvertNE"); // Invert prompts BufferedImage invertSWImage = new BufferedImage(32, 32, BufferedImage.TYPE_INT_ARGB); g = invertSWImage.createGraphics(); g.setComposite(AlphaComposite.getInstance(AlphaComposite.CLEAR, 0.0f)); rect = new Rectangle2D.Double(0, 0, 32, 32); g.fill(rect); g = invertSWImage.createGraphics(); imageIcon = new ImageIcon(this.getClass().getResource("/images/assembly/small-sw-invert.png"), "invert"); g.drawImage(imageIcon.getImage(), 0, 0, null); if (isWindows) { invertSWImage = windowsCreateCursor(invertSWImage, 240); } invertSWCursor = getToolkit().createCustomCursor(invertSWImage, new Point(8, 6), "InvertSW"); // Cut prompts BufferedImage scissorImage = new BufferedImage(32, 32, BufferedImage.TYPE_INT_ARGB); g = scissorImage.createGraphics(); g.setComposite(AlphaComposite.getInstance(AlphaComposite.CLEAR, 0.0f)); rect = new Rectangle2D.Double(0, 0, 32, 32); g.fill(rect); g = scissorImage.createGraphics(); imageIcon = new ImageIcon(this.getClass().getResource("/images/assembly/small-scissors.png"), "cut"); g.drawImage(imageIcon.getImage(), 0, 0, null); if (isWindows) { scissorImage = windowsCreateCursor(scissorImage, 141); } scissorCursor = getToolkit().createCustomCursor(scissorImage, new Point(8, 6), "Scissors"); // Group prompts BufferedImage groupNEImage = new BufferedImage(32, 32, BufferedImage.TYPE_INT_ARGB); g = groupNEImage.createGraphics(); g.setComposite(AlphaComposite.getInstance(AlphaComposite.CLEAR, 0.0f)); g.addRenderingHints(new RenderingHints(RenderingHints.KEY_RENDERING, RenderingHints.VALUE_RENDER_QUALITY)); rect = new Rectangle2D.Double(0, 0, 32, 32); g.fill(rect); g = groupNEImage.createGraphics(); imageIcon = new ImageIcon(this.getClass().getResource("/images/layer/ur_clicked.png"), "grouptoggle"); g.drawImage(imageIcon.getImage(), 0, 0, 20, 20, null); groupNECursor = getToolkit().createCustomCursor(groupNEImage, new Point(8, 6), "GroupNE"); BufferedImage groupSWImage = new BufferedImage(32, 32, BufferedImage.TYPE_INT_ARGB); g = groupSWImage.createGraphics(); g.setComposite(AlphaComposite.getInstance(AlphaComposite.CLEAR, 0.0f)); g.addRenderingHints(new RenderingHints(RenderingHints.KEY_RENDERING, RenderingHints.VALUE_RENDER_QUALITY)); rect = new Rectangle2D.Double(0, 0, 32, 32); g.fill(rect); g = groupSWImage.createGraphics(); imageIcon = new ImageIcon(this.getClass().getResource("/images/layer/ll_clicked.png"), "grouptoggle"); g.drawImage(imageIcon.getImage(), 0, 0, 20, 20, null); groupSWCursor = getToolkit().createCustomCursor(groupSWImage, new Point(8, 6), "GroupSW"); } private BufferedImage windowsCreateCursor(BufferedImage img, int thresholdVal) { try { int size = 32; BufferedImage image = new BufferedImage(size, size, BufferedImage.TYPE_INT_RGB); BufferedImage image2 = new BufferedImage(size, size, BufferedImage.TYPE_INT_ARGB); Graphics2D g = image.createGraphics(); Graphics2D g2 = image2.createGraphics(); g.setColor(Color.white); g.fillRect(0, 0, size, size); // turn on anti-aliasing. g.setStroke(new BasicStroke(4.0f)); // 4-pixel lines g.setRenderingHint(RenderingHints.KEY_ANTIALIASING, RenderingHints.VALUE_ANTIALIAS_ON); g.setRenderingHint(RenderingHints.KEY_INTERPOLATION, RenderingHints.VALUE_INTERPOLATION_BILINEAR); g.setColor(new Color(0.5f, 0f, 0f)); g.drawImage(img, 0, 0, null, null); g2.drawImage(image, 0, 0, null, null); for (int y = 0 ; y < size ; y++) { for (int x = 0 ; x < size ; x++) { int rgb = image.getRGB(x, y); int blue = rgb & 0xff; int green = (rgb & 0xff00) >> 8; int red = (rgb & 0xff0000) >> 16; if (red >= thresholdVal && green >= thresholdVal && blue >= thresholdVal) { // make white transparent image2.setRGB(x, y, 0); } } } return image2; } catch (Exception exp) { exp.printStackTrace(); return null; } } public void exitActionPerformed() { int option = 0; if (SuperAdapter.assemblyModeCurrentlyActive) { setDefaultCloseOperation(DO_NOTHING_ON_CLOSE); option = JOptionPane.showConfirmDialog(null, "Are you sure you want to exit? Make sure you have saved any important assembly changes.", "Warning", JOptionPane.YES_NO_OPTION); } if (option == 0) { setVisible(false); dispose(); String autoSaveFileName = DirectoryManager.getHiCDirectory() + "/" + System.nanoTime() + ".review.autosave.assembly"; try { autoSaveFileName = DirectoryManager.getHiCDirectory() + "/" + (SuperAdapter.getDatasetTitle().split(".+?/(?=[^/]+$)")[1]).split("\\.(?=[^\\.]+$)")[0] + ".review.autosave.assembly"; } catch (Exception e) { System.err.println("Unable to get desired file name"); System.err.println(e.getLocalizedMessage()); } File autoSaveFile = new File(autoSaveFileName); autoSaveFile.delete(); System.out.println("Exiting Main Window"); System.exit(0); } } /** * Utility function to execute a task in a worker thread. The method is on MainWindow because the glassPane * is used to display a wait cursor and block events. * * @param runnable Thread * @return thread */ public Future executeLongRunningTask(final Runnable runnable, final String caller) { return executeLongRunningTask(runnable, caller, "Loading..."); } public Future executeLongRunningTask(final Runnable runnable, final String caller, final String message) { if (HiCGlobals.printVerboseComments) { System.out.println("long_execute " + caller); } Callable wrapper = new Callable() { public Object call() { MainWindow.this.showDisabledGlassPane(caller, message); try { runnable.run(); return "done"; } catch (Exception error) { error.printStackTrace(); return "error"; } finally { MainWindow.this.hideDisabledGlassPane(caller); } } }; return threadExecutor.submit(wrapper); } private void showDisabledGlassPane(String caller, String displayMessage) { disabledGlassPane.activate(displayMessage); LayersPanel.disabledGlassPane.activate(displayMessage); if (HiCGlobals.printVerboseComments) { System.out.println("Loading " + caller); } } private void initializeGlassPaneListening() { rootPane.setGlassPane(disabledGlassPane); } private void hideDisabledGlassPane(String caller) {//getRootPane().getContentPane() if (HiCGlobals.printVerboseComments) { System.out.println("Done loading " + caller); } disabledGlassPane.deactivate(); LayersPanel.disabledGlassPane.deactivate(); } public void updateNamesFromImport(String path) { superAdapter.updatePrevStateNameFromImport(path); } } ================================================ FILE: src/juicebox/ProcessHelper.java ================================================ /* * The MIT License (MIT) * * Copyright (c) 2011-2020 Broad Institute, Aiden Lab, Rice University, Baylor College of Medicine * * Permission is hereby granted, free of charge, to any person obtaining a copy * of this software and associated documentation files (the "Software"), to deal * in the Software without restriction, including without limitation the rights * to use, copy, modify, merge, publish, distribute, sublicense, and/or sell * copies of the Software, and to permit persons to whom the Software is * furnished to do so, subject to the following conditions: * * The above copyright notice and this permission notice shall be included in * all copies or substantial portions of the Software. * * THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR * IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, * FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE * AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER * LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, * OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN * THE SOFTWARE. */ package juicebox; import java.io.File; import java.io.IOException; import java.util.ArrayList; import java.util.List; import java.util.Map; /** * Created by nchernia on 12/23/15. */ public class ProcessHelper { public ProcessHelper() { } public Process startNewJavaProcess() throws IOException { ProcessBuilder processBuilder = createProcess(); processBuilder.redirectErrorStream(true); // redirect error stream to output stream processBuilder.redirectOutput(ProcessBuilder.Redirect.INHERIT); return processBuilder.start(); } private ProcessBuilder createProcess() { String jvm = System.getProperty("java.home") + File.separator + "bin" + File.separator + "java"; String classpath = System.getProperty("java.class.path"); //System.err.println("classpath: " + classpath); // String workingDirectory = System.getProperty("user.dir"); // String[] options = optionsAsString.split(" "); List command = new ArrayList<>(); command.add(jvm); String url = System.getProperty("jnlp.loadMenu"); if (url != null) { System.err.println(url); command.add("-Djnlp.loadMenu=" + url); // String[] options = {"-Xmx2000m", "-Djnlp.loadMenu=" + url}; // command.addAll(Arrays.asList(options)); } command.add("-Xmx5000m"); // command.addAll(Arrays.asList(options)); command.add(MainWindow.class.getCanonicalName()); // command.addAll(Arrays.asList(arguments)); ProcessBuilder processBuilder = new ProcessBuilder(command); Map environment = processBuilder.environment(); environment.put("CLASSPATH", classpath); return processBuilder; } } ================================================ FILE: src/juicebox/Unused.java ================================================ /* * The MIT License (MIT) * * Copyright (c) 2011-2020 Broad Institute, Aiden Lab, Rice University, Baylor College of Medicine * * Permission is hereby granted, free of charge, to any person obtaining a copy * of this software and associated documentation files (the "Software"), to deal * in the Software without restriction, including without limitation the rights * to use, copy, modify, merge, publish, distribute, sublicense, and/or sell * copies of the Software, and to permit persons to whom the Software is * furnished to do so, subject to the following conditions: * * The above copyright notice and this permission notice shall be included in * all copies or substantial portions of the Software. * * THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR * IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, * FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE * AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER * LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, * OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN * THE SOFTWARE. */ package juicebox; /** * TODO These should probably be deleted, but keeping them until respective author decides/refactors * Created by muhammadsaadshamim on 8/3/15. */ class Unused { /* private static void writeMergedNoDupsFromTimeSeq(String seqPath, String newPath) { List listPositions = new ArrayList<>(); try (BufferedReader br = new BufferedReader(new FileReader(seqPath))) { for (String line; (line = br.readLine()) != null; ) { String[] parts = line.split(","); listPositions.add(new Integer[]{Integer.parseInt(parts[0]), Integer.parseInt(parts[1])}); } } catch (Exception ignored) { ignored.printStackTrace(); } try { PrintWriter p0 = new PrintWriter(new FileWriter(newPath)); for (int i = 0; i < listPositions.size(); i++) { Integer[] pos_xy_1 = listPositions.get(i); for (int j = i; j < listPositions.size(); j++) { Integer[] pos_xy_2 = listPositions.get(j); double value = 1. / Math.max(1, Math.sqrt((pos_xy_1[0] - pos_xy_2[0]) ^ 2 + (pos_xy_1[1] - pos_xy_2[1]) ^ 2)); float conv_val = (float) value; if (!Float.isNaN(conv_val) && conv_val > 0) { p0.println("0 art " + i + " 0 16 art " + j + " 1 " + conv_val); } } } p0.close(); } catch (IOException ignored) { ignored.printStackTrace(); } } Iterator iter = zd.getNewContactRecordIterator(); while (iter.hasNext()) { ContactRecord cr = iter.next(); final int x = cr.getBinX(); final int y = cr.getBinY(); final float counts = cr.getCounts(); if(!indexToRegion.containsKey(x)){ indexToRegion.put(x, new LocalGenomeRegion(x)); } if(!indexToRegion.containsKey(y)){ indexToRegion.put(y, new LocalGenomeRegion(y)); } if(x != y){ indexToRegion.get(x).addNeighbor(y, counts); indexToRegion.get(y).addNeighbor(x, counts); } } private void loadNormalizationVector(File file, HiC hic) throws IOException { BufferedReader reader = new BufferedReader(new InputStreamReader(new FileInputStream(file)), HiCGlobals.bufferSize); String nextLine = reader.readLine(); String[] tokens = Globals.singleTabMultiSpacePattern.split(nextLine); int resolution = Integer.valueOf(tokens[0]); int vectorLength = Integer.valueOf(tokens[1]); int expectedLength = Integer.valueOf(tokens[2]); ChromosomeHandler chromosomeHandler = hic.getChromosomeHandler(); double[] nv = new double[vectorLength]; double[] exp = new double[expectedLength]; for (int i = 0; i < nv.length; i++) { nextLine = reader.readLine(); tokens = Globals.singleTabMultiSpacePattern.split(nextLine); nv[i] = Double.valueOf(tokens[0]); } for (int i = 0; i < exp.length; i++) { nextLine = reader.readLine(); tokens = Globals.singleTabMultiSpacePattern.split(nextLine); exp[i] = Double.valueOf(tokens[0]); } int location1 = 0; for (Chromosome c1 : chromosomeHandler.getChromosomeArrayWithoutAllByAll()) { int chrBinned = c1.getLength() / resolution + 1; double[] chrNV = new double[chrBinned]; for (int i = 0; i < chrNV.length; i++) { chrNV[i] = nv[location1]; location1++; } //hic.getDataset().putCustomNormalizationVector(c1.getIndex(), resolution, chrNV, exp); } } */ } ================================================ FILE: src/juicebox/assembly/AssemblyFileExporter.java ================================================ /* * The MIT License (MIT) * * Copyright (c) 2011-2021 Broad Institute, Aiden Lab, Rice University, Baylor College of Medicine * * Permission is hereby granted, free of charge, to any person obtaining a copy * of this software and associated documentation files (the "Software"), to deal * in the Software without restriction, including without limitation the rights * to use, copy, modify, merge, publish, distribute, sublicense, and/or sell * copies of the Software, and to permit persons to whom the Software is * furnished to do so, subject to the following conditions: * * The above copyright notice and this permission notice shall be included in * all copies or substantial portions of the Software. * * THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR * IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, * FITNESS FOR A PARTICULAR PURPOSE AND NON-INFRINGEMENT. IN NO EVENT SHALL THE * AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER * LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, * OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN * THE SOFTWARE. */ package juicebox.assembly; import java.io.IOException; import java.io.PrintWriter; import java.util.Iterator; import java.util.List; /** * Created by nathanielmusial on 6/29/17. */ public class AssemblyFileExporter { private final String outputFilePath; private final List listOfScaffolds; private final List> listOfSuperscaffolds; private final List listOfBundledScaffolds; public AssemblyFileExporter(AssemblyScaffoldHandler assemblyScaffoldHandler, String outputFilePath) { this.outputFilePath = outputFilePath; this.listOfScaffolds = assemblyScaffoldHandler.getListOfScaffolds(); this.listOfSuperscaffolds = assemblyScaffoldHandler.getListOfSuperscaffolds(); this.listOfBundledScaffolds = assemblyScaffoldHandler.getListOfBundledScaffolds(); } public void exportAssemblyFile() { try { exportAssembly(); } catch (IOException exception) { System.out.println("Exporting failed..."); } } private void exportAssembly() throws IOException { PrintWriter assemblyWriter = new PrintWriter(buildAssemblyOutputPath(), "UTF-8"); int last = 0; for (Scaffold scaffold : listOfScaffolds) { if (scaffold.getName().equals("unattempted:::debris")) { continue; } assemblyWriter.print(">" + scaffold.toString() + "\n"); // Use print to account for OS difference in control characters last = scaffold.getIndexId(); } if (listOfBundledScaffolds.size() > 0) { for (String row : listOfBundledScaffolds) { String[] splitRow = row.split(" "); last += 1; assemblyWriter.print(splitRow[0] + " " + last + " " + splitRow[2] + "\n"); } } for (List row : listOfSuperscaffolds) { if (listOfBundledScaffolds.size() > 0 && row.get(0) == listOfScaffolds.size()) { continue; } assemblyWriter.print(superscaffoldToString(row) + "\n"); } if (listOfBundledScaffolds.size() > 0) { for (int i = listOfScaffolds.size(); i <= last; i++) assemblyWriter.print(i + "\n"); } assemblyWriter.close(); } private String superscaffoldToString(List scaffoldRow) { StringBuilder stringBuilder = new StringBuilder(); Iterator iterator = scaffoldRow.iterator(); while (iterator.hasNext()) { stringBuilder.append(iterator.next()); if (iterator.hasNext()) { stringBuilder.append(" "); } } return stringBuilder.toString(); } private String buildAssemblyOutputPath() { return this.outputFilePath + ".assembly"; } } ================================================ FILE: src/juicebox/assembly/AssemblyFileImporter.java ================================================ /* * The MIT License (MIT) * * Copyright (c) 2011-2021 Broad Institute, Aiden Lab, Rice University, Baylor College of Medicine * * Permission is hereby granted, free of charge, to any person obtaining a copy * of this software and associated documentation files (the "Software"), to deal * in the Software without restriction, including without limitation the rights * to use, copy, modify, merge, publish, distribute, sublicense, and/or sell * copies of the Software, and to permit persons to whom the Software is * furnished to do so, subject to the following conditions: * * The above copyright notice and this permission notice shall be included in * all copies or substantial portions of the Software. * * THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR * IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, * FITNESS FOR A PARTICULAR PURPOSE AND NON-INFRINGEMENT. IN NO EVENT SHALL THE * AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER * LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, * OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN * THE SOFTWARE. */ package juicebox.assembly; import juicebox.HiCGlobals; import juicebox.gui.SuperAdapter; import java.io.File; import java.io.IOException; import java.util.ArrayList; import java.util.List; import java.util.Scanner; /** * Created by ranganmostofa on 6/29/17. */ public class AssemblyFileImporter { public List listOfUnattempted; private SuperAdapter superAdapter = null; // single file format private String assemblyFilePath; private boolean modified = false; //private int bundleSize=15000; //user-defined presumably private boolean needsBundling = false; private final int bundleSize = 0; //temporary? bundle everything you can private List listOfScaffolds; private List> listOfSuperscaffolds; private AssemblyScaffoldHandler assemblyScaffoldHandler; private List rawFileData; public AssemblyFileImporter(String assemblyFilePath, boolean modified) { this.assemblyFilePath = assemblyFilePath; this.modified = modified; } public AssemblyFileImporter(SuperAdapter superAdapter) { this.superAdapter = superAdapter; } public AssemblyFileImporter() { } public void importAssembly() { listOfScaffolds = new ArrayList<>(); listOfSuperscaffolds = new ArrayList<>(); listOfUnattempted = new ArrayList<>(); try { if (assemblyFilePath != null) { rawFileData = readFile(assemblyFilePath); parseAssemblyFile(); } if (!modified) setInitialState(); else setModifiedInitialState(); } catch (IOException exception) { System.err.println("Error reading files!"); } updateAssemblyScale(); assemblyScaffoldHandler = new AssemblyScaffoldHandler(listOfScaffolds, listOfSuperscaffolds, listOfUnattempted); } //at some point TODO: sandboxed to assembly // private void parseChromSizes() { // for (Chromosome chr : superAdapter.getHiC().getChromosomeHandler().getChromosomeArrayWithoutAllByAll()) { // Scaffold scaffold = new Scaffold(chr.getName(), chr.getIndex(), chr.getLength()); // listOfScaffolds.add(scaffold); // listOfSuperscaffolds.add(Arrays.asList(chr.getIndex())); // } // } private int updateAssemblyScale() { long totalLength = 0; for (Scaffold fragmentProperty : listOfScaffolds) { totalLength += fragmentProperty.getLength(); } HiCGlobals.hicMapScale = (int) (1 + totalLength / 2100000000); return (int) (totalLength / HiCGlobals.hicMapScale); // in case decide to use for validation so that not to count again } private void parseAssemblyFileNoBundling() throws IOException { try { for (String row : rawFileData) { if (row.startsWith(">")) { String[] splitRow = row.split(" "); // Name<\s>ID<\s>length Scaffold scaffold = new Scaffold(splitRow[0].substring(1), Integer.parseInt(splitRow[1]), Integer.parseInt(splitRow[2])); listOfScaffolds.add(scaffold); } else { List superscaffold = new ArrayList<>(); for (String index : row.split(" ")) { superscaffold.add(Integer.parseInt(index)); } listOfSuperscaffolds.add(superscaffold); } } } catch (NumberFormatException e) { e.printStackTrace(); System.err.println("Errors in format"); } } private void parseAssemblyFile() throws IOException { if (!needsBundling) { parseAssemblyFileNoBundling(); return; } try { long len = 0; int start = 0; int prev = 0; int i = 0; int input_start = 0; List name = new ArrayList<>(); List size = new ArrayList<>(); List asm = new ArrayList<>(); for (String row : rawFileData) { String[] splitRow = row.split(" "); if (splitRow[0].startsWith(">")) { int clen = Integer.parseInt(splitRow[2]); int id = Integer.parseInt(splitRow[1]); if (clen >= bundleSize && input_start != 0) { input_start = 0; } if (clen < bundleSize && input_start == 0) { input_start = id; } len += clen; name.add(splitRow[0]); size.add(clen); } else { asm.add(splitRow); if (splitRow.length != 1) { start = 0; continue; } i = Integer.parseInt(splitRow[0]); if (i <= 0) { start = 0; continue; } if (name.get(i - 1).contains(":::fragment_")) { start = 0; continue; } if (start <= 0 || i != prev + 1) { start = i; } prev = i; } } if ((bundleSize != 0 && input_start == 0) || (start == i)) { System.err.println("Nothing to bundle!"); } if (bundleSize != 0 && input_start > start) { start = input_start; System.err.println("Warning: cannot bundle everything under " + bundleSize + "bp"); } //safeguard against accidentally bundling more than one has originally bundled if (modified && start > 1) { List originalScaffolds = AssemblyHeatmapHandler.getSuperAdapter().getAssemblyStateTracker().getInitialAssemblyScaffoldHandler().getListOfScaffolds(); while (true) { long tentativeUnbundled = 0; for (int j = 0; j < start - 1; j++) { tentativeUnbundled += size.get(j); } if (tentativeUnbundled < len - originalScaffolds.get(originalScaffolds.size() - 1).getLength()) { start++; continue; } if (tentativeUnbundled > len - originalScaffolds.get(originalScaffolds.size() - 1).getLength()) { System.err.println("Something's wrong!"); } break; } } long bundlelen = 0; for (i = 1; i < start; i++) { Scaffold scaffold = new Scaffold(name.get(i - 1).substring(1), i, size.get(i - 1)); listOfScaffolds.add(scaffold); bundlelen += size.get(i - 1); } for (i = start; i <= name.size(); i++) { listOfUnattempted.add(name.get(i - 1) + " " + i + " " + size.get(i - 1)); } for (String[] asmLine : asm) { if (Integer.parseInt(asmLine[0]) == start) { break; } List superscaffold = new ArrayList<>(); for (String index : asmLine) { superscaffold.add(Integer.parseInt(index)); } listOfSuperscaffolds.add(superscaffold); } listOfScaffolds.add(new Scaffold("unattempted:::debris", start, len - bundlelen)); List superscaffold = new ArrayList<>(); superscaffold.add(start); listOfSuperscaffolds.add(superscaffold); } catch (NumberFormatException e) { e.printStackTrace(); System.err.println("Errors in format"); } } private void setInitialState() { long shift = 0; for (List row : listOfSuperscaffolds) { for (Integer entry : row) { int fragmentIterator = Math.abs(entry) - 1; listOfScaffolds.get(fragmentIterator).setOriginallyInverted(false); if (entry < 0) { listOfScaffolds.get(fragmentIterator).setOriginallyInverted(true); } else if (entry == 0) { System.err.println("Something is wrong with the input."); // should not happen } listOfScaffolds.get(fragmentIterator).setOriginalStart(shift); shift += listOfScaffolds.get(fragmentIterator).getLength(); } } } private void setModifiedInitialState() { List originalScaffolds = AssemblyHeatmapHandler.getSuperAdapter().getAssemblyStateTracker().getInitialAssemblyScaffoldHandler().getListOfScaffolds(); long modifiedShift = 0; int originalScaffoldIterator = 0; Scaffold originalScaffold = originalScaffolds.get(originalScaffoldIterator); long containingStart = originalScaffold.getOriginalStart(); long containingEnd = originalScaffold.getOriginalEnd(); for (Scaffold modifiedScaffold : listOfScaffolds) { modifiedScaffold.setOriginallyInverted(originalScaffold.getOriginallyInverted()); if (!modifiedScaffold.getOriginallyInverted()) { modifiedScaffold.setOriginalStart(containingStart); containingStart += modifiedScaffold.getLength(); } else { modifiedScaffold.setOriginalStart(containingEnd - modifiedScaffold.getLength()); containingEnd -= modifiedScaffold.getLength(); } // trace movement along the original feature modifiedShift += modifiedScaffold.getLength(); // check if need to switch to next original feature if (modifiedShift == originalScaffold.getLength()) { if (originalScaffoldIterator == originalScaffolds.size() - 1) { if (modifiedScaffold != listOfScaffolds.get(listOfScaffolds.size() - 1)) { System.err.println("Modified assembly incompatible with the original one."); } break; } originalScaffoldIterator++; originalScaffold = originalScaffolds.get(originalScaffoldIterator); containingStart = originalScaffold.getOriginalStart(); containingEnd = originalScaffold.getOriginalEnd(); modifiedShift = 0; } } //TODO: more safeguards e.g. by name } List readFile(String filePath) throws IOException { List fileData = new ArrayList<>(); File file = new File(filePath); if (file.length() > 1000000 && !modified) { //launch dialog to confirm with the user if (SuperAdapter.showConfirmDialog("The assembly file is large. Do you want to try and bundle small sequences?") == 0) { needsBundling = true; } } //for modified use replicate what's in the current map if (modified) { List listOfScaffolds = AssemblyHeatmapHandler.getSuperAdapter().getAssemblyStateTracker().getInitialAssemblyScaffoldHandler().getListOfScaffolds(); if (listOfScaffolds.get(listOfScaffolds.size() - 1).getName().contentEquals("unattempted:::debris")) { needsBundling = true; } } Scanner scanner = new Scanner(file); while (scanner.hasNext()) { fileData.add(scanner.nextLine()); } return fileData; } public AssemblyScaffoldHandler getAssemblyScaffoldHandler() { return assemblyScaffoldHandler; } } ================================================ FILE: src/juicebox/assembly/AssemblyHeatmapHandler.java ================================================ /* * The MIT License (MIT) * * Copyright (c) 2011-2020 Broad Institute, Aiden Lab, Rice University, Baylor College of Medicine * * Permission is hereby granted, free of charge, to any person obtaining a copy * of this software and associated documentation files (the "Software"), to deal * in the Software without restriction, including without limitation the rights * to use, copy, modify, merge, publish, distribute, sublicense, and/or sell * copies of the Software, and to permit persons to whom the Software is * furnished to do so, subject to the following conditions: * * The above copyright notice and this permission notice shall be included in * all copies or substantial portions of the Software. * * THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR * IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, * FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE * AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER * LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, * OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN * THE SOFTWARE. */ package juicebox.assembly; import juicebox.HiCGlobals; import juicebox.data.Block; import juicebox.data.ContactRecord; import juicebox.gui.SuperAdapter; import java.util.ArrayList; import java.util.Collections; import java.util.List; /** * Created by muhammadsaadshamim on 4/17/17. */ public class AssemblyHeatmapHandler { private static SuperAdapter superAdapter; private static List listOfOSortedAggregateScaffolds = new ArrayList<>(); // Does not seem to offer any speedup. // private static Scaffold guessScaffold = null; public static void setListOfOSortedAggregateScaffolds(List listOfAggregateScaffolds) { AssemblyHeatmapHandler.listOfOSortedAggregateScaffolds = new ArrayList<>(listOfAggregateScaffolds); Collections.sort(listOfOSortedAggregateScaffolds, Scaffold.originalStateComparator); } public static SuperAdapter getSuperAdapter() { return AssemblyHeatmapHandler.superAdapter; } public static void setSuperAdapter(SuperAdapter superAdapter) { AssemblyHeatmapHandler.superAdapter = superAdapter; } public static Block modifyBlock(Block block, String key, int binSize, int chr1Idx, int chr2Idx) { //temp fix for AllByAll. TODO: trace this! if (chr1Idx == 0 && chr2Idx == 0) { binSize = 1000 * binSize; // AllByAll is measured in kb } List alteredContacts = new ArrayList<>(); for (ContactRecord record : block.getContactRecords()) { int alteredAsmBinX = getAlteredAsmBin(record.getBinX(), binSize); int alteredAsmBinY = getAlteredAsmBin(record.getBinY(), binSize); if (alteredAsmBinX == -1 || alteredAsmBinY == -1) { alteredContacts.add(record); } else { if (alteredAsmBinX > alteredAsmBinY) { alteredContacts.add(new ContactRecord( alteredAsmBinY, alteredAsmBinX, record.getCounts())); } else { alteredContacts.add(new ContactRecord( alteredAsmBinX, alteredAsmBinY, record.getCounts())); } } } block = new Block(block.getNumber(), alteredContacts, key); return block; } private static int getAlteredAsmBin(int binValue, int binSize) { long originalFirstNucleotide = (long) (binValue * HiCGlobals.hicMapScale * binSize + 1); long currentFirstNucleotide; Scaffold aggregateScaffold = lookUpOriginalAggregateScaffold(originalFirstNucleotide); if (aggregateScaffold != null) { if (!aggregateScaffold.getInvertedVsInitial()) { currentFirstNucleotide = (aggregateScaffold.getCurrentStart() + originalFirstNucleotide - aggregateScaffold.getOriginalStart()); } else { currentFirstNucleotide = (aggregateScaffold.getCurrentEnd() - originalFirstNucleotide + 2 - (long) (HiCGlobals.hicMapScale * binSize) + aggregateScaffold.getOriginalStart()); } return (int) ((currentFirstNucleotide - 1) / (HiCGlobals.hicMapScale * binSize)); } return -1; } private static Scaffold lookUpOriginalAggregateScaffold(long genomicPos) { // Does not seem to offer much advantage // if (guessScaffold!=null && guessScaffold.getOriginalStart()=genomicPos){ // return guessScaffold; // } Scaffold tmp = new Scaffold("tmp", 1, 1); tmp.setOriginalStart(genomicPos); int idx = Collections.binarySearch(listOfOSortedAggregateScaffolds, tmp, Scaffold.originalStateComparator); if (-idx - 2 >= 0) { return listOfOSortedAggregateScaffolds.get(-idx - 2); } else return null; } } ================================================ FILE: src/juicebox/assembly/AssemblyOperationExecutor.java ================================================ /* * The MIT License (MIT) * * Copyright (c) 2011-2021 Broad Institute, Aiden Lab, Rice University, Baylor College of Medicine * * Permission is hereby granted, free of charge, to any person obtaining a copy * of this software and associated documentation files (the "Software"), to deal * in the Software without restriction, including without limitation the rights * to use, copy, modify, merge, publish, distribute, sublicense, and/or sell * copies of the Software, and to permit persons to whom the Software is * furnished to do so, subject to the following conditions: * * The above copyright notice and this permission notice shall be included in * all copies or substantial portions of the Software. * * THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR * IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, * FITNESS FOR A PARTICULAR PURPOSE AND NON-INFRINGEMENT. IN NO EVENT SHALL THE * AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER * LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, * OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN * THE SOFTWARE. */ package juicebox.assembly; import juicebox.HiC; import juicebox.HiCGlobals; import juicebox.gui.SuperAdapter; import juicebox.track.feature.Feature2D; import java.util.List; /** * Created by nathanielmusial on 7/10/17. */ public class AssemblyOperationExecutor { public static void splitContig(Feature2D originalContig, Feature2D debrisContig, SuperAdapter superAdapter, HiC hic, boolean moveTo) { AssemblyScaffoldHandler assemblyScaffoldHandler = superAdapter.getAssemblyStateTracker().getNewAssemblyHandler(); assemblyScaffoldHandler.editScaffold(originalContig, debrisContig); performAssemblyAction(superAdapter, assemblyScaffoldHandler, true); } public static void invertSelection(SuperAdapter superAdapter, List selectedFeatures) { if (selectedFeatures != null && !selectedFeatures.isEmpty()) { AssemblyScaffoldHandler assemblyScaffoldHandler = superAdapter.getAssemblyStateTracker().getNewAssemblyHandler(); assemblyScaffoldHandler.invertSelection(selectedFeatures); performAssemblyAction(superAdapter, assemblyScaffoldHandler, true); } } public static void moveSelection(SuperAdapter superAdapter, List selectedFeatures, Feature2D featureOrigin) { if (selectedFeatures != null && !selectedFeatures.isEmpty()) { AssemblyScaffoldHandler assemblyScaffoldHandler = superAdapter.getAssemblyStateTracker().getNewAssemblyHandler(); assemblyScaffoldHandler.moveSelection(selectedFeatures, featureOrigin); performAssemblyAction(superAdapter, assemblyScaffoldHandler, true); } } public static void moveAndDisperseSelection(SuperAdapter superAdapter, List selectedFeatures, Feature2D featureOrigin) { if (selectedFeatures != null && !selectedFeatures.isEmpty()) { AssemblyScaffoldHandler assemblyScaffoldHandler = superAdapter.getAssemblyStateTracker().getNewAssemblyHandler(); assemblyScaffoldHandler.moveSelection(selectedFeatures, featureOrigin); assemblyScaffoldHandler.multiSplit(selectedFeatures); performAssemblyAction(superAdapter, assemblyScaffoldHandler, true); } } public static void toggleGroup(SuperAdapter superAdapter, Feature2D upstreamFeature2D, Feature2D downstreamFeature2D) { if (upstreamFeature2D != null && downstreamFeature2D != null) { AssemblyScaffoldHandler assemblyScaffoldHandler = superAdapter.getAssemblyStateTracker().getNewAssemblyHandler(); assemblyScaffoldHandler.toggleGroup(upstreamFeature2D, downstreamFeature2D); performAssemblyAction(superAdapter, assemblyScaffoldHandler, HiCGlobals.phasing); } } public static void multiMerge(SuperAdapter superAdapter, List selectedFeatures) { if (selectedFeatures != null && !selectedFeatures.isEmpty()) { AssemblyScaffoldHandler assemblyScaffoldHandler = superAdapter.getAssemblyStateTracker().getNewAssemblyHandler(); assemblyScaffoldHandler.multiMerge(selectedFeatures.get(0), selectedFeatures.get(selectedFeatures.size() - 1)); performAssemblyAction(superAdapter, assemblyScaffoldHandler, false); } } public static void multiSplit(SuperAdapter superAdapter, List selectedFeatures) { if (selectedFeatures != null && !selectedFeatures.isEmpty()) { AssemblyScaffoldHandler assemblyScaffoldHandler = superAdapter.getAssemblyStateTracker().getNewAssemblyHandler(); assemblyScaffoldHandler.multiSplit(selectedFeatures); performAssemblyAction(superAdapter, assemblyScaffoldHandler, false); } } public static void phaseMerge(SuperAdapter superAdapter, List selectedFeatures) { if (selectedFeatures != null && !selectedFeatures.isEmpty()) { AssemblyScaffoldHandler assemblyScaffoldHandler = superAdapter.getAssemblyStateTracker().getNewAssemblyHandler(); assemblyScaffoldHandler.phaseMerge(selectedFeatures); performAssemblyAction(superAdapter, assemblyScaffoldHandler, true); } } private static void performAssemblyAction(final SuperAdapter superAdapter, final AssemblyScaffoldHandler assemblyScaffoldHandler, final Boolean refreshMap) { superAdapter.getAssemblyStateTracker().assemblyActionPerformed(assemblyScaffoldHandler, refreshMap); if (refreshMap) superAdapter.safeClearAllMZDCache(); } } ================================================ FILE: src/juicebox/assembly/AssemblyScaffoldHandler.java ================================================ /* * The MIT License (MIT) * * Copyright (c) 2011-2021 Broad Institute, Aiden Lab, Rice University, Baylor College of Medicine * * Permission is hereby granted, free of charge, to any person obtaining a copy * of this software and associated documentation files (the "Software"), to deal * in the Software without restriction, including without limitation the rights * to use, copy, modify, merge, publish, distribute, sublicense, and/or sell * copies of the Software, and to permit persons to whom the Software is * furnished to do so, subject to the following conditions: * * The above copyright notice and this permission notice shall be included in * all copies or substantial portions of the Software. * * THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR * IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, * FITNESS FOR A PARTICULAR PURPOSE AND NON-INFRINGEMENT. IN NO EVENT SHALL THE * AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER * LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, * OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN * THE SOFTWARE. */ package juicebox.assembly; import juicebox.HiCGlobals; import juicebox.mapcolorui.Feature2DHandler; import juicebox.track.feature.Feature2D; import juicebox.track.feature.Feature2DList; import java.awt.*; import java.util.List; import java.util.*; /** * Created by nathanielmusial on 6/30/17. */ public class AssemblyScaffoldHandler { //constants, have just one attribute private final String unsignedScaffoldIdAttributeKey = "Scaffold #"; private final String signedScaffoldIdAttributeKey = "Signed scaffold #"; private final String scaffoldNameAttributeKey = "Scaffold name"; private final String superScaffoldIdAttributeKey = "Superscaffold #"; private final String superScaffoldNameAttributeKey = "Superscaffold name"; // formalities private final int chrIndex = 1; private final String chrName = "assembly"; //scaffolds and superscaffolds private List listOfScaffolds = new ArrayList<>(); private List> listOfSuperscaffolds = new ArrayList<>(); // aggregates private List listOfAggregateScaffolds = new ArrayList<>(); private List listOfBundledScaffolds = new ArrayList<>(); private Feature2DHandler scaffoldFeature2DHandler; private Feature2DHandler superscaffoldFeature2DHandler; public AssemblyScaffoldHandler(List listOfScaffolds, List> listOfSuperscaffolds) { this.listOfScaffolds = listOfScaffolds; this.listOfSuperscaffolds = listOfSuperscaffolds; updateAssembly(true); } public AssemblyScaffoldHandler(List listOfScaffolds, List> listOfSuperscaffolds, List bundled) { this.listOfScaffolds = listOfScaffolds; this.listOfSuperscaffolds = listOfSuperscaffolds; this.listOfBundledScaffolds = bundled; updateAssembly(true); } public AssemblyScaffoldHandler(AssemblyScaffoldHandler assemblyScaffoldHandler) { this.listOfScaffolds = assemblyScaffoldHandler.cloneScaffolds(); this.listOfSuperscaffolds = assemblyScaffoldHandler.cloneSuperscaffolds(); this.listOfBundledScaffolds = assemblyScaffoldHandler.getListOfBundledScaffolds(); this.scaffoldFeature2DHandler = assemblyScaffoldHandler.getScaffoldFeature2DHandler(); this.superscaffoldFeature2DHandler = assemblyScaffoldHandler.getSuperscaffoldFeature2DHandler(); this.listOfAggregateScaffolds = assemblyScaffoldHandler.getListOfAggregateScaffolds(); //updateAssembly(true); } private List cloneScaffolds() { List newListOfScaffolds = new ArrayList<>(); for (Scaffold scaffold : listOfScaffolds) { newListOfScaffolds.add(new Scaffold(scaffold)); } return newListOfScaffolds; } private List> cloneSuperscaffolds() { List> newListOfSuperScaffolds = new ArrayList<>(); for (List superscaffold : listOfSuperscaffolds) { newListOfSuperScaffolds.add(new ArrayList<>(superscaffold)); } return newListOfSuperScaffolds; } public List getListOfScaffolds() { return listOfScaffolds; } public List> getListOfSuperscaffolds() { return listOfSuperscaffolds; } public void updateAssembly(boolean refreshMap) { if (!refreshMap) { updateSuperscaffolds(); return; } int signScafId; long scaffoldShift = 0; long superscaffoldShift = 0; int aggregateScaffoldCounter = 1; Scaffold nextScaffold = null; Scaffold aggregateScaffold = null; Scaffold tempAggregateScaffold = null; Feature2DList scaffoldFeature2DList = new Feature2DList(); Feature2DList superscaffoldFeature2DList = new Feature2DList(); listOfAggregateScaffolds = new ArrayList<>(); for (int i = 0; i < listOfSuperscaffolds.size(); i++) { for (int j = 0; j < listOfSuperscaffolds.get(i).size(); j++) { if (i == 0 && j == 0) { // first scaffold signScafId = listOfSuperscaffolds.get(i).get(j); nextScaffold = listOfScaffolds.get(Math.abs(signScafId) - 1); nextScaffold.setCurrentStart(scaffoldShift); nextScaffold.setInvertedVsInitial(false); if (signScafId < 0 && (!listOfScaffolds.get(Math.abs(signScafId) - 1).getOriginallyInverted()) || signScafId > 0 && listOfScaffolds.get(Math.abs(signScafId) - 1).getOriginallyInverted()) { nextScaffold.setInvertedVsInitial(true); } scaffoldFeature2DList.add(chrIndex, chrIndex, nextScaffold.getCurrentFeature2D()); scaffoldShift += nextScaffold.getLength(); // first aggregate aggregateScaffold = new Scaffold(nextScaffold); aggregateScaffold.setIndexId(aggregateScaffoldCounter); aggregateScaffold.setOriginallyInverted(false); continue; } // rest of scaffolds signScafId = listOfSuperscaffolds.get(i).get(j); nextScaffold = listOfScaffolds.get(Math.abs(signScafId) - 1); nextScaffold.setCurrentStart(scaffoldShift); nextScaffold.setInvertedVsInitial(false); if (signScafId < 0 && (!listOfScaffolds.get(Math.abs(signScafId) - 1).getOriginallyInverted()) || signScafId > 0 && listOfScaffolds.get(Math.abs(signScafId) - 1).getOriginallyInverted()) { nextScaffold.setInvertedVsInitial(true); } scaffoldFeature2DList.add(chrIndex, chrIndex, nextScaffold.getCurrentFeature2D()); scaffoldShift += nextScaffold.getLength(); // try to aggregate tempAggregateScaffold = aggregateScaffold.mergeWith(nextScaffold); if (tempAggregateScaffold == null) { // if merge failed dump current aggregate listOfAggregateScaffolds.add(aggregateScaffold); // start next aggregate aggregateScaffoldCounter++; aggregateScaffold = new Scaffold(nextScaffold); aggregateScaffold.setIndexId(aggregateScaffoldCounter); aggregateScaffold.setOriginallyInverted(false); } else { aggregateScaffold = tempAggregateScaffold; } } Feature2D superscaffoldFeature2D = populateSuperscaffoldFeature2D(superscaffoldShift, scaffoldShift, i); superscaffoldFeature2DList.add(chrIndex, chrIndex, superscaffoldFeature2D); superscaffoldShift = scaffoldShift; } listOfAggregateScaffolds.add(aggregateScaffold); // create scaffold feature handler scaffoldFeature2DHandler = new Feature2DHandler(scaffoldFeature2DList); //scaffoldFeature2DHandler.setSparsePlottingEnabled(true); // Uncomment to visualize aggregate scaffold boundaries // for (Scaffold temp : listOfAggregateScaffolds){ // temp.setAssociatedFeatureColor(Color.black); // superscaffoldFeature2DList.add(chrIndex, chrIndex, temp.getCurrentFeature2D()); // } // create superscaffold feature handler superscaffoldFeature2DHandler = new Feature2DHandler(superscaffoldFeature2DList); AssemblyHeatmapHandler.setListOfOSortedAggregateScaffolds(listOfAggregateScaffolds); // aggregate list is already sorted, no need to sort again // System.out.println("update assembly: " + listOfAggregateScaffolds.size()); } private Feature2D populateSuperscaffoldFeature2D(long start, long end, int i) { Map attributes = new HashMap<>(); attributes.put(superScaffoldIdAttributeKey, String.valueOf(i + 1)); attributes.put(superScaffoldNameAttributeKey, listOfScaffolds.get(Math.abs(listOfSuperscaffolds.get(i).get(0)) - 1).getName()); return new Feature2D(Feature2D.FeatureType.SUPERSCAFFOLD, chrName, (int) (start / HiCGlobals.hicMapScale), (int) (end / HiCGlobals.hicMapScale), chrName, (int) (start / HiCGlobals.hicMapScale), (int) (end / HiCGlobals.hicMapScale), new Color(0, 0, 255), attributes); } private void updateSuperscaffolds() { Feature2DList superscaffoldFeature2DList = new Feature2DList(); long superscaffoldStart = 0; for (int superscaffold = 0; superscaffold < listOfSuperscaffolds.size(); superscaffold++) { long superscaffoldLength = 0; for (int scaffold : listOfSuperscaffolds.get(superscaffold)) { superscaffoldLength += listOfScaffolds.get(Math.abs(scaffold) - 1).getLength(); } Feature2D superscaffoldFeature2D = populateSuperscaffoldFeature2D(superscaffoldStart, superscaffoldStart + superscaffoldLength, superscaffold); superscaffoldFeature2DList.add(chrIndex, chrIndex, superscaffoldFeature2D); superscaffoldStart += superscaffoldLength; } superscaffoldFeature2DHandler = new Feature2DHandler(superscaffoldFeature2DList); } //************************** Communication with Feature2D ***************************// private int getSignedIndexFromScaffoldFeature2D(Feature2D scaffoldFeature2D) { if (scaffoldFeature2D.getFeatureType() == Feature2D.FeatureType.SCAFFOLD) { return Integer.parseInt(scaffoldFeature2D.getAttribute(signedScaffoldIdAttributeKey)); } else { return 0; } } private int getUnSignedIndexFromScaffoldFeature2D(Feature2D scaffoldFeature2D) { if (scaffoldFeature2D.getFeatureType() == Feature2D.FeatureType.SCAFFOLD) { return Integer.parseInt(scaffoldFeature2D.getAttribute(unsignedScaffoldIdAttributeKey)); } else { return 0; } } public Scaffold getScaffoldFromFeature(Feature2D scaffoldFeature2D) { if (scaffoldFeature2D.getFeatureType() == Feature2D.FeatureType.SCAFFOLD) { int i = getUnSignedIndexFromScaffoldFeature2D(scaffoldFeature2D) - 1; return listOfScaffolds.get(i); } return null; } public Scaffold getAggegateScaffoldFromFeature(Feature2D aggregateScaffoldFeature2D) { if (aggregateScaffoldFeature2D.getFeatureType() == Feature2D.FeatureType.SCAFFOLD) { int i = getUnSignedIndexFromScaffoldFeature2D(aggregateScaffoldFeature2D) - 1; return listOfAggregateScaffolds.get(i); } return null; } //************************************** Actions **************************************// //**** Split fragment ****// public void editScaffold(Feature2D targetFeature, Feature2D debrisFeature) { Scaffold targetScaffold = getScaffoldFromFeature(targetFeature); // do not allow for splitting debris scaffoldFeature2DList, TODO: should probably also handle at the level of prompts if (targetScaffold.isDebris()) { return; } // calculate split with respect to fragment long startCut; long endCut; if (targetScaffold.getSignIndexId() > 0) { startCut = (long) (debrisFeature.getStart1() * HiCGlobals.hicMapScale) - targetScaffold.getCurrentStart(); endCut = (long) (debrisFeature.getEnd1() * HiCGlobals.hicMapScale) - targetScaffold.getCurrentStart(); } else { startCut = (long) (targetScaffold.getCurrentEnd() - debrisFeature.getEnd1() * HiCGlobals.hicMapScale); endCut = (long) (targetScaffold.getCurrentEnd() - debrisFeature.getStart1() * HiCGlobals.hicMapScale); } editCprops(targetScaffold, startCut, endCut); editAsm(targetScaffold); } private void editAsm(Scaffold scaffold) { List debrisSuperscaffold = new ArrayList<>(); for (List listOfSuperscaffold : listOfSuperscaffolds) { int scaffoldId = scaffold.getIndexId(); for (int j = 0; j < listOfSuperscaffold.size(); j++) { listOfSuperscaffold.set(j, modifyScaffoldId(listOfSuperscaffold.get(j), scaffoldId)); } if (listOfSuperscaffold.contains(scaffoldId)) { listOfSuperscaffold.add(listOfSuperscaffold.indexOf(scaffoldId) + 1, scaffoldId + 2); debrisSuperscaffold.add(scaffoldId + 1); } else if (listOfSuperscaffold.contains(-scaffoldId)) { listOfSuperscaffold.add(listOfSuperscaffold.indexOf(-scaffoldId), -scaffoldId - 2); debrisSuperscaffold.add(-scaffoldId - 1); } } listOfSuperscaffolds.add(debrisSuperscaffold); } private int modifyScaffoldId(int index, int cutElementId) { if (Math.abs(index) <= cutElementId) { return index; } else { if (index > 0) { return index + 2; } else { return index - 2; } } } private void editCprops(Scaffold targetScaffold, long startCut, long endCut) { List newListOfScaffolds = new ArrayList<>(); //List addedProperties = new ArrayList<>(); int startingFragmentNumber; for (Scaffold scaffoldProperty : listOfScaffolds) { if (scaffoldProperty.getIndexId() < targetScaffold.getIndexId()) { newListOfScaffolds.add(scaffoldProperty); } else if (scaffoldProperty.getIndexId() == targetScaffold.getIndexId()) { startingFragmentNumber = scaffoldProperty.getFragmentNumber(); if (startingFragmentNumber == 0) { startingFragmentNumber++; } // first ever split newListOfScaffolds.add(new Scaffold(scaffoldProperty.getOriginalScaffoldName() + ":::fragment_" + (startingFragmentNumber), scaffoldProperty.getIndexId(), startCut)); newListOfScaffolds.add(new Scaffold(scaffoldProperty.getOriginalScaffoldName() + ":::fragment_" + (startingFragmentNumber + 1) + ":::debris", scaffoldProperty.getIndexId() + 1, endCut - startCut)); newListOfScaffolds.add(new Scaffold(scaffoldProperty.getOriginalScaffoldName() + ":::fragment_" + (startingFragmentNumber + 2), scaffoldProperty.getIndexId() + 2, scaffoldProperty.getLength() - endCut)); // set their initial properties int lastIndexScaffolds = newListOfScaffolds.size(); if (!targetScaffold.getOriginallyInverted()) { newListOfScaffolds.get(lastIndexScaffolds - 3).setOriginalStart(targetScaffold.getOriginalStart()); newListOfScaffolds.get(lastIndexScaffolds - 3).setOriginallyInverted(false); newListOfScaffolds.get(lastIndexScaffolds - 2) .setOriginalStart(targetScaffold.getOriginalStart() + startCut); newListOfScaffolds.get(lastIndexScaffolds - 2).setOriginallyInverted(false); newListOfScaffolds.get(lastIndexScaffolds - 1) .setOriginalStart(targetScaffold.getOriginalStart() + endCut); newListOfScaffolds.get(lastIndexScaffolds - 1).setOriginallyInverted(false); } else { newListOfScaffolds.get(lastIndexScaffolds - 1).setOriginalStart(targetScaffold.getOriginalStart()); newListOfScaffolds.get(lastIndexScaffolds - 1).setOriginallyInverted(true); newListOfScaffolds.get(lastIndexScaffolds - 2) .setOriginalStart(targetScaffold.getOriginalEnd() - endCut - 1); newListOfScaffolds.get(lastIndexScaffolds - 2).setOriginallyInverted(true); newListOfScaffolds.get(lastIndexScaffolds - 3) .setOriginalStart(targetScaffold.getOriginalEnd() - startCut - 1); newListOfScaffolds.get(lastIndexScaffolds - 3).setOriginallyInverted(true); } } else { if (scaffoldProperty.getOriginalScaffoldName().equals(targetScaffold.getOriginalScaffoldName())) { if (scaffoldProperty.isDebris()) { scaffoldProperty.setName(scaffoldProperty.getOriginalScaffoldName() + ":::fragment_" + (scaffoldProperty.getFragmentNumber() + 2) + ":::debris"); } else { scaffoldProperty.setName(scaffoldProperty.getOriginalScaffoldName() + ":::fragment_" + (scaffoldProperty.getFragmentNumber() + 2)); } } scaffoldProperty.setIndexId(scaffoldProperty.getIndexId() + 2); newListOfScaffolds.add(scaffoldProperty); } } listOfScaffolds.clear(); listOfScaffolds.addAll(newListOfScaffolds); } //**** Inversion ****// public void invertSelection(List scaffoldFeatures) { int id1 = getSignedIndexFromScaffoldFeature2D(scaffoldFeatures.get(0)); int id2 = getSignedIndexFromScaffoldFeature2D(scaffoldFeatures.get(scaffoldFeatures.size() - 1)); int gid1 = getSuperscaffoldId(id1); int gid2 = getSuperscaffoldId(id2); if (gid1 != gid2 && listOfSuperscaffolds.get(gid1).indexOf(id1) != 0) { splitSuperscaffold(gid1, listOfSuperscaffolds.get(gid1).get(listOfSuperscaffolds.get(gid1).indexOf(id1) - 1)); gid1 = getSuperscaffoldId(id1); gid2 = getSuperscaffoldId(id2); } if (gid1 != gid2 && listOfSuperscaffolds.get(gid2).indexOf(id2) != listOfSuperscaffolds.get(gid2).size() - 1) { splitSuperscaffold(gid2, id2); gid1 = getSuperscaffoldId(id1); gid2 = getSuperscaffoldId(id2); } //update scaffold inversion status for (Feature2D feature : scaffoldFeatures) { getScaffoldFromFeature(feature).toggleInversion(); } if (gid1 == gid2) { Collections.reverse(listOfSuperscaffolds.get(gid1) .subList(listOfSuperscaffolds.get(gid1).indexOf(id1), listOfSuperscaffolds.get(gid2).indexOf(id2) + 1)); for (int i = listOfSuperscaffolds.get(gid1).indexOf(id2); i <= listOfSuperscaffolds.get(gid2).indexOf(id1); i++) { listOfSuperscaffolds.get(gid1).set(i, -1 * listOfSuperscaffolds.get(gid1).get(i)); } } else { List> newListOfSuperscaffolds = new ArrayList<>(); for (int i = 0; i <= listOfSuperscaffolds.size() - 1; i++) { if (i >= gid1 && i <= gid2) { newListOfSuperscaffolds.add(listOfSuperscaffolds.get(gid2 - i + gid1)); Collections.reverse(newListOfSuperscaffolds.get(i)); for (int j = 0; j <= newListOfSuperscaffolds.get(i).size() - 1; j++) { newListOfSuperscaffolds.get(i).set(j, -1 * newListOfSuperscaffolds.get(i).get(j)); } } else { newListOfSuperscaffolds.add(listOfSuperscaffolds.get(i)); } } listOfSuperscaffolds.clear(); listOfSuperscaffolds.addAll(newListOfSuperscaffolds); } } //**** Move selection ****// void moveSelection(List selectedFeatures, Feature2D upstreamFeature) { // note assumes sorted int id1 = getSignedIndexFromScaffoldFeature2D(selectedFeatures.get(0)); int id2 = getSignedIndexFromScaffoldFeature2D(selectedFeatures.get(selectedFeatures.size() - 1)); int gid1 = getSuperscaffoldId(id1); int gid2 = getSuperscaffoldId(id2); // initialize id3 and gid3 int id3 = 0; int gid3 = -1; if (upstreamFeature != null) { // initialize id3 and gid3 if not inserting to top id3 = getSignedIndexFromScaffoldFeature2D(upstreamFeature); gid3 = getSuperscaffoldId(id3); // check if selectedFeatures span multiple groups paste split at destination if (gid1 != gid2 & listOfSuperscaffolds.get(gid3).indexOf(id3) != listOfSuperscaffolds.get(gid3).size() - 1) { // handles pasting scaffolds from multiple groups into another group splitSuperscaffold(gid3, id3); gid1 = getSuperscaffoldId(id1); gid2 = getSuperscaffoldId(id2); gid3 = getSuperscaffoldId(id3); } } List> newSuperscaffolds = new ArrayList<>(); List> tempSuperscaffolds = new ArrayList<>(); List truncatedSuperscaffold = new ArrayList<>(); int shiftSuperscaffold = 0; for (int i = 0; i <= listOfSuperscaffolds.size() - 1; i++) { if (i == gid1 && i == gid2) { tempSuperscaffolds.add(listOfSuperscaffolds.get(gid1).subList(listOfSuperscaffolds.get(gid1).indexOf(id1), listOfSuperscaffolds.get(gid2).indexOf(id2) + 1)); if (listOfSuperscaffolds.get(gid1).indexOf(id1) != 0) { truncatedSuperscaffold.addAll(listOfSuperscaffolds.get(gid1).subList(0, listOfSuperscaffolds.get(gid1).indexOf(id1))); } if (listOfSuperscaffolds.get(gid2).indexOf(id2) != listOfSuperscaffolds.get(gid2).size() - 1) { truncatedSuperscaffold.addAll(listOfSuperscaffolds.get(gid2).subList(1 + listOfSuperscaffolds.get(gid2).indexOf(id2), listOfSuperscaffolds.get(gid2).size())); } if (!truncatedSuperscaffold.isEmpty()) { newSuperscaffolds.add(truncatedSuperscaffold); } else { shiftSuperscaffold++; } } else if (gid1 != gid2 && i == gid1) { tempSuperscaffolds.add(listOfSuperscaffolds.get(gid1).subList(listOfSuperscaffolds.get(gid1).indexOf(id1), listOfSuperscaffolds.get(gid1).size())); if (listOfSuperscaffolds.get(gid1).indexOf(id1) != 0) { newSuperscaffolds.add(listOfSuperscaffolds.get(gid1).subList(0, listOfSuperscaffolds.get(gid1).indexOf(id1))); } else { shiftSuperscaffold++; } } else if (i > gid1 && i < gid2) { //gid1 != gid2 is covered/inherent to the condition tempSuperscaffolds.add(listOfSuperscaffolds.get(i)); shiftSuperscaffold++; } else if (gid1 != gid2 && i == gid2) { tempSuperscaffolds.add(listOfSuperscaffolds.get(gid2).subList(0, 1 + listOfSuperscaffolds.get(gid2).indexOf(id2))); if (listOfSuperscaffolds.get(gid2).indexOf(id2) != listOfSuperscaffolds.get(gid2).size() - 1) { newSuperscaffolds.add(listOfSuperscaffolds.get(gid2).subList(1 + listOfSuperscaffolds.get(gid2).indexOf(id2), listOfSuperscaffolds.get(gid2).size())); } else { shiftSuperscaffold++; } } else { newSuperscaffolds.add(listOfSuperscaffolds.get(i)); } } // check if inserting to top through PASTETOP if (upstreamFeature != null) { int newgid3 = gid3; if (gid3 > gid2) { // if moving a superscaffold downstream newgid3 -= shiftSuperscaffold; } if (listOfSuperscaffolds.get(gid3).indexOf(id3) == listOfSuperscaffolds.get(gid3).size() - 1) { newSuperscaffolds.addAll(newgid3 + 1, tempSuperscaffolds); } else { int pasteIndex = listOfSuperscaffolds.get(gid3).indexOf(id3); if (gid1 == gid3 && gid2 == gid3 && listOfSuperscaffolds.get(gid3).indexOf(id3) > listOfSuperscaffolds.get(gid3).indexOf(id2)) { pasteIndex -= listOfSuperscaffolds.get(gid3).size() - truncatedSuperscaffold.size(); } newSuperscaffolds.get(newgid3).addAll(pasteIndex + 1, tempSuperscaffolds.get(0)); } } else // if inserting to top, add all scaffolds to index 0 newSuperscaffolds.addAll(0, tempSuperscaffolds); listOfSuperscaffolds.clear(); listOfSuperscaffolds.addAll(newSuperscaffolds); } //**** Group toggle ****// public void toggleGroup(Feature2D upstreamFeature2D, Feature2D downstreamFeature2D) { int id1 = getSignedIndexFromScaffoldFeature2D(upstreamFeature2D); int id2 = getSignedIndexFromScaffoldFeature2D(downstreamFeature2D); //should not happen, other sanity checks? if (id1 == id2) { return; } int super1 = getSuperscaffoldId(id1); int super2 = getSuperscaffoldId(id2); if (super1 == super2) { splitSuperscaffold(super1, id1); } else { mergeSuperScaffolds(super1, super2); } } public void multiMerge(Feature2D firstFeature, Feature2D lastFeature) { int super1 = getSuperscaffoldId(getSignedIndexFromScaffoldFeature2D(firstFeature)); int super2 = getSuperscaffoldId(getSignedIndexFromScaffoldFeature2D(lastFeature)); mergeSuperScaffolds(super1, super2); } // public void phaseMerge(List selectedFeatures) { // // List> newSuperscaffolds = new ArrayList<>(); // // List newSuperscaffold = new ArrayList<>(); // List newAltSuperscaffold = new ArrayList<>(); // // for (Feature2D feature : selectedFeatures) { // int id = getSignedIndexFromScaffoldFeature2D(feature); // newSuperscaffold.add(id); // } // Collections.sort(newSuperscaffold); // for (int i : newSuperscaffold) { // if (i % 2 == 0) // newAltSuperscaffold.add(i - 1); // else // newAltSuperscaffold.add(i + 1); // } // // boolean test = true; // for (List superscaffold : listOfSuperscaffolds) { // // if (Collections.disjoint(listOfSuperscaffolds.get(i), newSuperscaffold)) { // if (!newSuperscaffold.contains(superscaffold.get(0)) && !newAltSuperscaffold.contains(superscaffold.get(0))) { // newSuperscaffolds.add(superscaffold); // } else { // if (test) { // if (getSuperscaffoldId(newSuperscaffold.get(0)) < getSuperscaffoldId(newAltSuperscaffold.get(0))) { // newSuperscaffolds.add(newSuperscaffold); // newSuperscaffolds.add(newAltSuperscaffold); // } else { // newSuperscaffolds.add(newAltSuperscaffold); // newSuperscaffolds.add(newSuperscaffold); // } // test = false; // } // continue; // } // } // // listOfSuperscaffolds.clear(); // listOfSuperscaffolds.addAll(newSuperscaffolds); // } public void multiSplit(List selectedFeatures) { int id1 = getSignedIndexFromScaffoldFeature2D(selectedFeatures.get(0)); int id2 = getSignedIndexFromScaffoldFeature2D(selectedFeatures.get(selectedFeatures.size() - 1)); int super1 = getSuperscaffoldId(id1); int super2 = getSuperscaffoldId(id2); multiSplitSuperscaffolds(id1, id2, super1, super2); } // SuperScaffold manipulations private void mergeSuperScaffolds (int super1, int super2){ if (HiCGlobals.phasing) { List idListToMerge = new ArrayList<>(); idListToMerge.add(super1); idListToMerge.add(super2); phaseMerge(idListToMerge); return; } List> newSuperscaffolds = new ArrayList<>(); for (int i = 0; i < listOfSuperscaffolds.size(); i++) { if(i>super1 && i<=super2){ newSuperscaffolds.get(super1).addAll(listOfSuperscaffolds.get(i)); }else{ newSuperscaffolds.add(listOfSuperscaffolds.get(i)); } } listOfSuperscaffolds.clear(); listOfSuperscaffolds.addAll(newSuperscaffolds); } public void phaseMerge(List idListToMerge) { List> newSuperscaffolds = new ArrayList<>(); List newSuperscaffold = new ArrayList<>(); List newAltSuperscaffold = new ArrayList<>(); List altIdListToMerge = new ArrayList<>(); for (int i : idListToMerge) { newSuperscaffold.addAll(listOfSuperscaffolds.get(i)); if (i % 2 == 0) { altIdListToMerge.add(i + 1); } else { altIdListToMerge.add(i - 1); } } idListToMerge.addAll(altIdListToMerge); Collections.sort(idListToMerge); boolean altGoesFirst = false; if (altIdListToMerge.contains(idListToMerge.get(0))) { altGoesFirst = true; } if (!HiCGlobals.noSortInPhasing) Collections.sort(newSuperscaffold); for (int i : newSuperscaffold) { if (i % 2 == 0) newAltSuperscaffold.add(i - 1); else { newAltSuperscaffold.add(i + 1); } } for (int i = 0; i < listOfSuperscaffolds.size(); i++) { List superscaffold = listOfSuperscaffolds.get(i); if (!idListToMerge.contains(Integer.valueOf(i))) { newSuperscaffolds.add(superscaffold); } else if (i == idListToMerge.get(0)) { if (!altGoesFirst) { newSuperscaffolds.add(newSuperscaffold); newSuperscaffolds.add(newAltSuperscaffold); } else { newSuperscaffolds.add(newAltSuperscaffold); newSuperscaffolds.add(newSuperscaffold); } } } listOfSuperscaffolds.clear(); listOfSuperscaffolds.addAll(newSuperscaffolds); } private void splitSuperscaffold(int superscaffoldId, int scaffoldId) { if (HiCGlobals.phasing) { if (superscaffoldId % 2 != 0) { superscaffoldId -= 1; if (scaffoldId % 2 == 0) { scaffoldId -= 1; } else { scaffoldId += 1; } } } List> newSuperscaffolds = new ArrayList<>(); for (int i = 0; i < listOfSuperscaffolds.size(); i++) { if (i == superscaffoldId) { int breakPointIndex = listOfSuperscaffolds.get(superscaffoldId).indexOf(scaffoldId); newSuperscaffolds.add(listOfSuperscaffolds.get(superscaffoldId) .subList(0, 1 + breakPointIndex)); if (HiCGlobals.phasing) { newSuperscaffolds.add(listOfSuperscaffolds.get(superscaffoldId + 1) .subList(0, 1 + breakPointIndex)); } newSuperscaffolds.add(listOfSuperscaffolds.get(superscaffoldId) .subList(1 + breakPointIndex, listOfSuperscaffolds.get(superscaffoldId).size())); if (HiCGlobals.phasing) { newSuperscaffolds.add(listOfSuperscaffolds.get(superscaffoldId + 1) .subList(1 + breakPointIndex, listOfSuperscaffolds.get(superscaffoldId + 1).size())); i++; } } else { newSuperscaffolds.add(listOfSuperscaffolds.get(i)); } } listOfSuperscaffolds.clear(); listOfSuperscaffolds.addAll(newSuperscaffolds); } private void multiSplitSuperscaffolds(int id1, int id2, int super1, int super2) { List> newSuperscaffolds = new ArrayList<>(); int startPoint = listOfSuperscaffolds.get(super1).indexOf(id1); int endPoint = listOfSuperscaffolds.get(super2).indexOf(id2); int jstart, jend; boolean addEndScaff = false; newSuperscaffolds.addAll(listOfSuperscaffolds.subList(0, super1)); for (int i = super1; i <= super2; i++) { jstart = 0; jend = listOfSuperscaffolds.get(i).size() - 1; // If at first superscaffold and selected start scaffold not at beginning of current superscaffold if (i == super1 && startPoint != 0) { jstart = startPoint; // Add rest of superscaffold to its own superscaffold newSuperscaffolds.add(listOfSuperscaffolds.get(i).subList(0, jstart)); } // If at last superscaffold and selected end scaffold not at end of current superscaffold if (i == super2 && endPoint != jend) { jend = endPoint; addEndScaff = true; } // Add each inner scaffold to its own superscaffold group for (int j = jstart; j <= jend; j++) { newSuperscaffolds.add(Arrays.asList(listOfSuperscaffolds.get(i).get(j))); } // If did not end at last scaffold in last superscaffold selected if (addEndScaff) { // Add rest of superscaffold to its own superscaffold newSuperscaffolds.add(listOfSuperscaffolds.get(i).subList(jend + 1, listOfSuperscaffolds.get(i).size())); } } newSuperscaffolds.addAll(listOfSuperscaffolds.subList(super2 + 1, listOfSuperscaffolds.size())); listOfSuperscaffolds.clear(); listOfSuperscaffolds.addAll(newSuperscaffolds); } //**** Utility functions ****// private int getSuperscaffoldId(int scaffoldId) { int i = 0; for (List scaffoldRow : listOfSuperscaffolds) { for (int index : scaffoldRow) { if (Math.abs(index) == Math.abs(scaffoldId)) { return i; } } i++; } System.err.println("Cannot find superscaffold containing scaffold " + scaffoldId); return -1; } @Override public String toString() { return Arrays.toString(listOfSuperscaffolds.toArray()); } public Feature2DHandler getScaffoldFeature2DHandler() { return scaffoldFeature2DHandler; } public Feature2DHandler getSuperscaffoldFeature2DHandler() { return superscaffoldFeature2DHandler; } public List getListOfAggregateScaffolds() { return listOfAggregateScaffolds; } public List getIntersectingAggregateFeatures(long genomicPos1, long genomicPos2) { Scaffold tmp = new Scaffold("tmp", 1, 1); tmp.setCurrentStart(genomicPos1); int idx1 = Collections.binarySearch(listOfAggregateScaffolds, tmp); idx1 = Math.max(-idx1 - 2, 0); tmp.setCurrentStart(genomicPos2); int idx2 = Collections.binarySearch(listOfAggregateScaffolds, tmp); if (-idx2 - 2 < 0) { idx2 = listOfAggregateScaffolds.size() - 1; } else { idx2 = -idx2 - 2; } return listOfAggregateScaffolds.subList(idx1, idx2 + 1); } public List getListOfBundledScaffolds() { return listOfBundledScaffolds; } } ================================================ FILE: src/juicebox/assembly/AssemblyStateTracker.java ================================================ /* * The MIT License (MIT) * * Copyright (c) 2011-2020 Broad Institute, Aiden Lab, Rice University, Baylor College of Medicine * * Permission is hereby granted, free of charge, to any person obtaining a copy * of this software and associated documentation files (the "Software"), to deal * in the Software without restriction, including without limitation the rights * to use, copy, modify, merge, publish, distribute, sublicense, and/or sell * copies of the Software, and to permit persons to whom the Software is * furnished to do so, subject to the following conditions: * * The above copyright notice and this permission notice shall be included in * all copies or substantial portions of the Software. * * THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR * IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, * FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE * AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER * LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, * OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN * THE SOFTWARE. */ package juicebox.assembly; import juicebox.DirectoryManager; import juicebox.HiCGlobals; import juicebox.gui.SuperAdapter; import java.util.Stack; /** * Created by nathanielmusial on 7/5/17. */ public class AssemblyStateTracker { private final Stack undoStack; private final Stack redoStack; private final AssemblyScaffoldHandler initialAssemblyScaffoldHandler; private final SuperAdapter superAdapter; private final String autoSaveFileName; private int counter = 0; public AssemblyStateTracker(AssemblyScaffoldHandler assemblyScaffoldHandler, SuperAdapter superAdapter) { undoStack = new Stack<>(); undoStack.push(assemblyScaffoldHandler); redoStack = new Stack<>(); this.initialAssemblyScaffoldHandler = assemblyScaffoldHandler; this.superAdapter = superAdapter; this.autoSaveFileName = DirectoryManager.getHiCDirectory() + "/" + (SuperAdapter.getDatasetTitle().split(".+?/(?=[^/]+$)")[1]).split("\\.(?=[^\\.]+$)")[0] + ".review.autosave"; } public AssemblyScaffoldHandler getAssemblyHandler() { return undoStack.peek(); } public AssemblyScaffoldHandler getNewAssemblyHandler() { return new AssemblyScaffoldHandler(undoStack.peek()); } public void resetState() { undoStack.clear(); assemblyActionPerformed(initialAssemblyScaffoldHandler, true); superAdapter.safeClearAllMZDCache(); } public AssemblyScaffoldHandler getInitialAssemblyScaffoldHandler() { return initialAssemblyScaffoldHandler; } public void assemblyActionPerformed(AssemblyScaffoldHandler assemblyScaffoldHandler, boolean refreshMap) { counter++; redoStack.clear(); undoStack.push(assemblyScaffoldHandler); if (counter % 20 == 0) { if (HiCGlobals.phasing) { PsfFileExporter psfFileExporter = new PsfFileExporter(assemblyScaffoldHandler, autoSaveFileName); psfFileExporter.exportPsfFile(); } else { AssemblyFileExporter assemblyFileExporter = new AssemblyFileExporter(assemblyScaffoldHandler, autoSaveFileName); assemblyFileExporter.exportAssemblyFile(); } } while (undoStack.size() > 50) { //keeps stack at size of 50 or less undoStack.remove(0); } assemblyScaffoldHandler.updateAssembly(refreshMap); regenerateLayers(refreshMap); } private void regenerateLayers(boolean refreshMap) { AssemblyScaffoldHandler assemblyScaffoldHandler = undoStack.peek(); if (refreshMap) { superAdapter.getMainLayer().getFeatureHandler().setLoopList(assemblyScaffoldHandler.getScaffoldFeature2DHandler().getAllVisibleLoops()); } superAdapter.getGroupLayer().getFeatureHandler().setLoopList(assemblyScaffoldHandler.getSuperscaffoldFeature2DHandler().getAllVisibleLoops()); } public boolean checkUndo() { return undoStack.size() > 1; } public void undo() { if (checkUndo()) { redoStack.push(undoStack.pop()); undoStack.peek().updateAssembly(true); regenerateLayers(true); superAdapter.safeClearAllMZDCache(); } } public boolean checkRedo() { return !redoStack.empty(); } public void redo() { if (checkRedo()) { undoStack.push(redoStack.pop()); undoStack.peek().updateAssembly(true); regenerateLayers(true); superAdapter.safeClearAllMZDCache(); } } } ================================================ FILE: src/juicebox/assembly/IGVFeatureCopy.java ================================================ /* * The MIT License (MIT) * * Copyright (c) 2011-2020 Broad Institute, Aiden Lab, Rice University, Baylor College of Medicine * * Permission is hereby granted, free of charge, to any person obtaining a copy * of this software and associated documentation files (the "Software"), to deal * in the Software without restriction, including without limitation the rights * to use, copy, modify, merge, publish, distribute, sublicense, and/or sell * copies of the Software, and to permit persons to whom the Software is * furnished to do so, subject to the following conditions: * * The above copyright notice and this permission notice shall be included in * all copies or substantial portions of the Software. * * THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR * IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, * FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE * AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER * LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, * OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN * THE SOFTWARE. */ // Created by Santiago Garcia Acosta July 4, 2018. package juicebox.assembly; import org.broad.igv.feature.Exon; import org.broad.igv.feature.IGVFeature; import org.broad.igv.feature.Strand; import org.broad.igv.track.WindowFunction; import org.broad.igv.util.collections.MultiMap; import java.awt.*; import java.util.List; public class IGVFeatureCopy implements IGVFeature { private final IGVFeature origFeat; private final String type; private final String id; private final String description; private final String url; private final String name; private final String chr; private final String contig; private Strand strand; private final int length; private final MultiMap attributes; private final float score; private List exons; private Color color; private int start; private int end; public static boolean colorFeaturesChk = false; public IGVFeatureCopy(IGVFeature feature) { this.origFeat = feature; this.type = feature.getType(); this.id = feature.getIdentifier(); this.description = feature.getDescription(); this.url = feature.getURL(); this.color = feature.getColor(); this.attributes = feature.getAttributes(); this.name = feature.getName(); this.chr = feature.getChr(); this.score = feature.getScore(); this.contig = feature.getContig(); this.start = feature.getStart(); this.end = feature.getEnd(); this.length = feature.getLength(); this.strand = feature.getStrand(); this.exons = feature.getExons(); } public void updateExons(List newExons) { exons = newExons; } public void updateStrand(Strand curStrand, boolean inversionState, boolean isBed) { Strand newStrand; if (!inversionState) { newStrand = curStrand; } else { if (colorFeaturesChk && isBed && color != null) { // Update color to complement color int r = color.getRed(); int g = color.getGreen(); int b = color.getBlue(); color = new Color(~r & 0xff, ~g & 0xff, ~b & 0xff); } // Update strand orientation if (curStrand == Strand.POSITIVE) { newStrand = Strand.NEGATIVE; } else if (curStrand == Strand.NEGATIVE) { newStrand = Strand.POSITIVE; } else { newStrand = strand; } } this.strand = newStrand; } public static void invertColorFeaturesChk() { colorFeaturesChk = !colorFeaturesChk; } public void setStart(int newStart) { this.start = newStart; } public void setEnd(int newEnd) { this.end = newEnd; } public int getStart() { return start; } public int getEnd() { return end; } public int getLength() { return java.lang.Math.abs(end - start); } public String getType() { return type; } public String getIdentifier() { return id; } public String getDescription() { return description; } public Strand getStrand() { return strand; } public MultiMap getAttributes() { return attributes; } public boolean contains(IGVFeature var1) { return origFeat.contains(var1); } public boolean contains(double var1) { return origFeat.contains(var1); } public List getExons() { return exons; } public Color getColor() { return color; } public String getURL() { return url; } public String getName() { return name; } public String getChr() { return chr; } public float getScore() { return score; } public String getValueString(double var1, int mouseX, WindowFunction var3) { return origFeat.getValueString(var1, mouseX, var3); } public String getContig() { return contig; } } ================================================ FILE: src/juicebox/assembly/OneDimAssemblyTrackLifter.java ================================================ /* * The MIT License (MIT) * * Copyright (c) 2011-2020 Broad Institute, Aiden Lab, Rice University, Baylor College of Medicine * * Permission is hereby granted, free of charge, to any person obtaining a copy * of this software and associated documentation files (the "Software"), to deal * in the Software without restriction, including without limitation the rights * to use, copy, modify, merge, publish, distribute, sublicense, and/or sell * copies of the Software, and to permit persons to whom the Software is * furnished to do so, subject to the following conditions: * * The above copyright notice and this permission notice shall be included in * all copies or substantial portions of the Software. * * THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR * IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, * FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE * AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER * LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, * OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN * THE SOFTWARE. */ package juicebox.assembly; import juicebox.HiC; import juicebox.HiCGlobals; import juicebox.data.basics.Chromosome; import juicebox.track.*; import juicebox.windowui.HiCZoom; import org.broad.igv.feature.Exon; import org.broad.igv.feature.IGVFeature; import org.broad.igv.track.WindowFunction; import java.util.ArrayList; import java.util.HashMap; import java.util.List; /** * Created by dudcha on 11/17/17. */ public class OneDimAssemblyTrackLifter { public static HiCDataPoint[] liftDataArray(HiCDataSource dataSource, HiC hic, Chromosome chromosome, int binX1, int binX2, HiCGridAxis gridAxis, double scaleFactor, WindowFunction windowFunction) { HiCZoom zoom = hic.getZoom(); // get aggregate scaffold handler AssemblyScaffoldHandler aFragHandler = AssemblyHeatmapHandler.getSuperAdapter().getAssemblyStateTracker().getAssemblyHandler(); final int binSize = zoom.getBinSize(); long actualBinSize = binSize; if (chromosome.getIndex() == 0) { actualBinSize = 1000 * actualBinSize; } List xAxisAggregateScaffolds = aFragHandler.getIntersectingAggregateFeatures( (long) (actualBinSize * binX1 * HiCGlobals.hicMapScale), (long) (actualBinSize * binX2 * HiCGlobals.hicMapScale)); List modifiedDataPoints = new ArrayList<>(); int x1pos, x2pos; for (Scaffold xScaffold : xAxisAggregateScaffolds) { x1pos = (int) (xScaffold.getOriginalStart() / HiCGlobals.hicMapScale); x2pos = (int) (xScaffold.getOriginalEnd() / HiCGlobals.hicMapScale); // have to case long because of thumbnail, maybe fix thumbnail instead if (xScaffold.getCurrentStart() < actualBinSize * binX1 * HiCGlobals.hicMapScale) { if (!xScaffold.getInvertedVsInitial()) { x1pos = (int) ((xScaffold.getOriginalStart() + actualBinSize * binX1 * HiCGlobals.hicMapScale - xScaffold.getCurrentStart()) / HiCGlobals.hicMapScale); } else { x2pos = (int) ((xScaffold.getOriginalStart() - actualBinSize * binX1 * HiCGlobals.hicMapScale + xScaffold.getCurrentEnd()) / HiCGlobals.hicMapScale); } } if (xScaffold.getCurrentEnd() > actualBinSize * binX2 * HiCGlobals.hicMapScale) { if (!xScaffold.getInvertedVsInitial()) { x2pos = (int) ((xScaffold.getOriginalStart() + actualBinSize * binX2 * HiCGlobals.hicMapScale - xScaffold.getCurrentStart()) / HiCGlobals.hicMapScale); } else { x1pos = (int) ((xScaffold.getOriginalStart() - actualBinSize * binX2 * HiCGlobals.hicMapScale + xScaffold.getCurrentEnd()) / HiCGlobals.hicMapScale); } } HiCDataPoint[] dataArray = dataSource.getData(chromosome, (int) (x1pos / actualBinSize), (int) (x2pos / actualBinSize), gridAxis, scaleFactor, windowFunction); for (HiCDataPoint point : dataArray) { // disregard points outside of the bin positions for this aggregate scaffold if (point.getBinNumber() < (int) (x1pos / actualBinSize) || point.getBinNumber() > (int) (x2pos / actualBinSize)) continue; long newStart; long newEnd; long newBin; if (!xScaffold.getInvertedVsInitial()) { newStart = (long) ((xScaffold.getCurrentStart() + HiCGlobals.hicMapScale * point.getGenomicStart() - xScaffold.getOriginalStart()) / HiCGlobals.hicMapScale); newBin = (long) ((xScaffold.getCurrentStart() + HiCGlobals.hicMapScale * point.getBinNumber() * binSize - xScaffold.getOriginalStart()) / HiCGlobals.hicMapScale / binSize); } else { newStart = (long) ((xScaffold.getCurrentEnd() - HiCGlobals.hicMapScale * point.getGenomicEnd() + xScaffold.getOriginalStart()) / HiCGlobals.hicMapScale); newBin = (long) ((xScaffold.getCurrentEnd() - HiCGlobals.hicMapScale * point.getBinNumber() * binSize + xScaffold.getOriginalStart()) / HiCGlobals.hicMapScale / binSize - 1); } newEnd = newStart + point.getGenomicEnd() - point.getGenomicStart(); if (point instanceof HiCCoverageDataSource.CoverageDataPoint) { HiCCoverageDataSource.CoverageDataPoint covPoint = (HiCCoverageDataSource.CoverageDataPoint) point; modifiedDataPoints.add(new HiCCoverageDataSource.CoverageDataPoint((int) (newStart / binSize), newStart, newEnd, covPoint.value)); } else if (point instanceof HiCDataAdapter.DataAccumulator) { HiCDataAdapter.DataAccumulator accumPoint = (HiCDataAdapter.DataAccumulator) point; HiCDataAdapter.DataAccumulator newAccumPoint = new HiCDataAdapter.DataAccumulator(newBin, accumPoint.width, newStart, newEnd); newAccumPoint.nPts = accumPoint.nPts; newAccumPoint.weightedSum = accumPoint.weightedSum; newAccumPoint.max = accumPoint.max; modifiedDataPoints.add(newAccumPoint); // if(accumPoint.getBinNumber()!=(double)newBin) // System.out.println(accumPoint.getBinNumber()+" "+(double)newBin); // why do these not match? } } } HiCDataPoint[] points = new HiCDataPoint[modifiedDataPoints.size()]; for (int i = 0; i < points.length; i++) { points[i] = modifiedDataPoints.get(i); } return points; } public static List liftIGVFeatures( HiC hic, Chromosome chromosome, int binX1, int binX2, HiCGridAxis gridAxis, ArrayList featureList, boolean isBed) { List newFeatureList = new ArrayList<>(); // Initialize HiCZoom zoom = hic.getZoom(); final double scaleFactor = hic.getScaleFactor(); AssemblyScaffoldHandler aFragHandler = AssemblyHeatmapHandler.getSuperAdapter().getAssemblyStateTracker().getAssemblyHandler(); final int binSize = zoom.getBinSize(); long actualBinSize = binSize; if (chromosome.getIndex() == 0) { actualBinSize *= 1000; } List xAxisAggregateScaffolds = aFragHandler.getIntersectingAggregateFeatures( (long) (actualBinSize * binX1 * HiCGlobals.hicMapScale), (long) (actualBinSize * binX2 * HiCGlobals.hicMapScale)); // Determine positions of all aggregate scaffolds int x1pos, x2pos; HashMap> scaffoldOriginalPositions = new HashMap<>(); for (Scaffold xScaffold : xAxisAggregateScaffolds) { ArrayList originalPositions = new ArrayList<>(2); x1pos = (int) (xScaffold.getOriginalStart() / HiCGlobals.hicMapScale); x2pos = (int) (xScaffold.getOriginalEnd() / HiCGlobals.hicMapScale); // Have to case long because of thumbnail, maybe fix thumbnail instead // Following results in "fragmentation" when feature is outside of window which may not be ideal if fragments are labeled in some matter // could fix by extending window boundaries to include intersecting feature boundaries if (xScaffold.getCurrentStart() < actualBinSize * binX1 * HiCGlobals.hicMapScale) { if (!xScaffold.getInvertedVsInitial()) { x1pos = (int) ((xScaffold.getOriginalStart() + actualBinSize * binX1 * HiCGlobals.hicMapScale - xScaffold.getCurrentStart()) / HiCGlobals.hicMapScale); } else { x2pos = (int) ((xScaffold.getOriginalStart() - actualBinSize * binX1 * HiCGlobals.hicMapScale + xScaffold.getCurrentEnd()) / HiCGlobals.hicMapScale); } } if (xScaffold.getCurrentEnd() > actualBinSize * binX2 * HiCGlobals.hicMapScale) { if (!xScaffold.getInvertedVsInitial()) { x2pos = (int) ((xScaffold.getOriginalStart() + actualBinSize * binX2 * HiCGlobals.hicMapScale - xScaffold.getCurrentStart()) / HiCGlobals.hicMapScale); } else { x1pos = (int) ((xScaffold.getOriginalStart() - actualBinSize * binX2 * HiCGlobals.hicMapScale + xScaffold.getCurrentEnd()) / HiCGlobals.hicMapScale); } } originalPositions.add(x1pos); originalPositions.add(x2pos); scaffoldOriginalPositions.put(xScaffold, originalPositions); } // Iterate over features and over the aggregate scaffolds the feature spans for (IGVFeature feature : featureList) { double bin1 = HiCFeatureTrack.getFractionalBin(feature.getStart(), scaleFactor, gridAxis); double bin2 = HiCFeatureTrack.getFractionalBin(feature.getEnd(), scaleFactor, gridAxis); IGVFeatureCopy featureFraction; for (Scaffold xScaffold : xAxisAggregateScaffolds) { x1pos = scaffoldOriginalPositions.get(xScaffold).get(0); x2pos = scaffoldOriginalPositions.get(xScaffold).get(1); if (bin2 < (int) (x1pos / actualBinSize) || bin1 > (int) (x2pos / actualBinSize)) { continue; } featureFraction = new IGVFeatureCopy(feature); if (feature.getStart()x2pos){featureFraction.setEnd(x2pos);} int newStart, newEnd; if (!xScaffold.getInvertedVsInitial()) { newStart = (int) ((xScaffold.getCurrentStart() + (HiCGlobals.hicMapScale * featureFraction.getStart()) - xScaffold.getOriginalStart()) / HiCGlobals.hicMapScale); } else { newStart = (int) ((xScaffold.getCurrentEnd() - (HiCGlobals.hicMapScale * featureFraction.getEnd()) + xScaffold.getOriginalStart()) / HiCGlobals.hicMapScale); } newEnd = newStart + featureFraction.getEnd() - featureFraction.getStart(); featureFraction.setStart(newStart); featureFraction.setEnd(newEnd); featureFraction.updateStrand(feature.getStrand(), xScaffold.getInvertedVsInitial(), isBed); // Update exons if (feature.getExons() != null) { List newExons = new ArrayList<>(); for (Exon exon : feature.getExons()) { double exonBin1 = HiCFeatureTrack.getFractionalBin(exon.getStart(), scaleFactor, gridAxis); double exonBin2 = HiCFeatureTrack.getFractionalBin(exon.getEnd(), scaleFactor, gridAxis); if (exonBin2 < (int) (x1pos / actualBinSize) || exonBin1 > (x2pos / actualBinSize)) { continue; } Exon newExon = new Exon(featureFraction.getChr(), exon.getStart(), exon.getEnd(), featureFraction.getStrand()); if (exon.getStart()x2pos){newExon.setEnd(x2pos);} int newExonStart, newExonEnd; if (!xScaffold.getInvertedVsInitial()) { newExonStart = (int) ((xScaffold.getCurrentStart() + (HiCGlobals.hicMapScale * newExon.getStart()) - xScaffold.getOriginalStart()) / HiCGlobals.hicMapScale); } else { newExonStart = (int) ((xScaffold.getCurrentEnd() - (HiCGlobals.hicMapScale * newExon.getEnd()) + xScaffold.getOriginalStart()) / HiCGlobals.hicMapScale); } newExonEnd = newExonStart + newExon.getEnd() - newExon.getStart(); newExon.setStart(newExonStart); newExon.setEnd(newExonEnd); newExons.add(newExon); } featureFraction.updateExons(newExons); } newFeatureList.add(featureFraction); } } return newFeatureList; } } ================================================ FILE: src/juicebox/assembly/PsfFileExporter.java ================================================ /* * The MIT License (MIT) * * Copyright (c) 2011-2020 Broad Institute, Aiden Lab * * Permission is hereby granted, free of charge, to any person obtaining a copy * of this software and associated documentation files (the "Software"), to deal * in the Software without restriction, including without limitation the rights * to use, copy, modify, merge, publish, distribute, sublicense, and/or sell * copies of the Software, and to permit persons to whom the Software is * furnished to do so, subject to the following conditions: * * The above copyright notice and this permission notice shall be included in * all copies or substantial portions of the Software. * * THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR * IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, * FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE * AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER * LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, * OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN * THE SOFTWARE. */ package juicebox.assembly; import java.io.IOException; import java.io.PrintWriter; import java.util.Iterator; import java.util.List; /** * Created by dudcha on 10/27/20. */ public class PsfFileExporter { private final String outputFilePath; private final List listOfScaffolds; private final List> listOfSuperscaffolds; public PsfFileExporter(AssemblyScaffoldHandler assemblyScaffoldHandler, String outputFilePath) { this.outputFilePath = outputFilePath; this.listOfScaffolds = assemblyScaffoldHandler.getListOfScaffolds(); this.listOfSuperscaffolds = assemblyScaffoldHandler.getListOfSuperscaffolds(); } public void exportPsfFile() { try { exportPsf(); } catch (IOException exception) { System.out.println("Exporting failed..."); } } private void exportPsf() throws IOException { PrintWriter assemblyWriter = new PrintWriter(buildPsfOutputPath(), "UTF-8"); String name = ""; for (Scaffold scaffold : listOfScaffolds) { int id = scaffold.getIndexId(); if (id % 2 == 0) { String[] splitName = scaffold.getName().split(":"); assemblyWriter.print(">" + name + " " + splitName[2] + " " + (id / 2) + "\n"); name = ""; } else { name = scaffold.getName().replace(":", " "); } } for (int i = 0; i < listOfSuperscaffolds.size(); i++) { if (i % 2 != 0) { continue; } List row = listOfSuperscaffolds.get(i); assemblyWriter.print(superscaffoldToString(row) + "\n"); } assemblyWriter.close(); } private String superscaffoldToString(List scaffoldRow) { StringBuilder stringBuilder = new StringBuilder(); Iterator iterator = scaffoldRow.iterator(); while (iterator.hasNext()) { int i = iterator.next(); if (i % 2 == 0) { i = -i / 2; } else { i = (i + 1) / 2; } stringBuilder.append(i); if (iterator.hasNext()) { stringBuilder.append(" "); } } return stringBuilder.toString(); } private String buildPsfOutputPath() { return this.outputFilePath + ".psf"; } } ================================================ FILE: src/juicebox/assembly/PsfFileImporter.java ================================================ /* * The MIT License (MIT) * * Copyright (c) 2011-2020 Broad Institute, Aiden Lab * * Permission is hereby granted, free of charge, to any person obtaining a copy * of this software and associated documentation files (the "Software"), to deal * in the Software without restriction, including without limitation the rights * to use, copy, modify, merge, publish, distribute, sublicense, and/or sell * copies of the Software, and to permit persons to whom the Software is * furnished to do so, subject to the following conditions: * * The above copyright notice and this permission notice shall be included in * all copies or substantial portions of the Software. * * THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR * IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, * FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE * AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER * LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, * OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN * THE SOFTWARE. */ package juicebox.assembly; import juicebox.HiCGlobals; import juicebox.gui.SuperAdapter; import java.io.File; import java.io.IOException; import java.util.ArrayList; import java.util.List; import java.util.Scanner; /** * Created by dudcha on 10/19/20. */ public class PsfFileImporter extends AssemblyFileImporter { private SuperAdapter superAdapter = null; // single file format private String psfFilePath; private boolean modified = false; private List listOfScaffolds; private List> listOfSuperscaffolds; private AssemblyScaffoldHandler assemblyScaffoldHandler; private List rawFileData; public PsfFileImporter(String psfFilePath, boolean modified) { this.psfFilePath = psfFilePath; this.modified = modified; } @Override public void importAssembly() { importPsf(); } public void importPsf() { listOfScaffolds = new ArrayList<>(); listOfSuperscaffolds = new ArrayList<>(); try { if (psfFilePath != null) { rawFileData = readFile(psfFilePath); parsePsfFile(); } if (!modified) setInitialState(); else setModifiedInitialState(); } catch (IOException exception) { System.err.println("Error reading files!"); } updateAssemblyScale(); assemblyScaffoldHandler = new AssemblyScaffoldHandler(listOfScaffolds, listOfSuperscaffolds); } private int updateAssemblyScale() { long totalLength = 0; for (Scaffold fragmentProperty : listOfScaffolds) { totalLength += fragmentProperty.getLength(); } HiCGlobals.hicMapScale = (int) (1 + totalLength / 2100000000); return (int) (totalLength / HiCGlobals.hicMapScale); // in case decide to use for validation so that not to count again } private void parsePsfFile() throws IOException { try { for (String row : rawFileData) { if (row.startsWith(">")) { String[] splitRow = row.split(" "); // Chr Pos Ref_var Alt_var ID int id = Integer.parseInt(splitRow[4]); Scaffold scaffold = new Scaffold(splitRow[0].substring(1) + ":" + splitRow[1] + ":" + splitRow[2], 2 * id - 1, 1000); listOfScaffolds.add(scaffold); scaffold = new Scaffold(splitRow[0].substring(1) + ":" + splitRow[1] + ":" + splitRow[3], 2 * id, 1000); listOfScaffolds.add(scaffold); } else { List superscaffold = new ArrayList<>(); List altSuperscaffold = new ArrayList<>(); for (String index : row.split(" ")) { int id = Integer.parseInt(index); if (id > 0) { superscaffold.add(2 * id - 1); altSuperscaffold.add(2 * id); } else { altSuperscaffold.add(-2 * id - 1); superscaffold.add(-2 * id); } } listOfSuperscaffolds.add(superscaffold); listOfSuperscaffolds.add(altSuperscaffold); } } } catch (NumberFormatException e) { e.printStackTrace(); System.err.println("Errors in format"); } } private void setInitialState() { long shift = 0; for (List row : listOfSuperscaffolds) { for (Integer entry : row) { int fragmentIterator = Math.abs(entry) - 1; listOfScaffolds.get(fragmentIterator).setOriginallyInverted(false); if (entry < 0) { listOfScaffolds.get(fragmentIterator).setOriginallyInverted(true); } else if (entry == 0) { System.err.println("Something is wrong with the input."); // should not happen } listOfScaffolds.get(fragmentIterator).setOriginalStart(shift); shift += listOfScaffolds.get(fragmentIterator).getLength(); } } } private void setModifiedInitialState() { List originalScaffolds = AssemblyHeatmapHandler.getSuperAdapter().getAssemblyStateTracker().getInitialAssemblyScaffoldHandler().getListOfScaffolds(); for (int i = 0; i < listOfScaffolds.size(); i++) { listOfScaffolds.get(i).setOriginallyInverted(false); listOfScaffolds.get(i).setOriginalStart(originalScaffolds.get(i).getOriginalStart()); } } List readFile(String filePath) throws IOException { List fileData = new ArrayList<>(); File file = new File(filePath); Scanner scanner = new Scanner(file); while (scanner.hasNext()) { fileData.add(scanner.nextLine()); } return fileData; } public AssemblyScaffoldHandler getAssemblyScaffoldHandler() { return assemblyScaffoldHandler; } } ================================================ FILE: src/juicebox/assembly/Scaffold.java ================================================ /* * The MIT License (MIT) * * Copyright (c) 2011-2020 Broad Institute, Aiden Lab, Rice University, Baylor College of Medicine * * Permission is hereby granted, free of charge, to any person obtaining a copy * of this software and associated documentation files (the "Software"), to deal * in the Software without restriction, including without limitation the rights * to use, copy, modify, merge, publish, distribute, sublicense, and/or sell * copies of the Software, and to permit persons to whom the Software is * furnished to do so, subject to the following conditions: * * The above copyright notice and this permission notice shall be included in * all copies or substantial portions of the Software. * * THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR * IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, * FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE * AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER * LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, * OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN * THE SOFTWARE. */ package juicebox.assembly; import juicebox.HiCGlobals; import juicebox.data.feature.Feature; import juicebox.track.feature.Feature2D; import java.awt.*; import java.util.Comparator; import java.util.HashMap; import java.util.Map; import java.util.Objects; /** * Created by dudcha on 10/10/17. * todo rename locus or something generic, with motifanchor extending from this */ public class Scaffold extends Feature implements Comparable { public static final Comparator originalStateComparator = new Comparator() { public int compare(Scaffold o1, Scaffold o2) { // System.out.println("I am in originalstatscomparator"); if (o1.getOriginalStart() == o2.getOriginalStart()) { return -Long.compare(o1.length, o2.length); } return Long.compare(o1.getOriginalStart(), o2.getOriginalStart()); } }; public final String chrName = "assembly"; //constants private final String unsignedScaffoldIdAttributeKey = "Scaffold #"; private final String signedScaffoldIdAttributeKey = "Signed scaffold #"; private final String scaffoldNameAttributeKey = "Scaffold name"; // formality private final Integer chrIndex = 1; private final Color defaultColor = new Color(0, 255, 0); //invariant properties public String name; private int indexId; //initial state private long originalStart; private boolean isOriginallyInverted; //current state private boolean isInvertedVsInitial; private long currentStart; private long length; // Main Constructor public Scaffold(String name, int indexId, long length) { this.name = name; this.indexId = indexId; this.length = length; } // Copy Constructor public Scaffold(Scaffold scaffold) { // invariant properties this.name = scaffold.name; this.indexId = scaffold.indexId; this.length = scaffold.length; // initial state this.originalStart = scaffold.originalStart; this.isOriginallyInverted = scaffold.isOriginallyInverted; // current state this.currentStart = scaffold.currentStart; this.isInvertedVsInitial = scaffold.isInvertedVsInitial; } // Invariant properties getters and setters public String getName() { return name; } public void setName(String name) { this.name = name; } public int getIndexId() { return indexId; } public void setIndexId(int indexId) { this.indexId = indexId; } public long getLength() { return length; } public void setLength(long length) { this.length = length; } // Original state getters and setters public long getOriginalStart() { return originalStart; } public void setOriginalStart(long originalStart) { this.originalStart = originalStart; } public boolean getOriginallyInverted() { return isOriginallyInverted; } public void setOriginallyInverted(boolean originallyInverted) { this.isOriginallyInverted = originallyInverted; } // Current state getters and setters public long getCurrentStart() { return currentStart; } public void setCurrentStart(long currentStart) { this.currentStart = currentStart; } // todo refactor ; always inverted; rename var; what exactly does invertedVsInitial mean? public boolean getInvertedVsInitial() { return isInvertedVsInitial; } public void setInvertedVsInitial(boolean invertedVsInitial) { this.isInvertedVsInitial = invertedVsInitial; } // convenience methods public int getSignIndexId() { if ((!getOriginallyInverted()) && (!isInvertedVsInitial) || getOriginallyInverted() && isInvertedVsInitial) { return indexId; } else { return -indexId; } } public Feature2D getCurrentFeature2D() { Map attributes = new HashMap<>(); attributes.put(scaffoldNameAttributeKey, this.getName()); attributes.put(signedScaffoldIdAttributeKey, String.valueOf(this.getSignIndexId())); attributes.put(unsignedScaffoldIdAttributeKey, String.valueOf(this.getIndexId())); return new Feature2D(Feature2D.FeatureType.SCAFFOLD, chrName, scale(this.getCurrentStart()), scale(this.getCurrentEnd()), chrName, scale(this.getCurrentStart()), scale(this.getCurrentEnd()), defaultColor, attributes); } private int scale(long longCoordinate) { return (int) (longCoordinate / HiCGlobals.hicMapScale); } public boolean isDebris() { return name.contains(":::debris"); } public String getOriginalScaffoldName() { if (name.contains(":::fragment_")) { return name.split(":::fragment_")[0]; } else { return name; } } public int getFragmentNumber() { if (name.contains(":::fragment_")) { String temp = name.split(":::fragment_")[1]; if (temp.contains(":::debris")) { return Integer.parseInt(temp.split(":::debris")[0]); } else { return Integer.parseInt(temp); //can just parse int from string } } else { return 0; } } public long getOriginalEnd() { return originalStart + length; } public long getCurrentEnd() { return currentStart + length; } public void toggleInversion() { isInvertedVsInitial = !isInvertedVsInitial; } public Scaffold mergeWith(Scaffold scaffold) { if (this.getOriginalEnd() == scaffold.getOriginalStart() && scaffold.isInvertedVsInitial == this.isInvertedVsInitial && !this.isInvertedVsInitial) { this.length = this.length + scaffold.length; return this; } if (scaffold.getOriginalEnd() == this.originalStart && scaffold.isInvertedVsInitial == this.isInvertedVsInitial && this.isInvertedVsInitial) { this.setOriginalStart(scaffold.getOriginalStart()); this.length = this.length + scaffold.length; return this; } return null; } @Override public String getKey() { return "" + chrIndex; } @Override public Feature deepClone() { return new Scaffold(name, indexId, length); } @Override public boolean equals(Object obj) { if (obj == null) { return false; } if (getClass() != obj.getClass()) { return false; } if (this == obj) { return true; } Scaffold o = (Scaffold) obj; if (chrIndex.equals(o.chrIndex)) { if (length == o.length) { return currentStart == o.currentStart; } } return false; } @Override public String toString() { return name + " " + indexId + " " + length; } @Override public int hashCode() { return Objects.hash(currentStart, length, HiCGlobals.hicMapScale); } @Override public int compareTo(Scaffold o) { // System.out.println("I am in standard comparator"); if (currentStart == o.currentStart) { // System.out.println(-(new Long(length)).compareTo(o.length)); return -Long.compare(length, o.length); } // System.out.println((new Long(currentStart)).compareTo(o.currentStart)); return Long.compare(currentStart, o.currentStart); } private boolean currentContains(long x) { return x >= currentStart && x <= getCurrentEnd(); } private boolean originalContains(long x) { return x >= originalStart && x <= getOriginalEnd(); } } ================================================ FILE: src/juicebox/data/AbstractDatasetReader.java ================================================ /* * The MIT License (MIT) * * Copyright (c) 2011-2022 Broad Institute, Aiden Lab, Rice University, Baylor College of Medicine * * Permission is hereby granted, free of charge, to any person obtaining a copy * of this software and associated documentation files (the "Software"), to deal * in the Software without restriction, including without limitation the rights * to use, copy, modify, merge, publish, distribute, sublicense, and/or sell * copies of the Software, and to permit persons to whom the Software is * furnished to do so, subject to the following conditions: * * The above copyright notice and this permission notice shall be included in * all copies or substantial portions of the Software. * * THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR * IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, * FITNESS FOR A PARTICULAR PURPOSE AND NON-INFRINGEMENT. IN NO EVENT SHALL THE * AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER * LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, * OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN * THE SOFTWARE. */ package juicebox.data; import juicebox.HiC; import juicebox.HiCGlobals; import juicebox.windowui.HiCZoom; import juicebox.windowui.NormalizationType; import org.broad.igv.util.FileUtils; import org.broad.igv.util.ParsingUtils; import org.broad.igv.util.collections.DoubleArrayList; import java.io.BufferedReader; import java.io.IOException; import java.io.InputStreamReader; /** * Abstract base class for methods that can be shared by V1 and V2 readers. * * @author jrobinso * Date: 12/22/12 * Time: 10:15 AM */ public abstract class AbstractDatasetReader implements DatasetReader { final String path; AbstractDatasetReader(String path) { this.path = path; } public String getPath() { return path; } @Override public double[] readEigenvector(String chrName, HiCZoom zoom, int number, String type) { double[] eigenvector = null; // If there's an eigenvector file load it String rootPath = FileUtils.getParent(path); String folder = rootPath + "/" + chrName; String eigenFile = "eigen" + "_" + chrName + "_" + chrName + "_" + zoom.getBinSize() + "_" + type + ".wig"; String fullPath = folder + "/" + eigenFile; if (FileUtils.resourceExists(fullPath)) { System.out.println("Reading " + fullPath); // Lots of assumptions made here about structure of wig file BufferedReader br = null; try { br = ParsingUtils.openBufferedReader(fullPath); br = new BufferedReader(new InputStreamReader(ParsingUtils.openInputStream(fullPath)), HiCGlobals.bufferSize); String nextLine = br.readLine(); // The track line, ignored DoubleArrayList arrayList = new DoubleArrayList(10000); // TODO -- can size this exactly while ((nextLine = br.readLine()) != null) { if (nextLine.startsWith("track") || nextLine.startsWith("fixedStep") || nextLine.startsWith("#")) { continue; } try { arrayList.add(Double.parseDouble(nextLine)); } catch (NumberFormatException e) { arrayList.add(Double.NaN); } } return arrayList.toArray(); } catch (IOException e) { System.err.println("Error reading eigenvector " + e.getLocalizedMessage()); } finally { if (br != null) try { br.close(); } catch (IOException e) { System.err.println("Error reading eigenvector " + e.getLocalizedMessage()); } } } else { System.out.println("Can't find eigenvector" + fullPath); } return null; } @Override public NormalizationVector readNormalizationVector(NormalizationType type, int chrIdx, HiC.Unit unit, int binSize) throws IOException { return null; // Override as necessary } } ================================================ FILE: src/juicebox/data/BinReader.java ================================================ /* * The MIT License (MIT) * * Copyright (c) 2011-2021 Broad Institute, Aiden Lab, Rice University, Baylor College of Medicine * * Permission is hereby granted, free of charge, to any person obtaining a copy * of this software and associated documentation files (the "Software"), to deal * in the Software without restriction, including without limitation the rights * to use, copy, modify, merge, publish, distribute, sublicense, and/or sell * copies of the Software, and to permit persons to whom the Software is * furnished to do so, subject to the following conditions: * * The above copyright notice and this permission notice shall be included in * all copies or substantial portions of the Software. * * THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR * IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, * FITNESS FOR A PARTICULAR PURPOSE AND NON-INFRINGEMENT. IN NO EVENT SHALL THE * AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER * LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, * OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN * THE SOFTWARE. */ package juicebox.data; import htsjdk.tribble.util.LittleEndianInputStream; import java.io.IOException; import java.util.List; public class BinReader { public static void handleBinType(LittleEndianInputStream dis, byte type, int binXOffset, int binYOffset, List records, boolean useShortBinX, boolean useShortBinY, boolean useShort) throws IOException { if (type == 1) { if (useShortBinX && useShortBinY) { handleBothShorts(dis, binXOffset, binYOffset, useShort, records); } else if (useShortBinX) { handleShortX(dis, binXOffset, binYOffset, useShort, records); } else if (useShortBinY) { handleShortY(dis, binXOffset, binYOffset, useShort, records); } else { handleBothInts(dis, binXOffset, binYOffset, useShort, records); } } else if (type == 2) { int nPts = dis.readInt(); int w = dis.readShort(); for (int i = 0; i < nPts; i++) { //int idx = (p.y - binOffset2) * w + (p.x - binOffset1); int row = i / w; int col = i - row * w; int bin1 = binXOffset + col; int bin2 = binYOffset + row; if (useShort) { short counts = dis.readShort(); if (counts != Short.MIN_VALUE) { records.add(new ContactRecord(bin1, bin2, counts)); } } else { float counts = dis.readFloat(); if (!Float.isNaN(counts)) { records.add(new ContactRecord(bin1, bin2, counts)); } } } } else { throw new RuntimeException("Unknown block type: " + type); } } private static void handleBothInts(LittleEndianInputStream dis, int binXOffset, int binYOffset, boolean useShort, List records) throws IOException { int rowCount = dis.readInt(); for (int i = 0; i < rowCount; i++) { int binY = binYOffset + dis.readInt(); int colCount = dis.readInt(); for (int j = 0; j < colCount; j++) { int binX = binXOffset + dis.readInt(); float counts = useShort ? dis.readShort() : dis.readFloat(); records.add(new ContactRecord(binX, binY, counts)); } } } private static void handleShortY(LittleEndianInputStream dis, int binXOffset, int binYOffset, boolean useShort, List records) throws IOException { int rowCount = dis.readShort(); for (int i = 0; i < rowCount; i++) { int binY = binYOffset + dis.readShort(); int colCount = dis.readInt(); for (int j = 0; j < colCount; j++) { int binX = binXOffset + dis.readInt(); float counts = useShort ? dis.readShort() : dis.readFloat(); records.add(new ContactRecord(binX, binY, counts)); } } } private static void handleShortX(LittleEndianInputStream dis, int binXOffset, int binYOffset, boolean useShort, List records) throws IOException { int rowCount = dis.readInt(); for (int i = 0; i < rowCount; i++) { int binY = binYOffset + dis.readInt(); int colCount = dis.readShort(); for (int j = 0; j < colCount; j++) { int binX = binXOffset + dis.readShort(); float counts = useShort ? dis.readShort() : dis.readFloat(); records.add(new ContactRecord(binX, binY, counts)); } } } private static void handleBothShorts(LittleEndianInputStream dis, int binXOffset, int binYOffset, boolean useShort, List records) throws IOException { int rowCount = dis.readShort(); for (int i = 0; i < rowCount; i++) { int binY = binYOffset + dis.readShort(); int colCount = dis.readShort(); for (int j = 0; j < colCount; j++) { int binX = binXOffset + dis.readShort(); float counts = useShort ? dis.readShort() : dis.readFloat(); records.add(new ContactRecord(binX, binY, counts)); } } } } ================================================ FILE: src/juicebox/data/Block.java ================================================ /* * The MIT License (MIT) * * Copyright (c) 2011-2020 Broad Institute, Aiden Lab, Rice University, Baylor College of Medicine * * Permission is hereby granted, free of charge, to any person obtaining a copy * of this software and associated documentation files (the "Software"), to deal * in the Software without restriction, including without limitation the rights * to use, copy, modify, merge, publish, distribute, sublicense, and/or sell * copies of the Software, and to permit persons to whom the Software is * furnished to do so, subject to the following conditions: * * The above copyright notice and this permission notice shall be included in * all copies or substantial portions of the Software. * * THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR * IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, * FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE * AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER * LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, * OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN * THE SOFTWARE. */ package juicebox.data; //import java.awt.*; //import java.util.List; import java.util.ArrayList; import java.util.List; import java.util.Random; /** * @author jrobinso * @since Aug 10, 2010 */ public class Block { private final int number; private final String uniqueRegionID; private final List records; public Block(int number, String regionID) { this.number = number; records = new ArrayList<>(); uniqueRegionID = regionID + "_" + number; } public Block(int number, List records, String regionID) { this.number = number; this.records = records; this.uniqueRegionID = regionID + "_" + number; } public int getNumber() { return number; } public String getUniqueRegionID() { return uniqueRegionID; } public List getContactRecords() { return records; } public List getContactRecords(double subsampleFraction, Random randomSubsampleGenerator) { List newRecords = new ArrayList<>(); for (ContactRecord i : records) { int newBinX = i.getBinX(); int newBinY = i.getBinY(); int newCounts = 0; for (int j = 0; j < (int) i.getCounts(); j++) { if ( subsampleFraction <= 1 && subsampleFraction > 0 && randomSubsampleGenerator.nextDouble() <= subsampleFraction) { newCounts += 1; } } newRecords.add(new ContactRecord(newBinX, newBinY, (float) newCounts)); } return newRecords; } public void clear() { records.clear(); } } ================================================ FILE: src/juicebox/data/BlockIndex.java ================================================ /* * The MIT License (MIT) * * Copyright (c) 2011-2020 Broad Institute, Aiden Lab, Rice University, Baylor College of Medicine * * Permission is hereby granted, free of charge, to any person obtaining a copy * of this software and associated documentation files (the "Software"), to deal * in the Software without restriction, including without limitation the rights * to use, copy, modify, merge, publish, distribute, sublicense, and/or sell * copies of the Software, and to permit persons to whom the Software is * furnished to do so, subject to the following conditions: * * The above copyright notice and this permission notice shall be included in * all copies or substantial portions of the Software. * * THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR * IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, * FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE * AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER * LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, * OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN * THE SOFTWARE. */ package juicebox.data; import htsjdk.tribble.util.LittleEndianInputStream; import juicebox.tools.utils.original.IndexEntry; import java.io.IOException; import java.util.ArrayList; import java.util.HashMap; import java.util.List; import java.util.Map; public class BlockIndex { protected final Map blockIndex; protected final int numBlocks; public BlockIndex(int nBlocks) { numBlocks = nBlocks; blockIndex = new HashMap<>(nBlocks); } public void populateBlocks(LittleEndianInputStream dis) throws IOException { for (int b = 0; b < numBlocks; b++) { int blockNumber = dis.readInt(); long filePosition = dis.readLong(); int blockSizeInBytes = dis.readInt(); blockIndex.put(blockNumber, new IndexEntry(filePosition, blockSizeInBytes)); } } public List getBlockNumbers() { return new ArrayList<>(blockIndex.keySet()); } public Integer getBlockSize(int num) { if (blockIndex.containsKey(num)) { return blockIndex.get(num).size; } else { return null; } } public IndexEntry getBlock(int blockNumber) { return blockIndex.get(blockNumber); } } ================================================ FILE: src/juicebox/data/ChromosomeHandler.java ================================================ /* * The MIT License (MIT) * * Copyright (c) 2011-2021 Broad Institute, Aiden Lab, Rice University, Baylor College of Medicine * * Permission is hereby granted, free of charge, to any person obtaining a copy * of this software and associated documentation files (the "Software"), to deal * in the Software without restriction, including without limitation the rights * to use, copy, modify, merge, publish, distribute, sublicense, and/or sell * copies of the Software, and to permit persons to whom the Software is * furnished to do so, subject to the following conditions: * * The above copyright notice and this permission notice shall be included in * all copies or substantial portions of the Software. * * THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR * IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, * FITNESS FOR A PARTICULAR PURPOSE AND NON-INFRINGEMENT. IN NO EVENT SHALL THE * AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER * LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, * OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN * THE SOFTWARE. */ package juicebox.data; import juicebox.Context; import juicebox.data.anchor.*; import juicebox.data.basics.Chromosome; import juicebox.data.feature.FeatureFunction; import juicebox.data.feature.GenomeWideList; import juicebox.track.feature.Feature2DList; import org.broad.igv.util.Pair; import java.io.File; import java.util.*; /** * Created by muhammadsaadshamim on 8/3/16. */ public class ChromosomeHandler { private static final String GENOMEWIDE_CHR = "GENOMEWIDE"; public final static int CUSTOM_CHROMOSOME_BUFFER = 10; // todo make to smallest value of resolution private static final String CHR_ALL = "All"; private final Map chromosomeMap = new HashMap<>(); private final Map> customChromosomeRegions = new HashMap<>(); private final List cleanedChromosomes; private final String genomeID; private final long[] chromosomeBoundaries; private final Chromosome[] chromosomesArray; private final Chromosome[] chromosomeArrayWithoutAllByAll; private final Chromosome[] chromosomeArrayAutosomesOnly; public ChromosomeHandler(List chromosomes, String genomeID, boolean inferID) { this(chromosomes, genomeID, inferID, true); } public ChromosomeHandler(List chromosomes, String genomeID, boolean inferID, boolean createAllChr) { if (inferID) { String inferGenomeId = inferGenomeId(); // if cannot find matching genomeID, set based on file if (inferGenomeId != null) { this.genomeID = inferGenomeId; } else { this.genomeID = genomeID; } } else { this.genomeID = genomeID; } // set the global chromosome list if (createAllChr) { long genomeLength = getTotalLengthOfAllChromosomes(chromosomes); chromosomes.set(0, new Chromosome(0, cleanUpName(CHR_ALL), (int) (genomeLength / 1000))); } cleanedChromosomes = initializeCleanedChromosomesList(chromosomes); Pair> outputs = initializeInternalVariables(); chromosomeBoundaries = outputs.getFirst(); chromosomesArray = outputs.getSecond().get(0); chromosomeArrayWithoutAllByAll = outputs.getSecond().get(1); chromosomeArrayAutosomesOnly = outputs.getSecond().get(2); } public static boolean isWholeGenomeView(Context xContext, Context yContext) { return isAllByAll(xContext.getChromosome()) && isAllByAll(yContext.getChromosome()); } public String cleanUpName(String name) { if (genomeID.equalsIgnoreCase("hg19")) { return name.trim().toLowerCase().replaceAll("chr", "").toUpperCase(); } return name; } public static boolean isAllByAll(String name) { return name.toLowerCase().contains("all"); } public static void sort(List indices) { indices.sort(new ChromosomeComparator()); } /** * Set intersection * http://stackoverflow.com/questions/7574311/efficiently-compute-intersection-of-two-sets-in-java * * @param collection1 * @param collection2 * @return intersection of set1 and set2 */ private static Set getSetIntersection(Collection collection1, Collection collection2) { Set set1 = new HashSet<>(collection1); Set set2 = new HashSet<>(collection2); boolean set1IsLarger = set1.size() > set2.size(); Set cloneSet = new HashSet<>(set1IsLarger ? set2 : set1); // TODO: Chromosome defines hashcode based on index + length, but this is incorrect since index can be arbitrary cloneSet.retainAll(set1IsLarger ? set1 : set2); return cloneSet; } public static boolean isAllByAll(Chromosome chromosome) { return isAllByAll(chromosome.getName()); } private GenomeWideList generateChromDotSizesBedFile() { GenomeWideList chromDotSizes = new GenomeWideList<>(this); for (Chromosome c : getChromosomeArray()) { if (isAllByAll(c) || isGenomeWide(c)) continue; MotifAnchor chromAnchor = new MotifAnchor(c.getName(), 0, (int) c.getLength(), c.getName()); // not implemented or called List anchors = new ArrayList<>(); anchors.add(chromAnchor); chromDotSizes.setFeatures("" + c.getIndex(), anchors); } return chromDotSizes; } private boolean isGenomeWide(Chromosome chromosome) { return isGenomeWide(chromosome.getName()); } private boolean isGenomeWide(String name) { return cleanUpName(name).equalsIgnoreCase(GENOMEWIDE_CHR); } public Chromosome addGenomeWideChromosome() { GenomeWideList chromDotSizes = generateChromDotSizesBedFile(); return addCustomChromosome(chromDotSizes, cleanUpName(GENOMEWIDE_CHR)); } public Chromosome generateAssemblyChromosome() { // long genomeLength = 0; // for (Chromosome c : chromosomes) { // if (c != null) genomeLength += c.getLength(); // } // return genomeLength; //TODO: handle scaling int size = (int) getTotalLengthOfAllChromosomes(Arrays.asList(this.chromosomeArrayWithoutAllByAll)); int newIndex = cleanedChromosomes.size(); Chromosome newChr = new Chromosome(newIndex, "pseudoassembly", size); cleanedChromosomes.add(newChr); chromosomeMap.put(newChr.getName(), newChr); return newChr; } public Chromosome generateCustomChromosomeFromBED(File file, int minSize) { GenomeWideList regionsInCustomChromosome = GenericLocusParser.loadFromBEDFile(this, file.getAbsolutePath()); MotifAnchorTools.mergeAndExpandSmallAnchors(regionsInCustomChromosome, minSize); String cleanedUpName = cleanUpName(file.getName()); return addCustomChromosome(regionsInCustomChromosome, cleanedUpName); } public Chromosome addCustomChromosome(Feature2DList featureList, String chrName) { GenomeWideList featureAnchors = MotifAnchorTools.extractAllAnchorsFromAllFeatures(featureList, this); String cleanedUpName = cleanUpName(chrName); return addCustomChromosome(featureAnchors, cleanedUpName); } private int getTotalLengthOfAllRegionsInBedFile(GenomeWideList regionsInCustomChromosome) { final int[] customGenomeLength = new int[]{0}; regionsInCustomChromosome.processLists(new FeatureFunction() { @Override public void process(String chr, List featureList) { for (GenericLocus c : featureList) { if (c != null) customGenomeLength[0] += c.getWidth() + CUSTOM_CHROMOSOME_BUFFER; } } }); return customGenomeLength[0]; } private Chromosome addCustomChromosome(GenomeWideList regionsInCustomChromosome, String cleanedUpName) { int size = getTotalLengthOfAllRegionsInBedFile(regionsInCustomChromosome); int newIndex = cleanedChromosomes.size(); customChromosomeRegions.put(newIndex, regionsInCustomChromosome); Chromosome newChr = new Chromosome(newIndex, cleanedUpName, size); cleanedChromosomes.add(newChr); chromosomeMap.put(newChr.getName(), newChr); return newChr; } private List initializeCleanedChromosomesList(List chromosomes) { List cleanedChromosomes = new ArrayList<>(); for (Chromosome c : chromosomes) { String cleanName = cleanUpName(c.getName()); Chromosome cleanChromosome = new Chromosome(c.getIndex(), cleanName, c.getLength()); cleanedChromosomes.add(cleanChromosome); } return cleanedChromosomes; } private Pair> initializeInternalVariables() { for (Chromosome c : cleanedChromosomes) { chromosomeMap.put(c.getName(), c); if (c.getName().equalsIgnoreCase("MT")) { chromosomeMap.put("M", c); // special case for mitochondria } } // for all-by-all view long[] chromosomeBoundaries = new long[cleanedChromosomes.size() - 1]; long bound = 0; for (int i = 1; i < cleanedChromosomes.size(); i++) { Chromosome c = cleanedChromosomes.get(i); bound += (c.getLength() / 1000); chromosomeBoundaries[i - 1] = bound; } Chromosome[] chromosomesArray = cleanedChromosomes.toArray(new Chromosome[cleanedChromosomes.size()]); // array without all by all Chromosome[] chromosomeArrayWithoutAllByAll = new Chromosome[chromosomesArray.length - 1]; System.arraycopy(chromosomesArray, 1, chromosomeArrayWithoutAllByAll, 0, chromosomesArray.length - 1); // array without X and Y List autosomes = new ArrayList<>(); for (Chromosome chr : chromosomeArrayWithoutAllByAll) { if (chr.getName().toLowerCase().contains("x") || chr.getName().toLowerCase().contains("y") || chr.getName().toLowerCase().contains("m")) continue; autosomes.add(chr); } Chromosome[] chromosomeArrayAutosomesOnly = new Chromosome[autosomes.size()]; for (int i = 0; i < autosomes.size(); i++) { chromosomeArrayAutosomesOnly[i] = autosomes.get(i); } List outputs = new ArrayList<>(); outputs.add(chromosomesArray); outputs.add(chromosomeArrayWithoutAllByAll); outputs.add(chromosomeArrayAutosomesOnly); return new Pair<>(chromosomeBoundaries, outputs); } private long getTotalLengthOfAllChromosomes(List chromosomes) { long genomeLength = 0; for (Chromosome c : chromosomes) { if (c != null) genomeLength += c.getLength(); } return genomeLength; } public String getGenomeID() { return genomeID; } public boolean isCustomChromosome(Chromosome chromosome) { return isCustomChromosome(chromosome.getIndex()); } private boolean isCustomChromosome(int index) { return customChromosomeRegions.containsKey(index); } public Chromosome getChromosomeFromName(String name) { return chromosomeMap.get(cleanUpName(name)); } public boolean doesNotContainChromosome(String name) { return !chromosomeMap.containsKey(cleanUpName(name)); } public int size() { return chromosomesArray.length; } public long[] getChromosomeBoundaries() { return chromosomeBoundaries; } public Chromosome[] getChromosomeArray() { return chromosomesArray; } public Chromosome getChromosomeFromIndex(int indx) { return chromosomesArray[indx]; } public ChromosomeHandler getIntersectionWith(ChromosomeHandler handler2) { Set intersection = getSetIntersection(cleanedChromosomes, handler2.cleanedChromosomes); if (intersection.isEmpty()) { return null; } List newSetOfChrs = new ArrayList<>(); long genomeLength = getTotalLengthOfAllChromosomes(cleanedChromosomes); newSetOfChrs.add(new Chromosome(0, CHR_ALL, (int) (genomeLength / 1000))); for (Chromosome chromosome : cleanedChromosomes) { if (!isAllByAll(chromosome) && intersection.contains(chromosome)) { newSetOfChrs.add(chromosome); } } return new ChromosomeHandler(newSetOfChrs, genomeID, false); } public Chromosome[] getAutosomalChromosomesArray() { return chromosomeArrayAutosomesOnly; } public Chromosome[] getChromosomeArrayWithoutAllByAll() { return chromosomeArrayWithoutAllByAll; } public GenomeWideList getListOfRegionsInCustomChromosome(Integer index) { return customChromosomeRegions.get(index); } public String inferGenomeId() { List chrom_sizes = Arrays.asList("hg19", "hg38", "b37", "hg18", "mm10", "mm9", "GRCm38", "aedAeg1", "anasPlat1", "assembly", "bTaurus3", "calJac3", "canFam3", "capHir1", "dm3", "dMel", "EBV", "equCab2", "felCat8", "galGal4", "hg18", "loxAfr3", "macMul1", "macMulBaylor", "oryCun2", "oryLat2", "panTro4", "Pf3D7", "ratNor5", "ratNor6", "sacCer3", "sCerS288c", "spretus", "susScr3", "TAIR10"); for (String id : chrom_sizes) { ChromosomeHandler handler = HiCFileTools.loadChromosomes(id); for (Chromosome chr : handler.cleanedChromosomes) { for (Chromosome chr2 : this.cleanedChromosomes) { if (!chr.getName().equalsIgnoreCase("ALL") && chr.getName().equals(chr2.getName()) && chr.getLength() == chr2.getLength()) { return id; } } } // this is more elegant but there's a problem with the Chromosome hashCode //ChromosomeHandler handler1 = this.getIntersectionWith(handler); //if (handler1 != null && handler1.size() > 1) { // return id; //} } return null; } public Chromosome[] extractOddOrEvenAutosomes(boolean extractOdd) { List subset = new ArrayList<>(); for (Chromosome chromosome : chromosomeArrayAutosomesOnly) { if (extractOdd && chromosome.getIndex() % 2 == 1) { subset.add(chromosome); } else if (!extractOdd && chromosome.getIndex() % 2 == 0) { subset.add(chromosome); } } Chromosome[] subsetArray = new Chromosome[subset.size()]; for (int i = 0; i < subset.size(); i++) { subsetArray[i] = subset.get(i); } return subsetArray; } static class ChromosomeComparator implements Comparator { @Override public int compare(Chromosome a, Chromosome b) { Integer aIndx = a.getIndex(); Integer bIndx = b.getIndex(); return aIndx.compareTo(bIndx); } } public Pair splitAutosomesIntoHalves() { int n = chromosomeArrayAutosomesOnly.length; int autosomesLength = 0; for (Chromosome chrom : chromosomeArrayAutosomesOnly) { autosomesLength += chrom.getLength(); } int halfLength = autosomesLength / 2; // default assume chromosomes ordered with biggest first // so for human, assuming first 8 chroms int firstBatchUpToChr = n / 3 + 1; long prevLength = 0; for (int i = 0; i < n / 2; i++) { long newLength = prevLength + chromosomeArrayAutosomesOnly[i].getLength(); if (prevLength <= halfLength && newLength >= halfLength) { // midpoint found if (Math.abs(prevLength - halfLength) < Math.abs(newLength - halfLength)) { firstBatchUpToChr = i - 1; } else { firstBatchUpToChr = i; } break; } prevLength = newLength; } System.out.println("Splitting chromosomes; " + chromosomeArrayAutosomesOnly[0].getName() + " to " + chromosomeArrayAutosomesOnly[firstBatchUpToChr].getName() + " and " + chromosomeArrayAutosomesOnly[firstBatchUpToChr + 1].getName() + " to " + chromosomeArrayAutosomesOnly[n - 1].getName()); Chromosome[] rowsChromosomes = new Chromosome[firstBatchUpToChr]; Chromosome[] colsChromosomes = new Chromosome[n - firstBatchUpToChr]; for (int i = 0; i < n; i++) { if (i < firstBatchUpToChr) { rowsChromosomes[i] = chromosomeArrayAutosomesOnly[i]; } else { colsChromosomes[i - firstBatchUpToChr] = chromosomeArrayAutosomesOnly[i]; } } return new Pair<>(rowsChromosomes, colsChromosomes); } public Pair splitAutosomesAndSkipByTwos() { int n = chromosomeArrayAutosomesOnly.length; List part1 = new ArrayList<>(); List part2 = new ArrayList<>(); part1.add(chromosomeArrayAutosomesOnly[0]); int i = 1; int counterOffset = 0; boolean addToFirstOne = false; while (i < n) { if (addToFirstOne) { part1.add(chromosomeArrayAutosomesOnly[i]); } else { part2.add(chromosomeArrayAutosomesOnly[i]); } counterOffset++; i++; if (counterOffset == 2) { addToFirstOne = !addToFirstOne; counterOffset = 0; } } return new Pair<>(chromosomeListToArray(part1), chromosomeListToArray(part2)); } private Chromosome[] chromosomeListToArray(List chromosomes) { Chromosome[] array = new Chromosome[chromosomes.size()]; for (int i = 0; i < chromosomes.size(); i++) { array[i] = chromosomes.get(i); } return array; } } ================================================ FILE: src/juicebox/data/CombinedDatasetReader.java ================================================ /* * The MIT License (MIT) * * Copyright (c) 2011-2023 Broad Institute, Aiden Lab, Rice University, Baylor College of Medicine * * Permission is hereby granted, free of charge, to any person obtaining a copy * of this software and associated documentation files (the "Software"), to deal * in the Software without restriction, including without limitation the rights * to use, copy, modify, merge, publish, distribute, sublicense, and/or sell * copies of the Software, and to permit persons to whom the Software is * furnished to do so, subject to the following conditions: * * The above copyright notice and this permission notice shall be included in * all copies or substantial portions of the Software. * * THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR * IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, * FITNESS FOR A PARTICULAR PURPOSE AND NON-INFRINGEMENT. IN NO EVENT SHALL THE * AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER * LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, * OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN * THE SOFTWARE. */ package juicebox.data; import juicebox.HiC; import juicebox.HiCGlobals; import juicebox.MainWindow; import juicebox.data.basics.ListOfDoubleArrays; import juicebox.windowui.HiCZoom; import juicebox.windowui.NormalizationType; import javax.swing.*; import java.awt.event.ActionListener; import java.io.IOException; import java.text.DecimalFormat; import java.text.ParseException; import java.util.*; //import java.util.List; /** * @author jrobinso * Date: 12/22/12 * Time: 10:10 AM */ public class CombinedDatasetReader implements DatasetReader { private final List readers; private boolean hasFrags; private int version; public CombinedDatasetReader(List readers) { this.readers = readers; } @Override public Dataset read() throws IOException { // Temporarily create a dataset for each reader, then merge them List tmpDatasets = new ArrayList<>(); version = 100000; for (DatasetReader r : readers) { Dataset ds = r.read(); if (ds == null) { System.err.println("Dataset is null!! : " + r.getPath()); } else { tmpDatasets.add(ds); } version = Math.min(version, r.getVersion()); } return mergeDatasets(tmpDatasets); } @Override public boolean isActive() { /* do nothing boolean atLeastOneIsActive = false; for(DatasetReaderV2 reader : readers){ atLeastOneIsActive = atLeastOneIsActive || reader.isActive(); } return atLeastOneIsActive; */ return true; } @Override public void setActive(boolean status) { // do nothing } @Override public int getVersion() { // Version is the minimum of all constituent datasets return version; } @Override public String getPath() { // we use this for peaks and blocks list, maybe the best thing to do is to somehow combine them return "combined_dataset"; } @Override public List getCheckBoxes(List actionListeners) { List allBoxes = new ArrayList<>(); for (DatasetReaderV2 reader : readers) { allBoxes.addAll(reader.getCheckBoxes(actionListeners)); } return allBoxes; } // todo this just picks the normalization for the first map rather doing an appropriate calculation @Override public NormalizationVector getNormalizationVector(int chr1Idx, HiCZoom zoom, NormalizationType normalizationType) { return readers.get(0).getNormalizationVector(chr1Idx, zoom, normalizationType); } @Override public int getDepthBase() { return readers.get(0).getDepthBase(); } /** * @param key -- string identifier for matrix, concatenation of chromosome names * @return Merged matrices read in * @throws IOException */ @Override public Matrix readMatrix(String key) throws IOException { // List tmpDatasets = new ArrayList<>(); for (DatasetReader r : readers) { if (r.isActive()) { Matrix m = r.readMatrix(key); if (m == null) { System.err.println("Matrix Region is null!! : " + r.getPath()); System.err.println("Key " + m.getKey()); } else { tmpDatasets.add(m); } } } if (tmpDatasets.size() == 0) { return null; } else if (tmpDatasets.size() == 1) { return tmpDatasets.get(0); } else { return mergeMatrices(tmpDatasets); } } @Override public Block readNormalizedBlock(int blockNumber, MatrixZoomData zd, NormalizationType no) throws IOException { List blockList = Collections.synchronizedList(new ArrayList<>()); for (DatasetReader r : readers) { if (r.isActive()) { Block cb = r.readNormalizedBlock(blockNumber, zd, no); if (cb != null) { blockList.add(cb); } } } String key = zd.getBlockKey(blockNumber, no); return blockList.size() == 0 ? new Block(blockNumber, key) : mergeBlocks(blockList, key); } /** * Return the block numbers of all occupied blocks. * * @param matrixZoomData Matrix * @return block numbers */ @Override public List getBlockNumbers(MatrixZoomData matrixZoomData) { Set blockNumberSet = new HashSet<>(); for (DatasetReader r : readers) { if (r.isActive()) { blockNumberSet.addAll(r.getBlockNumbers(matrixZoomData)); } } List blockNumbers = new ArrayList<>(blockNumberSet); Collections.sort(blockNumbers); return blockNumbers; } @Override public Integer getBlockSize(MatrixZoomData zd, int blockNum) { Integer blockSize = 0; for (DatasetReader r : readers) { if (r.isActive()) { Integer tmpBlockSize = r.getBlockSize(zd, blockNum); if (tmpBlockSize != null) { blockSize += tmpBlockSize; } } } if (blockSize != 0) { return blockSize; } else { return null; } } @Override public double[] readEigenvector(String chr, HiCZoom zoom, int number, String type) { // Eigenvectors not supported for combined datasets return null; } @Override public NormalizationVector readNormalizationVector(NormalizationType type, int chrIdx, HiC.Unit unit, int binSize) { return null; // Undefined for combined datasets } @Override public NormalizationVector readNormalizationVectorPart(NormalizationType type, int chrIdx, HiC.Unit unit, int binSize, int bound1, int bound2) { return null; //Undefined for combined datasets } @Override public ListOfDoubleArrays readExpectedVectorPart(long position, long nVals) { return null; } /** * Return a dataset that is an "intersection" of the supplied datasets. * * @param datasetList List of datasets to merge * @return new dataset */ private Dataset mergeDatasets(List datasetList) { Dataset dataset = new Dataset(this); final Dataset firstDataset = datasetList.get(0); dataset.genomeId = firstDataset.getGenomeId(); dataset.setChromosomeHandler(firstDataset.getChromosomeHandler()); String enzyme = firstDataset.getRestrictionEnzyme(); hasFrags = enzyme != null; if (hasFrags) { for (Dataset ds : datasetList) { if (!ds.getRestrictionEnzyme().equals(enzyme)) { hasFrags = false; break; } } } //Set zoomSet = new HashSet<>(firstDataset.getBpZooms()); // only retain resolutions in common between all datasets dataset.bpZooms = firstDataset.getBpZooms(); for (Dataset ds : datasetList) { for (HiCZoom zoom: ds.getBpZooms()) { if (!(dataset.bpZooms.contains(zoom))) { dataset.bpZooms.add(zoom); } } // dataset.bpZooms.retainAll(ds.getBpZooms()); } dataset.bpZooms.sort(Collections.reverseOrder()); if (hasFrags) { dataset.fragZooms = firstDataset.getFragZooms(); for (Dataset ds : datasetList) { dataset.fragZooms.retainAll(ds.getFragZooms()); } dataset.setFragmentCounts(firstDataset.getFragmentCounts()); } // Expected values, just sum // Map key == unit_binSize Map dfMap = new HashMap<>(); Collection keys = firstDataset.getExpectedValueFunctionMap().keySet(); Set zoomsToRemove = new HashSet<>(); for (String key : keys) { if (!hasFrags && key.startsWith(HiC.Unit.FRAG.toString())) continue; List evFunctions = new ArrayList<>(); boolean haveAll = true; for (Dataset ds : datasetList) { final ExpectedValueFunction e = ds.getExpectedValueFunctionMap().get(key); if (e == null) { int idx = key.lastIndexOf("_"); String zoomKey = key.substring(0, idx); zoomsToRemove.add(zoomKey); haveAll = false; break; } else { evFunctions.add(e); } } if (haveAll) { ExpectedValueFunction combinedEV = mergeExpectedValues(evFunctions); dfMap.put(key, combinedEV); } } dataset.expectedValueFunctionMap = dfMap; /*if (zoomsToRemove.size() > 0) { List trimmedBpZooms = new ArrayList<>(dataset.bpZooms.size()); for (HiCZoom zoom : dataset.bpZooms) { if (!zoomsToRemove.contains(zoom.getKey())) { trimmedBpZooms.add(zoom); } } dataset.bpZooms = trimmedBpZooms; if (hasFrags) { List trimmedFragZooms = new ArrayList<>(dataset.bpZooms.size()); for (HiCZoom zoom : dataset.fragZooms) { if (!zoomsToRemove.contains(zoom.getKey())) { trimmedFragZooms.add(zoom); } } dataset.fragZooms = trimmedFragZooms; } } */ ArrayList statisticsList = new ArrayList<>(); ArrayList graphsList = new ArrayList<>(); HashSet reList = new HashSet<>(); for (Dataset ds : datasetList) { try { statisticsList.add(ds.getStatistics()); graphsList.add(ds.getGraphs()); reList.add(ds.getRestrictionEnzyme()); } catch (Exception e) { // TODO - test on hic file with no stats file specified e.printStackTrace(); if (HiCGlobals.guiIsCurrentlyActive) JOptionPane.showMessageDialog(MainWindow.getInstance(), "Unable to retrieve statistics for one of the maps.", "Error", JOptionPane.ERROR_MESSAGE); } } Map attributes = new HashMap<>(); attributes.put("statistics", mergeStatistics(statisticsList)); attributes.put("graphs", mergeGraphs(graphsList)); dataset.setAttributes(attributes); Iterator it = reList.iterator(); StringBuilder newRestrictionEnzyme = new StringBuilder(); while (it.hasNext()) newRestrictionEnzyme.append(it.next()).append(" "); dataset.restrictionEnzyme = newRestrictionEnzyme.toString(); // Set normalization types (for menu) LinkedHashSet normTypes = new LinkedHashSet<>(); for (Dataset ds : datasetList) { List tmp = ds.getNormalizationTypes(); if (tmp != null) normTypes.addAll(tmp); } for (Dataset ds : datasetList) { List tmp = ds.getNormalizationTypes(); if (tmp != null) normTypes.retainAll(tmp); } dataset.setNormalizationTypes(new ArrayList<>(normTypes)); return dataset; } private ExpectedValueFunction mergeExpectedValues(List densityFunctions) { try { ExpectedValueFunction protoFunction = densityFunctions.get(0); int binSize = protoFunction.getBinSize(); HiC.Unit unit = protoFunction.getUnit(); NormalizationType type = protoFunction.getNormalizationType(); long len = protoFunction.getLength(); for (ExpectedValueFunction df : densityFunctions) { if (df.getBinSize() != binSize || !df.getUnit().equals(unit) || df.getNormalizationType() != type) { throw new RuntimeException("Attempt to merge incompatible expected values"); } len = Math.min(df.getLength(), len); } ListOfDoubleArrays expectedValues = new ListOfDoubleArrays(len); for (ExpectedValueFunction df : densityFunctions) { expectedValues.addValuesFrom(df.getExpectedValuesNoNormalization()); } return new ExpectedValueFunctionImpl(protoFunction.getNormalizationType(), protoFunction.getUnit(), protoFunction.getBinSize(), expectedValues, null); } catch (Exception e) { e.printStackTrace(); //To change body of catch statement use File | Settings | File Templates. return null; } } private String mergeStatistics(List statisticsList) { LinkedHashMap statsMap = new LinkedHashMap<>(); int numberFiles = statisticsList.size(); StringBuilder newStatistics = new StringBuilder(); for (String stats : statisticsList) { if (stats == null) return null; Scanner scanner = new Scanner(stats).useDelimiter("\n"); while (scanner.hasNext()) { String[] results = scanner.next().split(":"); if (results.length == 2) { String key = results[0]; String prevValue = statsMap.get(key); String value = results[1]; int index = value.indexOf("("); if (index > -1) value = value.substring(0, index); if (prevValue == null) { statsMap.put(key, value); } else { statsMap.put(key, prevValue + ";" + value); } } } } DecimalFormat decimalFormat = new DecimalFormat(); for (Map.Entry e : statsMap.entrySet()) { String key = e.getKey(); String value = e.getValue(); String[] results = value.split(";"); if (results.length == numberFiles) { boolean add = true; long tmp = 0; for (int i = 0; i < numberFiles; i++) { try { tmp += decimalFormat.parse(results[i].trim()).longValue(); } catch (ParseException exception) { add = false; } //tmp += Long.valueOf(results[i].trim()); } if (add) newStatistics.append(key).append(": ").append(decimalFormat.format(tmp)).append("\n"); } } return newStatistics.toString(); } private String mergeGraphs(List graphsList) { long[] A = new long[2000]; int[] mapq1 = new int[201]; int[] mapq2 = new int[201]; int[] mapq3 = new int[201]; int[] inner = new int[100]; int[] outer = new int[100]; int[] right = new int[100]; int[] left = new int[100]; for (String graphs : graphsList) { if (graphs == null) { return null; } Scanner scanner = new Scanner(graphs); try { while (true) { if (scanner.next().equals("[")) break; } //while (!scanner.next().equals("[")) ; for (int idx = 0; idx < 2000; idx++) { A[idx] += scanner.nextLong(); } while (true) { if (scanner.next().equals("[")) break; } //while (!scanner.next().equals("[")) ; for (int idx = 0; idx < 201; idx++) { mapq1[idx] += scanner.nextInt(); mapq2[idx] += scanner.nextInt(); mapq3[idx] += scanner.nextInt(); } while (true) { if (scanner.next().equals("[")) break; } //while (!scanner.next().equals("[")) ; for (int idx = 0; idx < 100; idx++) { inner[idx] += scanner.nextInt(); outer[idx] += scanner.nextInt(); right[idx] += scanner.nextInt(); left[idx] += scanner.nextInt(); } } catch (NoSuchElementException exception) { System.err.println("Graphing file improperly formatted"); return null; } } StringBuilder newGraph = new StringBuilder("A = [\n"); for (int idx = 0; idx < 2000; idx++) newGraph.append(A[idx]).append(" "); newGraph.append("];\n"); newGraph.append("B = [\n"); for (int idx = 0; idx < 201; idx++) newGraph.append(mapq1[idx]).append(" ").append(mapq2[idx]).append(" ").append(mapq3[idx]).append("\n"); newGraph.append("];\n"); newGraph.append("D = [\n"); for (int idx = 0; idx < 100; idx++) newGraph.append(inner[idx]).append(" ").append(outer[idx]).append(" ").append(right[idx]).append(" ").append(left[idx]).append("\n"); newGraph.append("];\n"); return newGraph.toString(); } private Matrix mergeMatrices(List matrixList) { Map averageCount = new HashMap<>(); Map sumCount = new HashMap<>(); List newMatrixZoomData = new ArrayList<>(); Set bpBinSizesSet = new HashSet<>(); Set fragBinSizesSet = new HashSet<>(); for (Matrix matrix : matrixList) { for (MatrixZoomData zd : matrix.bpZoomData) { String key = zd.getKey(); Double avg = averageCount.get(key); Double sum = sumCount.get(key); if (avg == null) { averageCount.put(key, zd.getAverageCount()); } else if (avg >= 0) { averageCount.put(key, avg + zd.getAverageCount()); } if (sum == null) { sumCount.put(key, zd.getSumCount()); } else if (sum >= 0) { sumCount.put(key, sum + zd.getSumCount()); } newMatrixZoomData.add(zd); bpBinSizesSet.add(zd.getBinSize()); } if (hasFrags) { for (MatrixZoomData zd : matrix.fragZoomData) { String key = zd.getKey(); Double avg = averageCount.get(key); if (avg == null) { averageCount.put(key, zd.getAverageCount()); } else if (avg >= 0) { averageCount.put(key, avg + zd.getAverageCount()); } fragBinSizesSet.add(zd.getBinSize()); } } } Matrix mergedMatrix = matrixList.get(0); ArrayList bpBinSizes = new ArrayList<>(bpBinSizesSet); Collections.sort(bpBinSizes, Collections.reverseOrder()); mergedMatrix.setBpBinSizes(bpBinSizes); for (MatrixZoomData zd : newMatrixZoomData) { zd.reader = this; String key = zd.getKey(); if (averageCount.containsKey(key)) { zd.setAverageCount(averageCount.get(key)); } if (sumCount.containsKey(key)) { zd.setSumCount(sumCount.get(key)); } } mergedMatrix.bpZoomData = newMatrixZoomData; /* for (MatrixZoomData zd : mergedMatrix.bpZoomData) { zd.reader = this; String key = zd.getKey(); if (averageCount.containsKey(key)) { zd.setAverageCount(averageCount.get(key)); } }*/ if (hasFrags) { ArrayList fragBinSizes = new ArrayList<>(fragBinSizesSet); Collections.sort(fragBinSizes, Collections.reverseOrder()); mergedMatrix.setFragBinSizes(fragBinSizes); for (MatrixZoomData zd : mergedMatrix.fragZoomData) { zd.reader = this; String key = zd.getKey(); if (averageCount.containsKey(key)) { zd.setAverageCount(averageCount.get(key)); } if (sumCount.containsKey(key)) { zd.setSumCount(sumCount.get(key)); } } } else { mergedMatrix.fragZoomData = null; } return mergedMatrix; } /** * Merge the contact records from multiple blocks to create a new block. Contact records are sorted in row then * column order. * * @param blockList Blocks to merge * @param blockKey * @return new Block */ private Block mergeBlocks(List blockList, String blockKey) { // First combine contact records for all blocks final Block firstBlock = blockList.get(0); int repSize = firstBlock.getContactRecords().size(); int blockNumber = firstBlock.getNumber(); // TODO -- this should be checked, all blocks should have same number HashMap mergedRecordMap = new HashMap<>(blockList.size() * repSize * 2); for (Block b : blockList) { Collection records = b.getContactRecords(); for (ContactRecord rec : records) { String key = rec.getBinX() + "_" + rec.getBinY(); ContactRecord mergedRecord = mergedRecordMap.get(key); if (mergedRecord == null) { mergedRecord = new ContactRecord(rec.getBinX(), rec.getBinY(), rec.getCounts()); mergedRecordMap.put(key, mergedRecord); } else { mergedRecord.incrementCount(rec.getCounts()); } } } List mergedRecords = new ArrayList<>(mergedRecordMap.values()); return new Block(blockNumber, mergedRecords, blockKey); } } ================================================ FILE: src/juicebox/data/CombinedExpectedValueFunction.java ================================================ /* * The MIT License (MIT) * * Copyright (c) 2011-2020 Broad Institute, Aiden Lab, Rice University, Baylor College of Medicine * * Permission is hereby granted, free of charge, to any person obtaining a copy * of this software and associated documentation files (the "Software"), to deal * in the Software without restriction, including without limitation the rights * to use, copy, modify, merge, publish, distribute, sublicense, and/or sell * copies of the Software, and to permit persons to whom the Software is * furnished to do so, subject to the following conditions: * * The above copyright notice and this permission notice shall be included in * all copies or substantial portions of the Software. * * THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR * IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, * FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE * AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER * LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, * OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN * THE SOFTWARE. */ package juicebox.data; import juicebox.HiC; import juicebox.data.basics.ListOfDoubleArrays; import juicebox.windowui.NormalizationType; import java.util.ArrayList; import java.util.List; //import java.util.Map; /** * @author jrobinso * Date: 12/26/12 * Time: 9:30 PM */ public class CombinedExpectedValueFunction implements ExpectedValueFunction { private final List densityFunctions; private ListOfDoubleArrays expectedValuesNoNormalization = null; public CombinedExpectedValueFunction(ExpectedValueFunction densityFunction) { this.densityFunctions = new ArrayList<>(); densityFunctions.add(densityFunction); } public void addDensityFunction(ExpectedValueFunction densityFunction) { // TODO -- verify same unit, binsize, type, denisty array size densityFunctions.add(densityFunction); } @Override public double getExpectedValue(int chrIdx, long distance) { double sum = 0; for (ExpectedValueFunction df : densityFunctions) { sum += df.getExpectedValue(chrIdx, distance); } return sum; } @Override public ListOfDoubleArrays getExpectedValuesWithNormalization(int chrIdx) { if (expectedValuesNoNormalization.getLength() > 0) { ListOfDoubleArrays normedExpectedValues = new ListOfDoubleArrays(expectedValuesNoNormalization.getLength()); for (long i = 0; i < normedExpectedValues.getLength(); i++) { for (ExpectedValueFunction df : densityFunctions) { normedExpectedValues.addTo(i, df.getExpectedValue(chrIdx, i)); } } return normedExpectedValues; } else { System.err.println("Expected values array is empty"); return null; } } @Override public ListOfDoubleArrays getExpectedValuesNoNormalization() { if (expectedValuesNoNormalization != null) return expectedValuesNoNormalization; long length = 0; for (ExpectedValueFunction df : densityFunctions) { // Removed cast to ExpectedValueFunctionImpl; change back if errors length = Math.max(length, df.getExpectedValuesNoNormalization().getLength()); } expectedValuesNoNormalization = new ListOfDoubleArrays(length); for (ExpectedValueFunction df : densityFunctions) { expectedValuesNoNormalization.addValuesFrom(df.getExpectedValuesNoNormalization()); } return expectedValuesNoNormalization; } @Override public long getLength() { return densityFunctions.get(0).getLength(); } @Override public NormalizationType getNormalizationType() { return densityFunctions.get(0).getNormalizationType(); } @Override public HiC.Unit getUnit() { return densityFunctions.get(0).getUnit(); } @Override public int getBinSize() { return densityFunctions.get(0).getBinSize(); } } ================================================ FILE: src/juicebox/data/ContactRecord.java ================================================ /* * The MIT License (MIT) * * Copyright (c) 2011-2021 Broad Institute, Aiden Lab, Rice University, Baylor College of Medicine * * Permission is hereby granted, free of charge, to any person obtaining a copy * of this software and associated documentation files (the "Software"), to deal * in the Software without restriction, including without limitation the rights * to use, copy, modify, merge, publish, distribute, sublicense, and/or sell * copies of the Software, and to permit persons to whom the Software is * furnished to do so, subject to the following conditions: * * The above copyright notice and this permission notice shall be included in * all copies or substantial portions of the Software. * * THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR * IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, * FITNESS FOR A PARTICULAR PURPOSE AND NON-INFRINGEMENT. IN NO EVENT SHALL THE * AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER * LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, * OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN * THE SOFTWARE. */ package juicebox.data; import juicebox.windowui.NormalizationType; import java.util.Objects; /** * @author jrobinso * @since Aug 3, 2010 */ public class ContactRecord implements Comparable { /** * Bin number in x coordinate */ private final int binX; /** * Bin number in y coordinate */ private final int binY; /** * Total number of counts, or cumulative score */ private float counts; public ContactRecord(int binX, int binY, float counts) { this.binX = binX; this.binY = binY; this.counts = counts; } public void incrementCount(float score) { counts += score; } public int getBinX() { return binX; } public int getBinY() { return binY; } public float getCounts() { return counts; } @Override public int compareTo(ContactRecord contactRecord) { if (this.binX != contactRecord.binX) { return binX - contactRecord.binX; } else if (this.binY != contactRecord.binY) { return binY - contactRecord.binY; } else return 0; } public String toString() { return "" + binX + " " + binY + " " + counts; } @Override public int hashCode() { return Objects.hash(binX, binY, counts); } @Override public boolean equals(Object obj) { if (this == obj) return true; if (obj == null) return false; if (getClass() != obj.getClass()) return false; return compareTo((ContactRecord) obj) == 0; } public String getKey(NormalizationType normalizationType) { return binX + "_" + binY + "_" + normalizationType; } } ================================================ FILE: src/juicebox/data/CustomMatrixZoomData.java ================================================ /* * The MIT License (MIT) * * Copyright (c) 2011-2021 Broad Institute, Aiden Lab, Rice University, Baylor College of Medicine * * Permission is hereby granted, free of charge, to any person obtaining a copy * of this software and associated documentation files (the "Software"), to deal * in the Software without restriction, including without limitation the rights * to use, copy, modify, merge, publish, distribute, sublicense, and/or sell * copies of the Software, and to permit persons to whom the Software is * furnished to do so, subject to the following conditions: * * The above copyright notice and this permission notice shall be included in * all copies or substantial portions of the Software. * * THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR * IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, * FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE * AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER * LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, * OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN * THE SOFTWARE. */ package juicebox.data; import juicebox.HiCGlobals; import juicebox.data.anchor.GenericLocus; import juicebox.data.anchor.MotifAnchor; import juicebox.data.basics.Chromosome; import juicebox.data.censoring.CustomMZDRegionHandler; import juicebox.data.censoring.RegionPair; import juicebox.windowui.HiCZoom; import juicebox.windowui.NormalizationType; import org.broad.igv.util.Pair; import org.broad.igv.util.collections.LRUCache; import java.io.IOException; import java.util.*; import java.util.concurrent.ConcurrentHashMap; import java.util.concurrent.ExecutorService; import java.util.concurrent.TimeUnit; import java.util.concurrent.atomic.AtomicInteger; /** * Created by muhammadsaadshamim on 7/21/17. */ public class CustomMatrixZoomData extends MatrixZoomData { private final Map zoomDatasForDifferentRegions = new HashMap<>(); private final Map>> allBlockCaches = new HashMap<>(); private final CustomMZDRegionHandler rTreeHandler = new CustomMZDRegionHandler(); private final ChromosomeHandler handler; public CustomMatrixZoomData(Chromosome chr1, Chromosome chr2, ChromosomeHandler handler, HiCZoom zoom, DatasetReader reader) { super(chr1, chr2, zoom, -1, -1, new int[0], new int[0], reader); this.handler = handler; rTreeHandler.initialize(chr1, chr2, zoom, handler); } private boolean isImportant = false; public void expandAvailableZoomDatas(String regionKey, MatrixZoomData zd) { if (getZoom().equals(zd.getZoom())) { zoomDatasForDifferentRegions.put(regionKey, zd); } } private static Block modifyBlock(Block block, String key, MatrixZoomData zd, RegionPair rp) { int binSize = zd.getBinSize(); int chr1Idx = zd.getChr1Idx(); int chr2Idx = zd.getChr2Idx(); List alteredContacts = new ArrayList<>(); for (ContactRecord record : block.getContactRecords()) { long newX = record.getBinX() * binSize; if (newX >= rp.xRegion.getX1() && newX <= rp.xRegion.getX2()) { newX = rp.xTransRegion.getX1() + newX - rp.xRegion.getX1(); } else { continue; } long newY = record.getBinY() * binSize; if (newY >= rp.yRegion.getX1() && newY <= rp.yRegion.getX2()) { newY = rp.yTransRegion.getX1() + newY - rp.yRegion.getX1(); } else { continue; } int newBinX = (int) (newX / binSize); int newBinY = (int) (newY / binSize); if (chr1Idx == chr2Idx && newBinY < newBinX) { alteredContacts.add(new ContactRecord(newBinY, newBinX, record.getCounts())); } else { alteredContacts.add(new ContactRecord(newBinX, newBinY, record.getCounts())); } } //System.out.println("num orig records "+block.getContactRecords().size()+ " after alter "+alteredContacts.size()+" bnum "+block.getNumber()); return new Block(block.getNumber(), alteredContacts, key + rp.getDescription()); } @Override public List getNormalizedBlocksOverlapping(long binX1, long binY1, long binX2, long binY2, final NormalizationType norm, boolean isImportant, boolean fillUnderDiagonal) { this.isImportant = isImportant; int resolution = zoom.getBinSize(); //if(isImportant) System.out.println("zt12 "+resolution+" --x "+binX1+" "+binX2+" y "+binY1+" "+binY2); long gx1 = (binX1 * resolution); long gy1 = (binY1 * resolution); long gx2 = (binX2 * resolution); long gy2 = (binY2 * resolution); return addNormalizedBlocksToListByGenomeCoordinates(gx1, gy1, gx2, gy2, norm); } @Override public void printFullDescription() { System.out.println("Custom Chromosome: " + chr1.getName() + " - " + chr2.getName()); System.out.println("unit: " + zoom.getUnit()); System.out.println("binSize (bp): " + zoom.getBinSize()); } private List addNormalizedBlocksToListByGenomeCoordinates(long gx1, long gy1, long gx2, long gy2, final NormalizationType no) { List blockList = Collections.synchronizedList(new ArrayList<>()); Map>> blocksNumsToLoadForZd = new ConcurrentHashMap<>(); // remember these are pseudo genome coordinates // x window //net.sf.jsi.Rectangle currentWindow = new net.sf.jsi.Rectangle(gx1, gx1, gx2, gx2); List> xAxisRegions = rTreeHandler.getIntersectingFeatures(chr1.getName(), gx1, gx2); // y window //currentWindow = new net.sf.jsi.Rectangle(gy1, gy1, gy2, gy2); List> yAxisRegions = rTreeHandler.getIntersectingFeatures(chr2.getName(), gy1, gy2); if (isImportant) { if (HiCGlobals.printVerboseComments) System.out.println("num x regions " + xAxisRegions.size() + " num y regions " + yAxisRegions.size()); } if (xAxisRegions.size() < 1) { System.err.println("no x?"); } if (yAxisRegions.size() < 1) { System.err.println("no y?"); } ExecutorService executor = HiCGlobals.newFixedThreadPool(); // todo change to be by chromosome? for (Pair xRegion : xAxisRegions) { for (Pair yRegion : yAxisRegions) { Runnable worker = new Runnable() { @Override public void run() { RegionPair rp = RegionPair.generateRegionPair(xRegion, yRegion, handler); MatrixZoomData zd = zoomDatasForDifferentRegions.get(Matrix.generateKey(rp.xI, rp.yI)); if (zd == null || rp == null) return; synchronized (blocksNumsToLoadForZd) { if (!blocksNumsToLoadForZd.containsKey(zd)) { blocksNumsToLoadForZd.put(zd, new HashMap<>()); } if (!blocksNumsToLoadForZd.get(zd).containsKey(rp)) { blocksNumsToLoadForZd.get(zd).put(rp, new ArrayList<>()); } } // todo mss custom matrix zd doesn't have long support yet List tempBlockNumbers = zd.getBlockNumbersForRegionFromGenomePosition(rp.getOriginalGenomeRegion()); synchronized (blocksNumsToLoadForZd) { for (int blockNumber : tempBlockNumbers) { String key = zd.getBlockKey(blockNumber, no); if (HiCGlobals.useCache && allBlockCaches.containsKey(zd) && allBlockCaches.get(zd).containsKey(rp) && allBlockCaches.get(zd).get(rp).containsKey(key)) { synchronized (blockList) { blockList.add(allBlockCaches.get(zd).get(rp).get(key)); } } else if (blocksNumsToLoadForZd.containsKey(zd) && blocksNumsToLoadForZd.get(zd).containsKey(rp)) { blocksNumsToLoadForZd.get(zd).get(rp).add(blockNumber); } else { System.err.println("Something went wrong CZDErr3 " + zd.getDescription() + " rp " + rp.getDescription() + " block num " + blockNumber); } } } } }; executor.execute(worker); } } executor.shutdown(); // Wait until all threads finish while (!executor.isTerminated()) { } // Actually load new blocks actuallyLoadGivenBlocks(blockList, no, blocksNumsToLoadForZd); //System.out.println("num blocks post "+blockList.size()); if (blockList.size() < 1) { if (HiCGlobals.printVerboseComments) System.err.println("no blocks?? for num x regions " + xAxisRegions.size() + " num y regions " + yAxisRegions.size()); } return blockList; } /** * not quite an override since inputs are different, but naming preserved as parent class * * @param blockList * @param no * @param blocksNumsToLoadForZd */ private void actuallyLoadGivenBlocks(final List blockList, final NormalizationType no, Map>> blocksNumsToLoadForZd) { final AtomicInteger errorCounter = new AtomicInteger(); ExecutorService service = HiCGlobals.newFixedThreadPool(); long[] timesPassed = new long[3]; long overallTimeStart = System.currentTimeMillis(); for (final MatrixZoomData zd : blocksNumsToLoadForZd.keySet()) { final Map> blockNumberMap = blocksNumsToLoadForZd.get(zd); for (final RegionPair rp : blockNumberMap.keySet()) { Runnable loader = new Runnable() { @Override public void run() { for (final int blockNum : blockNumberMap.get(rp)) { try { long time0 = System.currentTimeMillis(); String key = zd.getBlockKey(blockNum, no); long time1 = System.currentTimeMillis(); Block b = reader.readNormalizedBlock(blockNum, zd, no); long time2 = System.currentTimeMillis(); if (b == null) { b = new Block(blockNum, key + rp.getDescription()); // An empty block } else { b = modifyBlock(b, key, zd, rp); } long time3 = System.currentTimeMillis(); if (HiCGlobals.useCache) { synchronized (allBlockCaches) { if (!allBlockCaches.containsKey(zd)) { allBlockCaches.put(zd, new HashMap<>()); } if (!allBlockCaches.get(zd).containsKey(rp)) { allBlockCaches.get(zd).put(rp, new LRUCache<>(50)); } allBlockCaches.get(zd).get(rp).put(key, b); } } blockList.add(b); synchronized (timesPassed) { timesPassed[0] += time1 - time0; timesPassed[1] += time2 - time1; timesPassed[2] += time3 - time2; } } catch (IOException e) { System.err.println("--e0 " + zd.getDescription() + " - " + rp.getDescription()); errorCounter.incrementAndGet(); } } } }; service.submit(loader); } } // done submitting all jobs service.shutdown(); // Wait until all threads finish while (!service.isTerminated()) { } // wait for all to finish try { service.awaitTermination(Long.MAX_VALUE, TimeUnit.NANOSECONDS); } catch (InterruptedException e) { //String.format("Pending tasks: %d", executor.getQueue().size()) System.err.println("Error loading custom mzd data " + e.getLocalizedMessage()); if (HiCGlobals.printVerboseComments) { e.printStackTrace(); } } long timeFinalOverall = System.currentTimeMillis(); //System.out.println("Time taken in actuallyLoadGivenBlocks (seconds): " + timesPassed[0] / 1000.0 + " - " + timesPassed[1] / 1000.0 + " - " + timesPassed[2] / 1000.0); if (HiCGlobals.printVerboseComments) { System.out.println("Time taken overall breakdown (seconds): " + DatasetReaderV2.globalTimeDiffThings[0] + " - " + DatasetReaderV2.globalTimeDiffThings[1] + " - " + DatasetReaderV2.globalTimeDiffThings[2] + " - " + DatasetReaderV2.globalTimeDiffThings[3] + " - " + DatasetReaderV2.globalTimeDiffThings[4] ); System.out.println("Time taken overall (seconds): " + (overallTimeStart - timeFinalOverall) / 1000.0); } // error printing if (errorCounter.get() > 0) { System.err.println(errorCounter.get() + " errors while reading blocks"); } } public List getBoundariesOfCustomChromosomeX() { return rTreeHandler.getBoundariesOfCustomChromosomeX(); } public List getBoundariesOfCustomChromosomeY() { return rTreeHandler.getBoundariesOfCustomChromosomeY(); } // TODO get Expected should be appropriately caculated in the custom regions public double getExpected(int binX, int binY, ExpectedValueFunction df) { // x window int gx1 = binX * zoom.getBinSize(); net.sf.jsi.Rectangle currentWindow = new net.sf.jsi.Rectangle(gx1, gx1, gx1, gx1); List> xRegions = rTreeHandler.getIntersectingFeatures(chr1.getName(), gx1); // y window int gy1 = binY * zoom.getBinSize(); currentWindow = new net.sf.jsi.Rectangle(gy1, gy1, gy1, gy1); List> yRegions = rTreeHandler.getIntersectingFeatures(chr2.getName(), gy1); RegionPair rp = RegionPair.generateRegionPair(xRegions.get(0), yRegions.get(0), handler); MatrixZoomData zd = zoomDatasForDifferentRegions.get(Matrix.generateKey(rp.xI, rp.yI)); return zd.getAverageCount(); /* if(rp.xI == rp.yI){ if (df != null) { int dist = Math.abs(binX - binY); return df.getExpectedValue(rp.xI, dist); } } else { return zd.getAverageCount(); } return 0; */ } @Override public double getAverageCount() { return 10; //todo } public List> getRTreeHandlerIntersectingFeatures(String name, int g1, int g2) { return rTreeHandler.getIntersectingFeatures(name, g1, g2); } } ================================================ FILE: src/juicebox/data/Dataset.java ================================================ /* * The MIT License (MIT) * * Copyright (c) 2011-2023 Broad Institute, Aiden Lab, Rice University, Baylor College of Medicine * * Permission is hereby granted, free of charge, to any person obtaining a copy * of this software and associated documentation files (the "Software"), to deal * in the Software without restriction, including without limitation the rights * to use, copy, modify, merge, publish, distribute, sublicense, and/or sell * copies of the Software, and to permit persons to whom the Software is * furnished to do so, subject to the following conditions: * * The above copyright notice and this permission notice shall be included in * all copies or substantial portions of the Software. * * THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR * IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, * FITNESS FOR A PARTICULAR PURPOSE AND NON-INFRINGEMENT. IN NO EVENT SHALL THE * AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER * LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, * OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN * THE SOFTWARE. */ package juicebox.data; import com.google.common.primitives.Ints; import juicebox.HiC; import juicebox.HiCGlobals; import juicebox.data.basics.Chromosome; import juicebox.tools.dev.Private; import juicebox.tools.utils.original.Preprocessor; import juicebox.windowui.HiCZoom; import juicebox.windowui.NormalizationHandler; import juicebox.windowui.NormalizationType; import org.broad.igv.util.FileUtils; import org.broad.igv.util.Pair; import org.broad.igv.util.ResourceLocator; import org.broad.igv.util.collections.LRUCache; import javax.swing.*; import java.awt.event.ActionListener; import java.io.IOException; import java.text.DecimalFormat; import java.text.NumberFormat; import java.text.ParseException; import java.util.*; /** * @author jrobinso * @since Aug 12, 2010 */ public class Dataset { private final Map matrices = new HashMap<>(625); private final DatasetReader reader; private final LRUCache eigenvectorCache; private final LRUCache normalizationVectorCache; private final Map normalizationsVectorsOnlySavedInRAMCache; Map expectedValueFunctionMap; String genomeId; String restrictionEnzyme = null; List bpZooms, dynamicZooms, fragZooms; private int v9DepthBase = 0; private List bpZoomResolutions; private Map attributes; private Map fragmentCounts; protected NormalizationHandler normalizationHandler = new NormalizationHandler(); private List normalizationTypes; private ChromosomeHandler chromosomeHandler; public Dataset(DatasetReader reader) { this.reader = reader; eigenvectorCache = new LRUCache<>(25); normalizationVectorCache = new LRUCache<>(25); normalizationsVectorsOnlySavedInRAMCache = new HashMap<>(); normalizationTypes = new ArrayList<>(); } public Matrix getMatrix(Chromosome chr1, Chromosome chr2) { // order is arbitrary, convention is lower # chr first if (chr1 == null || chr2 == null) return null; //System.out.println("from dataset"); String key = Matrix.generateKey(chr1, chr2); Matrix m = matrices.get(key); if (m == null && reader != null) { try { // custom chromosome is handled as separate case //if (chromosomeHandler.isCustomAPAChromosome(chr1) || chromosomeHandler.isCustomAPAChromosome(chr2)) { // System.err.println("APA Index key is " + key); // m = Matrix.createCustomChromosomeMatrix(chr1, chr2, chromosomeHandler, matrices, reader); //} else if (chromosomeHandler.isCustomChromosome(chr1) || chromosomeHandler.isCustomChromosome(chr2)) { if (HiCGlobals.printVerboseComments) System.out.println("Custom Chromosome Index key is " + key); m = Matrix.createCustomChromosomeMatrix(chr1, chr2, chromosomeHandler, matrices, reader); } else if (HiCGlobals.isAssemblyMatCheck) { m = Matrix.createAssemblyChromosomeMatrix(chromosomeHandler, matrices, reader); } else { m = reader.readMatrix(key); } matrices.put(key, m); } catch (Exception e) { System.err.println("Error fetching matrix for: " + chr1.getName() + "-" + chr2.getName() + " in " + reader.getPath()); e.printStackTrace(); } } return m; } public void addDynamicResolution(int newRes) { int highRes = -1; for (int potentialRes : bpZoomResolutions) { if (potentialRes < newRes && potentialRes > highRes && newRes % potentialRes == 0) { highRes = potentialRes; } } if (highRes < 0) { System.err.println("No suitable higher resolution found"); return; } for (Matrix matrix : matrices.values()) { matrix.createDynamicResolutionMZD(new Pair<>(newRes, highRes), true); } dynamicZooms.add(new HiCZoom(HiC.Unit.BP, newRes)); } public ResourceLocator getSubcompartments() { ResourceLocator locator = null; String path = reader.getPath(); //Special case for combined maps: if (path == null) { return null; } if (path.contains("gm12878/in-situ/combined")) { path = path.substring(0, path.lastIndexOf('.')); if (path.lastIndexOf("_30") > -1) { path = path.substring(0, path.lastIndexOf("_30")); } String location = path + "_subcompartments.bed"; locator = new ResourceLocator(location); locator.setName("Subcompartments"); } return locator; } public ResourceLocator getSuperLoops() { ResourceLocator locator = null; String path = reader.getPath(); //Special case for combined maps: if (path == null) { return null; } if (path.contains("gm12878/in-situ/combined")) { path = path.substring(0, path.lastIndexOf('.')); if (path.lastIndexOf("_30") > -1) { path = path.substring(0, path.lastIndexOf("_30")); } String location = path + "_chrX_superloop_list.txt"; locator = new ResourceLocator(location); locator.setName("ChrX super loops"); } return locator; } public ResourceLocator getPeaks() { String path = reader.getPath(); //Special case for combined maps: if (path == null) { return null; } path = path.substring(0, path.lastIndexOf('.')); if (path.lastIndexOf("_30") > -1) { path = path.substring(0, path.lastIndexOf("_30")); } String location = path + "_peaks.txt"; if (FileUtils.resourceExists(location)) { return new ResourceLocator(location); } else { location = path + "_loops.txt"; if (FileUtils.resourceExists(location)) { return new ResourceLocator(location); } else { return null; } } } public ResourceLocator getBlocks() { String path = reader.getPath(); //Special case for combined maps: if (path == null) { return null; } path = path.substring(0, path.lastIndexOf('.')); if (path.lastIndexOf("_30") > -1) { path = path.substring(0, path.lastIndexOf("_30")); } String location = path + "_blocks.txt"; if (FileUtils.resourceExists(location)) { return new ResourceLocator(location); } else { location = path + "_domains.txt"; if (FileUtils.resourceExists(location)) { return new ResourceLocator(location); } else { return null; } } } public void setAttributes(Map map) { this.attributes = map; try { v9DepthBase = Integer.parseInt(attributes.get(Preprocessor.V9_DEPTH_BASE)); } catch (Exception e) { v9DepthBase = 0; } } public List getNormalizationTypes() { return normalizationTypes; } public void setNormalizationTypes(List normalizationTypes) { this.normalizationTypes = normalizationTypes; } public void addNormalizationType(NormalizationType type) { if (!normalizationTypes.contains(type)) normalizationTypes.add(type); } public int getNumberZooms(HiC.Unit unit) { return unit == HiC.Unit.BP ? bpZooms.size() + dynamicZooms.size() : fragZooms.size(); } // todo deprecate public HiCZoom getZoom(HiC.Unit unit, int index) { return unit == HiC.Unit.BP ? bpZooms.get(index) : fragZooms.get(index); } public HiCZoom getZoomForBPResolution(Integer resolution) { for (HiCZoom zoom : bpZooms) { if (zoom.getBinSize() == resolution) { return zoom; } } for (HiCZoom zoom : dynamicZooms) { if (zoom.getBinSize() == resolution) { return zoom; } } return null; } public ExpectedValueFunction getExpectedValues(HiCZoom zoom, NormalizationType type) { if (expectedValueFunctionMap == null || zoom == null || type == null) return null; String key = ExpectedValueFunctionImpl.getKey(zoom, type); return expectedValueFunctionMap.get(key); } public ExpectedValueFunction getExpectedValuesOrExit(HiCZoom zoom, NormalizationType type, Chromosome chromosome, boolean isIntra) { ExpectedValueFunction df = getExpectedValues(zoom, type); if (isIntra && df == null) { System.err.println("O/E data not available at " + chromosome.getName() + " " + zoom + " " + type); System.exit(14); } return df; } public Map getExpectedValueFunctionMap() { return expectedValueFunctionMap; } public void setExpectedValueFunctionMap(Map df) { this.expectedValueFunctionMap = df; } public ChromosomeHandler getChromosomeHandler() { return chromosomeHandler; } public void setChromosomeHandler(ChromosomeHandler chromosomeHandler) { this.chromosomeHandler = chromosomeHandler; } public int getVersion() { return reader.getVersion(); } public String getGenomeId() { return genomeId; } public void setGenomeId(String genomeId) { if (genomeId.equals("GRCm38")) genomeId = "mm10"; this.genomeId = genomeId; } public String getRestrictionEnzyme() { return restrictionEnzyme; } void setRestrictionEnzyme(int nSites) { restrictionEnzyme = findRestrictionEnzyme(nSites); } private String getSoftware() { if (attributes != null) return attributes.get(Preprocessor.SOFTWARE); else return null; } public String getHiCFileScalingFactor() { if (attributes != null) return attributes.get(Preprocessor.HIC_FILE_SCALING); else return null; } public String getStatistics() { String stats = null; if (attributes != null) stats = attributes.get(Preprocessor.STATISTICS); if (stats != null && (!stats.contains("")) && HiCGlobals.guiIsCurrentlyActive) { return convertStats(stats); } return stats; } private String convertStats(String oldStats) { HashMap statsMap = new HashMap<>(); StringTokenizer lines = new StringTokenizer(oldStats, "\n"); DecimalFormat decimalFormat = new DecimalFormat("0.00%"); NumberFormat numberFormat = NumberFormat.getNumberInstance(Locale.US); while (lines.hasMoreTokens()) { String current = lines.nextToken(); StringTokenizer colon = new StringTokenizer(current, ":"); if (colon.countTokens() != 2) { System.err.println("Incorrect form in original statistics attribute. Offending line:"); System.err.println(current); } else { // Appears to be correct format, convert files as appropriate String label = colon.nextToken(); String value = colon.nextToken(); statsMap.put(label, value); } } String newStats = ""; int sequenced = -1; int unique = -1; newStats += "
\n" + " "; newStats += ""; if (statsMap.containsKey("Experiment description")) { String value = statsMap.get("Experiment description").trim(); if (!value.isEmpty()) newStats += ""; } if (getSoftware() != null) { newStats += ""; } if (getHiCFileScalingFactor() != null) { newStats += ""; } newStats += "\n" + " "; newStats += ""; newStats += ""; /*
Experiment Information
Experiment #: "; String filename = reader.getPath(); boolean mapq30 = filename.lastIndexOf("_30") > 0; String[] parts = filename.split("/"); newStats += parts[parts.length - 2]; newStats += "
Restriction Enzyme:"; newStats += getRestrictionEnzyme() + "
Experiment Description:" + value + "
Software: " + getSoftware() + "
File Scaling: " + getHiCFileScalingFactor() + "
Alignment Information
Reference Genome:" + genomeId + "
MAPQ Threshold: "; if (mapq30) newStats += "30"; else newStats += "1"; newStats += "
Experiment Information
Experiment #: HIC034
Cell Type: GM12878
Protocol: dilution
Restriction Enzyme:HindIII
Crosslinking: 1% FA, 10min, RT
Biotin Base: bio-dCTP
Ligation Volume: 8ml
Alignment Information
Reference Genome:hg19
MAPQ Threshold: 1
Sequencing Information
Instrument: HiSeq 2000
Read 1 Length: 101
Read 2 Length: 101
*/ newStats += ""; if (statsMap.containsKey("Total") || statsMap.containsKey("Sequenced Read Pairs")) { newStats += ""; newStats += ""; String value = ""; try { if (statsMap.containsKey("Total")) value = statsMap.get("Total").trim(); else value = statsMap.get("Sequenced Read Pairs").trim(); sequenced = numberFormat.parse(value).intValue(); } catch (ParseException error) { sequenced = -1; } newStats += ""; // TODO: add in Total Bases } if (statsMap.containsKey(" Regular") || statsMap.containsKey(" Normal Paired")) { newStats += ""; newStats += ""; newStats += ""; newStats += ""; } if (statsMap.containsKey(" Normal chimeric") || statsMap.containsKey(" Chimeric Paired")) { newStats += ""; newStats += ""; } if (statsMap.containsKey(" Abnormal chimeric") || statsMap.containsKey(" Chimeric Ambiguous")) { newStats += ""; newStats += ""; } if (statsMap.containsKey(" Unmapped")) { newStats += ""; newStats += ""; } newStats += ""; newStats += ""; if (statsMap.containsKey(" Total alignable reads") || statsMap.containsKey("Alignable (Normal+Chimeric Paired)")) { newStats += ""; newStats += ""; } if (statsMap.containsKey("Total reads after duplication removal")) { newStats += ""; String value = statsMap.get("Total reads after duplication removal"); try { unique = numberFormat.parse(value.trim()).intValue(); } catch (ParseException error) { unique = -1; } newStats += ""; } else if (statsMap.containsKey("Unique Reads")) { newStats += ""; String value = statsMap.get("Unique Reads"); newStats += ""; if (value.indexOf('(') >= 0) { value = value.substring(0, value.indexOf('(')); } try { unique = numberFormat.parse(value.trim()).intValue(); } catch (ParseException error) { unique = -1; } } if (statsMap.containsKey("Duplicate reads")) { newStats += ""; String value = statsMap.get("Duplicate reads"); newStats += ""; } else if (statsMap.containsKey("PCR Duplicates")) { newStats += ""; newStats += ""; } if (statsMap.containsKey("Optical duplicates")) { newStats += ""; String value = statsMap.get("Optical duplicates"); int num; try { num = numberFormat.parse(value.trim()).intValue(); } catch (ParseException error) { num = -1; } if (sequenced != -1 && num != -1) { newStats += " (" + decimalFormat.format(num / (float) sequenced) + ")"; } newStats += ""; } else if (statsMap.containsKey("Optical Duplicates")) { newStats += ""; newStats += ""; } if (statsMap.containsKey("Library complexity (new)") || statsMap.containsKey("Library Complexity Estimate")) { newStats += ""; newStats += ""; } newStats += ""; newStats += ""; if (statsMap.containsKey("Intra-fragment Reads")) { newStats += ""; String value = statsMap.get("Intra-fragment Reads"); if (value.indexOf('(') > 0) value = value.substring(0, value.indexOf('(')); newStats += ""; } if (statsMap.containsKey("Non-uniquely Aligning Reads")) { newStats += ""; String value = statsMap.get("Non-uniquely Aligning Reads"); newStats += ""; } else if (statsMap.containsKey("Below MAPQ Threshold")) { newStats += ""; newStats += ""; } if (statsMap.containsKey("Total reads in current file")) { newStats += ""; String value = statsMap.get("Total reads in current file"); newStats += ""; // Error checking if (statsMap.containsKey("HiC Contacts")) { int num2; try { num2 = numberFormat.parse(statsMap.get("HiC Contacts").trim()).intValue(); } catch (ParseException error) { num2 = -1; } if (num != num2) { System.err.println("Check files -- \"HiC Contacts\" should be the same as \"Total reads in current file\""); } } } else if (statsMap.containsKey("Hi-C Contacts")) { newStats += ""; newStats += ""; } if (statsMap.containsKey("Ligations") || statsMap.containsKey(" Ligation Motif Present")) { newStats += ""; String value = statsMap.containsKey("Ligations") ? statsMap.get("Ligations") : statsMap.get(" Ligation Motif Present"); newStats += ""; } if (statsMap.containsKey("Five prime") && statsMap.containsKey("Three prime")) { newStats += ""; String value = statsMap.get("Five prime"); value = value.substring(value.indexOf('(') + 1); value = value.substring(0, value.indexOf('%')); int num1 = Math.round(Float.parseFloat(value)); value = statsMap.get("Three prime"); value = value.substring(value.indexOf('(') + 1); value = value.substring(0, value.indexOf('%')); int num2 = Math.round(Float.parseFloat(value)); newStats += ""; } else if (statsMap.containsKey(" 3' Bias (Long Range)")) { newStats += ""; newStats += ""; } if (statsMap.containsKey("Inner") && statsMap.containsKey("Outer") && statsMap.containsKey("Left") && statsMap.containsKey("Right")) { newStats += ""; String value = statsMap.get("Left"); value = value.substring(value.indexOf('(') + 1); value = value.substring(0, value.indexOf('%')); int num1 = Math.round(Float.parseFloat(value)); value = statsMap.get("Inner"); value = value.substring(value.indexOf('(') + 1); value = value.substring(0, value.indexOf('%')); int num2 = Math.round(Float.parseFloat(value)); value = statsMap.get("Outer"); value = value.substring(value.indexOf('(') + 1); value = value.substring(0, value.indexOf('%')); int num3 = Math.round(Float.parseFloat(value)); value = statsMap.get("Right"); value = value.substring(value.indexOf('(') + 1); value = value.substring(0, value.indexOf('%')); int num4 = Math.round(Float.parseFloat(value)); newStats += ""; } else if (statsMap.containsKey(" Pair Type %(L-I-O-R)")) { newStats += ""; newStats += ""; } newStats += ""; newStats += ""; if (statsMap.containsKey("Inter")) { newStats += ""; String value = statsMap.get("Inter"); newStats += ""; } else if (statsMap.containsKey("Inter-chromosomal")) { newStats += ""; newStats += ""; } if (statsMap.containsKey("Intra")) { newStats += ""; String value = statsMap.get("Intra"); newStats += ""; } else if (statsMap.containsKey("Intra-chromosomal")) { newStats += ""; newStats += ""; } if (statsMap.containsKey("Small")) { newStats += ""; String value = statsMap.get("Small"); newStats += ""; } else if (statsMap.containsKey("Short Range (<20Kb)")) { newStats += ""; newStats += ""; } if (statsMap.containsKey("Large")) { newStats += ""; String value = statsMap.get("Large"); newStats += ""; } else if (statsMap.containsKey("Long Range (>20Kb)")) { newStats += ""; newStats += ""; } // Error checking if (statsMap.containsKey("Unique Reads")) { int num; try { num = numberFormat.parse(statsMap.get("Unique Reads").trim()).intValue(); } catch (ParseException error) { num = -1; } if (num != unique) { System.err.println("Check files -- \"Unique Reads\" should be the same as \"Total reads after duplication removal\""); } } return newStats; } public String getGraphs() { if (attributes == null) return null; return attributes.get(Preprocessor.GRAPHS); } public List getBpZooms() { List zooms = new ArrayList<>(bpZooms); zooms.addAll(dynamicZooms); zooms.sort(Collections.reverseOrder()); return zooms; } public void setBpZooms(int[] bpBinSizes) { bpZoomResolutions = Ints.asList(bpBinSizes); bpZooms = new ArrayList<>(bpBinSizes.length); for (int bpBinSize : bpZoomResolutions) { bpZooms.add(new HiCZoom(HiC.Unit.BP, bpBinSize)); } dynamicZooms = new ArrayList<>(); } public List getFragZooms() { return fragZooms; } public void setFragZooms(int[] fragBinSizes) { // Don't show fragments in restricted mode // if (MainWindow.isRestricted()) return; this.fragZooms = new ArrayList<>(fragBinSizes.length); for (int fragBinSize : fragBinSizes) { fragZooms.add(new HiCZoom(HiC.Unit.FRAG, fragBinSize)); } } public boolean hasFrags() { return fragZooms != null && fragZooms.size() > 0; } public Map getFragmentCounts() { return fragmentCounts; } public void setFragmentCounts(Map map) { fragmentCounts = map; } /** * Return the "next" zoom level, relative to the current one, in the direction indicated * * @param zoom - current zoom level * @param useIncreasingOrder -- direction, true == increasing resolution, false decreasing * @return Next zoom level */ public HiCZoom getNextZoom(HiCZoom zoom, boolean useIncreasingOrder) { final HiC.Unit currentUnit = zoom.getUnit(); List zoomList = currentUnit == HiC.Unit.BP ? getBpZooms() : fragZooms; // TODO MSS - is there a reason not to just rewrite this using indexOf? cleaner? if (useIncreasingOrder) { for (int i = 0; i < zoomList.size() - 1; i++) { if (zoom.equals(zoomList.get(i))) return zoomList.get(i + 1); } return zoomList.get(zoomList.size() - 1); } else { // Decreasing for (int i = zoomList.size() - 1; i > 0; i--) { if (zoom.equals(zoomList.get(i))) { return zoomList.get(i - 1); } } return zoomList.get(0); } } public double[] getEigenvector(Chromosome chr, HiCZoom zoom, int number, NormalizationType type) { String key = chr.getName() + "_" + zoom.getKey() + "_" + number + "_" + type; if (!eigenvectorCache.containsKey(key)) { double[] eigenvector; //eigenvector = reader.readEigenvector(chr.getName(), zoom, number, type.toString()); ExpectedValueFunction df = getExpectedValues(zoom, type); Matrix m = getMatrix(chr, chr); MatrixZoomData mzd = m.getZoomData(zoom); if (df != null && mzd.getPearsons(df) != null && zoom.getBinSize() >= HiCGlobals.MAX_EIGENVECTOR_ZOOM) { eigenvector = mzd.computeEigenvector(df, number); } else { eigenvector = new double[0]; } eigenvectorCache.put(key, eigenvector); } return eigenvectorCache.get(key); } public NormalizationVector getNormalizationVector(int chrIdx, HiCZoom zoom, NormalizationType type) { String key = NormalizationVector.getKey(type, chrIdx, zoom.getUnit().toString(), zoom.getBinSize()); if (normalizationsVectorsOnlySavedInRAMCache.containsKey(key)) { return normalizationsVectorsOnlySavedInRAMCache.get(key); } if (type.equals(NormalizationHandler.NONE)) { return null; } else if (!normalizationVectorCache.containsKey(key)) { try { NormalizationVector nv = reader.readNormalizationVector(type, chrIdx, zoom.getUnit(), zoom.getBinSize()); normalizationVectorCache.put(key, nv); } catch (IOException e) { normalizationVectorCache.put(key, null); } } return normalizationVectorCache.get(key); } public NormalizationVector getPartNormalizationVector(int chrIdx, HiCZoom zoom, NormalizationType type, int bound1, int bound2) { String key = NormalizationVector.getKey(type, chrIdx, zoom.getUnit().toString(), zoom.getBinSize()); NormalizationVector nv; if (type.equals(NormalizationHandler.NONE)) { return null; } else { try { nv = reader.readNormalizationVectorPart(type, chrIdx, zoom.getUnit(), zoom.getBinSize(), bound1, bound2); } catch (IOException e) { return null; } } return nv; } public void addNormalizationVectorDirectlyToRAM(NormalizationVector normalizationVector) { normalizationsVectorsOnlySavedInRAMCache.put(normalizationVector.getKey(), normalizationVector); } private String findRestrictionEnzyme(int sites) { if (genomeId == null) return null; if (Private.assessGenomeForRE(genomeId)) { if (sites == 13393) return "DpnII/MboI"; } else if (Private.assessGenomeForRE3(genomeId)) { if (sites == 465673) return "DpnII/MboI"; } else if (Private.assessGenomeForRE4(genomeId)) { if (sites == 801622) return "DpnII/MboI"; } else if (genomeId.equals("canFam3")) { if (sites == 345776) return "DpnII/MboI"; } else if (genomeId.equals("dMel")) { // arm_2L if (sites == 60924) return "DpnII/MboI"; if (sites == 6742) return "HindIII"; return Private.reForDMEL(sites); } else if (genomeId.equals("hg18")) { if (sites == 575605) return "DpnII/MboI"; return Private.reForHG18(sites); } else if (genomeId.equals("hg19") || Private.assessGenomeForRE2(genomeId)) { if (sites == 576357) return "DpnII/MboI"; if (sites == 64395) return "HindIII"; if (sites == 59852) return "NcoI"; return Private.reForHG19(sites); } else if (genomeId.equals("mm9")) { // chr1 if (sites == 479082) return "DpnII/MboI"; if (sites == 62882) return "HindIII"; if (sites == 60953) return "NcoI"; return Private.reForMM9(sites); } else if (genomeId.equals("mm10")) { if (sites == 480062) return "DpnII/MboI"; if (sites == 63013) return "HindIII"; } else if (genomeId.equals("Pf3D7")) { if (sites == 13) return "DpnII/MboI"; } else if (genomeId.equals("sCerS288c")) { if (sites == 65) return "HindIII"; // chrI } return null; } public void setAttributes(String key, String value) { if (this.attributes == null) { attributes = new HashMap<>(); } attributes.put(key, value); } public List getCheckBoxes(List actionListeners) { return reader.getCheckBoxes(actionListeners); } public List getAllPossibleResolutions() { List resolutions = new ArrayList<>(); resolutions.addAll(bpZooms); resolutions.addAll(dynamicZooms); resolutions.addAll(fragZooms); return resolutions; } public NormalizationHandler getNormalizationHandler() { return normalizationHandler; } public int getDepthBase() { return v9DepthBase; } public void clearCache(boolean onlyClearInter) { for (Matrix matrix : matrices.values()) { for (HiCZoom zoom : getBpZooms()) { try { matrix.getZoomData(zoom).clearCache(onlyClearInter); } catch (Exception e) { if (HiCGlobals.printVerboseComments) { System.err.println("Clearing err: " + e.getLocalizedMessage()); } } } } } public void clearCache(boolean onlyClearInter, HiCZoom zoom) { for (Matrix matrix : matrices.values()) { try { matrix.getZoomData(zoom).clearCache(onlyClearInter); } catch (Exception e) { if (HiCGlobals.printVerboseComments) { System.err.println("Clearing z_err: " + e.getLocalizedMessage()); } } } } } ================================================ FILE: src/juicebox/data/DatasetReader.java ================================================ /* * The MIT License (MIT) * * Copyright (c) 2011-2022 Broad Institute, Aiden Lab, Rice University, Baylor College of Medicine * * Permission is hereby granted, free of charge, to any person obtaining a copy * of this software and associated documentation files (the "Software"), to deal * in the Software without restriction, including without limitation the rights * to use, copy, modify, merge, publish, distribute, sublicense, and/or sell * copies of the Software, and to permit persons to whom the Software is * furnished to do so, subject to the following conditions: * * The above copyright notice and this permission notice shall be included in * all copies or substantial portions of the Software. * * THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR * IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, * FITNESS FOR A PARTICULAR PURPOSE AND NON-INFRINGEMENT. IN NO EVENT SHALL THE * AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER * LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, * OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN * THE SOFTWARE. */ package juicebox.data; import juicebox.HiC; import juicebox.data.basics.ListOfDoubleArrays; import juicebox.windowui.HiCZoom; import juicebox.windowui.NormalizationType; import javax.swing.*; import java.awt.event.ActionListener; import java.io.IOException; import java.util.List; /** * @author jrobinso * Date: 10/17/12 * Time: 8:38 AM */ public interface DatasetReader { boolean isActive(); void setActive(boolean status); int getVersion(); Dataset read() throws IOException; Matrix readMatrix(String key) throws IOException; Block readNormalizedBlock(int blockNumber, MatrixZoomData zd, NormalizationType no) throws IOException; /** * Return the list of occupied block numbers for the given matrix. * * @param matrixZoomData * @return */ List getBlockNumbers(MatrixZoomData matrixZoomData); Integer getBlockSize(MatrixZoomData matrixZoomData, int blockNum); double[] readEigenvector(String chrName, HiCZoom zoom, int number, String type); NormalizationVector readNormalizationVector(NormalizationType type, int chrIdx, HiC.Unit unit, int binSize) throws IOException; NormalizationVector readNormalizationVectorPart(NormalizationType type, int chrIdx, HiC.Unit unit, int binSize, int bound1, int bound2) throws IOException; ListOfDoubleArrays readExpectedVectorPart(long position, long nVals) throws IOException; String getPath(); List getCheckBoxes(List actionListeners); NormalizationVector getNormalizationVector(int chr1Idx, HiCZoom zoom, NormalizationType normalizationType); int getDepthBase(); } ================================================ FILE: src/juicebox/data/DatasetReaderFactory.java ================================================ /* * The MIT License (MIT) * * Copyright (c) 2011-2020 Broad Institute, Aiden Lab, Rice University, Baylor College of Medicine * * Permission is hereby granted, free of charge, to any person obtaining a copy * of this software and associated documentation files (the "Software"), to deal * in the Software without restriction, including without limitation the rights * to use, copy, modify, merge, publish, distribute, sublicense, and/or sell * copies of the Software, and to permit persons to whom the Software is * furnished to do so, subject to the following conditions: * * The above copyright notice and this permission notice shall be included in * all copies or substantial portions of the Software. * * THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR * IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, * FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE * AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER * LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, * OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN * THE SOFTWARE. */ package juicebox.data; import htsjdk.samtools.seekablestream.SeekableHTTPStream; import htsjdk.samtools.seekablestream.SeekableStream; import htsjdk.tribble.util.LittleEndianInputStream; import juicebox.HiCGlobals; import juicebox.gui.SuperAdapter; import org.broad.igv.ui.util.MessageUtils; import java.io.BufferedInputStream; import java.io.FileInputStream; import java.io.IOException; import java.net.MalformedURLException; import java.net.URL; import java.util.ArrayList; import java.util.List; /** * @author jrobinso * Date: 12/22/12 * Time: 1:06 PM */ public class DatasetReaderFactory { public static DatasetReader getReader(List fileList) throws IOException { if (fileList.size() == 1) { String file = fileList.get(0); return getReaderForFile(file); } else { List readers = new ArrayList<>(fileList.size()); for (String f : fileList) { DatasetReaderV2 r = getReaderForFile(f); if (r != null) { readers.add(r); } } return new CombinedDatasetReader(readers); } } private static DatasetReaderV2 getReaderForFile(String file) throws IOException { String magicString = getMagicString(file); if(magicString != null) { if (magicString.equals("HIC")) { return new DatasetReaderV2(file); } else { System.err.println("This version is deprecated and is no longer supported."); //reader = new DatasetReaderV1(file); // file not actually read, usually canceled the read of password-protected file //if (reader.getVersion() == -1) } } return null; } static String getMagicString(String path) throws IOException { SeekableStream stream = null; LittleEndianInputStream dis = null; try { stream = new SeekableHTTPStream(new URL(path)); // IGVSeekableStreamFactory.getStreamFor(path); dis = new LittleEndianInputStream(new BufferedInputStream(stream)); } catch (MalformedURLException e) { try { dis = new LittleEndianInputStream(new FileInputStream(path)); } catch (Exception e2) { if (HiCGlobals.guiIsCurrentlyActive) { SuperAdapter.showMessageDialog("File could not be found\n(" + path + ")"); } else { MessageUtils.showErrorMessage("File could not be found\n(" + path + ")", e2); } } } finally { if (stream != null) stream.close(); } if (dis != null) { return dis.readString(); } return null; } } ================================================ FILE: src/juicebox/data/DatasetReaderV2.java ================================================ /* * The MIT License (MIT) * * Copyright (c) 2011-2022 Broad Institute, Aiden Lab, Rice University, Baylor College of Medicine * * Permission is hereby granted, free of charge, to any person obtaining a copy * of this software and associated documentation files (the "Software"), to deal * in the Software without restriction, including without limitation the rights * to use, copy, modify, merge, publish, distribute, sublicense, and/or sell * copies of the Software, and to permit persons to whom the Software is * furnished to do so, subject to the following conditions: * * The above copyright notice and this permission notice shall be included in * all copies or substantial portions of the Software. * * THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR * IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, * FITNESS FOR A PARTICULAR PURPOSE AND NON-INFRINGEMENT. IN NO EVENT SHALL THE * AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER * LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, * OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN * THE SOFTWARE. */ package juicebox.data; import htsjdk.samtools.seekablestream.SeekableStream; import htsjdk.tribble.util.LittleEndianInputStream; import juicebox.HiC; import juicebox.HiCGlobals; import juicebox.data.basics.Chromosome; import juicebox.data.basics.ListOfDoubleArrays; import juicebox.tools.utils.original.IndexEntry; import juicebox.tools.utils.original.LargeIndexEntry; import juicebox.windowui.HiCZoom; import juicebox.windowui.NormalizationHandler; import juicebox.windowui.NormalizationType; import org.broad.igv.Globals; import org.broad.igv.exceptions.HttpResponseException; import org.broad.igv.util.CompressionUtils; import org.broad.igv.util.Pair; import org.broad.igv.util.ParsingUtils; import org.broad.igv.util.stream.IGVSeekableStreamFactory; import javax.swing.*; import java.awt.event.ActionEvent; import java.awt.event.ActionListener; import java.io.*; import java.util.*; import java.util.concurrent.atomic.AtomicBoolean; /** * @author jrobinso * @since Aug 17, 2010 */ public class DatasetReaderV2 extends AbstractDatasetReader { private static final int maxLengthEntryName = 100; private static final int MAX_BYTE_READ_SIZE = Integer.MAX_VALUE - 10; /** * Cache of chromosome name -> array of restriction sites */ private final Map fragmentSitesCache = new HashMap<>(); private final Map masterIndex = new HashMap<>(); private Map normVectorIndex; private final Dataset dataset; private int version = -1; private Map fragmentSitesIndex; private final Map blockIndexMap = new HashMap<>(); private long masterIndexPos; private long normVectorFilePosition; private long nviHeaderPosition; private boolean activeStatus = true; public static double[] globalTimeDiffThings = new double[5]; private final IGVSeekableStreamFactory streamFactory = IGVSeekableStreamFactory.getInstance(); private final CompressionUtils compressionUtils = new CompressionUtils(); public DatasetReaderV2(String path) throws IOException { super(path); dataset = new Dataset(this); } @Override public Dataset read() throws IOException { try { SeekableStream stream = getValidStream(); long position = 0L; // Read the header LittleEndianInputStream dis = new LittleEndianInputStream(new BufferedInputStream(stream, HiCGlobals.bufferSize)); String magicString = dis.readString(); position += magicString.length() + 1; if (!magicString.equals("HIC")) { throw new IOException("Magic string is not HIC, this does not appear to be a hic file."); } version = dis.readInt(); position += 4; if (HiCGlobals.guiIsCurrentlyActive) { System.out.println("HiC file version: " + version); } //System.out.println("HiC file version: " + version); masterIndexPos = dis.readLong(); position += 8; // will set genomeId below String genomeId = dis.readString(); position += genomeId.length() + 1; if (version > 8) { // read NVI todo nviHeaderPosition = position; // todo use long nvi = dis.readLong(); long nviSize = dis.readLong(); position += 16; } Map attributes = new HashMap<>(); // Attributes (key-value pairs) if (version > 4) { int nAttributes = dis.readInt(); position += 4; for (int i = 0; i < nAttributes; i++) { String key = dis.readString(); position += key.length() + 1; String value = dis.readString(); position += value.length() + 1; attributes.put(key, value); } } dataset.setAttributes(attributes); if (dataset.getHiCFileScalingFactor() != null) { HiCGlobals.hicMapScale = Double.parseDouble(dataset.getHiCFileScalingFactor()); } // Read chromosome dictionary int nchrs = dis.readInt(); position += 4; List chromosomes = new ArrayList<>(nchrs); for (int i = 0; i < nchrs; i++) { String name = dis.readString(); position += name.length() + 1; long size; if (version > 8) { size = dis.readLong(); position += 8; } else { size = dis.readInt(); position += 4; } chromosomes.add(new Chromosome(i, name, size)); } boolean createWholeChr = false; ChromosomeHandler chromosomeHandler = new ChromosomeHandler(chromosomes, genomeId, createWholeChr, true); dataset.setChromosomeHandler(chromosomeHandler); // guess genomeID from chromosomes String genomeId1 = chromosomeHandler.getGenomeID(); // if cannot find matching genomeID, set based on file dataset.setGenomeId(genomeId1); int nBpResolutions = dis.readInt(); position += 4; int[] bpBinSizes = new int[nBpResolutions]; for (int i = 0; i < nBpResolutions; i++) { bpBinSizes[i] = dis.readInt(); position += 4; } dataset.setBpZooms(bpBinSizes); int nFragResolutions = dis.readInt(); position += 4; int[] fragBinSizes = new int[nFragResolutions]; for (int i = 0; i < nFragResolutions; i++) { fragBinSizes[i] = dis.readInt(); position += 4; } dataset.setFragZooms(fragBinSizes); // Now we need to skip through stream reading # fragments, stream on buffer is not needed so null it to // prevent accidental use dis = null; if (nFragResolutions > 0) { stream.seek(position); fragmentSitesIndex = new HashMap<>(); Map map = new HashMap<>(); String firstChrName = null; for (int i = 0; i < nchrs; i++) { String chr = chromosomes.get(i).getName(); if (!chr.equals(Globals.CHR_ALL)) { firstChrName = chr; } byte[] buffer = new byte[4]; stream.readFully(buffer); int nSites = (new LittleEndianInputStream(new ByteArrayInputStream(buffer))).readInt(); position += 4; FragIndexEntry entry = new FragIndexEntry(position, nSites); fragmentSitesIndex.put(chr, entry); map.put(chr, nSites); stream.skip(nSites * 4); position += nSites * 4; } if (firstChrName != null) { dataset.setRestrictionEnzyme(map.get(firstChrName)); } dataset.setFragmentCounts(map); } readFooter(masterIndexPos); stream.close(); } catch (IOException e) { System.err.println("Error reading dataset" + e.getLocalizedMessage()); throw e; } return dataset; } private SeekableStream getValidStream() throws IOException { SeekableStream stream; do { stream = streamFactory.getStreamFor(path); } while (stream == null); return stream; } @Override public List getCheckBoxes(List actionListeners) { String truncatedName = HiCFileTools.getTruncatedText(getPath(), maxLengthEntryName); final JCheckBox checkBox = new JCheckBox(truncatedName); checkBox.setSelected(isActive()); checkBox.setToolTipText(getPath()); actionListeners.add(new ActionListener() { @Override public void actionPerformed(ActionEvent e) { setActive(checkBox.isSelected()); } }); List checkBoxList = new ArrayList<>(); checkBoxList.add(checkBox); return checkBoxList; } @Override public NormalizationVector getNormalizationVector(int chr1Idx, HiCZoom zoom, NormalizationType normalizationType) { return dataset.getNormalizationVector(chr1Idx, zoom, normalizationType); } @Override public int getDepthBase() { return dataset.getDepthBase(); } private Pair readMatrixZoomData(Chromosome chr1, Chromosome chr2, int[] chr1Sites, int[] chr2Sites, long filePointer) throws IOException { SeekableStream stream = getValidStream(); stream.seek(filePointer); LittleEndianInputStream dis = new LittleEndianInputStream(new BufferedInputStream(stream, HiCGlobals.bufferSize)); String hicUnitStr = dis.readString(); HiC.Unit unit = HiC.valueOfUnit(hicUnitStr); dis.readInt(); // Old "zoom" index -- not used // Stats. Not used yet, but we need to read them anyway double sumCounts = dis.readFloat(); float occupiedCellCount = dis.readFloat(); float stdDev = dis.readFloat(); float percent95 = dis.readFloat(); int binSize = dis.readInt(); HiCZoom zoom = new HiCZoom(unit, binSize); // TODO: Default binSize value for "ALL" is 6197... // (actually (genomeLength/1000)/500; depending on bug fix, could be 6191 for hg19); // We need to make sure our maps hold a valid binSize value as default. int blockBinCount = dis.readInt(); int blockColumnCount = dis.readInt(); MatrixZoomData zd = new MatrixZoomData(chr1, chr2, zoom, blockBinCount, blockColumnCount, chr1Sites, chr2Sites, this); int nBlocks = dis.readInt(); long currentFilePointer = filePointer + (9 * 4) + hicUnitStr.getBytes().length + 1; // i think 1 byte for 0 terminated string? if (binSize < 50 && HiCGlobals.allowDynamicBlockIndex) { int maxPossibleBlockNumber = blockColumnCount * blockColumnCount - 1; DynamicBlockIndex blockIndex = new DynamicBlockIndex(getValidStream(), nBlocks, maxPossibleBlockNumber, currentFilePointer); synchronized (blockIndexMap) { blockIndexMap.put(zd.getKey(), blockIndex); } } else { BlockIndex blockIndex = new BlockIndex(nBlocks); blockIndex.populateBlocks(dis); synchronized (blockIndexMap) { blockIndexMap.put(zd.getKey(), blockIndex); } } currentFilePointer += (nBlocks * 16L); long nBins1 = chr1.getLength() / binSize; long nBins2 = chr2.getLength() / binSize; double avgCount = (sumCounts / nBins1) / nBins2; // <= trying to avoid overflows zd.setAverageCount(avgCount); zd.setSumCount(sumCounts); stream.close(); return new Pair<>(zd, currentFilePointer); } private String checkGraphs(String graphs) { boolean reset = false; if (graphs == null) reset = true; else { Scanner scanner = new Scanner(graphs); try { while (!scanner.next().equals("[")) ; for (int idx = 0; idx < 2000; idx++) { scanner.nextLong(); } while (!scanner.next().equals("[")) ; for (int idx = 0; idx < 201; idx++) { scanner.nextInt(); scanner.nextInt(); scanner.nextInt(); } while (!scanner.next().equals("[")) ; for (int idx = 0; idx < 100; idx++) { scanner.nextInt(); scanner.nextInt(); scanner.nextInt(); scanner.nextInt(); } } catch (NoSuchElementException exception) { reset = true; } } /* if (reset) { try { graphs = readGraphs(null); } catch (IOException e) { graphs = null; } }*/ return graphs; } private String readGraphs(String graphFileName) throws IOException { String graphs; try (BufferedReader reader = ParsingUtils.openBufferedReader(graphFileName)) { if (reader == null) return null; StringBuilder builder = new StringBuilder(); String nextLine; while ((nextLine = reader.readLine()) != null) { builder.append(nextLine); builder.append("\n"); } graphs = builder.toString(); } catch (IOException e) { System.err.println("Error while reading graphs file: " + e); graphs = null; } return graphs; } @Override public boolean isActive() { return activeStatus; } @Override public void setActive(boolean status) { activeStatus = status; } @Override public int getVersion() { return version; } public long getNviHeaderPosition() { return nviHeaderPosition; } private void readFooter(long position) throws IOException { SeekableStream stream = getValidStream(); stream.seek(position); long currentPosition = position; //Get the size in bytes of the v5 footer, that is the footer up to normalization and normalized expected values byte[] buffer; long nBytes; LittleEndianInputStream dis; if (version > 8) { buffer = new byte[8]; stream.read(buffer); dis = new LittleEndianInputStream(new ByteArrayInputStream(buffer)); nBytes = dis.readLong(); currentPosition += 8; normVectorFilePosition = masterIndexPos + nBytes + 8; // 8 bytes for the buffer size } else { buffer = new byte[4]; stream.read(buffer); dis = new LittleEndianInputStream(new ByteArrayInputStream(buffer)); nBytes = dis.readInt(); currentPosition += 4; normVectorFilePosition = masterIndexPos + nBytes + 4; // 4 bytes for the buffer size } //List disList = new ArrayList<>(); //long nBytesCounter = nBytes; //while (nBytesCounter > (Integer.MAX_VALUE-10)) { // buffer = new byte[(Integer.MAX_VALUE - 10)]; // stream.read(buffer); // disList.add(new ByteArrayInputStream(buffer)); // nBytesCounter = nBytesCounter - (Integer.MAX_VALUE - 10); //} //buffer = new byte[(int) nBytesCounter]; //stream.read(buffer); //disList.add(new ByteArrayInputStream(buffer)); //dis = new LittleEndianInputStream(new SequenceInputStream(Collections.enumeration(disList))); dis = new LittleEndianInputStream(new BufferedInputStream(stream, HiCGlobals.bufferSize)); int nEntries = dis.readInt(); currentPosition += 4; //System.err.println(nEntries); for (int i = 0; i < nEntries; i++) { String key = dis.readString(); currentPosition += (key.length() + 1); long filePosition = dis.readLong(); int sizeInBytes = dis.readInt(); currentPosition += 12; synchronized (masterIndex) { masterIndex.put(key, new IndexEntry(filePosition, sizeInBytes)); } } Map expectedValuesMap = new LinkedHashMap<>(); // Expected values from non-normalized matrix int nExpectedValues = dis.readInt(); currentPosition += 4; //System.err.println(nExpectedValues); for (int i = 0; i < nExpectedValues; i++) { NormalizationType no = NormalizationHandler.NONE; String unitString = dis.readString(); currentPosition += (unitString.length() + 1); HiC.Unit unit = HiC.valueOfUnit(unitString); int binSize = dis.readInt(); currentPosition += 4; String key = unitString + "_" + binSize + "_" + no; long nValues; if (version > 8) { nValues = dis.readLong(); currentPosition += 8; } else { nValues = dis.readInt(); currentPosition += 4; } //System.err.println(nValues); if (binSize >= 500) { ListOfDoubleArrays values = new ListOfDoubleArrays(nValues); if (version > 8) { currentPosition += readVectorOfFloats(dis, nValues, values); } else { currentPosition += readVectorOfDoubles(dis, nValues, values); } //System.out.println(binSize + " " + stream.position()); int nNormalizationFactors = dis.readInt(); currentPosition += 4; NormFactorMapReader hmReader = new NormFactorMapReader(nNormalizationFactors, version, dis); currentPosition += hmReader.getOffset(); expectedValuesMap.put(key, new ExpectedValueFunctionImpl(no, unit, binSize, values, hmReader.getNormFactors())); } else { long skipPosition = currentPosition; long expectedVectorIndexPosition = currentPosition; if (version > 8) { skipPosition += (nValues * 4); } else { skipPosition += (nValues * 8); } stream.seek(skipPosition); dis = new LittleEndianInputStream(new BufferedInputStream(stream, HiCGlobals.bufferSize)); //long skipPosition = stream.position(); int nNormalizationFactors = dis.readInt(); currentPosition = skipPosition + 4; NormFactorMapReader hmReader = new NormFactorMapReader(nNormalizationFactors, version, dis); currentPosition += hmReader.getOffset(); expectedValuesMap.put(key, new ExpectedValueFunctionImpl(no, unit, binSize, nValues, expectedVectorIndexPosition, hmReader.getNormFactors(), this)); } } dataset.setExpectedValueFunctionMap(expectedValuesMap); // Normalized expected values (v6 and greater only) if (version >= 6) { //System.out.println(stream.position()); //System.out.println(normVectorFilePosition); stream.seek(normVectorFilePosition); currentPosition = normVectorFilePosition; dis = new LittleEndianInputStream(new BufferedInputStream(stream, HiCGlobals.bufferSize)); int nNormExpectedValueVectors; try { nNormExpectedValueVectors = dis.readInt(); currentPosition += 4; //System.out.println(nExpectedValues); } catch (EOFException | HttpResponseException e) { if (HiCGlobals.printVerboseComments) { System.out.println("No normalization vectors"); } return; } for (int i = 0; i < nNormExpectedValueVectors; i++) { String typeString = dis.readString(); currentPosition += (typeString.length() + 1); String unitString = dis.readString(); currentPosition += (unitString.length() + 1); HiC.Unit unit = HiC.valueOfUnit(unitString); int binSize = dis.readInt(); currentPosition += 4; String key = unitString + "_" + binSize + "_" + typeString; //System.out.println(key); long nValues; if (version > 8) { nValues = dis.readLong(); currentPosition += 8; //System.out.println(nValues); } else { nValues = dis.readInt(); currentPosition += 4; } if (binSize >= 500) { ListOfDoubleArrays values = new ListOfDoubleArrays(nValues); if (version > 8) { currentPosition += readVectorOfFloats(dis, nValues, values); } else { currentPosition += readVectorOfDoubles(dis, nValues, values); } int nNormalizationFactors = dis.readInt(); currentPosition += 4; NormFactorMapReader hmReader = new NormFactorMapReader(nNormalizationFactors, version, dis); currentPosition += hmReader.getOffset(); NormalizationType type = dataset.getNormalizationHandler().getNormTypeFromString(typeString); ExpectedValueFunction df = new ExpectedValueFunctionImpl(type, unit, binSize, values, hmReader.getNormFactors()); expectedValuesMap.put(key, df); } else { long skipPosition = currentPosition; long expectedVectorIndexPosition = currentPosition; if (version > 8) { skipPosition += (nValues * 4); } else { skipPosition += (nValues * 8); } stream.seek(skipPosition); dis = new LittleEndianInputStream(new BufferedInputStream(stream, HiCGlobals.bufferSize)); //long skipPosition = stream.position(); int nNormalizationFactors = dis.readInt(); if (HiCGlobals.guiIsCurrentlyActive && HiCGlobals.printVerboseComments) { System.out.println(currentPosition + " " + skipPosition + " " + nValues + " " + nNormalizationFactors); } currentPosition = skipPosition + 4; NormFactorMapReader hmReader = new NormFactorMapReader(nNormalizationFactors, version, dis); currentPosition += hmReader.getOffset(); NormalizationType type = dataset.getNormalizationHandler().getNormTypeFromString(typeString); ExpectedValueFunction df = new ExpectedValueFunctionImpl(type, unit, binSize, nValues, expectedVectorIndexPosition, hmReader.getNormFactors(), this); expectedValuesMap.put(key, df); } } // Normalization vectors (indexed) if (HiCGlobals.printVerboseComments) { System.out.println("NVI " + currentPosition); } int nNormVectors = dis.readInt(); normVectorIndex = new HashMap<>(nNormVectors * 2); for (int i = 0; i < nNormVectors; i++) { NormalizationType type = dataset.getNormalizationHandler().getNormTypeFromString(dis.readString()); int chrIdx = dis.readInt(); String unit = dis.readString(); int resolution = dis.readInt(); long filePosition = dis.readLong(); long sizeInBytes = version > 8 ? dis.readLong() : dis.readInt(); String key = NormalizationVector.getKey(type, chrIdx, unit, resolution); dataset.addNormalizationType(type); normVectorIndex.put(key, new LargeIndexEntry(filePosition, sizeInBytes)); } } stream.close(); } private long readVectorOfFloats(LittleEndianInputStream dis, long nValues, ListOfDoubleArrays values) throws IOException { for (long j = 0; j < nValues; j++) { values.set(j, dis.readFloat()); } return 4 * nValues; } private long readVectorOfDoubles(LittleEndianInputStream dis, long nValues, ListOfDoubleArrays values) throws IOException { for (long j = 0; j < nValues; j++) { values.set(j, dis.readDouble()); } return 8 * nValues; } private int[] readSites(long position, int nSites) throws IOException { IndexEntry idx = new IndexEntry(position, 4 + nSites * 4); byte[] buffer = seekAndFullyReadCompressedBytes(idx); LittleEndianInputStream les = new LittleEndianInputStream(new ByteArrayInputStream(buffer)); int[] sites = new int[nSites]; for (int s = 0; s < nSites; s++) { sites[s] = les.readInt(); } return sites; } @Override public Matrix readMatrix(String key) throws IOException { IndexEntry idx = masterIndex.get(key); if (idx == null) { return null; } byte[] buffer = seekAndFullyReadCompressedBytes(idx); LittleEndianInputStream dis = new LittleEndianInputStream(new ByteArrayInputStream(buffer)); int c1 = dis.readInt(); int c2 = dis.readInt(); // TODO weird bug // interesting bug with local files; difficult to reliably repeat, but just occurs on loading a region // indices that are read (c1, c2) seem to be excessively large / wrong // maybe some int overflow is occurring? // uncomment next 2 lines to help debug // System.err.println("read in mtrx indcs "+c1+ " " +c2+" key "+key+" idx "+idx.position+ // " sz "+idx.size+ " "+stream.getSource()+" "+stream.position()+" "+stream ); if (c1 < 0 || c1 > dataset.getChromosomeHandler().getChromosomeArray().length || c2 < 0 || c2 > dataset.getChromosomeHandler().getChromosomeArray().length) { System.err.println("WEIRD BUG HAPPENED AGAIN!!"); return null; } Chromosome chr1 = dataset.getChromosomeHandler().getChromosomeFromIndex(c1); Chromosome chr2 = dataset.getChromosomeHandler().getChromosomeFromIndex(c2); // # of resolution levels (bp and frags) int nResolutions = dis.readInt(); long currentFilePosition = idx.position + 12; List zdList = new ArrayList<>(); int[] chr1Sites = retrieveFragmentSitesFromCache(chr1); int[] chr2Sites = retrieveFragmentSitesFromCache(chr2); for (int i = 0; i < nResolutions; i++) { try { Pair result = readMatrixZoomData(chr1, chr2, chr1Sites, chr2Sites, currentFilePosition); zdList.add(result.getFirst()); currentFilePosition = result.getSecond(); } catch (Exception ee) { System.err.println("Weird error happened with trying to read MZD at currentFilePosition: " + currentFilePosition); ee.printStackTrace(); } } return new Matrix(c1, c2, zdList); } int getFragCount(Chromosome chromosome) { FragIndexEntry entry = null; if (fragmentSitesIndex != null) entry = fragmentSitesIndex.get(chromosome.getName()); if (entry != null) { return entry.nSites; } else return -1; } private synchronized int[] retrieveFragmentSitesFromCache(Chromosome chromosome) throws IOException { int[] chrSites = fragmentSitesCache.get(chromosome.getName()); if (chrSites == null && fragmentSitesIndex != null) { FragIndexEntry entry = fragmentSitesIndex.get(chromosome.getName()); if (entry != null && entry.nSites > 0) { chrSites = readSites(entry.position, entry.nSites); } fragmentSitesCache.put(chromosome.getName(), chrSites); } return chrSites; } private final AtomicBoolean useMainCompression = new AtomicBoolean(); @Override public List getBlockNumbers(MatrixZoomData zd) { BlockIndex blockIndex = blockIndexMap.get(zd.getKey()); return blockIndex == null ? null : blockIndex.getBlockNumbers(); } @Override public Integer getBlockSize(MatrixZoomData zd, int blockNum) { BlockIndex blockIndex = blockIndexMap.get(zd.getKey()); Integer blockSize; if (blockIndex != null) { blockSize = blockIndex.getBlockSize(blockNum); } else { blockSize = null; } return blockSize; } public Map getNormVectorIndex() { return normVectorIndex; } public long getNormFilePosition() { return version <= 5 ? (new File(this.path)).length() : normVectorFilePosition; } static class FragIndexEntry { final long position; final int nSites; FragIndexEntry(long position, int nSites) { this.position = position; this.nSites = nSites; } } @Override public NormalizationVector readNormalizationVector(NormalizationType type, int chrIdx, HiC.Unit unit, int binSize) throws IOException { String key = NormalizationVector.getKey(type, chrIdx, unit.toString(), binSize); if (normVectorIndex == null) return null; LargeIndexEntry idx = normVectorIndex.get(key); boolean useVCForVCSQRT = false; if (idx == null && type.equals(NormalizationHandler.VC_SQRT)) { key = NormalizationVector.getKey(NormalizationHandler.VC, chrIdx, unit.toString(), binSize); idx = normVectorIndex.get(key); useVCForVCSQRT = true; } if (idx == null) return null; List buffer = seekAndFullyReadLargeCompressedBytes(idx); List disList = new ArrayList<>(); for (int i = 0; i < buffer.size(); i++) { disList.add(new ByteArrayInputStream(buffer.get(i))); } LittleEndianInputStream dis = new LittleEndianInputStream(new SequenceInputStream(Collections.enumeration(disList))); long nValues; if (version > 8) { nValues = dis.readLong(); } else { nValues = dis.readInt(); } ListOfDoubleArrays values = new ListOfDoubleArrays(nValues); boolean allNaN = true; for (long i = 0; i < nValues; i++) { double val = version > 8 ? (double) dis.readFloat() : dis.readDouble(); if (!useVCForVCSQRT) { values.set(i, val); } else { values.set(i, Math.sqrt(val)); } if (!Double.isNaN(val)) { allNaN = false; } } if (allNaN) return null; else return new NormalizationVector(type, chrIdx, unit, binSize, values); } @Override public NormalizationVector readNormalizationVectorPart(NormalizationType type, int chrIdx, HiC.Unit unit, int binSize, int bound1, int bound2) throws IOException { String key = NormalizationVector.getKey(type, chrIdx, unit.toString(), binSize); if (normVectorIndex == null) return null; LargeIndexEntry idx = normVectorIndex.get(key); boolean useVCForVCSQRT = false; if (idx == null && type.equals(NormalizationHandler.VC_SQRT)) { key = NormalizationVector.getKey(NormalizationHandler.VC, chrIdx, unit.toString(), binSize); idx = normVectorIndex.get(key); useVCForVCSQRT = true; } if (idx == null) return null; long partPosition = version > 8 ? idx.position + 8 + 4*bound1 : idx.position + 4 + 8*bound1; long partSize = version > 8 ? (bound2-bound1+1) * 4 : (bound2-bound1+1) * 8; LargeIndexEntry partIdx = new LargeIndexEntry(partPosition, partSize); List buffer = seekAndFullyReadLargeCompressedBytes(partIdx); List disList = new ArrayList<>(); for (int i = 0; i < buffer.size(); i++) { disList.add(new ByteArrayInputStream(buffer.get(i))); } LittleEndianInputStream dis = new LittleEndianInputStream(new SequenceInputStream(Collections.enumeration(disList))); long nValues = bound2-bound1+1; ListOfDoubleArrays values = new ListOfDoubleArrays(nValues); boolean allNaN = true; for (long i = 0; i < nValues; i++) { double val = version > 8 ? (double) dis.readFloat() : dis.readDouble(); if (!useVCForVCSQRT) { values.set(i, val); } else { values.set(i, Math.sqrt(val)); } if (!Double.isNaN(val)) { allNaN = false; } } if (allNaN) return null; else return new NormalizationVector(type, chrIdx, unit, binSize, values); } @Override public ListOfDoubleArrays readExpectedVectorPart(long position, long nVals) throws IOException { long size = version > 8 ? nVals * 4 : nVals * 8; LargeIndexEntry idx = new LargeIndexEntry(position, size); List buffer = seekAndFullyReadLargeCompressedBytes(idx); List disList = new ArrayList<>(); for (int i = 0; i < buffer.size(); i++) { disList.add(new ByteArrayInputStream(buffer.get(i))); } LittleEndianInputStream dis = new LittleEndianInputStream(new SequenceInputStream(Collections.enumeration(disList))); ListOfDoubleArrays values = new ListOfDoubleArrays(nVals); for (int i = 0; i < nVals; i++) { double val = version > 8 ? dis.readFloat() : dis.readDouble(); values.set(i, val); } return values; } private byte[] seekAndFullyReadCompressedBytes(IndexEntry idx) throws IOException { byte[] compressedBytes = new byte[idx.size]; SeekableStream stream = getValidStream(); stream.seek(idx.position); stream.readFully(compressedBytes); stream.close(); return compressedBytes; } private List seekAndFullyReadLargeCompressedBytes(LargeIndexEntry idx) throws IOException { List compressedBytes = new ArrayList<>(); long counter = idx.size; while (counter > MAX_BYTE_READ_SIZE) { compressedBytes.add(new byte[MAX_BYTE_READ_SIZE]); counter = counter - MAX_BYTE_READ_SIZE; } compressedBytes.add(new byte[(int) counter]); SeekableStream stream = getValidStream(); stream.seek(idx.position); for (int i = 0; i < compressedBytes.size(); i++) { stream.readFully(compressedBytes.get(i)); } stream.close(); return compressedBytes; } @Override public Block readNormalizedBlock(int blockNumber, MatrixZoomData zd, NormalizationType no) throws IOException { if (no == null) { throw new IOException("Norm " + no + " is null"); } else if (no.equals(NormalizationHandler.NONE)) { return readBlock(blockNumber, zd); } else { long[] timeDiffThings = new long[4]; timeDiffThings[0] = System.currentTimeMillis(); NormalizationVector nv1 = dataset.getNormalizationVector(zd.getChr1Idx(), zd.getZoom(), no); NormalizationVector nv2 = dataset.getNormalizationVector(zd.getChr2Idx(), zd.getZoom(), no); if (nv1 == null || nv2 == null) { if (HiCGlobals.printVerboseComments) { // todo should this print an error always instead? System.err.println("Norm " + no + " missing for: " + zd.getDescription()); System.err.println(nv1 + " - " + nv2); } return null; } ListOfDoubleArrays nv1Data = nv1.getData(); ListOfDoubleArrays nv2Data = nv2.getData(); timeDiffThings[1] = System.currentTimeMillis(); Block rawBlock = readBlock(blockNumber, zd); timeDiffThings[2] = System.currentTimeMillis(); if (rawBlock == null) return null; Collection records = rawBlock.getContactRecords(); List normRecords = new ArrayList<>(records.size()); for (ContactRecord rec : records) { int x = rec.getBinX(); int y = rec.getBinY(); double denominator = nv1Data.get(x) * nv2Data.get(y); float counts = (float) (rec.getCounts() / denominator); if (!Float.isNaN(counts)) { normRecords.add(new ContactRecord(x, y, counts)); } } timeDiffThings[3] = System.currentTimeMillis(); return new Block(blockNumber, normRecords, zd.getBlockKey(blockNumber, no)); } } private Block readBlock(int blockNumber, MatrixZoomData zd) throws IOException { long[] timeDiffThings = new long[6]; timeDiffThings[0] = System.currentTimeMillis(); Block b = null; BlockIndex blockIndex = blockIndexMap.get(zd.getKey()); if (blockIndex != null) { IndexEntry idx = blockIndex.getBlock(blockNumber); if (idx != null) { //System.out.println(" blockIndexPosition:" + idx.position); timeDiffThings[1] = System.currentTimeMillis(); byte[] compressedBytes = seekAndFullyReadCompressedBytes(idx); timeDiffThings[2] = System.currentTimeMillis(); byte[] buffer; try { buffer = decompress(compressedBytes); timeDiffThings[3] = System.currentTimeMillis(); } catch (Exception e) { throw new RuntimeException("Block read error: " + e.getMessage()); } LittleEndianInputStream dis = new LittleEndianInputStream(new ByteArrayInputStream(buffer)); int nRecords = dis.readInt(); List records = new ArrayList<>(nRecords); timeDiffThings[4] = System.currentTimeMillis(); if (version < 7) { for (int i = 0; i < nRecords; i++) { int binX = dis.readInt(); int binY = dis.readInt(); float counts = dis.readFloat(); records.add(new ContactRecord(binX, binY, counts)); } } else { int binXOffset = dis.readInt(); int binYOffset = dis.readInt(); boolean useShort = dis.readByte() == 0; boolean useShortBinX = true, useShortBinY = true; if (version > 8) { useShortBinX = dis.readByte() == 0; useShortBinY = dis.readByte() == 0; } byte type = dis.readByte(); BinReader.handleBinType(dis, type, binXOffset, binYOffset, records, useShortBinX, useShortBinY, useShort); } b = new Block(blockNumber, records, zd.getBlockKey(blockNumber, NormalizationHandler.NONE)); timeDiffThings[5] = System.currentTimeMillis(); for (int ii = 0; ii < timeDiffThings.length - 1; ii++) { globalTimeDiffThings[ii] += (timeDiffThings[ii + 1] - timeDiffThings[ii]) / 1000.0; } } } // If no block exists, mark with an "empty block" to prevent further attempts if (b == null) { b = new Block(blockNumber, zd.getBlockKey(blockNumber, NormalizationHandler.NONE)); } return b; } private byte[] decompress(byte[] compressedBytes) { return compressionUtils.decompress(compressedBytes); } } ================================================ FILE: src/juicebox/data/DynamicBlock.java ================================================ /* * The MIT License (MIT) * * Copyright (c) 2011-2020 Broad Institute, Aiden Lab, Rice University, Baylor College of Medicine * * Permission is hereby granted, free of charge, to any person obtaining a copy * of this software and associated documentation files (the "Software"), to deal * in the Software without restriction, including without limitation the rights * to use, copy, modify, merge, publish, distribute, sublicense, and/or sell * copies of the Software, and to permit persons to whom the Software is * furnished to do so, subject to the following conditions: * * The above copyright notice and this permission notice shall be included in * all copies or substantial portions of the Software. * * THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR * IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, * FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE * AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER * LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, * OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN * THE SOFTWARE. */ package juicebox.data; import java.util.ArrayList; import java.util.HashSet; import java.util.List; import java.util.Set; public class DynamicBlock extends Block { Set recordSet = new HashSet<>(); public DynamicBlock(int number, ContactRecord record, String regionID) { super(number, null, regionID); recordSet.add(record); } @Override public List getContactRecords() { return new ArrayList<>(recordSet); } public void addContactRecord(ContactRecord cr) { recordSet.add(cr); } } ================================================ FILE: src/juicebox/data/DynamicBlockIndex.java ================================================ /* * The MIT License (MIT) * * Copyright (c) 2011-2020 Broad Institute, Aiden Lab, Rice University, Baylor College of Medicine * * Permission is hereby granted, free of charge, to any person obtaining a copy * of this software and associated documentation files (the "Software"), to deal * in the Software without restriction, including without limitation the rights * to use, copy, modify, merge, publish, distribute, sublicense, and/or sell * copies of the Software, and to permit persons to whom the Software is * furnished to do so, subject to the following conditions: * * The above copyright notice and this permission notice shall be included in * all copies or substantial portions of the Software. * * THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR * IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, * FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE * AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER * LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, * OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN * THE SOFTWARE. */ package juicebox.data; import htsjdk.samtools.seekablestream.SeekableStream; import htsjdk.tribble.util.LittleEndianInputStream; import juicebox.tools.utils.original.IndexEntry; import java.io.BufferedInputStream; import java.io.ByteArrayInputStream; import java.io.IOException; import java.util.List; public class DynamicBlockIndex extends BlockIndex { private final int maxBlocks; private final long minPosition, maxPosition; private Integer blockNumberRangeMin = null, blockNumberRangeMax = null; private Long mapFileBoundsMin = null, mapFileBoundsMax = null; private final SeekableStream stream; public DynamicBlockIndex(SeekableStream stream, int numBlocks, int maxBlocks, long minPosition) { super(numBlocks); this.stream = stream; this.maxBlocks = maxBlocks; this.minPosition = minPosition; maxPosition = minPosition + numBlocks * 16; } @Override public List getBlockNumbers() { // cause break - should not be called for this type of indexing return null; } @Override public IndexEntry getBlock(int blockNumber) { if (blockNumber > maxBlocks) { return null; } else if (blockIndex.containsKey(blockNumber)) { return blockIndex.get(blockNumber); } else if (blockNumber == 0) { try { return searchForBlockIndexEntry(blockNumber, this.minPosition, this.minPosition + 16); } catch (Exception e) { return null; } } else { long minPosition = this.minPosition; long maxPosition = this.maxPosition; if (blockNumberRangeMin != null && mapFileBoundsMin != null) { if (blockNumber < blockNumberRangeMin) { maxPosition = mapFileBoundsMin; } else if (blockNumber > blockNumberRangeMax) { minPosition = mapFileBoundsMax; } } if (maxPosition - minPosition < 16) { return null; } else { try { return searchForBlockIndexEntry(blockNumber, minPosition, maxPosition); } catch (Exception e) { return null; } } } } // Search entry for blockNumber between file positions boundsMin and boundsMax // boundsMin is guaranteed to start at the beginning of an entry, boundsMax at the end private IndexEntry searchForBlockIndexEntry(int blockNumber, long boundsMin, long boundsMax) throws IOException { int chunkSize = 1600000; if (boundsMax - boundsMin < chunkSize) { synchronized (stream) { stream.seek(boundsMin); LittleEndianInputStream dis = new LittleEndianInputStream(new BufferedInputStream(stream)); Integer firstBlockNumber = null; Integer lastBlockNumber = null; long pointer = boundsMin; while (pointer < boundsMax) { int blockNumberFound = dis.readInt(); long filePosition = dis.readLong(); int blockSizeInBytes = dis.readInt(); blockIndex.put(blockNumberFound, new IndexEntry(filePosition, blockSizeInBytes)); if (firstBlockNumber == null) firstBlockNumber = blockNumberFound; lastBlockNumber = blockNumberFound; pointer += 16; } // recent memory mapFileBoundsMin = boundsMin; mapFileBoundsMax = boundsMax; blockNumberRangeMin = firstBlockNumber; blockNumberRangeMax = lastBlockNumber; } return blockIndex.get(blockNumber); } // Midpoint in units of 16 byte chunks int nEntries = (int) ((boundsMax - boundsMin) / 16); long positionToSeek = boundsMin + (long) Math.floor(nEntries / 2f) * 16; int blockNumberFound, blockSizeInBytes; long filePosition; synchronized (stream) { stream.seek(positionToSeek); byte[] buffer = new byte[16]; stream.readFully(buffer); LittleEndianInputStream dis = new LittleEndianInputStream(new ByteArrayInputStream(buffer)); blockNumberFound = dis.readInt(); filePosition = dis.readLong(); blockSizeInBytes = dis.readInt(); } if (blockNumberFound == blockNumber) { blockIndex.put(blockNumberFound, new IndexEntry(filePosition, blockSizeInBytes)); return blockIndex.get(blockNumber); } else if (blockNumber > blockNumberFound) { return searchForBlockIndexEntry(blockNumber, positionToSeek + 16, boundsMax); } else { return searchForBlockIndexEntry(blockNumber, boundsMin, positionToSeek); } } } ================================================ FILE: src/juicebox/data/DynamicMatrixZoomData.java ================================================ /* * The MIT License (MIT) * * Copyright (c) 2011-2020 Broad Institute, Aiden Lab, Rice University, Baylor College of Medicine * * Permission is hereby granted, free of charge, to any person obtaining a copy * of this software and associated documentation files (the "Software"), to deal * in the Software without restriction, including without limitation the rights * to use, copy, modify, merge, publish, distribute, sublicense, and/or sell * copies of the Software, and to permit persons to whom the Software is * furnished to do so, subject to the following conditions: * * The above copyright notice and this permission notice shall be included in * all copies or substantial portions of the Software. * * THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR * IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, * FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE * AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER * LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, * OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN * THE SOFTWARE. */ package juicebox.data; import juicebox.windowui.HiCZoom; import juicebox.windowui.NormalizationType; import java.util.*; public class DynamicMatrixZoomData extends MatrixZoomData { private final MatrixZoomData higherResZD; private final int scaleFactor; /** * Constructor, sets the grid axes. Called when read from file. * * @param zoom */ public DynamicMatrixZoomData(HiCZoom zoom, MatrixZoomData higherResZD) { super(higherResZD.chr1, higherResZD.chr2, zoom, higherResZD.blockBinCount, higherResZD.blockColumnCount, new int[0], new int[0], null); this.higherResZD = higherResZD; scaleFactor = zoom.getBinSize() / higherResZD.getBinSize(); } @Override public List getNormalizedBlocksOverlapping(long binX1, long binY1, long binX2, long binY2, final NormalizationType norm, boolean isImportant, boolean fillUnderDiagonal) { // for V8 will be ints int higherBinX1 = (int) (binX1 * scaleFactor); int higherBinY1 = (int) (binY1 * scaleFactor); int higherBinX2 = (int) (binX2 * scaleFactor); int higherBinY2 = (int) (binY2 * scaleFactor); List blocksFromHigherRes = higherResZD.getNormalizedBlocksOverlapping(higherBinX1, higherBinY1, higherBinX2, higherBinY2, norm, isImportant, fillUnderDiagonal); return createBlocksForLowerRes(blocksFromHigherRes, norm); } private List createBlocksForLowerRes(List highResBlocks, NormalizationType norm) { Map> condensedRecords = new HashMap<>(); for (Block b : highResBlocks) { for (ContactRecord record : b.getContactRecords()) { int binX = record.getBinX() / scaleFactor; int binY = record.getBinY() / scaleFactor; float counts = record.getCounts(); if (!condensedRecords.containsKey(binX)) { condensedRecords.put(binX, new HashMap<>()); } if (condensedRecords.get(binX).containsKey(binY)) { condensedRecords.get(binX).get(binY).incrementCount(counts); } else { ContactRecord recordNew = new ContactRecord(binX, binY, counts); condensedRecords.get(binX).put(binY, recordNew); } } } Set blockNumbers = new HashSet<>(); for (int bx : condensedRecords.keySet()) { int cx = bx / blockBinCount; Map yMap = condensedRecords.get(bx); for (int by : yMap.keySet()) { ContactRecord cr = yMap.get(by); int ry = by / blockBinCount; int blockNumber = ry * blockColumnCount + cx; blockNumbers.add(blockNumber); String key = getBlockKey(blockNumber, norm); DynamicBlock b; if (blockCache.containsKey(key)) { b = (DynamicBlock) blockCache.get(key); b.addContactRecord(cr); } else { DynamicBlock block = new DynamicBlock(blockNumber, cr, key); blockCache.put(key, block); } } } List blockList = new ArrayList<>(); for (Integer num : blockNumbers) { blockList.add(blockCache.get(getBlockKey(num, norm))); } return blockList; } @Override public void printFullDescription() { System.out.println("Dynamic Resolution Chromosome: " + chr1.getName() + " - " + chr2.getName()); System.out.println("unit: " + zoom.getUnit()); System.out.println("binSize (bp): " + zoom.getBinSize()); } } ================================================ FILE: src/juicebox/data/ExpectedValueFunction.java ================================================ /* * The MIT License (MIT) * * Copyright (c) 2011-2021 Broad Institute, Aiden Lab, Rice University, Baylor College of Medicine * * Permission is hereby granted, free of charge, to any person obtaining a copy * of this software and associated documentation files (the "Software"), to deal * in the Software without restriction, including without limitation the rights * to use, copy, modify, merge, publish, distribute, sublicense, and/or sell * copies of the Software, and to permit persons to whom the Software is * furnished to do so, subject to the following conditions: * * The above copyright notice and this permission notice shall be included in * all copies or substantial portions of the Software. * * THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR * IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, * FITNESS FOR A PARTICULAR PURPOSE AND NON-INFRINGEMENT. IN NO EVENT SHALL THE * AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER * LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, * OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN * THE SOFTWARE. */ package juicebox.data; import juicebox.HiC; import juicebox.data.basics.ListOfDoubleArrays; import juicebox.windowui.NormalizationType; /** * @author jrobinso * Date: 12/26/12 * Time: 9:30 PM */ public interface ExpectedValueFunction { double getExpectedValue(int chrIdx, long distance); long getLength(); NormalizationType getNormalizationType(); HiC.Unit getUnit(); int getBinSize(); ListOfDoubleArrays getExpectedValuesNoNormalization(); ListOfDoubleArrays getExpectedValuesWithNormalization(int chrIdx); } ================================================ FILE: src/juicebox/data/ExpectedValueFunctionImpl.java ================================================ /* * The MIT License (MIT) * * Copyright (c) 2011-2020 Broad Institute, Aiden Lab, Rice University, Baylor College of Medicine * * Permission is hereby granted, free of charge, to any person obtaining a copy * of this software and associated documentation files (the "Software"), to deal * in the Software without restriction, including without limitation the rights * to use, copy, modify, merge, publish, distribute, sublicense, and/or sell * copies of the Software, and to permit persons to whom the Software is * furnished to do so, subject to the following conditions: * * The above copyright notice and this permission notice shall be included in * all copies or substantial portions of the Software. * * THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR * IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, * FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE * AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER * LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, * OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN * THE SOFTWARE. */ package juicebox.data; import juicebox.HiC; import juicebox.data.basics.ListOfDoubleArrays; import juicebox.windowui.HiCZoom; import juicebox.windowui.NormalizationType; import java.io.IOException; import java.util.Map; /** * Utility holder for Density calculation, for O/E maps. * * @author Jim Robinson * @author Neva Cherniavsky * @since 8/27/12 */ public class ExpectedValueFunctionImpl implements ExpectedValueFunction { private final DatasetReader reader; private int version = -1; private final int binSize; private final NormalizationType type; private final HiC.Unit unit; private final Map normFactors; private ListOfDoubleArrays expectedValues; private final long nValues; private final long filePosition; private long streamBound1 = 0; private long streamBound2 = 0; private final int streamSize = 500000; public ExpectedValueFunctionImpl(NormalizationType type, HiC.Unit unit, int binSize, ListOfDoubleArrays expectedValues, Map normFactors) { this.type = type; this.unit = unit; this.binSize = binSize; this.normFactors = normFactors; this.expectedValues = expectedValues; this.nValues = expectedValues.getLength(); this.filePosition = 0; this.reader = null; } public ExpectedValueFunctionImpl(NormalizationType type, HiC.Unit unit, int binSize, long nValues, long filePosition, Map normFactors, DatasetReader reader) { this.type = type; this.unit = unit; this.binSize = binSize; this.normFactors = normFactors; this.expectedValues = null; this.nValues = nValues; this.filePosition = filePosition; this.reader = reader; this.version = reader.getVersion(); } public static String getKey(HiCZoom zoom, NormalizationType normType) { return zoom.getKey() + "_" + normType; } // This is exposed for testing, should not use directly public Map getNormFactors() { return normFactors; } /** * Expected value vector. No chromosome normalization * * @return Genome-wide expected value vector */ @Override public ListOfDoubleArrays getExpectedValuesNoNormalization() { if (expectedValues == null && (streamBound1==0 && streamBound2 == 0)) { try { expectedValues = reader.readExpectedVectorPart(filePosition, nValues); streamBound1 = 0; streamBound2 = 0; } catch (IOException e) { System.err.println("Error reading expected vector"); e.printStackTrace(); } } return expectedValues; } /** * Gets the expected value, distance and coverage normalized, chromosome-length normalized * * @param chrIdx Chromosome index * @param distance Distance from diagonal in bins * @return Expected value, distance and coverage normalized */ @Override public double getExpectedValue(int chrIdx, long distance) { double normFactor = 1.0; long streamIndex; if (normFactors != null && normFactors.containsKey(chrIdx)) { normFactor = normFactors.get(chrIdx); } if (expectedValues == null) { streamBound1 = Math.max(0, distance-(streamSize/2)); streamBound2 = streamBound1 + streamSize; long position = version > 8? filePosition + (streamBound1*4): filePosition + (streamBound1*8); try { expectedValues = reader.readExpectedVectorPart(position, streamSize); } catch (IOException e) { System.err.println("Error reading expected vector"); e.printStackTrace(); } } if (streamBound1==0 && streamBound2==0) { if (expectedValues.getLength() > 0) { if (distance >= expectedValues.getLength()) { return expectedValues.getLastValue() / normFactor; } else { return expectedValues.get(distance) / normFactor; } } else { System.err.println("Expected values array is empty"); return -1; } } else if (distance >= streamBound1 && distance < streamBound2) { streamIndex = distance - streamBound1; return expectedValues.get(streamIndex) / normFactor; } else { streamBound1 = Math.max(0, distance-(streamSize/2)); streamBound2 = streamBound1 + streamSize; long position = version > 8? filePosition + (streamBound1*4): filePosition + (streamBound1*8); try { expectedValues = reader.readExpectedVectorPart(position, streamSize); } catch (IOException e) { System.err.println("Error reading expected vector"); e.printStackTrace(); } streamIndex = distance - streamBound1; return expectedValues.get(streamIndex) / normFactor; } } @Override public ListOfDoubleArrays getExpectedValuesWithNormalization(int chrIdx) { if (expectedValues == null && (streamBound1==0 && streamBound2 == 0)) { try { expectedValues = reader.readExpectedVectorPart(filePosition, nValues); streamBound1 = 0; streamBound2 = 0; } catch (IOException e) { System.err.println("Error reading expected vector"); e.printStackTrace(); } } double normFactor = 1.0; if (normFactors != null && normFactors.containsKey(chrIdx)) { normFactor = normFactors.get(chrIdx); } if (expectedValues.getLength() > 0) { ListOfDoubleArrays normedExpectedValues = expectedValues.deepClone(); normedExpectedValues.multiplyEverythingBy(1.0 / normFactor); return normedExpectedValues; } else { System.err.println("Expected values array is empty"); return null; } } @Override public long getLength() { return nValues; } @Override public NormalizationType getNormalizationType() { return type; } @Override public HiC.Unit getUnit() { return unit; } @Override public int getBinSize() { return binSize; } } ================================================ FILE: src/juicebox/data/GeneLocation.java ================================================ /* * The MIT License (MIT) * * Copyright (c) 2011-2020 Broad Institute, Aiden Lab, Rice University, Baylor College of Medicine * * Permission is hereby granted, free of charge, to any person obtaining a copy * of this software and associated documentation files (the "Software"), to deal * in the Software without restriction, including without limitation the rights * to use, copy, modify, merge, publish, distribute, sublicense, and/or sell * copies of the Software, and to permit persons to whom the Software is * furnished to do so, subject to the following conditions: * * The above copyright notice and this permission notice shall be included in * all copies or substantial portions of the Software. * * THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR * IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, * FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE * AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER * LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, * OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN * THE SOFTWARE. */ package juicebox.data; import juicebox.data.basics.Chromosome; public class GeneLocation { private final Chromosome chromosome; private final int centerPosition; public GeneLocation(Chromosome chromosome, int centerPosition) { this.chromosome = chromosome; this.centerPosition = centerPosition; } public int getCenterPosition() { return centerPosition; } public Chromosome getChromosome() { return chromosome; } } ================================================ FILE: src/juicebox/data/HiCFileLoader.java ================================================ /* * The MIT License (MIT) * * Copyright (c) 2011-2020 Broad Institute, Aiden Lab, Rice University, Baylor College of Medicine * * Permission is hereby granted, free of charge, to any person obtaining a copy * of this software and associated documentation files (the "Software"), to deal * in the Software without restriction, including without limitation the rights * to use, copy, modify, merge, publish, distribute, sublicense, and/or sell * copies of the Software, and to permit persons to whom the Software is * furnished to do so, subject to the following conditions: * * The above copyright notice and this permission notice shall be included in * all copies or substantial portions of the Software. * * THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR * IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, * FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE * AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER * LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, * OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN * THE SOFTWARE. */ package juicebox.data; import juicebox.HiCGlobals; import juicebox.gui.SuperAdapter; import juicebox.windowui.LoadDialog; import juicebox.windowui.RecentMenu; import org.broad.igv.Globals; import org.broad.igv.ui.util.FileDialogUtils; import org.broad.igv.ui.util.MessageUtils; import org.broad.igv.util.ParsingUtils; import javax.swing.*; import java.io.File; import java.io.FilenameFilter; import java.io.IOException; import java.io.InputStream; import java.net.MalformedURLException; import java.net.URL; import java.util.ArrayList; import java.util.Collections; import java.util.List; import java.util.Properties; import java.util.prefs.Preferences; /** * Created by muhammadsaadshamim on 8/4/15. */ public class HiCFileLoader { private static Properties properties; private static LoadDialog loadDialog = null; private static String propertiesFileURL = null; private static final String RECENT_PROPERTIES_FILE = "recentPropertiesFile"; public static File loadMenuItemActionPerformed(SuperAdapter superAdapter, boolean control, File openHiCPath) { FilenameFilter hicFilter = new FilenameFilter() { public boolean accept(File dir, String name) { return name.toLowerCase().endsWith(".hic"); } }; File[] files = FileDialogUtils.chooseMultiple("Choose Hi-C file(s)", openHiCPath, hicFilter); if (files != null && files.length > 0) { List fileNames = new ArrayList<>(); StringBuilder str = new StringBuilder(); String path = ""; for (File f : files) { fileNames.add(f.getAbsolutePath()); str.append(f.getName()).append(" "); path = f.getAbsolutePath(); } openHiCPath = new File(path); superAdapter.addRecentMapMenuEntry(str.toString().trim() + RecentMenu.delimiter + files[0].getAbsolutePath(), true); superAdapter.safeLoad(fileNames, control, str.toString()); } return openHiCPath; } public static void loadFromRecentActionPerformed(SuperAdapter superAdapter, String url, String title, boolean control) { if (url != null) { superAdapter.addRecentMapMenuEntry(title.trim() + RecentMenu.delimiter + url, true); superAdapter.safeLoad(Collections.singletonList(url), control, title); } } public static void loadFromURLActionPerformed(SuperAdapter superAdapter, boolean control) { String urlString = JOptionPane.showInputDialog("Enter URLs (separated by commas): "); if (urlString != null && urlString.length() > 0) { try { if (HiCFileTools.isDropboxURL(urlString)) { urlString = HiCFileTools.cleanUpDropboxURL(urlString); } urlString = urlString.trim(); String[] urls = urlString.split(","); List urlList = new ArrayList<>(); StringBuilder title = new StringBuilder(); for (String url : urls) { urlList.add(url); title.append((new URL(url)).getPath()).append(" "); } superAdapter.safeLoad(urlList, control, title.toString()); } catch (MalformedURLException e1) { superAdapter.launchFileLoadingError(urlString); } } } public static void loadFromListActionPerformed(SuperAdapter superAdapter, boolean control) { if (loadDialog == null) { initProperties(); loadDialog = superAdapter.launchLoadFileDialog(properties); if (!loadDialog.getSuccess()) { loadDialog = null; return; } } loadDialog.setControl(control); loadDialog.setVisible(true); } private static void initProperties() { try { if (propertiesFileURL == null) { try { Preferences prefs = Preferences.userNodeForPackage(Globals.class); String potentialURL = prefs.get(RECENT_PROPERTIES_FILE, null); if (potentialURL != null && potentialURL.length() > 0 && potentialURL.endsWith(".properties")) { propertiesFileURL = potentialURL; } } catch (Exception ignored) { } if (propertiesFileURL == null) propertiesFileURL = System.getProperty("jnlp.loadMenu"); if (propertiesFileURL == null) propertiesFileURL = HiCGlobals.defaultPropertiesURL; } InputStream is = ParsingUtils.openInputStream(propertiesFileURL); properties = new Properties(); if (is != null) { properties.load(is); } } catch (Exception error) { boolean fileFailedToLoad = true; if (!propertiesFileURL.equals(HiCGlobals.defaultPropertiesURL)) { try { loadPropertiesViaURL(HiCGlobals.defaultPropertiesURL); fileFailedToLoad = false; } catch (Exception ignored) { } } if (fileFailedToLoad) { System.err.println("Can't find properties file for loading list - internet likely disconnected" + error.getLocalizedMessage()); } } } private static void loadPropertiesViaURL(String url) throws IOException { InputStream is = ParsingUtils.openInputStream(url); properties = new Properties(); if (is != null) { properties.load(is); } } public static void changeJuiceboxPropertiesFile(String newURL) { boolean providedURLIsValid = true; try { InputStream is = ParsingUtils.openInputStream(newURL); properties = new Properties(); if (is != null) { properties.load(is); } } catch (Exception error) { providedURLIsValid = false; if (HiCGlobals.guiIsCurrentlyActive) { SuperAdapter.showMessageDialog("Can't find/load specified properties file"); } else { MessageUtils.showErrorMessage("Can't find/load specified properties file", error); } } // if no exception has been thrown at this point, the url is a valid one if (providedURLIsValid) { setPropertiesFileURL(newURL); loadDialog = null; } } private static void setPropertiesFileURL(String propertiesFileURL) { HiCFileLoader.propertiesFileURL = propertiesFileURL; Preferences prefs = Preferences.userNodeForPackage(Globals.class); prefs.put(RECENT_PROPERTIES_FILE, propertiesFileURL); } } ================================================ FILE: src/juicebox/data/HiCFileTools.java ================================================ /* * The MIT License (MIT) * * Copyright (c) 2011-2020 Broad Institute, Aiden Lab, Rice University, Baylor College of Medicine * * Permission is hereby granted, free of charge, to any person obtaining a copy * of this software and associated documentation files (the "Software"), to deal * in the Software without restriction, including without limitation the rights * to use, copy, modify, merge, publish, distribute, sublicense, and/or sell * copies of the Software, and to permit persons to whom the Software is * furnished to do so, subject to the following conditions: * * The above copyright notice and this permission notice shall be included in * all copies or substantial portions of the Software. * * THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR * IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, * FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE * AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER * LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, * OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN * THE SOFTWARE. */ package juicebox.data; import juicebox.HiCGlobals; import juicebox.data.basics.Chromosome; import juicebox.data.basics.ListOfDoubleArrays; import juicebox.tools.chrom.sizes.ChromosomeSizes; import juicebox.tools.utils.common.MatrixTools; import juicebox.windowui.HiCZoom; import juicebox.windowui.NormalizationType; import org.apache.commons.math.linear.RealMatrix; import java.io.*; import java.util.*; import java.util.regex.Pattern; /** * Created by muhammadsaadshamim on 5/12/15. */ public class HiCFileTools { public static Dataset extractDatasetForCLT(List files, boolean allowPrinting) { Dataset dataset = null; try { DatasetReader reader = null; if (files.size() == 1) { if (allowPrinting) System.out.println("Reading file: " + files.get(0)); String magicString = DatasetReaderFactory.getMagicString(files.get(0)); if (magicString.equals("HIC")) { reader = new DatasetReaderV2(files.get(0)); } else { System.err.println("This version of HIC is no longer supported"); System.exit(32); } dataset = reader.read(); } else { if (allowPrinting) System.out.println("Reading summed files: " + files); reader = DatasetReaderFactory.getReader(files); if (reader == null) { System.err.println("Error while reading files"); System.exit(33); } else { dataset = reader.read(); } } HiCGlobals.verifySupportedHiCFileVersion(reader.getVersion()); } catch (Exception e) { System.err.println("Could not read hic file: " + e.getMessage()); System.exit(34); //e.printStackTrace(); } return dataset; } public static DatasetReader extractDatasetReaderForCLT(List files, boolean allowPrinting) { DatasetReader reader = null; try { if (files.size() == 1) { if (allowPrinting) System.out.println("Reading file: " + files.get(0)); String magicString = DatasetReaderFactory.getMagicString(files.get(0)); if (magicString.equals("HIC")) { reader = new DatasetReaderV2(files.get(0)); } else { System.err.println("This version of HIC is no longer supported"); System.exit(32); } } else { if (allowPrinting) System.out.println("Reading summed files: " + files); reader = DatasetReaderFactory.getReader(files); if (reader == null) { System.err.println("Error while reading files"); System.exit(33); } } } catch (Exception e) { System.err.println("Could not read hic file: " + e.getMessage()); System.exit(34); //e.printStackTrace(); } return reader; } /** * Load the list of chromosomes based on given genome id or file * * @param idOrFile string * @return list of chromosomes */ public static ChromosomeHandler loadChromosomes(String idOrFile) { InputStream is = null; try { // Note: to get this to work, had to edit Intellij settings // so that "?*.sizes" are considered sources to be copied to class path is = ChromosomeSizes.class.getResourceAsStream(idOrFile + ".chrom.sizes"); if (is == null) { // Not an ID, see if its a file File file = new File(idOrFile); try { if (file.exists()) { is = new FileInputStream(file); } else { System.err.println("Could not find chromosome sizes file for: " + idOrFile); System.exit(35); } } catch (Exception e) { e.printStackTrace(); } } List chromosomes = new ArrayList<>(); chromosomes.add(0, null); // Index 0 reserved for "whole genome" pseudo-chromosome Pattern pattern = Pattern.compile("\\s+"); BufferedReader reader = new BufferedReader(new InputStreamReader(is), HiCGlobals.bufferSize); String nextLine; int idx = 1; try { while ((nextLine = reader.readLine()) != null) { String[] tokens = pattern.split(nextLine); if (tokens.length == 2) { String name = tokens[0]; int length = Integer.parseInt(tokens[1]); chromosomes.add(idx, new Chromosome(idx, name, length)); idx++; } else { System.out.println("Skipping " + nextLine); } } } catch (Exception e) { e.printStackTrace(); } // "pseudo-chromosome" All taken care of by by chromosome handler return new ChromosomeHandler(chromosomes, idOrFile, false); } finally { if (is != null) { try { is.close(); } catch (Exception e) { e.printStackTrace(); } } } } /** * Given an array of possible resolutions, returns the actual resolutions available in the dataset * * @param availableZooms * @param resolutions * @return finalResolutions Set */ public static List filterResolutions(List availableZooms, int[] resolutions) { TreeSet resSet = new TreeSet<>(); for (HiCZoom zoom : availableZooms) { resSet.add(zoom.getBinSize()); } List finalResolutions = new ArrayList<>(); for (int res : resolutions) { finalResolutions.add(closestValue(res, resSet)); } return finalResolutions; } private static int closestValue(int val, TreeSet valSet) { int floorVal; try { // sometimes no lower value is available and throws NPE floorVal = valSet.floor(val); } catch (Exception e) { return valSet.ceiling(val); } int ceilVal; try { // sometimes no higher value is available and throws NPE ceilVal = valSet.ceiling(val); } catch (Exception e) { return floorVal; } if (Math.abs(ceilVal - val) < Math.abs(val - floorVal)) return ceilVal; return floorVal; } public static ChromosomeHandler getChromosomeSetIntersection(ChromosomeHandler handler1, ChromosomeHandler handler2) { return handler1.getIntersectionWith(handler2); } public static Set getZoomSetIntersection(Collection collection1, Collection collection2) { Set set1 = new HashSet<>(collection1); Set set2 = new HashSet<>(collection2); boolean set1IsLarger = set1.size() > set2.size(); Set cloneSet = new HashSet<>(set1IsLarger ? set2 : set1); cloneSet.retainAll(set1IsLarger ? set1 : set2); return cloneSet; } /** * For each given chromosome name, find its equivalent Chromosome object * * @param chromosomesSpecified by strings * @param handler as Chromosome objects * @return the specified Chromosomes corresponding to the given strings */ public static ChromosomeHandler stringToChromosomes(List chromosomesSpecified, ChromosomeHandler handler) { List chromosomes = new ArrayList<>(); chromosomes.add(0, null); for (String strKey : chromosomesSpecified) { boolean chrFound = false; for (Chromosome chrKey : handler.getChromosomeArray()) { if (equivalentChromosome(strKey, chrKey)) { chromosomes.add(chrKey); chrFound = true; break; } } if (!chrFound) { System.err.println("Chromosome " + strKey + " not found"); } } return new ChromosomeHandler(chromosomes, handler.getGenomeID(), false); } /** * Evaluates whether the same chromosome is being referenced by the token * * @param token * @param chr * @return */ public static boolean equivalentChromosome(String token, Chromosome chr) { String token2 = token.toLowerCase().replaceAll("chr", ""); String chrName = chr.getName().toLowerCase().replaceAll("chr", ""); return token2.equals(chrName); } public static PrintWriter openWriter(File file) { try { file.createNewFile(); file.setWritable(true); return new PrintWriter(new BufferedWriter(new FileWriter(file)), true); } catch (IOException e) { System.out.println("I/O error opening file."); System.exit(37); } return null; } public static RealMatrix extractLocalBoundedRegion(MatrixZoomData zd, int limStart, int limEnd, int n, NormalizationType normalizationType, boolean fillUnderDiagonal) throws IOException { return extractLocalBoundedRegion(zd, limStart, limEnd, limStart, limEnd, n, n, normalizationType, fillUnderDiagonal); } public static RealMatrix extractLocalBoundedRegion(MatrixZoomData zd, int binXStart, int binYStart, int numRows, int numCols, NormalizationType normalizationType, boolean fillUnderDiagonal) throws IOException { return extractLocalBoundedRegion(zd, binXStart, binXStart + numRows, binYStart, binYStart + numCols, numRows, numCols, normalizationType, fillUnderDiagonal); } /** * Extracts matrix from hic file for a specified region. * By default, only the top right part of the matrix is returned if the matrix is on the diagonal. * * @return section of the matrix */ public static RealMatrix extractLocalBoundedRegion(MatrixZoomData zd, long binXStart, long binXEnd, long binYStart, long binYEnd, int numRows, int numCols, NormalizationType normalizationType, boolean fillUnderDiagonal) throws IOException { // numRows/numCols is just to ensure a set size in case bounds are approximate // left upper corner is reference for 0,0 List blocks = getAllRegionBlocks(zd, binXStart, binXEnd, binYStart, binYEnd, normalizationType, fillUnderDiagonal); RealMatrix data = MatrixTools.cleanArray2DMatrix(numRows, numCols); if (blocks.size() > 0) { for (Block b : blocks) { if (b != null) { for (ContactRecord rec : b.getContactRecords()) { // only called for small regions - should not exceed int int relativeX = (int) (rec.getBinX() - binXStart); int relativeY = (int) (rec.getBinY() - binYStart); if (relativeX >= 0 && relativeX < numRows) { if (relativeY >= 0 && relativeY < numCols) { data.addToEntry(relativeX, relativeY, rec.getCounts()); } } if (fillUnderDiagonal) { relativeX = (int) (rec.getBinY() - binXStart); relativeY = (int) (rec.getBinX() - binYStart); if (relativeX >= 0 && relativeX < numRows) { if (relativeY >= 0 && relativeY < numCols) { data.addToEntry(relativeX, relativeY, rec.getCounts()); } } } } } } } // force cleanup blocks = null; //System.gc(); return data; } public static List getAllRegionBlocks(MatrixZoomData zd, long binXStart, long binXEnd, long binYStart, long binYEnd, NormalizationType normalizationType, boolean fillUnderDiagonal) throws IOException { List blocks = Collections.synchronizedList(new ArrayList<>()); int numDataReadingErrors = 0; try { blocks.addAll(zd.getNormalizedBlocksOverlapping(binXStart, binYStart, binXEnd, binYEnd, normalizationType, false, fillUnderDiagonal)); } catch (Exception e) { triggerNormError(normalizationType); if (HiCGlobals.printVerboseComments) { System.err.println("You do not have " + normalizationType + " normalized maps available for this resolution/region:"); System.err.println("x1 " + binXStart + " x2 " + binXEnd + " y1 " + binYStart + " y2 " + binYEnd + " res " + zd.getBinSize()); System.err.println("Map is likely too sparse or a different normalization/resolution should be chosen."); e.printStackTrace(); System.exit(38); } } if (HiCGlobals.printVerboseComments && numDataReadingErrors > 0) { //System.err.println(numDataReadingErrors + " errors while reading data from region. Map is likely too sparse"); triggerNormError(normalizationType); } return blocks; } public static ListOfDoubleArrays extractChromosomeExpectedVector(Dataset ds, int index, HiCZoom zoom, NormalizationType normalization) { ExpectedValueFunction expectedValueFunction = ds.getExpectedValues(zoom, normalization); long n = expectedValueFunction.getLength(); ListOfDoubleArrays expectedVector = new ListOfDoubleArrays(n); for (long i = 0; i < n; i++) { expectedVector.set(i, expectedValueFunction.getExpectedValue(index, i)); } return expectedVector; } public static void triggerNormError(NormalizationType normalizationType) throws IOException { System.err.println(); System.err.println("You do not have " + normalizationType + " normalized maps available for this resolution/region."); System.err.println("Region is likely too sparse/does not exist, or a different normalization/resolution should be chosen."); throw new IOException("Norm could not be found"); } /** * @param directoryPath * @return valid directory for unix/windows or exits with error code */ public static File createValidDirectory(String directoryPath) { File outputDirectory = new File(directoryPath); if (!outputDirectory.exists() || !outputDirectory.isDirectory()) { if (!outputDirectory.mkdir()) { System.err.println("Couldn't create output directory " + directoryPath); System.exit(40); } } return outputDirectory; } public static String getTruncatedText(String text, int maxLengthEntryName) { String truncatedName = text; if (truncatedName.length() > maxLengthEntryName) { truncatedName = text.substring(0, maxLengthEntryName / 2 - 1); truncatedName += "..."; truncatedName += text.substring(text.length() - maxLengthEntryName / 2); } return truncatedName; } public static boolean isDropboxURL(String url) { return url.contains("dropbox.com"); } public static String cleanUpDropboxURL(String url) { return url.replace("?dl=0", "") .replace("://www.dropbox.com", "://dl.dropboxusercontent.com"); } public static MatrixZoomData getMatrixZoomData(Dataset ds, Chromosome chrom1, Chromosome chrom2, HiCZoom zoom) { Matrix matrix = ds.getMatrix(chrom1, chrom2); if (matrix == null || zoom == null) return null; return matrix.getZoomData(zoom); } public static MatrixZoomData getMatrixZoomData(Dataset ds, Chromosome chrom1, Chromosome chrom2, int resolution) { return getMatrixZoomData(ds, chrom1, chrom2, ds.getZoomForBPResolution(resolution)); } } ================================================ FILE: src/juicebox/data/Matrix.java ================================================ /* * The MIT License (MIT) * * Copyright (c) 2011-2020 Broad Institute, Aiden Lab, Rice University, Baylor College of Medicine * * Permission is hereby granted, free of charge, to any person obtaining a copy * of this software and associated documentation files (the "Software"), to deal * in the Software without restriction, including without limitation the rights * to use, copy, modify, merge, publish, distribute, sublicense, and/or sell * copies of the Software, and to permit persons to whom the Software is * furnished to do so, subject to the following conditions: * * The above copyright notice and this permission notice shall be included in * all copies or substantial portions of the Software. * * THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR * IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, * FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE * AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER * LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, * OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN * THE SOFTWARE. */ package juicebox.data; import juicebox.HiC; import juicebox.HiCGlobals; import juicebox.data.anchor.GenericLocus; import juicebox.data.anchor.MotifAnchor; import juicebox.data.basics.Chromosome; import juicebox.data.feature.FeatureFunction; import juicebox.data.feature.GenomeWideList; import juicebox.windowui.HiCZoom; import org.broad.igv.util.Pair; import java.util.*; /** * @author jrobinso * @since Aug 12, 2010 */ public class Matrix { private final int chr1; private final int chr2; private final static Set> dynamicZoomResolutions = new HashSet<>(); protected List bpZoomData = new ArrayList<>(); protected List fragZoomData = new ArrayList<>(); protected List dynamicBPZoomData = new ArrayList<>(); protected List bpBinSizes = new ArrayList<>(); protected List fragBinSizes = new ArrayList<>(); private final Comparator comparator = new Comparator() { @Override public int compare(MatrixZoomData o1, MatrixZoomData o2) { return o2.getBinSize() - o1.getBinSize(); } }; /** * Constructor for creating a matrix from precomputed data. * * @param chr1 * @param chr2 * @param zoomDataList */ public Matrix(int chr1, int chr2, List zoomDataList) { this.chr1 = chr1; this.chr2 = chr2; initZoomDataMap(zoomDataList); } public static Matrix createCustomChromosomeMatrix(Chromosome chr1, Chromosome chr2, ChromosomeHandler handler, final Map matrices, DatasetReader reader) { // TODO some weird null error when X chr in bed file? List indicesForChr1 = getIndicesFromSubChromosomes(handler, chr1); List indicesForChr2; if (chr1.getIndex() == chr2.getIndex()) { indicesForChr2 = new ArrayList<>(indicesForChr1); } else { indicesForChr2 = getIndicesFromSubChromosomes(handler, chr2); } if (HiCGlobals.printVerboseComments) { System.out.println("Indices_1 " + indicesForChr1); System.out.println("Indices_2 " + indicesForChr2); } // TODO need to sort first!! Chromosome newChr1 = chr1, newChr2 = chr2; if (chr1.getIndex() != chr2.getIndex() && indicesForChr1.get(0).getIndex() > indicesForChr2.get(0).getIndex()) { newChr1 = chr2; newChr2 = chr1; } Map customZDs = new HashMap<>(); // ensure all regions loaded for (Chromosome i : indicesForChr1) { for (Chromosome j : indicesForChr2) { //System.out.println("from mtrx"); String key = Matrix.generateKey(i, j); try { Matrix m = matrices.get(key); if (m == null) { // TODO sometimes this fails once or twice, but later succeeds - // TODO high priority, needs to be fixed int numAttempts = 0; while (m == null && numAttempts < 3) { numAttempts++; try { m = reader.readMatrix(key); } catch (Exception ignored) { } } if (m == null) { if (HiCGlobals.printVerboseComments) { System.out.println("nothing found for cc4 " + i.getName() + " - " + j.getName()); } continue; } matrices.put(key, m); } for (MatrixZoomData zd : m.bpZoomData) { updateCustomZoomDataRegions(newChr1, newChr2, handler, key, zd, customZDs, reader); } for (MatrixZoomData zd : m.dynamicBPZoomData) { updateCustomZoomDataRegions(newChr1, newChr2, handler, key, zd, customZDs, reader); } for (MatrixZoomData zd : m.fragZoomData) { updateCustomZoomDataRegions(newChr1, newChr2, handler, key, zd, customZDs, reader); } } catch (Exception ee) { System.err.println("Custom Chr Region Missing " + key); //ee.printStackTrace(); } if (HiCGlobals.printVerboseComments) System.out.println("completed cc4 " + i.getName() + " - " + j.getName()); } } return new Matrix(chr1.getIndex(), chr2.getIndex(), new ArrayList<>(customZDs.values())); } private void initZoomDataMap(List zoomDataList) { for (MatrixZoomData zd : zoomDataList) { if (zd.getZoom().getUnit() == HiC.Unit.BP) { bpZoomData.add(zd); } else { fragZoomData.add(zd); } // Zooms should be sorted, but in case they are not... bpZoomData.sort(comparator); fragZoomData.sort(comparator); } for (Pair resPair : dynamicZoomResolutions) { try { createDynamicResolutionMZD(resPair, false); } catch (Exception e) { System.err.println("Dynamic resolution could not be made"); } } dynamicBPZoomData.sort(comparator); } public static String generateKey(int chr1, int chr2) { if (chr2 < chr1) return "" + chr2 + "_" + chr1; return "" + chr1 + "_" + chr2; } public static Matrix createAssemblyChromosomeMatrix(ChromosomeHandler handler, final Map matrices, DatasetReader reader) { Map assemblyZDs = new HashMap<>(); Matrix matrix = null; int numAttempts = 0; while (matrix == null && numAttempts < 3) { try { matrix = reader.readMatrix("1_1"); } catch (Exception ignored) { numAttempts++; } } long length = handler.getChromosomeFromName("pseudoassembly").getLength(); // TODO: scaling; also maybe chromosome ends need to shift to start with new bin at every zoom? for (MatrixZoomData zd : matrix.bpZoomData) { // todo @dudcha is this done for resolutions where conversion will be lossy? assemblyZDs.put(zd.getZoom(), new MatrixZoomData(handler.getChromosomeFromName("pseudoassembly"), handler.getChromosomeFromName("pseudoassembly"), zd.getZoom(), (int) (length / zd.getBinSize()), (int) (length / zd.getBinSize()), null, null, reader)); } //TODO: assumption that we are doing this before modifying the handler // for (Chromosome i : handler.getChromosomeArrayWithoutAllByAll()) { // for (Chromosome j : handler.getChromosomeArrayWithoutAllByAll()) { // // //System.out.println("from mtrx"); // String key = Matrix.generateKey(i, j); // try { // Matrix m = matrices.get(key); // if (m == null) { // // TODO sometimes this fails once or twice, but later succeeds - // // TODO high priority, needs to be fixed?????? // int numAttempts = 0; // while (m == null && numAttempts < 3) { // try { // m = reader.readMatrix(key); // } catch (Exception ignored) { // numAttempts++; // } // } // // for(MatrixZoomData tempMatrixZoomData : m.bpZoomData){ // tempMatrixZoomData. // } // // // // modify m for each zoom //// matrices.put(key, m); //perhaps move it to the end // } // for (MatrixZoomData zd : m.bpZoomData) { // updateCustomZoomDataRegions(newChr1, newChr2, handler, key, zd, assemblyZDs, reader); // } //// for (MatrixZoomData zd : m.fragZoomData) { //// updateCustomZoomDataRegions(newChr1, newChr2, handler, key, zd, customZDs, reader); //// } // } catch (Exception ee) { // System.err.println("Everything failed in creatingAssemblyChromosomeMatrix " + key); // ee.printStackTrace(); // } // } // } Matrix m = new Matrix(handler.size(), handler.size(), new ArrayList<>(assemblyZDs.values())); matrices.put(generateKey(handler.size(), handler.size()), m); return m; } public void createDynamicResolutionMZD(Pair resPair, boolean addToSet) { int newRes = resPair.getFirst(); int highRes = resPair.getSecond(); MatrixZoomData highMZD = getZoomData(new HiCZoom(HiC.Unit.BP, highRes)); MatrixZoomData newMZD = new DynamicMatrixZoomData(new HiCZoom(HiC.Unit.BP, newRes), highMZD); if (addToSet) { dynamicZoomResolutions.add(resPair); } dynamicBPZoomData.add(newMZD); } private static List getIndicesFromSubChromosomes(final ChromosomeHandler handler, Chromosome chromosome) { final List indices = new ArrayList<>(); if (handler.isCustomChromosome(chromosome)) { GenomeWideList regions = handler.getListOfRegionsInCustomChromosome(chromosome.getIndex()); regions.processLists(new FeatureFunction() { @Override public void process(String chr, List featureList) { if (featureList.size() > 0) { Chromosome chromosomeN = handler.getChromosomeFromName(chr); if (chromosomeN != null) { indices.add(chromosomeN); } } } }); } else { indices.add(chromosome); } ChromosomeHandler.sort(indices); return indices; } private static void updateCustomZoomDataRegions(Chromosome chr1, Chromosome chr2, ChromosomeHandler handler, String regionKey, MatrixZoomData zd, Map customZDs, DatasetReader reader) { if (!customZDs.containsKey(zd.getZoom())) { customZDs.put(zd.getZoom(), new CustomMatrixZoomData(chr1, chr2, handler, zd.getZoom(), reader)); } customZDs.get(zd.getZoom()).expandAvailableZoomDatas(regionKey, zd); } public static String generateKey(Chromosome chr1, Chromosome chr2) { int t1 = Math.min(chr1.getIndex(), chr2.getIndex()); int t2 = Math.max(chr1.getIndex(), chr2.getIndex()); return generateKey(t1, t2); } public String getKey() { return generateKey(chr1, chr2); } public MatrixZoomData getFirstZoomData() { if (bpZoomData != null && bpZoomData.size() > 0) { return getFirstZoomData(HiC.Unit.BP); } else { return getFirstZoomData(HiC.Unit.FRAG); } } public MatrixZoomData getFirstZoomData(HiC.Unit unit) { if (unit == HiC.Unit.BP) { return bpZoomData != null && bpZoomData.size() > 0 ? bpZoomData.get(0) : null; } else { return fragZoomData != null && fragZoomData.size() > 0 ? fragZoomData.get(0) : null; } } public MatrixZoomData getFirstPearsonZoomData(HiC.Unit unit) { if (unit == HiC.Unit.BP) { return bpZoomData != null ? bpZoomData.get(2) : null; } else { return fragZoomData != null ? fragZoomData.get(2) : null; } } public MatrixZoomData getZoomData(HiCZoom zoom) { int targetZoom = zoom.getBinSize(); List zdList = (zoom.getUnit() == HiC.Unit.BP) ? bpZoomData : fragZoomData; //linear search for bin size, the lists are not large for (MatrixZoomData zd : zdList) { if (zd.getBinSize() == targetZoom) { return zd; } } for (MatrixZoomData zd : dynamicBPZoomData) { if (zd.getBinSize() == targetZoom) { return zd; } } // special exception for all by all if (chr1 == 0 && chr2 == 0) { MatrixZoomData closestValue = zdList.get(0); int distance = Math.abs(closestValue.getBinSize() - targetZoom); for (MatrixZoomData zd : zdList) { int cdistance = Math.abs(zd.getBinSize() - targetZoom); if (cdistance < distance) { closestValue = zd; distance = cdistance; } } return closestValue; } return null; } public MatrixZoomData getZoomData(int index) { if (index < bpBinSizes.size()) { HiCZoom zoom = new HiCZoom(HiC.Unit.BP, bpBinSizes.get(index)); return getZoomData(zoom); } else if (index >= bpBinSizes.size() && index < (bpBinSizes.size()+fragBinSizes.size())) { HiCZoom zoom = new HiCZoom(HiC.Unit.FRAG, fragBinSizes.get(index)); return getZoomData(zoom); } else { return null; } } public int getNumBPResolutions() { return bpBinSizes.size(); } public int getNumFragResolutions() { return fragBinSizes.size(); } public boolean isNotIntra() { return chr1 != chr2; } public int getChr1Idx() { return chr1; } public int getChr2Idx() { return chr2; } public void setBpBinSizes(ArrayList bpBinSizes) { this.bpBinSizes = bpBinSizes; } public void setFragBinSizes(ArrayList fragBinSizes) { this.fragBinSizes = fragBinSizes; } } ================================================ FILE: src/juicebox/data/MatrixZoomData.java ================================================ /* * The MIT License (MIT) * * Copyright (c) 2011-2021 Broad Institute, Aiden Lab, Rice University, Baylor College of Medicine * * Permission is hereby granted, free of charge, to any person obtaining a copy * of this software and associated documentation files (the "Software"), to deal * in the Software without restriction, including without limitation the rights * to use, copy, modify, merge, publish, distribute, sublicense, and/or sell * copies of the Software, and to permit persons to whom the Software is * furnished to do so, subject to the following conditions: * * The above copyright notice and this permission notice shall be included in * all copies or substantial portions of the Software. * * THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR * IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, * FITNESS FOR A PARTICULAR PURPOSE AND NON-INFRINGEMENT. IN NO EVENT SHALL THE * AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER * LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, * OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN * THE SOFTWARE. */ package juicebox.data; import htsjdk.tribble.util.LittleEndianOutputStream; import juicebox.HiC; import juicebox.HiCGlobals; import juicebox.assembly.AssemblyHeatmapHandler; import juicebox.assembly.AssemblyScaffoldHandler; import juicebox.assembly.Scaffold; import juicebox.data.basics.Chromosome; import juicebox.data.iterator.IteratorContainer; import juicebox.data.iterator.ListOfListGenerator; import juicebox.data.iterator.ZDIteratorContainer; import juicebox.data.v9depth.LogDepth; import juicebox.data.v9depth.V9Depth; import juicebox.gui.SuperAdapter; import juicebox.matrix.BasicMatrix; import juicebox.matrix.RealMatrixWrapper; import juicebox.tools.clt.old.Pearsons; import juicebox.tools.utils.original.*; import juicebox.track.HiCFixedGridAxis; import juicebox.track.HiCFragmentAxis; import juicebox.track.HiCGridAxis; import juicebox.windowui.HiCZoom; import juicebox.windowui.MatrixType; import juicebox.windowui.NormalizationHandler; import juicebox.windowui.NormalizationType; import org.apache.commons.math3.linear.Array2DRowRealMatrix; import org.apache.commons.math3.linear.EigenDecomposition; import org.apache.commons.math3.linear.RealMatrix; import org.apache.commons.math3.linear.RealVector; import org.broad.igv.tdf.BufferedByteWriter; import org.broad.igv.util.Pair; import org.broad.igv.util.collections.DownsampledDoubleArrayList; import org.broad.igv.util.collections.LRUCache; import java.awt.*; import java.io.ByteArrayOutputStream; import java.io.File; import java.io.IOException; import java.io.PrintWriter; import java.util.*; import java.util.List; import java.util.concurrent.ConcurrentHashMap; import java.util.concurrent.ExecutorService; import java.util.concurrent.Executors; import java.util.concurrent.TimeUnit; import java.util.concurrent.atomic.AtomicInteger; import java.util.zip.Deflater; public class MatrixZoomData { final Chromosome chr1; // Chromosome on the X axis final Chromosome chr2; // Chromosome on the Y axis private final boolean isIntra; final HiCZoom zoom; // Unit and bin size private final HiCGridAxis xGridAxis; private final HiCGridAxis yGridAxis; // Observed values are organized into sub-matrices ("blocks") protected final int blockBinCount; // block size in bins protected final int blockColumnCount; // number of block columns // Cache the last 20 blocks loaded protected final LRUCache blockCache = new LRUCache<>(500); private final HashMap pearsonsMap; private final HashMap normSquaredMaps; //private BigContactRecordList localCacheOfRecords = null; private final V9Depth v9Depth; private double sumCount = -1; private double averageCount = -1; protected DatasetReader reader; private IteratorContainer iteratorContainer = null; public long blockIndexPosition; /** * Constructor, sets the grid axes. Called when read from file. * * @param chr1 Chromosome 1 * @param chr2 Chromosome 2 * @param zoom Zoom (bin size and BP or FRAG) * @param blockBinCount Number of bins divided by number of columns (around 1000) * @param blockColumnCount Number of bins divided by 1000 (BLOCK_SIZE) * @param chr1Sites Used for looking up fragment * @param chr2Sites Used for looking up fragment * @param reader Pointer to file reader */ public MatrixZoomData(Chromosome chr1, Chromosome chr2, HiCZoom zoom, int blockBinCount, int blockColumnCount, int[] chr1Sites, int[] chr2Sites, DatasetReader reader) { this.chr1 = chr1; this.chr2 = chr2; this.zoom = zoom; this.isIntra = chr1.getIndex() == chr2.getIndex(); this.reader = reader; this.blockBinCount = blockBinCount; if (reader.getVersion() > 8) { v9Depth = V9Depth.setDepthMethod(reader.getDepthBase(), blockBinCount); } else { v9Depth = new LogDepth(2, blockBinCount); } this.blockColumnCount = blockColumnCount; long correctedBinCount = blockBinCount; if (!(this instanceof DynamicMatrixZoomData)) { if (reader.getVersion() < 8 && chr1.getLength() < chr2.getLength()) { boolean isFrag = zoom.getUnit() == HiC.Unit.FRAG; long len1 = chr1.getLength(); long len2 = chr2.getLength(); if (chr1Sites != null && chr2Sites != null && isFrag) { len1 = chr1Sites.length + 1; len2 = chr2Sites.length + 1; } long nBinsX = Math.max(len1, len2) / zoom.getBinSize() + 1; correctedBinCount = nBinsX / blockColumnCount + 1; } } if (this instanceof CustomMatrixZoomData || this instanceof DynamicMatrixZoomData) { this.xGridAxis = new HiCFixedGridAxis(chr1.getLength() / zoom.getBinSize() + 1, zoom.getBinSize(), null); this.yGridAxis = new HiCFixedGridAxis(chr2.getLength() / zoom.getBinSize() + 1, zoom.getBinSize(), null); } else if (zoom.getUnit() == HiC.Unit.BP) { this.xGridAxis = new HiCFixedGridAxis(correctedBinCount * blockColumnCount, zoom.getBinSize(), chr1Sites); this.yGridAxis = new HiCFixedGridAxis(correctedBinCount * blockColumnCount, zoom.getBinSize(), chr2Sites); } else if (zoom.getUnit() == HiC.Unit.FRAG) { this.xGridAxis = new HiCFragmentAxis(zoom.getBinSize(), chr1Sites, chr1.getLength()); this.yGridAxis = new HiCFragmentAxis(zoom.getBinSize(), chr2Sites, chr2.getLength()); } else { System.err.println("Requested " + zoom.getUnit() + " unit; error encountered"); this.xGridAxis = null; this.yGridAxis = null; } pearsonsMap = new HashMap<>(); normSquaredMaps = new HashMap<>(); } public Chromosome getChr1() { return chr1; } public Chromosome getChr2() { return chr2; } public HiCGridAxis getXGridAxis() { return xGridAxis; } public HiCGridAxis getYGridAxis() { return yGridAxis; } public int getBinSize() { return zoom.getBinSize(); } public int getChr1Idx() { return chr1.getIndex(); } public int getChr2Idx() { return chr2.getIndex(); } public HiCZoom getZoom() { return zoom; } public int getBlockColumnCount() { return blockColumnCount; } public int getBlockBinCount() { return blockBinCount; } public String getKey() { return chr1.getName() + "_" + chr2.getName() + "_" + zoom.getKey(); } // i think this is how it should be? todo sxxgrc please confirm use case private String getKey(int chr1, int chr2) { return chr1 + "_" + chr2 + "_" + zoom.getKey(); } public String getBlockKey(int blockNumber, NormalizationType no) { return getKey() + "_" + blockNumber + "_" + no; } public String getNormLessBlockKey(Block block) { return getKey() + "_" + block.getNumber() + "_" + block.getUniqueRegionID(); } private String getBlockKey(int blockNumber, NormalizationType no, int chr1, int chr2) { return getKey(chr1, chr2) + "_" + blockNumber + "_" + no; } public String getColorScaleKey(MatrixType displayOption, NormalizationType n1, NormalizationType n2) { return getKey() + displayOption + "_" + n1 + "_" + n2; } public String getTileKey(int tileRow, int tileColumn, MatrixType displayOption) { return getKey() + "_" + tileRow + "_" + tileColumn + "_ " + displayOption; } /** * Return the blocks of normalized, observed values overlapping the rectangular region specified. * The units are "bins" * * @param binY1 leftmost position in "bins" * @param binX2 rightmost position in "bins" * @param binY2 bottom position in "bins" * @param no normalization type * @param isImportant used for debugging * @return List of overlapping blocks, normalized */ public List getNormalizedBlocksOverlapping(long binX1, long binY1, long binX2, long binY2, final NormalizationType no, boolean isImportant, boolean fillUnderDiagonal) { final List blockList = Collections.synchronizedList(new ArrayList<>()); if (reader.getVersion() > 8 && isIntra) { return addNormalizedBlocksToListV9(blockList, (int) binX1, (int) binY1, (int) binX2, (int) binY2, no); } else { if (HiCGlobals.isAssemblyMatCheck) { return addNormalizedBlocksToList(blockList, (int) binX1, (int) binY1, (int) binX2, (int) binY2, no, 1, 1); } else if (SuperAdapter.assemblyModeCurrentlyActive && !HiCGlobals.isAssemblyMatCheck) { return addNormalizedBlocksToListAssembly(blockList, (int) binX1, (int) binY1, (int) binX2, (int) binY2, no); } else { return addNormalizedBlocksToList(blockList, (int) binX1, (int) binY1, (int) binX2, (int) binY2, no, fillUnderDiagonal); } } } /** * // for reference * public int getBlockNumberVersion9(int binI, int binJ) { * //int numberOfBlocksOnDiagonal = numberOfBinsInThisIntraMatrixAtResolution / blockSizeInBinCount + 1; * // assuming number of blocks on diagonal is blockClolumnSize * int depth = v9Depth.getDepth(binI, binJ); * int positionAlongDiagonal = ((binI + binJ) / 2 / blockBinCount); * return getBlockNumberVersion9FromPADAndDepth(positionAlongDiagonal, depth); * } *

* public int[] getBlockBoundsFromNumberVersion9Up(int blockNumber) { * int positionAlongDiagonal = blockNumber % blockColumnCount; * int depth = blockNumber / blockColumnCount; * int avgPosition1 = positionAlongDiagonal * blockBinCount; * int avgPosition2 = (positionAlongDiagonal + 1) * blockBinCount; * double difference1 = (Math.pow(2, depth) - 1) * blockBinCount * Math.sqrt(2); * double difference2 = (Math.pow(2, depth + 1) - 1) * blockBinCount * Math.sqrt(2); * int c1 = avgPosition1 + (int) difference1 / 2 - 1; * int c2 = avgPosition2 + (int) difference2 / 2 + 1; * int r1 = avgPosition1 - (int) difference2 / 2 - 1; * int r2 = avgPosition2 - (int) difference1 / 2 + 1; * return new int[]{c1, c2, r1, r2}; * } *

* public int[] getBlockBoundsFromNumberVersion8Below(int blockNumber) { * int c = (blockNumber % blockColumnCount); * int r = blockNumber / blockColumnCount; * int c1 = c * blockBinCount; * int c2 = c1 + blockBinCount - 1; * int r1 = r * blockBinCount; * int r2 = r1 + blockBinCount - 1; * return new int[]{c1, c2, r1, r2}; * } */ public int getBlockNumberVersion9FromPADAndDepth(int positionAlongDiagonal, int depth) { return depth * blockColumnCount + positionAlongDiagonal; } private void populateBlocksToLoadV9(int positionAlongDiagonal, int depth, NormalizationType no, List blockList, Set blocksToLoad) { int blockNumber = getBlockNumberVersion9FromPADAndDepth(positionAlongDiagonal, depth); String key = getBlockKey(blockNumber, no); Block b; if (HiCGlobals.useCache && blockCache.containsKey(key)) { b = blockCache.get(key); blockList.add(b); } else { blocksToLoad.add(blockNumber); } } private List addNormalizedBlocksToListV9(final List blockList, int binX1, int binY1, int binX2, int binY2, final NormalizationType norm) { Set blocksToLoad = new HashSet<>(); // PAD = positionAlongDiagonal (~projected) // Depth is axis perpendicular to diagonal; nearer means closer to diagonal int translatedLowerPAD = (binX1 + binY1) / 2 / blockBinCount; int translatedHigherPAD = (binX2 + binY2) / 2 / blockBinCount + 1; int translatedNearerDepth = v9Depth.getDepth(binX1, binY2); int translatedFurtherDepth = v9Depth.getDepth(binX2, binY1); // because code above assume above diagonal; but we could be below diagonal int nearerDepth = Math.min(translatedNearerDepth, translatedFurtherDepth); if ((binX1 > binY2 && binX2 < binY1) || (binX2 > binY1 && binX1 < binY2)) { nearerDepth = 0; } int furtherDepth = Math.max(translatedNearerDepth, translatedFurtherDepth) + 1; // +1; integer divide rounds down for (int depth = nearerDepth; depth <= furtherDepth; depth++) { for (int pad = translatedLowerPAD; pad <= translatedHigherPAD; pad++) { populateBlocksToLoadV9(pad, depth, norm, blockList, blocksToLoad); } } actuallyLoadGivenBlocks(blockList, blocksToLoad, norm); return new ArrayList<>(new HashSet<>(blockList)); } private void populateBlocksToLoad(int r, int c, NormalizationType no, List blockList, Set blocksToLoad) { int blockNumber = r * getBlockColumnCount() + c; String key = getBlockKey(blockNumber, no); Block b; if (HiCGlobals.useCache && blockCache.containsKey(key)) { b = blockCache.get(key); blockList.add(b); } else { blocksToLoad.add(blockNumber); } } /** * Return the blocks of normalized, observed values overlapping the rectangular region specified. * * @param binY1 leftmost position in "bins" * @param binX2 rightmost position in "bins" * @param binY2 bottom position in "bins" * @param norm normalization type * @return List of overlapping blocks, normalized */ private List addNormalizedBlocksToList(final List blockList, int binX1, int binY1, int binX2, int binY2, final NormalizationType norm, boolean getBelowDiagonal) { Set blocksToLoad = new HashSet<>(); // have to do this regardless (just in case) int col1 = binX1 / blockBinCount; int row1 = binY1 / blockBinCount; int col2 = binX2 / blockBinCount; int row2 = binY2 / blockBinCount; for (int r = row1; r <= row2; r++) { for (int c = col1; c <= col2; c++) { populateBlocksToLoad(r, c, norm, blockList, blocksToLoad); } } if (getBelowDiagonal && binY1 < binX2) { for (int r = row1; r <= row2; r++) { for (int c = col1; c <= col2; c++) { populateBlocksToLoad(c, r, norm, blockList, blocksToLoad); } } } actuallyLoadGivenBlocks(blockList, blocksToLoad, norm); return new ArrayList<>(new HashSet<>(blockList)); } private List addNormalizedBlocksToList(final List blockList, int binX1, int binY1, int binX2, int binY2, final NormalizationType no, int chr1, int chr2) { Set blocksToLoad = new HashSet<>(); // for V8 - these will always be ints // have to do this regardless (just in case) int col1 = binX1 / blockBinCount; int row1 = binY1 / blockBinCount; int col2 = binX2 / blockBinCount; int row2 = binY2 / blockBinCount; for (int r = row1; r <= row2; r++) { for (int c = col1; c <= col2; c++) { populateBlocksToLoad(r, c, no, blockList, blocksToLoad); } } actuallyLoadGivenBlocks(blockList, blocksToLoad, no, chr1, chr2); // System.out.println("I am block size: " + blockList.size()); // System.out.println("I am first block: " + blockList.get(0).getNumber()); return new ArrayList<>(new HashSet<>(blockList)); } private List addNormalizedBlocksToListAssembly(final List blockList, int binX1, int binY1, int binX2, int binY2, final NormalizationType no) { Set blocksToLoad = new HashSet<>(); // get aggregate scaffold handler AssemblyScaffoldHandler aFragHandler = AssemblyHeatmapHandler.getSuperAdapter().getAssemblyStateTracker().getAssemblyHandler(); final int binSize = zoom.getBinSize(); long actualBinSize = binSize; if (chr1.getIndex() == 0 && chr2.getIndex() == 0) { actualBinSize = 1000 * actualBinSize; } List xAxisAggregateScaffolds = aFragHandler.getIntersectingAggregateFeatures( (long) (actualBinSize * binX1 * HiCGlobals.hicMapScale), (long) (actualBinSize * binX2 * HiCGlobals.hicMapScale)); List yAxisAggregateScaffolds = aFragHandler.getIntersectingAggregateFeatures( (long) (actualBinSize * binY1 * HiCGlobals.hicMapScale), (long) (actualBinSize * binY2 * HiCGlobals.hicMapScale)); long x1pos, x2pos, y1pos, y2pos; for (Scaffold xScaffold : xAxisAggregateScaffolds) { if (HiCGlobals.phasing && xScaffold.getLength() < (actualBinSize / 2) * HiCGlobals.hicMapScale) { continue; } for (Scaffold yScaffold : yAxisAggregateScaffolds) { if (HiCGlobals.phasing && yScaffold.getLength() < (actualBinSize / 2) * HiCGlobals.hicMapScale) { continue; } x1pos = (long) (xScaffold.getOriginalStart() / HiCGlobals.hicMapScale); x2pos = (long) (xScaffold.getOriginalEnd() / HiCGlobals.hicMapScale); y1pos = (long) (yScaffold.getOriginalStart() / HiCGlobals.hicMapScale); y2pos = (long) (yScaffold.getOriginalEnd() / HiCGlobals.hicMapScale); // have to case long because of thumbnail, maybe fix thumbnail instead if (xScaffold.getCurrentStart() < actualBinSize * binX1 * HiCGlobals.hicMapScale) { if (!xScaffold.getInvertedVsInitial()) { x1pos = (int) ((xScaffold.getOriginalStart() + actualBinSize * binX1 * HiCGlobals.hicMapScale - xScaffold.getCurrentStart()) / HiCGlobals.hicMapScale); } else { x2pos = (int) ((xScaffold.getOriginalStart() - actualBinSize * binX1 * HiCGlobals.hicMapScale + xScaffold.getCurrentEnd()) / HiCGlobals.hicMapScale); } } if (yScaffold.getCurrentStart() < actualBinSize * binY1 * HiCGlobals.hicMapScale) { if (!yScaffold.getInvertedVsInitial()) { y1pos = (int) ((yScaffold.getOriginalStart() + actualBinSize * binY1 * HiCGlobals.hicMapScale - yScaffold.getCurrentStart()) / HiCGlobals.hicMapScale); } else { y2pos = (int) ((yScaffold.getOriginalStart() - actualBinSize * binY1 * HiCGlobals.hicMapScale + yScaffold.getCurrentEnd()) / HiCGlobals.hicMapScale); } } if (xScaffold.getCurrentEnd() > actualBinSize * binX2 * HiCGlobals.hicMapScale) { if (!xScaffold.getInvertedVsInitial()) { x2pos = (int) ((xScaffold.getOriginalStart() + actualBinSize * binX2 * HiCGlobals.hicMapScale - xScaffold.getCurrentStart()) / HiCGlobals.hicMapScale); } else { x1pos = (int) ((xScaffold.getOriginalStart() - actualBinSize * binX2 * HiCGlobals.hicMapScale + xScaffold.getCurrentEnd()) / HiCGlobals.hicMapScale); } } if (yScaffold.getCurrentEnd() > actualBinSize * binY2 * HiCGlobals.hicMapScale) { if (!yScaffold.getInvertedVsInitial()) { y2pos = (int) ((yScaffold.getOriginalStart() + actualBinSize * binY2 * HiCGlobals.hicMapScale - yScaffold.getCurrentStart()) / HiCGlobals.hicMapScale); } else { y1pos = (int) ((yScaffold.getOriginalStart() - actualBinSize * binY2 * HiCGlobals.hicMapScale + yScaffold.getCurrentEnd()) / HiCGlobals.hicMapScale); } } long[] genomePosition = new long[]{ x1pos, x2pos, y1pos, y2pos }; List tempBlockNumbers = getBlockNumbersForRegionFromGenomePosition(genomePosition); for (int blockNumber : tempBlockNumbers) { if (!blocksToLoad.contains(blockNumber)) { String key = getBlockKey(blockNumber, no); Block b; //temp fix for AllByAll. TODO: trace this! if (HiCGlobals.useCache && blockCache.containsKey(key)) { b = blockCache.get(key); blockList.add(b); } else { blocksToLoad.add(blockNumber); } } } } } // Remove basic duplicates here // Actually load new blocks actuallyLoadGivenBlocks(blockList, blocksToLoad, no); return new ArrayList<>(new HashSet<>(blockList)); } // private List retrieveContigsIntersectingWithWindow(Feature2DHandler handler, Rectangle currentWindow) { // List xAxisFeatures; // if (chr1.getIndex() == 0 && chr2.getIndex() == 0) { // xAxisFeatures = handler.getIntersectingFeatures(1, 1, currentWindow, true); // // helps with disappearing heatmap but doesn't fix everything // } else { // xAxisFeatures = handler.getIntersectingFeatures(chr1.getIndex(), chr2.getIndex(), currentWindow, true); // } // List axisContigs = new ArrayList<>(); // for (Feature2D feature2D : new HashSet<>(xAxisFeatures)) { // axisContigs.add(feature2D.toContig()); // } // Collections.sort(axisContigs); // return AssemblyHeatmapHandler.mergeRedundantContiguousContigs(axisContigs); // } private void actuallyLoadGivenBlocks(final List blockList, Set blocksToLoad, final NormalizationType no) { final AtomicInteger errorCounter = new AtomicInteger(); ExecutorService service = HiCGlobals.newFixedThreadPool(); final int binSize = getBinSize(); final int chr1Index = chr1.getIndex(); final int chr2Index = chr2.getIndex(); for (final int blockNumber : blocksToLoad) { Runnable loader = new Runnable() { @Override public void run() { try { String key = getBlockKey(blockNumber, no); Block b = reader.readNormalizedBlock(blockNumber, MatrixZoomData.this, no); if (b == null) { b = new Block(blockNumber, key); // An empty block } //Run out of memory if do it here if (SuperAdapter.assemblyModeCurrentlyActive) { b = AssemblyHeatmapHandler.modifyBlock(b, key, binSize, chr1Index, chr2Index); } if (HiCGlobals.useCache) { blockCache.put(key, b); } blockList.add(b); } catch (IOException e) { errorCounter.incrementAndGet(); } } }; service.submit(loader); } // done submitting all jobs service.shutdown(); // wait for all to finish try { service.awaitTermination(Long.MAX_VALUE, TimeUnit.NANOSECONDS); } catch (InterruptedException e) { System.err.println("Error loading mzd data " + e.getLocalizedMessage()); if (HiCGlobals.printVerboseComments) { e.printStackTrace(); } } // error printing if (errorCounter.get() > 0) { System.err.println(errorCounter.get() + " errors while reading blocks"); } } private void actuallyLoadGivenBlocks(final List blockList, Set blocksToLoad, final NormalizationType no, final int chr1Id, final int chr2Id) { final AtomicInteger errorCounter = new AtomicInteger(); ExecutorService service = Executors.newFixedThreadPool(200); final int binSize = getBinSize(); for (final int blockNumber : blocksToLoad) { Runnable loader = new Runnable() { @Override public void run() { try { String key = getBlockKey(blockNumber, no, chr1Id, chr2Id); Block b = reader.readNormalizedBlock(blockNumber, MatrixZoomData.this, no); if (b == null) { b = new Block(blockNumber, key); // An empty block } //Run out of memory if do it here if (SuperAdapter.assemblyModeCurrentlyActive) { b = AssemblyHeatmapHandler.modifyBlock(b, key, binSize, chr1Id, chr2Id); } if (HiCGlobals.useCache) { blockCache.put(key, b); } blockList.add(b); } catch (IOException e) { errorCounter.incrementAndGet(); } } }; service.submit(loader); } // done submitting all jobs service.shutdown(); // wait for all to finish try { service.awaitTermination(Long.MAX_VALUE, TimeUnit.NANOSECONDS); } catch (InterruptedException e) { System.err.println("Error loading mzd data " + e.getLocalizedMessage()); if (HiCGlobals.printVerboseComments) { e.printStackTrace(); } } // error printing if (errorCounter.get() > 0) { System.err.println(errorCounter.get() + " errors while reading blocks"); } } /** * Return the observed value at the specified location. Supports tooltip text * This implementation is naive, but might get away with it for tooltip. * * @param binX X bin * @param binY Y bin * @param normalizationType Normalization type */ public float getObservedValue(int binX, int binY, NormalizationType normalizationType) { // Intra stores only lower diagonal if (chr1 == chr2) { if (binX > binY) { int tmp = binX; //noinspection SuspiciousNameCombination binX = binY; binY = tmp; } } List blocks = getNormalizedBlocksOverlapping(binX, binY, binX, binY, normalizationType, false, false); if (blocks == null) return 0; for (Block b : blocks) { for (ContactRecord rec : b.getContactRecords()) { if (rec.getBinX() == binX && rec.getBinY() == binY) { return rec.getCounts(); } } } // No record found for this bin return 0; } // /** // * Return a slice of the matrix at the specified Y been as a list of wiggle scores // * // * @param binY // */ // public List getSlice(int startBinX, int endBinX, int binY, NormalizationType normalizationType) { // // // Intra stores only lower diagonal // if (chr1 == chr2) { // if (binX > binY) { // int tmp = binX; // binX = binY; // binY = tmp; // // } // } // // List blocks = getNormalizedBlocksOverlapping(binX, binY, binX, binY, normalizationType); // if (blocks == null) return 0; // for (Block b : blocks) { // for (ContactRecord rec : b.getContactRecords()) { // if (rec.getBinX() == binX && rec.getBinY() == binY) { // return rec.getCounts(); // } // } // } // // No record found for this bin // return 0; // } /** * Computes eigenvector from Pearson's. * * @param df Expected values, needed to get Pearson's * @param which Which eigenvector; 0 is principal. * @return Eigenvector */ public double[] computeEigenvector(ExpectedValueFunction df, int which) { BasicMatrix pearsons = getPearsons(df); if (pearsons == null) { return null; } int dim = pearsons.getRowDimension(); BitSet bitSet = new BitSet(dim); for (int i = 0; i < dim; i++) { float tmp = pearsons.getEntry(i, i); if (tmp > .999) { // checking if diagonal is 1 bitSet.set(i); } } int[] newPosToOrig = getMapNewPosToOriginal(dim, bitSet); RealMatrix subMatrix = getSubsetOfMatrix(newPosToOrig, bitSet.cardinality(), pearsons); RealVector rv = (new EigenDecomposition(subMatrix)).getEigenvector(which); double[] ev = rv.toArray(); int size = pearsons.getColumnDimension(); double[] eigenvector = new double[size]; Arrays.fill(eigenvector, Double.NaN); for (int i = 0; i < newPosToOrig.length; i++) { int oldI = newPosToOrig[i]; eigenvector[oldI] = ev[i]; } return eigenvector; } private RealMatrix getSubsetOfMatrix(int[] newPosToOrig, int subsetN, BasicMatrix pearsons) { double[][] data = new double[subsetN][subsetN]; for (int newI = 0; newI < newPosToOrig.length; newI++) { int oldI = newPosToOrig[newI]; for (int newJ = newI; newJ < newPosToOrig.length; newJ++) { int oldJ = newPosToOrig[newJ]; float tmp = pearsons.getEntry(oldI, oldJ); data[newI][newJ] = tmp; data[newJ][newI] = tmp; } } return new Array2DRowRealMatrix(data); } private int[] getMapNewPosToOriginal(int dim, BitSet bitSet) { int[] newPosToOrig = new int[bitSet.cardinality()]; int count = 0; for (int i = 0; i < dim; i++) { if (bitSet.get(i)) { newPosToOrig[count++] = i; } } return newPosToOrig; } public BasicMatrix getNormSquared(NormalizationType normalizationType) { if (normSquaredMaps.containsKey(normalizationType) && normSquaredMaps.get(normalizationType) != null) { return normSquaredMaps.get(normalizationType); } // otherwise calculate BasicMatrix normSquared = computeNormSquared(normalizationType); normSquaredMaps.put(normalizationType, normSquared); return normSquared; } // todo only compute local region at high resolution otherwise memory gets exceeded // todo deprecate private BasicMatrix computeNormSquared(NormalizationType normalizationType) { double[] nv1Data = reader.getNormalizationVector(getChr1Idx(), getZoom(), normalizationType).getData().getValues().get(0); double[] nv2Data = reader.getNormalizationVector(getChr2Idx(), getZoom(), normalizationType).getData().getValues().get(0); double[][] matrix = new double[nv1Data.length][nv2Data.length]; for (int i = 0; i < nv1Data.length; i++) { for (int j = 0; j < nv2Data.length; j++) { int diff = Math.max(1, Math.abs(i - j)); matrix[i][j] = 1 / (nv1Data[i] * nv2Data[j] * diff * diff * diff * diff); } } return new RealMatrixWrapper(new Array2DRowRealMatrix(matrix)); } /** * Returns the Pearson's matrix; read if available (currently commented out), calculate if small enough. * * @param df Expected values * @return Pearson's matrix or null if not able to calculate or read */ public BasicMatrix getPearsons(ExpectedValueFunction df) { boolean readPearsons = false; // check if were able to read in // try to get from local cache BasicMatrix pearsons = pearsonsMap.get(df.getNormalizationType()); if (pearsons != null) { return pearsons; } // we weren't able to read in the Pearsons. check that the resolution is low enough to calculate if (!readPearsons && (zoom.getUnit() == HiC.Unit.BP && zoom.getBinSize() >= HiCGlobals.MAX_PEARSON_ZOOM) || (zoom.getUnit() == HiC.Unit.FRAG && zoom.getBinSize() >= HiCGlobals.MAX_PEARSON_ZOOM/1000)) { pearsons = computePearsons(df); pearsonsMap.put(df.getNormalizationType(), pearsons); } return pearsonsMap.get(df.getNormalizationType()); } /** * Returns Pearson value at given bin X and Y * * @param binX X bin * @param binY Y bin * @param type Normalization type * @return Pearson's value at this location */ public float getPearsonValue(int binX, int binY, NormalizationType type) { BasicMatrix pearsons = pearsonsMap.get(type); if (pearsons != null) { return pearsons.getEntry(binX, binY); } else { return 0; } } /** * Compute the Pearson's. Read in the observed, calculate O/E from the expected value function, subtract the row * means, compute the Pearson's correlation on that matrix * * @param df Expected value * @return Pearson's correlation matrix */ private BasicMatrix computePearsons(ExpectedValueFunction df) { if (chr1 != chr2) { throw new RuntimeException("Cannot compute pearsons for non-diagonal matrices"); } int dim; if (zoom.getUnit() == HiC.Unit.BP) { dim = (int) (chr1.getLength() / zoom.getBinSize()) + 1; } else { dim = ((DatasetReaderV2) reader).getFragCount(chr1) / zoom.getBinSize() + 1; } // Compute O/E column vectors double[][] oeMatrix = new double[dim][dim]; BitSet bitSet = new BitSet(dim); populateOEMatrixAndBitset(oeMatrix, bitSet, df); BasicMatrix pearsons; if (HiCGlobals.guiIsCurrentlyActive) { // todo ask Neva pearsons = Pearsons.computeParallelizedPearsons(oeMatrix, dim, bitSet); } else { pearsons = Pearsons.computePearsons(oeMatrix, dim, bitSet); } pearsonsMap.put(df.getNormalizationType(), pearsons); return pearsons; } private void populateOEMatrixAndBitset(double[][] oeMatrix, BitSet bitSet, ExpectedValueFunction df) { Iterator iterator = getNewContactRecordIterator(); while (iterator.hasNext()) { ContactRecord record = iterator.next(); float counts = record.getCounts(); if (Float.isNaN(counts)) continue; int i = record.getBinX(); int j = record.getBinY(); int dist = Math.abs(i - j); double expected = df.getExpectedValue(chr1.getIndex(), dist); double oeValue = counts / expected; oeMatrix[i][j] = oeValue; oeMatrix[j][i] = oeValue; bitSet.set(i); bitSet.set(j); } } /** * Utility for printing description of this matrix. */ public String getDescription() { return chr1.getName() + " - " + chr2.getName() + " - " + getZoom(); } public void printFullDescription() { System.out.println("Chromosomes: " + chr1.getName() + " - " + chr2.getName()); System.out.println("unit: " + zoom.getUnit()); System.out.println("binSize (bp): " + zoom.getBinSize()); System.out.println("blockBinCount (bins): " + blockBinCount); System.out.println("blockColumnCount (columns): " + blockColumnCount); System.out.println("Block size (bp): " + blockBinCount * zoom.getBinSize()); System.out.println(); } public List getBlockNumbers() { return reader.getBlockNumbers(this); } /** * For a specified region, select the block numbers corresponding to it * * @param regionIndices * @return */ List getBlockNumbersForRegionFromGenomePosition(long[] regionIndices) { int resolution = zoom.getBinSize(); long[] regionBinIndices = new long[4]; for (int i = 0; i < regionBinIndices.length; i++) { regionBinIndices[i] = regionIndices[i] / resolution; } return getBlockNumbersForRegionFromBinPosition(regionBinIndices); } // todo V9 needs a diff method private List getBlockNumbersForRegionFromBinPosition(long[] regionIndices) { // cast should be fine - this is for V8 int col1 = (int) (regionIndices[0] / blockBinCount); int col2 = (int) ((regionIndices[1] + 1) / blockBinCount); int row1 = (int) (regionIndices[2] / blockBinCount); int row2 = (int) ((regionIndices[3] + 1) / blockBinCount); // first check the upper triangular matrix Set blocksSet = new HashSet<>(); for (int r = row1; r <= row2; r++) { for (int c = col1; c <= col2; c++) { int blockNumber = r * getBlockColumnCount() + c; blocksSet.add(blockNumber); } } // check region part that overlaps with lower left triangle // but only if intrachromosomal if (chr1.getIndex() == chr2.getIndex()) { for (int r = col1; r <= col2; r++) { for (int c = row1; c <= row2; c++) { int blockNumber = r * getBlockColumnCount() + c; blocksSet.add(blockNumber); } } } List blocksToIterateOver = new ArrayList<>(blocksSet); Collections.sort(blocksToIterateOver); return blocksToIterateOver; } public void dump(PrintWriter printWriter, LittleEndianOutputStream les, NormalizationType norm, MatrixType matrixType, boolean useRegionIndices, long[] regionIndices, ExpectedValueFunction df, boolean dense) throws IOException { // determine which output will be used if (printWriter == null && les == null) { printWriter = new PrintWriter(System.out); } boolean usePrintWriter = printWriter != null && les == null; boolean isIntraChromosomal = chr1.getIndex() == chr2.getIndex(); // Get the block index keys, and sort List blocksToIterateOver; if (useRegionIndices) { blocksToIterateOver = getBlockNumbersForRegionFromGenomePosition(regionIndices); } else { blocksToIterateOver = reader.getBlockNumbers(this); Collections.sort(blocksToIterateOver); } if (!dense) { for (Integer blockNumber : blocksToIterateOver) { Block b = reader.readNormalizedBlock(blockNumber, MatrixZoomData.this, norm); if (b != null) { for (ContactRecord rec : b.getContactRecords()) { float counts = rec.getCounts(); int x = rec.getBinX(); int y = rec.getBinY(); int xActual = x * zoom.getBinSize(); int yActual = y * zoom.getBinSize(); float oeVal = 0f; if (matrixType == MatrixType.OE) { double expected = 0; if (chr1 == chr2) { if (df != null) { int dist = Math.abs(x - y); expected = df.getExpectedValue(chr1.getIndex(), dist); } } else { expected = (averageCount > 0 ? averageCount : 1); } double observed = rec.getCounts(); // Observed is already normalized oeVal = (float) (observed / expected); } if (!useRegionIndices || // i.e. use full matrix // or check regions that overlap with upper left (xActual >= regionIndices[0] && xActual <= regionIndices[1] && yActual >= regionIndices[2] && yActual <= regionIndices[3]) || // or check regions that overlap with lower left (isIntraChromosomal && yActual >= regionIndices[0] && yActual <= regionIndices[1] && xActual >= regionIndices[2] && xActual <= regionIndices[3])) { // but leave in upper right triangle coordinates if (usePrintWriter) { if (matrixType == MatrixType.OBSERVED) { printWriter.println(xActual + "\t" + yActual + "\t" + counts); } else if (matrixType == MatrixType.OE) { printWriter.println(xActual + "\t" + yActual + "\t" + oeVal); } } else { // TODO I suspect this is wrong - should be writing xActual - but this is for binary dumping and we never use it if (matrixType == MatrixType.OBSERVED) { les.writeInt(x); les.writeInt(y); les.writeFloat(counts); } else if (matrixType == MatrixType.OE) { les.writeInt(x); les.writeInt(y); les.writeFloat(oeVal); } } } } } } } else { int maxX = 0; int maxY = 0; for (Integer blockNumber : blocksToIterateOver) { Block b = reader.readNormalizedBlock(blockNumber, MatrixZoomData.this, norm); if (b != null) { for (ContactRecord rec : b.getContactRecords()) { int x = rec.getBinX(); int y = rec.getBinY(); if (maxX < x) maxX = x; if (maxY < y) maxY = y; } } } if (isIntraChromosomal) { if (maxX < maxY) { maxX = maxY; } else { maxY = maxX; } } maxX++; maxY++; float[][] matrix = new float[maxX][maxY]; // auto initialized to 0 for (Integer blockNumber : blocksToIterateOver) { Block b = reader.readNormalizedBlock(blockNumber, MatrixZoomData.this, norm); if (b != null) { for (ContactRecord rec : b.getContactRecords()) { float counts = rec.getCounts(); int x = rec.getBinX(); int y = rec.getBinY(); int xActual = x * zoom.getBinSize(); int yActual = y * zoom.getBinSize(); float oeVal = 0f; if (matrixType == MatrixType.OE) { int dist = Math.abs(x - y); double expected = 0; try { expected = df.getExpectedValue(chr1.getIndex(), dist); } catch (Exception e) { e.printStackTrace(); //To change body of catch statement use File | Settings | File Templates. } double observed = rec.getCounts(); // Observed is already normalized oeVal = (float) (observed / expected); } if (!useRegionIndices || // i.e. use full matrix // or check regions that overlap with upper left (xActual >= regionIndices[0] && xActual <= regionIndices[1] && yActual >= regionIndices[2] && yActual <= regionIndices[3]) || // or check regions that overlap with lower left (isIntraChromosomal && yActual >= regionIndices[0] && yActual <= regionIndices[1] && xActual >= regionIndices[2] && xActual <= regionIndices[3])) { if (matrixType == MatrixType.OBSERVED) { matrix[x][y] = counts; if (isIntraChromosomal) { matrix[y][x] = counts; } // printWriter.println(xActual + "\t" + yActual + "\t" + counts); } else if (matrixType == MatrixType.OE) { matrix[x][y] = oeVal; if (isIntraChromosomal) { matrix[y][x] = oeVal; } // printWriter.println(xActual + "\t" + yActual + "\t" + oeVal); } } } } } if (usePrintWriter) { for (int i = 0; i < maxX; i++) { for (int j = 0; j < maxY; j++) { printWriter.print(matrix[i][j] + "\t"); } printWriter.println(); } } else { for (int i = 0; i < maxX; i++) { for (int j = 0; j < maxY; j++) { les.writeFloat(matrix[i][j]); } } } } if (usePrintWriter) { printWriter.close(); } else { les.close(); } } public void dump1DTrackFromCrossHairAsWig(PrintWriter printWriter, long binStartPosition, boolean isIntraChromosomal, long[] regionBinIndices, NormalizationType norm, MatrixType matrixType) { if (!MatrixType.isObservedOrControl(matrixType)) { System.out.println("This feature is only available for Observed or Control views"); return; } int binCounter = 0; // Get the block index keys, and sort List blocksToIterateOver = getBlockNumbersForRegionFromBinPosition(regionBinIndices); Collections.sort(blocksToIterateOver); for (Integer blockNumber : blocksToIterateOver) { Block b = null; try { b = reader.readNormalizedBlock(blockNumber, MatrixZoomData.this, norm); } catch (Exception e) { System.err.println("Skipping block " + blockNumber); } if (b != null) { for (ContactRecord rec : b.getContactRecords()) { float counts = rec.getCounts(); int x = rec.getBinX(); int y = rec.getBinY(); if ( //check regions that overlap with upper left (x >= regionBinIndices[0] && x <= regionBinIndices[1] && y >= regionBinIndices[2] && y <= regionBinIndices[3]) || // or check regions that overlap with lower left (isIntraChromosomal && x >= regionBinIndices[2] && x <= regionBinIndices[3] && y >= regionBinIndices[0] && y <= regionBinIndices[1])) { // but leave in upper right triangle coordinates if (x == binStartPosition) { while (binCounter < y) { printWriter.println("0"); binCounter++; } } else if (y == binStartPosition) { while (binCounter < x) { printWriter.println("0"); binCounter++; } } else { System.err.println("Something went wrong while generating 1D track"); System.err.println("Improper input was likely provided"); } printWriter.println(counts); binCounter++; } } } } } /** * Returns the average count * * @return Average count */ public double getAverageCount() { return averageCount; } public double getSumCount() { return sumCount; } /** * Sets the average count * * @param averageCount Average count to set */ public void setAverageCount(double averageCount) { this.averageCount = averageCount; } public void setSumCount(double sumCount) { this.sumCount = sumCount; } public void clearCache(boolean onlyClearInter) { if (onlyClearInter && isIntra) return; if (HiCGlobals.useCache) { blockCache.clear(); } if (iteratorContainer != null) { iteratorContainer.clear(); iteratorContainer = null; } } private Iterator getNewContactRecordIterator() { return getIteratorContainer().getNewContactRecordIterator(); //return new ContactRecordIterator(reader, this, blockCache); } public IteratorContainer getIteratorContainer() { if (iteratorContainer == null) { iteratorContainer = ListOfListGenerator.createFromZD(reader, this, blockCache); } return iteratorContainer; } public IteratorContainer getFromFileIteratorContainer() { return new ZDIteratorContainer(reader, this, blockCache); } // Merge and write out blocks one at a time. public Pair,ExpectedValueCalculation> mergeAndWriteBlocks(LittleEndianOutputStream los, Deflater compressor, boolean calculateExpecteds, Map fragmentCountMap, ChromosomeHandler chromosomeHandler, double subsampleFraction, Random randomSubsampleGenerator) throws IOException { List sortedBlockNumbers = reader.getBlockNumbers(this); List indexEntries = new ArrayList<>(); ExpectedValueCalculation zoomCalc; if (calculateExpecteds) { zoomCalc = new ExpectedValueCalculation(chromosomeHandler, zoom.getBinSize(), fragmentCountMap, NormalizationHandler.NONE); } else { zoomCalc = null; } for (int i = 0; i < sortedBlockNumbers.size(); i++) { Block currentBlock = reader.readNormalizedBlock(sortedBlockNumbers.get(i), this, NormalizationHandler.NONE); int num = sortedBlockNumbers.get(i); // Output block long position = los.getWrittenCount(); writeBlock(currentBlock, los, compressor, zoomCalc, subsampleFraction, randomSubsampleGenerator); long size = los.getWrittenCount() - position; indexEntries.add(new IndexEntry(num, position, (int) size)); //System.err.println(num + " " + position + " " + size); } return new Pair<>(indexEntries, zoomCalc); } // Merge and write out blocks multithreaded. public Pair,ExpectedValueCalculation> mergeAndWriteBlocks(LittleEndianOutputStream[] losArray, Deflater compressor, int whichZoom, int numResolutions, boolean calculateExpecteds, Map fragmentCountMap, ChromosomeHandler chromosomeHandler, double subsampleFraction, Random randomSubsampleGenerator) { List sortedBlockNumbers = reader.getBlockNumbers(this); int numCPUThreads = (losArray.length - 1) / numResolutions; List sortedBlockSizes = new ArrayList<>(); long totalBlockSize = 0; for (int i = 0; i < sortedBlockNumbers.size(); i++) { int blockSize = reader.getBlockSize(this, sortedBlockNumbers.get(i)); sortedBlockSizes.add(blockSize); totalBlockSize += blockSize; } ExecutorService executor = Executors.newFixedThreadPool(numCPUThreads); Map blockChunkSizes = new ConcurrentHashMap<>(numCPUThreads); Map> chunkBlockIndexes = new ConcurrentHashMap<>(numCPUThreads); ExpectedValueCalculation zoomCalc; Map localExpectedValueCalculations; if (calculateExpecteds) { zoomCalc = new ExpectedValueCalculation(chromosomeHandler, zoom.getBinSize(), fragmentCountMap, NormalizationHandler.NONE); localExpectedValueCalculations = new ConcurrentHashMap<>(numCPUThreads); } else { zoomCalc = null; localExpectedValueCalculations = null; } int placeholder = 0; for (int l = 0; l < numCPUThreads; l++) { final int threadNum = l; final int whichLos = numCPUThreads * whichZoom + threadNum; final long blockSizePerThread = (long) Math.floor(1.5 * (long) Math.floor(totalBlockSize / numCPUThreads)); final int startBlock; if (l == 0) { startBlock = 0; } else { startBlock = placeholder; } int tmpEnd = startBlock + ((int) Math.floor((double) sortedBlockNumbers.size() / numCPUThreads)) - 1; long tmpBlockSize = 0; int tmpEnd2 = 0; for (int b = startBlock; b <= tmpEnd; b++) { tmpBlockSize += sortedBlockSizes.get(b); if (tmpBlockSize > blockSizePerThread) { tmpEnd2 = b-1; break; } } if (tmpEnd2 > 0) { tmpEnd = tmpEnd2; } if (l + 1 == numCPUThreads && tmpEnd < sortedBlockNumbers.size()-1) { tmpEnd = sortedBlockNumbers.size()-1; } final int endBlock = tmpEnd; placeholder = endBlock + 1; //System.err.println(binSize + " " + blockNumbers.size() + " " + sortedBlockNumbers.length + " " + startBlock + " " + endBlock); if (startBlock > endBlock) { blockChunkSizes.put(threadNum,(long) 0); continue; } List indexEntries = new ArrayList<>(); final ExpectedValueCalculation calc; if (calculateExpecteds) { calc = new ExpectedValueCalculation(chromosomeHandler, zoom.getBinSize(), fragmentCountMap, NormalizationHandler.NONE); } else { calc = null; } Runnable worker = new Runnable() { @Override public void run() { try { writeBlockChunk(startBlock, endBlock, sortedBlockNumbers, losArray, whichLos, indexEntries, calc, subsampleFraction, randomSubsampleGenerator); } catch (Exception e) { e.printStackTrace(); } chunkBlockIndexes.put(whichLos,indexEntries); if (calculateExpecteds) { localExpectedValueCalculations.put(threadNum, calc); } } }; executor.execute(worker); } executor.shutdown(); // Wait until all threads finish while (!executor.isTerminated()) { try { Thread.sleep(50); } catch (InterruptedException e) { System.err.println(e.getLocalizedMessage()); } } long adjust = 0; for (int i = 0; i < losArray.length; i++) { blockChunkSizes.put(i, losArray[i].getWrittenCount()); if (i < numCPUThreads*whichZoom) { adjust += blockChunkSizes.get(i); } } List finalIndexEntries = new ArrayList<>(); for (int i = numCPUThreads*whichZoom ; i < numCPUThreads * (whichZoom + 1); i++) { adjust += blockChunkSizes.get(i); if (chunkBlockIndexes.get(i) != null) { for (int j = 0; j < chunkBlockIndexes.get(i).size(); j++) { long newPos = chunkBlockIndexes.get(i).get(j).position + adjust; //System.err.println(chunkBlockIndexes.get(i).get(j).id + " " + newPos + " " + chunkBlockIndexes.get(i).get(j).size); finalIndexEntries.add(new IndexEntry(chunkBlockIndexes.get(i).get(j).id, chunkBlockIndexes.get(i).get(j).position + adjust, chunkBlockIndexes.get(i).get(j).size)); } } } for (int l = 0; l < numCPUThreads; l++) { if (calculateExpecteds) { ExpectedValueCalculation tmpCalc = localExpectedValueCalculations.get(l); if (tmpCalc != null) { zoomCalc.merge(tmpCalc); } tmpCalc = null; } } return new Pair<>(finalIndexEntries, zoomCalc); } private void writeBlockChunk(int startBlock, int endBlock, List sortedBlockNumbers, LittleEndianOutputStream[] losArray, int threadNum, List indexEntries, ExpectedValueCalculation calc, double subsampleFraction, Random randomSubsampleGenerator) throws IOException{ Deflater compressor = new Deflater(); compressor.setLevel(Deflater.DEFAULT_COMPRESSION); //System.err.println(threadBlocks.length); for (int i = startBlock; i <= endBlock; i++) { Block currentBlock = reader.readNormalizedBlock(sortedBlockNumbers.get(i), this, NormalizationHandler.NONE); int num = sortedBlockNumbers.get(i); if (currentBlock != null) { long position = losArray[threadNum + 1].getWrittenCount(); writeBlock(currentBlock, losArray[threadNum + 1], compressor, calc, subsampleFraction, randomSubsampleGenerator); long size = losArray[threadNum + 1].getWrittenCount() - position; indexEntries.add(new IndexEntry(num, position, (int) size)); } currentBlock.clear(); //System.err.println("Used Memory after writing block " + i); //System.err.println(Runtime.getRuntime().totalMemory() - Runtime.getRuntime().freeMemory()); } } /** * Note -- compressed * * @param block Block to write * @throws IOException */ protected void writeBlock(Block block, LittleEndianOutputStream los, Deflater compressor, ExpectedValueCalculation calc, double subsampleFraction, Random randomSubsampleGenerator) throws IOException { final List records; if (subsampleFraction < 1) { records = block.getContactRecords(subsampleFraction, randomSubsampleGenerator);// getContactRecords(); } else { records = block.getContactRecords(); } // System.out.println("Write contact records : records count = " + records.size()); // Count records first int nRecords = records.size(); BufferedByteWriter buffer = new BufferedByteWriter(nRecords * 12); buffer.putInt(nRecords); // Find extents of occupied cells int binXOffset = Integer.MAX_VALUE; int binYOffset = Integer.MAX_VALUE; int binXMax = 0; int binYMax = 0; for (ContactRecord entry : records) { binXOffset = Math.min(binXOffset, entry.getBinX()); binYOffset = Math.min(binYOffset, entry.getBinY()); binXMax = Math.max(binXMax, entry.getBinX()); binYMax = Math.max(binYMax, entry.getBinY()); } buffer.putInt(binXOffset); buffer.putInt(binYOffset); // Sort keys in row-major order records.sort(new Comparator() { @Override public int compare(ContactRecord o1, ContactRecord o2) { if (o1.getBinY() != o2.getBinY()) { return o1.getBinY() - o2.getBinY(); } else { return o1.getBinX() - o2.getBinX(); } } }); ContactRecord lastRecord = records.get(records.size() - 1); final short w = (short) (binXMax - binXOffset + 1); final int w1 = binXMax - binXOffset + 1; final int w2 = binYMax - binYOffset + 1; boolean isInteger = true; float maxCounts = 0; LinkedHashMap> rows = new LinkedHashMap<>(); for (ContactRecord record : records) { float counts = record.getCounts(); if (counts >= 0) { isInteger = isInteger && (Math.floor(counts) == counts); maxCounts = Math.max(counts, maxCounts); final int px = record.getBinX() - binXOffset; final int py = record.getBinY() - binYOffset; if (calc != null && chr1.getIndex() == chr2.getIndex()) { calc.addDistance(chr1.getIndex(), record.getBinX(), record.getBinY(), counts); } List row = rows.get(py); if (row == null) { row = new ArrayList<>(10); rows.put(py, row); } row.add(new ContactRecord(px, py, counts)); } } // Compute size for each representation and choose smallest boolean useShort = isInteger && (maxCounts < Short.MAX_VALUE); boolean useShortBinX = w1 < Short.MAX_VALUE; boolean useShortBinY = w2 < Short.MAX_VALUE; int valueSize = useShort ? 2 : 4; int lorSize = 0; int nDensePts = (lastRecord.getBinY() - binYOffset) * w + (lastRecord.getBinX() - binXOffset) + 1; int denseSize = nDensePts * valueSize; for (List row : rows.values()) { lorSize += 4 + row.size() * valueSize; } buffer.put((byte) (useShort ? 0 : 1)); buffer.put((byte) (useShortBinX ? 0 : 1)); buffer.put((byte) (useShortBinY ? 0 : 1)); //dense calculation is incorrect for v9 denseSize = Integer.MAX_VALUE; if (lorSize < denseSize) { buffer.put((byte) 1); // List of rows representation if (useShortBinY) { buffer.putShort((short) rows.size()); // # of rows } else { buffer.putInt(rows.size()); // # of rows } for (Map.Entry> entry : rows.entrySet()) { int py = entry.getKey(); List row = entry.getValue(); if (useShortBinY) { buffer.putShort((short) py); // Row number } else { buffer.putInt(py); // Row number } if (useShortBinX) { buffer.putShort((short) row.size()); // size of row } else { buffer.putInt(row.size()); // size of row } for (ContactRecord contactRecord : row) { if (useShortBinX) { buffer.putShort((short) (contactRecord.getBinX())); } else { buffer.putInt(contactRecord.getBinX()); } final float counts = contactRecord.getCounts(); if (useShort) { buffer.putShort((short) counts); } else { buffer.putFloat(counts); } } } } else { buffer.put((byte) 2); // Dense matrix buffer.putInt(nDensePts); buffer.putShort(w); int lastIdx = 0; for (ContactRecord p : records) { int idx = (p.getBinY() - binYOffset) * w + (p.getBinX() - binXOffset); for (int i = lastIdx; i < idx; i++) { // Filler value if (useShort) { buffer.putShort(Short.MIN_VALUE); } else { buffer.putFloat(Float.NaN); } } float counts = p.getCounts(); if (useShort) { buffer.putShort((short) counts); } else { buffer.putFloat(counts); } lastIdx = idx + 1; } } byte[] bytes = buffer.getBytes(); byte[] compressedBytes = compress(bytes, compressor); los.write(compressedBytes); } /** * todo should this be synchronized? * * @param data * @param compressor * @return */ protected byte[] compress(byte[] data, Deflater compressor) { // Give the compressor the data to compress compressor.reset(); compressor.setInput(data); compressor.finish(); // Create an expandable byte array to hold the compressed data. // You cannot use an array that's the same size as the orginal because // there is no guarantee that the compressed data will be smaller than // the uncompressed data. ByteArrayOutputStream bos = new ByteArrayOutputStream(data.length); // Compress the data byte[] buf = new byte[1024]; while (!compressor.finished()) { int count = compressor.deflate(buf); bos.write(buf, 0, count); } try { bos.close(); } catch (IOException e) { System.err.println("Error clossing ByteArrayOutputStream"); e.printStackTrace(); } return bos.toByteArray(); } // Merge and write out blocks multithreaded. public ExpectedValueCalculation computeExpected(boolean calculateExpecteds, Map fragmentCountMap, ChromosomeHandler chromosomeHandler, int numCPUThreads) { List sortedBlockNumbers = reader.getBlockNumbers(this); List sortedBlockSizes = new ArrayList<>(); long totalBlockSize = 0; for (int i = 0; i < sortedBlockNumbers.size(); i++) { int blockSize = reader.getBlockSize(this, sortedBlockNumbers.get(i)); sortedBlockSizes.add(blockSize); totalBlockSize += blockSize; } ExecutorService executor = Executors.newFixedThreadPool(numCPUThreads); Map blockChunkSizes = new ConcurrentHashMap<>(numCPUThreads); ExpectedValueCalculation zoomCalc; Map localExpectedValueCalculations; if (calculateExpecteds) { zoomCalc = new ExpectedValueCalculation(chromosomeHandler, zoom.getBinSize(), fragmentCountMap, NormalizationHandler.NONE); localExpectedValueCalculations = new ConcurrentHashMap<>(numCPUThreads); } else { zoomCalc = null; localExpectedValueCalculations = null; } int placeholder = 0; for (int l = 0; l < numCPUThreads; l++) { final int threadNum = l; final long blockSizePerThread = (long) Math.floor(1.5 * (long) Math.floor(totalBlockSize / numCPUThreads)); final int startBlock; if (l == 0) { startBlock = 0; } else { startBlock = placeholder; } int tmpEnd = startBlock + ((int) Math.floor((double) sortedBlockNumbers.size() / numCPUThreads)) - 1; long tmpBlockSize = 0; int tmpEnd2 = 0; for (int b = startBlock; b <= tmpEnd; b++) { tmpBlockSize += sortedBlockSizes.get(b); if (tmpBlockSize > blockSizePerThread) { tmpEnd2 = b-1; break; } } if (tmpEnd2 > 0) { tmpEnd = tmpEnd2; } if (l + 1 == numCPUThreads && tmpEnd < sortedBlockNumbers.size()-1) { tmpEnd = sortedBlockNumbers.size()-1; } final int endBlock = tmpEnd; placeholder = endBlock + 1; //System.err.println(binSize + " " + blockNumbers.size() + " " + sortedBlockNumbers.length + " " + startBlock + " " + endBlock); if (startBlock > endBlock) { blockChunkSizes.put(threadNum,(long) 0); continue; } List indexEntries = new ArrayList<>(); final ExpectedValueCalculation calc; if (calculateExpecteds) { calc = new ExpectedValueCalculation(chromosomeHandler, zoom.getBinSize(), fragmentCountMap, NormalizationHandler.NONE); } else { calc = null; } Runnable worker = new Runnable() { @Override public void run() { try { calculateExpectedBlockChunk(startBlock, endBlock, sortedBlockNumbers, calc); } catch (Exception e) { e.printStackTrace(); } if (calculateExpecteds) { localExpectedValueCalculations.put(threadNum, calc); } } }; executor.execute(worker); } executor.shutdown(); // Wait until all threads finish while (!executor.isTerminated()) { try { Thread.sleep(50); } catch (InterruptedException e) { System.err.println(e.getLocalizedMessage()); } } for (int l = 0; l < numCPUThreads; l++) { if (calculateExpecteds) { ExpectedValueCalculation tmpCalc = localExpectedValueCalculations.get(l); if (tmpCalc != null) { zoomCalc.merge(tmpCalc); } tmpCalc = null; } } return zoomCalc; } private void calculateExpectedBlockChunk(int startBlock, int endBlock, List sortedBlockNumbers, ExpectedValueCalculation calc ) throws IOException{ //System.err.println(threadBlocks.length); for (int i = startBlock; i <= endBlock; i++) { Block currentBlock = reader.readNormalizedBlock(sortedBlockNumbers.get(i), this, NormalizationHandler.NONE); int num = sortedBlockNumbers.get(i); if (currentBlock != null) { calcExpectedBlock(currentBlock, calc); } currentBlock.clear(); //System.err.println("Used Memory after writing block " + i); //System.err.println(Runtime.getRuntime().totalMemory() - Runtime.getRuntime().freeMemory()); } } protected void calcExpectedBlock(Block block, ExpectedValueCalculation calc) throws IOException { final List records = block.getContactRecords();// getContactRecords(); // System.out.println("Write contact records : records count = " + records.size()); // Count records first int nRecords = records.size(); // Find extents of occupied cells int binXOffset = Integer.MAX_VALUE; int binYOffset = Integer.MAX_VALUE; int binXMax = 0; int binYMax = 0; for (ContactRecord entry : records) { binXOffset = Math.min(binXOffset, entry.getBinX()); binYOffset = Math.min(binYOffset, entry.getBinY()); binXMax = Math.max(binXMax, entry.getBinX()); binYMax = Math.max(binYMax, entry.getBinY()); } // Sort keys in row-major order records.sort(new Comparator() { @Override public int compare(ContactRecord o1, ContactRecord o2) { if (o1.getBinY() != o2.getBinY()) { return o1.getBinY() - o2.getBinY(); } else { return o1.getBinX() - o2.getBinX(); } } }); ContactRecord lastRecord = records.get(records.size() - 1); final short w = (short) (binXMax - binXOffset + 1); final int w1 = binXMax - binXOffset + 1; final int w2 = binYMax - binYOffset + 1; boolean isInteger = true; float maxCounts = 0; for (ContactRecord record : records) { float counts = record.getCounts(); if (counts >= 0) { isInteger = isInteger && (Math.floor(counts) == counts); maxCounts = Math.max(counts, maxCounts); final int px = record.getBinX() - binXOffset; final int py = record.getBinY() - binYOffset; if (calc != null && chr1.getIndex() == chr2.getIndex()) { calc.addDistance(chr1.getIndex(), record.getBinX(), record.getBinY(), counts); } } } } } ================================================ FILE: src/juicebox/data/NormFactorMapReader.java ================================================ /* * The MIT License (MIT) * * Copyright (c) 2011-2021 Broad Institute, Aiden Lab, Rice University, Baylor College of Medicine * * Permission is hereby granted, free of charge, to any person obtaining a copy * of this software and associated documentation files (the "Software"), to deal * in the Software without restriction, including without limitation the rights * to use, copy, modify, merge, publish, distribute, sublicense, and/or sell * copies of the Software, and to permit persons to whom the Software is * furnished to do so, subject to the following conditions: * * The above copyright notice and this permission notice shall be included in * all copies or substantial portions of the Software. * * THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR * IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, * FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE * AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER * LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, * OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN * THE SOFTWARE. */ package juicebox.data; import htsjdk.tribble.util.LittleEndianInputStream; import java.io.IOException; import java.util.LinkedHashMap; import java.util.Map; public class NormFactorMapReader { private final int version, nFactors; private final Map normFactors = new LinkedHashMap<>(); public NormFactorMapReader(int nFactors, int version, LittleEndianInputStream dis) throws IOException { this.version = version; this.nFactors = nFactors; for (int j = 0; j < nFactors; j++) { int chrIdx = dis.readInt(); if (version > 8) { normFactors.put(chrIdx, (double) dis.readFloat()); } else { normFactors.put(chrIdx, dis.readDouble()); } } } public Map getNormFactors() { return normFactors; } public int getOffset() { if (version > 8) { return 8 * nFactors; } else { return 12 * nFactors; } } } ================================================ FILE: src/juicebox/data/NormalizationVector.java ================================================ /* * The MIT License (MIT) * * Copyright (c) 2011-2021 Broad Institute, Aiden Lab, Rice University, Baylor College of Medicine * * Permission is hereby granted, free of charge, to any person obtaining a copy * of this software and associated documentation files (the "Software"), to deal * in the Software without restriction, including without limitation the rights * to use, copy, modify, merge, publish, distribute, sublicense, and/or sell * copies of the Software, and to permit persons to whom the Software is * furnished to do so, subject to the following conditions: * * The above copyright notice and this permission notice shall be included in * all copies or substantial portions of the Software. * * THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR * IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, * FITNESS FOR A PARTICULAR PURPOSE AND NON-INFRINGEMENT. IN NO EVENT SHALL THE * AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER * LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, * OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN * THE SOFTWARE. */ package juicebox.data; import juicebox.HiC; import juicebox.data.basics.Chromosome; import juicebox.data.basics.ListOfDoubleArrays; import juicebox.data.basics.ListOfFloatArrays; import juicebox.data.iterator.IteratorContainer; import juicebox.tools.utils.norm.ZeroScale; import juicebox.windowui.HiCZoom; import juicebox.windowui.NormalizationType; /** * @author jrobinso * Date: 2/10/13 * Time: 9:19 AM */ public class NormalizationVector { private final NormalizationType type; private final int chrIdx; private final HiC.Unit unit; private final int resolution; private final ListOfDoubleArrays data; private boolean needsToBeScaledTo = false; public NormalizationVector(NormalizationType type, int chrIdx, HiC.Unit unit, int resolution, ListOfDoubleArrays data) { this.type = type; this.chrIdx = chrIdx; this.unit = unit; this.resolution = resolution; this.data = data; } public NormalizationVector(NormalizationType type, int chrIdx, HiC.Unit unit, int resolution, ListOfDoubleArrays data, boolean needsToBeScaledTo) { this(type, chrIdx, unit, resolution, data); this.needsToBeScaledTo = needsToBeScaledTo; } public static String getKey(NormalizationType type, int chrIdx, String unit, int resolution) { return type + "_" + chrIdx + "_" + unit + "_" + resolution; } public int getChrIdx() { return chrIdx; } public int getResolution() { return resolution; } public String getKey() { return NormalizationVector.getKey(type, chrIdx, unit.toString(), resolution); } public ListOfDoubleArrays getData() { return data; } public boolean doesItNeedToBeScaledTo() { return needsToBeScaledTo; } public NormalizationVector mmbaScaleToVector(Dataset ds) { Chromosome chromosome = ds.getChromosomeHandler().getChromosomeFromIndex(chrIdx); MatrixZoomData zd = HiCFileTools.getMatrixZoomData(ds, chromosome, chromosome, new HiCZoom(unit, resolution)); if (zd == null) return null; return mmbaScaleToVector(zd.getIteratorContainer()); } public NormalizationVector mmbaScaleToVector(IteratorContainer ic) { ListOfFloatArrays newNormVector = ZeroScale.scale(ic, data.convertToFloats(), getKey()); if (newNormVector != null) { newNormVector = ZeroScale.normalizeVectorByScaleFactor(newNormVector, ic); } ListOfDoubleArrays newDoubleNormVector = newNormVector.convertToDoubles(); return new NormalizationVector(type, chrIdx, unit, resolution, newDoubleNormVector); } } ================================================ FILE: src/juicebox/data/ZoomAction.java ================================================ /* * The MIT License (MIT) * * Copyright (c) 2011-2020 Broad Institute, Aiden Lab, Rice University, Baylor College of Medicine * * Permission is hereby granted, free of charge, to any person obtaining a copy * of this software and associated documentation files (the "Software"), to deal * in the Software without restriction, including without limitation the rights * to use, copy, modify, merge, publish, distribute, sublicense, and/or sell * copies of the Software, and to permit persons to whom the Software is * furnished to do so, subject to the following conditions: * * The above copyright notice and this permission notice shall be included in * all copies or substantial portions of the Software. * * THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR * IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, * FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE * AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER * LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, * OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN * THE SOFTWARE. */ package juicebox.data; import juicebox.HiC; import juicebox.windowui.HiCZoom; /** * Created by ranganmostofa on 7/8/17. */ public class ZoomAction { private final String chromosomeX, chromosomeY; private final HiCZoom hiCZoom; private final long genomeX, genomeY; private double scaleFactor; private final boolean resetZoom; private final HiC.ZoomCallType zoomCallType; private final int resolutionLocked; public ZoomAction(String chromosomeX, String chromosomeY, HiCZoom hiCZoom, long genomeX, long genomeY, double scaleFactor, boolean resetZoom, HiC.ZoomCallType zoomCallType, int resolutionLocked) { this.chromosomeX = chromosomeX; this.chromosomeY = chromosomeY; this.hiCZoom = hiCZoom; this.genomeX = genomeX; this.genomeY = genomeY; this.scaleFactor = scaleFactor; this.resetZoom = resetZoom; this.zoomCallType = zoomCallType; this.resolutionLocked = resolutionLocked; } public boolean equals(ZoomAction other) { return this == other || other != null && chromosomeX.equals(other.getChromosomeX()) && chromosomeY.equals(other.getChromosomeY()) && hiCZoom.equals(other.getHiCZoom()) && genomeX == other.getGenomeX() && genomeY == other.getGenomeY() && scaleFactor == other.getScaleFactor() && resetZoom == other.getResetZoom() && zoomCallType == other.getZoomCallType() && resolutionLocked == other.getResolutionLocked(); } public String getChromosomeX() { return this.chromosomeX; } public String getChromosomeY() { return this.chromosomeY; } public HiCZoom getHiCZoom() { return this.hiCZoom; } public long getGenomeX() { return this.genomeX; } public long getGenomeY() { return this.genomeY; } public double getScaleFactor() { return this.scaleFactor; } public void setScaleFactor(double newScaleFactor) { this.scaleFactor = newScaleFactor; } public boolean getResetZoom() { return this.resetZoom; } public HiC.ZoomCallType getZoomCallType() { return this.zoomCallType; } public int getResolutionLocked() { return this.resolutionLocked; } } ================================================ FILE: src/juicebox/data/ZoomActionTracker.java ================================================ /* * The MIT License (MIT) * * Copyright (c) 2011-2020 Broad Institute, Aiden Lab, Rice University, Baylor College of Medicine * * Permission is hereby granted, free of charge, to any person obtaining a copy * of this software and associated documentation files (the "Software"), to deal * in the Software without restriction, including without limitation the rights * to use, copy, modify, merge, publish, distribute, sublicense, and/or sell * copies of the Software, and to permit persons to whom the Software is * furnished to do so, subject to the following conditions: * * The above copyright notice and this permission notice shall be included in * all copies or substantial portions of the Software. * * THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR * IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, * FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE * AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER * LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, * OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN * THE SOFTWARE. */ package juicebox.data; import java.util.Stack; /** * Created by ranganmostofa on 7/8/17. */ public class ZoomActionTracker { private final int stackSizeLimit = 100; private ZoomAction currentZoomAction; private final Stack undoZoomActions = new Stack<>(); private final Stack redoZoomActions = new Stack<>(); public void undoZoom() { if (validateUndoZoom()) { redoZoomActions.push(undoZoomActions.pop()); setCurrentZoomAction(undoZoomActions.peek()); } } public void redoZoom() { if (validateRedoZoom()) { undoZoomActions.push(redoZoomActions.pop()); setCurrentZoomAction(undoZoomActions.peek()); } } public boolean validateUndoZoom() { return undoZoomActions.size() > 1; } public boolean validateRedoZoom() { return !redoZoomActions.isEmpty(); } public void addZoomState(ZoomAction newZoomAction) { undoZoomActions.add(newZoomAction); setCurrentZoomAction(undoZoomActions.peek()); redoZoomActions.clear(); if (undoZoomActions.size() > stackSizeLimit) { undoZoomActions.remove(0); } } public void clear() { this.currentZoomAction = null; this.undoZoomActions.clear(); this.redoZoomActions.clear(); } public boolean equals(ZoomActionTracker other) { if (this == other) return true; if (other != null) { if (this.undoZoomActions.equals(other.getUndoZoomActions())) { if (this.redoZoomActions.equals(other.getRedoZoomActions())) { return this.currentZoomAction.equals(other.getCurrentZoomAction()); } } } return false; } public ZoomAction getCurrentZoomAction() { return this.currentZoomAction; } private void setCurrentZoomAction(ZoomAction zoomAction) { this.currentZoomAction = zoomAction; } private Stack getUndoZoomActions() { return this.undoZoomActions; } private Stack getRedoZoomActions() { return this.redoZoomActions; } } ================================================ FILE: src/juicebox/data/anchor/BEDTools.java ================================================ /* * The MIT License (MIT) * * Copyright (c) 2011-2020 Broad Institute, Aiden Lab * * Permission is hereby granted, free of charge, to any person obtaining a copy * of this software and associated documentation files (the "Software"), to deal * in the Software without restriction, including without limitation the rights * to use, copy, modify, merge, publish, distribute, sublicense, and/or sell * copies of the Software, and to permit persons to whom the Software is * furnished to do so, subject to the following conditions: * * The above copyright notice and this permission notice shall be included in * all copies or substantial portions of the Software. * * THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR * IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, * FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE * AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER * LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, * OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN * THE SOFTWARE. */ package juicebox.data.anchor; import java.util.*; /** * Created by muhammadsaadshamim on 11/17/15. */ class BEDTools { /** * BEDTools port of merge based on * http://bedtools.readthedocs.org/en/latest/content/tools/merge.html *

* NOTE - only default functionality supported at present (no additional flags) * * @param anchors * @return merged list of anchors */ public static List merge(List anchors) { Collections.sort(anchors); Set merged = new HashSet<>(); if (anchors.size() > 0) { GenericLocus current = (GenericLocus) anchors.get(0).deepClone(); for (GenericLocus anchor : anchors) { if (anchor.hasOverlapWith(current)) { current.mergeWith(anchor); } else { merged.add(current); current = (GenericLocus) anchor.deepClone(); } } merged.add(current); // in case last merger missed (i.e. boolean evaluated to true) } return new ArrayList<>(merged); } public static List mergeTakeSmaller(List anchors) { Collections.sort(anchors); Set merged = new HashSet<>(); if (anchors.size() > 0) { GenericLocus current = (GenericLocus) anchors.get(0).deepClone(); for (GenericLocus anchor : anchors) { if (anchor.hasOverlapWith(current)) { current.mergeWithTakeSmaller(anchor); } else { merged.add(current); current = (GenericLocus) anchor.deepClone(); } } merged.add(current); // in case last merger missed (i.e. boolean evaluated to true) } return new ArrayList<>(merged); } /** * BEDTools port of intersect based on * http://bedtools.readthedocs.org/en/latest/content/tools/intersect.html *

* NOTE - only default functionality supported at present (no additional flags) * * @param topAnchors * @param bottomAnchors * @return intersection of two anchor lists */ public static List intersect(List topAnchors, List bottomAnchors, boolean conductFullIntersection) { Collections.sort(topAnchors); Collections.sort(bottomAnchors); Set intersected = new HashSet<>(); int topIndex = 0; int bottomIndex = 0; int maxTopIndex = topAnchors.size(); int maxBottomIndex = bottomAnchors.size(); while (topIndex < maxTopIndex && bottomIndex < maxBottomIndex) { GenericLocus topAnchor = topAnchors.get(topIndex); GenericLocus bottomAnchor = bottomAnchors.get(bottomIndex); if (topAnchor.hasOverlapWith(bottomAnchor) || bottomAnchor.hasOverlapWith(topAnchor)) { //List tempIntersected = new ArrayList(); // iterate over all possible intersections with top element for (int i = bottomIndex; i < maxBottomIndex; i++) { GenericLocus newAnchor = bottomAnchors.get(i); if (topAnchor.hasOverlapWith(newAnchor) || newAnchor.hasOverlapWith(topAnchor)) { intersected.add(intersection(topAnchor, newAnchor, conductFullIntersection)); } else { break; } } // iterate over all possible intersections with bottom element // start from +1 because +0 checked in the for loop above for (int i = topIndex + 1; i < maxTopIndex; i++) { GenericLocus newAnchor = topAnchors.get(i); if (bottomAnchor.hasOverlapWith(newAnchor) || newAnchor.hasOverlapWith(bottomAnchor)) { intersected.add(intersection(bottomAnchor, newAnchor, conductFullIntersection)); } else { break; } } //intersected.addAll(merge(tempIntersected)); // increment both topIndex++; bottomIndex++; } else if (topAnchor.isStrictlyToTheLeftOf(bottomAnchor)) { topIndex++; } else if (topAnchor.isStrictlyToTheRightOf(bottomAnchor)) { bottomIndex++; } else { System.err.println("Error while intersecting anchors."); System.err.println(topAnchor + " & " + bottomAnchor); } } return new ArrayList<>(intersected); } /** * @param anchor1 * @param anchor2 * @return intersection of anchor1 and anchor2 */ private static GenericLocus intersection(GenericLocus anchor1, GenericLocus anchor2, boolean conductFullIntersection) { if (anchor1.getChr().equals(anchor2.getChr())) { long start = Math.max(anchor1.getX1(), anchor2.getX1()); long end = Math.min(anchor1.getX2(), anchor2.getX2()); if (start > end) { System.err.println("err _ " + start + " " + end); } GenericLocus intersectedMotif; if (anchor1 instanceof MotifAnchor || anchor2 instanceof MotifAnchor) { intersectedMotif = new MotifAnchor(anchor1.getChr(), start, end); } else { intersectedMotif = new GenericLocus(anchor1.getChr(), start, end); } // if all secondary attributes are also to be copied if (conductFullIntersection) { if (anchor1 instanceof MotifAnchor) { if (((MotifAnchor) anchor1).hasFIMOAttributes()) { ((MotifAnchor) intersectedMotif).addFIMOAttributesFrom((MotifAnchor) anchor1); } } else if (anchor2 instanceof MotifAnchor) { if (((MotifAnchor) anchor2).hasFIMOAttributes()) { ((MotifAnchor) intersectedMotif).addFIMOAttributesFrom((MotifAnchor) anchor2); } } intersectedMotif.addFeatureReferencesFrom(anchor1); intersectedMotif.addFeatureReferencesFrom(anchor2); } return intersectedMotif; } else { System.err.println("Error calculating intersection of anchors"); System.err.println(anchor1 + " & " + anchor2); } return null; } public static List preservativeIntersect(List topAnchors, List bottomAnchors, boolean conductFullIntersection) { Collections.sort(topAnchors); Collections.sort(bottomAnchors); Set intersected = new HashSet<>(); int topIndex = 0; int bottomIndex = 0; int maxTopIndex = topAnchors.size(); int maxBottomIndex = bottomAnchors.size(); while (topIndex < maxTopIndex && bottomIndex < maxBottomIndex) { GenericLocus topAnchor = topAnchors.get(topIndex); GenericLocus bottomAnchor = bottomAnchors.get(bottomIndex); if (topAnchor.hasOverlapWith(bottomAnchor) || bottomAnchor.hasOverlapWith(topAnchor)) { // iterate over all possible intersections with top element //List tempIntersection = new ArrayList(); for (int i = bottomIndex; i < maxBottomIndex; i++) { GenericLocus newAnchor = bottomAnchors.get(i); if (topAnchor.hasOverlapWith(newAnchor) || newAnchor.hasOverlapWith(topAnchor)) { intersected.add(preservativeIntersection(topAnchor, newAnchor, conductFullIntersection)); } else { break; } } // iterate over all possible intersections with bottom element // start from +1 because +0 checked in the for loop above for (int i = topIndex + 1; i < maxTopIndex; i++) { GenericLocus newAnchor = topAnchors.get(i); if (bottomAnchor.hasOverlapWith(newAnchor) || newAnchor.hasOverlapWith(bottomAnchor)) { intersected.add(preservativeIntersection(newAnchor, bottomAnchor, conductFullIntersection)); } else { break; } } //intersected.addAll(merge(tempIntersection)); // increment both topIndex++; bottomIndex++; } else if (topAnchor.isStrictlyToTheLeftOf(bottomAnchor)) { topIndex++; } else if (topAnchor.isStrictlyToTheRightOf(bottomAnchor)) { bottomIndex++; } else { System.err.println("Error while intersecting anchors."); System.err.println(topAnchor + " & " + bottomAnchor); } } return new ArrayList<>(intersected); } /** * @param anchor1 * @param anchor2 * @return preservative intersection of anchor1 and anchor2 */ private static GenericLocus preservativeIntersection(GenericLocus anchor1, GenericLocus anchor2, boolean conductFullIntersection) { if (anchor1.getChr().equals(anchor2.getChr())) { GenericLocus intersectedMotif; if (anchor1 instanceof MotifAnchor) { intersectedMotif = (MotifAnchor) anchor1.deepClone(); } else if (anchor2 instanceof MotifAnchor) { intersectedMotif = (MotifAnchor) anchor1.cloneToMotifAnchor(); } else { intersectedMotif = (GenericLocus) anchor1.deepClone(); } // if all secondary attributes are also to be copied if (conductFullIntersection) { if (anchor2 instanceof MotifAnchor) { if (((MotifAnchor) anchor2).hasFIMOAttributes()) { ((MotifAnchor) intersectedMotif).addFIMOAttributesFrom((MotifAnchor) anchor2); } } intersectedMotif.addFeatureReferencesFrom(anchor2); } return intersectedMotif; } else { System.err.println("Error calculating preservative intersection of anchors"); System.err.println(anchor1 + " & " + anchor2); } return null; } } ================================================ FILE: src/juicebox/data/anchor/GenericLocus.java ================================================ /* * The MIT License (MIT) * * Copyright (c) 2011-2020 Broad Institute, Aiden Lab * * Permission is hereby granted, free of charge, to any person obtaining a copy * of this software and associated documentation files (the "Software"), to deal * in the Software without restriction, including without limitation the rights * to use, copy, modify, merge, publish, distribute, sublicense, and/or sell * copies of the Software, and to permit persons to whom the Software is * furnished to do so, subject to the following conditions: * * The above copyright notice and this permission notice shall be included in * all copies or substantial portions of the Software. * * THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR * IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, * FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE * AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER * LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, * OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN * THE SOFTWARE. */ package juicebox.data.anchor; import juicebox.data.feature.Feature; import juicebox.track.feature.Feature2D; import java.util.ArrayList; import java.util.List; import java.util.Objects; public class GenericLocus extends Feature implements Comparable { // critical components of a motif anchor protected final String chr; // references to original features if applicable protected final List originalFeatures1 = new ArrayList<>(); protected final List originalFeatures2 = new ArrayList<>(); protected long x1, x2; protected String name = ""; /** * Inititalize locus given parameters (e.g. from BED file) * * @param chr * @param x1 * @param x2 */ public GenericLocus(String chr, long x1, long x2) { this.chr = chr; if (x1 <= x2) { // x1 < x2 this.x1 = x1; this.x2 = x2; } else { System.err.println("Improperly formatted Motif file: chr " + chr + " x1 " + x1 + " x2 " + x2); // todo throw new InvalidObjectException(); } } public GenericLocus(String chr, int x1, int x2, String name) { this(chr, x1, x2); this.name = name; } /** * Inititalize anchor given parameters (e.g. from feature list) * * @param chrIndex * @param x1 * @param x2 * @param originalFeatures1 * @param originalFeatures2 */ public GenericLocus(String chrIndex, long x1, long x2, List originalFeatures1, List originalFeatures2) { this(chrIndex, x1, x2); this.originalFeatures1.addAll(originalFeatures1); this.originalFeatures2.addAll(originalFeatures2); } @Override public String getKey() { return "" + chr; } @Override public Feature deepClone() { GenericLocus clone = new GenericLocus(chr, x1, x2, originalFeatures1, originalFeatures2); clone.name = name; return clone; } public Feature cloneToMotifAnchor() { MotifAnchor clone = new MotifAnchor(chr, x1, x2, originalFeatures1, originalFeatures2); clone.name = name; return clone; } /** * @return chromosome name */ public String getChr() { return chr; } /** * @return start point */ public long getX1() { return x1; } /** * @return end point */ public long getX2() { return x2; } /** * @return width of this anchor */ public int getWidth() { return (int) (x2 - x1); } /** * Expand this anchor (symmetrically) by the width given * * @param width */ public void widenMargins(int width) { x1 = x1 - width / 2; x2 = x2 + width / 2; } /** * @param x * @return true if x is within bounds of anchor */ public boolean contains(long x) { return x >= x1 && x <= x2; } /** * @param anchor * @return true if this is strictly left of given anchor */ public boolean isStrictlyToTheLeftOf(GenericLocus anchor) { return x2 < anchor.x1; } /** * @param anchor * @return true if this is strictly right of given anchor */ public boolean isStrictlyToTheRightOf(GenericLocus anchor) { return anchor.x2 < x1; } /** * @param anchor * @return true if given anchor overlaps at either edge with this anchor */ public boolean hasOverlapWith(GenericLocus anchor) { return chr.equalsIgnoreCase(anchor.chr) && (this.contains(anchor.x1) || this.contains(anchor.x2) || anchor.contains(x1) || anchor.contains(x2)); } public void mergeWith(GenericLocus anchor) { if (chr.equalsIgnoreCase(anchor.chr)) { x1 = Math.min(x1, anchor.x1); x2 = Math.max(x2, anchor.x2); addFeatureReferencesFrom(anchor); } else { System.err.println("Attempted to merge anchors on different chromosomes"); System.err.println(this + " & " + anchor); } } public void mergeWithTakeSmaller(GenericLocus anchor) { if (chr.equalsIgnoreCase(anchor.chr)) { if (anchor.x1 >= x1 && anchor.x2 <= x2) { x1 = anchor.x1; x2 = anchor.x2; } else if (x1 >= anchor.x1 && x2 <= anchor.x2) { x1 = x1; x2 = x2; } else { x1 = Math.min(x1, anchor.x1); x2 = Math.max(x2, anchor.x2); } addFeatureReferencesFrom(anchor); } else { System.err.println("Attempted to merge anchors on different chromosomes"); System.err.println(this + " & " + anchor); } } @Override public String toString() { String chrString = chr.startsWith("chr") ? chr.substring(3) : chr; return "chr" + chrString + "\t" + x1 + "\t" + x2; } @Override public boolean equals(Object obj) { if (this == obj) { return true; } if (obj instanceof GenericLocus) { GenericLocus o = (GenericLocus) obj; return chr.equalsIgnoreCase(o.chr) && x1 == o.x1 && x2 == o.x2; } return false; } @Override public int hashCode() { return Objects.hash(x2, chr, x1); } @Override public int compareTo(GenericLocus o) { if (chr.equalsIgnoreCase(o.chr)) { if (x1 == o.x1) { return Long.compare(x2, o.x2); } return Long.compare(x1, o.x1); } return chr.compareTo(o.chr); } public void addFeatureReferencesFrom(GenericLocus anchor) { originalFeatures1.addAll(anchor.originalFeatures1); originalFeatures2.addAll(anchor.originalFeatures2); } public void updateOriginalFeatures(String prefix) { if ((originalFeatures1.size() > 0 || originalFeatures2.size() > 0)) { for (Feature2D feature : originalFeatures1) { feature.addStringAttribute(prefix+"_start_1", "" + x1); feature.addStringAttribute(prefix+"_end_1", "" + x2); } for (Feature2D feature : originalFeatures2) { feature.addStringAttribute(prefix+"_start_2", "" + x1); feature.addStringAttribute(prefix+"_end_2", "" + x2); } } } public List getOriginalFeatures1() { return originalFeatures1; } public List getOriginalFeatures2() { return originalFeatures2; } public boolean isDirectionalAnchor(boolean direction) { if (direction) { return originalFeatures1.size() > 0 && originalFeatures2.size() == 0; } else { return originalFeatures2.size() > 0 && originalFeatures1.size() == 0; } } public String getName() { return name; } } ================================================ FILE: src/juicebox/data/anchor/GenericLocusParser.java ================================================ /* * The MIT License (MIT) * * Copyright (c) 2011-2020 Broad Institute, Aiden Lab * * Permission is hereby granted, free of charge, to any person obtaining a copy * of this software and associated documentation files (the "Software"), to deal * in the Software without restriction, including without limitation the rights * to use, copy, modify, merge, publish, distribute, sublicense, and/or sell * copies of the Software, and to permit persons to whom the Software is * furnished to do so, subject to the following conditions: * * The above copyright notice and this permission notice shall be included in * all copies or substantial portions of the Software. * * THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR * IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, * FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE * AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER * LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, * OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN * THE SOFTWARE. */ package juicebox.data.anchor; import juicebox.HiCGlobals; import juicebox.data.ChromosomeHandler; import juicebox.data.basics.Chromosome; import juicebox.data.feature.GenomeWideList; import org.broad.igv.Globals; import org.broad.igv.util.ParsingUtils; import java.io.BufferedReader; import java.io.IOException; import java.io.InputStreamReader; import java.util.ArrayList; import java.util.HashSet; import java.util.List; import java.util.Set; public class GenericLocusParser { /** * @param handler * @param bedFilePath * @return List of motif anchors from the provided bed file */ public static GenomeWideList loadFromBEDFile(ChromosomeHandler handler, String bedFilePath) { List anchors = new ArrayList<>(); try { //BufferedReader br = ParsingUtils.openBufferedReader(bedFilePath); BufferedReader br = new BufferedReader(new InputStreamReader(ParsingUtils.openInputStream(bedFilePath)), HiCGlobals.bufferSize); anchors.addAll(parseBEDFile(br, handler)); } catch (IOException ec) { ec.printStackTrace(); } return new GenomeWideList<>(handler, anchors); } /** * Methods for handling BED Files */ /** * Helper function for actually parsing BED file * Ignores any attributes beyond the third column (i.e. just chr and positions are read) * * @param bufferedReader * @param handler * @return list of motifs * @throws IOException */ private static List parseBEDFile(BufferedReader bufferedReader, ChromosomeHandler handler) throws IOException { Set anchors = new HashSet<>(); String nextLine; int errorCount = 0; while ((nextLine = bufferedReader.readLine()) != null) { String[] tokens = Globals.tabPattern.split(nextLine); String chr1Name; int start1, end1; if (tokens[0].startsWith("chr") && tokens.length > 2) { // valid line chr1Name = tokens[0]; start1 = Integer.parseInt(tokens[1]); end1 = Integer.parseInt(tokens[2]); Chromosome chr = handler.getChromosomeFromName(chr1Name); if (chr == null) { if (errorCount < 10) { System.out.println("Skipping line: " + nextLine); } else if (errorCount == 10) { System.err.println("Maximum error count exceeded. Further errors will not be logged"); } errorCount++; continue; } anchors.add(new GenericLocus(chr.getName(), start1, end1)); } } if (anchors.size() < 1) System.err.println("BED File empty - file may have problems or error was encountered"); bufferedReader.close(); return new ArrayList<>(anchors); } } ================================================ FILE: src/juicebox/data/anchor/GenericLocusTools.java ================================================ /* * The MIT License (MIT) * * Copyright (c) 2011-2020 Broad Institute, Aiden Lab * * Permission is hereby granted, free of charge, to any person obtaining a copy * of this software and associated documentation files (the "Software"), to deal * in the Software without restriction, including without limitation the rights * to use, copy, modify, merge, publish, distribute, sublicense, and/or sell * copies of the Software, and to permit persons to whom the Software is * furnished to do so, subject to the following conditions: * * The above copyright notice and this permission notice shall be included in * all copies or substantial portions of the Software. * * THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR * IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, * FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE * AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER * LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, * OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN * THE SOFTWARE. */ package juicebox.data.anchor; import juicebox.HiCGlobals; import juicebox.data.ChromosomeHandler; import juicebox.data.basics.Chromosome; import juicebox.data.feature.FeatureFilter; import juicebox.data.feature.GenomeWideList; import juicebox.gui.SuperAdapter; import juicebox.track.feature.Feature2D; import juicebox.track.feature.Feature2DList; import juicebox.track.feature.FeatureFunction; import org.broad.igv.ui.util.MessageUtils; import java.util.ArrayList; import java.util.List; public class GenericLocusTools { /** * @param features * @return anchor list from features (i.e. split anchor1 and anchor2) */ public static GenomeWideList extractAnchorsFromIntrachromosomalFeatures(Feature2DList features, final boolean onlyUninitializedFeatures, final ChromosomeHandler handler, int expandSize) { final GenomeWideList extractedAnchorList = new GenomeWideList<>(handler); features.processLists(new FeatureFunction() { @Override public void process(String chr, List feature2DList) { List anchors = new ArrayList<>(); for (Feature2D f : feature2DList) { anchors.addAll(f.getAnchors(onlyUninitializedFeatures, handler)); } String newKey = chr.split("_")[0].replace("chr", ""); extractedAnchorList.setFeatures(newKey, anchors); } }); mergeAnchors(extractedAnchorList); expandSmallAnchors(extractedAnchorList, expandSize); return extractedAnchorList; } public static GenomeWideList extractAllAnchorsFromAllFeatures(Feature2DList features, final ChromosomeHandler handler) { final GenomeWideList extractedAnchorList = new GenomeWideList<>(handler); features.processLists(new FeatureFunction() { @Override public void process(String chr, List feature2DList) { for (Feature2D f : feature2DList) { Chromosome chrom = handler.getChromosomeFromName((f.getChr1())); extractedAnchorList.addFeature(chrom.getName(), new GenericLocus(chrom.getName(), f.getStart1(), f.getEnd1())); chrom = handler.getChromosomeFromName((f.getChr2())); extractedAnchorList.addFeature(chrom.getName(), new GenericLocus(chrom.getName(), f.getStart2(), f.getEnd2())); } } }); mergeAndExpandSmallAnchors(extractedAnchorList, getMinSizeForExpansionFromGUI()); return extractedAnchorList; } public static int getMinSizeForExpansionFromGUI() { int minSize = 10000; String newSize = MessageUtils.showInputDialog("Specify a minimum size for 1D anchors", "" + minSize); try { minSize = Integer.parseInt(newSize); } catch (Exception e) { if (HiCGlobals.guiIsCurrentlyActive) { SuperAdapter.showMessageDialog("Invalid integer, using default size " + minSize); } else { MessageUtils.showMessage("Invalid integer, using default size " + minSize); } } return minSize; } /** * Merge anchors which have overlap */ private static void mergeAnchors(GenomeWideList anchorList) { anchorList.filterLists(new FeatureFilter() { @Override public List filter(String chr, List anchorList) { return BEDTools.merge(anchorList); } }); } private static void mergeAnchorsTakeSmaller(GenomeWideList anchorList) { anchorList.filterLists(new FeatureFilter() { @Override public List filter(String chr, List anchorList) { return BEDTools.mergeTakeSmaller(anchorList); } }); } /** * update the original features that the motifs belong to */ public static void updateOriginalFeatures(GenomeWideList anchorList, String prefix) { anchorList.processLists(new juicebox.data.feature.FeatureFunction() { @Override public void process(String chr, List anchorList) { for (GenericLocus anchor : anchorList) { anchor.updateOriginalFeatures(prefix); } } }); } /** * Merge anchors which have overlap */ public static void intersectLists(final GenomeWideList firstList, final GenomeWideList secondList, final boolean conductFullIntersection) { firstList.filterLists(new FeatureFilter() { @Override public List filter(String key, List anchorList) { if (secondList.containsKey(key)) { return BEDTools.intersect(anchorList, secondList.getFeatures(key), conductFullIntersection); } else { return new ArrayList<>(); } } }); } public static void preservativeIntersectLists(final GenomeWideList firstList, final GenomeWideList secondList, final boolean conductFullIntersection) { firstList.filterLists(new FeatureFilter() { @Override public List filter(String key, List anchorList) { if (secondList.containsKey(key)) { return BEDTools.preservativeIntersect(anchorList, secondList.getFeatures(key), conductFullIntersection); } else { return new ArrayList<>(); } } }); } /** * Guarantees that all anchors have minimum width of gapThreshold */ private static void expandSmallAnchors(GenomeWideList anchorList, final int gapThreshold) { anchorList.processLists(new juicebox.data.feature.FeatureFunction() { @Override public void process(String chr, List anchorList) { expandSmallAnchors(anchorList, gapThreshold); } }); } /** * Guarantees that all anchors have minimum width of gapThreshold * PreProcessing step for anchors in MotifFinder code * derived from: * (awk on BED file) ... if($3-$2<15000){d=15000-($3-$2); print $1 \"\\t\" $2-int(d/2) \"\\t\" $3+int(d/2) * * @param anchors */ private static void expandSmallAnchors(List anchors, int gapThreshold) { for (GenericLocus anchor : anchors) { int width = anchor.getWidth(); if (width < gapThreshold) { anchor.widenMargins(gapThreshold - width); } } } // true --> upstream public static GenomeWideList extractDirectionalAnchors(GenomeWideList featureAnchors, final boolean direction) { final GenomeWideList directionalAnchors = new GenomeWideList<>(); featureAnchors.processLists(new juicebox.data.feature.FeatureFunction() { @Override public void process(String chr, List featureList) { for (GenericLocus anchor : featureList) { if (anchor.isDirectionalAnchor(direction)) { directionalAnchors.addFeature(chr, anchor); } } } }); return directionalAnchors; } public static void mergeAndExpandSmallAnchors(GenomeWideList regionsInCustomChromosome, int minSize) { mergeAnchors(regionsInCustomChromosome); expandSmallAnchors(regionsInCustomChromosome, minSize); mergeAnchors(regionsInCustomChromosome); } public static void callMergeAnchors(GenomeWideList locusList) { mergeAnchorsTakeSmaller(locusList); } } ================================================ FILE: src/juicebox/data/anchor/MotifAnchor.java ================================================ /* * The MIT License (MIT) * * Copyright (c) 2011-2020 Broad Institute, Aiden Lab * * Permission is hereby granted, free of charge, to any person obtaining a copy * of this software and associated documentation files (the "Software"), to deal * in the Software without restriction, including without limitation the rights * to use, copy, modify, merge, publish, distribute, sublicense, and/or sell * copies of the Software, and to permit persons to whom the Software is * furnished to do so, subject to the following conditions: * * The above copyright notice and this permission notice shall be included in * all copies or substantial portions of the Software. * * THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR * IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, * FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE * AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER * LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, * OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN * THE SOFTWARE. */ package juicebox.data.anchor; import juicebox.data.feature.Feature; import juicebox.track.feature.Feature2D; import juicebox.track.feature.Feature2DWithMotif; import java.util.ArrayList; import java.util.List; import java.util.Objects; /** * Created by muhammadsaadshamim on 9/28/15. * todo rename locus or something generic, with motifanchor extending from this */ public class MotifAnchor extends GenericLocus { public static boolean uniquenessShouldSupercedeConvergentRule = true; private static int posCount = 0; private static int negCount = 0; // critical components of a motif anchor // references to original features if applicable private boolean strand; // fimo output loaded as attributes private boolean fimoAttributesHaveBeenInitialized = false; private double score = 0, pValue, qValue; private String sequence; /** * Inititalize anchor given parameters (e.g. from BED file) * * @param chr * @param x1 * @param x2 */ public MotifAnchor(String chr, long x1, long x2) { super(chr, x1, x2); } public MotifAnchor(String chr, int x1, int x2, String name) { super(chr, x1, x2, name); } /** * Inititalize anchor given parameters (e.g. from feature list) * * @param chrIndex * @param x1 * @param x2 * @param originalFeatures1 * @param originalFeatures2 */ public MotifAnchor(String chrIndex, long x1, long x2, List originalFeatures1, List originalFeatures2) { super(chrIndex, x1, x2, originalFeatures1, originalFeatures2); } @Override public String getKey() { return "" + chr; } @Override public Feature deepClone() { MotifAnchor clone = new MotifAnchor(chr, x1, x2, originalFeatures1, originalFeatures2); clone.name = name; if (fimoAttributesHaveBeenInitialized) { clone.setFIMOAttributes(score, pValue, qValue, strand, sequence); } return clone; } @Override public Feature cloneToMotifAnchor() { return deepClone(); } @Override public String toString() { return "chr" + chr + "\t" + x1 + "\t" + x2; } @Override public boolean equals(Object obj) { if (this == obj) { return true; } if (obj instanceof MotifAnchor) { MotifAnchor o = (MotifAnchor) obj; return chr.equalsIgnoreCase(o.chr) && x1 == o.x1 && x2 == o.x2; } return false; } @Override public int hashCode() { return Objects.hash(x2, chr, x1); } @Override public int compareTo(GenericLocus o) { if (chr.equalsIgnoreCase(o.chr)) { if (x1 == o.x1) { if (o instanceof MotifAnchor) { if (x2 == o.x2 && sequence != null && ((MotifAnchor) o).sequence != null) { return sequence.compareTo(((MotifAnchor) o).sequence); } } return Long.compare(x2, o.x2); } return Long.compare(x1, o.x1); } return chr.compareTo(o.chr); } public void setFIMOAttributes(double score, double pValue, double qValue, boolean strand, String sequence) { this.score = score; this.pValue = pValue; this.qValue = qValue; this.strand = strand; this.sequence = sequence; fimoAttributesHaveBeenInitialized = true; } public double getScore() { return score; } public boolean hasFIMOAttributes() { return fimoAttributesHaveBeenInitialized; } public void addFIMOAttributesFrom(MotifAnchor anchor) { setFIMOAttributes(anchor.score, anchor.pValue, anchor.qValue, anchor.strand, anchor.sequence); } public void addFeatureReferencesFrom(MotifAnchor anchor) { originalFeatures1.addAll(anchor.originalFeatures1); originalFeatures2.addAll(anchor.originalFeatures2); } public void updateOriginalFeatures(boolean uniqueStatus, int specificStatus) { if ((originalFeatures1.size() > 0 || originalFeatures2.size() > 0)) { if (fimoAttributesHaveBeenInitialized) { if (specificStatus == 1) { for (Feature2D feature : originalFeatures1) { if (feature instanceof Feature2DWithMotif) { if (strand || uniqueStatus) { posCount++; ((Feature2DWithMotif) feature).updateMotifData(strand, uniqueStatus, sequence, x1, x2, true, score); } } } } else if (specificStatus == -1) { for (Feature2D feature : originalFeatures2) { if (feature instanceof Feature2DWithMotif) { if (!strand || uniqueStatus) { negCount++; ((Feature2DWithMotif) feature).updateMotifData(strand, uniqueStatus, sequence, x1, x2, false, score); } } } } else { for (Feature2D feature : originalFeatures1) { if (feature instanceof Feature2DWithMotif) { if (strand || uniqueStatus) { posCount++; ((Feature2DWithMotif) feature).updateMotifData(strand, uniqueStatus, sequence, x1, x2, true, score); } } } for (Feature2D feature : originalFeatures2) { if (feature instanceof Feature2DWithMotif) { if (!strand || uniqueStatus) { negCount++; ((Feature2DWithMotif) feature).updateMotifData(strand, uniqueStatus, sequence, x1, x2, false, score); } } } } } else { System.err.println("Attempting to assign motifs on incomplete anchor"); } } } public String getSequence() { return sequence; } /** * @return true if positive strand, false if negative strand */ public boolean getStrand() { return strand; } } ================================================ FILE: src/juicebox/data/anchor/MotifAnchorParser.java ================================================ /* * The MIT License (MIT) * * Copyright (c) 2011-2021 Broad Institute, Aiden Lab, Rice University, Baylor College of Medicine * * Permission is hereby granted, free of charge, to any person obtaining a copy * of this software and associated documentation files (the "Software"), to deal * in the Software without restriction, including without limitation the rights * to use, copy, modify, merge, publish, distribute, sublicense, and/or sell * copies of the Software, and to permit persons to whom the Software is * furnished to do so, subject to the following conditions: * * The above copyright notice and this permission notice shall be included in * all copies or substantial portions of the Software. * * THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR * IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, * FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE * AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER * LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, * OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN * THE SOFTWARE. */ package juicebox.data.anchor; import juicebox.HiCGlobals; import juicebox.data.ChromosomeHandler; import juicebox.data.HiCFileTools; import juicebox.data.basics.Chromosome; import juicebox.data.feature.FeatureFilter; import juicebox.data.feature.GenomeWideList; import org.broad.igv.Globals; import org.broad.igv.util.ParsingUtils; import java.io.*; import java.net.URL; import java.net.URLConnection; import java.util.ArrayList; import java.util.HashSet; import java.util.List; import java.util.Set; import java.util.zip.GZIPInputStream; /** * Created by muhammadsaadshamim on 10/26/15. *

* Parses the .txt file of motifs created by FIMO *

* FIMO - */ public class MotifAnchorParser { public static GenomeWideList loadMotifsFromGenomeID(String genomeID, FeatureFilter anchorFilter) { return loadGlobalMotifs("", genomeID, anchorFilter, MotifLocation.VIA_ID); } public static GenomeWideList loadMotifsFromLocalFile(String path, String genomeID, FeatureFilter anchorFilter) { return loadGlobalMotifs(path, genomeID, anchorFilter, MotifLocation.LOCAL); } public static GenomeWideList loadMotifsFromURL(String path, String genomeID, FeatureFilter anchorFilter) { return loadGlobalMotifs(path, genomeID, anchorFilter, MotifLocation.URL); } private static GenomeWideList loadGlobalMotifs(String path, String genomeID, FeatureFilter anchorFilter, MotifLocation motifLocation) { InputStream is = null; BufferedReader reader = null; GenomeWideList newAnchorList; try { // locate file from appropriate source and creat input stream is = ParsingUtils.openInputStream(extractProperMotifFilePath(genomeID, path, motifLocation)); reader = new BufferedReader(new InputStreamReader(is), HiCGlobals.bufferSize); } catch (Exception e) { System.err.println("Unable to create input stream for global motifs " + motifLocation); System.exit(49); } finally { ChromosomeHandler handler = HiCFileTools.loadChromosomes(genomeID); Set anchors = new HashSet<>(); try { if (reader != null) { anchors.addAll(parseGlobalMotifFile(reader, handler)); } } catch (Exception e3) { //e3.printStackTrace(); System.err.println("Unable to parse motif file"); System.exit(50); } if (is != null) { try { is.close(); } catch (Exception e4) { System.err.println("Error closing file stream for motif file"); //e4.printStackTrace(); } } newAnchorList = new GenomeWideList<>(handler, new ArrayList<>(anchors)); } if (anchorFilter != null) newAnchorList.filterLists(anchorFilter); return newAnchorList; } private static String extractProperMotifFilePath(String genomeID, String path, MotifLocation motifLocation) { String filePath = path; try { if (motifLocation == MotifLocation.VIA_ID) { String newURL = "https://hicfiles.s3.amazonaws.com/internal/motifs/" + genomeID + ".motifs.txt"; filePath = downloadFromUrl(new URL(newURL), "motifs"); } else if (motifLocation == MotifLocation.URL) { filePath = downloadFromUrl(new URL(path), "motifs"); } } catch (Exception e) { System.err.println("Unable to find proper file via " + motifLocation); System.exit(51); } return filePath; } private static GenomeWideList parseMotifFile(String path, ChromosomeHandler handler, FeatureFilter anchorFilter) { List anchors = new ArrayList<>(); try { //BufferedReader br = ParsingUtils.openBufferedReader(path); BufferedReader br = new BufferedReader(new InputStreamReader(ParsingUtils.openInputStream(path)), HiCGlobals.bufferSize); anchors.addAll(parseGlobalMotifFile(br, handler)); } catch (IOException ec) { ec.printStackTrace(); } GenomeWideList newAnchorList = new GenomeWideList<>(handler, anchors); if (anchorFilter != null) newAnchorList.filterLists(anchorFilter); return newAnchorList; } /** * Parses a motif file (assumes FIMO output format) * * @param bufferedReader * @param handler * @return list of motifs and their attributes (score, sequence, etc) * @throws IOException */ private static List parseGlobalMotifFile(BufferedReader bufferedReader, ChromosomeHandler handler) throws IOException { Set anchors = new HashSet<>(); String nextLine; // skip header bufferedReader.readLine(); //String[] headers = Globals.tabPattern.split(nextLine); //pattern_name sequence_name start stop strand score p-value q-value matched sequence //CTCF_REN chr12 121937865 121937884 + 28.6735 5.86e-13 0.00113 GCGGCCACCAGGGGGCGCCC //OR IF FILTERED LIST //CTCF_M1_FLIPPED chr10:100420000-100425000 4400 4413 - 18.2569 4.1e-07 0.00811 TCCAGTAGATGGCG int errorCount = 0; while ((nextLine = bufferedReader.readLine()) != null) { String[] tokens = Globals.tabPattern.split(nextLine); if (tokens.length != 9) { String text = "Improperly formatted FIMO output file: \npattern_name\tsequence_name\t" + "start\tstop\tstrand\tscore\tp-value\tq-value\tmatched_sequence"; System.err.println(text); System.exit(52); } boolean strand; String chr1Name, sequence; int start1, end1; double score, pValue, qValue; try { if (tokens[1].contains(":")) {// behavior when filtered list provided String[] splitToken = tokens[1].split(":"); String[] indices = splitToken[1].split("-"); chr1Name = splitToken[0]; start1 = Integer.parseInt(indices[0]) + Integer.parseInt(indices[2]); end1 = Integer.parseInt(indices[1]) + Integer.parseInt(indices[3]); } else {//default format all tabs chr1Name = tokens[1]; start1 = Integer.parseInt(tokens[2]); end1 = Integer.parseInt(tokens[3]); } strand = tokens[4].contains("+"); score = Double.parseDouble(tokens[5]); pValue = Double.parseDouble(tokens[6]); qValue = Double.parseDouble(tokens[7]); sequence = tokens[8]; Chromosome chr = handler.getChromosomeFromName(chr1Name); if (chr == null) { if (HiCGlobals.printVerboseComments) { if (errorCount < 10) { System.out.println("Skipping line: " + nextLine); } else if (errorCount == 10) { System.err.println("Maximum error count exceeded. Further errors will not be logged"); } } errorCount++; continue; } MotifAnchor anchor = new MotifAnchor(chr.getName(), start1, end1); anchor.setFIMOAttributes(score, pValue, qValue, strand, sequence); anchors.add(anchor); } catch (Exception e) { String text = "Improperly formatted FIMO output file: \npattern_name\tsequence_name\t" + "start\tstop\tstrand\tscore\tp-value\tq-value\tmatched_sequence"; System.err.println(text); System.exit(53); } } bufferedReader.close(); return new ArrayList<>(anchors); } /** * @param handler * @param bedFilePath * @return List of motif anchors from the provided bed file */ public static GenomeWideList loadFromBEDFile(ChromosomeHandler handler, String bedFilePath) { List anchors = new ArrayList<>(); try { //BufferedReader br = ParsingUtils.openBufferedReader(bedFilePath); BufferedReader br = new BufferedReader(new InputStreamReader(ParsingUtils.openInputStream(bedFilePath)), HiCGlobals.bufferSize); anchors.addAll(parseBEDFile(br, handler)); } catch (IOException ec) { ec.printStackTrace(); } return new GenomeWideList<>(handler, anchors); } /** * Methods for handling BED Files */ /** * Helper function for actually parsing BED file * Ignores any attributes beyond the third column (i.e. just chr and positions are read) * * @param bufferedReader * @param handler * @return list of motifs * @throws IOException */ private static List parseBEDFile(BufferedReader bufferedReader, ChromosomeHandler handler) throws IOException { Set anchors = new HashSet<>(); String nextLine; int errorCount = 0; while ((nextLine = bufferedReader.readLine()) != null) { String[] tokens = Globals.tabPattern.split(nextLine); String chr1Name; int start1, end1; if (tokens[0].startsWith("chr") && tokens.length > 2) { // valid line chr1Name = tokens[0]; start1 = Integer.parseInt(tokens[1]); end1 = Integer.parseInt(tokens[2]); Chromosome chr = handler.getChromosomeFromName(chr1Name); if (chr == null) { if (errorCount < 10) { System.out.println("Skipping line: " + nextLine); } else if (errorCount == 10) { System.err.println("Maximum error count exceeded. Further errors will not be logged"); } errorCount++; continue; } anchors.add(new MotifAnchor(chr.getName(), start1, end1)); } } if (anchors.size() < 1) System.err.println("BED File empty - file may have problems or error was encountered"); bufferedReader.close(); return new ArrayList<>(anchors); } /** * http://kamwo.me/java-download-file-from-url-to-temp-directory/ * * @param url * @param localFilename * @return * @throws IOException */ public static String downloadFromUrl(URL url, String localFilename) throws IOException { InputStream is = null; FileOutputStream fos = null; String tempDir = System.getProperty("java.io.tmpdir"); File outputFile = new File(tempDir, localFilename); try { URLConnection urlConn = url.openConnection(); is = urlConn.getInputStream(); fos = new FileOutputStream(outputFile); byte[] buffer = new byte[HiCGlobals.bufferSize]; int length; // read from source and write into local file while ((length = is.read(buffer)) > 0) { fos.write(buffer, 0, length); } return outputFile.getAbsolutePath(); } finally { try { if (is != null) { is.close(); } } finally { if (fos != null) { fos.close(); } } } } public static String uncompressFromGzip(String compressedFile, String decompressedFile) throws IOException { InputStream fileIn = null; GZIPInputStream gZIPInputStream = null; FileOutputStream fileOutputStream = null; String tempDir = System.getProperty("java.io.tmpdir"); File outputFile = new File(tempDir, decompressedFile); try { byte[] buffer = new byte[HiCGlobals.bufferSize]; fileIn = new FileInputStream(compressedFile); gZIPInputStream = new GZIPInputStream(fileIn); fileOutputStream = new FileOutputStream(outputFile); int bytes_read; while ((bytes_read = gZIPInputStream.read(buffer)) > 0) { fileOutputStream.write(buffer, 0, bytes_read); } gZIPInputStream.close(); fileOutputStream.close(); System.out.println("The file was decompressed successfully!"); return outputFile.getAbsolutePath(); } finally { try { if (fileIn != null) { fileIn.close(); } if (gZIPInputStream != null) { gZIPInputStream.close(); } } finally { if (fileOutputStream != null) { fileOutputStream.close(); } } } } public enum MotifLocation {VIA_ID, URL, LOCAL} } ================================================ FILE: src/juicebox/data/anchor/MotifAnchorTools.java ================================================ /* * The MIT License (MIT) * * Copyright (c) 2011-2020 Broad Institute, Aiden Lab * * Permission is hereby granted, free of charge, to any person obtaining a copy * of this software and associated documentation files (the "Software"), to deal * in the Software without restriction, including without limitation the rights * to use, copy, modify, merge, publish, distribute, sublicense, and/or sell * copies of the Software, and to permit persons to whom the Software is * furnished to do so, subject to the following conditions: * * The above copyright notice and this permission notice shall be included in * all copies or substantial portions of the Software. * * THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR * IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, * FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE * AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER * LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, * OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN * THE SOFTWARE. */ package juicebox.data.anchor; import juicebox.HiCGlobals; import juicebox.data.feature.FeatureFilter; import juicebox.data.feature.GenomeWideList; import juicebox.track.feature.Feature2D; import juicebox.track.feature.Feature2DList; import juicebox.track.feature.FeatureFunction; import java.util.*; /** * Created by muhammadsaadshamim on 9/28/15. */ public class MotifAnchorTools extends GenericLocusTools { /** * update the original features that the motifs belong to */ public static void updateOriginalFeatures(GenomeWideList anchorList, final boolean uniqueStatus, final int specificStatus) { anchorList.processLists(new juicebox.data.feature.FeatureFunction() { @Override public void process(String chr, List anchorList) { for (MotifAnchor anchor : anchorList) { anchor.updateOriginalFeatures(uniqueStatus, specificStatus); } } }); } /** * Guarantees that all anchors have minimum width of gapThreshold */ private static void expandSmallAnchors(GenomeWideList anchorList, final int gapThreshold) { anchorList.processLists(new juicebox.data.feature.FeatureFunction() { @Override public void process(String chr, List anchorList) { expandSmallAnchors(anchorList, gapThreshold); } }); } /** * Guarantees that all anchors have minimum width of gapThreshold * PreProcessing step for anchors in MotifFinder code * derived from: * (awk on BED file) ... if($3-$2<15000){d=15000-($3-$2); print $1 \"\\t\" $2-int(d/2) \"\\t\" $3+int(d/2) * * @param anchors */ private static void expandSmallAnchors(List anchors, int gapThreshold) { for (MotifAnchor anchor : anchors) { int width = anchor.getWidth(); if (width < gapThreshold) { anchor.widenMargins(gapThreshold - width); } } } /** * @param anchors * @param threshold * @return unique motifs within a given threshold from a given AnchorList */ public static GenomeWideList extractUniqueMotifs(GenomeWideList anchors, final int threshold) { GenomeWideList uniqueAnchors = anchors.deepClone(); uniqueAnchors.filterLists(new FeatureFilter() { @Override public List filter(String chr, List anchorList) { // bin the motifs within resolution/threshold Map> uniqueMapping = new HashMap<>(); for (MotifAnchor motif : anchorList) { String key = (motif.getX1() / threshold) + "_" + (motif.getX2() / threshold); if (uniqueMapping.containsKey(key)) { uniqueMapping.get(key).add(motif); } else { List motifList = new ArrayList<>(); motifList.add(motif); uniqueMapping.put(key, motifList); } } // select for bins with only one value List uniqueMotifs = new ArrayList<>(); for (List motifList : uniqueMapping.values()) { if (motifList.size() == 1) { uniqueMotifs.add(motifList.get(0)); } } return uniqueMotifs; } }); return uniqueAnchors; } /** * @param anchors * @param threshold * @return best (highest scoring) motifs within a given threshold from a given anchors list */ public static GenomeWideList extractBestMotifs(GenomeWideList anchors, final int threshold) { GenomeWideList bestAnchors = anchors.deepClone(); bestAnchors.filterLists(new FeatureFilter() { @Override public List filter(String chr, List anchorList) { // bin the motifs within resolution/threshold, saving only the highest scoring motif Map bestMapping = new HashMap<>(); for (MotifAnchor motif : anchorList) { String key = (motif.getX1() / threshold) + "_" + (motif.getX2() / threshold); if (bestMapping.containsKey(key)) { if (bestMapping.get(key).getScore() < motif.getScore()) { bestMapping.put(key, motif); } } else { bestMapping.put(key, motif); } } return new ArrayList<>(bestMapping.values()); } }); return bestAnchors; } public static MotifAnchor searchForFeature(final String chrID, final String sequence, GenomeWideList anchorList) { final MotifAnchor[] anchor = new MotifAnchor[1]; anchorList.processLists(new juicebox.data.feature.FeatureFunction() { @Override public void process(String chr, List featureList) { for (MotifAnchor motif : featureList) { if (motif.getChr().equalsIgnoreCase(chrID) && motif.getSequence().equals(sequence)) { anchor[0] = (MotifAnchor) motif.deepClone(); } } } }); return anchor[0]; } public static MotifAnchor searchForFeature(final String chrID, final int start, final int end, GenomeWideList anchorList) { final MotifAnchor[] anchor = new MotifAnchor[1]; anchorList.processLists(new juicebox.data.feature.FeatureFunction() { @Override public void process(String chr, List featureList) { for (MotifAnchor motif : featureList) { if (motif.getChr().equalsIgnoreCase(chrID) && motif.getX1() == start && motif.getX2() == end) { anchor[0] = (MotifAnchor) motif.deepClone(); } } } }); return anchor[0]; } public static MotifAnchor searchForFeatureWithin(final String chrID, final int start, final int end, GenomeWideList anchorList) { final MotifAnchor[] anchor = new MotifAnchor[1]; anchorList.processLists(new juicebox.data.feature.FeatureFunction() { @Override public void process(String chr, List featureList) { for (MotifAnchor motif : featureList) { if (motif.getChr().equalsIgnoreCase(chrID) && motif.getX1() >= start && motif.getX2() <= end) { anchor[0] = (MotifAnchor) motif.deepClone(); } } } }); return anchor[0]; } public static List searchForFeaturesWithin(final String chrID, final int start, final int end, GenomeWideList anchorList) { final List anchors = new ArrayList<>(); anchorList.processLists(new juicebox.data.feature.FeatureFunction() { @Override public void process(String chr, List featureList) { for (MotifAnchor motif : featureList) { if (motif.getChr().equalsIgnoreCase(chrID) && motif.getX1() >= start && motif.getX2() <= end) { anchors.add((MotifAnchor) motif.deepClone()); } } } }); return anchors; } public static void retainProteinsInLocus(final GenomeWideList firstList, final GenomeWideList secondList, final boolean retainUniqueSites, final boolean copyFeatureReferences) { firstList.filterLists(new FeatureFilter() { @Override public List filter(String key, List anchorList) { if (secondList.containsKey(key)) { return retainProteinsInLocus(anchorList, secondList.getFeatures(key), retainUniqueSites, copyFeatureReferences); } else { return new ArrayList<>(); } } }); } private static List retainProteinsInLocus(List topAnchors, List baseList, boolean retainUniqueSites, boolean copyFeatureReferences) { Map> bottomListToTopList = new HashMap<>(); for (GenericLocus anchor : baseList) { bottomListToTopList.put(anchor, new HashSet<>()); } int topIndex = 0; int bottomIndex = 0; int maxTopIndex = topAnchors.size(); int maxBottomIndex = baseList.size(); Collections.sort(topAnchors); Collections.sort(baseList); while (topIndex < maxTopIndex && bottomIndex < maxBottomIndex) { GenericLocus topAnchor = topAnchors.get(topIndex); GenericLocus bottomAnchor = baseList.get(bottomIndex); if (topAnchor.hasOverlapWith(bottomAnchor) || bottomAnchor.hasOverlapWith(topAnchor)) { bottomListToTopList.get(bottomAnchor).add(topAnchor); // iterate over all possible intersections with top element for (int i = bottomIndex; i < maxBottomIndex; i++) { GenericLocus newAnchor = baseList.get(i); if (topAnchor.hasOverlapWith(newAnchor) || newAnchor.hasOverlapWith(topAnchor)) { bottomListToTopList.get(newAnchor).add(topAnchor); } else { break; } } // iterate over all possible intersections with bottom element // start from +1 because +0 checked in the for loop above for (int i = topIndex + 1; i < maxTopIndex; i++) { GenericLocus newAnchor = topAnchors.get(i); if (bottomAnchor.hasOverlapWith(newAnchor) || newAnchor.hasOverlapWith(bottomAnchor)) { bottomListToTopList.get(bottomAnchor).add(newAnchor); } else { break; } } // increment both topIndex++; bottomIndex++; } else if (topAnchor.isStrictlyToTheLeftOf(bottomAnchor)) { topIndex++; } else if (topAnchor.isStrictlyToTheRightOf(bottomAnchor)) { bottomIndex++; } else { System.err.println("Error while intersecting anchors."); System.err.println(topAnchor + " & " + bottomAnchor); } } List uniqueAnchors = new ArrayList<>(); if (copyFeatureReferences) { for (GenericLocus anchor : bottomListToTopList.keySet()) { for (GenericLocus anchor2 : bottomListToTopList.get(anchor)) { anchor2.addFeatureReferencesFrom(anchor); } } } if (retainUniqueSites) { for (Set motifs : bottomListToTopList.values()) { if (motifs.size() == 1) { uniqueAnchors.addAll(motifs); } } } else { for (Set motifs : bottomListToTopList.values()) { if (motifs.size() > 1) { uniqueAnchors.addAll(motifs); } } } return uniqueAnchors; } public static void retainBestMotifsInLocus(final GenomeWideList firstList, final GenomeWideList secondList) { firstList.filterLists(new FeatureFilter() { @Override public List filter(String key, List anchorList) { if (secondList.containsKey(key)) { return retainBestMotifsInLocus(anchorList, secondList.getFeatures(key)); } else { return new ArrayList<>(); } } }); } private static List retainBestMotifsInLocus(List topAnchors, List baseList) { Map> bottomListToTopList = new HashMap<>(); for (GenericLocus anchor : baseList) { bottomListToTopList.put(anchor, new HashSet<>()); } int topIndex = 0; int bottomIndex = 0; int maxTopIndex = topAnchors.size(); int maxBottomIndex = baseList.size(); Collections.sort(topAnchors); Collections.sort(baseList); while (topIndex < maxTopIndex && bottomIndex < maxBottomIndex) { MotifAnchor topAnchor = topAnchors.get(topIndex); GenericLocus bottomAnchor = baseList.get(bottomIndex); if (topAnchor.hasOverlapWith(bottomAnchor) || bottomAnchor.hasOverlapWith(topAnchor)) { bottomListToTopList.get(bottomAnchor).add(topAnchor); // iterate over all possible intersections with top element for (int i = bottomIndex; i < maxBottomIndex; i++) { GenericLocus newAnchor = baseList.get(i); if (topAnchor.hasOverlapWith(newAnchor) || newAnchor.hasOverlapWith(topAnchor)) { bottomListToTopList.get(newAnchor).add(topAnchor); } else { break; } } // iterate over all possible intersections with bottom element // start from +1 because +0 checked in the for loop above for (int i = topIndex + 1; i < maxTopIndex; i++) { MotifAnchor newAnchor = topAnchors.get(i); if (bottomAnchor.hasOverlapWith(newAnchor) || newAnchor.hasOverlapWith(bottomAnchor)) { bottomListToTopList.get(bottomAnchor).add(newAnchor); } else { break; } } // increment both topIndex++; bottomIndex++; } else if (topAnchor.isStrictlyToTheLeftOf(bottomAnchor)) { topIndex++; } else if (topAnchor.isStrictlyToTheRightOf(bottomAnchor)) { bottomIndex++; } else { System.err.println("Error while intersecting anchors."); System.err.println(topAnchor + " & " + bottomAnchor); } } for (GenericLocus anchor : bottomListToTopList.keySet()) { for (MotifAnchor anchor2 : bottomListToTopList.get(anchor)) { anchor2.addFeatureReferencesFrom(anchor); if (HiCGlobals.printVerboseComments) { if (anchor2.getSequence().equals("TGAGTCACTAGAGGGAGGCA")) { System.out.println(bottomListToTopList.get(anchor)); } } } } List uniqueAnchors = new ArrayList<>(); for (Set motifs : bottomListToTopList.values()) { if (motifs.size() == 1) { uniqueAnchors.addAll(motifs); } else if (motifs.size() > 1) { MotifAnchor best = motifs.iterator().next(); for (MotifAnchor an : motifs) { if (an.getScore() > best.getScore()) { best = an; } } uniqueAnchors.add(best); } } return uniqueAnchors; } public static int[] calculateConvergenceHistogram(Feature2DList features) { // ++, +- (convergent), -+ (divergent), --, other (incomplete) final int[] results = new int[6]; features.processLists(new FeatureFunction() { @Override public void process(String chr, List feature2DList) { for (Feature2D feature : feature2DList) { results[feature.toFeature2DWithMotif().getConvergenceStatus()]++; } } }); return results; } } ================================================ FILE: src/juicebox/data/basics/Chromosome.java ================================================ /* * The MIT License (MIT) * * Copyright (c) 2011-2021 Broad Institute, Aiden Lab, Rice University, Baylor College of Medicine * * Permission is hereby granted, free of charge, to any person obtaining a copy * of this software and associated documentation files (the "Software"), to deal * in the Software without restriction, including without limitation the rights * to use, copy, modify, merge, publish, distribute, sublicense, and/or sell * copies of the Software, and to permit persons to whom the Software is * furnished to do so, subject to the following conditions: * * The above copyright notice and this permission notice shall be included in * all copies or substantial portions of the Software. * * THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR * IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, * FITNESS FOR A PARTICULAR PURPOSE AND NON-INFRINGEMENT. IN NO EVENT SHALL THE * AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER * LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, * OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN * THE SOFTWARE. */ package juicebox.data.basics; import java.util.Objects; public class Chromosome { private final String name; private int index; private long length = 0; public Chromosome(int index, String name, long length) { this.index = index; this.name = name; this.length = length; } public int getIndex() { return this.index; } public void setIndex(int ii) { this.index = ii; } public long getLength() { return this.length; } public String getName() { return this.name; } public String toString() { return this.name; } public boolean equals(Object obj) { return obj instanceof Chromosome && ((Chromosome) obj).getIndex() == this.getIndex() && ((Chromosome) obj).getLength() == this.getLength(); } public int hashCode() { return Objects.hash(this.index, this.length); } public org.broad.igv.feature.Chromosome toIGVChromosome() { return new org.broad.igv.feature.Chromosome(index, name, (int) length); // assumed for IGV } } ================================================ FILE: src/juicebox/data/basics/ListOfDoubleArrays.java ================================================ /* * The MIT License (MIT) * * Copyright (c) 2011-2021 Broad Institute, Aiden Lab, Rice University, Baylor College of Medicine * * Permission is hereby granted, free of charge, to any person obtaining a copy * of this software and associated documentation files (the "Software"), to deal * in the Software without restriction, including without limitation the rights * to use, copy, modify, merge, publish, distribute, sublicense, and/or sell * copies of the Software, and to permit persons to whom the Software is * furnished to do so, subject to the following conditions: * * The above copyright notice and this permission notice shall be included in * all copies or substantial portions of the Software. * * THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR * IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, * FITNESS FOR A PARTICULAR PURPOSE AND NON-INFRINGEMENT. IN NO EVENT SHALL THE * AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER * LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, * OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN * THE SOFTWARE. */ package juicebox.data.basics; import java.util.ArrayList; import java.util.Arrays; import java.util.List; /** * can't use because we need to instantiate the array, otherwise that would have been nice */ public class ListOfDoubleArrays { private final long DEFAULT_LENGTH = Integer.MAX_VALUE - 10; private final long overallLength; private final List internalList = new ArrayList<>(); public ListOfDoubleArrays(long length) { this.overallLength = length; long tempLength = length; while (tempLength > 0) { if (tempLength < DEFAULT_LENGTH) { internalList.add(new double[(int) tempLength]); break; } else { internalList.add(new double[(int) DEFAULT_LENGTH]); tempLength -= DEFAULT_LENGTH; } } } public ListOfDoubleArrays(long totSize, double defaultValue) { this(totSize); for (double[] array : internalList) { Arrays.fill(array, defaultValue); } } public void clear() { internalList.clear(); } public double get(long index) { if (index < overallLength) { int pseudoRow = (int) (index / DEFAULT_LENGTH); int pseudoCol = (int) (index % DEFAULT_LENGTH); return internalList.get(pseudoRow)[pseudoCol]; } else { System.err.println("long index exceeds max size of list of arrays while getting: " + index + " " + overallLength); Exception ioe = new Exception(); ioe.printStackTrace(); return Double.NaN; } } public void set(long index, double value) { if (index < overallLength) { int pseudoRow = (int) (index / DEFAULT_LENGTH); int pseudoCol = (int) (index % DEFAULT_LENGTH); internalList.get(pseudoRow)[pseudoCol] = value; } else { System.err.println("long index exceeds max size of list of arrays while setting"); } } public long getLength() { return overallLength; } public ListOfDoubleArrays deepClone() { ListOfDoubleArrays clone = new ListOfDoubleArrays(overallLength); for (int k = 0; k < internalList.size(); k++) { System.arraycopy(internalList.get(k), 0, clone.internalList.get(k), 0, internalList.get(k).length); } return clone; } public void divideBy(long index, double value) { if (index < overallLength) { int pseudoRow = (int) (index / DEFAULT_LENGTH); int pseudoCol = (int) (index % DEFAULT_LENGTH); internalList.get(pseudoRow)[pseudoCol] /= value; } else { System.err.println("long index exceeds max size of list of arrays while dividing"); } } public void multiplyBy(long index, double value) { if (index < overallLength) { int pseudoRow = (int) (index / DEFAULT_LENGTH); int pseudoCol = (int) (index % DEFAULT_LENGTH); internalList.get(pseudoRow)[pseudoCol] *= value; } else { System.err.println("long index exceeds max size of list of arrays while mutiplying"); } } public void addTo(long index, double value) { if (index < overallLength) { int pseudoRow = (int) (index / DEFAULT_LENGTH); int pseudoCol = (int) (index % DEFAULT_LENGTH); try { internalList.get(pseudoRow)[pseudoCol] += value; } catch (Exception e) { System.err.println(index + " " + pseudoCol); e.printStackTrace(); } } else { System.err.println("long index exceeds max size of list of arrays while adding: " + index + " " + overallLength); Exception ioe = new Exception(); ioe.printStackTrace(); } } public void addValuesFrom(ListOfDoubleArrays other) { if (overallLength == other.overallLength) { for (int i = 0; i < internalList.size(); i++) { for (int j = 0; j < internalList.get(i).length; j++) { internalList.get(i)[j] += other.internalList.get(i)[j]; } } } else { System.err.println("Adding objects of different sizes!"); } } public double getFirstValue() { return internalList.get(0)[0]; } public double getLastValue() { double[] temp = internalList.get(internalList.size() - 1); return temp[temp.length - 1]; } public List getValues() { return internalList; } public void multiplyEverythingBy(double val) { for (double[] array : internalList) { for (int k = 0; k < array.length; k++) { array[k] *= val; } } } public ListOfFloatArrays convertToFloats() { ListOfFloatArrays newList = new ListOfFloatArrays(overallLength); for (int j = 0; j < internalList.size(); j++) { for (int k = 0; k < internalList.get(j).length; k++) { newList.getValues().get(j)[k] = (float) internalList.get(j)[k]; } } return newList; } } ================================================ FILE: src/juicebox/data/basics/ListOfFloatArrays.java ================================================ /* * The MIT License (MIT) * * Copyright (c) 2011-2021 Broad Institute, Aiden Lab, Rice University, Baylor College of Medicine * * Permission is hereby granted, free of charge, to any person obtaining a copy * of this software and associated documentation files (the "Software"), to deal * in the Software without restriction, including without limitation the rights * to use, copy, modify, merge, publish, distribute, sublicense, and/or sell * copies of the Software, and to permit persons to whom the Software is * furnished to do so, subject to the following conditions: * * The above copyright notice and this permission notice shall be included in * all copies or substantial portions of the Software. * * THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR * IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, * FITNESS FOR A PARTICULAR PURPOSE AND NON-INFRINGEMENT. IN NO EVENT SHALL THE * AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER * LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, * OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN * THE SOFTWARE. */ package juicebox.data.basics; import java.util.ArrayList; import java.util.Arrays; import java.util.List; /** * can't use because we need to instantiate the array, otherwise that would have been nice */ public class ListOfFloatArrays { private final long DEFAULT_LENGTH = Integer.MAX_VALUE - 10; private final long overallLength; private final List internalList = new ArrayList<>(); public ListOfFloatArrays(long length) { this.overallLength = length; long tempLength = length; while (tempLength > 0) { if (tempLength < DEFAULT_LENGTH) { internalList.add(new float[(int) tempLength]); break; } else { internalList.add(new float[(int) DEFAULT_LENGTH]); tempLength -= DEFAULT_LENGTH; } } } public ListOfFloatArrays(long totSize, float defaultValue) { this(totSize); for (float[] array : internalList) { Arrays.fill(array, defaultValue); } } public void clear() { internalList.clear(); } public float get(long index) { if (index < overallLength) { int pseudoRow = (int) (index / DEFAULT_LENGTH); int pseudoCol = (int) (index % DEFAULT_LENGTH); return internalList.get(pseudoRow)[pseudoCol]; } else { System.err.println("long index exceeds max size of list of arrays while getting: " + index + " " + overallLength); Exception ioe = new Exception(); ioe.printStackTrace(); return Float.NaN; } } public void set(long index, float value) { if (index < overallLength) { int pseudoRow = (int) (index / DEFAULT_LENGTH); int pseudoCol = (int) (index % DEFAULT_LENGTH); internalList.get(pseudoRow)[pseudoCol] = value; } else { System.err.println("long index exceeds max size of list of arrays while setting"); } } public long getLength() { return overallLength; } public long getMaxRow() { long maxIndex = 0; float maxVal = 0; for (int index = 0; index < overallLength; index++) { int pseudoRow = (int) (index / DEFAULT_LENGTH); int pseudoCol = (int) (index % DEFAULT_LENGTH); if (maxVal < internalList.get(pseudoRow)[pseudoCol]) { maxVal = internalList.get(pseudoRow)[pseudoCol]; maxIndex = index; } } return maxIndex; } public ListOfFloatArrays deepClone() { ListOfFloatArrays clone = new ListOfFloatArrays(overallLength); for (int k = 0; k < internalList.size(); k++) { System.arraycopy(internalList.get(k), 0, clone.internalList.get(k), 0, internalList.get(k).length); } return clone; } public void divideBy(long index, float value) { if (index < overallLength) { int pseudoRow = (int) (index / DEFAULT_LENGTH); int pseudoCol = (int) (index % DEFAULT_LENGTH); internalList.get(pseudoRow)[pseudoCol] /= value; } else { System.err.println("long index exceeds max size of list of arrays while dividing"); } } public void multiplyBy(long index, float value) { if (index < overallLength) { int pseudoRow = (int) (index / DEFAULT_LENGTH); int pseudoCol = (int) (index % DEFAULT_LENGTH); internalList.get(pseudoRow)[pseudoCol] *= value; } else { System.err.println("long index exceeds max size of list of arrays while mutiplying"); } } public void addTo(long index, float value) { if (index < overallLength) { int pseudoRow = (int) (index / DEFAULT_LENGTH); int pseudoCol = (int) (index % DEFAULT_LENGTH); try { internalList.get(pseudoRow)[pseudoCol] += value; } catch (Exception e) { System.err.println(index + " " + pseudoCol); e.printStackTrace(); } } else { System.err.println("long index exceeds max size of list of arrays while adding: " + index + " " + overallLength); Exception ioe = new Exception(); ioe.printStackTrace(); } } public void addValuesFrom(ListOfFloatArrays other) { if (overallLength == other.overallLength) { for (int i = 0; i < internalList.size(); i++) { float[] array = internalList.get(i); float[] otherArray = other.internalList.get(i); for (int j = 0; j < array.length; j++) { array[j] += otherArray[j]; } } } else { System.err.println("Adding objects of different sizes!"); } } public float getFirstValue() { return internalList.get(0)[0]; } public float getLastValue() { float[] temp = internalList.get(internalList.size() - 1); return temp[temp.length - 1]; } public List getValues() { return internalList; } public void multiplyEverythingBy(double val) { for (float[] array : internalList) { for (int k = 0; k < array.length; k++) { array[k] *= val; } } } public ListOfDoubleArrays convertToDoubles() { ListOfDoubleArrays newList = new ListOfDoubleArrays(overallLength); for (int j = 0; j < internalList.size(); j++) { float[] array = internalList.get(j); double[] newArray = newList.getValues().get(j); for (int k = 0; k < array.length; k++) { newArray[k] = array[k]; } } return newList; } } ================================================ FILE: src/juicebox/data/basics/ListOfIntArrays.java ================================================ /* * The MIT License (MIT) * * Copyright (c) 2011-2021 Broad Institute, Aiden Lab, Rice University, Baylor College of Medicine * * Permission is hereby granted, free of charge, to any person obtaining a copy * of this software and associated documentation files (the "Software"), to deal * in the Software without restriction, including without limitation the rights * to use, copy, modify, merge, publish, distribute, sublicense, and/or sell * copies of the Software, and to permit persons to whom the Software is * furnished to do so, subject to the following conditions: * * The above copyright notice and this permission notice shall be included in * all copies or substantial portions of the Software. * * THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR * IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, * FITNESS FOR A PARTICULAR PURPOSE AND NON-INFRINGEMENT. IN NO EVENT SHALL THE * AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER * LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, * OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN * THE SOFTWARE. */ package juicebox.data.basics; import java.util.ArrayList; import java.util.Arrays; import java.util.List; /** * can't use because we need to instantiate the array, otherwise that would have been nice */ public class ListOfIntArrays { private final int DEFAULT_LENGTH = Integer.MAX_VALUE - 10; private final long overallLength; private final List internalList = new ArrayList<>(); public ListOfIntArrays(long length) { this.overallLength = length; long tempLength = length; while (tempLength > 0) { if (tempLength < DEFAULT_LENGTH) { internalList.add(new int[(int) tempLength]); break; } else { internalList.add(new int[DEFAULT_LENGTH]); tempLength -= DEFAULT_LENGTH; } } } public ListOfIntArrays(long totSize, int defaultValue) { this(totSize); for (int[] array : internalList) { Arrays.fill(array, defaultValue); } } public void clear() { internalList.clear(); } public int get(long index) { if (index < overallLength) { int pseudoRow = (int) (index / DEFAULT_LENGTH); int pseudoCol = (int) (index % DEFAULT_LENGTH); return internalList.get(pseudoRow)[pseudoCol]; } else { System.err.println("long index exceeds max size of list of int arrays while getting"); return -Integer.MAX_VALUE; } } public void set(long index, int value) { long tempIndex = index; if (index < overallLength) { int pseudoRow = (int) (index / DEFAULT_LENGTH); int pseudoCol = (int) (index % DEFAULT_LENGTH); internalList.get(pseudoRow)[pseudoCol] = value; } else { System.err.println("long index exceeds max size of list of arrays while setting"); return; } //System.err.println("unusual - long index exceeds max size of list of arrays while setting"); } public long getLength() { return overallLength; } public ListOfIntArrays deepClone() { ListOfIntArrays clone = new ListOfIntArrays(overallLength); for (int k = 0; k < internalList.size(); k++) { System.arraycopy(internalList.get(k), 0, clone.internalList.get(k), 0, internalList.get(k).length); } return clone; } public void divideBy(long index, int value) { if (index < overallLength) { int pseudoRow = (int) (index / DEFAULT_LENGTH); int pseudoCol = (int) (index % DEFAULT_LENGTH); internalList.get(pseudoRow)[pseudoCol] /= value; } else { System.err.println("long index exceeds max size of list of arrays while dividing"); return; } System.err.println("unusual - long index exceeds max size of list of arrays while dividing"); } public void addValuesFrom(ListOfIntArrays other) { if (overallLength == other.overallLength) { for (int i = 0; i < internalList.size(); i++) { for (int j = 0; j < internalList.get(i).length; j++) { internalList.get(i)[j] += other.internalList.get(i)[j]; } } } else { System.err.println("Adding objects of different sizes!"); } } public void addTo(long index, int value) { if (index < overallLength) { int pseudoRow = (int) (index / DEFAULT_LENGTH); int pseudoCol = (int) (index % DEFAULT_LENGTH); internalList.get(pseudoRow)[pseudoCol] += value; } else { System.err.println("long index exceeds max size of list of arrays while adding"); } } public List getValues() { return internalList; } } ================================================ FILE: src/juicebox/data/binary_file_layout.txt ================================================ ------ Header ------ masterIndexPointer -------- Chr dictionary -------- numberOfChromosomes ------------ Chromosome // repeat for each chromosome ------------ name size --------- Attribute dictionary --------- attributeCount attKey attValue attKey attValue .... -------- Matrix -------- chr1 // lowest index chromosome chr2 // highest index chromosome numberOfZooms -------------- MatrixZoomData //repeat for each zoom -------------- zoom sum // Sum of counts over all records binSize // in bp blockBinCount // in # bin columns columnCount numberOfBlocks ----------- Block Index // repeat for each block ----------- blockNumber filePosition sizeInbytes ---------- Block // repeat for each block ---------- numberOfRecords ----------- ContactRecord // repeat for each contact record ----------- bin1 bin2 counts // int ------------ Master Index ------------ numberOfEntries ----- Entry // repeat for each entry ----- matrixKey // chr1_chr2 filePosition sizeInBytes ================================================ FILE: src/juicebox/data/censoring/CustomMZDRegionHandler.java ================================================ /* * The MIT License (MIT) * * Copyright (c) 2011-2020 Broad Institute, Aiden Lab, Rice University, Baylor College of Medicine * * Permission is hereby granted, free of charge, to any person obtaining a copy * of this software and associated documentation files (the "Software"), to deal * in the Software without restriction, including without limitation the rights * to use, copy, modify, merge, publish, distribute, sublicense, and/or sell * copies of the Software, and to permit persons to whom the Software is * furnished to do so, subject to the following conditions: * * The above copyright notice and this permission notice shall be included in * all copies or substantial portions of the Software. * * THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR * IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, * FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE * AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER * LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, * OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN * THE SOFTWARE. */ package juicebox.data.censoring; import juicebox.data.ChromosomeHandler; import juicebox.data.anchor.GenericLocus; import juicebox.data.anchor.MotifAnchor; import juicebox.data.basics.Chromosome; import juicebox.windowui.HiCZoom; import org.broad.igv.util.Pair; import java.util.*; public class CustomMZDRegionHandler { private final Map, List>> allRegionsForChr = new HashMap<>(); private final List boundariesOfCustomChromosomeX = new ArrayList<>(); private final List boundariesOfCustomChromosomeY = new ArrayList<>(); private static Pair, List> getAllRegionsFromSubChromosomes( final ChromosomeHandler handler, Chromosome chr) { if (handler.isCustomChromosome(chr)) { final List allRegions = new ArrayList<>(); final List translatedRegions = new ArrayList<>(); handler.getListOfRegionsInCustomChromosome(chr.getIndex()).processLists( new juicebox.data.feature.FeatureFunction() { @Override public void process(String chr, List featureList) { allRegions.addAll(featureList); } }); Collections.sort(allRegions); long previousEnd = 0; for (GenericLocus anchor : allRegions) { long currentEnd = previousEnd + anchor.getWidth(); GenericLocus anchor2 = new GenericLocus(chr.getName(), previousEnd, currentEnd); translatedRegions.add(anchor2); previousEnd = currentEnd + ChromosomeHandler.CUSTOM_CHROMOSOME_BUFFER; } return new Pair<>(allRegions, translatedRegions); } else { // just a standard chromosome final List allRegions = new ArrayList<>(); final List translatedRegions = new ArrayList<>(); allRegions.add(new GenericLocus(chr.getName(), 0, (int) chr.getLength())); translatedRegions.add(new GenericLocus(chr.getName(), 0, (int) chr.getLength())); return new Pair<>(allRegions, translatedRegions); } } /** * @param handler */ public void initialize(Chromosome chr1, Chromosome chr2, HiCZoom zoom, ChromosomeHandler handler) { allRegionsForChr.clear(); boundariesOfCustomChromosomeX.clear(); boundariesOfCustomChromosomeY.clear(); populateRegions(chr1, handler, boundariesOfCustomChromosomeX, zoom); if (chr1.getIndex() != chr2.getIndex()) { populateRegions(chr2, handler, boundariesOfCustomChromosomeY, zoom); } else { boundariesOfCustomChromosomeY.addAll(boundariesOfCustomChromosomeX); } } public List getBoundariesOfCustomChromosomeX() { return boundariesOfCustomChromosomeX; } public List getBoundariesOfCustomChromosomeY() { return boundariesOfCustomChromosomeY; } private void populateRegions(Chromosome chr, ChromosomeHandler handler, List boundaries, HiCZoom zoom) { String name = chr.getName(); Pair, List> allRegionsInfo = getAllRegionsFromSubChromosomes(handler, chr); if (allRegionsInfo != null) { allRegionsForChr.put(name, allRegionsInfo); List translatedRegions = allRegionsInfo.getSecond(); for (GenericLocus anchor : translatedRegions) { boundaries.add(anchor.getX2() / zoom.getBinSize()); } } } public List> getIntersectingFeatures(String name, long gx1, long gx2) { int idx1 = OneDimSearchUtils.indexedBinaryNearestSearch( allRegionsForChr.get(name).getSecond(), new MotifAnchor(name, gx1, gx1), true); int idx2 = OneDimSearchUtils.indexedBinaryNearestSearch( allRegionsForChr.get(name).getSecond(), new MotifAnchor(name, gx2, gx2), false); final List> foundFeatures = new ArrayList<>(); for (int i = idx1; i <= idx2; i++) { foundFeatures.add(new Pair<>( allRegionsForChr.get(name).getFirst().get(i), allRegionsForChr.get(name).getSecond().get(i))); } return foundFeatures; } public List> getIntersectingFeatures(String name, int gx1) { int idx1 = OneDimSearchUtils.indexedBinaryNearestSearch( allRegionsForChr.get(name).getSecond(), new MotifAnchor(name, gx1, gx1), true); final List> foundFeatures = new ArrayList<>(); if (idx1 > 0) { foundFeatures.add(new Pair<>( allRegionsForChr.get(name).getFirst().get(idx1), allRegionsForChr.get(name).getSecond().get(idx1))); } return foundFeatures; } } ================================================ FILE: src/juicebox/data/censoring/OneDimSearchUtils.java ================================================ /* * The MIT License (MIT) * * Copyright (c) 2011-2020 Broad Institute, Aiden Lab, Rice University, Baylor College of Medicine * * Permission is hereby granted, free of charge, to any person obtaining a copy * of this software and associated documentation files (the "Software"), to deal * in the Software without restriction, including without limitation the rights * to use, copy, modify, merge, publish, distribute, sublicense, and/or sell * copies of the Software, and to permit persons to whom the Software is * furnished to do so, subject to the following conditions: * * The above copyright notice and this permission notice shall be included in * all copies or substantial portions of the Software. * * THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR * IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, * FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE * AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER * LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, * OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN * THE SOFTWARE. */ package juicebox.data.censoring; import java.util.List; class OneDimSearchUtils { /** * Searches the specified list for the specified object or its closest * counter part using a modified binary search algorithm. The list must * be sorted into ascending order according to the natural ordering of * its elements prior to making this call. If it is not sorted, the * results are undefined. If the list contains multiple elements equal * to the specified object, there is no guarantee which one will be found. * * @param the class of the objects in the list * @param list the list to be searched. * @param key the key to be searched for. * @param useFloor to get the lesser of two indices given no exact match * @return the index of the search key, if it is contained in the list; */ public static int indexedBinaryNearestSearch(List> list, T key, boolean useFloor) { int low = 0; int high = list.size() - 1; if (useFloor && list.get(low).compareTo(key) > 0) { return low; } else if (!useFloor && list.get(high).compareTo(key) < 0) { return high; } while (low < high) { int mid = (low + high) >>> 1; int cmp = list.get(mid).compareTo(key); int cmpPlus1 = list.get(mid + 1).compareTo(key); if (cmpPlus1 < 0) { low = Math.min(high, mid + 1); } else if (cmp > 0) { high = Math.max(low, mid - 1); } else if (cmp == 0) { return mid; } else if (cmpPlus1 == 0) { return mid + 1; } else if (useFloor) { return mid; } else { return mid + 1; } if (high == low) { return low; } } System.err.println("something went wrong " + low + " " + high + " " + useFloor); return -(low); // key not found } } ================================================ FILE: src/juicebox/data/censoring/OneDimTrackCensoring.java ================================================ /* * The MIT License (MIT) * * Copyright (c) 2011-2020 Broad Institute, Aiden Lab, Rice University, Baylor College of Medicine * * Permission is hereby granted, free of charge, to any person obtaining a copy * of this software and associated documentation files (the "Software"), to deal * in the Software without restriction, including without limitation the rights * to use, copy, modify, merge, publish, distribute, sublicense, and/or sell * copies of the Software, and to permit persons to whom the Software is * furnished to do so, subject to the following conditions: * * The above copyright notice and this permission notice shall be included in * all copies or substantial portions of the Software. * * THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR * IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, * FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE * AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER * LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, * OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN * THE SOFTWARE. */ package juicebox.data.censoring; import juicebox.HiC; import juicebox.data.anchor.GenericLocus; import juicebox.data.anchor.MotifAnchor; import juicebox.data.basics.Chromosome; import juicebox.track.*; import juicebox.windowui.HiCZoom; import org.broad.igv.track.WindowFunction; import org.broad.igv.util.Pair; import java.util.ArrayList; import java.util.List; public class OneDimTrackCensoring { public static HiCDataPoint[] getFilteredData(HiCDataSource dataSource, HiC hic, Chromosome chromosome, int startBin, int endBin, HiCGridAxis gridAxis, double scaleFactor, WindowFunction windowFunction) { HiCZoom zoom; try { zoom = hic.getZd().getZoom(); } catch (Exception e) { return null; } // x window int binSize = zoom.getBinSize(); int gx1 = startBin * binSize; int gx2 = endBin * binSize; //net.sf.jsi.Rectangle currentWindow = new net.sf.jsi.Rectangle(gx1, gx1, gx2, gx2); List> axisRegions = hic.getRTreeHandlerIntersectingFeatures(chromosome.getName(), gx1, gx2); List dataPointArrays = new ArrayList<>(); for (Pair regionPair : axisRegions) { GenericLocus originalRegion = regionPair.getFirst(); GenericLocus translatedRegion = regionPair.getSecond(); Chromosome orig = hic.getChromosomeHandler().getChromosomeFromName(originalRegion.getChr()); HiCDataPoint[] array = dataSource.getData(orig, (int) (originalRegion.getX1() / binSize), (int) (originalRegion.getX2() / binSize), gridAxis, scaleFactor, windowFunction); HiCDataPoint[] translatedArray = OneDimTrackCensoring.translateDataPointArray(zoom.getBinSize(), array, originalRegion, translatedRegion); dataPointArrays.add(translatedArray); } return OneDimTrackCensoring.mergeDataPoints(dataPointArrays); } private static HiCDataPoint[] translateDataPointArray(int binSize, HiCDataPoint[] array, GenericLocus originalRegion, GenericLocus translatedRegion) { List translatedPoints = new ArrayList<>(); if (array.length > 0 && array[0] instanceof HiCCoverageDataSource.CoverageDataPoint) { for (HiCDataPoint pointGen : array) { HiCCoverageDataSource.CoverageDataPoint point = (HiCCoverageDataSource.CoverageDataPoint) pointGen; if (point.genomicStart >= originalRegion.getX1() && point.genomicEnd <= originalRegion.getX2()) { long newGStart = translatedRegion.getX1() + point.genomicStart - originalRegion.getX1(); long newGEnd = translatedRegion.getX1() + point.genomicEnd - originalRegion.getX1(); long newBinNum = newGStart / binSize; translatedPoints.add(new HiCCoverageDataSource.CoverageDataPoint((int) newBinNum, newGStart, newGEnd, point.value)); } } } else if (array.length > 0 && array[0] instanceof HiCDataAdapter.DataAccumulator) { for (HiCDataPoint pointGen : array) { HiCDataAdapter.DataAccumulator point = (HiCDataAdapter.DataAccumulator) pointGen; if (point.genomicStart >= originalRegion.getX1() && point.genomicEnd <= originalRegion.getX2()) { long newGStart = translatedRegion.getX1() + point.genomicStart - originalRegion.getX1(); long newGEnd = translatedRegion.getX1() + point.genomicEnd - originalRegion.getX1(); long newBinNum = newGStart / binSize; HiCDataAdapter.DataAccumulator accum = new HiCDataAdapter.DataAccumulator(newBinNum, point.width, newGStart, newGEnd); accum.nPts = point.nPts; accum.weightedSum = point.weightedSum; accum.max = point.max; translatedPoints.add(accum); } } } HiCDataPoint[] points = new HiCDataPoint[translatedPoints.size()]; for (int i = 0; i < points.length; i++) { points[i] = translatedPoints.get(i); } return points; } private static HiCDataPoint[] mergeDataPoints(List dataPointArrays) { int length = 0; for (HiCDataPoint[] array : dataPointArrays) { length += array.length; } HiCDataPoint[] mergedArray = new HiCDataPoint[length]; int index = 0; for (HiCDataPoint[] array : dataPointArrays) { System.arraycopy(array, 0, mergedArray, index, array.length); index += array.length; } return mergedArray; } } ================================================ FILE: src/juicebox/data/censoring/RegionPair.java ================================================ /* * The MIT License (MIT) * * Copyright (c) 2011-2020 Broad Institute, Aiden Lab, Rice University, Baylor College of Medicine * * Permission is hereby granted, free of charge, to any person obtaining a copy * of this software and associated documentation files (the "Software"), to deal * in the Software without restriction, including without limitation the rights * to use, copy, modify, merge, publish, distribute, sublicense, and/or sell * copies of the Software, and to permit persons to whom the Software is * furnished to do so, subject to the following conditions: * * The above copyright notice and this permission notice shall be included in * all copies or substantial portions of the Software. * * THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR * IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, * FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE * AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER * LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, * OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN * THE SOFTWARE. */ package juicebox.data.censoring; import juicebox.data.ChromosomeHandler; import juicebox.data.anchor.GenericLocus; import juicebox.data.anchor.MotifAnchor; import org.broad.igv.util.Pair; import java.util.Objects; public class RegionPair { public final int xI; public final int yI; public final GenericLocus xRegion; public final GenericLocus xTransRegion; public final GenericLocus yRegion; public final GenericLocus yTransRegion; private RegionPair(int xI, Pair xLocalRegion, int yI, Pair yLocalRegion) { this.xI = xI; this.yI = yI; this.xRegion = xLocalRegion.getFirst(); this.xTransRegion = xLocalRegion.getSecond(); this.yRegion = yLocalRegion.getFirst(); this.yTransRegion = yLocalRegion.getSecond(); } public static RegionPair generateRegionPair(Pair xRegion, Pair yRegion, ChromosomeHandler handler) { int xI = handler.getChromosomeFromName(xRegion.getFirst().getChr()).getIndex(); int yI = handler.getChromosomeFromName(yRegion.getFirst().getChr()).getIndex(); // todo debug for diff custom chrs against each other // return new RegionPair(xI, xRegion, yI, yRegion); if (xI <= yI) { return new RegionPair(xI, xRegion, yI, yRegion); } else { return new RegionPair(yI, yRegion, xI, xRegion); } } public String getDescription() { return "" + xI + "_" + yI + xRegion.toString() + xTransRegion.toString() + yRegion.toString() + yTransRegion.toString(); } public long[] getOriginalGenomeRegion() { return new long[]{ xRegion.getX1(), xRegion.getX2(), yRegion.getX1(), yRegion.getX2()}; } @Override public boolean equals(Object obj) { if (this == obj) return true; if (obj instanceof RegionPair) { RegionPair o = (RegionPair) obj; return xI == o.xI && yI == o.yI && xRegion.equals(o.xRegion) && xTransRegion.equals(o.xTransRegion) && yRegion.equals(o.yRegion) && yTransRegion.equals(o.yTransRegion); } return false; } @Override public int hashCode() { return Objects.hash(xI, yI, xRegion.hashCode(), xTransRegion.hashCode(), yRegion.hashCode(), yTransRegion.hashCode()); } } ================================================ FILE: src/juicebox/data/feature/Feature.java ================================================ /* * The MIT License (MIT) * * Copyright (c) 2011-2020 Broad Institute, Aiden Lab, Rice University, Baylor College of Medicine * * Permission is hereby granted, free of charge, to any person obtaining a copy * of this software and associated documentation files (the "Software"), to deal * in the Software without restriction, including without limitation the rights * to use, copy, modify, merge, publish, distribute, sublicense, and/or sell * copies of the Software, and to permit persons to whom the Software is * furnished to do so, subject to the following conditions: * * The above copyright notice and this permission notice shall be included in * all copies or substantial portions of the Software. * * THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR * IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, * FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE * AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER * LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, * OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN * THE SOFTWARE. */ package juicebox.data.feature; /** * Created by muhammadsaadshamim on 11/17/15. */ public abstract class Feature { public abstract String getKey(); public abstract Feature deepClone(); } ================================================ FILE: src/juicebox/data/feature/FeatureFilter.java ================================================ /* * The MIT License (MIT) * * Copyright (c) 2011-2020 Broad Institute, Aiden Lab, Rice University, Baylor College of Medicine * * Permission is hereby granted, free of charge, to any person obtaining a copy * of this software and associated documentation files (the "Software"), to deal * in the Software without restriction, including without limitation the rights * to use, copy, modify, merge, publish, distribute, sublicense, and/or sell * copies of the Software, and to permit persons to whom the Software is * furnished to do so, subject to the following conditions: * * The above copyright notice and this permission notice shall be included in * all copies or substantial portions of the Software. * * THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR * IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, * FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE * AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER * LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, * OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN * THE SOFTWARE. */ package juicebox.data.feature; import java.util.List; /** * Created by muhammadsaadshamim on 7/30/15. */ public interface FeatureFilter { List filter(String chr, List featureList); } ================================================ FILE: src/juicebox/data/feature/FeatureFunction.java ================================================ /* * The MIT License (MIT) * * Copyright (c) 2011-2020 Broad Institute, Aiden Lab, Rice University, Baylor College of Medicine * * Permission is hereby granted, free of charge, to any person obtaining a copy * of this software and associated documentation files (the "Software"), to deal * in the Software without restriction, including without limitation the rights * to use, copy, modify, merge, publish, distribute, sublicense, and/or sell * copies of the Software, and to permit persons to whom the Software is * furnished to do so, subject to the following conditions: * * The above copyright notice and this permission notice shall be included in * all copies or substantial portions of the Software. * * THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR * IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, * FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE * AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER * LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, * OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN * THE SOFTWARE. */ package juicebox.data.feature; import java.util.List; /** * Created by muhammadsaadshamim on 7/30/15. */ public interface FeatureFunction { void process(String chr, List featureList); } ================================================ FILE: src/juicebox/data/feature/GenomeWideList.java ================================================ /* * The MIT License (MIT) * * Copyright (c) 2011-2020 Broad Institute, Aiden Lab, Rice University, Baylor College of Medicine * * Permission is hereby granted, free of charge, to any person obtaining a copy * of this software and associated documentation files (the "Software"), to deal * in the Software without restriction, including without limitation the rights * to use, copy, modify, merge, publish, distribute, sublicense, and/or sell * copies of the Software, and to permit persons to whom the Software is * furnished to do so, subject to the following conditions: * * The above copyright notice and this permission notice shall be included in * all copies or substantial portions of the Software. * * THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR * IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, * FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE * AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER * LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, * OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN * THE SOFTWARE. */ package juicebox.data.feature; import juicebox.data.ChromosomeHandler; import juicebox.data.basics.Chromosome; import java.io.File; import java.io.FileWriter; import java.io.IOException; import java.util.*; /** * Created by muhammadsaadshamim on 11/17/15. */ public class GenomeWideList { /** * Genome-wide list of features, where each string is a key for an * inter or intra-chromosomal region */ private final Map> featureLists = new HashMap<>(); /** Constructors**/ /** * Private constructor only used for cloning * todo delete / make private @mss */ public GenomeWideList() { } /** * @param handler */ public GenomeWideList(ChromosomeHandler handler) { for (Chromosome c : handler.getChromosomeArray()) { featureLists.put("" + c.getIndex(), new ArrayList<>()); } } /** * @param handler * @param features to be added to list */ public GenomeWideList(ChromosomeHandler handler, List features) { this(handler); addAll(features); } /** * Basic methods/functions */ /** * Initialize a genome wide list using an existing list (creates deep copy) * * @param gwList */ public GenomeWideList(final GenomeWideList gwList) { processLists(new FeatureFunction() { @Override public void process(String chr, List featureList) { if (gwList.containsKey(chr)) { addAll(gwList.getFeatures(chr)); } } }); } /** * @param key * @return */ public boolean containsKey(String key) { return featureLists.containsKey(key); } /** * @param key * @param features */ public synchronized void setFeatures(String key, List features) { featureLists.put(key, features); } /** * @param key * @return features for corresponding region */ public List getFeatures(String key) { return featureLists.get(key); } /** * @return number of features in full list */ public synchronized int size() { int val = 0; for (List features : featureLists.values()) { val += features.size(); } return val; } /** * @param features to be added to this list (deep copy) */ @SuppressWarnings("unchecked") public synchronized void addAll(List features) { for (T feature : features) { featureLists.get(feature.getKey()).add((T) feature.deepClone()); } } /** * pass interface implementing a filter for anchors * * @param filter */ public synchronized void filterLists(FeatureFilter filter) { for (String chr : featureLists.keySet()) { featureLists.put(chr, filter.filter(chr, featureLists.get(chr))); } } /** methods to create copies **/ /** * pass interface implementing a process for all anchors * * @param function */ public synchronized void processLists(FeatureFunction function) { for (String key : featureLists.keySet()) { function.process(key, featureLists.get(key)); } } /** * @return deep copy of the anchor list */ public GenomeWideList deepClone() { GenomeWideList clone = new GenomeWideList<>(); for (String key : featureLists.keySet()) { clone.featureLists.put(key, cloneFeatureList(featureLists.get(key))); } return clone; } /** * @param features * @return deep copy of the list of features */ @SuppressWarnings("unchecked") private List cloneFeatureList(List features) { List clonedFeatures = new ArrayList<>(); for (T feature : features) { clonedFeatures.add((T) feature.deepClone());//feature.deepClone() } return clonedFeatures; } /** * @return set of keys for genome-wide regions (i.e. category/location keys) */ public Set keySet() { return featureLists.keySet(); } /** * Add feature to genome-wide list with specified key * * @param key * @param feature */ public synchronized void addFeature(String key, T feature) { if (featureLists.containsKey(key)) { featureLists.get(key).add(feature); } else { List features = new ArrayList<>(); features.add(feature); featureLists.put(key, features); } } public void simpleExport(final File file) { try { final FileWriter fw = new FileWriter(file); processLists(new FeatureFunction() { @Override public void process(String chr, List featureList) { for (T t : featureList) { try { if (fw != null) fw.write(t.toString() + "\n"); } catch (IOException e) { System.err.println("Unable to write to file for exporting GWList"); } } } }); try { fw.close(); } catch (IOException e) { System.err.println("Unable to close file for exporting GWList"); } } catch (IOException e) { System.err.println("Unable to open file for exporting GWList"); } } } ================================================ FILE: src/juicebox/data/iterator/BigContactRecordList.java ================================================ /* * The MIT License (MIT) * * Copyright (c) 2011-2021 Broad Institute, Aiden Lab, Rice University, Baylor College of Medicine * * Permission is hereby granted, free of charge, to any person obtaining a copy * of this software and associated documentation files (the "Software"), to deal * in the Software without restriction, including without limitation the rights * to use, copy, modify, merge, publish, distribute, sublicense, and/or sell * copies of the Software, and to permit persons to whom the Software is * furnished to do so, subject to the following conditions: * * The above copyright notice and this permission notice shall be included in * all copies or substantial portions of the Software. * * THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR * IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, * FITNESS FOR A PARTICULAR PURPOSE AND NON-INFRINGEMENT. IN NO EVENT SHALL THE * AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER * LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, * OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN * THE SOFTWARE. */ package juicebox.data.iterator; import juicebox.data.ContactRecord; import java.util.*; public class BigContactRecordList { private static final int MAX_LIMIT = Integer.MAX_VALUE - 10; private List> internalList = new ArrayList<>(); private long numOfContactRecords = 0; public static BigContactRecordList populateListOfListsFromSingleIterator(Iterator iterator) { BigContactRecordList allRecords = new BigContactRecordList(); List tempList = new ArrayList<>(); int counter = 0; while (iterator.hasNext()) { tempList.add(iterator.next()); counter++; if (counter > MAX_LIMIT) { allRecords.addSubList(tempList); tempList = new ArrayList<>(); counter = 0; } } if (tempList.size() > 0) { allRecords.addSubList(tempList); } return allRecords; } public void addAllSubLists(BigContactRecordList other) { internalList.addAll(other.internalList); for (List records : other.internalList) { numOfContactRecords += records.size(); } } private void addSubList(List cList) { internalList.add(cList); numOfContactRecords += cList.size(); } public long getTotalSize() { return numOfContactRecords; } public int getNumLists() { return internalList.size(); } public List getSubList(int index) { return internalList.get(index); } public void clear() { for (List cList : internalList) { cList.clear(); } internalList.clear(); internalList = new ArrayList<>(); numOfContactRecords = 0; } public void sort() { internalList.sort(Comparator.comparing(o -> o.get(0))); } public void collapse() { System.out.println("Was n " + internalList.size()); int numFinList = (int) Math.max(numOfContactRecords / 200000000, 20); List> newInternalList = new ArrayList<>(); int[] countForList = new int[numFinList]; Arrays.fill(countForList, 0); for (int z = 0; z < numFinList; z++) { newInternalList.add(new ArrayList<>()); } for (List subList : internalList) { int whichIndexToAddTo = getIndexOfMin(countForList); countForList[whichIndexToAddTo] += subList.size(); newInternalList.get(whichIndexToAddTo).addAll(subList); } internalList.clear(); internalList = newInternalList; System.out.println("Now is n " + internalList.size()); } private int getIndexOfMin(int[] counts) { int minIndex = 0; for (int k = 1; k < counts.length; k++) { if (counts[k] < counts[minIndex]) { minIndex = k; } } return minIndex; } } ================================================ FILE: src/juicebox/data/iterator/ContactRecordIterator.java ================================================ /* * The MIT License (MIT) * * Copyright (c) 2011-2021 Broad Institute, Aiden Lab, Rice University, Baylor College of Medicine * * Permission is hereby granted, free of charge, to any person obtaining a copy * of this software and associated documentation files (the "Software"), to deal * in the Software without restriction, including without limitation the rights * to use, copy, modify, merge, publish, distribute, sublicense, and/or sell * copies of the Software, and to permit persons to whom the Software is * furnished to do so, subject to the following conditions: * * The above copyright notice and this permission notice shall be included in * all copies or substantial portions of the Software. * * THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR * IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, * FITNESS FOR A PARTICULAR PURPOSE AND NON-INFRINGEMENT. IN NO EVENT SHALL THE * AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER * LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, * OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN * THE SOFTWARE. */ package juicebox.data.iterator; import juicebox.HiCGlobals; import juicebox.data.Block; import juicebox.data.ContactRecord; import juicebox.data.DatasetReader; import juicebox.data.MatrixZoomData; import juicebox.windowui.NormalizationHandler; import org.broad.igv.util.collections.LRUCache; import java.io.IOException; import java.util.Iterator; import java.util.List; public /** * Class for iterating over the contact records */ class ContactRecordIterator implements Iterator { private final List blockNumbers; private int blockIdx; private Iterator currentBlockIterator; private final DatasetReader reader; private final MatrixZoomData zd; private final LRUCache blockCache; /** * Initializes the iterator */ ContactRecordIterator(DatasetReader reader, MatrixZoomData zd, LRUCache blockCache) { this.reader = reader; this.zd = zd; this.blockCache = blockCache; this.blockIdx = -1; this.blockNumbers = reader.getBlockNumbers(zd); } /** * Indicates whether or not there is another block waiting; checks current block * iterator and creates a new one if need be * * @return true if there is another block to be read */ @Override public boolean hasNext() { if (currentBlockIterator != null && currentBlockIterator.hasNext()) { return true; } else { blockIdx++; if (blockNumbers != null && blockIdx < blockNumbers.size()) { try { int blockNumber = blockNumbers.get(blockIdx); // Optionally check the cache String key = zd.getBlockKey(blockNumber, NormalizationHandler.NONE); Block nextBlock; if (HiCGlobals.useCache && blockCache.containsKey(key)) { nextBlock = blockCache.get(key); } else { nextBlock = reader.readNormalizedBlock(blockNumber, zd, NormalizationHandler.NONE); } currentBlockIterator = nextBlock.getContactRecords().iterator(); return true; } catch (IOException e) { System.err.println("Error fetching block " + e.getMessage()); return false; } } } return false; } /** * Returns the next contact record * * @return The next contact record */ @Override public ContactRecord next() { return currentBlockIterator == null ? null : currentBlockIterator.next(); } /** * Not supported */ @Override public void remove() { //Not supported throw new RuntimeException("remove() is not supported"); } } ================================================ FILE: src/juicebox/data/iterator/CoupledIteratorAndOffset.java ================================================ /* * The MIT License (MIT) * * Copyright (c) 2011-2021 Broad Institute, Aiden Lab, Rice University, Baylor College of Medicine * * Permission is hereby granted, free of charge, to any person obtaining a copy * of this software and associated documentation files (the "Software"), to deal * in the Software without restriction, including without limitation the rights * to use, copy, modify, merge, publish, distribute, sublicense, and/or sell * copies of the Software, and to permit persons to whom the Software is * furnished to do so, subject to the following conditions: * * The above copyright notice and this permission notice shall be included in * all copies or substantial portions of the Software. * * THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR * IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, * FITNESS FOR A PARTICULAR PURPOSE AND NON-INFRINGEMENT. IN NO EVENT SHALL THE * AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER * LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, * OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN * THE SOFTWARE. */ package juicebox.data.iterator; import juicebox.data.ContactRecord; import java.util.Iterator; public class CoupledIteratorAndOffset implements Iterator { private final Iterator internalIterator; private final int xOffset, yOffset; public CoupledIteratorAndOffset(Iterator iterator, int xOffset, int yOffset) { internalIterator = iterator; this.xOffset = xOffset; this.yOffset = yOffset; } @Override public boolean hasNext() { return internalIterator.hasNext(); } @Override public ContactRecord next() { ContactRecord cr = internalIterator.next(); int binX = cr.getBinX() + xOffset; int binY = cr.getBinY() + yOffset; return new ContactRecord(binX, binY, cr.getCounts()); } } ================================================ FILE: src/juicebox/data/iterator/GWIteratorContainer.java ================================================ /* * The MIT License (MIT) * * Copyright (c) 2011-2021 Broad Institute, Aiden Lab, Rice University, Baylor College of Medicine * * Permission is hereby granted, free of charge, to any person obtaining a copy * of this software and associated documentation files (the "Software"), to deal * in the Software without restriction, including without limitation the rights * to use, copy, modify, merge, publish, distribute, sublicense, and/or sell * copies of the Software, and to permit persons to whom the Software is * furnished to do so, subject to the following conditions: * * The above copyright notice and this permission notice shall be included in * all copies or substantial portions of the Software. * * THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR * IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, * FITNESS FOR A PARTICULAR PURPOSE AND NON-INFRINGEMENT. IN NO EVENT SHALL THE * AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER * LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, * OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN * THE SOFTWARE. */ package juicebox.data.iterator; import juicebox.data.ChromosomeHandler; import juicebox.data.ContactRecord; import juicebox.data.Dataset; import juicebox.data.basics.Chromosome; import juicebox.data.basics.ListOfFloatArrays; import juicebox.tools.dev.ParallelizedJuicerTools; import juicebox.windowui.HiCZoom; import java.util.Iterator; import java.util.List; import java.util.concurrent.atomic.AtomicInteger; public class GWIteratorContainer extends IteratorContainer { private final Dataset dataset; private final ChromosomeHandler handler; private final HiCZoom zoom; private final boolean includeIntra; public GWIteratorContainer(Dataset dataset, ChromosomeHandler handler, HiCZoom zoom, boolean includeIntra) { super(calculateMatrixSize(handler, zoom)); this.dataset = dataset; this.handler = handler; this.zoom = zoom; this.includeIntra = includeIntra; } private static long calculateMatrixSize(ChromosomeHandler handler, HiCZoom zoom) { long totalSize = 0; for (Chromosome c1 : handler.getChromosomeArrayWithoutAllByAll()) { totalSize += (c1.getLength() / zoom.getBinSize()) + 1; } return totalSize; } @Override public Iterator getNewContactRecordIterator() { return new GenomeWideIterator(dataset, handler, zoom, includeIntra); } public List> getAllFromFileContactRecordIterators() { return GenomeWideIterator.getAllFromFileIterators(dataset, handler, zoom, includeIntra); } @Override public ListOfFloatArrays sparseMultiply(ListOfFloatArrays vector, long vectorLength) { final ListOfFloatArrays totalSumVector = new ListOfFloatArrays(vectorLength); List> allIterators = getAllFromFileContactRecordIterators(); AtomicInteger index = new AtomicInteger(0); ParallelizedJuicerTools.launchParallelizedCode(numCPUMatrixThreads, () -> { int i = index.getAndIncrement(); ListOfFloatArrays accumSumVector = new ListOfFloatArrays(vectorLength); while (i < allIterators.size()) { accumSumVector.addValuesFrom(ZDIteratorContainer.matrixVectorMultiplyOnIterator( allIterators.get(i), vector, vectorLength)); i = index.getAndIncrement(); } synchronized (totalSumVector) { totalSumVector.addValuesFrom(accumSumVector); } }); allIterators.clear(); return totalSumVector; } @Override public void clear() { // null, doesn't need to clean anything } } ================================================ FILE: src/juicebox/data/iterator/GenomeWideIterator.java ================================================ /* * The MIT License (MIT) * * Copyright (c) 2011-2021 Broad Institute, Aiden Lab, Rice University, Baylor College of Medicine * * Permission is hereby granted, free of charge, to any person obtaining a copy * of this software and associated documentation files (the "Software"), to deal * in the Software without restriction, including without limitation the rights * to use, copy, modify, merge, publish, distribute, sublicense, and/or sell * copies of the Software, and to permit persons to whom the Software is * furnished to do so, subject to the following conditions: * * The above copyright notice and this permission notice shall be included in * all copies or substantial portions of the Software. * * THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR * IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, * FITNESS FOR A PARTICULAR PURPOSE AND NON-INFRINGEMENT. IN NO EVENT SHALL THE * AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER * LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, * OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN * THE SOFTWARE. */ package juicebox.data.iterator; import juicebox.data.*; import juicebox.data.basics.Chromosome; import juicebox.windowui.HiCZoom; import java.util.ArrayList; import java.util.Iterator; import java.util.List; public class GenomeWideIterator implements Iterator { private final Chromosome[] chromosomes; private final boolean includeIntra; private final HiCZoom zoom; private final Dataset dataset; private Iterator currentIterator = null; private int recentAddX = 0; private int recentAddY = 0; private int c1i = 0, c2i = 0; public GenomeWideIterator(Dataset dataset, ChromosomeHandler handler, HiCZoom zoom, boolean includeIntra) { this.chromosomes = handler.getChromosomeArrayWithoutAllByAll(); this.includeIntra = includeIntra; this.zoom = zoom; this.dataset = dataset; getNextIterator(); } @Override public boolean hasNext() { if (currentIterator.hasNext()) { return true; } else { recentAddY += chromosomes[c2i].getLength() / zoom.getBinSize() + 1; c2i++; } return getNextIterator(); } public static List> getAllFromFileIterators(Dataset dataset, ChromosomeHandler handler, HiCZoom zoom, boolean includeIntra) { Chromosome[] chromosomes = handler.getChromosomeArrayWithoutAllByAll(); List> allIterators = new ArrayList<>(); int xOffset = 0; for (int i = 0; i < chromosomes.length; i++) { Chromosome c1 = chromosomes[i]; int yOffset = 0 + xOffset; for (int j = i; j < chromosomes.length; j++) { Chromosome c2 = chromosomes[j]; if (c1.getIndex() < c2.getIndex() || (c1.equals(c2) && includeIntra)) { MatrixZoomData zd = HiCFileTools.getMatrixZoomData(dataset, c1, c2, zoom); if (zd != null) { IteratorContainer ic = zd.getFromFileIteratorContainer(); Iterator iterator = ic.getNewContactRecordIterator(); if (iterator != null && iterator.hasNext()) { allIterators.add(new CoupledIteratorAndOffset(iterator, xOffset, yOffset)); } } } yOffset += c2.getLength() / zoom.getBinSize() + 1; } xOffset += c1.getLength() / zoom.getBinSize() + 1; } return allIterators; } private boolean getNextIterator() { while (c1i < chromosomes.length) { Chromosome c1 = chromosomes[c1i]; while (c2i < chromosomes.length) { Chromosome c2 = chromosomes[c2i]; if (c1.getIndex() < c2.getIndex() || (c1.equals(c2) && includeIntra)) { MatrixZoomData zd = HiCFileTools.getMatrixZoomData(dataset, c1, c2, zoom); if (zd != null) { Iterator newIterator = zd.getFromFileIteratorContainer().getNewContactRecordIterator(); if (newIterator != null && newIterator.hasNext()) { currentIterator = new CoupledIteratorAndOffset(newIterator, recentAddX, recentAddY); return true; } } } recentAddY += c2.getLength() / zoom.getBinSize() + 1; c2i++; } recentAddX += c1.getLength() / zoom.getBinSize() + 1; recentAddY = 0 + recentAddX; c1i++; c2i = c1i; } return false; } @Override public ContactRecord next() { return currentIterator.next(); } } ================================================ FILE: src/juicebox/data/iterator/IteratorContainer.java ================================================ /* * The MIT License (MIT) * * Copyright (c) 2011-2021 Broad Institute, Aiden Lab, Rice University, Baylor College of Medicine * * Permission is hereby granted, free of charge, to any person obtaining a copy * of this software and associated documentation files (the "Software"), to deal * in the Software without restriction, including without limitation the rights * to use, copy, modify, merge, publish, distribute, sublicense, and/or sell * copies of the Software, and to permit persons to whom the Software is * furnished to do so, subject to the following conditions: * * The above copyright notice and this permission notice shall be included in * all copies or substantial portions of the Software. * * THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR * IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, * FITNESS FOR A PARTICULAR PURPOSE AND NON-INFRINGEMENT. IN NO EVENT SHALL THE * AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER * LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, * OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN * THE SOFTWARE. */ package juicebox.data.iterator; import juicebox.data.ContactRecord; import juicebox.data.basics.ListOfDoubleArrays; import juicebox.data.basics.ListOfFloatArrays; import java.util.Iterator; public abstract class IteratorContainer { private final long matrixSize; private long numberOfContactRecords = -1; public static int numCPUMatrixThreads = 10; public IteratorContainer(long matrixSize) { this.matrixSize = matrixSize; } abstract public Iterator getNewContactRecordIterator(); protected void setNumberOfContactRecords(long numberOfContactRecords) { this.numberOfContactRecords = numberOfContactRecords; } public long getNumberOfContactRecords() { if (numberOfContactRecords > 0) return numberOfContactRecords; numberOfContactRecords = 0; Iterator iterator = getNewContactRecordIterator(); while (iterator.hasNext()) { iterator.next(); numberOfContactRecords++; } return numberOfContactRecords; } public long getMatrixSize() { return matrixSize; } public boolean getIsThereEnoughMemoryForNormCalculation() { // when using an iterator, we basically only worry // about the vector of row sums // float is 4 bytes; one for each row return matrixSize * 4 < Runtime.getRuntime().maxMemory(); } public abstract ListOfFloatArrays sparseMultiply(ListOfFloatArrays vector, long vectorLength); public abstract void clear(); protected static ListOfFloatArrays[] getArrayOfFloatVectors(int size, long vectorLength) { ListOfFloatArrays[] array = new ListOfFloatArrays[size]; for (int i = 0; i < size; i++) { array[i] = new ListOfFloatArrays(vectorLength); } return array; } protected static ListOfDoubleArrays[] getArrayOfDoubleVectors(int size, long vectorLength) { ListOfDoubleArrays[] array = new ListOfDoubleArrays[size]; for (int i = 0; i < size; i++) { array[i] = new ListOfDoubleArrays(vectorLength); } return array; } } ================================================ FILE: src/juicebox/data/iterator/ListIteratorContainer.java ================================================ /* * The MIT License (MIT) * * Copyright (c) 2011-2021 Broad Institute, Aiden Lab, Rice University, Baylor College of Medicine * * Permission is hereby granted, free of charge, to any person obtaining a copy * of this software and associated documentation files (the "Software"), to deal * in the Software without restriction, including without limitation the rights * to use, copy, modify, merge, publish, distribute, sublicense, and/or sell * copies of the Software, and to permit persons to whom the Software is * furnished to do so, subject to the following conditions: * * The above copyright notice and this permission notice shall be included in * all copies or substantial portions of the Software. * * THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR * IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, * FITNESS FOR A PARTICULAR PURPOSE AND NON-INFRINGEMENT. IN NO EVENT SHALL THE * AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER * LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, * OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN * THE SOFTWARE. */ package juicebox.data.iterator; import juicebox.data.ContactRecord; import juicebox.data.basics.ListOfDoubleArrays; import juicebox.data.basics.ListOfFloatArrays; import juicebox.tools.dev.ParallelizedJuicerTools; import java.util.Iterator; import java.util.List; import java.util.concurrent.atomic.AtomicInteger; public class ListIteratorContainer extends IteratorContainer { private final List readList; public ListIteratorContainer(List readList, long matrixSize) { super(matrixSize); setNumberOfContactRecords(readList.size()); this.readList = readList; } @Override public Iterator getNewContactRecordIterator() { return readList.iterator(); } @Override public boolean getIsThereEnoughMemoryForNormCalculation() { // float is 4 bytes; one for each row (row sums) // 12 bytes (2 ints, 1 float) for contact record return 4 * getMatrixSize() + 12 * getNumberOfContactRecords() < Runtime.getRuntime().maxMemory(); } public static ListOfFloatArrays sparseMultiplyByListContacts(List readList, ListOfFloatArrays vector, long vectorLength, int numThreads) { final ListOfDoubleArrays totalSumVector = new ListOfDoubleArrays(vectorLength); int[] cutoffs = ParallelizedListOperations.createCutoffs(numThreads, readList.size()); AtomicInteger index = new AtomicInteger(0); ParallelizedJuicerTools.launchParallelizedCode(numThreads, () -> { int sIndx = index.getAndIncrement(); ListOfDoubleArrays sumVector = new ListOfDoubleArrays(vectorLength); for (int i = cutoffs[sIndx]; i < cutoffs[sIndx + 1]; i++) { ContactRecord cr = readList.get(i); matrixVectorMult(vector, sumVector, cr); } synchronized (totalSumVector) { totalSumVector.addValuesFrom(sumVector); } }); return totalSumVector.convertToFloats(); } public static void matrixVectorMult(ListOfFloatArrays vector, ListOfDoubleArrays sumVector, ContactRecord cr) { int x = cr.getBinX(); int y = cr.getBinY(); double counts = cr.getCounts(); if (x == y) { counts *= .5; } sumVector.addTo(x, counts * vector.get(y)); sumVector.addTo(y, counts * vector.get(x)); } @Override public ListOfFloatArrays sparseMultiply(ListOfFloatArrays vector, long vectorLength) { return sparseMultiplyByListContacts(readList, vector, vectorLength, numCPUMatrixThreads); } @Override public void clear() { readList.clear(); } } ================================================ FILE: src/juicebox/data/iterator/ListOfListGenerator.java ================================================ /* * The MIT License (MIT) * * Copyright (c) 2011-2021 Broad Institute, Aiden Lab, Rice University, Baylor College of Medicine * * Permission is hereby granted, free of charge, to any person obtaining a copy * of this software and associated documentation files (the "Software"), to deal * in the Software without restriction, including without limitation the rights * to use, copy, modify, merge, publish, distribute, sublicense, and/or sell * copies of the Software, and to permit persons to whom the Software is * furnished to do so, subject to the following conditions: * * The above copyright notice and this permission notice shall be included in * all copies or substantial portions of the Software. * * THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR * IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, * FITNESS FOR A PARTICULAR PURPOSE AND NON-INFRINGEMENT. IN NO EVENT SHALL THE * AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER * LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, * OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN * THE SOFTWARE. */ package juicebox.data.iterator; import juicebox.HiCGlobals; import juicebox.data.*; import juicebox.tools.dev.ParallelizedJuicerTools; import juicebox.windowui.HiCZoom; import org.broad.igv.util.collections.LRUCache; import java.util.Iterator; import java.util.List; import java.util.concurrent.atomic.AtomicInteger; public class ListOfListGenerator { public static IteratorContainer createFromZD(DatasetReader reader, MatrixZoomData matrixZoomData, LRUCache blockCache) { IteratorContainer ic = new ZDIteratorContainer(reader, matrixZoomData, blockCache); return tryToCreateIteratorInRAM(ic); } public static IteratorContainer createForWholeGenome(Dataset dataset, ChromosomeHandler chromosomeHandler, HiCZoom zoom, boolean includeIntraData) { IteratorContainer ic = new GWIteratorContainer(dataset, chromosomeHandler, zoom, includeIntraData); return tryToCreateIteratorInRAM(ic); } private static IteratorContainer tryToCreateIteratorInRAM(IteratorContainer ic0) { if (HiCGlobals.USE_ITERATOR_NOT_ALL_IN_RAM) { return ic0; } try { // we should count once to ensure this is reasonable to do so memory-wise boolean shouldFitInMemory = true; if (HiCGlobals.CHECK_RAM_USAGE) { shouldFitInMemory = checkMemory(ic0); } if (shouldFitInMemory) { BigContactRecordList allContactRecords = populateListOfLists(ic0); long numOfContactRecords = allContactRecords.getTotalSize(); IteratorContainer newIC = new ListOfListIteratorContainer(allContactRecords, ic0.getMatrixSize(), numOfContactRecords); return newIC; } } catch (Exception e) { System.err.println(e.getLocalizedMessage()); System.err.println("Will use default iterator"); } return ic0; } private static BigContactRecordList populateListOfLists(IteratorContainer ic) { if (ic instanceof GWIteratorContainer) { List> iterators = ((GWIteratorContainer) ic).getAllFromFileContactRecordIterators(); BigContactRecordList allRecords = new BigContactRecordList(); AtomicInteger index = new AtomicInteger(0); ParallelizedJuicerTools.launchParallelizedCode(IteratorContainer.numCPUMatrixThreads, () -> { int i = index.getAndIncrement(); BigContactRecordList recordsForThread = new BigContactRecordList(); while (i < iterators.size()) { BigContactRecordList recordsForIter = BigContactRecordList.populateListOfListsFromSingleIterator(iterators.get(i)); recordsForThread.addAllSubLists(recordsForIter); i = index.getAndIncrement(); } synchronized (allRecords) { allRecords.addAllSubLists(recordsForThread); } }); return allRecords; } else { return BigContactRecordList.populateListOfListsFromSingleIterator(ic.getNewContactRecordIterator()); } } private static boolean checkMemory(IteratorContainer ic) { long ramForRowSums = ic.getMatrixSize() * 4; long ramForAllContactRecords = ic.getNumberOfContactRecords() * 12; return ramForRowSums + ramForAllContactRecords < Runtime.getRuntime().maxMemory(); } } ================================================ FILE: src/juicebox/data/iterator/ListOfListIterator.java ================================================ /* * The MIT License (MIT) * * Copyright (c) 2011-2021 Broad Institute, Aiden Lab, Rice University, Baylor College of Medicine * * Permission is hereby granted, free of charge, to any person obtaining a copy * of this software and associated documentation files (the "Software"), to deal * in the Software without restriction, including without limitation the rights * to use, copy, modify, merge, publish, distribute, sublicense, and/or sell * copies of the Software, and to permit persons to whom the Software is * furnished to do so, subject to the following conditions: * * The above copyright notice and this permission notice shall be included in * all copies or substantial portions of the Software. * * THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR * IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, * FITNESS FOR A PARTICULAR PURPOSE AND NON-INFRINGEMENT. IN NO EVENT SHALL THE * AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER * LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, * OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN * THE SOFTWARE. */ package juicebox.data.iterator; import juicebox.data.ContactRecord; import java.util.Iterator; public class ListOfListIterator implements Iterator { private final BigContactRecordList allContactRecords; private Iterator currentIterator = null; private int currentListIndex = 0; public ListOfListIterator(BigContactRecordList allContactRecords) { this.allContactRecords = allContactRecords; getNextIterator(); } @Override public boolean hasNext() { if (currentIterator.hasNext()) { return true; } else { currentListIndex++; } return getNextIterator(); } private boolean getNextIterator() { while (currentListIndex < allContactRecords.getNumLists()) { currentIterator = allContactRecords.getSubList(currentListIndex).iterator(); if (currentIterator.hasNext()) { return true; } currentListIndex++; } return false; } @Override public ContactRecord next() { return currentIterator.next(); } } ================================================ FILE: src/juicebox/data/iterator/ListOfListIteratorContainer.java ================================================ /* * The MIT License (MIT) * * Copyright (c) 2011-2021 Broad Institute, Aiden Lab, Rice University, Baylor College of Medicine * * Permission is hereby granted, free of charge, to any person obtaining a copy * of this software and associated documentation files (the "Software"), to deal * in the Software without restriction, including without limitation the rights * to use, copy, modify, merge, publish, distribute, sublicense, and/or sell * copies of the Software, and to permit persons to whom the Software is * furnished to do so, subject to the following conditions: * * The above copyright notice and this permission notice shall be included in * all copies or substantial portions of the Software. * * THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR * IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, * FITNESS FOR A PARTICULAR PURPOSE AND NON-INFRINGEMENT. IN NO EVENT SHALL THE * AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER * LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, * OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN * THE SOFTWARE. */ package juicebox.data.iterator; import juicebox.data.ContactRecord; import juicebox.data.basics.ListOfDoubleArrays; import juicebox.data.basics.ListOfFloatArrays; import juicebox.tools.dev.ParallelizedJuicerTools; import java.util.Iterator; import java.util.List; import java.util.concurrent.atomic.AtomicInteger; public class ListOfListIteratorContainer extends IteratorContainer { private final BigContactRecordList allContactRecords; public ListOfListIteratorContainer(BigContactRecordList allContactRecords, long matrixSize, long totalNumberOfContacts) { super(matrixSize); setNumberOfContactRecords(totalNumberOfContacts); this.allContactRecords = allContactRecords; } @Override public Iterator getNewContactRecordIterator() { return new ListOfListIterator(allContactRecords); } @Override public boolean getIsThereEnoughMemoryForNormCalculation() { // float is 4 bytes; one for each row (row sums) // 12 bytes (2 ints, 1 float) for contact record return 4 * getMatrixSize() + 12 * getNumberOfContactRecords() < Runtime.getRuntime().maxMemory(); } @Override public ListOfFloatArrays sparseMultiply(ListOfFloatArrays vector, long vectorLength) { if (allContactRecords.getNumLists() < numCPUMatrixThreads) { final ListOfFloatArrays totalSumVector = new ListOfFloatArrays(vectorLength); for (int k = 0; k < allContactRecords.getNumLists(); k++) { List contactRecords = allContactRecords.getSubList(k); totalSumVector.addValuesFrom(ListIteratorContainer.sparseMultiplyByListContacts( contactRecords, vector, vectorLength, numCPUMatrixThreads)); } return totalSumVector; } return sparseMultiplyAcrossLists(vector, vectorLength); } @Override public void clear() { allContactRecords.clear(); } private ListOfFloatArrays sparseMultiplyAcrossLists(ListOfFloatArrays vector, long vectorLength) { final ListOfDoubleArrays totalSumVector = new ListOfDoubleArrays(vectorLength); AtomicInteger index = new AtomicInteger(0); ParallelizedJuicerTools.launchParallelizedCode(numCPUMatrixThreads, () -> { int sIndx = index.getAndIncrement(); ListOfDoubleArrays sumVector = new ListOfDoubleArrays(vectorLength); while (sIndx < allContactRecords.getNumLists()) { for (ContactRecord cr : allContactRecords.getSubList(sIndx)) { ListIteratorContainer.matrixVectorMult(vector, sumVector, cr); } sIndx = index.getAndIncrement(); } synchronized (totalSumVector) { totalSumVector.addValuesFrom(sumVector); } }); return totalSumVector.convertToFloats(); } } ================================================ FILE: src/juicebox/data/iterator/ParallelizedListOperations.java ================================================ /* * The MIT License (MIT) * * Copyright (c) 2011-2021 Broad Institute, Aiden Lab, Rice University, Baylor College of Medicine * * Permission is hereby granted, free of charge, to any person obtaining a copy * of this software and associated documentation files (the "Software"), to deal * in the Software without restriction, including without limitation the rights * to use, copy, modify, merge, publish, distribute, sublicense, and/or sell * copies of the Software, and to permit persons to whom the Software is * furnished to do so, subject to the following conditions: * * The above copyright notice and this permission notice shall be included in * all copies or substantial portions of the Software. * * THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR * IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, * FITNESS FOR A PARTICULAR PURPOSE AND NON-INFRINGEMENT. IN NO EVENT SHALL THE * AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER * LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, * OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN * THE SOFTWARE. */ package juicebox.data.iterator; public class ParallelizedListOperations { public static int[] createCutoffs(int n, int listSize) { int[] cutoffs = new int[n + 1]; int increment = listSize / n; for (int k = 1; k < n; k++) { cutoffs[k] = k * increment; } cutoffs[0] = 0; cutoffs[n] = listSize; return cutoffs; } } ================================================ FILE: src/juicebox/data/iterator/ZDIteratorContainer.java ================================================ /* * The MIT License (MIT) * * Copyright (c) 2011-2021 Broad Institute, Aiden Lab, Rice University, Baylor College of Medicine * * Permission is hereby granted, free of charge, to any person obtaining a copy * of this software and associated documentation files (the "Software"), to deal * in the Software without restriction, including without limitation the rights * to use, copy, modify, merge, publish, distribute, sublicense, and/or sell * copies of the Software, and to permit persons to whom the Software is * furnished to do so, subject to the following conditions: * * The above copyright notice and this permission notice shall be included in * all copies or substantial portions of the Software. * * THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR * IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, * FITNESS FOR A PARTICULAR PURPOSE AND NON-INFRINGEMENT. IN NO EVENT SHALL THE * AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER * LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, * OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN * THE SOFTWARE. */ package juicebox.data.iterator; import juicebox.data.Block; import juicebox.data.ContactRecord; import juicebox.data.DatasetReader; import juicebox.data.MatrixZoomData; import juicebox.data.basics.ListOfDoubleArrays; import juicebox.data.basics.ListOfFloatArrays; import org.broad.igv.util.collections.LRUCache; import java.util.Iterator; public class ZDIteratorContainer extends IteratorContainer { private final LRUCache blockCache; private final DatasetReader reader; private final MatrixZoomData zd; public ZDIteratorContainer(DatasetReader reader, MatrixZoomData zd, LRUCache blockCache) { super(zd.getXGridAxis().getBinCount()); this.reader = reader; this.zd = zd; this.blockCache = blockCache; } @Override public Iterator getNewContactRecordIterator() { return new ContactRecordIterator(reader, zd, blockCache); } public static ListOfFloatArrays matrixVectorMultiplyOnIterator(Iterator iterator, ListOfFloatArrays vector, long vectorLength) { ListOfDoubleArrays sumVector = new ListOfDoubleArrays(vectorLength); while (iterator.hasNext()) { ContactRecord cr = iterator.next(); ListIteratorContainer.matrixVectorMult(vector, sumVector, cr); } return sumVector.convertToFloats(); } @Override public ListOfFloatArrays sparseMultiply(ListOfFloatArrays vector, long vectorLength) { return matrixVectorMultiplyOnIterator(getNewContactRecordIterator(), vector, vectorLength); } @Override public void clear() { //blockCache.clear(); } } ================================================ FILE: src/juicebox/data/v9depth/ConstantDepth.java ================================================ /* * The MIT License (MIT) * * Copyright (c) 2011-2021 Broad Institute, Aiden Lab, Rice University, Baylor College of Medicine * * Permission is hereby granted, free of charge, to any person obtaining a copy * of this software and associated documentation files (the "Software"), to deal * in the Software without restriction, including without limitation the rights * to use, copy, modify, merge, publish, distribute, sublicense, and/or sell * copies of the Software, and to permit persons to whom the Software is * furnished to do so, subject to the following conditions: * * The above copyright notice and this permission notice shall be included in * all copies or substantial portions of the Software. * * THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR * IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, * FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE * AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER * LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, * OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN * THE SOFTWARE. */ package juicebox.data.v9depth; public class ConstantDepth extends V9Depth { public ConstantDepth(int base, int blockBinCount) { super(blockBinCount); this.BASE = Math.abs(base); } @Override protected int logBase(double v) { return (int) Math.abs(v / BASE); } } ================================================ FILE: src/juicebox/data/v9depth/LogDepth.java ================================================ /* * The MIT License (MIT) * * Copyright (c) 2011-2021 Broad Institute, Aiden Lab, Rice University, Baylor College of Medicine * * Permission is hereby granted, free of charge, to any person obtaining a copy * of this software and associated documentation files (the "Software"), to deal * in the Software without restriction, including without limitation the rights * to use, copy, modify, merge, publish, distribute, sublicense, and/or sell * copies of the Software, and to permit persons to whom the Software is * furnished to do so, subject to the following conditions: * * The above copyright notice and this permission notice shall be included in * all copies or substantial portions of the Software. * * THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR * IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, * FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE * AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER * LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, * OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN * THE SOFTWARE. */ package juicebox.data.v9depth; public class LogDepth extends V9Depth { public LogDepth(int base, int blockBinCount) { super(blockBinCount); this.BASE = Math.log(base); } @Override protected int logBase(double v) { return (int) (Math.log(1 + v) / BASE); } } ================================================ FILE: src/juicebox/data/v9depth/V9Depth.java ================================================ /* * The MIT License (MIT) * * Copyright (c) 2011-2021 Broad Institute, Aiden Lab, Rice University, Baylor College of Medicine * * Permission is hereby granted, free of charge, to any person obtaining a copy * of this software and associated documentation files (the "Software"), to deal * in the Software without restriction, including without limitation the rights * to use, copy, modify, merge, publish, distribute, sublicense, and/or sell * copies of the Software, and to permit persons to whom the Software is * furnished to do so, subject to the following conditions: * * The above copyright notice and this permission notice shall be included in * all copies or substantial portions of the Software. * * THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR * IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, * FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE * AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER * LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, * OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN * THE SOFTWARE. */ package juicebox.data.v9depth; public abstract class V9Depth { protected final int blockBinCount; protected double BASE; V9Depth(int blockBinCount) { this.blockBinCount = blockBinCount; } public static V9Depth setDepthMethod(int depthBase, int blockBinCount) { if (depthBase > 1) { return new LogDepth(depthBase, blockBinCount); } else if (depthBase < 0) { return new ConstantDepth(-depthBase, blockBinCount); } // Default return new LogDepth(2, blockBinCount); } public int getDepth(int val1, int val2) { return logBase(Math.abs(val1 - val2) / Math.sqrt(2) / blockBinCount); } protected abstract int logBase(double value); } ================================================ FILE: src/juicebox/encode/EncodeFileBrowser.java ================================================ /* * The MIT License (MIT) * * Copyright (c) 2011-2021 Broad Institute, Aiden Lab, Rice University, Baylor College of Medicine * * Permission is hereby granted, free of charge, to any person obtaining a copy * of this software and associated documentation files (the "Software"), to deal * in the Software without restriction, including without limitation the rights * to use, copy, modify, merge, publish, distribute, sublicense, and/or sell * copies of the Software, and to permit persons to whom the Software is * furnished to do so, subject to the following conditions: * * The above copyright notice and this permission notice shall be included in * all copies or substantial portions of the Software. * * THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR * IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, * FITNESS FOR A PARTICULAR PURPOSE AND NON-INFRINGEMENT. IN NO EVENT SHALL THE * AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER * LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, * OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN * THE SOFTWARE. */ package juicebox.encode; import com.jidesoft.swing.JideBoxLayout; import juicebox.HiCGlobals; import org.broad.igv.Globals; import org.broad.igv.ui.IGV; import org.broad.igv.util.Pair; import org.broad.igv.util.ParsingUtils; import org.broad.igv.util.ResourceLocator; import javax.swing.*; import javax.swing.border.EmptyBorder; import javax.swing.event.DocumentEvent; import javax.swing.event.DocumentListener; import javax.swing.text.NumberFormatter; import java.awt.*; import java.awt.event.ActionEvent; import java.awt.event.ActionListener; import java.io.BufferedReader; import java.io.IOException; import java.io.InputStream; import java.io.InputStreamReader; import java.text.ParseException; import java.util.List; import java.util.*; import java.util.regex.Matcher; import java.util.regex.Pattern; /** * @author Jim Robinson */ public class EncodeFileBrowser extends JDialog { private static final long serialVersionUID = 9000016; private static final Map instanceMap = Collections.synchronizedMap(new HashMap<>()); private static final NumberFormatter numberFormatter = new NumberFormatter(); private final EncodeTableModel model; private JTable table; private JTextField filterTextField; private JLabel rowCountLabel; private boolean canceled; private EncodeFileBrowser(Frame owner, EncodeTableModel model) { super(owner); this.model = model; setModal(true); initComponents(); init(model); } public synchronized static EncodeFileBrowser getInstance(String genomeId) throws IOException { String encodeGenomeId = getEncodeGenomeId(genomeId); EncodeFileBrowser instance = instanceMap.get(encodeGenomeId); if (instance == null) { Pair> records = getEncodeFileRecords(encodeGenomeId); if (records == null) { return null; } Frame parent = IGV.hasInstance() ? IGV.getMainFrame() : null; instance = new EncodeFileBrowser(parent, new EncodeTableModel(records.getFirst(), records.getSecond())); instanceMap.put(encodeGenomeId, instance); } return instance; } private static String getEncodeGenomeId(String genomeId) { if (genomeId.equals("b37") || genomeId.equals("1kg_v37")) return "hg19"; else if (genomeId.equals("hg38")) return "GRCh38"; else return genomeId; } private static Pair> getEncodeFileRecords(String genomeId) throws IOException { boolean urlVersion = false; InputStream is = null; try { //is = EncodeFileBrowser.class.getResourceAsStream("encode." + genomeId + ".txt"); //if (is == null) { try { is = ParsingUtils.openInputStream("https://s3.amazonaws.com/igv.org.app/encode/" + getEncodeGenomeId(genomeId) + ".txt.gz"); urlVersion = true; } catch (Exception error) { return null; } //} BufferedReader reader = new BufferedReader(new InputStreamReader(is), HiCGlobals.bufferSize); String[] headers = Globals.tabPattern.split(reader.readLine()); List records = new ArrayList<>(20000); String nextLine; int pathLocation = 0; if (urlVersion) { pathLocation = Arrays.asList(headers).indexOf("HREF"); } while ((nextLine = reader.readLine()) != null) { if (!nextLine.startsWith("#")) { String[] tokens = Globals.tabPattern.split(nextLine, -1); String path = tokens[pathLocation]; // Filter BAMs for hic if (path == null || path.endsWith("bam")) continue; if (urlVersion) path = "https://www.encodeproject.org" + path; Map attributes = new HashMap<>(); for (int i = 0; i < headers.length; i++) { String value = i < tokens.length ? tokens[i] : ""; if (value.length() > 0) { attributes.put(headers[i], value); } } final EncodeFileRecord record = new EncodeFileRecord(path, attributes); if (record.hasMetaData()) records.add(record); } } return new Pair<>(headers, records); } finally { if (is != null) is.close(); } } private void init(final EncodeTableModel model) { setModal(true); setTitle("Encode Production Data"); table.setAutoCreateRowSorter(true); table.setModel(model); table.setRowSorter(model.getSorter()); try { rowCountLabel.setText(numberFormatter.valueToString(table.getRowCount()) + " rows"); } catch (ParseException e) { e.printStackTrace(); } table.setRowSelectionAllowed(false); table.setColumnSelectionAllowed(false); filterTextField.getDocument().addDocumentListener( new DocumentListener() { public void changedUpdate(DocumentEvent e) { updateFilter(); } public void insertUpdate(DocumentEvent e) { updateFilter(); } public void removeUpdate(DocumentEvent e) { updateFilter(); } }); } /** * Update the row filter regular expression from the expression in * the text box. */ private void updateFilter() { RowFilter rf = null; //If current expression doesn't parse, don't update. try { rf = new RegexFilter(filterTextField.getText()); } catch (java.util.regex.PatternSyntaxException | ClassCastException e) { return; } model.getSorter().setRowFilter(rf); try { rowCountLabel.setText(numberFormatter.valueToString(table.getRowCount()) + " rows"); } catch (ParseException e) { e.printStackTrace(); //To change body of catch statement use File | Settings | File Templates. } } private void loadButtonActionPerformed(ActionEvent e) { canceled = false; setVisible(false); } private void cancelButtonActionPerformed(ActionEvent e) { canceled = true; setVisible(false); } public boolean isCanceled() { return canceled; } /** * @return the list of VISIBLE selected records. Filtered records are not returned even if record.selected == true * @throws java.io.IOException */ public List getSelectedRecords() { List selectedRecords = new ArrayList<>(); List allRecords = model.getRecords(); int rowCount = table.getRowCount(); for (int i = 0; i < rowCount; i++) { int modelIdx = table.convertRowIndexToModel(i); EncodeFileRecord record = allRecords.get(modelIdx); if (record.isSelected()) { selectedRecords.add(record); } } return selectedRecords; } public void checkEncodeTracks(String track) { List allRecords = model.getRecords(); int rowCount = table.getRowCount(); for (int i = 0; i < rowCount; i++) { int modelIdx = table.convertRowIndexToModel(i); EncodeFileRecord record = allRecords.get(modelIdx); if (record.getTrackName().contains(track)) { record.setSelected(true); } } } public void remove(ResourceLocator locator) { List allRecords = model.getRecords(); int rowCount = table.getRowCount(); int i = 0; boolean notFound = true; while (i < rowCount && notFound) { int modelIdx = table.convertRowIndexToModel(i); EncodeFileRecord record = allRecords.get(modelIdx); ResourceLocator rl = new ResourceLocator(record.getPath()); rl.setName(record.getTrackName()); if (rl.equals(locator)) { record.setSelected(false); notFound = false; } i++; } } private void initComponents() { JPanel dialogPane = new JPanel(); JPanel contentPanel = new JPanel(); JScrollPane scrollPane1 = new JScrollPane(); table = new JTable(); JPanel filterPanel = new JPanel(); JLabel filterLabel = new JLabel(); filterTextField = new JTextField(); rowCountLabel = new JLabel(); JPanel buttonBar = new JPanel(); JButton okButton = new JButton(); JButton cancelButton = new JButton(); getRootPane().setDefaultButton(okButton); final String filterToolTip = "Enter multiple filter strings separated by commas. e.g. GM12878, ChipSeq"; filterLabel.setToolTipText(filterToolTip); filterTextField.setToolTipText(filterToolTip); //======== this ======== Container contentPane = getContentPane(); contentPane.setLayout(new BorderLayout()); //======== dialogPane ======== dialogPane.setBorder(new EmptyBorder(12, 12, 12, 12)); dialogPane.setLayout(new BorderLayout()); //======== contentPanel ======== contentPanel.setLayout(new BorderLayout(0, 10)); //======== scrollPane1 ======== scrollPane1.setViewportView(table); contentPanel.add(scrollPane1, BorderLayout.CENTER); //======== panel1 ======== filterPanel.setLayout(new JideBoxLayout(filterPanel, JideBoxLayout.X_AXIS, 5)); //---- label1 ---- filterLabel.setText("Filter:"); filterPanel.add(filterLabel, JideBoxLayout.FIX); //---- filterTextField ---- filterPanel.add(filterTextField, JideBoxLayout.VARY); rowCountLabel.setHorizontalAlignment(JLabel.RIGHT); JPanel sillyPanel = new JPanel(); sillyPanel.setLayout(new JideBoxLayout(sillyPanel, JideBoxLayout.X_AXIS, 0)); sillyPanel.setPreferredSize(new Dimension(100, 28)); sillyPanel.add(rowCountLabel, JideBoxLayout.VARY); filterPanel.add(sillyPanel, JideBoxLayout.FIX); contentPanel.add(filterPanel, BorderLayout.NORTH); dialogPane.add(contentPanel, BorderLayout.CENTER); //======== buttonBar ======== buttonBar.setBorder(new EmptyBorder(12, 0, 0, 0)); buttonBar.setLayout(new GridBagLayout()); ((GridBagLayout) buttonBar.getLayout()).columnWidths = new int[]{0, 85, 80}; ((GridBagLayout) buttonBar.getLayout()).columnWeights = new double[]{1.0, 0.0, 0.0}; //---- okButton ---- okButton.setText("Load"); okButton.addActionListener(new ActionListener() { @Override public void actionPerformed(ActionEvent e) { loadButtonActionPerformed(e); } }); buttonBar.add(okButton, new GridBagConstraints(1, 0, 1, 1, 0.0, 0.0, GridBagConstraints.CENTER, GridBagConstraints.BOTH, new Insets(0, 0, 0, 5), 0, 0)); //---- cancelButton ---- cancelButton.setText("Cancel"); cancelButton.addActionListener(new ActionListener() { @Override public void actionPerformed(ActionEvent e) { cancelButtonActionPerformed(e); } }); buttonBar.add(cancelButton, new GridBagConstraints(2, 0, 1, 1, 0.0, 0.0, GridBagConstraints.CENTER, GridBagConstraints.BOTH, new Insets(0, 0, 0, 0), 0, 0)); dialogPane.add(buttonBar, BorderLayout.SOUTH); contentPane.add(dialogPane, BorderLayout.CENTER); setSize(700, 620); setLocationRelativeTo(getOwner()); } private class RegexFilter extends RowFilter { List> matchers; RegexFilter(String text) { if (text == null) { throw new IllegalArgumentException("Pattern must be non-null"); } matchers = new ArrayList<>(); String[] tokens = Globals.whitespacePattern.split(text); for (String t : tokens) { // If token contains an = sign apply to specified column only String column = "*"; String value = t.trim(); if (t.contains("=")) { String[] kv = Globals.equalPattern.split(t); if (kv.length > 1) { column = kv[0].trim(); value = kv[1].trim(); } else { value = kv[0]; // Value is column name until more input is entered } } matchers.add(new Pair<>(column, Pattern.compile("(?i)" + value).matcher(""))); } } /** * Include row if each matcher succeeds in at least one column. In other words all the conditions * are combined with "and" * * @param value value to check * @return if matched */ @Override public boolean include(Entry value) { for (Pair entry : matchers) { String column = entry.getFirst(); Matcher matcher = entry.getSecond(); // Search for a match in at least one column. The first column is the checkbox. boolean found = false; // Pessimistic int nColumns = table.getColumnCount(); for (int index = 1; index < nColumns; index++) { // Include column headings in search. This is to prevent premature filtering when entering a // specific column condition (e.g. cataType=ChipSeq) matcher.reset(table.getColumnName(index).toLowerCase()); if (matcher.find()) { found = true; break; } boolean wildcard = column.equals("*"); if (wildcard || column.equalsIgnoreCase(table.getColumnName(index))) { matcher.reset(value.getStringValue(index)); if (matcher.find()) { found = true; break; } } } if (!found) return false; } return true; // If we get here we matched them all } } } ================================================ FILE: src/juicebox/encode/EncodeFileRecord.java ================================================ /* * The MIT License (MIT) * * Copyright (c) 2011-2020 Broad Institute, Aiden Lab, Rice University, Baylor College of Medicine * * Permission is hereby granted, free of charge, to any person obtaining a copy * of this software and associated documentation files (the "Software"), to deal * in the Software without restriction, including without limitation the rights * to use, copy, modify, merge, publish, distribute, sublicense, and/or sell * copies of the Software, and to permit persons to whom the Software is * furnished to do so, subject to the following conditions: * * The above copyright notice and this permission notice shall be included in * all copies or substantial portions of the Software. * * THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR * IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, * FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE * AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER * LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, * OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN * THE SOFTWARE. */ package juicebox.encode; import java.io.File; import java.util.Collection; import java.util.Map; /** * @author jrobinso * Date: 10/31/13 * Time: 10:11 PM */ public class EncodeFileRecord { private final String path; private final Map attributes; private boolean selected = false; private String trackName; public EncodeFileRecord(String path, Map attributes) { this.path = path; this.attributes = attributes; } public String getPath() { return path; } public String getFileType() { //String off trailing gz, if present String filetype = path; if (filetype.endsWith(".gz")) { filetype = filetype.substring(0, filetype.length() - 3); } int idx = filetype.lastIndexOf("."); return filetype.substring(idx + 1); } public String getAttributeValue(String name) { String value = attributes.get(name); if (name.equals("type") && value == null) value = getFileType(); return value; } public Collection getAttributeNames() { return attributes.keySet(); } public boolean containsText(String filter) { for (String value : attributes.values()) { if (value.contains(filter)) return true; } return false; } boolean isSelected() { return selected; } public void setSelected(boolean selected) { this.selected = selected; } /** * Return a friendly name for the track. Unfortunately it is neccessary to hardcode certain attributes. * * @return */ public String getTrackName() { if (trackName == null) { StringBuilder sb = new StringBuilder(); if (attributes.containsKey("cell")) sb.append(attributes.get("cell")).append(" "); if (attributes.containsKey("antibody")) sb.append(attributes.get("antibody")).append(" "); if (attributes.containsKey("dataType")) sb.append(attributes.get("dataType")).append(" "); if (attributes.containsKey("view")) sb.append(attributes.get("view")).append(" "); if (attributes.containsKey("replicate")) sb.append("rep ").append(attributes.get("replicate")); trackName = sb.toString().trim(); if (sb.length() == 0) trackName = (new File(path)).getName(); } return trackName; } /** * Test if record has a eough of meta-data to be interpretable * * @return */ public boolean hasMetaData() { return (attributes.containsKey("cell")) || (attributes.containsKey("antibody") || attributes.containsKey("Biosample")); } } ================================================ FILE: src/juicebox/encode/EncodeTableModel.java ================================================ /* * The MIT License (MIT) * * Copyright (c) 2011-2021 Broad Institute, Aiden Lab, Rice University, Baylor College of Medicine * * Permission is hereby granted, free of charge, to any person obtaining a copy * of this software and associated documentation files (the "Software"), to deal * in the Software without restriction, including without limitation the rights * to use, copy, modify, merge, publish, distribute, sublicense, and/or sell * copies of the Software, and to permit persons to whom the Software is * furnished to do so, subject to the following conditions: * * The above copyright notice and this permission notice shall be included in * all copies or substantial portions of the Software. * * THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR * IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, * FITNESS FOR A PARTICULAR PURPOSE AND NON-INFRINGEMENT. IN NO EVENT SHALL THE * AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER * LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, * OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN * THE SOFTWARE. */ package juicebox.encode; import javax.swing.table.AbstractTableModel; import javax.swing.table.TableModel; import javax.swing.table.TableRowSorter; import javax.swing.table.TableStringConverter; import java.util.ArrayList; import java.util.List; /** * //wgEncodeBroadHistoneGm12878H3k4me1StdSig.bigWig * // size=346M; * // dateSubmitted=2009-01-05; * // dataType=ChipSeq; * // cell=GM12878; * // antibody=H3K4me1; * // control=std; * // expId=33; * // setType=exp; * // controlId=GM12878/Input/std; * // subId=2804; * // dataVersion=ENCODE Jan 2011 Freeze; * // dateResubmitted=2010-11-05; * // grant=Bernstein; * // lab=Broad; * // view=Signal; * // type=bigWig; * // dccAccession=wgEncodeEH000033; * // origAssembly=hg18 * * @author jrobinso * Date: 10/31/13 * Time: 10:09 PM */ class EncodeTableModel extends AbstractTableModel { private static final long serialVersionUID = 9000015; private final String[] columnHeadings; private final List records; private final TableRowSorter sorter; public EncodeTableModel(String[] headings, List records) { this.records = records; List tmp = new ArrayList<>(); tmp.add(""); // Checkbox heading for (String h : headings) { String heading = h.trim(); if (heading.length() > 0 && !"path".equals(heading)) { tmp.add(heading); } } //tmp.add("path"); columnHeadings = tmp.toArray(new String[tmp.size()]); sorter = new TableRowSorter<>(this); sorter.setStringConverter(new TableStringConverter() { @Override public String toString(TableModel model, int row, int column) { final Object value = model.getValueAt(row, column); return value == null ? "" : value.toString(); } }); } public TableRowSorter getSorter() { return sorter; } @Override public Class getColumnClass(int columnIndex) { return columnIndex == 0 ? Boolean.class : String.class; } @Override public String getColumnName(int column) { return columnHeadings[column]; } @Override public int getRowCount() { return records.size(); } @Override public int getColumnCount() { return columnHeadings.length; } @Override public Object getValueAt(int rowIndex, int columnIndex) { if (rowIndex >= records.size() || columnIndex >= columnHeadings.length) { return null; } EncodeFileRecord record = records.get(rowIndex); if (columnIndex == 0) { return record.isSelected(); } else { String att = columnHeadings[columnIndex]; return record.getAttributeValue(att); } } @Override public boolean isCellEditable(int rowIndex, int columnIndex) { return columnIndex == 0; } @Override public void setValueAt(Object value, int row, int col) { if (col == 0) { records.get(row).setSelected((Boolean) value); } fireTableCellUpdated(row, col); } public List getRecords() { return records; } } ================================================ FILE: src/juicebox/encode/UCSCEncodeUtils.java ================================================ /* * The MIT License (MIT) * * Copyright (c) 2011-2020 Broad Institute, Aiden Lab, Rice University, Baylor College of Medicine * * Permission is hereby granted, free of charge, to any person obtaining a copy * of this software and associated documentation files (the "Software"), to deal * in the Software without restriction, including without limitation the rights * to use, copy, modify, merge, publish, distribute, sublicense, and/or sell * copies of the Software, and to permit persons to whom the Software is * furnished to do so, subject to the following conditions: * * The above copyright notice and this permission notice shall be included in * all copies or substantial portions of the Software. * * THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR * IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, * FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE * AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER * LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, * OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN * THE SOFTWARE. */ package juicebox.encode; import juicebox.HiCGlobals; import org.broad.igv.Globals; import org.broad.igv.util.HttpUtils; import org.broad.igv.util.ParsingUtils; import java.io.*; import java.util.*; /** * @author jrobinso * Date: 10/31/13 * Time: 12:16 PM */ class UCSCEncodeUtils { private static final HashSet labs = new HashSet<>(); private static final HashSet dataTypes = new HashSet<>(); private static final HashSet cells = new HashSet<>(); private static final HashSet antibodies = new HashSet<>(); private static final HashSet fileTypes = new HashSet<>(); private static final HashSet allHeaders = new LinkedHashSet<>(); private static final List rnaChipQualifiers = Arrays.asList("CellTotal", "Longnonpolya", "Longpolya", "NucleolusTotal", "ChromatinTotal", "ChromatinTotal", "NucleoplasmTotal"); private static final String[] columnHeadings = {"cell", "dataType", "antibody", "view", "replicate", "type", "lab"}; private static final HashSet knownFileTypes = new HashSet<>(Arrays.asList("bam", "bigBed", "bed", "bb", "bw", "bigWig", "gtf", "broadPeak", "narrowPeak", "gff")); public static void main(String[] args) throws IOException { // List records = new ArrayList(); // parseFilesDotTxt(args[0], records); // PrintWriter pw = new PrintWriter(new BufferedWriter(new FileWriter(args[1]))); // // pw.print("path"); // for (String h : EncodeTableModel.columnHeadings) { // pw.print("\t"); // pw.print(h); // } // pw.println(); // // for (EncodeFileRecord rec : records) { // pw.print(rec.getPath()); // for (String h : EncodeTableModel.columnHeadings) { // pw.print("\t"); // String value = rec.getAttributeValue(h); // pw.print(value == null ? "" : value); // } // pw.println(); // } // pw.close(); updateEncodeTableFile(args[0], args[1]); } private static List parseTableFile(String url) throws IOException { List records = new ArrayList<>(20000); BufferedReader reader = null; //reader = ParsingUtils.openBufferedReader(url); reader = new BufferedReader(new InputStreamReader(ParsingUtils.openInputStream(url)), HiCGlobals.bufferSize); String[] headers = Globals.tabPattern.split(reader.readLine()); String nextLine; while ((nextLine = reader.readLine()) != null) { if (!nextLine.startsWith("#")) { String[] tokens = Globals.tabPattern.split(nextLine, -1); String path = tokens[0]; Map attributes = new HashMap<>(); for (int i = 0; i < headers.length; i++) { String value = tokens[i]; if (value.length() > 0) { attributes.put(headers[i], value); } } records.add(new EncodeFileRecord(path, attributes)); } } return records; } private static void updateEncodeTableFile(String inputFile, String outputFile) throws IOException { List records = new ArrayList<>(); BufferedReader reader = null; //reader = ParsingUtils.openBufferedReader(inputFile); reader = new BufferedReader(new InputStreamReader(ParsingUtils.openInputStream(inputFile)), HiCGlobals.bufferSize); String rootPath = reader.readLine(); String hub = null; String nextLine; while ((nextLine = reader.readLine()) != null) { if (nextLine.startsWith("#")) { if (nextLine.startsWith("#hub=")) { hub = nextLine.substring(5); } } else { String dir = nextLine.equals(".") ? rootPath : rootPath + nextLine; String filesDotTxt = dir + "/files.txt"; try { if (HttpUtils.getInstance().resourceAvailable(filesDotTxt)) { parseFilesDotTxt(filesDotTxt, records); } } catch (IOException e) { // e.printStackTrace(); //To change body of catch statement use File | Settings | File Templates. } } } for (String dt : fileTypes) System.out.println(dt); outputRecords(outputFile, records, hub); } private static void outputRecords(String outputFile, List records, String hub) throws IOException { PrintWriter pw = new PrintWriter(new BufferedWriter(new FileWriter(outputFile))); pw.print("path"); for (String h : columnHeadings) { pw.print("\t"); pw.print(h); } if (hub != null) { pw.print("\thub"); } pw.println(); for (EncodeFileRecord rec : records) { pw.print(rec.getPath()); for (String h : columnHeadings) { pw.print("\t"); String value = rec.getAttributeValue(h); pw.print(value == null ? "" : value); } if (hub != null) { pw.print("\t" + hub); } pw.println(); } pw.close(); } private static void parseFilesDotTxt(String url, List fileRecords) throws IOException { BufferedReader reader = null; //reader = ParsingUtils.openBufferedReader(url); reader = new BufferedReader(new InputStreamReader(ParsingUtils.openInputStream(url)), HiCGlobals.bufferSize); String nextLine; while ((nextLine = reader.readLine()) != null) { String[] tokens = Globals.tabPattern.split(nextLine); if (tokens.length < 2) continue; String fn = tokens[0]; String[] attributes = Globals.semicolonPattern.split(tokens[1]); LinkedHashMap kvalues = new LinkedHashMap<>(); for (String tk : attributes) { String[] kv = Globals.equalPattern.split(tk); if (kv.length > 1) { kvalues.put(kv[0].trim(), kv[1].trim()); allHeaders.add(kv[0].trim()); } } // Hack for RnaChip -- need this to disambiguate them if ("RnaChip".equals(kvalues.get("dataType"))) { for (String qual : rnaChipQualifiers) { if (fn.contains(qual)) { kvalues.put("antibody", qual); } } } String path = fn.startsWith("http") ? fn : url.replace("files.txt", fn); EncodeFileRecord df = new EncodeFileRecord(path, kvalues); if (knownFileTypes.contains(df.getFileType())) { fileRecords.add(df); } dataTypes.add(df.getAttributeValue("dataType")); antibodies.add(df.getAttributeValue("antibody")); cells.add(df.getAttributeValue("cell")); labs.add(df.getAttributeValue("lab")); fileTypes.add(df.getFileType()); } reader.close(); } /* File types bam bigBed shortFrags csqual spikeins bai pdf bed matrix bigWig tab bed9 bedCluster peptideMapping csfasta gtf fastq broadPeak narrowPeak gff bedRrbs bedRnaElements tgz bedLogR peaks */ } ================================================ FILE: src/juicebox/encode/encode.hg18.txt ================================================ path cell dataType antibody view replicate type lab http://hgdownload.cse.ucsc.edu/goldenPath/hg18/encodeDCC/wgEncodeBroadChipSeq/wgEncodeBroadChipSeqPeaksGm12878Ctcf.broadPeak.gz GM12878 ChipSeq CTCF Peaks broadPeak Broad http://hgdownload.cse.ucsc.edu/goldenPath/hg18/encodeDCC/wgEncodeBroadChipSeq/wgEncodeBroadChipSeqPeaksGm12878H3k27ac.broadPeak.gz GM12878 ChipSeq H3K27ac Peaks broadPeak Broad http://hgdownload.cse.ucsc.edu/goldenPath/hg18/encodeDCC/wgEncodeBroadChipSeq/wgEncodeBroadChipSeqPeaksGm12878H3k27me3.broadPeak.gz GM12878 ChipSeq H3K27me3 Peaks broadPeak Broad http://hgdownload.cse.ucsc.edu/goldenPath/hg18/encodeDCC/wgEncodeBroadChipSeq/wgEncodeBroadChipSeqPeaksGm12878H3k36me3.broadPeak.gz GM12878 ChipSeq H3K36me3 Peaks broadPeak Broad http://hgdownload.cse.ucsc.edu/goldenPath/hg18/encodeDCC/wgEncodeBroadChipSeq/wgEncodeBroadChipSeqPeaksGm12878H3k4me1.broadPeak.gz GM12878 ChipSeq H3K4me1 Peaks broadPeak Broad http://hgdownload.cse.ucsc.edu/goldenPath/hg18/encodeDCC/wgEncodeBroadChipSeq/wgEncodeBroadChipSeqPeaksGm12878H3k4me2.broadPeak.gz GM12878 ChipSeq H3K4me2 Peaks broadPeak Broad http://hgdownload.cse.ucsc.edu/goldenPath/hg18/encodeDCC/wgEncodeBroadChipSeq/wgEncodeBroadChipSeqPeaksGm12878H3k4me3.broadPeak.gz GM12878 ChipSeq H3K4me3 Peaks broadPeak Broad http://hgdownload.cse.ucsc.edu/goldenPath/hg18/encodeDCC/wgEncodeBroadChipSeq/wgEncodeBroadChipSeqPeaksGm12878H3k9ac.broadPeak.gz GM12878 ChipSeq H3K9ac Peaks broadPeak Broad http://hgdownload.cse.ucsc.edu/goldenPath/hg18/encodeDCC/wgEncodeBroadChipSeq/wgEncodeBroadChipSeqPeaksGm12878H4k20me1.broadPeak.gz GM12878 ChipSeq H4K20me1 Peaks broadPeak Broad http://hgdownload.cse.ucsc.edu/goldenPath/hg18/encodeDCC/wgEncodeBroadChipSeq/wgEncodeBroadChipSeqPeaksH1hescCtcf.broadPeak.gz H1-hESC ChipSeq CTCF Peaks broadPeak Broad http://hgdownload.cse.ucsc.edu/goldenPath/hg18/encodeDCC/wgEncodeBroadChipSeq/wgEncodeBroadChipSeqPeaksH1hescH3k27me3.broadPeak.gz H1-hESC ChipSeq H3K27me3 Peaks broadPeak Broad http://hgdownload.cse.ucsc.edu/goldenPath/hg18/encodeDCC/wgEncodeBroadChipSeq/wgEncodeBroadChipSeqPeaksH1hescH3k36me3.broadPeak.gz H1-hESC ChipSeq H3K36me3 Peaks broadPeak Broad http://hgdownload.cse.ucsc.edu/goldenPath/hg18/encodeDCC/wgEncodeBroadChipSeq/wgEncodeBroadChipSeqPeaksH1hescH3k4me1.broadPeak.gz H1-hESC ChipSeq H3K4me1 Peaks broadPeak Broad http://hgdownload.cse.ucsc.edu/goldenPath/hg18/encodeDCC/wgEncodeBroadChipSeq/wgEncodeBroadChipSeqPeaksH1hescH3k4me2.broadPeak.gz H1-hESC ChipSeq H3K4me2 Peaks broadPeak Broad http://hgdownload.cse.ucsc.edu/goldenPath/hg18/encodeDCC/wgEncodeBroadChipSeq/wgEncodeBroadChipSeqPeaksH1hescH3k4me3.broadPeak.gz H1-hESC ChipSeq H3K4me3 Peaks broadPeak Broad http://hgdownload.cse.ucsc.edu/goldenPath/hg18/encodeDCC/wgEncodeBroadChipSeq/wgEncodeBroadChipSeqPeaksH1hescH3k9ac.broadPeak.gz H1-hESC ChipSeq H3K9ac Peaks broadPeak Broad 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http://hgdownload.cse.ucsc.edu/goldenPath/hg18/encodeDCC/wgEncodeBroadChipSeq/wgEncodeBroadChipSeqPeaksNhlfH3k9ac.broadPeak.gz NHLF ChipSeq H3K9ac Peaks broadPeak Broad http://hgdownload.cse.ucsc.edu/goldenPath/hg18/encodeDCC/wgEncodeBroadChipSeq/wgEncodeBroadChipSeqPeaksNhlfH4k20me1.broadPeak.gz NHLF ChipSeq H4K20me1 Peaks broadPeak Broad http://hgdownload.cse.ucsc.edu/goldenPath/hg18/encodeDCC/wgEncodeBroadHmm/wgEncodeBroadHmmGm12878HMM.bed.gz GM12878 Combined HMM bed Broad http://hgdownload.cse.ucsc.edu/goldenPath/hg18/encodeDCC/wgEncodeBroadHmm/wgEncodeBroadHmmH1hescHMM.bed.gz H1-hESC Combined HMM bed Broad http://hgdownload.cse.ucsc.edu/goldenPath/hg18/encodeDCC/wgEncodeBroadHmm/wgEncodeBroadHmmHepg2HMM.bed.gz HepG2 Combined HMM bed Broad http://hgdownload.cse.ucsc.edu/goldenPath/hg18/encodeDCC/wgEncodeBroadHmm/wgEncodeBroadHmmHmecHMM.bed.gz HMEC Combined HMM bed Broad http://hgdownload.cse.ucsc.edu/goldenPath/hg18/encodeDCC/wgEncodeBroadHmm/wgEncodeBroadHmmHsmmHMM.bed.gz HSMM 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http://hgdownload.cse.ucsc.edu/goldenPath/hg18/encodeDCC/wgEncodeChromatinMap/wgEncodeDukeDNaseSeqPeaksGm18507.narrowPeak.gz GM18507 DnaseSeq Peaks narrowPeak Duke http://hgdownload.cse.ucsc.edu/goldenPath/hg18/encodeDCC/wgEncodeChromatinMap/wgEncodeDukeDNaseSeqPeaksGm19238V2.narrowPeak.gz GM19238 DnaseSeq Peaks narrowPeak Duke http://hgdownload.cse.ucsc.edu/goldenPath/hg18/encodeDCC/wgEncodeChromatinMap/wgEncodeDukeDNaseSeqPeaksGm19239V2.narrowPeak.gz GM19239 DnaseSeq Peaks narrowPeak Duke http://hgdownload.cse.ucsc.edu/goldenPath/hg18/encodeDCC/wgEncodeChromatinMap/wgEncodeDukeDNaseSeqPeaksGm19240V2.narrowPeak.gz GM19240 DnaseSeq Peaks narrowPeak Duke http://hgdownload.cse.ucsc.edu/goldenPath/hg18/encodeDCC/wgEncodeChromatinMap/wgEncodeDukeDNaseSeqPeaksH1hescV2.narrowPeak.gz H1-hESC DnaseSeq Peaks narrowPeak Duke http://hgdownload.cse.ucsc.edu/goldenPath/hg18/encodeDCC/wgEncodeChromatinMap/wgEncodeDukeDNaseSeqPeaksH9es.narrowPeak.gz H9ES DnaseSeq Peaks narrowPeak Duke http://hgdownload.cse.ucsc.edu/goldenPath/hg18/encodeDCC/wgEncodeChromatinMap/wgEncodeDukeDNaseSeqPeaksHelas3Ifna4h.narrowPeak.gz HeLa-S3 DnaseSeq Peaks narrowPeak Duke http://hgdownload.cse.ucsc.edu/goldenPath/hg18/encodeDCC/wgEncodeChromatinMap/wgEncodeDukeDNaseSeqPeaksHelas3V3.narrowPeak.gz HeLa-S3 DnaseSeq Peaks narrowPeak Duke http://hgdownload.cse.ucsc.edu/goldenPath/hg18/encodeDCC/wgEncodeChromatinMap/wgEncodeDukeDNaseSeqPeaksHepg2V3.narrowPeak.gz HepG2 DnaseSeq Peaks narrowPeak Duke http://hgdownload.cse.ucsc.edu/goldenPath/hg18/encodeDCC/wgEncodeChromatinMap/wgEncodeDukeDNaseSeqPeaksHsmm.narrowPeak.gz HSMM DnaseSeq Peaks narrowPeak Duke http://hgdownload.cse.ucsc.edu/goldenPath/hg18/encodeDCC/wgEncodeChromatinMap/wgEncodeDukeDNaseSeqPeaksHsmmt.narrowPeak.gz HSMMtube DnaseSeq Peaks narrowPeak Duke http://hgdownload.cse.ucsc.edu/goldenPath/hg18/encodeDCC/wgEncodeChromatinMap/wgEncodeDukeDNaseSeqPeaksHuvecV2.narrowPeak.gz HUVEC DnaseSeq Peaks narrowPeak Duke 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http://hgdownload.cse.ucsc.edu/goldenPath/hg18/encodeDCC/wgEncodeUwAffyExonArray/wgEncodeUwAffyExonArraySimpleSignalRep1Mcf7.broadPeak.gz MCF-7 AffyExonArray SimpleSignal 1 broadPeak UW http://hgdownload.cse.ucsc.edu/goldenPath/hg18/encodeDCC/wgEncodeUwAffyExonArray/wgEncodeUwAffyExonArraySimpleSignalRep1Nb4V2.broadPeak.gz NB4 AffyExonArray SimpleSignal 1 broadPeak UW http://hgdownload.cse.ucsc.edu/goldenPath/hg18/encodeDCC/wgEncodeUwAffyExonArray/wgEncodeUwAffyExonArraySimpleSignalRep1Nhdfneo.broadPeak.gz NHDF-neo AffyExonArray SimpleSignal 1 broadPeak UW http://hgdownload.cse.ucsc.edu/goldenPath/hg18/encodeDCC/wgEncodeUwAffyExonArray/wgEncodeUwAffyExonArraySimpleSignalRep1Nhek.broadPeak.gz NHEK AffyExonArray SimpleSignal 1 broadPeak UW http://hgdownload.cse.ucsc.edu/goldenPath/hg18/encodeDCC/wgEncodeUwAffyExonArray/wgEncodeUwAffyExonArraySimpleSignalRep1Nhlf.broadPeak.gz NHLF AffyExonArray SimpleSignal 1 broadPeak UW http://hgdownload.cse.ucsc.edu/goldenPath/hg18/encodeDCC/wgEncodeUwAffyExonArray/wgEncodeUwAffyExonArraySimpleSignalRep1Panc1.broadPeak.gz PANC-1 AffyExonArray SimpleSignal 1 broadPeak UW http://hgdownload.cse.ucsc.edu/goldenPath/hg18/encodeDCC/wgEncodeUwAffyExonArray/wgEncodeUwAffyExonArraySimpleSignalRep1Saec.broadPeak.gz SAEC AffyExonArray SimpleSignal 1 broadPeak UW http://hgdownload.cse.ucsc.edu/goldenPath/hg18/encodeDCC/wgEncodeUwAffyExonArray/wgEncodeUwAffyExonArraySimpleSignalRep1SkmcV2.broadPeak.gz SKMC AffyExonArray SimpleSignal 1 broadPeak UW http://hgdownload.cse.ucsc.edu/goldenPath/hg18/encodeDCC/wgEncodeUwAffyExonArray/wgEncodeUwAffyExonArraySimpleSignalRep1Sknshra.broadPeak.gz SK-N-SH_RA AffyExonArray 1 broadPeak UW http://hgdownload.cse.ucsc.edu/goldenPath/hg18/encodeDCC/wgEncodeUwAffyExonArray/wgEncodeUwAffyExonArraySimpleSignalRep1Th1.broadPeak.gz Th1 AffyExonArray 1 broadPeak UW http://hgdownload.cse.ucsc.edu/goldenPath/hg18/encodeDCC/wgEncodeUwAffyExonArray/wgEncodeUwAffyExonArraySimpleSignalRep2Ag04449.broadPeak.gz AG04449 AffyExonArray SimpleSignal 2 broadPeak UW http://hgdownload.cse.ucsc.edu/goldenPath/hg18/encodeDCC/wgEncodeUwAffyExonArray/wgEncodeUwAffyExonArraySimpleSignalRep2Ag04450.broadPeak.gz AG04450 AffyExonArray SimpleSignal 2 broadPeak UW http://hgdownload.cse.ucsc.edu/goldenPath/hg18/encodeDCC/wgEncodeUwAffyExonArray/wgEncodeUwAffyExonArraySimpleSignalRep2Ag09309.broadPeak.gz AG09309 AffyExonArray SimpleSignal 2 broadPeak UW http://hgdownload.cse.ucsc.edu/goldenPath/hg18/encodeDCC/wgEncodeUwAffyExonArray/wgEncodeUwAffyExonArraySimpleSignalRep2Ag09319.broadPeak.gz AG09319 AffyExonArray SimpleSignal 2 broadPeak UW http://hgdownload.cse.ucsc.edu/goldenPath/hg18/encodeDCC/wgEncodeUwAffyExonArray/wgEncodeUwAffyExonArraySimpleSignalRep2Ag10803.broadPeak.gz AG10803 AffyExonArray SimpleSignal 2 broadPeak UW http://hgdownload.cse.ucsc.edu/goldenPath/hg18/encodeDCC/wgEncodeUwAffyExonArray/wgEncodeUwAffyExonArraySimpleSignalRep2Bjtert.broadPeak.gz BJ AffyExonArray SimpleSignal 2 broadPeak UW http://hgdownload.cse.ucsc.edu/goldenPath/hg18/encodeDCC/wgEncodeUwAffyExonArray/wgEncodeUwAffyExonArraySimpleSignalRep2Caco2.broadPeak.gz Caco-2 AffyExonArray SimpleSignal 2 broadPeak UW http://hgdownload.cse.ucsc.edu/goldenPath/hg18/encodeDCC/wgEncodeUwAffyExonArray/wgEncodeUwAffyExonArraySimpleSignalRep2Gm06990.broadPeak.gz GM06990 AffyExonArray 2 broadPeak UW http://hgdownload.cse.ucsc.edu/goldenPath/hg18/encodeDCC/wgEncodeUwAffyExonArray/wgEncodeUwAffyExonArraySimpleSignalRep2Hae.broadPeak.gz HAEpiC AffyExonArray SimpleSignal 2 broadPeak UW http://hgdownload.cse.ucsc.edu/goldenPath/hg18/encodeDCC/wgEncodeUwAffyExonArray/wgEncodeUwAffyExonArraySimpleSignalRep2Hcf.broadPeak.gz HCF AffyExonArray SimpleSignal 2 broadPeak UW http://hgdownload.cse.ucsc.edu/goldenPath/hg18/encodeDCC/wgEncodeUwAffyExonArray/wgEncodeUwAffyExonArraySimpleSignalRep2Hcm.broadPeak.gz HCM AffyExonArray SimpleSignal 2 broadPeak UW http://hgdownload.cse.ucsc.edu/goldenPath/hg18/encodeDCC/wgEncodeUwAffyExonArray/wgEncodeUwAffyExonArraySimpleSignalRep2Hcpe.broadPeak.gz HCPEpiC AffyExonArray SimpleSignal 2 broadPeak UW http://hgdownload.cse.ucsc.edu/goldenPath/hg18/encodeDCC/wgEncodeUwAffyExonArray/wgEncodeUwAffyExonArraySimpleSignalRep2Hee.broadPeak.gz HEEpiC AffyExonArray SimpleSignal 2 broadPeak UW http://hgdownload.cse.ucsc.edu/goldenPath/hg18/encodeDCC/wgEncodeUwAffyExonArray/wgEncodeUwAffyExonArraySimpleSignalRep2Helas3V2.broadPeak.gz HeLa-S3 AffyExonArray SimpleSignal 2 broadPeak UW http://hgdownload.cse.ucsc.edu/goldenPath/hg18/encodeDCC/wgEncodeUwAffyExonArray/wgEncodeUwAffyExonArraySimpleSignalRep2Hepg2.broadPeak.gz HepG2 AffyExonArray 2 broadPeak UW http://hgdownload.cse.ucsc.edu/goldenPath/hg18/encodeDCC/wgEncodeUwAffyExonArray/wgEncodeUwAffyExonArraySimpleSignalRep2Hipe.broadPeak.gz HIPEpiC AffyExonArray SimpleSignal 2 broadPeak UW http://hgdownload.cse.ucsc.edu/goldenPath/hg18/encodeDCC/wgEncodeUwAffyExonArray/wgEncodeUwAffyExonArraySimpleSignalRep2Hnpce.broadPeak.gz HNPCEpiC AffyExonArray SimpleSignal 2 broadPeak UW http://hgdownload.cse.ucsc.edu/goldenPath/hg18/encodeDCC/wgEncodeUwAffyExonArray/wgEncodeUwAffyExonArraySimpleSignalRep2Hrcepic.broadPeak.gz HRCEpiC AffyExonArray 2 broadPeak UW http://hgdownload.cse.ucsc.edu/goldenPath/hg18/encodeDCC/wgEncodeUwAffyExonArray/wgEncodeUwAffyExonArraySimpleSignalRep2Hre.broadPeak.gz HRE AffyExonArray 2 broadPeak UW http://hgdownload.cse.ucsc.edu/goldenPath/hg18/encodeDCC/wgEncodeUwAffyExonArray/wgEncodeUwAffyExonArraySimpleSignalRep2Hrpe.broadPeak.gz HRPEpiC AffyExonArray SimpleSignal 2 broadPeak UW http://hgdownload.cse.ucsc.edu/goldenPath/hg18/encodeDCC/wgEncodeUwAffyExonArray/wgEncodeUwAffyExonArraySimpleSignalRep2Jurkat.broadPeak.gz Jurkat AffyExonArray SimpleSignal 2 broadPeak UW http://hgdownload.cse.ucsc.edu/goldenPath/hg18/encodeDCC/wgEncodeUwAffyExonArray/wgEncodeUwAffyExonArraySimpleSignalRep2K562.broadPeak.gz K562 AffyExonArray SimpleSignal 2 broadPeak UW http://hgdownload.cse.ucsc.edu/goldenPath/hg18/encodeDCC/wgEncodeUwAffyExonArray/wgEncodeUwAffyExonArraySimpleSignalRep2Mcf7.broadPeak.gz MCF-7 AffyExonArray SimpleSignal 2 broadPeak UW http://hgdownload.cse.ucsc.edu/goldenPath/hg18/encodeDCC/wgEncodeUwAffyExonArray/wgEncodeUwAffyExonArraySimpleSignalRep2Nb4.broadPeak.gz NB4 AffyExonArray SimpleSignal 2 broadPeak UW http://hgdownload.cse.ucsc.edu/goldenPath/hg18/encodeDCC/wgEncodeUwAffyExonArray/wgEncodeUwAffyExonArraySimpleSignalRep2Nhdfneo.broadPeak.gz NHDF-neo AffyExonArray SimpleSignal 2 broadPeak UW http://hgdownload.cse.ucsc.edu/goldenPath/hg18/encodeDCC/wgEncodeUwAffyExonArray/wgEncodeUwAffyExonArraySimpleSignalRep2Nhlf.broadPeak.gz NHLF AffyExonArray SimpleSignal 2 broadPeak UW http://hgdownload.cse.ucsc.edu/goldenPath/hg18/encodeDCC/wgEncodeUwAffyExonArray/wgEncodeUwAffyExonArraySimpleSignalRep2Panc1.broadPeak.gz PANC-1 AffyExonArray SimpleSignal 2 broadPeak UW http://hgdownload.cse.ucsc.edu/goldenPath/hg18/encodeDCC/wgEncodeUwAffyExonArray/wgEncodeUwAffyExonArraySimpleSignalRep2Saec.broadPeak.gz SAEC AffyExonArray SimpleSignal 2 broadPeak UW http://hgdownload.cse.ucsc.edu/goldenPath/hg18/encodeDCC/wgEncodeUwAffyExonArray/wgEncodeUwAffyExonArraySimpleSignalRep2Skmc.broadPeak.gz SKMC AffyExonArray SimpleSignal 2 broadPeak UW http://hgdownload.cse.ucsc.edu/goldenPath/hg18/encodeDCC/wgEncodeUwAffyExonArray/wgEncodeUwAffyExonArraySimpleSignalRep2Sknshra.broadPeak.gz SK-N-SH_RA AffyExonArray 2 broadPeak UW http://hgdownload.cse.ucsc.edu/goldenPath/hg18/encodeDCC/wgEncodeUwChIPSeq/wgEncodeUwChIPSeqHotspotsRep1BjH3k27me3.broadPeak.gz BJ ChipSeq H3K27me3 Hotspots 1 broadPeak UW http://hgdownload.cse.ucsc.edu/goldenPath/hg18/encodeDCC/wgEncodeUwChIPSeq/wgEncodeUwChIPSeqHotspotsRep1BjH3k36me3.broadPeak.gz BJ ChipSeq H3K36me3 Hotspots 1 broadPeak UW http://hgdownload.cse.ucsc.edu/goldenPath/hg18/encodeDCC/wgEncodeUwChIPSeq/wgEncodeUwChIPSeqHotspotsRep1BjH3k4me3.broadPeak.gz BJ ChipSeq H3K4me3 Hotspots 1 broadPeak UW http://hgdownload.cse.ucsc.edu/goldenPath/hg18/encodeDCC/wgEncodeUwChIPSeq/wgEncodeUwChIPSeqHotspotsRep1BjtertCtcf.broadPeak.gz BJ ChipSeq CTCF Hotspots 1 broadPeak UW http://hgdownload.cse.ucsc.edu/goldenPath/hg18/encodeDCC/wgEncodeUwChIPSeq/wgEncodeUwChIPSeqHotspotsRep1Caco2Ctcf.broadPeak.gz Caco-2 ChipSeq CTCF Hotspots 1 broadPeak UW http://hgdownload.cse.ucsc.edu/goldenPath/hg18/encodeDCC/wgEncodeUwChIPSeq/wgEncodeUwChIPSeqHotspotsRep1Caco2H3k27me3.broadPeak.gz Caco-2 ChipSeq H3K27me3 Hotspots 1 broadPeak UW http://hgdownload.cse.ucsc.edu/goldenPath/hg18/encodeDCC/wgEncodeUwChIPSeq/wgEncodeUwChIPSeqHotspotsRep1Caco2H3k36me3.broadPeak.gz Caco-2 ChipSeq H3K36me3 Hotspots 1 broadPeak UW http://hgdownload.cse.ucsc.edu/goldenPath/hg18/encodeDCC/wgEncodeUwChIPSeq/wgEncodeUwChIPSeqHotspotsRep1Caco2H3k4me3.broadPeak.gz Caco-2 ChipSeq H3K4me3 Hotspots 1 broadPeak UW http://hgdownload.cse.ucsc.edu/goldenPath/hg18/encodeDCC/wgEncodeUwChIPSeq/wgEncodeUwChIPSeqHotspotsRep1Gm06990Ctcf.broadPeak.gz GM06990 ChipSeq CTCF Hotspots 1 broadPeak UW http://hgdownload.cse.ucsc.edu/goldenPath/hg18/encodeDCC/wgEncodeUwChIPSeq/wgEncodeUwChIPSeqHotspotsRep1Gm06990H3k27me3.broadPeak.gz GM06990 ChipSeq H3K27me3 Hotspots 1 broadPeak UW http://hgdownload.cse.ucsc.edu/goldenPath/hg18/encodeDCC/wgEncodeUwChIPSeq/wgEncodeUwChIPSeqHotspotsRep1Gm06990H3k36me3.broadPeak.gz GM06990 ChipSeq H3K36me3 Hotspots 1 broadPeak UW http://hgdownload.cse.ucsc.edu/goldenPath/hg18/encodeDCC/wgEncodeUwChIPSeq/wgEncodeUwChIPSeqHotspotsRep1Gm06990H3k4me3.broadPeak.gz GM06990 ChipSeq H3K4me3 Hotspots 1 broadPeak UW http://hgdownload.cse.ucsc.edu/goldenPath/hg18/encodeDCC/wgEncodeUwChIPSeq/wgEncodeUwChIPSeqHotspotsRep1Gm12801Ctcf.broadPeak.gz GM12801 ChipSeq CTCF Hotspots 1 broadPeak UW http://hgdownload.cse.ucsc.edu/goldenPath/hg18/encodeDCC/wgEncodeUwChIPSeq/wgEncodeUwChIPSeqHotspotsRep1Gm12864Ctcf.broadPeak.gz GM12864 ChipSeq CTCF Hotspots 1 broadPeak UW http://hgdownload.cse.ucsc.edu/goldenPath/hg18/encodeDCC/wgEncodeUwChIPSeq/wgEncodeUwChIPSeqHotspotsRep1Gm12865Ctcf.broadPeak.gz GM12865 ChipSeq CTCF Hotspots 1 broadPeak UW http://hgdownload.cse.ucsc.edu/goldenPath/hg18/encodeDCC/wgEncodeUwChIPSeq/wgEncodeUwChIPSeqHotspotsRep1Gm12872Ctcf.broadPeak.gz GM12872 ChipSeq CTCF Hotspots 1 broadPeak UW http://hgdownload.cse.ucsc.edu/goldenPath/hg18/encodeDCC/wgEncodeUwChIPSeq/wgEncodeUwChIPSeqHotspotsRep1Gm12873Ctcf.broadPeak.gz GM12873 ChipSeq CTCF Hotspots 1 broadPeak UW http://hgdownload.cse.ucsc.edu/goldenPath/hg18/encodeDCC/wgEncodeUwChIPSeq/wgEncodeUwChIPSeqHotspotsRep1Gm12874Ctcf.broadPeak.gz GM12874 ChipSeq CTCF Hotspots 1 broadPeak UW http://hgdownload.cse.ucsc.edu/goldenPath/hg18/encodeDCC/wgEncodeUwChIPSeq/wgEncodeUwChIPSeqHotspotsRep1Gm12875Ctcf.broadPeak.gz GM12875 ChipSeq CTCF Hotspots 1 broadPeak UW http://hgdownload.cse.ucsc.edu/goldenPath/hg18/encodeDCC/wgEncodeUwChIPSeq/wgEncodeUwChIPSeqHotspotsRep1Gm12878Ctcf.broadPeak.gz GM12878 ChipSeq CTCF Hotspots 1 broadPeak UW http://hgdownload.cse.ucsc.edu/goldenPath/hg18/encodeDCC/wgEncodeUwChIPSeq/wgEncodeUwChIPSeqHotspotsRep1Gm12878H3k27me3.broadPeak.gz GM12878 ChipSeq H3K27me3 Hotspots 1 broadPeak UW http://hgdownload.cse.ucsc.edu/goldenPath/hg18/encodeDCC/wgEncodeUwChIPSeq/wgEncodeUwChIPSeqHotspotsRep1Gm12878H3k36me3.broadPeak.gz GM12878 ChipSeq H3K36me3 Hotspots 1 broadPeak UW http://hgdownload.cse.ucsc.edu/goldenPath/hg18/encodeDCC/wgEncodeUwChIPSeq/wgEncodeUwChIPSeqHotspotsRep1Gm12878H3k4me3.broadPeak.gz GM12878 ChipSeq H3K4me3 Hotspots 1 broadPeak UW http://hgdownload.cse.ucsc.edu/goldenPath/hg18/encodeDCC/wgEncodeUwChIPSeq/wgEncodeUwChIPSeqHotspotsRep1Hek293Ctcf.broadPeak.gz HEK293 ChipSeq CTCF Hotspots 1 broadPeak UW http://hgdownload.cse.ucsc.edu/goldenPath/hg18/encodeDCC/wgEncodeUwChIPSeq/wgEncodeUwChIPSeqHotspotsRep1Helas3Ctcf.broadPeak.gz HeLa-S3 ChipSeq CTCF Hotspots 1 broadPeak UW http://hgdownload.cse.ucsc.edu/goldenPath/hg18/encodeDCC/wgEncodeUwChIPSeq/wgEncodeUwChIPSeqHotspotsRep1Helas3H3k27me3.broadPeak.gz HeLa-S3 ChipSeq H3K27me3 Hotspots 1 broadPeak UW http://hgdownload.cse.ucsc.edu/goldenPath/hg18/encodeDCC/wgEncodeUwChIPSeq/wgEncodeUwChIPSeqHotspotsRep1Helas3H3k36me3.broadPeak.gz HeLa-S3 ChipSeq H3K36me3 Hotspots 1 broadPeak UW http://hgdownload.cse.ucsc.edu/goldenPath/hg18/encodeDCC/wgEncodeUwChIPSeq/wgEncodeUwChIPSeqHotspotsRep1Helas3H3k4me3.broadPeak.gz HeLa-S3 ChipSeq H3K4me3 Hotspots 1 broadPeak UW http://hgdownload.cse.ucsc.edu/goldenPath/hg18/encodeDCC/wgEncodeUwChIPSeq/wgEncodeUwChIPSeqHotspotsRep1Hepg2Ctcf.broadPeak.gz HepG2 ChipSeq CTCF Hotspots 1 broadPeak UW http://hgdownload.cse.ucsc.edu/goldenPath/hg18/encodeDCC/wgEncodeUwChIPSeq/wgEncodeUwChIPSeqHotspotsRep1Hepg2H3k27me3.broadPeak.gz HepG2 ChipSeq H3K27me3 Hotspots 1 broadPeak UW http://hgdownload.cse.ucsc.edu/goldenPath/hg18/encodeDCC/wgEncodeUwChIPSeq/wgEncodeUwChIPSeqHotspotsRep1Hepg2H3k36me3.broadPeak.gz HepG2 ChipSeq H3K36me3 Hotspots 1 broadPeak UW http://hgdownload.cse.ucsc.edu/goldenPath/hg18/encodeDCC/wgEncodeUwChIPSeq/wgEncodeUwChIPSeqHotspotsRep1Hepg2H3k4me3.broadPeak.gz HepG2 ChipSeq H3K4me3 Hotspots 1 broadPeak UW http://hgdownload.cse.ucsc.edu/goldenPath/hg18/encodeDCC/wgEncodeUwChIPSeq/wgEncodeUwChIPSeqHotspotsRep1Hl60Ctcf.broadPeak.gz HL-60 ChipSeq CTCF Hotspots 1 broadPeak UW http://hgdownload.cse.ucsc.edu/goldenPath/hg18/encodeDCC/wgEncodeUwChIPSeq/wgEncodeUwChIPSeqHotspotsRep1Hl60H3k4me3.broadPeak.gz HL-60 ChipSeq H3K4me3 Hotspots 1 broadPeak UW http://hgdownload.cse.ucsc.edu/goldenPath/hg18/encodeDCC/wgEncodeUwChIPSeq/wgEncodeUwChIPSeqHotspotsRep1HmecCtcf.broadPeak.gz HMEC ChipSeq CTCF Hotspots 1 broadPeak UW http://hgdownload.cse.ucsc.edu/goldenPath/hg18/encodeDCC/wgEncodeUwChIPSeq/wgEncodeUwChIPSeqHotspotsRep1HmecH3k27me3.broadPeak.gz HMEC ChipSeq H3K27me3 Hotspots 1 broadPeak UW http://hgdownload.cse.ucsc.edu/goldenPath/hg18/encodeDCC/wgEncodeUwChIPSeq/wgEncodeUwChIPSeqHotspotsRep1HreCtcf.broadPeak.gz HRE ChipSeq 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http://hgdownload.cse.ucsc.edu/goldenPath/hg18/encodeDCC/wgEncodeUwChIPSeq/wgEncodeUwChIPSeqHotspotsRep1HuvecH3k36me3.broadPeak.gz HUVEC ChipSeq H3K36me3 Hotspots 1 broadPeak UW http://hgdownload.cse.ucsc.edu/goldenPath/hg18/encodeDCC/wgEncodeUwChIPSeq/wgEncodeUwChIPSeqHotspotsRep1HuvecH3k4me3.broadPeak.gz HUVEC ChipSeq H3K4me3 Hotspots 1 broadPeak UW http://hgdownload.cse.ucsc.edu/goldenPath/hg18/encodeDCC/wgEncodeUwChIPSeq/wgEncodeUwChIPSeqHotspotsRep1K562Ctcf.broadPeak.gz K562 ChipSeq CTCF Hotspots 1 broadPeak UW http://hgdownload.cse.ucsc.edu/goldenPath/hg18/encodeDCC/wgEncodeUwChIPSeq/wgEncodeUwChIPSeqHotspotsRep1K562H3k27me3.broadPeak.gz K562 ChipSeq H3K27me3 Hotspots 1 broadPeak UW http://hgdownload.cse.ucsc.edu/goldenPath/hg18/encodeDCC/wgEncodeUwChIPSeq/wgEncodeUwChIPSeqHotspotsRep1K562H3k36me3.broadPeak.gz K562 ChipSeq H3K36me3 Hotspots 1 broadPeak UW http://hgdownload.cse.ucsc.edu/goldenPath/hg18/encodeDCC/wgEncodeUwChIPSeq/wgEncodeUwChIPSeqHotspotsRep1K562H3k4me3.broadPeak.gz K562 ChipSeq H3K4me3 Hotspots 1 broadPeak UW http://hgdownload.cse.ucsc.edu/goldenPath/hg18/encodeDCC/wgEncodeUwChIPSeq/wgEncodeUwChIPSeqHotspotsRep1NhekCtcf.broadPeak.gz NHEK ChipSeq CTCF Hotspots 1 broadPeak UW http://hgdownload.cse.ucsc.edu/goldenPath/hg18/encodeDCC/wgEncodeUwChIPSeq/wgEncodeUwChIPSeqHotspotsRep1NhekH3k27me3.broadPeak.gz NHEK ChipSeq H3K27me3 Hotspots 1 broadPeak UW http://hgdownload.cse.ucsc.edu/goldenPath/hg18/encodeDCC/wgEncodeUwChIPSeq/wgEncodeUwChIPSeqHotspotsRep1NhekH3k36me3.broadPeak.gz NHEK ChipSeq H3K36me3 Hotspots 1 broadPeak UW http://hgdownload.cse.ucsc.edu/goldenPath/hg18/encodeDCC/wgEncodeUwChIPSeq/wgEncodeUwChIPSeqHotspotsRep1NhekH3k4me3.broadPeak.gz NHEK ChipSeq H3K4me3 Hotspots 1 broadPeak UW http://hgdownload.cse.ucsc.edu/goldenPath/hg18/encodeDCC/wgEncodeUwChIPSeq/wgEncodeUwChIPSeqHotspotsRep1SaecCtcf.broadPeak.gz SAEC ChipSeq CTCF Hotspots 1 broadPeak UW http://hgdownload.cse.ucsc.edu/goldenPath/hg18/encodeDCC/wgEncodeUwChIPSeq/wgEncodeUwChIPSeqHotspotsRep1SaecH3k27me3.broadPeak.gz SAEC ChipSeq H3K27me3 Hotspots 1 broadPeak UW http://hgdownload.cse.ucsc.edu/goldenPath/hg18/encodeDCC/wgEncodeUwChIPSeq/wgEncodeUwChIPSeqHotspotsRep1SaecH3k36me3.broadPeak.gz SAEC ChipSeq H3K36me3 Hotspots 1 broadPeak UW http://hgdownload.cse.ucsc.edu/goldenPath/hg18/encodeDCC/wgEncodeUwChIPSeq/wgEncodeUwChIPSeqHotspotsRep1SaecH3k4me3.broadPeak.gz SAEC ChipSeq H3K4me3 Hotspots 1 broadPeak UW http://hgdownload.cse.ucsc.edu/goldenPath/hg18/encodeDCC/wgEncodeUwChIPSeq/wgEncodeUwChIPSeqHotspotsRep1SknshraCtcf.broadPeak.gz SK-N-SH_RA ChipSeq CTCF Hotspots 1 broadPeak UW http://hgdownload.cse.ucsc.edu/goldenPath/hg18/encodeDCC/wgEncodeUwChIPSeq/wgEncodeUwChIPSeqHotspotsRep1SknshraH3k27me3.broadPeak.gz SK-N-SH_RA ChipSeq H3K27me3 Hotspots 1 broadPeak UW http://hgdownload.cse.ucsc.edu/goldenPath/hg18/encodeDCC/wgEncodeUwChIPSeq/wgEncodeUwChIPSeqHotspotsRep1SknshraH3k36me3.broadPeak.gz SK-N-SH_RA ChipSeq H3K36me3 Hotspots 1 broadPeak UW http://hgdownload.cse.ucsc.edu/goldenPath/hg18/encodeDCC/wgEncodeUwChIPSeq/wgEncodeUwChIPSeqHotspotsRep1SknshraH3k4me3.broadPeak.gz SK-N-SH_RA ChipSeq H3K4me3 Hotspots 1 broadPeak UW http://hgdownload.cse.ucsc.edu/goldenPath/hg18/encodeDCC/wgEncodeUwChIPSeq/wgEncodeUwChIPSeqHotspotsRep1Werirb1Ctcf.broadPeak.gz WERI-Rb-1 ChipSeq CTCF Hotspots 1 broadPeak UW http://hgdownload.cse.ucsc.edu/goldenPath/hg18/encodeDCC/wgEncodeUwChIPSeq/wgEncodeUwChIPSeqHotspotsRep2BjH3k27me3.broadPeak.gz BJ ChipSeq H3K27me3 Hotspots 2 broadPeak UW http://hgdownload.cse.ucsc.edu/goldenPath/hg18/encodeDCC/wgEncodeUwChIPSeq/wgEncodeUwChIPSeqHotspotsRep2BjH3k36me3.broadPeak.gz BJ ChipSeq H3K36me3 Hotspots 2 broadPeak UW http://hgdownload.cse.ucsc.edu/goldenPath/hg18/encodeDCC/wgEncodeUwChIPSeq/wgEncodeUwChIPSeqHotspotsRep2BjH3k4me3.broadPeak.gz BJ ChipSeq H3K4me3 Hotspots 2 broadPeak UW http://hgdownload.cse.ucsc.edu/goldenPath/hg18/encodeDCC/wgEncodeUwChIPSeq/wgEncodeUwChIPSeqHotspotsRep2BjtertCtcf.broadPeak.gz BJ ChipSeq CTCF Hotspots 2 broadPeak UW http://hgdownload.cse.ucsc.edu/goldenPath/hg18/encodeDCC/wgEncodeUwChIPSeq/wgEncodeUwChIPSeqHotspotsRep2Caco2Ctcf.broadPeak.gz Caco-2 ChipSeq CTCF Hotspots 2 broadPeak UW http://hgdownload.cse.ucsc.edu/goldenPath/hg18/encodeDCC/wgEncodeUwChIPSeq/wgEncodeUwChIPSeqHotspotsRep2Caco2H3k27me3.broadPeak.gz Caco-2 ChipSeq H3K27me3 Hotspots 2 broadPeak UW http://hgdownload.cse.ucsc.edu/goldenPath/hg18/encodeDCC/wgEncodeUwChIPSeq/wgEncodeUwChIPSeqHotspotsRep2Caco2H3k36me3.broadPeak.gz Caco-2 ChipSeq H3K36me3 Hotspots 2 broadPeak UW http://hgdownload.cse.ucsc.edu/goldenPath/hg18/encodeDCC/wgEncodeUwChIPSeq/wgEncodeUwChIPSeqHotspotsRep2Caco2H3k4me3.broadPeak.gz Caco-2 ChipSeq H3K4me3 Hotspots 2 broadPeak UW http://hgdownload.cse.ucsc.edu/goldenPath/hg18/encodeDCC/wgEncodeUwChIPSeq/wgEncodeUwChIPSeqHotspotsRep2Gm06990Ctcf.broadPeak.gz GM06990 ChipSeq CTCF Hotspots 2 broadPeak UW http://hgdownload.cse.ucsc.edu/goldenPath/hg18/encodeDCC/wgEncodeUwChIPSeq/wgEncodeUwChIPSeqHotspotsRep2Gm06990H3k27me3.broadPeak.gz GM06990 ChipSeq H3K27me3 Hotspots 2 broadPeak UW http://hgdownload.cse.ucsc.edu/goldenPath/hg18/encodeDCC/wgEncodeUwChIPSeq/wgEncodeUwChIPSeqHotspotsRep2Gm06990H3k36me3.broadPeak.gz GM06990 ChipSeq H3K36me3 Hotspots 2 broadPeak UW http://hgdownload.cse.ucsc.edu/goldenPath/hg18/encodeDCC/wgEncodeUwChIPSeq/wgEncodeUwChIPSeqHotspotsRep2Gm06990H3k4me3.broadPeak.gz GM06990 ChipSeq H3K4me3 Hotspots 2 broadPeak UW http://hgdownload.cse.ucsc.edu/goldenPath/hg18/encodeDCC/wgEncodeUwChIPSeq/wgEncodeUwChIPSeqHotspotsRep2Gm12864Ctcf.broadPeak.gz GM12864 ChipSeq CTCF Hotspots 2 broadPeak UW http://hgdownload.cse.ucsc.edu/goldenPath/hg18/encodeDCC/wgEncodeUwChIPSeq/wgEncodeUwChIPSeqHotspotsRep2Gm12865Ctcf.broadPeak.gz GM12865 ChipSeq CTCF Hotspots 2 broadPeak UW http://hgdownload.cse.ucsc.edu/goldenPath/hg18/encodeDCC/wgEncodeUwChIPSeq/wgEncodeUwChIPSeqHotspotsRep2Gm12872Ctcf.broadPeak.gz GM12872 ChipSeq CTCF Hotspots 2 broadPeak UW http://hgdownload.cse.ucsc.edu/goldenPath/hg18/encodeDCC/wgEncodeUwChIPSeq/wgEncodeUwChIPSeqHotspotsRep2Gm12873Ctcf.broadPeak.gz GM12873 ChipSeq CTCF Hotspots 2 broadPeak UW http://hgdownload.cse.ucsc.edu/goldenPath/hg18/encodeDCC/wgEncodeUwChIPSeq/wgEncodeUwChIPSeqHotspotsRep2Gm12874Ctcf.broadPeak.gz GM12874 ChipSeq CTCF Hotspots 2 broadPeak UW http://hgdownload.cse.ucsc.edu/goldenPath/hg18/encodeDCC/wgEncodeUwChIPSeq/wgEncodeUwChIPSeqHotspotsRep2Gm12875Ctcf.broadPeak.gz GM12875 ChipSeq CTCF Hotspots 2 broadPeak UW http://hgdownload.cse.ucsc.edu/goldenPath/hg18/encodeDCC/wgEncodeUwChIPSeq/wgEncodeUwChIPSeqHotspotsRep2Gm12878Ctcf.broadPeak.gz GM12878 ChipSeq CTCF Hotspots 2 broadPeak UW http://hgdownload.cse.ucsc.edu/goldenPath/hg18/encodeDCC/wgEncodeUwChIPSeq/wgEncodeUwChIPSeqHotspotsRep2Gm12878H3k27me3.broadPeak.gz GM12878 ChipSeq H3K27me3 Hotspots 2 broadPeak UW http://hgdownload.cse.ucsc.edu/goldenPath/hg18/encodeDCC/wgEncodeUwChIPSeq/wgEncodeUwChIPSeqHotspotsRep2Gm12878H3k36me3.broadPeak.gz GM12878 ChipSeq H3K36me3 Hotspots 2 broadPeak UW http://hgdownload.cse.ucsc.edu/goldenPath/hg18/encodeDCC/wgEncodeUwChIPSeq/wgEncodeUwChIPSeqHotspotsRep2Gm12878H3k4me3.broadPeak.gz GM12878 ChipSeq H3K4me3 Hotspots 2 broadPeak UW http://hgdownload.cse.ucsc.edu/goldenPath/hg18/encodeDCC/wgEncodeUwChIPSeq/wgEncodeUwChIPSeqHotspotsRep2Hek293Ctcf.broadPeak.gz HEK293 ChipSeq CTCF Hotspots 2 broadPeak UW http://hgdownload.cse.ucsc.edu/goldenPath/hg18/encodeDCC/wgEncodeUwChIPSeq/wgEncodeUwChIPSeqHotspotsRep2Helas3Ctcf.broadPeak.gz HeLa-S3 ChipSeq CTCF Hotspots 2 broadPeak UW http://hgdownload.cse.ucsc.edu/goldenPath/hg18/encodeDCC/wgEncodeUwChIPSeq/wgEncodeUwChIPSeqHotspotsRep2Helas3H3k27me3.broadPeak.gz HeLa-S3 ChipSeq H3K27me3 Hotspots 2 broadPeak UW http://hgdownload.cse.ucsc.edu/goldenPath/hg18/encodeDCC/wgEncodeUwChIPSeq/wgEncodeUwChIPSeqHotspotsRep2Helas3H3k36me3.broadPeak.gz HeLa-S3 ChipSeq H3K36me3 Hotspots 2 broadPeak UW http://hgdownload.cse.ucsc.edu/goldenPath/hg18/encodeDCC/wgEncodeUwChIPSeq/wgEncodeUwChIPSeqHotspotsRep2Helas3H3k4me3.broadPeak.gz HeLa-S3 ChipSeq H3K4me3 Hotspots 2 broadPeak UW http://hgdownload.cse.ucsc.edu/goldenPath/hg18/encodeDCC/wgEncodeUwChIPSeq/wgEncodeUwChIPSeqHotspotsRep2Hepg2Ctcf.broadPeak.gz HepG2 ChipSeq CTCF Hotspots 2 broadPeak UW http://hgdownload.cse.ucsc.edu/goldenPath/hg18/encodeDCC/wgEncodeUwChIPSeq/wgEncodeUwChIPSeqHotspotsRep2Hepg2H3k27me3.broadPeak.gz HepG2 ChipSeq H3K27me3 Hotspots 2 broadPeak UW http://hgdownload.cse.ucsc.edu/goldenPath/hg18/encodeDCC/wgEncodeUwChIPSeq/wgEncodeUwChIPSeqHotspotsRep2Hepg2H3k4me3.broadPeak.gz HepG2 ChipSeq H3K4me3 Hotspots 2 broadPeak UW http://hgdownload.cse.ucsc.edu/goldenPath/hg18/encodeDCC/wgEncodeUwChIPSeq/wgEncodeUwChIPSeqHotspotsRep2Hl60H3k4me3.broadPeak.gz HL-60 ChipSeq H3K4me3 Hotspots 2 broadPeak UW http://hgdownload.cse.ucsc.edu/goldenPath/hg18/encodeDCC/wgEncodeUwChIPSeq/wgEncodeUwChIPSeqHotspotsRep2HreCtcf.broadPeak.gz HRE ChipSeq CTCF Hotspots 2 broadPeak UW http://hgdownload.cse.ucsc.edu/goldenPath/hg18/encodeDCC/wgEncodeUwChIPSeq/wgEncodeUwChIPSeqHotspotsRep2HreH3k27me3.broadPeak.gz HRE ChipSeq H3K27me3 Hotspots 2 broadPeak UW http://hgdownload.cse.ucsc.edu/goldenPath/hg18/encodeDCC/wgEncodeUwChIPSeq/wgEncodeUwChIPSeqHotspotsRep2HreH3k36me3.broadPeak.gz HRE ChipSeq H3K36me3 Hotspots 2 broadPeak UW http://hgdownload.cse.ucsc.edu/goldenPath/hg18/encodeDCC/wgEncodeUwChIPSeq/wgEncodeUwChIPSeqHotspotsRep2HreH3k4me3.broadPeak.gz HRE ChipSeq H3K4me3 Hotspots 2 broadPeak UW http://hgdownload.cse.ucsc.edu/goldenPath/hg18/encodeDCC/wgEncodeUwChIPSeq/wgEncodeUwChIPSeqHotspotsRep2HuvecCtcf.broadPeak.gz HUVEC ChipSeq CTCF Hotspots 2 broadPeak UW http://hgdownload.cse.ucsc.edu/goldenPath/hg18/encodeDCC/wgEncodeUwChIPSeq/wgEncodeUwChIPSeqHotspotsRep2HuvecH3k27me3.broadPeak.gz HUVEC ChipSeq H3K27me3 Hotspots 2 broadPeak UW http://hgdownload.cse.ucsc.edu/goldenPath/hg18/encodeDCC/wgEncodeUwChIPSeq/wgEncodeUwChIPSeqHotspotsRep2HuvecH3k36me3.broadPeak.gz HUVEC ChipSeq H3K36me3 Hotspots 2 broadPeak UW http://hgdownload.cse.ucsc.edu/goldenPath/hg18/encodeDCC/wgEncodeUwChIPSeq/wgEncodeUwChIPSeqHotspotsRep2HuvecH3k4me3.broadPeak.gz HUVEC ChipSeq H3K4me3 Hotspots 2 broadPeak UW http://hgdownload.cse.ucsc.edu/goldenPath/hg18/encodeDCC/wgEncodeUwChIPSeq/wgEncodeUwChIPSeqHotspotsRep2K562Ctcf.broadPeak.gz K562 ChipSeq CTCF Hotspots 2 broadPeak UW http://hgdownload.cse.ucsc.edu/goldenPath/hg18/encodeDCC/wgEncodeUwChIPSeq/wgEncodeUwChIPSeqHotspotsRep2K562H3k27me3.broadPeak.gz K562 ChipSeq H3K27me3 Hotspots 2 broadPeak UW http://hgdownload.cse.ucsc.edu/goldenPath/hg18/encodeDCC/wgEncodeUwChIPSeq/wgEncodeUwChIPSeqHotspotsRep2K562H3k36me3.broadPeak.gz K562 ChipSeq H3K36me3 Hotspots 2 broadPeak UW http://hgdownload.cse.ucsc.edu/goldenPath/hg18/encodeDCC/wgEncodeUwChIPSeq/wgEncodeUwChIPSeqHotspotsRep2NhekCtcf.broadPeak.gz NHEK ChipSeq CTCF Hotspots 2 broadPeak UW http://hgdownload.cse.ucsc.edu/goldenPath/hg18/encodeDCC/wgEncodeUwChIPSeq/wgEncodeUwChIPSeqHotspotsRep2NhekH3k27me3.broadPeak.gz NHEK ChipSeq H3K27me3 Hotspots 2 broadPeak UW http://hgdownload.cse.ucsc.edu/goldenPath/hg18/encodeDCC/wgEncodeUwChIPSeq/wgEncodeUwChIPSeqHotspotsRep2NhekH3k36me3.broadPeak.gz NHEK ChipSeq H3K36me3 Hotspots 2 broadPeak UW http://hgdownload.cse.ucsc.edu/goldenPath/hg18/encodeDCC/wgEncodeUwChIPSeq/wgEncodeUwChIPSeqHotspotsRep2NhekH3k4me3.broadPeak.gz NHEK ChipSeq H3K4me3 Hotspots 2 broadPeak UW http://hgdownload.cse.ucsc.edu/goldenPath/hg18/encodeDCC/wgEncodeUwChIPSeq/wgEncodeUwChIPSeqHotspotsRep2SaecCtcf.broadPeak.gz SAEC ChipSeq CTCF Hotspots 2 broadPeak UW http://hgdownload.cse.ucsc.edu/goldenPath/hg18/encodeDCC/wgEncodeUwChIPSeq/wgEncodeUwChIPSeqHotspotsRep2SaecH3k27me3.broadPeak.gz SAEC ChipSeq H3K27me3 Hotspots 2 broadPeak UW http://hgdownload.cse.ucsc.edu/goldenPath/hg18/encodeDCC/wgEncodeUwChIPSeq/wgEncodeUwChIPSeqHotspotsRep2SaecH3k36me3.broadPeak.gz SAEC ChipSeq H3K36me3 Hotspots 2 broadPeak UW http://hgdownload.cse.ucsc.edu/goldenPath/hg18/encodeDCC/wgEncodeUwChIPSeq/wgEncodeUwChIPSeqHotspotsRep2SaecH3k4me3.broadPeak.gz SAEC ChipSeq H3K4me3 Hotspots 2 broadPeak UW http://hgdownload.cse.ucsc.edu/goldenPath/hg18/encodeDCC/wgEncodeUwChIPSeq/wgEncodeUwChIPSeqHotspotsRep2SknshraCtcf.broadPeak.gz SK-N-SH_RA ChipSeq CTCF Hotspots 2 broadPeak UW http://hgdownload.cse.ucsc.edu/goldenPath/hg18/encodeDCC/wgEncodeUwChIPSeq/wgEncodeUwChIPSeqHotspotsRep2SknshraH3k27me3.broadPeak.gz SK-N-SH_RA ChipSeq H3K27me3 Hotspots 2 broadPeak UW http://hgdownload.cse.ucsc.edu/goldenPath/hg18/encodeDCC/wgEncodeUwChIPSeq/wgEncodeUwChIPSeqHotspotsRep2SknshraH3k36me3.broadPeak.gz SK-N-SH_RA ChipSeq H3K36me3 Hotspots 2 broadPeak UW http://hgdownload.cse.ucsc.edu/goldenPath/hg18/encodeDCC/wgEncodeUwChIPSeq/wgEncodeUwChIPSeqHotspotsRep2SknshraH3k4me3.broadPeak.gz SK-N-SH_RA ChipSeq H3K4me3 Hotspots 2 broadPeak UW http://hgdownload.cse.ucsc.edu/goldenPath/hg18/encodeDCC/wgEncodeUwChIPSeq/wgEncodeUwChIPSeqHotspotsRep2Werirb1Ctcf.broadPeak.gz WERI-Rb-1 ChipSeq CTCF Hotspots 2 broadPeak UW http://hgdownload.cse.ucsc.edu/goldenPath/hg18/encodeDCC/wgEncodeUwChIPSeq/wgEncodeUwChIPSeqPeaksGm12801Ctcf.narrowPeak.gz GM12801 ChipSeq CTCF Peaks narrowPeak UW http://hgdownload.cse.ucsc.edu/goldenPath/hg18/encodeDCC/wgEncodeUwChIPSeq/wgEncodeUwChIPSeqPeaksHepg2Ctcf.narrowPeak.gz HepG2 ChipSeq CTCF Peaks narrowPeak UW http://hgdownload.cse.ucsc.edu/goldenPath/hg18/encodeDCC/wgEncodeUwChIPSeq/wgEncodeUwChIPSeqPeaksHl60Ctcf.narrowPeak.gz HL-60 ChipSeq CTCF Peaks narrowPeak UW http://hgdownload.cse.ucsc.edu/goldenPath/hg18/encodeDCC/wgEncodeUwChIPSeq/wgEncodeUwChIPSeqPeaksHreCtcf.narrowPeak.gz HRE ChipSeq CTCF Peaks narrowPeak UW http://hgdownload.cse.ucsc.edu/goldenPath/hg18/encodeDCC/wgEncodeUwChIPSeq/wgEncodeUwChIPSeqPeaksRep1BjH3k27me3.narrowPeak.gz BJ ChipSeq H3K27me3 Peaks 1 narrowPeak UW http://hgdownload.cse.ucsc.edu/goldenPath/hg18/encodeDCC/wgEncodeUwChIPSeq/wgEncodeUwChIPSeqPeaksRep1BjH3k36me3.narrowPeak.gz BJ ChipSeq H3K36me3 Peaks 1 narrowPeak UW http://hgdownload.cse.ucsc.edu/goldenPath/hg18/encodeDCC/wgEncodeUwChIPSeq/wgEncodeUwChIPSeqPeaksRep1BjH3k4me3.narrowPeak.gz BJ ChipSeq H3K4me3 Peaks 1 narrowPeak UW http://hgdownload.cse.ucsc.edu/goldenPath/hg18/encodeDCC/wgEncodeUwChIPSeq/wgEncodeUwChIPSeqPeaksRep1BjtertCtcf.narrowPeak.gz BJ ChipSeq CTCF Peaks 1 narrowPeak UW http://hgdownload.cse.ucsc.edu/goldenPath/hg18/encodeDCC/wgEncodeUwChIPSeq/wgEncodeUwChIPSeqPeaksRep1Caco2Ctcf.narrowPeak.gz Caco-2 ChipSeq CTCF Peaks 1 narrowPeak UW http://hgdownload.cse.ucsc.edu/goldenPath/hg18/encodeDCC/wgEncodeUwChIPSeq/wgEncodeUwChIPSeqPeaksRep1Caco2H3k27me3.narrowPeak.gz Caco-2 ChipSeq H3K27me3 Peaks 1 narrowPeak UW http://hgdownload.cse.ucsc.edu/goldenPath/hg18/encodeDCC/wgEncodeUwChIPSeq/wgEncodeUwChIPSeqPeaksRep1Caco2H3k36me3.narrowPeak.gz Caco-2 ChipSeq H3K36me3 Peaks 1 narrowPeak UW http://hgdownload.cse.ucsc.edu/goldenPath/hg18/encodeDCC/wgEncodeUwChIPSeq/wgEncodeUwChIPSeqPeaksRep1Caco2H3k4me3.narrowPeak.gz Caco-2 ChipSeq H3K4me3 Peaks 1 narrowPeak UW http://hgdownload.cse.ucsc.edu/goldenPath/hg18/encodeDCC/wgEncodeUwChIPSeq/wgEncodeUwChIPSeqPeaksRep1Gm06990Ctcf.narrowPeak.gz GM06990 ChipSeq CTCF Peaks 1 narrowPeak UW http://hgdownload.cse.ucsc.edu/goldenPath/hg18/encodeDCC/wgEncodeUwChIPSeq/wgEncodeUwChIPSeqPeaksRep1Gm06990H3k27me3.narrowPeak.gz GM06990 ChipSeq H3K27me3 Peaks 1 narrowPeak UW http://hgdownload.cse.ucsc.edu/goldenPath/hg18/encodeDCC/wgEncodeUwChIPSeq/wgEncodeUwChIPSeqPeaksRep1Gm06990H3k36me3.narrowPeak.gz GM06990 ChipSeq H3K36me3 Peaks 1 narrowPeak UW http://hgdownload.cse.ucsc.edu/goldenPath/hg18/encodeDCC/wgEncodeUwChIPSeq/wgEncodeUwChIPSeqPeaksRep1Gm06990H3k4me3.narrowPeak.gz GM06990 ChipSeq H3K4me3 Peaks 1 narrowPeak UW http://hgdownload.cse.ucsc.edu/goldenPath/hg18/encodeDCC/wgEncodeUwChIPSeq/wgEncodeUwChIPSeqPeaksRep1Gm12864Ctcf.narrowPeak.gz GM12864 ChipSeq CTCF Peaks 1 narrowPeak UW http://hgdownload.cse.ucsc.edu/goldenPath/hg18/encodeDCC/wgEncodeUwChIPSeq/wgEncodeUwChIPSeqPeaksRep1Gm12865Ctcf.narrowPeak.gz GM12865 ChipSeq CTCF Peaks 1 narrowPeak UW http://hgdownload.cse.ucsc.edu/goldenPath/hg18/encodeDCC/wgEncodeUwChIPSeq/wgEncodeUwChIPSeqPeaksRep1Gm12872Ctcf.narrowPeak.gz GM12872 ChipSeq CTCF Peaks 1 narrowPeak UW http://hgdownload.cse.ucsc.edu/goldenPath/hg18/encodeDCC/wgEncodeUwChIPSeq/wgEncodeUwChIPSeqPeaksRep1Gm12873Ctcf.narrowPeak.gz GM12873 ChipSeq CTCF Peaks 1 narrowPeak UW http://hgdownload.cse.ucsc.edu/goldenPath/hg18/encodeDCC/wgEncodeUwChIPSeq/wgEncodeUwChIPSeqPeaksRep1Gm12874Ctcf.narrowPeak.gz GM12874 ChipSeq CTCF Peaks 1 narrowPeak UW http://hgdownload.cse.ucsc.edu/goldenPath/hg18/encodeDCC/wgEncodeUwChIPSeq/wgEncodeUwChIPSeqPeaksRep1Gm12875Ctcf.narrowPeak.gz GM12875 ChipSeq CTCF Peaks 1 narrowPeak UW http://hgdownload.cse.ucsc.edu/goldenPath/hg18/encodeDCC/wgEncodeUwChIPSeq/wgEncodeUwChIPSeqPeaksRep1Gm12878Ctcf.narrowPeak.gz GM12878 ChipSeq CTCF Peaks 1 narrowPeak UW http://hgdownload.cse.ucsc.edu/goldenPath/hg18/encodeDCC/wgEncodeUwChIPSeq/wgEncodeUwChIPSeqPeaksRep1Gm12878H3k27me3.narrowPeak.gz GM12878 ChipSeq H3K27me3 Peaks 1 narrowPeak UW http://hgdownload.cse.ucsc.edu/goldenPath/hg18/encodeDCC/wgEncodeUwChIPSeq/wgEncodeUwChIPSeqPeaksRep1Gm12878H3k36me3.narrowPeak.gz GM12878 ChipSeq H3K36me3 Peaks 1 narrowPeak UW http://hgdownload.cse.ucsc.edu/goldenPath/hg18/encodeDCC/wgEncodeUwChIPSeq/wgEncodeUwChIPSeqPeaksRep1Gm12878H3k4me3.narrowPeak.gz GM12878 ChipSeq H3K4me3 Peaks 1 narrowPeak UW http://hgdownload.cse.ucsc.edu/goldenPath/hg18/encodeDCC/wgEncodeUwChIPSeq/wgEncodeUwChIPSeqPeaksRep1Hek293Ctcf.narrowPeak.gz HEK293 ChipSeq CTCF Peaks 1 narrowPeak UW http://hgdownload.cse.ucsc.edu/goldenPath/hg18/encodeDCC/wgEncodeUwChIPSeq/wgEncodeUwChIPSeqPeaksRep1Helas3Ctcf.narrowPeak.gz HeLa-S3 ChipSeq CTCF Peaks 1 narrowPeak UW http://hgdownload.cse.ucsc.edu/goldenPath/hg18/encodeDCC/wgEncodeUwChIPSeq/wgEncodeUwChIPSeqPeaksRep1Helas3H3k27me3.narrowPeak.gz HeLa-S3 ChipSeq H3K27me3 Peaks 1 narrowPeak UW http://hgdownload.cse.ucsc.edu/goldenPath/hg18/encodeDCC/wgEncodeUwChIPSeq/wgEncodeUwChIPSeqPeaksRep1Helas3H3k36me3.narrowPeak.gz HeLa-S3 ChipSeq H3K36me3 Peaks 1 narrowPeak UW http://hgdownload.cse.ucsc.edu/goldenPath/hg18/encodeDCC/wgEncodeUwChIPSeq/wgEncodeUwChIPSeqPeaksRep1Helas3H3k4me3.narrowPeak.gz HeLa-S3 ChipSeq H3K4me3 Peaks 1 narrowPeak UW http://hgdownload.cse.ucsc.edu/goldenPath/hg18/encodeDCC/wgEncodeUwChIPSeq/wgEncodeUwChIPSeqPeaksRep1Hepg2H3k27me3.narrowPeak.gz HepG2 ChipSeq H3K27me3 Peaks 1 narrowPeak UW http://hgdownload.cse.ucsc.edu/goldenPath/hg18/encodeDCC/wgEncodeUwChIPSeq/wgEncodeUwChIPSeqPeaksRep1Hepg2H3k36me3.narrowPeak.gz HepG2 ChipSeq H3K36me3 Peaks 1 narrowPeak UW http://hgdownload.cse.ucsc.edu/goldenPath/hg18/encodeDCC/wgEncodeUwChIPSeq/wgEncodeUwChIPSeqPeaksRep1Hepg2H3k4me3.narrowPeak.gz HepG2 ChipSeq H3K4me3 Peaks 1 narrowPeak UW http://hgdownload.cse.ucsc.edu/goldenPath/hg18/encodeDCC/wgEncodeUwChIPSeq/wgEncodeUwChIPSeqPeaksRep1Hl60H3k4me3.narrowPeak.gz HL-60 ChipSeq H3K4me3 Peaks 1 narrowPeak UW http://hgdownload.cse.ucsc.edu/goldenPath/hg18/encodeDCC/wgEncodeUwChIPSeq/wgEncodeUwChIPSeqPeaksRep1HmecCtcf.narrowPeak.gz HMEC ChipSeq CTCF Peaks 1 narrowPeak UW http://hgdownload.cse.ucsc.edu/goldenPath/hg18/encodeDCC/wgEncodeUwChIPSeq/wgEncodeUwChIPSeqPeaksRep1HmecH3k27me3.narrowPeak.gz HMEC ChipSeq H3K27me3 Peaks 1 narrowPeak UW http://hgdownload.cse.ucsc.edu/goldenPath/hg18/encodeDCC/wgEncodeUwChIPSeq/wgEncodeUwChIPSeqPeaksRep1HreH3k27me3.narrowPeak.gz HRE ChipSeq H3K27me3 Peaks 1 narrowPeak UW http://hgdownload.cse.ucsc.edu/goldenPath/hg18/encodeDCC/wgEncodeUwChIPSeq/wgEncodeUwChIPSeqPeaksRep1HreH3k36me3.narrowPeak.gz HRE ChipSeq H3K36me3 Peaks 1 narrowPeak UW http://hgdownload.cse.ucsc.edu/goldenPath/hg18/encodeDCC/wgEncodeUwChIPSeq/wgEncodeUwChIPSeqPeaksRep1HreH3k4me3.narrowPeak.gz HRE ChipSeq H3K4me3 Peaks 1 narrowPeak UW http://hgdownload.cse.ucsc.edu/goldenPath/hg18/encodeDCC/wgEncodeUwChIPSeq/wgEncodeUwChIPSeqPeaksRep1HuvecCtcf.narrowPeak.gz HUVEC ChipSeq CTCF Peaks 1 narrowPeak UW http://hgdownload.cse.ucsc.edu/goldenPath/hg18/encodeDCC/wgEncodeUwChIPSeq/wgEncodeUwChIPSeqPeaksRep1HuvecH3k27me3.narrowPeak.gz HUVEC ChipSeq H3K27me3 Peaks 1 narrowPeak UW http://hgdownload.cse.ucsc.edu/goldenPath/hg18/encodeDCC/wgEncodeUwChIPSeq/wgEncodeUwChIPSeqPeaksRep1HuvecH3k36me3.narrowPeak.gz HUVEC ChipSeq H3K36me3 Peaks 1 narrowPeak UW http://hgdownload.cse.ucsc.edu/goldenPath/hg18/encodeDCC/wgEncodeUwChIPSeq/wgEncodeUwChIPSeqPeaksRep1HuvecH3k4me3.narrowPeak.gz HUVEC ChipSeq H3K4me3 Peaks 1 narrowPeak UW http://hgdownload.cse.ucsc.edu/goldenPath/hg18/encodeDCC/wgEncodeUwChIPSeq/wgEncodeUwChIPSeqPeaksRep1K562Ctcf.narrowPeak.gz K562 ChipSeq CTCF Peaks 1 narrowPeak UW http://hgdownload.cse.ucsc.edu/goldenPath/hg18/encodeDCC/wgEncodeUwChIPSeq/wgEncodeUwChIPSeqPeaksRep1K562H3k27me3.narrowPeak.gz K562 ChipSeq H3K27me3 Peaks 1 narrowPeak UW http://hgdownload.cse.ucsc.edu/goldenPath/hg18/encodeDCC/wgEncodeUwChIPSeq/wgEncodeUwChIPSeqPeaksRep1K562H3k36me3.narrowPeak.gz K562 ChipSeq H3K36me3 Peaks 1 narrowPeak UW http://hgdownload.cse.ucsc.edu/goldenPath/hg18/encodeDCC/wgEncodeUwChIPSeq/wgEncodeUwChIPSeqPeaksRep1K562H3k4me3.narrowPeak.gz K562 ChipSeq H3K4me3 Peaks 1 narrowPeak UW http://hgdownload.cse.ucsc.edu/goldenPath/hg18/encodeDCC/wgEncodeUwChIPSeq/wgEncodeUwChIPSeqPeaksRep1NhekCtcf.narrowPeak.gz NHEK ChipSeq CTCF Peaks 1 narrowPeak UW http://hgdownload.cse.ucsc.edu/goldenPath/hg18/encodeDCC/wgEncodeUwChIPSeq/wgEncodeUwChIPSeqPeaksRep1NhekH3k27me3.narrowPeak.gz NHEK ChipSeq H3K27me3 Peaks 1 narrowPeak UW http://hgdownload.cse.ucsc.edu/goldenPath/hg18/encodeDCC/wgEncodeUwChIPSeq/wgEncodeUwChIPSeqPeaksRep1NhekH3k36me3.narrowPeak.gz NHEK ChipSeq H3K36me3 Peaks 1 narrowPeak UW http://hgdownload.cse.ucsc.edu/goldenPath/hg18/encodeDCC/wgEncodeUwChIPSeq/wgEncodeUwChIPSeqPeaksRep1NhekH3k4me3.narrowPeak.gz NHEK ChipSeq H3K4me3 Peaks 1 narrowPeak UW http://hgdownload.cse.ucsc.edu/goldenPath/hg18/encodeDCC/wgEncodeUwChIPSeq/wgEncodeUwChIPSeqPeaksRep1SaecCtcf.narrowPeak.gz SAEC ChipSeq CTCF Peaks 1 narrowPeak UW http://hgdownload.cse.ucsc.edu/goldenPath/hg18/encodeDCC/wgEncodeUwChIPSeq/wgEncodeUwChIPSeqPeaksRep1SaecH3k27me3.narrowPeak.gz SAEC ChipSeq H3K27me3 Peaks 1 narrowPeak UW http://hgdownload.cse.ucsc.edu/goldenPath/hg18/encodeDCC/wgEncodeUwChIPSeq/wgEncodeUwChIPSeqPeaksRep1SaecH3k36me3.narrowPeak.gz SAEC ChipSeq H3K36me3 Peaks 1 narrowPeak UW http://hgdownload.cse.ucsc.edu/goldenPath/hg18/encodeDCC/wgEncodeUwChIPSeq/wgEncodeUwChIPSeqPeaksRep1SaecH3k4me3.narrowPeak.gz SAEC ChipSeq H3K4me3 Peaks 1 narrowPeak UW http://hgdownload.cse.ucsc.edu/goldenPath/hg18/encodeDCC/wgEncodeUwChIPSeq/wgEncodeUwChIPSeqPeaksRep1SknshraCtcf.narrowPeak.gz SK-N-SH_RA ChipSeq CTCF Peaks 1 narrowPeak UW http://hgdownload.cse.ucsc.edu/goldenPath/hg18/encodeDCC/wgEncodeUwChIPSeq/wgEncodeUwChIPSeqPeaksRep1SknshraH3k27me3.narrowPeak.gz SK-N-SH_RA ChipSeq H3K27me3 Peaks 1 narrowPeak UW http://hgdownload.cse.ucsc.edu/goldenPath/hg18/encodeDCC/wgEncodeUwChIPSeq/wgEncodeUwChIPSeqPeaksRep1SknshraH3k36me3.narrowPeak.gz SK-N-SH_RA ChipSeq H3K36me3 Peaks 1 narrowPeak UW http://hgdownload.cse.ucsc.edu/goldenPath/hg18/encodeDCC/wgEncodeUwChIPSeq/wgEncodeUwChIPSeqPeaksRep1SknshraH3k4me3.narrowPeak.gz SK-N-SH_RA ChipSeq H3K4me3 Peaks 1 narrowPeak UW http://hgdownload.cse.ucsc.edu/goldenPath/hg18/encodeDCC/wgEncodeUwChIPSeq/wgEncodeUwChIPSeqPeaksWerirb1Ctcf.narrowPeak.gz WERI-Rb-1 ChipSeq CTCF Peaks narrowPeak UW http://hgdownload.cse.ucsc.edu/goldenPath/hg18/encodeDCC/wgEncodeUwDGF/wgEncodeUwDGFHotspotsGm06990.broadPeak.gz GM06990 DGF Hotspots broadPeak Uw http://hgdownload.cse.ucsc.edu/goldenPath/hg18/encodeDCC/wgEncodeUwDGF/wgEncodeUwDGFHotspotsHepg2.broadPeak.gz HepG2 DGF Hotspots broadPeak Uw http://hgdownload.cse.ucsc.edu/goldenPath/hg18/encodeDCC/wgEncodeUwDGF/wgEncodeUwDGFHotspotsK562.broadPeak.gz K562 DGF Hotspots broadPeak Uw http://hgdownload.cse.ucsc.edu/goldenPath/hg18/encodeDCC/wgEncodeUwDGF/wgEncodeUwDGFHotspotsSknshra.broadPeak.gz SK-N-SH_RA DGF Hotspots broadPeak Uw http://hgdownload.cse.ucsc.edu/goldenPath/hg18/encodeDCC/wgEncodeUwDGF/wgEncodeUwDGFHotspotsTh1.broadPeak.gz Th1 DGF Hotspots broadPeak Uw http://hgdownload.cse.ucsc.edu/goldenPath/hg18/encodeDCC/wgEncodeUwDGF/wgEncodeUwDGFPeaksGm06990.narrowPeak.gz GM06990 DGF Peaks narrowPeak Uw http://hgdownload.cse.ucsc.edu/goldenPath/hg18/encodeDCC/wgEncodeUwDGF/wgEncodeUwDGFPeaksHepg2.narrowPeak.gz HepG2 DGF Peaks narrowPeak Uw http://hgdownload.cse.ucsc.edu/goldenPath/hg18/encodeDCC/wgEncodeUwDGF/wgEncodeUwDGFPeaksK562.narrowPeak.gz K562 DGF Peaks narrowPeak Uw http://hgdownload.cse.ucsc.edu/goldenPath/hg18/encodeDCC/wgEncodeUwDGF/wgEncodeUwDGFPeaksSknshra.narrowPeak.gz SK-N-SH_RA DGF Peaks narrowPeak Uw http://hgdownload.cse.ucsc.edu/goldenPath/hg18/encodeDCC/wgEncodeUwDGF/wgEncodeUwDGFPeaksTh1.narrowPeak.gz Th1 DGF Peaks narrowPeak Uw http://hgdownload.cse.ucsc.edu/goldenPath/hg18/encodeDCC/wgEncodeUwDnaseSeq/wgEncodeUwDnaseSeqHotspotsRep1Ag04449.broadPeak.gz AG04449 DnaseSeq Hotspots 1 broadPeak UW http://hgdownload.cse.ucsc.edu/goldenPath/hg18/encodeDCC/wgEncodeUwDnaseSeq/wgEncodeUwDnaseSeqHotspotsRep1Ag04450.broadPeak.gz AG04450 DnaseSeq Hotspots 1 broadPeak UW http://hgdownload.cse.ucsc.edu/goldenPath/hg18/encodeDCC/wgEncodeUwDnaseSeq/wgEncodeUwDnaseSeqHotspotsRep1Ag09309.broadPeak.gz AG09309 DnaseSeq Hotspots 1 broadPeak UW http://hgdownload.cse.ucsc.edu/goldenPath/hg18/encodeDCC/wgEncodeUwDnaseSeq/wgEncodeUwDnaseSeqHotspotsRep1Ag09319.broadPeak.gz AG09319 DnaseSeq Hotspots 1 broadPeak UW http://hgdownload.cse.ucsc.edu/goldenPath/hg18/encodeDCC/wgEncodeUwDnaseSeq/wgEncodeUwDnaseSeqHotspotsRep1Ag10803.broadPeak.gz AG10803 DnaseSeq Hotspots 1 broadPeak UW http://hgdownload.cse.ucsc.edu/goldenPath/hg18/encodeDCC/wgEncodeUwDnaseSeq/wgEncodeUwDnaseSeqHotspotsRep1Bjtert.broadPeak.gz BJ DnaseSeq Hotspots 1 broadPeak UW http://hgdownload.cse.ucsc.edu/goldenPath/hg18/encodeDCC/wgEncodeUwDnaseSeq/wgEncodeUwDnaseSeqHotspotsRep1Caco2.broadPeak.gz Caco-2 DnaseSeq Hotspots 1 broadPeak UW http://hgdownload.cse.ucsc.edu/goldenPath/hg18/encodeDCC/wgEncodeUwDnaseSeq/wgEncodeUwDnaseSeqHotspotsRep1Cmk.broadPeak.gz CMK DnaseSeq Hotspots 1 broadPeak UW http://hgdownload.cse.ucsc.edu/goldenPath/hg18/encodeDCC/wgEncodeUwDnaseSeq/wgEncodeUwDnaseSeqHotspotsRep1Gm06990.broadPeak.gz GM06990 DnaseSeq Hotspots 1 broadPeak UW http://hgdownload.cse.ucsc.edu/goldenPath/hg18/encodeDCC/wgEncodeUwDnaseSeq/wgEncodeUwDnaseSeqHotspotsRep1Gm12865.broadPeak.gz GM12865 DnaseSeq Hotspots 1 broadPeak UW http://hgdownload.cse.ucsc.edu/goldenPath/hg18/encodeDCC/wgEncodeUwDnaseSeq/wgEncodeUwDnaseSeqHotspotsRep1Gm12878.broadPeak.gz GM12878 DnaseSeq Hotspots 1 broadPeak UW http://hgdownload.cse.ucsc.edu/goldenPath/hg18/encodeDCC/wgEncodeUwDnaseSeq/wgEncodeUwDnaseSeqHotspotsRep1H1es.broadPeak.gz H1-hESC DnaseSeq Hotspots 1 broadPeak UW http://hgdownload.cse.ucsc.edu/goldenPath/hg18/encodeDCC/wgEncodeUwDnaseSeq/wgEncodeUwDnaseSeqHotspotsRep1H7es.broadPeak.gz H7-hESC DnaseSeq Hotspots 1 broadPeak UW http://hgdownload.cse.ucsc.edu/goldenPath/hg18/encodeDCC/wgEncodeUwDnaseSeq/wgEncodeUwDnaseSeqHotspotsRep1Hae.broadPeak.gz HAEpiC DnaseSeq Hotspots 1 broadPeak UW http://hgdownload.cse.ucsc.edu/goldenPath/hg18/encodeDCC/wgEncodeUwDnaseSeq/wgEncodeUwDnaseSeqHotspotsRep1Hcf.broadPeak.gz HCF DnaseSeq Hotspots 1 broadPeak UW http://hgdownload.cse.ucsc.edu/goldenPath/hg18/encodeDCC/wgEncodeUwDnaseSeq/wgEncodeUwDnaseSeqHotspotsRep1Hcm.broadPeak.gz HCM DnaseSeq Hotspots 1 broadPeak UW http://hgdownload.cse.ucsc.edu/goldenPath/hg18/encodeDCC/wgEncodeUwDnaseSeq/wgEncodeUwDnaseSeqHotspotsRep1Hcpe.broadPeak.gz HCPEpiC DnaseSeq Hotspots 1 broadPeak UW http://hgdownload.cse.ucsc.edu/goldenPath/hg18/encodeDCC/wgEncodeUwDnaseSeq/wgEncodeUwDnaseSeqHotspotsRep1Hee.broadPeak.gz HEEpiC DnaseSeq Hotspots 1 broadPeak UW http://hgdownload.cse.ucsc.edu/goldenPath/hg18/encodeDCC/wgEncodeUwDnaseSeq/wgEncodeUwDnaseSeqHotspotsRep1Helas3.broadPeak.gz HeLa-S3 DnaseSeq Hotspots 1 broadPeak UW http://hgdownload.cse.ucsc.edu/goldenPath/hg18/encodeDCC/wgEncodeUwDnaseSeq/wgEncodeUwDnaseSeqHotspotsRep1Hepg2.broadPeak.gz HepG2 DnaseSeq Hotspots 1 broadPeak UW http://hgdownload.cse.ucsc.edu/goldenPath/hg18/encodeDCC/wgEncodeUwDnaseSeq/wgEncodeUwDnaseSeqHotspotsRep1Hgf.broadPeak.gz HGF DnaseSeq Hotspots 1 broadPeak UW http://hgdownload.cse.ucsc.edu/goldenPath/hg18/encodeDCC/wgEncodeUwDnaseSeq/wgEncodeUwDnaseSeqHotspotsRep1Hl60V2.broadPeak.gz HL-60 DnaseSeq Hotspots 1 broadPeak UW http://hgdownload.cse.ucsc.edu/goldenPath/hg18/encodeDCC/wgEncodeUwDnaseSeq/wgEncodeUwDnaseSeqHotspotsRep1Hmec.broadPeak.gz HMEC DnaseSeq Hotspots 1 broadPeak UW http://hgdownload.cse.ucsc.edu/goldenPath/hg18/encodeDCC/wgEncodeUwDnaseSeq/wgEncodeUwDnaseSeqHotspotsRep1Hnpce.broadPeak.gz HNPCEpiC DnaseSeq Hotspots 1 broadPeak UW http://hgdownload.cse.ucsc.edu/goldenPath/hg18/encodeDCC/wgEncodeUwDnaseSeq/wgEncodeUwDnaseSeqHotspotsRep1Hrcepic.broadPeak.gz HRCEpiC DnaseSeq Hotspots 1 broadPeak UW http://hgdownload.cse.ucsc.edu/goldenPath/hg18/encodeDCC/wgEncodeUwDnaseSeq/wgEncodeUwDnaseSeqHotspotsRep1Hre.broadPeak.gz HRE DnaseSeq Hotspots 1 broadPeak UW http://hgdownload.cse.ucsc.edu/goldenPath/hg18/encodeDCC/wgEncodeUwDnaseSeq/wgEncodeUwDnaseSeqHotspotsRep1Hrpe.broadPeak.gz HRPEpiC DnaseSeq Hotspots 1 broadPeak UW http://hgdownload.cse.ucsc.edu/goldenPath/hg18/encodeDCC/wgEncodeUwDnaseSeq/wgEncodeUwDnaseSeqHotspotsRep1Huvec.broadPeak.gz HUVEC DnaseSeq Hotspots 1 broadPeak UW http://hgdownload.cse.ucsc.edu/goldenPath/hg18/encodeDCC/wgEncodeUwDnaseSeq/wgEncodeUwDnaseSeqHotspotsRep1Jurkat.broadPeak.gz Jurkat DnaseSeq Hotspots 1 broadPeak UW http://hgdownload.cse.ucsc.edu/goldenPath/hg18/encodeDCC/wgEncodeUwDnaseSeq/wgEncodeUwDnaseSeqHotspotsRep1K562.broadPeak.gz K562 DnaseSeq Hotspots 1 broadPeak UW http://hgdownload.cse.ucsc.edu/goldenPath/hg18/encodeDCC/wgEncodeUwDnaseSeq/wgEncodeUwDnaseSeqHotspotsRep1Mcf7.broadPeak.gz MCF-7 DnaseSeq Hotspots 1 broadPeak UW http://hgdownload.cse.ucsc.edu/goldenPath/hg18/encodeDCC/wgEncodeUwDnaseSeq/wgEncodeUwDnaseSeqHotspotsRep1Nb4V2.broadPeak.gz NB4 DnaseSeq Hotspots 1 broadPeak UW http://hgdownload.cse.ucsc.edu/goldenPath/hg18/encodeDCC/wgEncodeUwDnaseSeq/wgEncodeUwDnaseSeqHotspotsRep1Nhdfneo.broadPeak.gz NHDF-neo DnaseSeq Hotspots 1 broadPeak UW http://hgdownload.cse.ucsc.edu/goldenPath/hg18/encodeDCC/wgEncodeUwDnaseSeq/wgEncodeUwDnaseSeqHotspotsRep1Nhek.broadPeak.gz NHEK DnaseSeq Hotspots 1 broadPeak UW http://hgdownload.cse.ucsc.edu/goldenPath/hg18/encodeDCC/wgEncodeUwDnaseSeq/wgEncodeUwDnaseSeqHotspotsRep1Nhlf.broadPeak.gz NHLF DnaseSeq Hotspots 1 broadPeak UW http://hgdownload.cse.ucsc.edu/goldenPath/hg18/encodeDCC/wgEncodeUwDnaseSeq/wgEncodeUwDnaseSeqHotspotsRep1Panc1.broadPeak.gz PANC-1 DnaseSeq Hotspots 1 broadPeak UW http://hgdownload.cse.ucsc.edu/goldenPath/hg18/encodeDCC/wgEncodeUwDnaseSeq/wgEncodeUwDnaseSeqHotspotsRep1Saec.broadPeak.gz SAEC DnaseSeq Hotspots 1 broadPeak UW http://hgdownload.cse.ucsc.edu/goldenPath/hg18/encodeDCC/wgEncodeUwDnaseSeq/wgEncodeUwDnaseSeqHotspotsRep1SkmcV2.broadPeak.gz SKMC DnaseSeq Hotspots 1 broadPeak UW http://hgdownload.cse.ucsc.edu/goldenPath/hg18/encodeDCC/wgEncodeUwDnaseSeq/wgEncodeUwDnaseSeqHotspotsRep1Sknshra.broadPeak.gz SK-N-SH_RA DnaseSeq Hotspots 1 broadPeak UW http://hgdownload.cse.ucsc.edu/goldenPath/hg18/encodeDCC/wgEncodeUwDnaseSeq/wgEncodeUwDnaseSeqHotspotsRep1Th1.broadPeak.gz Th1 DnaseSeq Hotspots 1 broadPeak UW http://hgdownload.cse.ucsc.edu/goldenPath/hg18/encodeDCC/wgEncodeUwDnaseSeq/wgEncodeUwDnaseSeqHotspotsRep1Th2.broadPeak.gz Th2 DnaseSeq Hotspots 1 broadPeak UW http://hgdownload.cse.ucsc.edu/goldenPath/hg18/encodeDCC/wgEncodeUwDnaseSeq/wgEncodeUwDnaseSeqHotspotsRep2Ag04449.broadPeak.gz AG04449 DnaseSeq Hotspots 2 broadPeak UW http://hgdownload.cse.ucsc.edu/goldenPath/hg18/encodeDCC/wgEncodeUwDnaseSeq/wgEncodeUwDnaseSeqHotspotsRep2Ag04450.broadPeak.gz AG04450 DnaseSeq Hotspots 2 broadPeak UW http://hgdownload.cse.ucsc.edu/goldenPath/hg18/encodeDCC/wgEncodeUwDnaseSeq/wgEncodeUwDnaseSeqHotspotsRep2Ag09309.broadPeak.gz AG09309 DnaseSeq Hotspots 2 broadPeak UW http://hgdownload.cse.ucsc.edu/goldenPath/hg18/encodeDCC/wgEncodeUwDnaseSeq/wgEncodeUwDnaseSeqHotspotsRep2Ag09319.broadPeak.gz AG09319 DnaseSeq Hotspots 2 broadPeak UW http://hgdownload.cse.ucsc.edu/goldenPath/hg18/encodeDCC/wgEncodeUwDnaseSeq/wgEncodeUwDnaseSeqHotspotsRep2Ag10803.broadPeak.gz AG10803 DnaseSeq Hotspots 2 broadPeak UW http://hgdownload.cse.ucsc.edu/goldenPath/hg18/encodeDCC/wgEncodeUwDnaseSeq/wgEncodeUwDnaseSeqHotspotsRep2Bjtert.broadPeak.gz BJ DnaseSeq Hotspots 2 broadPeak UW http://hgdownload.cse.ucsc.edu/goldenPath/hg18/encodeDCC/wgEncodeUwDnaseSeq/wgEncodeUwDnaseSeqHotspotsRep2Caco2.broadPeak.gz Caco-2 DnaseSeq Hotspots 2 broadPeak UW http://hgdownload.cse.ucsc.edu/goldenPath/hg18/encodeDCC/wgEncodeUwDnaseSeq/wgEncodeUwDnaseSeqHotspotsRep2Gm06990.broadPeak.gz GM06990 DnaseSeq Hotspots 2 broadPeak UW http://hgdownload.cse.ucsc.edu/goldenPath/hg18/encodeDCC/wgEncodeUwDnaseSeq/wgEncodeUwDnaseSeqHotspotsRep2Gm12865.broadPeak.gz GM12865 DnaseSeq Hotspots 2 broadPeak UW http://hgdownload.cse.ucsc.edu/goldenPath/hg18/encodeDCC/wgEncodeUwDnaseSeq/wgEncodeUwDnaseSeqHotspotsRep2Gm12878.broadPeak.gz GM12878 DnaseSeq Hotspots 2 broadPeak UW http://hgdownload.cse.ucsc.edu/goldenPath/hg18/encodeDCC/wgEncodeUwDnaseSeq/wgEncodeUwDnaseSeqHotspotsRep2Hae.broadPeak.gz HAEpiC DnaseSeq Hotspots 2 broadPeak UW http://hgdownload.cse.ucsc.edu/goldenPath/hg18/encodeDCC/wgEncodeUwDnaseSeq/wgEncodeUwDnaseSeqHotspotsRep2Hcf.broadPeak.gz HCF DnaseSeq Hotspots 2 broadPeak UW http://hgdownload.cse.ucsc.edu/goldenPath/hg18/encodeDCC/wgEncodeUwDnaseSeq/wgEncodeUwDnaseSeqHotspotsRep2Hcm.broadPeak.gz HCM DnaseSeq Hotspots 2 broadPeak UW http://hgdownload.cse.ucsc.edu/goldenPath/hg18/encodeDCC/wgEncodeUwDnaseSeq/wgEncodeUwDnaseSeqHotspotsRep2Hcpe.broadPeak.gz HCPEpiC DnaseSeq Hotspots 2 broadPeak UW http://hgdownload.cse.ucsc.edu/goldenPath/hg18/encodeDCC/wgEncodeUwDnaseSeq/wgEncodeUwDnaseSeqHotspotsRep2Hee.broadPeak.gz HEEpiC DnaseSeq Hotspots 2 broadPeak UW http://hgdownload.cse.ucsc.edu/goldenPath/hg18/encodeDCC/wgEncodeUwDnaseSeq/wgEncodeUwDnaseSeqHotspotsRep2Helas3.broadPeak.gz HeLa-S3 DnaseSeq Hotspots 2 broadPeak UW http://hgdownload.cse.ucsc.edu/goldenPath/hg18/encodeDCC/wgEncodeUwDnaseSeq/wgEncodeUwDnaseSeqHotspotsRep2Hepg2.broadPeak.gz HepG2 DnaseSeq Hotspots 2 broadPeak UW http://hgdownload.cse.ucsc.edu/goldenPath/hg18/encodeDCC/wgEncodeUwDnaseSeq/wgEncodeUwDnaseSeqHotspotsRep2Hgf.broadPeak.gz HGF DnaseSeq Hotspots 2 broadPeak UW http://hgdownload.cse.ucsc.edu/goldenPath/hg18/encodeDCC/wgEncodeUwDnaseSeq/wgEncodeUwDnaseSeqHotspotsRep2Hl60.broadPeak.gz HL-60 DnaseSeq Hotspots 2 broadPeak UW http://hgdownload.cse.ucsc.edu/goldenPath/hg18/encodeDCC/wgEncodeUwDnaseSeq/wgEncodeUwDnaseSeqHotspotsRep2Hnpce.broadPeak.gz HNPCEpiC DnaseSeq Hotspots 2 broadPeak UW http://hgdownload.cse.ucsc.edu/goldenPath/hg18/encodeDCC/wgEncodeUwDnaseSeq/wgEncodeUwDnaseSeqHotspotsRep2Hrcepic.broadPeak.gz HRCEpiC DnaseSeq Hotspots 2 broadPeak UW http://hgdownload.cse.ucsc.edu/goldenPath/hg18/encodeDCC/wgEncodeUwDnaseSeq/wgEncodeUwDnaseSeqHotspotsRep2Hre.broadPeak.gz HRE DnaseSeq Hotspots 2 broadPeak UW http://hgdownload.cse.ucsc.edu/goldenPath/hg18/encodeDCC/wgEncodeUwDnaseSeq/wgEncodeUwDnaseSeqHotspotsRep2Hrpe.broadPeak.gz HRPEpiC DnaseSeq Hotspots 2 broadPeak UW http://hgdownload.cse.ucsc.edu/goldenPath/hg18/encodeDCC/wgEncodeUwDnaseSeq/wgEncodeUwDnaseSeqHotspotsRep2Jurkat.broadPeak.gz Jurkat DnaseSeq Hotspots 2 broadPeak UW http://hgdownload.cse.ucsc.edu/goldenPath/hg18/encodeDCC/wgEncodeUwDnaseSeq/wgEncodeUwDnaseSeqHotspotsRep2K562.broadPeak.gz K562 DnaseSeq Hotspots 2 broadPeak UW http://hgdownload.cse.ucsc.edu/goldenPath/hg18/encodeDCC/wgEncodeUwDnaseSeq/wgEncodeUwDnaseSeqHotspotsRep2Mcf7.broadPeak.gz MCF-7 DnaseSeq Hotspots 2 broadPeak UW http://hgdownload.cse.ucsc.edu/goldenPath/hg18/encodeDCC/wgEncodeUwDnaseSeq/wgEncodeUwDnaseSeqHotspotsRep2Nb4.broadPeak.gz NB4 DnaseSeq Hotspots 2 broadPeak UW http://hgdownload.cse.ucsc.edu/goldenPath/hg18/encodeDCC/wgEncodeUwDnaseSeq/wgEncodeUwDnaseSeqHotspotsRep2Nhdfneo.broadPeak.gz NHDF-neo DnaseSeq Hotspots 2 broadPeak UW http://hgdownload.cse.ucsc.edu/goldenPath/hg18/encodeDCC/wgEncodeUwDnaseSeq/wgEncodeUwDnaseSeqHotspotsRep2Nhlf.broadPeak.gz NHLF DnaseSeq Hotspots 2 broadPeak UW http://hgdownload.cse.ucsc.edu/goldenPath/hg18/encodeDCC/wgEncodeUwDnaseSeq/wgEncodeUwDnaseSeqHotspotsRep2Panc1.broadPeak.gz PANC-1 DnaseSeq Hotspots 2 broadPeak UW 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E2F6 Peaks narrowPeak USC http://hgdownload.cse.ucsc.edu/goldenPath/hg18/encodeDCC/wgEncodeYaleChIPseq/wgEncodeYaleChIPseqPeaksHelas3Ha.narrowPeak.gz HeLa-S3 ChipSeq HA-E2F1 Peaks narrowPeak USC http://hgdownload.cse.ucsc.edu/goldenPath/hg18/encodeDCC/wgEncodeYaleChIPseq/wgEncodeYaleChIPseqPeaksHelas3Ini1Musigg.narrowPeak.gz HeLa-S3 ChipSeq Ini1 Peaks narrowPeak Stanford http://hgdownload.cse.ucsc.edu/goldenPath/hg18/encodeDCC/wgEncodeYaleChIPseq/wgEncodeYaleChIPseqPeaksHelas3JundRabigg.narrowPeak.gz HeLa-S3 ChipSeq JunD Peaks narrowPeak Stanford http://hgdownload.cse.ucsc.edu/goldenPath/hg18/encodeDCC/wgEncodeYaleChIPseq/wgEncodeYaleChIPseqPeaksHelas3Largefragment.narrowPeak.gz HeLa-S3 ChipSeq Input Peaks narrowPeak Yale http://hgdownload.cse.ucsc.edu/goldenPath/hg18/encodeDCC/wgEncodeYaleChIPseq/wgEncodeYaleChIPseqPeaksHelas3Max.narrowPeak.gz HeLa-S3 ChipSeq Max Peaks narrowPeak Yale 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http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeAwgDnaseUniform/wgEncodeAwgDnaseUwHreUniPk.narrowPeak.gz HRE DnaseSeq Peaks narrowPeak UW Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeAwgDnaseUniform/wgEncodeAwgDnaseUwHrgecUniPk.narrowPeak.gz HRGEC DnaseSeq Peaks narrowPeak UW Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeAwgDnaseUniform/wgEncodeAwgDnaseUwHrpepicUniPk.narrowPeak.gz HRPEpiC DnaseSeq Peaks narrowPeak UW Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeAwgDnaseUniform/wgEncodeAwgDnaseUwHvmfUniPk.narrowPeak.gz HVMF DnaseSeq Peaks narrowPeak UW Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeAwgDnaseUniform/wgEncodeAwgDnaseUwJurkatUniPk.narrowPeak.gz Jurkat DnaseSeq Peaks narrowPeak UW Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeAwgDnaseUniform/wgEncodeAwgDnaseUwMonocytescd14ro01746UniPk.narrowPeak.gz Monocytes-CD14+_RO01746 DnaseSeq Peaks narrowPeak UW Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeAwgDnaseUniform/wgEncodeAwgDnaseUwNb4UniPk.narrowPeak.gz NB4 DnaseSeq Peaks narrowPeak UW Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeAwgDnaseUniform/wgEncodeAwgDnaseUwNhaUniPk.narrowPeak.gz NH-A DnaseSeq Peaks narrowPeak UW Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeAwgDnaseUniform/wgEncodeAwgDnaseUwNhdfadUniPk.narrowPeak.gz NHDF-Ad DnaseSeq Peaks narrowPeak UW Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeAwgDnaseUniform/wgEncodeAwgDnaseUwNhdfneoUniPk.narrowPeak.gz NHDF-neo DnaseSeq Peaks narrowPeak UW Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeAwgDnaseUniform/wgEncodeAwgDnaseUwNhlfUniPk.narrowPeak.gz NHLF DnaseSeq Peaks narrowPeak UW Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeAwgDnaseUniform/wgEncodeAwgDnaseUwNt2d1UniPk.narrowPeak.gz NT2-D1 DnaseSeq Peaks narrowPeak UW Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeAwgDnaseUniform/wgEncodeAwgDnaseUwPanc1UniPk.narrowPeak.gz PANC-1 DnaseSeq Peaks narrowPeak UW Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeAwgDnaseUniform/wgEncodeAwgDnaseUwPrecUniPk.narrowPeak.gz PrEC DnaseSeq Peaks narrowPeak UW Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeAwgDnaseUniform/wgEncodeAwgDnaseUwRptecUniPk.narrowPeak.gz RPTEC DnaseSeq Peaks narrowPeak UW Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeAwgDnaseUniform/wgEncodeAwgDnaseUwSaecUniPk.narrowPeak.gz SAEC DnaseSeq Peaks narrowPeak UW Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeAwgDnaseUniform/wgEncodeAwgDnaseUwSkmcUniPk.narrowPeak.gz SKMC DnaseSeq Peaks narrowPeak UW Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeAwgDnaseUniform/wgEncodeAwgDnaseUwSknmcUniPk.narrowPeak.gz SK-N-MC DnaseSeq Peaks narrowPeak UW Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeAwgDnaseUniform/wgEncodeAwgDnaseUwSknshraUniPk.narrowPeak.gz SK-N-SH_RA DnaseSeq Peaks narrowPeak UW Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeAwgDnaseUniform/wgEncodeAwgDnaseUwTh2UniPk.narrowPeak.gz Th2 DnaseSeq Peaks narrowPeak UW Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeAwgDnaseUniform/wgEncodeAwgDnaseUwWerirb1UniPk.narrowPeak.gz WERI-Rb-1 DnaseSeq Peaks narrowPeak UW Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeAwgDnaseUniform/wgEncodeAwgDnaseUwWi38UniPk.narrowPeak.gz WI-38 DnaseSeq Peaks narrowPeak UW Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeAwgDnaseUniform/wgEncodeAwgDnaseUwWi38tamoxifentamoxifenUniPk.narrowPeak.gz WI-38 DnaseSeq Peaks narrowPeak UW Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeAwgDnaseUniform/wgEncodeAwgDnaseUwdukeA549UniPk.narrowPeak.gz A549 DnaseSeq Peaks narrowPeak AWG Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeAwgDnaseUniform/wgEncodeAwgDnaseUwdukeGm12878UniPk.narrowPeak.gz GM12878 DnaseSeq Peaks narrowPeak AWG Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeAwgDnaseUniform/wgEncodeAwgDnaseUwdukeH1hescUniPk.narrowPeak.gz H1-hESC DnaseSeq Peaks narrowPeak AWG Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeAwgDnaseUniform/wgEncodeAwgDnaseUwdukeHelas3UniPk.narrowPeak.gz HeLa-S3 DnaseSeq Peaks narrowPeak AWG Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeAwgDnaseUniform/wgEncodeAwgDnaseUwdukeHepg2UniPk.narrowPeak.gz HepG2 DnaseSeq Peaks narrowPeak AWG Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeAwgDnaseUniform/wgEncodeAwgDnaseUwdukeHmecUniPk.narrowPeak.gz HMEC DnaseSeq Peaks narrowPeak AWG Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeAwgDnaseUniform/wgEncodeAwgDnaseUwdukeHsmmUniPk.narrowPeak.gz HSMM DnaseSeq Peaks narrowPeak AWG Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeAwgDnaseUniform/wgEncodeAwgDnaseUwdukeHsmmtubeUniPk.narrowPeak.gz HSMMtube DnaseSeq Peaks narrowPeak AWG Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeAwgDnaseUniform/wgEncodeAwgDnaseUwdukeHuvecUniPk.narrowPeak.gz HUVEC DnaseSeq Peaks narrowPeak AWG Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeAwgDnaseUniform/wgEncodeAwgDnaseUwdukeK562UniPk.narrowPeak.gz K562 DnaseSeq Peaks narrowPeak AWG Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeAwgDnaseUniform/wgEncodeAwgDnaseUwdukeLncapUniPk.narrowPeak.gz LNCaP DnaseSeq Peaks narrowPeak AWG Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeAwgDnaseUniform/wgEncodeAwgDnaseUwdukeMcf7UniPk.narrowPeak.gz MCF-7 DnaseSeq Peaks narrowPeak AWG Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeAwgDnaseUniform/wgEncodeAwgDnaseUwdukeNhekUniPk.narrowPeak.gz NHEK DnaseSeq Peaks narrowPeak AWG Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeAwgDnaseUniform/wgEncodeAwgDnaseUwdukeTh1UniPk.narrowPeak.gz Th1 DnaseSeq Peaks narrowPeak AWG Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeAwgTfbsUniform/wgEncodeAwgTfbsBroadDnd41CtcfUniPk.narrowPeak.gz Dnd41 ChipSeq CTCF Peaks narrowPeak Broad Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeAwgTfbsUniform/wgEncodeAwgTfbsBroadDnd41Ezh239875UniPk.narrowPeak.gz Dnd41 ChipSeq EZH2_(39875) Peaks narrowPeak Broad Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeAwgTfbsUniform/wgEncodeAwgTfbsBroadGm12878CtcfUniPk.narrowPeak.gz GM12878 ChipSeq CTCF Peaks narrowPeak Broad Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeAwgTfbsUniform/wgEncodeAwgTfbsBroadGm12878Ezh239875UniPk.narrowPeak.gz GM12878 ChipSeq EZH2_(39875) Peaks narrowPeak Broad Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeAwgTfbsUniform/wgEncodeAwgTfbsBroadH1hescChd1a301218aUniPk.narrowPeak.gz H1-hESC ChipSeq CHD1_(A301-218A) Peaks narrowPeak Broad Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeAwgTfbsUniform/wgEncodeAwgTfbsBroadH1hescCtcfUniPk.narrowPeak.gz H1-hESC ChipSeq CTCF Peaks narrowPeak Broad Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeAwgTfbsUniform/wgEncodeAwgTfbsBroadH1hescEzh239875UniPk.narrowPeak.gz H1-hESC ChipSeq EZH2_(39875) Peaks narrowPeak Broad Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeAwgTfbsUniform/wgEncodeAwgTfbsBroadH1hescJarid1aab26049UniPk.narrowPeak.gz H1-hESC ChipSeq JARID1A_(ab26049) Peaks narrowPeak Broad Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeAwgTfbsUniform/wgEncodeAwgTfbsBroadH1hescRbbp5a300109aUniPk.narrowPeak.gz H1-hESC ChipSeq RBBP5_(A300-109A) Peaks narrowPeak Broad Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeAwgTfbsUniform/wgEncodeAwgTfbsBroadHelas3CtcfUniPk.narrowPeak.gz HeLa-S3 ChipSeq CTCF Peaks narrowPeak Broad Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeAwgTfbsUniform/wgEncodeAwgTfbsBroadHelas3Ezh239875UniPk.narrowPeak.gz HeLa-S3 ChipSeq EZH2_(39875) Peaks narrowPeak Broad Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeAwgTfbsUniform/wgEncodeAwgTfbsBroadHelas3Pol2bUniPk.narrowPeak.gz HeLa-S3 ChipSeq Pol2(b) Peaks narrowPeak Broad Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeAwgTfbsUniform/wgEncodeAwgTfbsBroadHepg2CtcfUniPk.narrowPeak.gz HepG2 ChipSeq CTCF Peaks narrowPeak Broad Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeAwgTfbsUniform/wgEncodeAwgTfbsBroadHepg2Ezh239875UniPk.narrowPeak.gz HepG2 ChipSeq EZH2_(39875) Peaks narrowPeak Broad Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeAwgTfbsUniform/wgEncodeAwgTfbsBroadHmecCtcfUniPk.narrowPeak.gz HMEC ChipSeq CTCF Peaks narrowPeak Broad Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeAwgTfbsUniform/wgEncodeAwgTfbsBroadHmecEzh239875UniPk.narrowPeak.gz HMEC ChipSeq EZH2_(39875) Peaks narrowPeak Broad Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeAwgTfbsUniform/wgEncodeAwgTfbsBroadHsmmCtcfUniPk.narrowPeak.gz HSMM ChipSeq CTCF Peaks narrowPeak Broad Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeAwgTfbsUniform/wgEncodeAwgTfbsBroadHsmmEzh239875UniPk.narrowPeak.gz HSMM ChipSeq EZH2_(39875) Peaks narrowPeak Broad Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeAwgTfbsUniform/wgEncodeAwgTfbsBroadHsmmtCtcfUniPk.narrowPeak.gz HSMMtube ChipSeq CTCF Peaks narrowPeak Broad Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeAwgTfbsUniform/wgEncodeAwgTfbsBroadHsmmtEzh239875UniPk.narrowPeak.gz HSMMtube ChipSeq EZH2_(39875) Peaks narrowPeak Broad Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeAwgTfbsUniform/wgEncodeAwgTfbsBroadHuvecCtcfUniPk.narrowPeak.gz HUVEC ChipSeq CTCF Peaks narrowPeak Broad Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeAwgTfbsUniform/wgEncodeAwgTfbsBroadHuvecEzh239875UniPk.narrowPeak.gz HUVEC ChipSeq EZH2_(39875) Peaks narrowPeak Broad Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeAwgTfbsUniform/wgEncodeAwgTfbsBroadHuvecPol2bUniPk.narrowPeak.gz HUVEC ChipSeq Pol2(b) Peaks narrowPeak Broad Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeAwgTfbsUniform/wgEncodeAwgTfbsBroadK562Chd1a301218aUniPk.narrowPeak.gz K562 ChipSeq CHD1_(A301-218A) Peaks narrowPeak Broad Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeAwgTfbsUniform/wgEncodeAwgTfbsBroadK562CtcfUniPk.narrowPeak.gz K562 ChipSeq CTCF Peaks narrowPeak Broad Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeAwgTfbsUniform/wgEncodeAwgTfbsBroadK562Ezh239875UniPk.narrowPeak.gz K562 ChipSeq EZH2_(39875) Peaks narrowPeak Broad Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeAwgTfbsUniform/wgEncodeAwgTfbsBroadK562Hdac1sc6298UniPk.narrowPeak.gz K562 ChipSeq HDAC1_(SC-6298) Peaks narrowPeak Broad Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeAwgTfbsUniform/wgEncodeAwgTfbsBroadK562Hdac2a300705aUniPk.narrowPeak.gz K562 ChipSeq HDAC2_(A300-705A) Peaks narrowPeak Broad Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeAwgTfbsUniform/wgEncodeAwgTfbsBroadK562Hdac6a301341aUniPk.narrowPeak.gz K562 ChipSeq HDAC6_(A301-341A) Peaks narrowPeak Broad Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeAwgTfbsUniform/wgEncodeAwgTfbsBroadK562P300UniPk.narrowPeak.gz K562 ChipSeq p300 Peaks narrowPeak Broad Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeAwgTfbsUniform/wgEncodeAwgTfbsBroadK562Phf8a301772aUniPk.narrowPeak.gz K562 ChipSeq PHF8_(A301-772A) Peaks narrowPeak Broad Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeAwgTfbsUniform/wgEncodeAwgTfbsBroadK562Plu1UniPk.narrowPeak.gz K562 ChipSeq PLU1 Peaks narrowPeak Broad Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeAwgTfbsUniform/wgEncodeAwgTfbsBroadK562Pol2bUniPk.narrowPeak.gz K562 ChipSeq Pol2(b) Peaks narrowPeak Broad Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeAwgTfbsUniform/wgEncodeAwgTfbsBroadK562Rbbp5a300109aUniPk.narrowPeak.gz K562 ChipSeq RBBP5_(A300-109A) Peaks narrowPeak Broad Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeAwgTfbsUniform/wgEncodeAwgTfbsBroadK562Sap3039731UniPk.narrowPeak.gz K562 ChipSeq SAP30_(39731) Peaks narrowPeak Broad Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeAwgTfbsUniform/wgEncodeAwgTfbsBroadNhaCtcfUniPk.narrowPeak.gz NH-A ChipSeq CTCF Peaks narrowPeak Broad Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeAwgTfbsUniform/wgEncodeAwgTfbsBroadNhaEzh239875UniPk.narrowPeak.gz NH-A ChipSeq EZH2_(39875) Peaks narrowPeak Broad Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeAwgTfbsUniform/wgEncodeAwgTfbsBroadNhdfadCtcfUniPk.narrowPeak.gz NHDF-Ad ChipSeq CTCF Peaks narrowPeak Broad Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeAwgTfbsUniform/wgEncodeAwgTfbsBroadNhdfadEzh239875UniPk.narrowPeak.gz NHDF-Ad ChipSeq EZH2_(39875) Peaks narrowPeak Broad Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeAwgTfbsUniform/wgEncodeAwgTfbsBroadNhekCtcfUniPk.narrowPeak.gz NHEK ChipSeq CTCF Peaks narrowPeak Broad Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeAwgTfbsUniform/wgEncodeAwgTfbsBroadNhekEzh239875UniPk.narrowPeak.gz NHEK ChipSeq EZH2_(39875) Peaks narrowPeak Broad Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeAwgTfbsUniform/wgEncodeAwgTfbsBroadNhekPol2bUniPk.narrowPeak.gz NHEK ChipSeq Pol2(b) Peaks narrowPeak Broad Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeAwgTfbsUniform/wgEncodeAwgTfbsBroadNhlfCtcfUniPk.narrowPeak.gz NHLF ChipSeq CTCF Peaks narrowPeak Broad Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeAwgTfbsUniform/wgEncodeAwgTfbsBroadNhlfEzh239875UniPk.narrowPeak.gz NHLF ChipSeq EZH2_(39875) Peaks narrowPeak Broad Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeAwgTfbsUniform/wgEncodeAwgTfbsBroadOsteoblCtcfUniPk.narrowPeak.gz Osteobl ChipSeq CTCF Peaks narrowPeak Broad Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeAwgTfbsUniform/wgEncodeAwgTfbsHaibA549Atf3V0422111Etoh02UniPk.narrowPeak.gz A549 ChipSeq ATF3 Peaks narrowPeak HudsonAlpha Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeAwgTfbsUniform/wgEncodeAwgTfbsHaibA549Bcl3V0422111Etoh02UniPk.narrowPeak.gz A549 ChipSeq BCL3 Peaks narrowPeak HudsonAlpha Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeAwgTfbsUniform/wgEncodeAwgTfbsHaibA549Creb1sc240V0416102Dex100nmUniPk.narrowPeak.gz A549 ChipSeq CREB1_(SC-240) Peaks narrowPeak HudsonAlpha Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeAwgTfbsUniform/wgEncodeAwgTfbsHaibA549Ctcfsc5916Pcr1xDex100nmUniPk.narrowPeak.gz A549 ChipSeq CTCF_(SC-5916) Peaks narrowPeak HudsonAlpha Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeAwgTfbsUniform/wgEncodeAwgTfbsHaibA549Ctcfsc5916Pcr1xEtoh02UniPk.narrowPeak.gz A549 ChipSeq CTCF_(SC-5916) Peaks narrowPeak HudsonAlpha Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeAwgTfbsUniform/wgEncodeAwgTfbsHaibA549Elf1V0422111Etoh02UniPk.narrowPeak.gz A549 ChipSeq ELF1_(SC-631) Peaks narrowPeak HudsonAlpha Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeAwgTfbsUniform/wgEncodeAwgTfbsHaibA549Ets1V0422111Etoh02UniPk.narrowPeak.gz A549 ChipSeq ETS1 Peaks narrowPeak HudsonAlpha Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeAwgTfbsUniform/wgEncodeAwgTfbsHaibA549Fosl2V0422111Etoh02UniPk.narrowPeak.gz A549 ChipSeq FOSL2 Peaks narrowPeak HudsonAlpha Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeAwgTfbsUniform/wgEncodeAwgTfbsHaibA549Foxa1V0416102Dex100nmUniPk.narrowPeak.gz A549 ChipSeq FOXA1_(SC-101058) Peaks narrowPeak HudsonAlpha Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeAwgTfbsUniform/wgEncodeAwgTfbsHaibA549GabpV0422111Etoh02UniPk.narrowPeak.gz A549 ChipSeq GABP Peaks narrowPeak HudsonAlpha Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeAwgTfbsUniform/wgEncodeAwgTfbsHaibA549GrPcr1xDex500pmUniPk.narrowPeak.gz A549 ChipSeq GR Peaks narrowPeak HudsonAlpha Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeAwgTfbsUniform/wgEncodeAwgTfbsHaibA549GrPcr1xDex50nmUniPk.narrowPeak.gz A549 ChipSeq GR Peaks narrowPeak HudsonAlpha Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeAwgTfbsUniform/wgEncodeAwgTfbsHaibA549GrPcr1xDex5nmUniPk.narrowPeak.gz A549 ChipSeq GR Peaks narrowPeak HudsonAlpha Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeAwgTfbsUniform/wgEncodeAwgTfbsHaibA549GrPcr2xDex100nmUniPk.narrowPeak.gz A549 ChipSeq GR Peaks narrowPeak HudsonAlpha Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeAwgTfbsUniform/wgEncodeAwgTfbsHaibA549NrsfV0422111Etoh02UniPk.narrowPeak.gz A549 ChipSeq NRSF Peaks narrowPeak HudsonAlpha Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeAwgTfbsUniform/wgEncodeAwgTfbsHaibA549P300V0422111Etoh02UniPk.narrowPeak.gz A549 ChipSeq p300 Peaks narrowPeak HudsonAlpha Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeAwgTfbsUniform/wgEncodeAwgTfbsHaibA549Pol2Pcr2xDex100nmUniPk.narrowPeak.gz A549 ChipSeq Pol2 Peaks narrowPeak HudsonAlpha Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeAwgTfbsUniform/wgEncodeAwgTfbsHaibA549Pol2Pcr2xEtoh02UniPk.narrowPeak.gz A549 ChipSeq Pol2 Peaks narrowPeak HudsonAlpha Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeAwgTfbsUniform/wgEncodeAwgTfbsHaibA549Sin3ak20V0422111Etoh02UniPk.narrowPeak.gz A549 ChipSeq Sin3Ak-20 Peaks narrowPeak HudsonAlpha Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeAwgTfbsUniform/wgEncodeAwgTfbsHaibA549Six5V0422111Etoh02UniPk.narrowPeak.gz A549 ChipSeq SIX5 Peaks narrowPeak HudsonAlpha Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeAwgTfbsUniform/wgEncodeAwgTfbsHaibA549Taf1V0422111Etoh02UniPk.narrowPeak.gz A549 ChipSeq TAF1 Peaks narrowPeak HudsonAlpha Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeAwgTfbsUniform/wgEncodeAwgTfbsHaibA549Tcf12V0422111Etoh02UniPk.narrowPeak.gz A549 ChipSeq TCF12 Peaks narrowPeak HudsonAlpha Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeAwgTfbsUniform/wgEncodeAwgTfbsHaibA549Usf1Pcr1xDex100nmUniPk.narrowPeak.gz A549 ChipSeq USF-1 Peaks narrowPeak HudsonAlpha Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeAwgTfbsUniform/wgEncodeAwgTfbsHaibA549Usf1Pcr1xEtoh02UniPk.narrowPeak.gz A549 ChipSeq USF-1 Peaks narrowPeak HudsonAlpha Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeAwgTfbsUniform/wgEncodeAwgTfbsHaibA549Usf1V0422111Etoh02UniPk.narrowPeak.gz A549 ChipSeq USF-1 Peaks narrowPeak HudsonAlpha Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeAwgTfbsUniform/wgEncodeAwgTfbsHaibA549Yy1cV0422111Etoh02UniPk.narrowPeak.gz A549 ChipSeq YY1_(SC-281) Peaks narrowPeak HudsonAlpha Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeAwgTfbsUniform/wgEncodeAwgTfbsHaibA549Zbtb33V0422111Etoh02UniPk.narrowPeak.gz A549 ChipSeq ZBTB33 Peaks narrowPeak HudsonAlpha Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeAwgTfbsUniform/wgEncodeAwgTfbsHaibEcc1CtcfcV0416102Dm002p1hUniPk.narrowPeak.gz ECC-1 ChipSeq CTCF_(SC-5916) Peaks narrowPeak HudsonAlpha Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeAwgTfbsUniform/wgEncodeAwgTfbsHaibEcc1EraaV0416102Bpa1hUniPk.narrowPeak.gz ECC-1 ChipSeq ERalpha_a Peaks narrowPeak HudsonAlpha Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeAwgTfbsUniform/wgEncodeAwgTfbsHaibEcc1EralphaaV0416102Est10nm1hUniPk.narrowPeak.gz ECC-1 ChipSeq ERalpha_a Peaks narrowPeak HudsonAlpha Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeAwgTfbsUniform/wgEncodeAwgTfbsHaibEcc1EralphaaV0416102Gen1hUniPk.narrowPeak.gz ECC-1 ChipSeq ERalpha_a Peaks narrowPeak HudsonAlpha Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeAwgTfbsUniform/wgEncodeAwgTfbsHaibEcc1Foxa1sc6553V0416102Dm002p1hUniPk.narrowPeak.gz ECC-1 ChipSeq FOXA1_(SC-6553) Peaks narrowPeak HudsonAlpha Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeAwgTfbsUniform/wgEncodeAwgTfbsHaibEcc1GrV0416102Dex100nmUniPk.narrowPeak.gz ECC-1 ChipSeq GR Peaks narrowPeak HudsonAlpha Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeAwgTfbsUniform/wgEncodeAwgTfbsHaibEcc1Pol2V0416102Dm002p1hUniPk.narrowPeak.gz ECC-1 ChipSeq Pol2 Peaks narrowPeak HudsonAlpha Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeAwgTfbsUniform/wgEncodeAwgTfbsHaibGm12878Atf2sc81188V0422111UniPk.narrowPeak.gz GM12878 ChipSeq ATF2_(SC-81188) Peaks narrowPeak HudsonAlpha Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeAwgTfbsUniform/wgEncodeAwgTfbsHaibGm12878Atf3Pcr1xUniPk.narrowPeak.gz GM12878 ChipSeq ATF3 Peaks narrowPeak HudsonAlpha Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeAwgTfbsUniform/wgEncodeAwgTfbsHaibGm12878BatfPcr1xUniPk.narrowPeak.gz GM12878 ChipSeq BATF Peaks narrowPeak HudsonAlpha Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeAwgTfbsUniform/wgEncodeAwgTfbsHaibGm12878Bcl11aPcr1xUniPk.narrowPeak.gz GM12878 ChipSeq BCL11A Peaks narrowPeak HudsonAlpha Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeAwgTfbsUniform/wgEncodeAwgTfbsHaibGm12878Bcl3V0416101UniPk.narrowPeak.gz GM12878 ChipSeq BCL3 Peaks narrowPeak HudsonAlpha Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeAwgTfbsUniform/wgEncodeAwgTfbsHaibGm12878Bclaf101388V0416101UniPk.narrowPeak.gz GM12878 ChipSeq BCLAF1_(SC-101388) Peaks narrowPeak HudsonAlpha Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeAwgTfbsUniform/wgEncodeAwgTfbsHaibGm12878Cebpbsc150V0422111UniPk.narrowPeak.gz GM12878 ChipSeq CEBPB_(SC-150) Peaks narrowPeak HudsonAlpha Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeAwgTfbsUniform/wgEncodeAwgTfbsHaibGm12878Ebf1sc137065Pcr1xUniPk.narrowPeak.gz GM12878 ChipSeq EBF1_(SC-137065) Peaks narrowPeak HudsonAlpha Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeAwgTfbsUniform/wgEncodeAwgTfbsHaibGm12878Egr1Pcr2xUniPk.narrowPeak.gz GM12878 ChipSeq Egr-1 Peaks narrowPeak HudsonAlpha Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeAwgTfbsUniform/wgEncodeAwgTfbsHaibGm12878Elf1sc631V0416101UniPk.narrowPeak.gz GM12878 ChipSeq ELF1_(SC-631) Peaks narrowPeak HudsonAlpha Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeAwgTfbsUniform/wgEncodeAwgTfbsHaibGm12878Ets1Pcr1xUniPk.narrowPeak.gz GM12878 ChipSeq ETS1 Peaks narrowPeak HudsonAlpha Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeAwgTfbsUniform/wgEncodeAwgTfbsHaibGm12878Foxm1sc502V0422111UniPk.narrowPeak.gz GM12878 ChipSeq FOXM1_(SC-502) Peaks narrowPeak HudsonAlpha Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeAwgTfbsUniform/wgEncodeAwgTfbsHaibGm12878GabpPcr2xUniPk.narrowPeak.gz GM12878 ChipSeq GABP Peaks narrowPeak HudsonAlpha Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeAwgTfbsUniform/wgEncodeAwgTfbsHaibGm12878Irf4sc6059Pcr1xUniPk.narrowPeak.gz GM12878 ChipSeq IRF4_(SC-6059) Peaks narrowPeak HudsonAlpha Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeAwgTfbsUniform/wgEncodeAwgTfbsHaibGm12878Mef2aPcr1xUniPk.narrowPeak.gz GM12878 ChipSeq MEF2A Peaks narrowPeak HudsonAlpha Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeAwgTfbsUniform/wgEncodeAwgTfbsHaibGm12878Mef2csc13268V0416101UniPk.narrowPeak.gz GM12878 ChipSeq MEF2C_(SC-13268) Peaks narrowPeak HudsonAlpha Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeAwgTfbsUniform/wgEncodeAwgTfbsHaibGm12878Mta3sc81325V0422111UniPk.narrowPeak.gz GM12878 ChipSeq MTA3_(SC-81325) Peaks narrowPeak HudsonAlpha Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeAwgTfbsUniform/wgEncodeAwgTfbsHaibGm12878Nfatc1sc17834V0422111UniPk.narrowPeak.gz GM12878 ChipSeq NFATC1_(SC-17834) Peaks narrowPeak HudsonAlpha Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeAwgTfbsUniform/wgEncodeAwgTfbsHaibGm12878Nficsc81335V0422111UniPk.narrowPeak.gz GM12878 ChipSeq NFIC_(SC-81335) Peaks narrowPeak HudsonAlpha Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeAwgTfbsUniform/wgEncodeAwgTfbsHaibGm12878NrsfPcr1xUniPk.narrowPeak.gz GM12878 ChipSeq NRSF Peaks narrowPeak HudsonAlpha Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeAwgTfbsUniform/wgEncodeAwgTfbsHaibGm12878P300Pcr1xUniPk.narrowPeak.gz GM12878 ChipSeq p300 Peaks narrowPeak HudsonAlpha Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeAwgTfbsUniform/wgEncodeAwgTfbsHaibGm12878Pax5c20Pcr1xUniPk.narrowPeak.gz GM12878 ChipSeq PAX5-C20 Peaks narrowPeak HudsonAlpha Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeAwgTfbsUniform/wgEncodeAwgTfbsHaibGm12878Pax5n19Pcr1xUniPk.narrowPeak.gz GM12878 ChipSeq PAX5-N19 Peaks narrowPeak HudsonAlpha Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeAwgTfbsUniform/wgEncodeAwgTfbsHaibGm12878Pbx3Pcr1xUniPk.narrowPeak.gz GM12878 ChipSeq Pbx3 Peaks narrowPeak HudsonAlpha Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeAwgTfbsUniform/wgEncodeAwgTfbsHaibGm12878Pmlsc71910V0422111UniPk.narrowPeak.gz GM12878 ChipSeq PML_(SC-71910) Peaks narrowPeak HudsonAlpha Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeAwgTfbsUniform/wgEncodeAwgTfbsHaibGm12878Pol24h8Pcr1xUniPk.narrowPeak.gz GM12878 ChipSeq Pol2-4H8 Peaks narrowPeak HudsonAlpha Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeAwgTfbsUniform/wgEncodeAwgTfbsHaibGm12878Pol2Pcr2xUniPk.narrowPeak.gz GM12878 ChipSeq Pol2 Peaks narrowPeak HudsonAlpha Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeAwgTfbsUniform/wgEncodeAwgTfbsHaibGm12878Pou2f2Pcr1xUniPk.narrowPeak.gz GM12878 ChipSeq POU2F2 Peaks narrowPeak HudsonAlpha Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeAwgTfbsUniform/wgEncodeAwgTfbsHaibGm12878Pu1Pcr1xUniPk.narrowPeak.gz GM12878 ChipSeq PU.1 Peaks narrowPeak HudsonAlpha Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeAwgTfbsUniform/wgEncodeAwgTfbsHaibGm12878Rad21V0416101UniPk.narrowPeak.gz GM12878 ChipSeq Rad21 Peaks narrowPeak HudsonAlpha Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeAwgTfbsUniform/wgEncodeAwgTfbsHaibGm12878Runx3sc101553V0422111UniPk.narrowPeak.gz GM12878 ChipSeq RUNX3_(SC-101553) Peaks narrowPeak HudsonAlpha Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeAwgTfbsUniform/wgEncodeAwgTfbsHaibGm12878RxraPcr1xUniPk.narrowPeak.gz GM12878 ChipSeq RXRA Peaks narrowPeak HudsonAlpha Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeAwgTfbsUniform/wgEncodeAwgTfbsHaibGm12878Six5Pcr1xUniPk.narrowPeak.gz GM12878 ChipSeq SIX5 Peaks narrowPeak HudsonAlpha Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeAwgTfbsUniform/wgEncodeAwgTfbsHaibGm12878Sp1Pcr1xUniPk.narrowPeak.gz GM12878 ChipSeq SP1 Peaks narrowPeak HudsonAlpha Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeAwgTfbsUniform/wgEncodeAwgTfbsHaibGm12878SrfPcr2xUniPk.narrowPeak.gz GM12878 ChipSeq SRF Peaks narrowPeak HudsonAlpha Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeAwgTfbsUniform/wgEncodeAwgTfbsHaibGm12878Stat5asc74442V0422111UniPk.narrowPeak.gz GM12878 ChipSeq STAT5A_(SC-74442) Peaks narrowPeak HudsonAlpha Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeAwgTfbsUniform/wgEncodeAwgTfbsHaibGm12878Taf1Pcr1xUniPk.narrowPeak.gz GM12878 ChipSeq TAF1 Peaks narrowPeak HudsonAlpha Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeAwgTfbsUniform/wgEncodeAwgTfbsHaibGm12878Tcf12Pcr1xUniPk.narrowPeak.gz GM12878 ChipSeq TCF12 Peaks narrowPeak HudsonAlpha Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeAwgTfbsUniform/wgEncodeAwgTfbsHaibGm12878Tcf3Pcr1xUniPk.narrowPeak.gz GM12878 ChipSeq TCF3_(SC-349) Peaks narrowPeak HudsonAlpha Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeAwgTfbsUniform/wgEncodeAwgTfbsHaibGm12878Usf1Pcr2xUniPk.narrowPeak.gz GM12878 ChipSeq USF-1 Peaks narrowPeak HudsonAlpha Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeAwgTfbsUniform/wgEncodeAwgTfbsHaibGm12878Yy1sc281Pcr1xUniPk.narrowPeak.gz GM12878 ChipSeq YY1_(SC-281) Peaks narrowPeak HudsonAlpha Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeAwgTfbsUniform/wgEncodeAwgTfbsHaibGm12878Zbtb33Pcr1xUniPk.narrowPeak.gz GM12878 ChipSeq ZBTB33 Peaks narrowPeak HudsonAlpha Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeAwgTfbsUniform/wgEncodeAwgTfbsHaibGm12878Zeb1sc25388V0416102UniPk.narrowPeak.gz GM12878 ChipSeq ZEB1_(SC-25388) Peaks narrowPeak HudsonAlpha Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeAwgTfbsUniform/wgEncodeAwgTfbsHaibGm12891Pax5c20V0416101UniPk.narrowPeak.gz GM12891 ChipSeq PAX5-C20 Peaks narrowPeak HudsonAlpha Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeAwgTfbsUniform/wgEncodeAwgTfbsHaibGm12891Pol24h8Pcr1xUniPk.narrowPeak.gz GM12891 ChipSeq Pol2-4H8 Peaks narrowPeak HudsonAlpha Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeAwgTfbsUniform/wgEncodeAwgTfbsHaibGm12891Pol2Pcr1xUniPk.narrowPeak.gz GM12891 ChipSeq Pol2 Peaks narrowPeak HudsonAlpha Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeAwgTfbsUniform/wgEncodeAwgTfbsHaibGm12891Pou2f2Pcr1xUniPk.narrowPeak.gz GM12891 ChipSeq POU2F2 Peaks narrowPeak HudsonAlpha Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeAwgTfbsUniform/wgEncodeAwgTfbsHaibGm12891Pu1Pcr1xUniPk.narrowPeak.gz GM12891 ChipSeq PU.1 Peaks narrowPeak HudsonAlpha Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeAwgTfbsUniform/wgEncodeAwgTfbsHaibGm12891Taf1Pcr1xUniPk.narrowPeak.gz GM12891 ChipSeq TAF1 Peaks narrowPeak HudsonAlpha Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeAwgTfbsUniform/wgEncodeAwgTfbsHaibGm12891Yy1sc281V0416101UniPk.narrowPeak.gz GM12891 ChipSeq YY1_(SC-281) Peaks narrowPeak HudsonAlpha Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeAwgTfbsUniform/wgEncodeAwgTfbsHaibGm12892Pax5c20V0416101UniPk.narrowPeak.gz GM12892 ChipSeq PAX5-C20 Peaks narrowPeak HudsonAlpha Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeAwgTfbsUniform/wgEncodeAwgTfbsHaibGm12892Pol24h8V0416102UniPk.narrowPeak.gz GM12892 ChipSeq Pol2-4H8 Peaks narrowPeak HudsonAlpha Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeAwgTfbsUniform/wgEncodeAwgTfbsHaibGm12892Pol2V0416102UniPk.narrowPeak.gz GM12892 ChipSeq Pol2 Peaks narrowPeak HudsonAlpha Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeAwgTfbsUniform/wgEncodeAwgTfbsHaibGm12892Taf1V0416102UniPk.narrowPeak.gz GM12892 ChipSeq TAF1 Peaks narrowPeak HudsonAlpha Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeAwgTfbsUniform/wgEncodeAwgTfbsHaibGm12892Yy1V0416101UniPk.narrowPeak.gz GM12892 ChipSeq YY1 Peaks narrowPeak HudsonAlpha Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeAwgTfbsUniform/wgEncodeAwgTfbsHaibH1hescAtf2sc81188V0422111UniPk.narrowPeak.gz H1-hESC ChipSeq ATF2_(SC-81188) Peaks narrowPeak HudsonAlpha Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeAwgTfbsUniform/wgEncodeAwgTfbsHaibH1hescAtf3V0416102UniPk.narrowPeak.gz H1-hESC ChipSeq ATF3 Peaks narrowPeak HudsonAlpha Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeAwgTfbsUniform/wgEncodeAwgTfbsHaibH1hescBcl11aPcr1xUniPk.narrowPeak.gz H1-hESC ChipSeq BCL11A Peaks narrowPeak HudsonAlpha Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeAwgTfbsUniform/wgEncodeAwgTfbsHaibH1hescCtcfsc5916V0416102UniPk.narrowPeak.gz H1-hESC ChipSeq CTCF_(SC-5916) Peaks narrowPeak HudsonAlpha Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeAwgTfbsUniform/wgEncodeAwgTfbsHaibH1hescEgr1V0416102UniPk.narrowPeak.gz H1-hESC ChipSeq Egr-1 Peaks narrowPeak HudsonAlpha Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeAwgTfbsUniform/wgEncodeAwgTfbsHaibH1hescFosl1sc183V0416102UniPk.narrowPeak.gz H1-hESC ChipSeq FOSL1_(SC-183) Peaks narrowPeak HudsonAlpha Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeAwgTfbsUniform/wgEncodeAwgTfbsHaibH1hescGabpPcr1xUniPk.narrowPeak.gz H1-hESC ChipSeq GABP Peaks narrowPeak HudsonAlpha Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeAwgTfbsUniform/wgEncodeAwgTfbsHaibH1hescHdac2sc6296V0416102UniPk.narrowPeak.gz H1-hESC ChipSeq HDAC2_(SC-6296) Peaks narrowPeak HudsonAlpha Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeAwgTfbsUniform/wgEncodeAwgTfbsHaibH1hescJundV0416102UniPk.narrowPeak.gz H1-hESC ChipSeq JunD Peaks narrowPeak HudsonAlpha Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeAwgTfbsUniform/wgEncodeAwgTfbsHaibH1hescNanogsc33759V0416102UniPk.narrowPeak.gz H1-hESC ChipSeq NANOG_(SC-33759) Peaks narrowPeak HudsonAlpha Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeAwgTfbsUniform/wgEncodeAwgTfbsHaibH1hescNrsfV0416102UniPk.narrowPeak.gz H1-hESC ChipSeq NRSF Peaks narrowPeak HudsonAlpha Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeAwgTfbsUniform/wgEncodeAwgTfbsHaibH1hescP300V0416102UniPk.narrowPeak.gz H1-hESC ChipSeq p300 Peaks narrowPeak HudsonAlpha Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeAwgTfbsUniform/wgEncodeAwgTfbsHaibH1hescPol24h8V0416102UniPk.narrowPeak.gz H1-hESC ChipSeq Pol2-4H8 Peaks narrowPeak HudsonAlpha Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeAwgTfbsUniform/wgEncodeAwgTfbsHaibH1hescPol2V0416102UniPk.narrowPeak.gz H1-hESC ChipSeq Pol2 Peaks narrowPeak HudsonAlpha Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeAwgTfbsUniform/wgEncodeAwgTfbsHaibH1hescPou5f1sc9081V0416102UniPk.narrowPeak.gz H1-hESC ChipSeq POU5F1_(SC-9081) Peaks narrowPeak HudsonAlpha Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeAwgTfbsUniform/wgEncodeAwgTfbsHaibH1hescRad21V0416102UniPk.narrowPeak.gz H1-hESC ChipSeq Rad21 Peaks narrowPeak HudsonAlpha Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeAwgTfbsUniform/wgEncodeAwgTfbsHaibH1hescRxraV0416102UniPk.narrowPeak.gz H1-hESC ChipSeq RXRA Peaks narrowPeak HudsonAlpha Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeAwgTfbsUniform/wgEncodeAwgTfbsHaibH1hescSin3ak20Pcr1xUniPk.narrowPeak.gz H1-hESC ChipSeq Sin3Ak-20 Peaks narrowPeak HudsonAlpha Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeAwgTfbsUniform/wgEncodeAwgTfbsHaibH1hescSix5Pcr1xUniPk.narrowPeak.gz H1-hESC ChipSeq SIX5 Peaks narrowPeak HudsonAlpha Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeAwgTfbsUniform/wgEncodeAwgTfbsHaibH1hescSp1Pcr1xUniPk.narrowPeak.gz H1-hESC ChipSeq SP1 Peaks narrowPeak HudsonAlpha Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeAwgTfbsUniform/wgEncodeAwgTfbsHaibH1hescSp2V0422111UniPk.narrowPeak.gz H1-hESC ChipSeq SP2_(SC-643) Peaks narrowPeak HudsonAlpha Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeAwgTfbsUniform/wgEncodeAwgTfbsHaibH1hescSp4v20V0422111UniPk.narrowPeak.gz H1-hESC ChipSeq SP4_(V-20) Peaks narrowPeak HudsonAlpha Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeAwgTfbsUniform/wgEncodeAwgTfbsHaibH1hescSrfPcr1xUniPk.narrowPeak.gz H1-hESC ChipSeq SRF Peaks narrowPeak HudsonAlpha Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeAwgTfbsUniform/wgEncodeAwgTfbsHaibH1hescTaf1V0416102UniPk.narrowPeak.gz H1-hESC ChipSeq TAF1 Peaks narrowPeak HudsonAlpha Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeAwgTfbsUniform/wgEncodeAwgTfbsHaibH1hescTaf7sc101167V0416102UniPk.narrowPeak.gz H1-hESC ChipSeq TAF7_(SC-101167) Peaks narrowPeak HudsonAlpha Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeAwgTfbsUniform/wgEncodeAwgTfbsHaibH1hescTcf12Pcr1xUniPk.narrowPeak.gz H1-hESC ChipSeq TCF12 Peaks narrowPeak HudsonAlpha Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeAwgTfbsUniform/wgEncodeAwgTfbsHaibH1hescTead4sc101184V0422111UniPk.narrowPeak.gz H1-hESC ChipSeq TEAD4_(SC-101184) Peaks narrowPeak HudsonAlpha Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeAwgTfbsUniform/wgEncodeAwgTfbsHaibH1hescUsf1Pcr1xUniPk.narrowPeak.gz H1-hESC ChipSeq USF-1 Peaks narrowPeak HudsonAlpha Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeAwgTfbsUniform/wgEncodeAwgTfbsHaibH1hescYy1sc281V0416102UniPk.narrowPeak.gz H1-hESC ChipSeq YY1_(SC-281) Peaks narrowPeak HudsonAlpha Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeAwgTfbsUniform/wgEncodeAwgTfbsHaibHct116Pol24h8V0416101UniPk.narrowPeak.gz HCT-116 ChipSeq Pol2-4H8 Peaks narrowPeak HudsonAlpha Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeAwgTfbsUniform/wgEncodeAwgTfbsHaibHct116Yy1sc281V0416101UniPk.narrowPeak.gz HCT-116 ChipSeq YY1_(SC-281) Peaks narrowPeak HudsonAlpha Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeAwgTfbsUniform/wgEncodeAwgTfbsHaibHct116Zbtb33V0416101UniPk.narrowPeak.gz HCT-116 ChipSeq ZBTB33 Peaks narrowPeak HudsonAlpha Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeAwgTfbsUniform/wgEncodeAwgTfbsHaibHelas3GabpPcr1xUniPk.narrowPeak.gz HeLa-S3 ChipSeq GABP Peaks narrowPeak HudsonAlpha Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeAwgTfbsUniform/wgEncodeAwgTfbsHaibHelas3NrsfPcr1xUniPk.narrowPeak.gz HeLa-S3 ChipSeq NRSF Peaks narrowPeak HudsonAlpha Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeAwgTfbsUniform/wgEncodeAwgTfbsHaibHelas3Pol2Pcr1xUniPk.narrowPeak.gz HeLa-S3 ChipSeq Pol2 Peaks narrowPeak HudsonAlpha Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeAwgTfbsUniform/wgEncodeAwgTfbsHaibHelas3Taf1Pcr1xUniPk.narrowPeak.gz HeLa-S3 ChipSeq TAF1 Peaks narrowPeak HudsonAlpha Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeAwgTfbsUniform/wgEncodeAwgTfbsHaibHepg2Atf3V0416101UniPk.narrowPeak.gz HepG2 ChipSeq ATF3 Peaks narrowPeak HudsonAlpha Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeAwgTfbsUniform/wgEncodeAwgTfbsHaibHepg2Bhlhe40V0416101UniPk.narrowPeak.gz HepG2 ChipSeq BHLHE40 Peaks narrowPeak HudsonAlpha Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeAwgTfbsUniform/wgEncodeAwgTfbsHaibHepg2Cebpbsc150V0416101UniPk.narrowPeak.gz HepG2 ChipSeq CEBPB_(SC-150) Peaks narrowPeak HudsonAlpha Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeAwgTfbsUniform/wgEncodeAwgTfbsHaibHepg2Cebpdsc636V0416101UniPk.narrowPeak.gz HepG2 ChipSeq CEBPD_(SC-636) Peaks narrowPeak HudsonAlpha Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeAwgTfbsUniform/wgEncodeAwgTfbsHaibHepg2Ctcfsc5916V0416101UniPk.narrowPeak.gz HepG2 ChipSeq CTCF_(SC-5916) Peaks narrowPeak HudsonAlpha Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeAwgTfbsUniform/wgEncodeAwgTfbsHaibHepg2Elf1sc631V0416101UniPk.narrowPeak.gz HepG2 ChipSeq ELF1_(SC-631) Peaks narrowPeak HudsonAlpha Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeAwgTfbsUniform/wgEncodeAwgTfbsHaibHepg2Fosl2V0416101UniPk.narrowPeak.gz HepG2 ChipSeq FOSL2 Peaks narrowPeak HudsonAlpha Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeAwgTfbsUniform/wgEncodeAwgTfbsHaibHepg2Foxa1sc101058V0416101UniPk.narrowPeak.gz HepG2 ChipSeq FOXA1_(SC-101058) Peaks narrowPeak HudsonAlpha Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeAwgTfbsUniform/wgEncodeAwgTfbsHaibHepg2Foxa1sc6553V0416101UniPk.narrowPeak.gz HepG2 ChipSeq FOXA1_(SC-6553) Peaks narrowPeak HudsonAlpha Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeAwgTfbsUniform/wgEncodeAwgTfbsHaibHepg2Foxa2sc6554V0416101UniPk.narrowPeak.gz HepG2 ChipSeq FOXA2_(SC-6554) Peaks narrowPeak HudsonAlpha Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeAwgTfbsUniform/wgEncodeAwgTfbsHaibHepg2GabpPcr2xUniPk.narrowPeak.gz HepG2 ChipSeq GABP Peaks narrowPeak HudsonAlpha Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeAwgTfbsUniform/wgEncodeAwgTfbsHaibHepg2Hdac2sc6296V0416101UniPk.narrowPeak.gz HepG2 ChipSeq HDAC2_(SC-6296) Peaks narrowPeak HudsonAlpha Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeAwgTfbsUniform/wgEncodeAwgTfbsHaibHepg2Hnf4asc8987V0416101UniPk.narrowPeak.gz HepG2 ChipSeq HNF4A_(SC-8987) Peaks narrowPeak HudsonAlpha Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeAwgTfbsUniform/wgEncodeAwgTfbsHaibHepg2Hnf4gsc6558V0416101UniPk.narrowPeak.gz HepG2 ChipSeq HNF4G_(SC-6558) Peaks narrowPeak HudsonAlpha Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeAwgTfbsUniform/wgEncodeAwgTfbsHaibHepg2JundPcr1xUniPk.narrowPeak.gz HepG2 ChipSeq JunD Peaks narrowPeak HudsonAlpha Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeAwgTfbsUniform/wgEncodeAwgTfbsHaibHepg2Mbd4sc271530V0422111UniPk.narrowPeak.gz HepG2 ChipSeq MBD4_(SC-271530) Peaks narrowPeak HudsonAlpha Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeAwgTfbsUniform/wgEncodeAwgTfbsHaibHepg2Mybl2sc81192V0422111UniPk.narrowPeak.gz HepG2 ChipSeq MYBL2_(SC-81192) Peaks narrowPeak HudsonAlpha Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeAwgTfbsUniform/wgEncodeAwgTfbsHaibHepg2Nficsc81335V0422111UniPk.narrowPeak.gz HepG2 ChipSeq NFIC_(SC-81335) Peaks narrowPeak HudsonAlpha Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeAwgTfbsUniform/wgEncodeAwgTfbsHaibHepg2NrsfPcr2xUniPk.narrowPeak.gz HepG2 ChipSeq NRSF Peaks narrowPeak HudsonAlpha Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeAwgTfbsUniform/wgEncodeAwgTfbsHaibHepg2NrsfV0416101UniPk.narrowPeak.gz HepG2 ChipSeq NRSF Peaks narrowPeak HudsonAlpha Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeAwgTfbsUniform/wgEncodeAwgTfbsHaibHepg2P300V0416101UniPk.narrowPeak.gz HepG2 ChipSeq p300 Peaks narrowPeak HudsonAlpha Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeAwgTfbsUniform/wgEncodeAwgTfbsHaibHepg2Pol24h8V0416102UniPk.narrowPeak.gz HepG2 ChipSeq Pol2-4H8 Peaks narrowPeak HudsonAlpha Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeAwgTfbsUniform/wgEncodeAwgTfbsHaibHepg2Pol2Pcr2xUniPk.narrowPeak.gz HepG2 ChipSeq Pol2 Peaks narrowPeak HudsonAlpha Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeAwgTfbsUniform/wgEncodeAwgTfbsHaibHepg2Rad21V0416101UniPk.narrowPeak.gz HepG2 ChipSeq Rad21 Peaks narrowPeak HudsonAlpha Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeAwgTfbsUniform/wgEncodeAwgTfbsHaibHepg2RxraPcr1xUniPk.narrowPeak.gz HepG2 ChipSeq RXRA Peaks narrowPeak HudsonAlpha Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeAwgTfbsUniform/wgEncodeAwgTfbsHaibHepg2Sin3ak20Pcr1xUniPk.narrowPeak.gz HepG2 ChipSeq Sin3Ak-20 Peaks narrowPeak HudsonAlpha Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeAwgTfbsUniform/wgEncodeAwgTfbsHaibHepg2Sp1Pcr1xUniPk.narrowPeak.gz HepG2 ChipSeq SP1 Peaks narrowPeak HudsonAlpha Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeAwgTfbsUniform/wgEncodeAwgTfbsHaibHepg2Sp2V0422111UniPk.narrowPeak.gz HepG2 ChipSeq SP2_(SC-643) Peaks narrowPeak HudsonAlpha Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeAwgTfbsUniform/wgEncodeAwgTfbsHaibHepg2SrfV0416101UniPk.narrowPeak.gz HepG2 ChipSeq SRF Peaks narrowPeak HudsonAlpha Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeAwgTfbsUniform/wgEncodeAwgTfbsHaibHepg2Taf1Pcr2xUniPk.narrowPeak.gz HepG2 ChipSeq TAF1 Peaks narrowPeak HudsonAlpha Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeAwgTfbsUniform/wgEncodeAwgTfbsHaibHepg2Tcf12Pcr1xUniPk.narrowPeak.gz HepG2 ChipSeq TCF12 Peaks narrowPeak HudsonAlpha Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeAwgTfbsUniform/wgEncodeAwgTfbsHaibHepg2Tead4sc101184V0422111UniPk.narrowPeak.gz HepG2 ChipSeq TEAD4_(SC-101184) Peaks narrowPeak HudsonAlpha Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeAwgTfbsUniform/wgEncodeAwgTfbsHaibHepg2Usf1Pcr1xUniPk.narrowPeak.gz HepG2 ChipSeq USF-1 Peaks narrowPeak HudsonAlpha Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeAwgTfbsUniform/wgEncodeAwgTfbsHaibHepg2Yy1sc281V0416101UniPk.narrowPeak.gz HepG2 ChipSeq YY1_(SC-281) Peaks narrowPeak HudsonAlpha Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeAwgTfbsUniform/wgEncodeAwgTfbsHaibHepg2Zbtb33Pcr1xUniPk.narrowPeak.gz HepG2 ChipSeq ZBTB33 Peaks narrowPeak HudsonAlpha Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeAwgTfbsUniform/wgEncodeAwgTfbsHaibHepg2Zbtb7aV0416101UniPk.narrowPeak.gz HepG2 ChipSeq ZBTB7A_(SC-34508) Peaks narrowPeak HudsonAlpha Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeAwgTfbsUniform/wgEncodeAwgTfbsHaibHuvecPol24h8V0416101UniPk.narrowPeak.gz HUVEC ChipSeq Pol2-4H8 Peaks narrowPeak HudsonAlpha Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeAwgTfbsUniform/wgEncodeAwgTfbsHaibHuvecPol2Pcr1xUniPk.narrowPeak.gz HUVEC ChipSeq Pol2 Peaks narrowPeak HudsonAlpha Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeAwgTfbsUniform/wgEncodeAwgTfbsHaibK562Atf3V0416101UniPk.narrowPeak.gz K562 ChipSeq ATF3 Peaks narrowPeak HudsonAlpha Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeAwgTfbsUniform/wgEncodeAwgTfbsHaibK562Bcl3Pcr1xUniPk.narrowPeak.gz K562 ChipSeq BCL3 Peaks narrowPeak HudsonAlpha Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeAwgTfbsUniform/wgEncodeAwgTfbsHaibK562Bclaf101388Pcr1xUniPk.narrowPeak.gz K562 ChipSeq BCLAF1_(SC-101388) Peaks narrowPeak HudsonAlpha Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeAwgTfbsUniform/wgEncodeAwgTfbsHaibK562Cbx3sc101004V0422111UniPk.narrowPeak.gz K562 ChipSeq CBX3_(SC-101004) Peaks narrowPeak HudsonAlpha Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeAwgTfbsUniform/wgEncodeAwgTfbsHaibK562Cebpbsc150V0422111UniPk.narrowPeak.gz K562 ChipSeq CEBPB_(SC-150) Peaks narrowPeak HudsonAlpha Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeAwgTfbsUniform/wgEncodeAwgTfbsHaibK562CtcfcPcr1xUniPk.narrowPeak.gz K562 ChipSeq CTCF_(SC-5916) Peaks narrowPeak HudsonAlpha Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeAwgTfbsUniform/wgEncodeAwgTfbsHaibK562Ctcflsc98982V0416101UniPk.narrowPeak.gz K562 ChipSeq CTCFL_(SC-98982) Peaks narrowPeak HudsonAlpha Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeAwgTfbsUniform/wgEncodeAwgTfbsHaibK562E2f6V0416102UniPk.narrowPeak.gz K562 ChipSeq E2F6 Peaks narrowPeak HudsonAlpha Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeAwgTfbsUniform/wgEncodeAwgTfbsHaibK562Egr1V0416101UniPk.narrowPeak.gz K562 ChipSeq Egr-1 Peaks narrowPeak HudsonAlpha Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeAwgTfbsUniform/wgEncodeAwgTfbsHaibK562Elf1sc631V0416102UniPk.narrowPeak.gz K562 ChipSeq ELF1_(SC-631) Peaks narrowPeak HudsonAlpha Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeAwgTfbsUniform/wgEncodeAwgTfbsHaibK562Ets1V0416101UniPk.narrowPeak.gz K562 ChipSeq ETS1 Peaks narrowPeak HudsonAlpha Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeAwgTfbsUniform/wgEncodeAwgTfbsHaibK562Fosl1sc183V0416101UniPk.narrowPeak.gz K562 ChipSeq FOSL1_(SC-183) Peaks narrowPeak HudsonAlpha Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeAwgTfbsUniform/wgEncodeAwgTfbsHaibK562GabpV0416101UniPk.narrowPeak.gz K562 ChipSeq GABP Peaks narrowPeak HudsonAlpha Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeAwgTfbsUniform/wgEncodeAwgTfbsHaibK562Gata2sc267Pcr1xUniPk.narrowPeak.gz K562 ChipSeq GATA2_(SC-267) Peaks narrowPeak HudsonAlpha Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeAwgTfbsUniform/wgEncodeAwgTfbsHaibK562Hdac2sc6296V0416102UniPk.narrowPeak.gz K562 ChipSeq HDAC2_(SC-6296) Peaks narrowPeak HudsonAlpha Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeAwgTfbsUniform/wgEncodeAwgTfbsHaibK562MaxV0416102UniPk.narrowPeak.gz K562 ChipSeq Max Peaks narrowPeak HudsonAlpha Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeAwgTfbsUniform/wgEncodeAwgTfbsHaibK562Mef2aV0416101UniPk.narrowPeak.gz K562 ChipSeq MEF2A Peaks narrowPeak HudsonAlpha Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeAwgTfbsUniform/wgEncodeAwgTfbsHaibK562Nr2f2sc271940V0422111UniPk.narrowPeak.gz K562 ChipSeq NR2F2_(SC-271940) Peaks narrowPeak HudsonAlpha Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeAwgTfbsUniform/wgEncodeAwgTfbsHaibK562NrsfV0416102UniPk.narrowPeak.gz K562 ChipSeq NRSF Peaks narrowPeak HudsonAlpha Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeAwgTfbsUniform/wgEncodeAwgTfbsHaibK562Pmlsc71910V0422111UniPk.narrowPeak.gz K562 ChipSeq PML_(SC-71910) Peaks narrowPeak HudsonAlpha Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeAwgTfbsUniform/wgEncodeAwgTfbsHaibK562Pol24h8V0416101UniPk.narrowPeak.gz K562 ChipSeq Pol2-4H8 Peaks narrowPeak HudsonAlpha Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeAwgTfbsUniform/wgEncodeAwgTfbsHaibK562Pol2V0416101UniPk.narrowPeak.gz K562 ChipSeq Pol2 Peaks narrowPeak HudsonAlpha Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeAwgTfbsUniform/wgEncodeAwgTfbsHaibK562Pu1Pcr1xUniPk.narrowPeak.gz K562 ChipSeq PU.1 Peaks narrowPeak HudsonAlpha Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeAwgTfbsUniform/wgEncodeAwgTfbsHaibK562Rad21V0416102UniPk.narrowPeak.gz K562 ChipSeq Rad21 Peaks narrowPeak HudsonAlpha Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeAwgTfbsUniform/wgEncodeAwgTfbsHaibK562Sin3ak20V0416101UniPk.narrowPeak.gz K562 ChipSeq Sin3Ak-20 Peaks narrowPeak HudsonAlpha Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeAwgTfbsUniform/wgEncodeAwgTfbsHaibK562Six5Pcr1xUniPk.narrowPeak.gz K562 ChipSeq SIX5 Peaks narrowPeak HudsonAlpha Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeAwgTfbsUniform/wgEncodeAwgTfbsHaibK562Sp1Pcr1xUniPk.narrowPeak.gz K562 ChipSeq SP1 Peaks narrowPeak HudsonAlpha Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeAwgTfbsUniform/wgEncodeAwgTfbsHaibK562Sp2sc643V0416102UniPk.narrowPeak.gz K562 ChipSeq SP2_(SC-643) Peaks narrowPeak HudsonAlpha Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeAwgTfbsUniform/wgEncodeAwgTfbsHaibK562SrfV0416101UniPk.narrowPeak.gz K562 ChipSeq SRF Peaks narrowPeak HudsonAlpha Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeAwgTfbsUniform/wgEncodeAwgTfbsHaibK562Stat5asc74442V0422111UniPk.narrowPeak.gz K562 ChipSeq STAT5A_(SC-74442) Peaks narrowPeak HudsonAlpha Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeAwgTfbsUniform/wgEncodeAwgTfbsHaibK562Taf1V0416101UniPk.narrowPeak.gz K562 ChipSeq TAF1 Peaks narrowPeak HudsonAlpha Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeAwgTfbsUniform/wgEncodeAwgTfbsHaibK562Taf7sc101167V0416101UniPk.narrowPeak.gz K562 ChipSeq TAF7_(SC-101167) Peaks narrowPeak HudsonAlpha Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeAwgTfbsUniform/wgEncodeAwgTfbsHaibK562Tead4sc101184V0422111UniPk.narrowPeak.gz K562 ChipSeq TEAD4_(SC-101184) Peaks narrowPeak HudsonAlpha Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeAwgTfbsUniform/wgEncodeAwgTfbsHaibK562Thap1sc98174V0416101UniPk.narrowPeak.gz K562 ChipSeq THAP1_(SC-98174) Peaks narrowPeak HudsonAlpha Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeAwgTfbsUniform/wgEncodeAwgTfbsHaibK562Trim28sc81411V0422111UniPk.narrowPeak.gz K562 ChipSeq TRIM28_(SC-81411) Peaks narrowPeak HudsonAlpha Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeAwgTfbsUniform/wgEncodeAwgTfbsHaibK562Usf1V0416101UniPk.narrowPeak.gz K562 ChipSeq USF-1 Peaks narrowPeak HudsonAlpha Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeAwgTfbsUniform/wgEncodeAwgTfbsHaibK562Yy1V0416101UniPk.narrowPeak.gz K562 ChipSeq YY1_(SC-281) Peaks narrowPeak HudsonAlpha Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeAwgTfbsUniform/wgEncodeAwgTfbsHaibK562Yy1V0416102UniPk.narrowPeak.gz K562 ChipSeq YY1 Peaks narrowPeak HudsonAlpha Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeAwgTfbsUniform/wgEncodeAwgTfbsHaibK562Zbtb33Pcr1xUniPk.narrowPeak.gz K562 ChipSeq ZBTB33 Peaks narrowPeak HudsonAlpha Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeAwgTfbsUniform/wgEncodeAwgTfbsHaibK562Zbtb7asc34508V0416101UniPk.narrowPeak.gz K562 ChipSeq ZBTB7A_(SC-34508) Peaks narrowPeak HudsonAlpha Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeAwgTfbsUniform/wgEncodeAwgTfbsHaibPanc1NrsfPcr2xUniPk.narrowPeak.gz PANC-1 ChipSeq NRSF Peaks narrowPeak HudsonAlpha Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeAwgTfbsUniform/wgEncodeAwgTfbsHaibPanc1Pol24h8V0416101UniPk.narrowPeak.gz PANC-1 ChipSeq Pol2-4H8 Peaks narrowPeak HudsonAlpha Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeAwgTfbsUniform/wgEncodeAwgTfbsHaibPanc1Sin3ak20V0416101UniPk.narrowPeak.gz PANC-1 ChipSeq Sin3Ak-20 Peaks narrowPeak HudsonAlpha Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeAwgTfbsUniform/wgEncodeAwgTfbsHaibPfsk1Foxp2Pcr2xUniPk.narrowPeak.gz PFSK-1 ChipSeq FOXP2 Peaks narrowPeak HudsonAlpha Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeAwgTfbsUniform/wgEncodeAwgTfbsHaibPfsk1NrsfPcr2xUniPk.narrowPeak.gz PFSK-1 ChipSeq NRSF Peaks narrowPeak HudsonAlpha Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeAwgTfbsUniform/wgEncodeAwgTfbsHaibPfsk1Pol24h8V0416101UniPk.narrowPeak.gz narrowPeak Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeAwgTfbsUniform/wgEncodeAwgTfbsHaibPfsk1Sin3ak20V0416101UniPk.narrowPeak.gz PFSK-1 ChipSeq Sin3Ak-20 Peaks narrowPeak HudsonAlpha Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeAwgTfbsUniform/wgEncodeAwgTfbsHaibPfsk1Taf1V0416101UniPk.narrowPeak.gz PFSK-1 ChipSeq TAF1 Peaks narrowPeak HudsonAlpha Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeAwgTfbsUniform/wgEncodeAwgTfbsHaibSknmcFoxp2Pcr2xUniPk.narrowPeak.gz SK-N-MC ChipSeq FOXP2 Peaks narrowPeak HudsonAlpha Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeAwgTfbsUniform/wgEncodeAwgTfbsHaibSknmcPol24h8V0416101UniPk.narrowPeak.gz SK-N-MC ChipSeq Pol2-4H8 Peaks narrowPeak HudsonAlpha Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeAwgTfbsUniform/wgEncodeAwgTfbsHaibSknshNrsfPcr2xUniPk.narrowPeak.gz SK-N-SH ChipSeq NRSF Peaks narrowPeak HudsonAlpha Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeAwgTfbsUniform/wgEncodeAwgTfbsHaibSknshNrsfV0416101UniPk.narrowPeak.gz SK-N-SH ChipSeq NRSF Peaks narrowPeak HudsonAlpha Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeAwgTfbsUniform/wgEncodeAwgTfbsHaibSknshPol24h8V0416101UniPk.narrowPeak.gz SK-N-SH ChipSeq Pol2-4H8 Peaks narrowPeak HudsonAlpha Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeAwgTfbsUniform/wgEncodeAwgTfbsHaibSknshSin3ak20V0416101UniPk.narrowPeak.gz SK-N-SH ChipSeq Sin3Ak-20 Peaks narrowPeak HudsonAlpha Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeAwgTfbsUniform/wgEncodeAwgTfbsHaibSknshTaf1V0416101UniPk.narrowPeak.gz SK-N-SH ChipSeq TAF1 Peaks narrowPeak HudsonAlpha Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeAwgTfbsUniform/wgEncodeAwgTfbsHaibSknshraCtcfV0416102UniPk.narrowPeak.gz SK-N-SH_RA ChipSeq CTCF Peaks narrowPeak HudsonAlpha Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeAwgTfbsUniform/wgEncodeAwgTfbsHaibSknshraP300V0416102UniPk.narrowPeak.gz SK-N-SH_RA ChipSeq p300 Peaks narrowPeak HudsonAlpha Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeAwgTfbsUniform/wgEncodeAwgTfbsHaibSknshraRad21V0416102UniPk.narrowPeak.gz SK-N-SH_RA ChipSeq Rad21 Peaks narrowPeak HudsonAlpha Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeAwgTfbsUniform/wgEncodeAwgTfbsHaibSknshraUsf1sc8983V0416102UniPk.narrowPeak.gz SK-N-SH_RA ChipSeq USF1_(SC-8983) Peaks narrowPeak HudsonAlpha Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeAwgTfbsUniform/wgEncodeAwgTfbsHaibSknshraYy1sc281V0416102UniPk.narrowPeak.gz SK-N-SH_RA ChipSeq YY1_(SC-281) Peaks narrowPeak HudsonAlpha Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeAwgTfbsUniform/wgEncodeAwgTfbsHaibT47dCtcfsc5916V0416102Dm002p1hUniPk.narrowPeak.gz T-47D ChipSeq CTCF_(SC-5916) Peaks narrowPeak HudsonAlpha Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeAwgTfbsUniform/wgEncodeAwgTfbsHaibT47dEraaV0416102Bpa1hUniPk.narrowPeak.gz T-47D ChipSeq ERalpha_a Peaks narrowPeak HudsonAlpha Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeAwgTfbsUniform/wgEncodeAwgTfbsHaibT47dEralphaaPcr2xGen1hUniPk.narrowPeak.gz T-47D ChipSeq ERalpha_a Peaks narrowPeak HudsonAlpha Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeAwgTfbsUniform/wgEncodeAwgTfbsHaibT47dEralphaaV0416102Est10nm1hUniPk.narrowPeak.gz T-47D ChipSeq ERalpha_a Peaks narrowPeak HudsonAlpha Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeAwgTfbsUniform/wgEncodeAwgTfbsHaibT47dFoxa1sc6553V0416102Dm002p1hUniPk.narrowPeak.gz T-47D ChipSeq FOXA1_(SC-6553) Peaks narrowPeak HudsonAlpha Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeAwgTfbsUniform/wgEncodeAwgTfbsHaibT47dGata3sc268V0416102Dm002p1hUniPk.narrowPeak.gz T-47D ChipSeq GATA3_(SC-268) Peaks narrowPeak HudsonAlpha Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeAwgTfbsUniform/wgEncodeAwgTfbsHaibT47dP300V0416102Dm002p1hUniPk.narrowPeak.gz T-47D ChipSeq p300 Peaks narrowPeak HudsonAlpha Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeAwgTfbsUniform/wgEncodeAwgTfbsHaibU87NrsfPcr2xUniPk.narrowPeak.gz U87 ChipSeq NRSF Peaks narrowPeak HudsonAlpha Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeAwgTfbsUniform/wgEncodeAwgTfbsHaibU87Pol24h8V0416101UniPk.narrowPeak.gz U87 ChipSeq Pol2-4H8 Peaks narrowPeak HudsonAlpha Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeAwgTfbsUniform/wgEncodeAwgTfbsSydhA549Bhlhe40IggrabUniPk.narrowPeak.gz A549 ChipSeq BHLHE40 Peaks narrowPeak Stanford Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeAwgTfbsUniform/wgEncodeAwgTfbsSydhA549CebpbIggrabUniPk.narrowPeak.gz A549 ChipSeq CEBPB Peaks narrowPeak Stanford Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeAwgTfbsUniform/wgEncodeAwgTfbsSydhA549MaxIggrabUniPk.narrowPeak.gz A549 ChipSeq Max Peaks narrowPeak Stanford Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeAwgTfbsUniform/wgEncodeAwgTfbsSydhA549Pol2s2IggrabUniPk.narrowPeak.gz A549 ChipSeq Pol2(phosphoS2) Peaks narrowPeak Stanford Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeAwgTfbsUniform/wgEncodeAwgTfbsSydhA549Rad21IggrabUniPk.narrowPeak.gz A549 ChipSeq Rad21 Peaks narrowPeak Stanford Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeAwgTfbsUniform/wgEncodeAwgTfbsSydhGm08714Znf274UcdUniPk.narrowPeak.gz GM08714 ChipSeq ZNF274 Peaks narrowPeak USC Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeAwgTfbsUniform/wgEncodeAwgTfbsSydhGm10847NfkbTnfaIggrabUniPk.narrowPeak.gz GM10847 ChipSeq NFKB Peaks narrowPeak Stanford Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeAwgTfbsUniform/wgEncodeAwgTfbsSydhGm10847Pol2IggmusUniPk.narrowPeak.gz GM10847 ChipSeq Pol2 Peaks narrowPeak Stanford Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeAwgTfbsUniform/wgEncodeAwgTfbsSydhGm12878Bhlhe40cIggmusUniPk.narrowPeak.gz GM12878 ChipSeq BHLHE40_(NB100-1800) Peaks narrowPeak Stanford Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeAwgTfbsUniform/wgEncodeAwgTfbsSydhGm12878Brca1a300IggmusUniPk.narrowPeak.gz GM12878 ChipSeq BRCA1_(A300-000A) Peaks narrowPeak Stanford Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeAwgTfbsUniform/wgEncodeAwgTfbsSydhGm12878CfosUniPk.narrowPeak.gz GM12878 ChipSeq c-Fos Peaks narrowPeak Yale Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeAwgTfbsUniform/wgEncodeAwgTfbsSydhGm12878Chd1a301218aIggmusUniPk.narrowPeak.gz GM12878 ChipSeq CHD1_(A301-218A) Peaks narrowPeak Stanford Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeAwgTfbsUniform/wgEncodeAwgTfbsSydhGm12878Chd2ab68301IggmusUniPk.narrowPeak.gz GM12878 ChipSeq CHD2_(AB68301) Peaks narrowPeak Stanford Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeAwgTfbsUniform/wgEncodeAwgTfbsSydhGm12878Corestsc30189IggmusUniPk.narrowPeak.gz GM12878 ChipSeq COREST_(sc-30189) Peaks narrowPeak Stanford Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeAwgTfbsUniform/wgEncodeAwgTfbsSydhGm12878Ctcfsc15914c20UniPk.narrowPeak.gz GM12878 ChipSeq CTCF_(SC-15914) Peaks narrowPeak Stanford Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeAwgTfbsUniform/wgEncodeAwgTfbsSydhGm12878E2f4IggmusUniPk.narrowPeak.gz GM12878 ChipSeq E2F4 Peaks narrowPeak Stanford Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeAwgTfbsUniform/wgEncodeAwgTfbsSydhGm12878Ebf1sc137065UniPk.narrowPeak.gz GM12878 ChipSeq EBF1_(SC-137065) Peaks narrowPeak Stanford Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeAwgTfbsUniform/wgEncodeAwgTfbsSydhGm12878Elk112771IggmusUniPk.narrowPeak.gz GM12878 ChipSeq ELK1_(1277-1) Peaks narrowPeak Stanford Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeAwgTfbsUniform/wgEncodeAwgTfbsSydhGm12878Ikzf1iknuclaUniPk.narrowPeak.gz GM12878 ChipSeq IKZF1_(IkN)_(UCLA) Peaks narrowPeak USC Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeAwgTfbsUniform/wgEncodeAwgTfbsSydhGm12878JundUniPk.narrowPeak.gz GM12878 ChipSeq JunD Peaks narrowPeak Yale Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeAwgTfbsUniform/wgEncodeAwgTfbsSydhGm12878MaxIggmusUniPk.narrowPeak.gz GM12878 ChipSeq Max Peaks narrowPeak Stanford Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeAwgTfbsUniform/wgEncodeAwgTfbsSydhGm12878Mazab85725IggmusUniPk.narrowPeak.gz GM12878 ChipSeq MAZ_(ab85725) Peaks narrowPeak Stanford Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeAwgTfbsUniform/wgEncodeAwgTfbsSydhGm12878Mxi1IggmusUniPk.narrowPeak.gz GM12878 ChipSeq Mxi1_(AF4185) Peaks narrowPeak Stanford Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeAwgTfbsUniform/wgEncodeAwgTfbsSydhGm12878Nfe2sc22827UniPk.narrowPeak.gz GM12878 ChipSeq NF-E2_(SC-22827) Peaks narrowPeak Stanford Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeAwgTfbsUniform/wgEncodeAwgTfbsSydhGm12878NfkbTnfaIggrabUniPk.narrowPeak.gz GM12878 ChipSeq NFKB Peaks narrowPeak Stanford Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeAwgTfbsUniform/wgEncodeAwgTfbsSydhGm12878NfyaIggmusUniPk.narrowPeak.gz GM12878 ChipSeq NF-YA Peaks narrowPeak Harvard Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeAwgTfbsUniform/wgEncodeAwgTfbsSydhGm12878NfybIggmusUniPk.narrowPeak.gz GM12878 ChipSeq NF-YB Peaks narrowPeak Harvard Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeAwgTfbsUniform/wgEncodeAwgTfbsSydhGm12878Nrf1IggmusUniPk.narrowPeak.gz GM12878 ChipSeq Nrf1 Peaks narrowPeak Stanford Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeAwgTfbsUniform/wgEncodeAwgTfbsSydhGm12878P300IggmusUniPk.narrowPeak.gz GM12878 ChipSeq p300 Peaks narrowPeak Stanford Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeAwgTfbsUniform/wgEncodeAwgTfbsSydhGm12878P300bUniPk.narrowPeak.gz GM12878 ChipSeq p300_(SC-584) Peaks narrowPeak Stanford Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeAwgTfbsUniform/wgEncodeAwgTfbsSydhGm12878Pol2IggmusUniPk.narrowPeak.gz GM12878 ChipSeq Pol2 Peaks narrowPeak Stanford Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeAwgTfbsUniform/wgEncodeAwgTfbsSydhGm12878Pol2UniPk.narrowPeak.gz GM12878 ChipSeq Pol2 Peaks narrowPeak Yale Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeAwgTfbsUniform/wgEncodeAwgTfbsSydhGm12878Pol2s2IggmusUniPk.narrowPeak.gz GM12878 ChipSeq Pol2(phosphoS2) Peaks narrowPeak Stanford Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeAwgTfbsUniform/wgEncodeAwgTfbsSydhGm12878Pol3UniPk.narrowPeak.gz GM12878 ChipSeq Pol3 Peaks narrowPeak Yale Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeAwgTfbsUniform/wgEncodeAwgTfbsSydhGm12878Rad21IggrabUniPk.narrowPeak.gz GM12878 ChipSeq Rad21 Peaks narrowPeak Stanford Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeAwgTfbsUniform/wgEncodeAwgTfbsSydhGm12878Rfx5200401194IggmusUniPk.narrowPeak.gz GM12878 ChipSeq RFX5_(200-401-194) Peaks narrowPeak Stanford Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeAwgTfbsUniform/wgEncodeAwgTfbsSydhGm12878Sin3anb6001263IggmusUniPk.narrowPeak.gz GM12878 ChipSeq SIN3A_(NB600-1263) Peaks narrowPeak Stanford Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeAwgTfbsUniform/wgEncodeAwgTfbsSydhGm12878Smc3ab9263IggmusUniPk.narrowPeak.gz GM12878 ChipSeq SMC3_(ab9263) Peaks narrowPeak Stanford Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeAwgTfbsUniform/wgEncodeAwgTfbsSydhGm12878Stat1UniPk.narrowPeak.gz GM12878 ChipSeq STAT1 Peaks narrowPeak Stanford Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeAwgTfbsUniform/wgEncodeAwgTfbsSydhGm12878Stat3IggmusUniPk.narrowPeak.gz GM12878 ChipSeq STAT3 Peaks narrowPeak Stanford Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeAwgTfbsUniform/wgEncodeAwgTfbsSydhGm12878Tblr1ab24550IggmusUniPk.narrowPeak.gz GM12878 ChipSeq TBLR1_(ab24550) Peaks narrowPeak Stanford Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeAwgTfbsUniform/wgEncodeAwgTfbsSydhGm12878TbpIggmusUniPk.narrowPeak.gz GM12878 ChipSeq TBP Peaks narrowPeak Stanford Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeAwgTfbsUniform/wgEncodeAwgTfbsSydhGm12878Tr4UniPk.narrowPeak.gz GM12878 ChipSeq TR4 Peaks narrowPeak USC Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeAwgTfbsUniform/wgEncodeAwgTfbsSydhGm12878Usf2IggmusUniPk.narrowPeak.gz GM12878 ChipSeq USF2 Peaks narrowPeak Stanford Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeAwgTfbsUniform/wgEncodeAwgTfbsSydhGm12878WhipIggmusUniPk.narrowPeak.gz GM12878 ChipSeq WHIP Peaks narrowPeak Stanford Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeAwgTfbsUniform/wgEncodeAwgTfbsSydhGm12878Yy1UniPk.narrowPeak.gz GM12878 ChipSeq YY1 Peaks narrowPeak USC Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeAwgTfbsUniform/wgEncodeAwgTfbsSydhGm12878Znf143166181apUniPk.narrowPeak.gz GM12878 ChipSeq Znf143_(16618-1-AP) Peaks narrowPeak Stanford Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeAwgTfbsUniform/wgEncodeAwgTfbsSydhGm12878Znf274UniPk.narrowPeak.gz GM12878 ChipSeq ZNF274 Peaks narrowPeak USC Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeAwgTfbsUniform/wgEncodeAwgTfbsSydhGm12878Zzz3UniPk.narrowPeak.gz GM12878 ChipSeq ZZZ3 Peaks narrowPeak Harvard Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeAwgTfbsUniform/wgEncodeAwgTfbsSydhGm12891NfkbTnfaIggrabUniPk.narrowPeak.gz GM12891 ChipSeq NFKB Peaks narrowPeak Stanford Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeAwgTfbsUniform/wgEncodeAwgTfbsSydhGm12891Pol2IggmusUniPk.narrowPeak.gz GM12891 ChipSeq Pol2 Peaks narrowPeak Stanford Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeAwgTfbsUniform/wgEncodeAwgTfbsSydhGm12892NfkbTnfaIggrabUniPk.narrowPeak.gz GM12892 ChipSeq NFKB Peaks narrowPeak Stanford Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeAwgTfbsUniform/wgEncodeAwgTfbsSydhGm12892Pol2IggmusUniPk.narrowPeak.gz GM12892 ChipSeq Pol2 Peaks narrowPeak Stanford Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeAwgTfbsUniform/wgEncodeAwgTfbsSydhGm15510NfkbTnfaIggrabUniPk.narrowPeak.gz GM15510 ChipSeq NFKB Peaks narrowPeak Stanford Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeAwgTfbsUniform/wgEncodeAwgTfbsSydhGm15510Pol2IggmusUniPk.narrowPeak.gz GM15510 ChipSeq Pol2 Peaks narrowPeak Stanford Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeAwgTfbsUniform/wgEncodeAwgTfbsSydhGm18505NfkbTnfaIggrabUniPk.narrowPeak.gz GM18505 ChipSeq NFKB Peaks narrowPeak Stanford Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeAwgTfbsUniform/wgEncodeAwgTfbsSydhGm18505Pol2IggmusUniPk.narrowPeak.gz GM18505 ChipSeq Pol2 Peaks narrowPeak Stanford Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeAwgTfbsUniform/wgEncodeAwgTfbsSydhGm18526NfkbTnfaIggrabUniPk.narrowPeak.gz GM18526 ChipSeq NFKB Peaks narrowPeak Stanford Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeAwgTfbsUniform/wgEncodeAwgTfbsSydhGm18526Pol2IggmusUniPk.narrowPeak.gz GM18526 ChipSeq Pol2 Peaks narrowPeak Stanford Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeAwgTfbsUniform/wgEncodeAwgTfbsSydhGm18951NfkbTnfaIggrabUniPk.narrowPeak.gz GM18951 ChipSeq NFKB Peaks narrowPeak Stanford Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeAwgTfbsUniform/wgEncodeAwgTfbsSydhGm18951Pol2IggmusUniPk.narrowPeak.gz GM18951 ChipSeq Pol2 Peaks narrowPeak Stanford Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeAwgTfbsUniform/wgEncodeAwgTfbsSydhGm19099NfkbTnfaIggrabUniPk.narrowPeak.gz GM19099 ChipSeq NFKB Peaks narrowPeak Stanford Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeAwgTfbsUniform/wgEncodeAwgTfbsSydhGm19099Pol2IggmusUniPk.narrowPeak.gz GM19099 ChipSeq Pol2 Peaks narrowPeak Stanford Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeAwgTfbsUniform/wgEncodeAwgTfbsSydhGm19193NfkbTnfaIggrabUniPk.narrowPeak.gz GM19193 ChipSeq NFKB Peaks narrowPeak Stanford Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeAwgTfbsUniform/wgEncodeAwgTfbsSydhGm19193Pol2IggmusUniPk.narrowPeak.gz GM19193 ChipSeq Pol2 Peaks narrowPeak Stanford Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeAwgTfbsUniform/wgEncodeAwgTfbsSydhH1hescBach1sc14700IggrabUniPk.narrowPeak.gz H1-hESC ChipSeq Bach1_(sc-14700) Peaks narrowPeak Stanford Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeAwgTfbsUniform/wgEncodeAwgTfbsSydhH1hescBrca1IggrabUniPk.narrowPeak.gz H1-hESC ChipSeq BRCA1_(A300-000A) Peaks narrowPeak Stanford Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeAwgTfbsUniform/wgEncodeAwgTfbsSydhH1hescCebpbIggrabUniPk.narrowPeak.gz H1-hESC ChipSeq CEBPB Peaks narrowPeak Stanford Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeAwgTfbsUniform/wgEncodeAwgTfbsSydhH1hescChd1a301218aIggrabUniPk.narrowPeak.gz H1-hESC ChipSeq CHD1_(A301-218A) Peaks narrowPeak Stanford Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeAwgTfbsUniform/wgEncodeAwgTfbsSydhH1hescChd2IggrabUniPk.narrowPeak.gz H1-hESC ChipSeq CHD2_(AB68301) Peaks narrowPeak Stanford Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeAwgTfbsUniform/wgEncodeAwgTfbsSydhH1hescCjunIggrabUniPk.narrowPeak.gz H1-hESC ChipSeq c-Jun Peaks narrowPeak Stanford Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeAwgTfbsUniform/wgEncodeAwgTfbsSydhH1hescCmycIggrabUniPk.narrowPeak.gz H1-hESC ChipSeq c-Myc Peaks narrowPeak Stanford Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeAwgTfbsUniform/wgEncodeAwgTfbsSydhH1hescCtbp2UcdUniPk.narrowPeak.gz H1-hESC ChipSeq CtBP2 Peaks narrowPeak USC Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeAwgTfbsUniform/wgEncodeAwgTfbsSydhH1hescGtf2f1IggrabUniPk.narrowPeak.gz H1-hESC ChipSeq GTF2F1_(AB28179) Peaks narrowPeak Stanford Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeAwgTfbsUniform/wgEncodeAwgTfbsSydhH1hescJundIggrabUniPk.narrowPeak.gz H1-hESC ChipSeq JunD Peaks narrowPeak Stanford Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeAwgTfbsUniform/wgEncodeAwgTfbsSydhH1hescMafkIggrabUniPk.narrowPeak.gz H1-hESC ChipSeq MafK_(ab50322) Peaks narrowPeak Stanford Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeAwgTfbsUniform/wgEncodeAwgTfbsSydhH1hescMaxUcdUniPk.narrowPeak.gz H1-hESC ChipSeq Max Peaks narrowPeak USC Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeAwgTfbsUniform/wgEncodeAwgTfbsSydhH1hescMxi1IggrabUniPk.narrowPeak.gz H1-hESC ChipSeq Mxi1_(AF4185) Peaks narrowPeak Stanford Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeAwgTfbsUniform/wgEncodeAwgTfbsSydhH1hescNrf1IggrabUniPk.narrowPeak.gz H1-hESC ChipSeq Nrf1 Peaks narrowPeak Stanford Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeAwgTfbsUniform/wgEncodeAwgTfbsSydhH1hescRad21IggrabUniPk.narrowPeak.gz H1-hESC ChipSeq Rad21 Peaks narrowPeak Stanford Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeAwgTfbsUniform/wgEncodeAwgTfbsSydhH1hescRfx5200401194IggrabUniPk.narrowPeak.gz H1-hESC ChipSeq RFX5_(200-401-194) Peaks narrowPeak Stanford Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeAwgTfbsUniform/wgEncodeAwgTfbsSydhH1hescSin3anb6001263IggrabUniPk.narrowPeak.gz H1-hESC ChipSeq SIN3A_(NB600-1263) Peaks narrowPeak Stanford Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeAwgTfbsUniform/wgEncodeAwgTfbsSydhH1hescSuz12UcdUniPk.narrowPeak.gz H1-hESC ChipSeq SUZ12 Peaks narrowPeak USC Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeAwgTfbsUniform/wgEncodeAwgTfbsSydhH1hescTbpIggrabUniPk.narrowPeak.gz H1-hESC ChipSeq TBP Peaks narrowPeak Stanford Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeAwgTfbsUniform/wgEncodeAwgTfbsSydhH1hescUsf2IggrabUniPk.narrowPeak.gz H1-hESC ChipSeq USF2 Peaks narrowPeak Stanford Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeAwgTfbsUniform/wgEncodeAwgTfbsSydhH1hescZnf143IggrabUniPk.narrowPeak.gz H1-hESC ChipSeq Znf143_(16618-1-AP) Peaks narrowPeak Stanford Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeAwgTfbsUniform/wgEncodeAwgTfbsSydhHct116Pol2UcdUniPk.narrowPeak.gz HCT-116 ChipSeq Pol2 Peaks narrowPeak USC Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeAwgTfbsUniform/wgEncodeAwgTfbsSydhHct116Tcf7l2UcdUniPk.narrowPeak.gz HCT-116 ChipSeq TCF7L2 Peaks narrowPeak USC Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeAwgTfbsUniform/wgEncodeAwgTfbsSydhHek293Elk4UcdUniPk.narrowPeak.gz HEK293 ChipSeq ELK4 Peaks narrowPeak USC Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeAwgTfbsUniform/wgEncodeAwgTfbsSydhHek293Kap1UcdUniPk.narrowPeak.gz HEK293 ChipSeq KAP1 Peaks narrowPeak USC Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeAwgTfbsUniform/wgEncodeAwgTfbsSydhHek293Pol2UniPk.narrowPeak.gz HEK293 ChipSeq Pol2 Peaks narrowPeak Yale Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeAwgTfbsUniform/wgEncodeAwgTfbsSydhHek293Tcf7l2UcdUniPk.narrowPeak.gz HEK293 ChipSeq TCF7L2 Peaks narrowPeak USC Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeAwgTfbsUniform/wgEncodeAwgTfbsSydhHek293tZnf263UcdUniPk.narrowPeak.gz HEK293-T-REx ChipSeq ZNF263 Peaks narrowPeak USC Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeAwgTfbsUniform/wgEncodeAwgTfbsSydhHelas3Ap2alphaUniPk.narrowPeak.gz HeLa-S3 ChipSeq AP-2alpha Peaks narrowPeak USC Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeAwgTfbsUniform/wgEncodeAwgTfbsSydhHelas3Ap2gammaUniPk.narrowPeak.gz HeLa-S3 ChipSeq AP-2gamma Peaks narrowPeak USC Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeAwgTfbsUniform/wgEncodeAwgTfbsSydhHelas3Baf155IggmusUniPk.narrowPeak.gz HeLa-S3 ChipSeq BAF155 Peaks narrowPeak Stanford Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeAwgTfbsUniform/wgEncodeAwgTfbsSydhHelas3Baf170IggmusUniPk.narrowPeak.gz HeLa-S3 ChipSeq BAF170 Peaks narrowPeak Stanford Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeAwgTfbsUniform/wgEncodeAwgTfbsSydhHelas3Bdp1UniPk.narrowPeak.gz HeLa-S3 ChipSeq BDP1 Peaks narrowPeak Harvard Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeAwgTfbsUniform/wgEncodeAwgTfbsSydhHelas3Brca1a300IggrabUniPk.narrowPeak.gz HeLa-S3 ChipSeq BRCA1_(A300-000A) Peaks narrowPeak Stanford Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeAwgTfbsUniform/wgEncodeAwgTfbsSydhHelas3Brf1UniPk.narrowPeak.gz HeLa-S3 ChipSeq BRF1 Peaks narrowPeak Harvard Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeAwgTfbsUniform/wgEncodeAwgTfbsSydhHelas3Brf2UniPk.narrowPeak.gz HeLa-S3 ChipSeq BRF2 Peaks narrowPeak Harvard Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeAwgTfbsUniform/wgEncodeAwgTfbsSydhHelas3Brg1IggmusUniPk.narrowPeak.gz HeLa-S3 ChipSeq Brg1 Peaks narrowPeak Yale Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeAwgTfbsUniform/wgEncodeAwgTfbsSydhHelas3CebpbIggrabUniPk.narrowPeak.gz HeLa-S3 ChipSeq CEBPB Peaks narrowPeak Stanford Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeAwgTfbsUniform/wgEncodeAwgTfbsSydhHelas3CfosUniPk.narrowPeak.gz HeLa-S3 ChipSeq c-Fos Peaks narrowPeak Yale Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeAwgTfbsUniform/wgEncodeAwgTfbsSydhHelas3Chd2IggrabUniPk.narrowPeak.gz HeLa-S3 ChipSeq CHD2_(AB68301) Peaks narrowPeak Stanford Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeAwgTfbsUniform/wgEncodeAwgTfbsSydhHelas3CjunIggrabUniPk.narrowPeak.gz HeLa-S3 ChipSeq c-Jun Peaks narrowPeak Stanford Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeAwgTfbsUniform/wgEncodeAwgTfbsSydhHelas3CmycUniPk.narrowPeak.gz HeLa-S3 ChipSeq c-Myc Peaks narrowPeak Yale Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeAwgTfbsUniform/wgEncodeAwgTfbsSydhHelas3Corestsc30189IggrabUniPk.narrowPeak.gz HeLa-S3 ChipSeq COREST_(sc-30189) Peaks narrowPeak Stanford Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeAwgTfbsUniform/wgEncodeAwgTfbsSydhHelas3E2f1UniPk.narrowPeak.gz HeLa-S3 ChipSeq E2F1 Peaks narrowPeak USC Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeAwgTfbsUniform/wgEncodeAwgTfbsSydhHelas3E2f4UniPk.narrowPeak.gz HeLa-S3 ChipSeq E2F4 Peaks narrowPeak USC Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeAwgTfbsUniform/wgEncodeAwgTfbsSydhHelas3E2f6UniPk.narrowPeak.gz HeLa-S3 ChipSeq E2F6 Peaks narrowPeak USC Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeAwgTfbsUniform/wgEncodeAwgTfbsSydhHelas3Elk112771IggrabUniPk.narrowPeak.gz HeLa-S3 ChipSeq ELK1_(1277-1) Peaks narrowPeak Stanford Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeAwgTfbsUniform/wgEncodeAwgTfbsSydhHelas3Elk4UcdUniPk.narrowPeak.gz HeLa-S3 ChipSeq ELK4 Peaks narrowPeak USC Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeAwgTfbsUniform/wgEncodeAwgTfbsSydhHelas3Gtf2f1ab28179IggrabUniPk.narrowPeak.gz HeLa-S3 ChipSeq GTF2F1_(AB28179) Peaks narrowPeak Stanford Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeAwgTfbsUniform/wgEncodeAwgTfbsSydhHelas3Hae2f1UniPk.narrowPeak.gz HeLa-S3 ChipSeq HA-E2F1 Peaks narrowPeak USC Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeAwgTfbsUniform/wgEncodeAwgTfbsSydhHelas3Ini1IggmusUniPk.narrowPeak.gz HeLa-S3 ChipSeq Ini1 Peaks narrowPeak Stanford Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeAwgTfbsUniform/wgEncodeAwgTfbsSydhHelas3Irf3IggrabUniPk.narrowPeak.gz HeLa-S3 ChipSeq IRF3 Peaks narrowPeak Stanford Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeAwgTfbsUniform/wgEncodeAwgTfbsSydhHelas3JundIggrabUniPk.narrowPeak.gz HeLa-S3 ChipSeq JunD Peaks narrowPeak Stanford Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeAwgTfbsUniform/wgEncodeAwgTfbsSydhHelas3MafkIggrabUniPk.narrowPeak.gz HeLa-S3 ChipSeq MafK_(ab50322) Peaks narrowPeak Stanford Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeAwgTfbsUniform/wgEncodeAwgTfbsSydhHelas3MaxIggrabUniPk.narrowPeak.gz HeLa-S3 ChipSeq Max Peaks narrowPeak Stanford Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeAwgTfbsUniform/wgEncodeAwgTfbsSydhHelas3Mazab85725IggrabUniPk.narrowPeak.gz HeLa-S3 ChipSeq MAZ_(ab85725) Peaks narrowPeak Stanford Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeAwgTfbsUniform/wgEncodeAwgTfbsSydhHelas3Mxi1af4185IggrabUniPk.narrowPeak.gz HeLa-S3 ChipSeq Mxi1_(AF4185) Peaks narrowPeak Stanford Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeAwgTfbsUniform/wgEncodeAwgTfbsSydhHelas3NfyaIggrabUniPk.narrowPeak.gz HeLa-S3 ChipSeq NF-YA Peaks narrowPeak Harvard Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeAwgTfbsUniform/wgEncodeAwgTfbsSydhHelas3NfybIggrabUniPk.narrowPeak.gz HeLa-S3 ChipSeq NF-YB Peaks narrowPeak Harvard Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeAwgTfbsUniform/wgEncodeAwgTfbsSydhHelas3Nrf1IggmusUniPk.narrowPeak.gz HeLa-S3 ChipSeq Nrf1 Peaks narrowPeak Stanford Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeAwgTfbsUniform/wgEncodeAwgTfbsSydhHelas3P300sc584sc584IggrabUniPk.narrowPeak.gz HeLa-S3 ChipSeq p300_(SC-584) Peaks narrowPeak Stanford Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeAwgTfbsUniform/wgEncodeAwgTfbsSydhHelas3Pol2UniPk.narrowPeak.gz HeLa-S3 ChipSeq Pol2 Peaks narrowPeak Yale Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeAwgTfbsUniform/wgEncodeAwgTfbsSydhHelas3Pol2s2IggrabUniPk.narrowPeak.gz HeLa-S3 ChipSeq Pol2(phosphoS2) Peaks narrowPeak Stanford Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeAwgTfbsUniform/wgEncodeAwgTfbsSydhHelas3Prdm19115IggrabUniPk.narrowPeak.gz HeLa-S3 ChipSeq PRDM1_(9115) Peaks narrowPeak Stanford Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeAwgTfbsUniform/wgEncodeAwgTfbsSydhHelas3Rad21IggrabUniPk.narrowPeak.gz HeLa-S3 ChipSeq Rad21 Peaks narrowPeak Stanford Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeAwgTfbsUniform/wgEncodeAwgTfbsSydhHelas3Rfx5200401194IggrabUniPk.narrowPeak.gz HeLa-S3 ChipSeq RFX5_(200-401-194) Peaks narrowPeak Stanford Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeAwgTfbsUniform/wgEncodeAwgTfbsSydhHelas3Rpc155UniPk.narrowPeak.gz HeLa-S3 ChipSeq RPC155 Peaks narrowPeak Harvard Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeAwgTfbsUniform/wgEncodeAwgTfbsSydhHelas3Smc3ab9263IggrabUniPk.narrowPeak.gz HeLa-S3 ChipSeq SMC3_(ab9263) Peaks narrowPeak Stanford Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeAwgTfbsUniform/wgEncodeAwgTfbsSydhHelas3Spt20UniPk.narrowPeak.gz HeLa-S3 ChipSeq SPT20 Peaks narrowPeak Stanford Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeAwgTfbsUniform/wgEncodeAwgTfbsSydhHelas3Stat1Ifng30UniPk.narrowPeak.gz HeLa-S3 ChipSeq STAT1 Peaks narrowPeak Yale Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeAwgTfbsUniform/wgEncodeAwgTfbsSydhHelas3Stat3IggrabUniPk.narrowPeak.gz HeLa-S3 ChipSeq STAT3 Peaks narrowPeak Stanford Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeAwgTfbsUniform/wgEncodeAwgTfbsSydhHelas3TbpIggrabUniPk.narrowPeak.gz HeLa-S3 ChipSeq TBP Peaks narrowPeak Stanford Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeAwgTfbsUniform/wgEncodeAwgTfbsSydhHelas3Tcf7l2UcdUniPk.narrowPeak.gz HeLa-S3 ChipSeq TCF7L2 Peaks narrowPeak USC Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeAwgTfbsUniform/wgEncodeAwgTfbsSydhHelas3Tcf7l2c9b92565UcdUniPk.narrowPeak.gz HeLa-S3 ChipSeq TCF7L2_C9B9_(2565) Peaks narrowPeak USC Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeAwgTfbsUniform/wgEncodeAwgTfbsSydhHelas3Tf3c110UniPk.narrowPeak.gz HeLa-S3 ChipSeq TFIIIC-110 Peaks narrowPeak Harvard Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeAwgTfbsUniform/wgEncodeAwgTfbsSydhHelas3Tr4UniPk.narrowPeak.gz HeLa-S3 ChipSeq TR4 Peaks narrowPeak USC Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeAwgTfbsUniform/wgEncodeAwgTfbsSydhHelas3Usf2IggmusUniPk.narrowPeak.gz HeLa-S3 ChipSeq USF2 Peaks narrowPeak Stanford Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeAwgTfbsUniform/wgEncodeAwgTfbsSydhHelas3Zkscan1hpa006672IggrabUniPk.narrowPeak.gz HeLa-S3 ChipSeq ZKSCAN1_(HPA006672) Peaks narrowPeak Stanford Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeAwgTfbsUniform/wgEncodeAwgTfbsSydhHelas3Znf143IggrabUniPk.narrowPeak.gz HeLa-S3 ChipSeq Znf143_(16618-1-AP) Peaks narrowPeak Stanford Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeAwgTfbsUniform/wgEncodeAwgTfbsSydhHelas3Znf274UcdUniPk.narrowPeak.gz HeLa-S3 ChipSeq ZNF274 Peaks narrowPeak USC Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeAwgTfbsUniform/wgEncodeAwgTfbsSydhHelas3Zzz3UniPk.narrowPeak.gz HeLa-S3 ChipSeq ZZZ3 Peaks narrowPeak Harvard Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeAwgTfbsUniform/wgEncodeAwgTfbsSydhHepg2Arid3anb100279IggrabUniPk.narrowPeak.gz HepG2 ChipSeq ARID3A_(NB100-279) Peaks narrowPeak Stanford Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeAwgTfbsUniform/wgEncodeAwgTfbsSydhHepg2Bhlhe40cIggrabUniPk.narrowPeak.gz HepG2 ChipSeq BHLHE40_(NB100-1800) Peaks narrowPeak Stanford Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeAwgTfbsUniform/wgEncodeAwgTfbsSydhHepg2Brca1a300IggrabUniPk.narrowPeak.gz HepG2 ChipSeq BRCA1_(A300-000A) Peaks narrowPeak Stanford Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeAwgTfbsUniform/wgEncodeAwgTfbsSydhHepg2CebpbForsklnUniPk.narrowPeak.gz HepG2 ChipSeq CEBPB Peaks narrowPeak Stanford Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeAwgTfbsUniform/wgEncodeAwgTfbsSydhHepg2CebpbIggrabUniPk.narrowPeak.gz HepG2 ChipSeq CEBPB Peaks narrowPeak Stanford Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeAwgTfbsUniform/wgEncodeAwgTfbsSydhHepg2Chd2ab68301IggrabUniPk.narrowPeak.gz HepG2 ChipSeq CHD2_(AB68301) Peaks narrowPeak Stanford Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeAwgTfbsUniform/wgEncodeAwgTfbsSydhHepg2CjunIggrabUniPk.narrowPeak.gz HepG2 ChipSeq c-Jun Peaks narrowPeak Stanford Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeAwgTfbsUniform/wgEncodeAwgTfbsSydhHepg2Corestsc30189IggrabUniPk.narrowPeak.gz HepG2 ChipSeq COREST_(sc-30189) Peaks narrowPeak Stanford Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeAwgTfbsUniform/wgEncodeAwgTfbsSydhHepg2ErraForsklnUniPk.narrowPeak.gz HepG2 ChipSeq ERRA Peaks narrowPeak Stanford Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeAwgTfbsUniform/wgEncodeAwgTfbsSydhHepg2Grp20ForsklnUniPk.narrowPeak.gz HepG2 ChipSeq GRp20 Peaks narrowPeak Stanford Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeAwgTfbsUniform/wgEncodeAwgTfbsSydhHepg2Hnf4aForsklnUniPk.narrowPeak.gz HepG2 ChipSeq HNF4A Peaks narrowPeak Stanford Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeAwgTfbsUniform/wgEncodeAwgTfbsSydhHepg2Hsf1ForsklnUniPk.narrowPeak.gz HepG2 ChipSeq HSF1 Peaks narrowPeak Stanford Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeAwgTfbsUniform/wgEncodeAwgTfbsSydhHepg2Irf3IggrabUniPk.narrowPeak.gz HepG2 ChipSeq IRF3 Peaks narrowPeak Stanford Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeAwgTfbsUniform/wgEncodeAwgTfbsSydhHepg2JundIggrabUniPk.narrowPeak.gz HepG2 ChipSeq JunD Peaks narrowPeak Stanford Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeAwgTfbsUniform/wgEncodeAwgTfbsSydhHepg2Maffm8194IggrabUniPk.narrowPeak.gz HepG2 ChipSeq MafF_(M8194) Peaks narrowPeak Stanford Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeAwgTfbsUniform/wgEncodeAwgTfbsSydhHepg2Mafkab50322IggrabUniPk.narrowPeak.gz HepG2 ChipSeq MafK_(ab50322) Peaks narrowPeak Stanford Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeAwgTfbsUniform/wgEncodeAwgTfbsSydhHepg2Mafksc477IggrabUniPk.narrowPeak.gz HepG2 ChipSeq MafK_(SC-477) Peaks narrowPeak Stanford Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeAwgTfbsUniform/wgEncodeAwgTfbsSydhHepg2MaxIggrabUniPk.narrowPeak.gz HepG2 ChipSeq Max Peaks narrowPeak Stanford Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeAwgTfbsUniform/wgEncodeAwgTfbsSydhHepg2Mazab85725IggrabUniPk.narrowPeak.gz HepG2 ChipSeq MAZ_(ab85725) Peaks narrowPeak Stanford Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeAwgTfbsUniform/wgEncodeAwgTfbsSydhHepg2Mxi1UniPk.narrowPeak.gz HepG2 ChipSeq Mxi1_(AF4185) Peaks narrowPeak Stanford Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeAwgTfbsUniform/wgEncodeAwgTfbsSydhHepg2Nrf1IggrabUniPk.narrowPeak.gz HepG2 ChipSeq Nrf1 Peaks narrowPeak Stanford Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeAwgTfbsUniform/wgEncodeAwgTfbsSydhHepg2P300sc582IggrabUniPk.narrowPeak.gz HepG2 ChipSeq p300_(SC-584) Peaks narrowPeak Stanford Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeAwgTfbsUniform/wgEncodeAwgTfbsSydhHepg2Pgc1aForsklnUniPk.narrowPeak.gz HepG2 ChipSeq PGC1A Peaks narrowPeak Stanford Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeAwgTfbsUniform/wgEncodeAwgTfbsSydhHepg2Pol2ForsklnUniPk.narrowPeak.gz HepG2 ChipSeq Pol2 Peaks narrowPeak Stanford Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeAwgTfbsUniform/wgEncodeAwgTfbsSydhHepg2Pol2IggrabUniPk.narrowPeak.gz HepG2 ChipSeq Pol2 Peaks narrowPeak Stanford Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeAwgTfbsUniform/wgEncodeAwgTfbsSydhHepg2Pol2s2IggrabUniPk.narrowPeak.gz HepG2 ChipSeq Pol2(phosphoS2) Peaks narrowPeak Stanford Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeAwgTfbsUniform/wgEncodeAwgTfbsSydhHepg2Rad21IggrabUniPk.narrowPeak.gz HepG2 ChipSeq Rad21 Peaks narrowPeak Stanford Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeAwgTfbsUniform/wgEncodeAwgTfbsSydhHepg2Rfx5200401194IggrabUniPk.narrowPeak.gz HepG2 ChipSeq RFX5_(200-401-194) Peaks narrowPeak Stanford Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeAwgTfbsUniform/wgEncodeAwgTfbsSydhHepg2Smc3ab9263IggrabUniPk.narrowPeak.gz HepG2 ChipSeq SMC3_(ab9263) Peaks narrowPeak Stanford Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeAwgTfbsUniform/wgEncodeAwgTfbsSydhHepg2TbpIggrabUniPk.narrowPeak.gz HepG2 ChipSeq TBP Peaks narrowPeak Stanford Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeAwgTfbsUniform/wgEncodeAwgTfbsSydhHepg2Tcf7l2UcdUniPk.narrowPeak.gz HepG2 ChipSeq TCF7L2 Peaks narrowPeak USC Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeAwgTfbsUniform/wgEncodeAwgTfbsSydhHepg2Tr4UcdUniPk.narrowPeak.gz HepG2 ChipSeq TR4 Peaks narrowPeak USC Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeAwgTfbsUniform/wgEncodeAwgTfbsSydhHepg2Usf2IggrabUniPk.narrowPeak.gz HepG2 ChipSeq USF2 Peaks narrowPeak Stanford Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeAwgTfbsUniform/wgEncodeAwgTfbsSydhHepg2Znf274UcdUniPk.narrowPeak.gz HepG2 ChipSeq ZNF274 Peaks narrowPeak USC Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeAwgTfbsUniform/wgEncodeAwgTfbsSydhHuvecCfosUcdUniPk.narrowPeak.gz HUVEC ChipSeq c-Fos Peaks narrowPeak USC Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeAwgTfbsUniform/wgEncodeAwgTfbsSydhHuvecCjunUniPk.narrowPeak.gz HUVEC ChipSeq c-Jun Peaks narrowPeak Stanford Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeAwgTfbsUniform/wgEncodeAwgTfbsSydhHuvecGata2UcdUniPk.narrowPeak.gz HUVEC ChipSeq GATA-2 Peaks narrowPeak USC Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeAwgTfbsUniform/wgEncodeAwgTfbsSydhHuvecMaxUniPk.narrowPeak.gz HUVEC ChipSeq Max Peaks narrowPeak Stanford Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeAwgTfbsUniform/wgEncodeAwgTfbsSydhHuvecPol2UniPk.narrowPeak.gz HUVEC ChipSeq Pol2 Peaks narrowPeak Stanford Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeAwgTfbsUniform/wgEncodeAwgTfbsSydhImr90CebpbIggrabUniPk.narrowPeak.gz IMR90 ChipSeq CEBPB Peaks narrowPeak Stanford Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeAwgTfbsUniform/wgEncodeAwgTfbsSydhImr90CtcfbIggrabUniPk.narrowPeak.gz IMR90 ChipSeq CTCF_(SC-15914) Peaks narrowPeak Stanford Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeAwgTfbsUniform/wgEncodeAwgTfbsSydhImr90MafkIggrabUniPk.narrowPeak.gz IMR90 ChipSeq MafK_(ab50322) Peaks narrowPeak Stanford Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeAwgTfbsUniform/wgEncodeAwgTfbsSydhImr90Pol2IggrabUniPk.narrowPeak.gz IMR90 ChipSeq Pol2 Peaks narrowPeak Stanford Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeAwgTfbsUniform/wgEncodeAwgTfbsSydhImr90Rad21IggrabUniPk.narrowPeak.gz IMR90 ChipSeq Rad21 Peaks narrowPeak Stanford Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeAwgTfbsUniform/wgEncodeAwgTfbsSydhK562Arid3asc8821IggrabUniPk.narrowPeak.gz K562 ChipSeq ARID3A_(sc-8821) Peaks narrowPeak Stanford Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeAwgTfbsUniform/wgEncodeAwgTfbsSydhK562Atf106325UniPk.narrowPeak.gz K562 ChipSeq ATF1_(06-325) Peaks narrowPeak Harvard Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeAwgTfbsUniform/wgEncodeAwgTfbsSydhK562Atf3UniPk.narrowPeak.gz K562 ChipSeq ATF3 Peaks narrowPeak Harvard Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeAwgTfbsUniform/wgEncodeAwgTfbsSydhK562Bach1sc14700IggrabUniPk.narrowPeak.gz K562 ChipSeq Bach1_(sc-14700) Peaks narrowPeak Stanford Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeAwgTfbsUniform/wgEncodeAwgTfbsSydhK562Bdp1UniPk.narrowPeak.gz K562 ChipSeq BDP1 Peaks narrowPeak Harvard Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeAwgTfbsUniform/wgEncodeAwgTfbsSydhK562Bhlhe40nb100IggrabUniPk.narrowPeak.gz K562 ChipSeq BHLHE40_(NB100-1800) Peaks narrowPeak Stanford Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeAwgTfbsUniform/wgEncodeAwgTfbsSydhK562Brf1UniPk.narrowPeak.gz K562 ChipSeq BRF1 Peaks narrowPeak Harvard Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeAwgTfbsUniform/wgEncodeAwgTfbsSydhK562Brf2UniPk.narrowPeak.gz K562 ChipSeq BRF2 Peaks narrowPeak Harvard Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeAwgTfbsUniform/wgEncodeAwgTfbsSydhK562Brg1IggmusUniPk.narrowPeak.gz K562 ChipSeq Brg1 Peaks narrowPeak Stanford Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeAwgTfbsUniform/wgEncodeAwgTfbsSydhK562Ccnt2UniPk.narrowPeak.gz K562 ChipSeq CCNT2 Peaks narrowPeak Harvard Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeAwgTfbsUniform/wgEncodeAwgTfbsSydhK562CebpbIggrabUniPk.narrowPeak.gz K562 ChipSeq CEBPB Peaks narrowPeak Stanford Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeAwgTfbsUniform/wgEncodeAwgTfbsSydhK562CfosUniPk.narrowPeak.gz K562 ChipSeq c-Fos Peaks narrowPeak Yale Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeAwgTfbsUniform/wgEncodeAwgTfbsSydhK562Chd2ab68301IggrabUniPk.narrowPeak.gz K562 ChipSeq CHD2_(AB68301) Peaks narrowPeak Stanford Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeAwgTfbsUniform/wgEncodeAwgTfbsSydhK562CjunIfna30UniPk.narrowPeak.gz K562 ChipSeq c-Jun Peaks narrowPeak Stanford Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeAwgTfbsUniform/wgEncodeAwgTfbsSydhK562CjunIfna6hUniPk.narrowPeak.gz K562 ChipSeq c-Jun Peaks narrowPeak Yale Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeAwgTfbsUniform/wgEncodeAwgTfbsSydhK562CjunIfng30UniPk.narrowPeak.gz K562 ChipSeq c-Jun Peaks narrowPeak Yale Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeAwgTfbsUniform/wgEncodeAwgTfbsSydhK562CjunIfng6hUniPk.narrowPeak.gz K562 ChipSeq c-Jun Peaks narrowPeak Yale Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeAwgTfbsUniform/wgEncodeAwgTfbsSydhK562CjunUniPk.narrowPeak.gz K562 ChipSeq c-Jun Peaks narrowPeak Yale Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeAwgTfbsUniform/wgEncodeAwgTfbsSydhK562CmycIfna30UniPk.narrowPeak.gz K562 ChipSeq c-Myc Peaks narrowPeak Yale Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeAwgTfbsUniform/wgEncodeAwgTfbsSydhK562CmycIfna6hUniPk.narrowPeak.gz K562 ChipSeq c-Myc Peaks narrowPeak Yale Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeAwgTfbsUniform/wgEncodeAwgTfbsSydhK562CmycIfng30UniPk.narrowPeak.gz K562 ChipSeq c-Myc Peaks narrowPeak Stanford Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeAwgTfbsUniform/wgEncodeAwgTfbsSydhK562CmycIfng6hUniPk.narrowPeak.gz K562 ChipSeq c-Myc Peaks narrowPeak Yale Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeAwgTfbsUniform/wgEncodeAwgTfbsSydhK562CmycIggrabUniPk.narrowPeak.gz K562 ChipSeq c-Myc Peaks narrowPeak Stanford Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeAwgTfbsUniform/wgEncodeAwgTfbsSydhK562CmycUniPk.narrowPeak.gz K562 ChipSeq c-Myc Peaks narrowPeak Yale Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeAwgTfbsUniform/wgEncodeAwgTfbsSydhK562Corestab24166IggrabUniPk.narrowPeak.gz K562 ChipSeq COREST_(ab24166) Peaks narrowPeak Stanford Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeAwgTfbsUniform/wgEncodeAwgTfbsSydhK562Corestsc30189IggrabUniPk.narrowPeak.gz K562 ChipSeq COREST_(sc-30189) Peaks narrowPeak Stanford Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeAwgTfbsUniform/wgEncodeAwgTfbsSydhK562CtcfbIggrabUniPk.narrowPeak.gz K562 ChipSeq CTCF_(SC-15914) Peaks narrowPeak Stanford Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeAwgTfbsUniform/wgEncodeAwgTfbsSydhK562E2f4UcdUniPk.narrowPeak.gz K562 ChipSeq E2F4 Peaks narrowPeak USC Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeAwgTfbsUniform/wgEncodeAwgTfbsSydhK562E2f6UcdUniPk.narrowPeak.gz K562 ChipSeq E2F6 Peaks narrowPeak USC Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeAwgTfbsUniform/wgEncodeAwgTfbsSydhK562Elk112771IggrabUniPk.narrowPeak.gz K562 ChipSeq ELK1_(1277-1) Peaks narrowPeak Stanford Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeAwgTfbsUniform/wgEncodeAwgTfbsSydhK562Gata1UcdUniPk.narrowPeak.gz K562 ChipSeq GATA-1 Peaks narrowPeak USC Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeAwgTfbsUniform/wgEncodeAwgTfbsSydhK562Gata2UcdUniPk.narrowPeak.gz K562 ChipSeq GATA-2 Peaks narrowPeak USC Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeAwgTfbsUniform/wgEncodeAwgTfbsSydhK562Gtf2bUniPk.narrowPeak.gz K562 ChipSeq GTF2B Peaks narrowPeak Harvard Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeAwgTfbsUniform/wgEncodeAwgTfbsSydhK562Gtf2f1ab28179IggrabUniPk.narrowPeak.gz K562 ChipSeq GTF2F1_(AB28179) Peaks narrowPeak Stanford Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeAwgTfbsUniform/wgEncodeAwgTfbsSydhK562Hmgn3UniPk.narrowPeak.gz K562 ChipSeq HMGN3 Peaks narrowPeak Harvard Data 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http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeAwgTfbsUniform/wgEncodeAwgTfbsSydhK562NfybUniPk.narrowPeak.gz K562 ChipSeq NF-YB Peaks narrowPeak Stanford Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeAwgTfbsUniform/wgEncodeAwgTfbsSydhK562Nrf1IggrabUniPk.narrowPeak.gz K562 ChipSeq Nrf1 Peaks narrowPeak Stanford Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeAwgTfbsUniform/wgEncodeAwgTfbsSydhK562P300IggrabUniPk.narrowPeak.gz K562 ChipSeq p300 Peaks narrowPeak Stanford Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeAwgTfbsUniform/wgEncodeAwgTfbsSydhK562Pol2Ifna30UniPk.narrowPeak.gz K562 ChipSeq Pol2 Peaks narrowPeak Yale Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeAwgTfbsUniform/wgEncodeAwgTfbsSydhK562Pol2Ifna6hUniPk.narrowPeak.gz K562 ChipSeq Pol2 Peaks narrowPeak Yale Data 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http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeAwgTfbsUniform/wgEncodeAwgTfbsSydhMcf10aesE2f4TamHvdUniPk.narrowPeak.gz MCF10A-Er-Src ChipSeq E2F4 Peaks narrowPeak Harvard Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeAwgTfbsUniform/wgEncodeAwgTfbsSydhMcf10aesPol2Etoh01UniPk.narrowPeak.gz MCF10A-Er-Src ChipSeq Pol2 Peaks narrowPeak Harvard Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeAwgTfbsUniform/wgEncodeAwgTfbsSydhMcf10aesPol2TamUniPk.narrowPeak.gz MCF10A-Er-Src ChipSeq Pol2 Peaks narrowPeak Harvard Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeAwgTfbsUniform/wgEncodeAwgTfbsSydhMcf10aesStat3Etoh01UniPk.narrowPeak.gz MCF10A-Er-Src ChipSeq STAT3 Peaks narrowPeak Harvard Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeAwgTfbsUniform/wgEncodeAwgTfbsSydhMcf10aesStat3Etoh01bUniPk.narrowPeak.gz MCF10A-Er-Src ChipSeq STAT3 Peaks narrowPeak Harvard Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeAwgTfbsUniform/wgEncodeAwgTfbsSydhMcf10aesStat3Etoh01cUniPk.narrowPeak.gz MCF10A-Er-Src ChipSeq STAT3 Peaks narrowPeak Harvard Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeAwgTfbsUniform/wgEncodeAwgTfbsSydhMcf10aesStat3Tam112hHvdUniPk.narrowPeak.gz MCF10A-Er-Src ChipSeq STAT3 Peaks narrowPeak Harvard Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeAwgTfbsUniform/wgEncodeAwgTfbsSydhMcf10aesStat3TamUniPk.narrowPeak.gz MCF10A-Er-Src ChipSeq STAT3 Peaks narrowPeak Harvard Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeAwgTfbsUniform/wgEncodeAwgTfbsSydhMcf7Gata3UcdUniPk.narrowPeak.gz MCF-7 ChipSeq GATA3_(SC-268) Peaks narrowPeak USC Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeAwgTfbsUniform/wgEncodeAwgTfbsSydhMcf7Gata3sc269UcdUniPk.narrowPeak.gz MCF-7 ChipSeq GATA3_(SC-269) Peaks narrowPeak USC Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeAwgTfbsUniform/wgEncodeAwgTfbsSydhMcf7Hae2f1UcdUniPk.narrowPeak.gz MCF-7 ChipSeq HA-E2F1 Peaks narrowPeak USC Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeAwgTfbsUniform/wgEncodeAwgTfbsSydhMcf7Tcf7l2UcdUniPk.narrowPeak.gz MCF-7 ChipSeq TCF7L2 Peaks narrowPeak USC Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeAwgTfbsUniform/wgEncodeAwgTfbsSydhMcf7Znf217UcdUniPk.narrowPeak.gz MCF-7 ChipSeq ZNF217 Peaks narrowPeak USC Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeAwgTfbsUniform/wgEncodeAwgTfbsSydhNb4CmycUniPk.narrowPeak.gz NB4 ChipSeq c-Myc Peaks narrowPeak Stanford Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeAwgTfbsUniform/wgEncodeAwgTfbsSydhNb4MaxUniPk.narrowPeak.gz NB4 ChipSeq Max Peaks narrowPeak Stanford Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeAwgTfbsUniform/wgEncodeAwgTfbsSydhNb4Pol2UniPk.narrowPeak.gz NB4 ChipSeq Pol2 Peaks narrowPeak Yale Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeAwgTfbsUniform/wgEncodeAwgTfbsSydhNt2d1Suz12UcdUniPk.narrowPeak.gz NT2-D1 ChipSeq SUZ12 Peaks narrowPeak USC Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeAwgTfbsUniform/wgEncodeAwgTfbsSydhNt2d1Yy1UcdUniPk.narrowPeak.gz NT2-D1 ChipSeq YY1 Peaks narrowPeak USC Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeAwgTfbsUniform/wgEncodeAwgTfbsSydhNt2d1Znf274UcdUniPk.narrowPeak.gz NT2-D1 ChipSeq ZNF274 Peaks narrowPeak USC Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeAwgTfbsUniform/wgEncodeAwgTfbsSydhPanc1Tcf7l2UcdUniPk.narrowPeak.gz PANC-1 ChipSeq TCF7L2 Peaks narrowPeak USC Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeAwgTfbsUniform/wgEncodeAwgTfbsSydhPbdeGata1UcdUniPk.narrowPeak.gz PBDE ChipSeq GATA-1 Peaks narrowPeak USC Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeAwgTfbsUniform/wgEncodeAwgTfbsSydhPbdePol2UcdUniPk.narrowPeak.gz PBDE ChipSeq Pol2 Peaks narrowPeak USC Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeAwgTfbsUniform/wgEncodeAwgTfbsSydhPbdefetalGata1UcdUniPk.narrowPeak.gz PBDEFetal ChipSeq GATA-1 Peaks narrowPeak USC Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeAwgTfbsUniform/wgEncodeAwgTfbsSydhRajiPol2UcdUniPk.narrowPeak.gz Raji ChipSeq Pol2 Peaks narrowPeak USC Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeAwgTfbsUniform/wgEncodeAwgTfbsSydhShsy5yGata2UcdUniPk.narrowPeak.gz SH-SY5Y ChipSeq GATA-2 Peaks narrowPeak USC Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeAwgTfbsUniform/wgEncodeAwgTfbsSydhShsy5yGata3sc269sc269UcdUniPk.narrowPeak.gz SH-SY5Y ChipSeq GATA3_(SC-269) Peaks narrowPeak USC Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeAwgTfbsUniform/wgEncodeAwgTfbsSydhU2osKap1UcdUniPk.narrowPeak.gz U2OS ChipSeq KAP1 Peaks narrowPeak USC Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeAwgTfbsUniform/wgEncodeAwgTfbsSydhU2osSetdb1UcdUniPk.narrowPeak.gz U2OS ChipSeq SETDB1 Peaks narrowPeak USC Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeAwgTfbsUniform/wgEncodeAwgTfbsUchicagoK562EfosUniPk.narrowPeak.gz K562 ChipSeq eGFP-FOS Peaks narrowPeak UChicago Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeAwgTfbsUniform/wgEncodeAwgTfbsUchicagoK562Egata2UniPk.narrowPeak.gz K562 ChipSeq eGFP-GATA2 Peaks narrowPeak UChicago Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeAwgTfbsUniform/wgEncodeAwgTfbsUchicagoK562Ehdac8UniPk.narrowPeak.gz K562 ChipSeq eGFP-HDAC8 Peaks narrowPeak UChicago Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeAwgTfbsUniform/wgEncodeAwgTfbsUchicagoK562EjunbUniPk.narrowPeak.gz K562 ChipSeq eGFP-JunB Peaks narrowPeak UChicago Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeAwgTfbsUniform/wgEncodeAwgTfbsUchicagoK562EjundUniPk.narrowPeak.gz K562 ChipSeq eGFP-JunD Peaks narrowPeak UChicago Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeAwgTfbsUniform/wgEncodeAwgTfbsUtaA549CtcfUniPk.narrowPeak.gz A549 ChipSeq CTCF Peaks narrowPeak UT-A Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeAwgTfbsUniform/wgEncodeAwgTfbsUtaA549Pol2UniPk.narrowPeak.gz A549 ChipSeq Pol2 Peaks narrowPeak UT-A Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeAwgTfbsUniform/wgEncodeAwgTfbsUtaFibroblCtcfUniPk.narrowPeak.gz Fibrobl ChipSeq CTCF Peaks narrowPeak UT-A Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeAwgTfbsUniform/wgEncodeAwgTfbsUtaGlioblaCtcfUniPk.narrowPeak.gz Gliobla ChipSeq CTCF Peaks narrowPeak UT-A Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeAwgTfbsUniform/wgEncodeAwgTfbsUtaGlioblaPol2UniPk.narrowPeak.gz Gliobla ChipSeq Pol2 Peaks narrowPeak UT-A Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeAwgTfbsUniform/wgEncodeAwgTfbsUtaGm12878CmycUniPk.narrowPeak.gz GM12878 ChipSeq c-Myc Peaks narrowPeak UT-A Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeAwgTfbsUniform/wgEncodeAwgTfbsUtaGm12878CtcfUniPk.narrowPeak.gz GM12878 ChipSeq CTCF Peaks narrowPeak UT-A Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeAwgTfbsUniform/wgEncodeAwgTfbsUtaGm12878Pol2UniPk.narrowPeak.gz GM12878 ChipSeq Pol2 Peaks narrowPeak UT-A Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeAwgTfbsUniform/wgEncodeAwgTfbsUtaGm12891CtcfUniPk.narrowPeak.gz GM12891 ChipSeq CTCF Peaks narrowPeak UT-A Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeAwgTfbsUniform/wgEncodeAwgTfbsUtaGm12892CtcfUniPk.narrowPeak.gz GM12892 ChipSeq CTCF Peaks narrowPeak UT-A Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeAwgTfbsUniform/wgEncodeAwgTfbsUtaGm19238CtcfUniPk.narrowPeak.gz GM19238 ChipSeq CTCF Peaks narrowPeak UT-A Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeAwgTfbsUniform/wgEncodeAwgTfbsUtaGm19239CtcfUniPk.narrowPeak.gz GM19239 ChipSeq CTCF Peaks narrowPeak UT-A Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeAwgTfbsUniform/wgEncodeAwgTfbsUtaGm19240CtcfUniPk.narrowPeak.gz GM19240 ChipSeq CTCF Peaks narrowPeak UT-A Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeAwgTfbsUniform/wgEncodeAwgTfbsUtaH1hescCmycUniPk.narrowPeak.gz H1-hESC ChipSeq c-Myc Peaks narrowPeak UT-A Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeAwgTfbsUniform/wgEncodeAwgTfbsUtaH1hescCtcfUniPk.narrowPeak.gz H1-hESC ChipSeq CTCF Peaks narrowPeak UT-A Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeAwgTfbsUniform/wgEncodeAwgTfbsUtaH1hescPol2UniPk.narrowPeak.gz H1-hESC ChipSeq Pol2 Peaks narrowPeak UT-A Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeAwgTfbsUniform/wgEncodeAwgTfbsUtaHelas3CmycUniPk.narrowPeak.gz HeLa-S3 ChipSeq c-Myc Peaks narrowPeak UT-A Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeAwgTfbsUniform/wgEncodeAwgTfbsUtaHelas3CtcfUniPk.narrowPeak.gz HeLa-S3 ChipSeq CTCF Peaks narrowPeak UT-A Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeAwgTfbsUniform/wgEncodeAwgTfbsUtaHelas3Pol2UniPk.narrowPeak.gz HeLa-S3 ChipSeq Pol2 Peaks narrowPeak UT-A Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeAwgTfbsUniform/wgEncodeAwgTfbsUtaHepg2CmycUniPk.narrowPeak.gz HepG2 ChipSeq c-Myc Peaks narrowPeak UT-A Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeAwgTfbsUniform/wgEncodeAwgTfbsUtaHepg2CtcfUniPk.narrowPeak.gz HepG2 ChipSeq CTCF Peaks narrowPeak UT-A Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeAwgTfbsUniform/wgEncodeAwgTfbsUtaHepg2Pol2UniPk.narrowPeak.gz HepG2 ChipSeq Pol2 Peaks narrowPeak UT-A Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeAwgTfbsUniform/wgEncodeAwgTfbsUtaHuvecCmycUniPk.narrowPeak.gz HUVEC ChipSeq c-Myc Peaks narrowPeak UT-A Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeAwgTfbsUniform/wgEncodeAwgTfbsUtaHuvecCtcfUniPk.narrowPeak.gz HUVEC ChipSeq CTCF Peaks narrowPeak UT-A Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeAwgTfbsUniform/wgEncodeAwgTfbsUtaHuvecPol2UniPk.narrowPeak.gz HUVEC ChipSeq Pol2 Peaks narrowPeak UT-A Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeAwgTfbsUniform/wgEncodeAwgTfbsUtaK562CmycUniPk.narrowPeak.gz K562 ChipSeq c-Myc Peaks narrowPeak UT-A Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeAwgTfbsUniform/wgEncodeAwgTfbsUtaK562CtcfUniPk.narrowPeak.gz K562 ChipSeq CTCF Peaks narrowPeak UT-A Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeAwgTfbsUniform/wgEncodeAwgTfbsUtaK562Pol2UniPk.narrowPeak.gz K562 ChipSeq Pol2 Peaks narrowPeak UT-A Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeAwgTfbsUniform/wgEncodeAwgTfbsUtaMcf7CmycEstroUniPk.narrowPeak.gz MCF-7 ChipSeq c-Myc Peaks narrowPeak UT-A Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeAwgTfbsUniform/wgEncodeAwgTfbsUtaMcf7CmycSerumstimUniPk.narrowPeak.gz MCF-7 ChipSeq c-Myc Peaks narrowPeak UT-A Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeAwgTfbsUniform/wgEncodeAwgTfbsUtaMcf7CmycSerumstvdUniPk.narrowPeak.gz MCF-7 ChipSeq c-Myc Peaks narrowPeak UT-A Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeAwgTfbsUniform/wgEncodeAwgTfbsUtaMcf7CmycVehUniPk.narrowPeak.gz MCF-7 ChipSeq c-Myc Peaks narrowPeak UT-A Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeAwgTfbsUniform/wgEncodeAwgTfbsUtaMcf7CtcfEstroUniPk.narrowPeak.gz MCF-7 ChipSeq CTCF Peaks narrowPeak UT-A Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeAwgTfbsUniform/wgEncodeAwgTfbsUtaMcf7CtcfSerumstimUniPk.narrowPeak.gz MCF-7 ChipSeq CTCF Peaks narrowPeak UT-A Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeAwgTfbsUniform/wgEncodeAwgTfbsUtaMcf7CtcfSerumstvdUniPk.narrowPeak.gz MCF-7 ChipSeq CTCF Peaks narrowPeak UT-A Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeAwgTfbsUniform/wgEncodeAwgTfbsUtaMcf7CtcfUniPk.narrowPeak.gz MCF-7 ChipSeq CTCF Peaks narrowPeak UT-A Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeAwgTfbsUniform/wgEncodeAwgTfbsUtaMcf7CtcfVehUniPk.narrowPeak.gz MCF-7 ChipSeq CTCF Peaks narrowPeak UT-A Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeAwgTfbsUniform/wgEncodeAwgTfbsUtaMcf7Pol2SerumstimUniPk.narrowPeak.gz MCF-7 ChipSeq Pol2 Peaks narrowPeak UT-A Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeAwgTfbsUniform/wgEncodeAwgTfbsUtaMcf7Pol2SerumstvdUniPk.narrowPeak.gz MCF-7 ChipSeq Pol2 Peaks narrowPeak UT-A Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeAwgTfbsUniform/wgEncodeAwgTfbsUtaMcf7Pol2UniPk.narrowPeak.gz MCF-7 ChipSeq Pol2 Peaks narrowPeak UT-A Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeAwgTfbsUniform/wgEncodeAwgTfbsUtaNhekCtcfUniPk.narrowPeak.gz NHEK ChipSeq CTCF Peaks narrowPeak UT-A Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeAwgTfbsUniform/wgEncodeAwgTfbsUtaProgfibCtcfUniPk.narrowPeak.gz ProgFib ChipSeq CTCF Peaks narrowPeak UT-A Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeAwgTfbsUniform/wgEncodeAwgTfbsUtaProgfibPol2UniPk.narrowPeak.gz ProgFib ChipSeq Pol2 Peaks narrowPeak UT-A Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeAwgTfbsUniform/wgEncodeAwgTfbsUwA549CtcfUniPk.narrowPeak.gz A549 ChipSeq CTCF Peaks narrowPeak UW Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeAwgTfbsUniform/wgEncodeAwgTfbsUwAg04449CtcfUniPk.narrowPeak.gz AG04449 ChipSeq CTCF Peaks narrowPeak UW Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeAwgTfbsUniform/wgEncodeAwgTfbsUwAg04450CtcfUniPk.narrowPeak.gz AG04450 ChipSeq CTCF Peaks narrowPeak UW Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeAwgTfbsUniform/wgEncodeAwgTfbsUwAg09309CtcfUniPk.narrowPeak.gz AG09309 ChipSeq CTCF Peaks narrowPeak UW Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeAwgTfbsUniform/wgEncodeAwgTfbsUwAg09319CtcfUniPk.narrowPeak.gz AG09319 ChipSeq CTCF Peaks narrowPeak UW Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeAwgTfbsUniform/wgEncodeAwgTfbsUwAg10803CtcfUniPk.narrowPeak.gz AG10803 ChipSeq CTCF Peaks narrowPeak UW Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeAwgTfbsUniform/wgEncodeAwgTfbsUwAoafCtcfUniPk.narrowPeak.gz AoAF ChipSeq CTCF Peaks narrowPeak UW Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeAwgTfbsUniform/wgEncodeAwgTfbsUwBe2cCtcfUniPk.narrowPeak.gz BE2_C ChipSeq CTCF Peaks narrowPeak UW Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeAwgTfbsUniform/wgEncodeAwgTfbsUwBjCtcfUniPk.narrowPeak.gz BJ ChipSeq CTCF Peaks narrowPeak UW Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeAwgTfbsUniform/wgEncodeAwgTfbsUwCaco2CtcfUniPk.narrowPeak.gz Caco-2 ChipSeq CTCF Peaks narrowPeak UW Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeAwgTfbsUniform/wgEncodeAwgTfbsUwGm06990CtcfUniPk.narrowPeak.gz GM06990 ChipSeq CTCF Peaks narrowPeak UW Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeAwgTfbsUniform/wgEncodeAwgTfbsUwGm12801CtcfUniPk.narrowPeak.gz GM12801 ChipSeq CTCF Peaks narrowPeak UW Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeAwgTfbsUniform/wgEncodeAwgTfbsUwGm12864CtcfUniPk.narrowPeak.gz GM12864 ChipSeq CTCF Peaks narrowPeak UW Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeAwgTfbsUniform/wgEncodeAwgTfbsUwGm12865CtcfUniPk.narrowPeak.gz GM12865 ChipSeq CTCF Peaks narrowPeak UW Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeAwgTfbsUniform/wgEncodeAwgTfbsUwGm12872CtcfUniPk.narrowPeak.gz GM12872 ChipSeq CTCF Peaks narrowPeak UW Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeAwgTfbsUniform/wgEncodeAwgTfbsUwGm12873CtcfUniPk.narrowPeak.gz GM12873 ChipSeq CTCF Peaks narrowPeak UW Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeAwgTfbsUniform/wgEncodeAwgTfbsUwGm12874CtcfUniPk.narrowPeak.gz GM12874 ChipSeq CTCF Peaks narrowPeak UW Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeAwgTfbsUniform/wgEncodeAwgTfbsUwGm12875CtcfUniPk.narrowPeak.gz GM12875 ChipSeq CTCF Peaks narrowPeak UW Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeAwgTfbsUniform/wgEncodeAwgTfbsUwGm12878CtcfUniPk.narrowPeak.gz GM12878 ChipSeq CTCF Peaks narrowPeak UW Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeAwgTfbsUniform/wgEncodeAwgTfbsUwHacCtcfUniPk.narrowPeak.gz HAc ChipSeq CTCF Peaks narrowPeak UW Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeAwgTfbsUniform/wgEncodeAwgTfbsUwHaspCtcfUniPk.narrowPeak.gz HA-sp ChipSeq CTCF Peaks narrowPeak UW Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeAwgTfbsUniform/wgEncodeAwgTfbsUwHbmecCtcfUniPk.narrowPeak.gz HBMEC ChipSeq CTCF Peaks narrowPeak UW Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeAwgTfbsUniform/wgEncodeAwgTfbsUwHcfaaCtcfUniPk.narrowPeak.gz HCFaa ChipSeq CTCF Peaks narrowPeak UW Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeAwgTfbsUniform/wgEncodeAwgTfbsUwHcmCtcfUniPk.narrowPeak.gz HCM ChipSeq CTCF Peaks narrowPeak UW Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeAwgTfbsUniform/wgEncodeAwgTfbsUwHcpeCtcfUniPk.narrowPeak.gz HCPEpiC ChipSeq CTCF Peaks narrowPeak UW Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeAwgTfbsUniform/wgEncodeAwgTfbsUwHct116CtcfUniPk.narrowPeak.gz HCT-116 ChipSeq CTCF Peaks narrowPeak UW Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeAwgTfbsUniform/wgEncodeAwgTfbsUwHeeCtcfUniPk.narrowPeak.gz HEEpiC ChipSeq CTCF Peaks narrowPeak UW Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeAwgTfbsUniform/wgEncodeAwgTfbsUwHek293CtcfUniPk.narrowPeak.gz HEK293 ChipSeq CTCF Peaks narrowPeak UW Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeAwgTfbsUniform/wgEncodeAwgTfbsUwHelas3CtcfUniPk.narrowPeak.gz HeLa-S3 ChipSeq CTCF Peaks narrowPeak UW Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeAwgTfbsUniform/wgEncodeAwgTfbsUwHepg2CtcfUniPk.narrowPeak.gz HepG2 ChipSeq CTCF Peaks narrowPeak UW Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeAwgTfbsUniform/wgEncodeAwgTfbsUwHffCtcfUniPk.narrowPeak.gz HFF ChipSeq CTCF Peaks narrowPeak UW Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeAwgTfbsUniform/wgEncodeAwgTfbsUwHffmycCtcfUniPk.narrowPeak.gz HFF-Myc ChipSeq CTCF Peaks narrowPeak UW Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeAwgTfbsUniform/wgEncodeAwgTfbsUwHl60CtcfUniPk.narrowPeak.gz HL-60 ChipSeq CTCF Peaks narrowPeak UW Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeAwgTfbsUniform/wgEncodeAwgTfbsUwHmecCtcfUniPk.narrowPeak.gz HMEC ChipSeq CTCF Peaks narrowPeak UW Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeAwgTfbsUniform/wgEncodeAwgTfbsUwHmfCtcfUniPk.narrowPeak.gz HMF ChipSeq CTCF Peaks narrowPeak UW Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeAwgTfbsUniform/wgEncodeAwgTfbsUwHpafCtcfUniPk.narrowPeak.gz HPAF ChipSeq CTCF Peaks narrowPeak UW Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeAwgTfbsUniform/wgEncodeAwgTfbsUwHpfCtcfUniPk.narrowPeak.gz HPF ChipSeq CTCF Peaks narrowPeak UW Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeAwgTfbsUniform/wgEncodeAwgTfbsUwHreCtcfUniPk.narrowPeak.gz HRE ChipSeq CTCF Peaks narrowPeak UW Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeAwgTfbsUniform/wgEncodeAwgTfbsUwHrpeCtcfUniPk.narrowPeak.gz HRPEpiC ChipSeq CTCF Peaks narrowPeak UW Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeAwgTfbsUniform/wgEncodeAwgTfbsUwHuvecCtcfUniPk.narrowPeak.gz HUVEC ChipSeq CTCF Peaks narrowPeak UW Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeAwgTfbsUniform/wgEncodeAwgTfbsUwHvmfCtcfUniPk.narrowPeak.gz HVMF ChipSeq CTCF Peaks narrowPeak UW Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeAwgTfbsUniform/wgEncodeAwgTfbsUwK562CtcfUniPk.narrowPeak.gz K562 ChipSeq CTCF Peaks narrowPeak UW Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeAwgTfbsUniform/wgEncodeAwgTfbsUwMcf7CtcfUniPk.narrowPeak.gz MCF-7 ChipSeq CTCF Peaks narrowPeak UW Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeAwgTfbsUniform/wgEncodeAwgTfbsUwNb4CtcfUniPk.narrowPeak.gz NB4 ChipSeq CTCF Peaks narrowPeak UW Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeAwgTfbsUniform/wgEncodeAwgTfbsUwNhdfneoCtcfUniPk.narrowPeak.gz NHDF-neo ChipSeq CTCF Peaks narrowPeak UW Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeAwgTfbsUniform/wgEncodeAwgTfbsUwNhekCtcfUniPk.narrowPeak.gz NHEK ChipSeq CTCF Peaks narrowPeak UW Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeAwgTfbsUniform/wgEncodeAwgTfbsUwNhlfCtcfUniPk.narrowPeak.gz NHLF ChipSeq CTCF Peaks narrowPeak UW Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeAwgTfbsUniform/wgEncodeAwgTfbsUwRptecCtcfUniPk.narrowPeak.gz RPTEC ChipSeq CTCF Peaks narrowPeak UW Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeAwgTfbsUniform/wgEncodeAwgTfbsUwSaecCtcfUniPk.narrowPeak.gz SAEC ChipSeq CTCF Peaks narrowPeak UW Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeAwgTfbsUniform/wgEncodeAwgTfbsUwSknshraCtcfUniPk.narrowPeak.gz SK-N-SH_RA ChipSeq CTCF Peaks narrowPeak UW Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeAwgTfbsUniform/wgEncodeAwgTfbsUwWerirb1CtcfUniPk.narrowPeak.gz 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http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeBroadHistone/wgEncodeBroadHistoneDnd41Ezh239875Sig.bigWig Dnd41 ChipSeq EZH2_(39875) Signal bigWig Broad Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeBroadHistone/wgEncodeBroadHistoneDnd41H2azAlnRep1.bam Dnd41 ChipSeq H2A.Z Alignments 1 bam Broad Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeBroadHistone/wgEncodeBroadHistoneDnd41H2azAlnRep2.bam Dnd41 ChipSeq H2A.Z Alignments 2 bam Broad Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeBroadHistone/wgEncodeBroadHistoneDnd41H2azPk.broadPeak.gz Dnd41 ChipSeq H2A.Z Peaks broadPeak Broad Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeBroadHistone/wgEncodeBroadHistoneDnd41H2azSig.bigWig Dnd41 ChipSeq H2A.Z Signal bigWig Broad Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeBroadHistone/wgEncodeBroadHistoneDnd41H3k04me1AlnRep1.bam Dnd41 ChipSeq H3K4me1 Alignments 1 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ChipSeq H3K4me3 Signal bigWig Broad Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeBroadHistone/wgEncodeBroadHistoneDnd41H3k09acAlnRep1.bam Dnd41 ChipSeq H3K9ac Alignments 1 bam Broad Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeBroadHistone/wgEncodeBroadHistoneDnd41H3k09acAlnRep2.bam Dnd41 ChipSeq H3K9ac Alignments 2 bam Broad Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeBroadHistone/wgEncodeBroadHistoneDnd41H3k09acPk.broadPeak.gz Dnd41 ChipSeq H3K9ac Peaks broadPeak Broad Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeBroadHistone/wgEncodeBroadHistoneDnd41H3k09acSig.bigWig Dnd41 ChipSeq H3K9ac Signal bigWig Broad Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeBroadHistone/wgEncodeBroadHistoneDnd41H3k09me3AlnRep1.bam Dnd41 ChipSeq H3K9me3 Alignments 1 bam Broad Data 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ChipSeq H3K27ac Peaks broadPeak Broad Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeBroadHistone/wgEncodeBroadHistoneDnd41H3k27acSig.bigWig Dnd41 ChipSeq H3K27ac Signal bigWig Broad Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeBroadHistone/wgEncodeBroadHistoneDnd41H3k27me3AlnRep1.bam Dnd41 ChipSeq H3K27me3 Alignments 1 bam Broad Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeBroadHistone/wgEncodeBroadHistoneDnd41H3k27me3AlnRep2.bam Dnd41 ChipSeq H3K27me3 Alignments 2 bam Broad Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeBroadHistone/wgEncodeBroadHistoneDnd41H3k27me3Pk.broadPeak.gz Dnd41 ChipSeq H3K27me3 Peaks broadPeak Broad Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeBroadHistone/wgEncodeBroadHistoneDnd41H3k27me3Sig.bigWig Dnd41 ChipSeq H3K27me3 Signal bigWig Broad Data 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ChipSeq H3K79me2 Alignments 2 bam Broad Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeBroadHistone/wgEncodeBroadHistoneDnd41H3k79me2Pk.broadPeak.gz Dnd41 ChipSeq H3K79me2 Peaks broadPeak Broad Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeBroadHistone/wgEncodeBroadHistoneDnd41H3k79me2Sig.bigWig Dnd41 ChipSeq H3K79me2 Signal bigWig Broad Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeBroadHistone/wgEncodeBroadHistoneDnd41H4k20me1AlnRep1.bam Dnd41 ChipSeq H4K20me1 Alignments 1 bam Broad Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeBroadHistone/wgEncodeBroadHistoneDnd41H4k20me1AlnRep2.bam Dnd41 ChipSeq H4K20me1 Alignments 2 bam Broad Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeBroadHistone/wgEncodeBroadHistoneDnd41H4k20me1Pk.broadPeak.gz Dnd41 ChipSeq H4K20me1 Peaks broadPeak Broad Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeBroadHistone/wgEncodeBroadHistoneDnd41H4k20me1Sig.bigWig Dnd41 ChipSeq H4K20me1 Signal bigWig Broad Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeBroadHistone/wgEncodeBroadHistoneGm12878ControlStdAlnRep1.bam GM12878 ChipSeq Input Alignments 1 bam Broad Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeBroadHistone/wgEncodeBroadHistoneGm12878ControlStdAlnRep2.bam GM12878 ChipSeq Input Alignments 2 bam Broad Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeBroadHistone/wgEncodeBroadHistoneGm12878ControlStdSig.bigWig GM12878 ChipSeq Input Signal bigWig Broad Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeBroadHistone/wgEncodeBroadHistoneGm12878CtcfStdAlnRep1.bam GM12878 ChipSeq CTCF Alignments 1 bam Broad Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeBroadHistone/wgEncodeBroadHistoneGm12878CtcfStdAlnRep2.bam GM12878 ChipSeq CTCF Alignments 2 bam Broad Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeBroadHistone/wgEncodeBroadHistoneGm12878CtcfStdPk.broadPeak.gz GM12878 ChipSeq CTCF Peaks broadPeak Broad Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeBroadHistone/wgEncodeBroadHistoneGm12878CtcfStdSig.bigWig GM12878 ChipSeq CTCF Signal bigWig Broad Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeBroadHistone/wgEncodeBroadHistoneGm12878Ezh239875AlnRep1.bam GM12878 ChipSeq EZH2_(39875) Alignments 1 bam Broad Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeBroadHistone/wgEncodeBroadHistoneGm12878Ezh239875AlnRep2.bam GM12878 ChipSeq EZH2_(39875) Alignments 2 bam Broad Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeBroadHistone/wgEncodeBroadHistoneGm12878Ezh239875Pk.broadPeak.gz GM12878 ChipSeq EZH2_(39875) Peaks broadPeak Broad Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeBroadHistone/wgEncodeBroadHistoneGm12878Ezh239875Sig.bigWig GM12878 ChipSeq EZH2_(39875) Signal bigWig Broad Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeBroadHistone/wgEncodeBroadHistoneGm12878H2azStdAlnRep1.bam GM12878 ChipSeq H2A.Z Alignments 1 bam Broad Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeBroadHistone/wgEncodeBroadHistoneGm12878H2azStdAlnRep2.bam GM12878 ChipSeq H2A.Z Alignments 2 bam Broad Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeBroadHistone/wgEncodeBroadHistoneGm12878H2azStdPk.broadPeak.gz GM12878 ChipSeq H2A.Z Peaks broadPeak Broad Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeBroadHistone/wgEncodeBroadHistoneGm12878H2azStdSig.bigWig GM12878 ChipSeq H2A.Z Signal bigWig Broad Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeBroadHistone/wgEncodeBroadHistoneGm12878H3k04me1StdAlnRep1V2.bam GM12878 ChipSeq H3K4me1 Alignments 1 bam Broad Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeBroadHistone/wgEncodeBroadHistoneGm12878H3k04me1StdPkV2.broadPeak.gz GM12878 ChipSeq H3K4me1 Peaks broadPeak Broad Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeBroadHistone/wgEncodeBroadHistoneGm12878H3k04me1StdSigV2.bigWig GM12878 ChipSeq H3K4me1 Signal bigWig Broad Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeBroadHistone/wgEncodeBroadHistoneGm12878H3k04me3StdAlnRep2V2.bam GM12878 ChipSeq H3K4me3 Alignments 2 bam Broad Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeBroadHistone/wgEncodeBroadHistoneGm12878H3k04me3StdPkV2.broadPeak.gz GM12878 ChipSeq H3K4me3 Peaks broadPeak Broad Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeBroadHistone/wgEncodeBroadHistoneGm12878H3k04me3StdSigV2.bigWig GM12878 ChipSeq H3K4me3 Signal bigWig Broad Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeBroadHistone/wgEncodeBroadHistoneGm12878H3k27acStdAlnRep1.bam GM12878 ChipSeq H3K27ac Alignments 1 bam Broad Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeBroadHistone/wgEncodeBroadHistoneGm12878H3k27acStdAlnRep2.bam GM12878 ChipSeq H3K27ac Alignments 2 bam Broad Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeBroadHistone/wgEncodeBroadHistoneGm12878H3k27acStdPk.broadPeak.gz GM12878 ChipSeq H3K27ac Peaks broadPeak Broad Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeBroadHistone/wgEncodeBroadHistoneGm12878H3k27acStdSig.bigWig GM12878 ChipSeq H3K27ac Signal bigWig Broad Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeBroadHistone/wgEncodeBroadHistoneGm12878H3k27me3StdAlnRep1.bam GM12878 ChipSeq H3K27me3 Alignments 1 bam Broad Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeBroadHistone/wgEncodeBroadHistoneGm12878H3k27me3StdAlnRep2.bam GM12878 ChipSeq H3K27me3 Alignments 2 bam Broad Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeBroadHistone/wgEncodeBroadHistoneGm12878H3k27me3StdAlnRep3V2.bam GM12878 ChipSeq H3K27me3 Alignments 3 bam Broad Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeBroadHistone/wgEncodeBroadHistoneGm12878H3k27me3StdPk.broadPeak.gz GM12878 ChipSeq H3K27me3 Peaks broadPeak Broad Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeBroadHistone/wgEncodeBroadHistoneGm12878H3k27me3StdPkV2.broadPeak.gz GM12878 ChipSeq H3K27me3 Peaks broadPeak Broad Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeBroadHistone/wgEncodeBroadHistoneGm12878H3k27me3StdSig.bigWig GM12878 ChipSeq H3K27me3 Signal bigWig Broad Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeBroadHistone/wgEncodeBroadHistoneGm12878H3k27me3StdSigV2.bigWig GM12878 ChipSeq H3K27me3 Signal bigWig Broad Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeBroadHistone/wgEncodeBroadHistoneGm12878H3k36me3StdAlnRep1.bam GM12878 ChipSeq H3K36me3 Alignments 1 bam Broad Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeBroadHistone/wgEncodeBroadHistoneGm12878H3k36me3StdAlnRep2.bam GM12878 ChipSeq H3K36me3 Alignments 2 bam Broad Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeBroadHistone/wgEncodeBroadHistoneGm12878H3k36me3StdPk.broadPeak.gz GM12878 ChipSeq H3K36me3 Peaks broadPeak Broad Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeBroadHistone/wgEncodeBroadHistoneGm12878H3k36me3StdSig.bigWig GM12878 ChipSeq H3K36me3 Signal bigWig Broad Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeBroadHistone/wgEncodeBroadHistoneGm12878H3k4me1StdAlnRep1.bam GM12878 ChipSeq H3K4me1 Alignments 1 bam Broad Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeBroadHistone/wgEncodeBroadHistoneGm12878H3k4me1StdAlnRep2.bam GM12878 ChipSeq H3K4me1 Alignments 2 bam Broad Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeBroadHistone/wgEncodeBroadHistoneGm12878H3k4me1StdPk.broadPeak.gz GM12878 ChipSeq H3K4me1 Peaks broadPeak Broad Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeBroadHistone/wgEncodeBroadHistoneGm12878H3k4me1StdSig.bigWig GM12878 ChipSeq H3K4me1 Signal bigWig Broad Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeBroadHistone/wgEncodeBroadHistoneGm12878H3k4me2StdAlnRep1.bam GM12878 ChipSeq H3K4me2 Alignments 1 bam Broad Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeBroadHistone/wgEncodeBroadHistoneGm12878H3k4me2StdAlnRep2.bam GM12878 ChipSeq H3K4me2 Alignments 2 bam Broad Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeBroadHistone/wgEncodeBroadHistoneGm12878H3k4me2StdPk.broadPeak.gz GM12878 ChipSeq H3K4me2 Peaks broadPeak Broad Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeBroadHistone/wgEncodeBroadHistoneGm12878H3k4me2StdSig.bigWig GM12878 ChipSeq H3K4me2 Signal bigWig Broad Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeBroadHistone/wgEncodeBroadHistoneGm12878H3k4me3StdAlnRep1.bam GM12878 ChipSeq H3K4me3 Alignments 1 bam Broad Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeBroadHistone/wgEncodeBroadHistoneGm12878H3k4me3StdAlnRep2.bam GM12878 ChipSeq H3K4me3 Alignments 2 bam Broad Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeBroadHistone/wgEncodeBroadHistoneGm12878H3k4me3StdPk.broadPeak.gz GM12878 ChipSeq H3K4me3 Peaks broadPeak Broad Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeBroadHistone/wgEncodeBroadHistoneGm12878H3k4me3StdSig.bigWig GM12878 ChipSeq H3K4me3 Signal bigWig Broad Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeBroadHistone/wgEncodeBroadHistoneGm12878H3k79me2StdAlnRep1.bam GM12878 ChipSeq H3K79me2 Alignments 1 bam Broad Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeBroadHistone/wgEncodeBroadHistoneGm12878H3k79me2StdAlnRep2.bam GM12878 ChipSeq H3K79me2 Alignments 2 bam Broad Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeBroadHistone/wgEncodeBroadHistoneGm12878H3k79me2StdPk.broadPeak.gz GM12878 ChipSeq H3K79me2 Peaks broadPeak Broad Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeBroadHistone/wgEncodeBroadHistoneGm12878H3k79me2StdSig.bigWig GM12878 ChipSeq H3K79me2 Signal bigWig Broad Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeBroadHistone/wgEncodeBroadHistoneGm12878H3k9acStdAlnRep1.bam GM12878 ChipSeq H3K9ac Alignments 1 bam Broad Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeBroadHistone/wgEncodeBroadHistoneGm12878H3k9acStdAlnRep2.bam GM12878 ChipSeq H3K9ac Alignments 2 bam Broad Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeBroadHistone/wgEncodeBroadHistoneGm12878H3k9acStdPk.broadPeak.gz GM12878 ChipSeq H3K9ac Peaks broadPeak Broad Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeBroadHistone/wgEncodeBroadHistoneGm12878H3k9acStdSig.bigWig GM12878 ChipSeq H3K9ac Signal bigWig Broad Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeBroadHistone/wgEncodeBroadHistoneGm12878H3k9me3StdAlnRep1.bam GM12878 ChipSeq H3K9me3 Alignments 1 bam Broad Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeBroadHistone/wgEncodeBroadHistoneGm12878H3k9me3StdAlnRep2.bam GM12878 ChipSeq H3K9me3 Alignments 2 bam Broad Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeBroadHistone/wgEncodeBroadHistoneGm12878H3k9me3StdAlnRep3.bam GM12878 ChipSeq H3K9me3 Alignments 3 bam Broad Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeBroadHistone/wgEncodeBroadHistoneGm12878H3k9me3StdPk.broadPeak.gz GM12878 ChipSeq H3K9me3 Peaks broadPeak Broad Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeBroadHistone/wgEncodeBroadHistoneGm12878H3k9me3StdSig.bigWig GM12878 ChipSeq H3K9me3 Signal bigWig Broad Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeBroadHistone/wgEncodeBroadHistoneGm12878H4k20me1StdAlnRep1.bam GM12878 ChipSeq H4K20me1 Alignments 1 bam Broad Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeBroadHistone/wgEncodeBroadHistoneGm12878H4k20me1StdAlnRep2.bam GM12878 ChipSeq H4K20me1 Alignments 2 bam Broad Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeBroadHistone/wgEncodeBroadHistoneGm12878H4k20me1StdPk.broadPeak.gz GM12878 ChipSeq H4K20me1 Peaks broadPeak Broad Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeBroadHistone/wgEncodeBroadHistoneGm12878H4k20me1StdSig.bigWig GM12878 ChipSeq H4K20me1 Signal bigWig Broad Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeBroadHistone/wgEncodeBroadHistoneH1hescChd1a301218aStdAlnRep1.bam H1-hESC ChipSeq CHD1_(A301-218A) Alignments 1 bam Broad Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeBroadHistone/wgEncodeBroadHistoneH1hescChd1a301218aStdAlnRep2.bam H1-hESC ChipSeq CHD1_(A301-218A) Alignments 2 bam Broad Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeBroadHistone/wgEncodeBroadHistoneH1hescChd1a301218aStdPk.broadPeak.gz H1-hESC ChipSeq CHD1_(A301-218A) Peaks broadPeak Broad Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeBroadHistone/wgEncodeBroadHistoneH1hescChd1a301218aStdSig.bigWig H1-hESC ChipSeq CHD1_(A301-218A) Signal bigWig Broad Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeBroadHistone/wgEncodeBroadHistoneH1hescChd7a301223a1AlnRep1.bam H1-hESC ChipSeq CHD7_(A301-223A-1) Alignments 1 bam Broad Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeBroadHistone/wgEncodeBroadHistoneH1hescChd7a301223a1Pk.broadPeak.gz H1-hESC ChipSeq CHD7_(A301-223A-1) Peaks broadPeak Broad Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeBroadHistone/wgEncodeBroadHistoneH1hescChd7a301223a1Sig.bigWig H1-hESC ChipSeq CHD7_(A301-223A-1) Signal bigWig Broad Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeBroadHistone/wgEncodeBroadHistoneH1hescControlStdAlnRep1.bam H1-hESC ChipSeq Input Alignments 1 bam Broad Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeBroadHistone/wgEncodeBroadHistoneH1hescControlStdAlnRep2.bam H1-hESC ChipSeq Input Alignments 2 bam Broad Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeBroadHistone/wgEncodeBroadHistoneH1hescControlStdSig.bigWig H1-hESC ChipSeq Input Signal bigWig Broad Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeBroadHistone/wgEncodeBroadHistoneH1hescCtcfStdAlnRep1.bam H1-hESC ChipSeq CTCF Alignments 1 bam Broad Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeBroadHistone/wgEncodeBroadHistoneH1hescCtcfStdAlnRep2.bam H1-hESC ChipSeq CTCF Alignments 2 bam Broad Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeBroadHistone/wgEncodeBroadHistoneH1hescCtcfStdPk.broadPeak.gz H1-hESC ChipSeq CTCF Peaks broadPeak Broad Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeBroadHistone/wgEncodeBroadHistoneH1hescCtcfStdSig.bigWig H1-hESC ChipSeq CTCF Signal bigWig Broad Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeBroadHistone/wgEncodeBroadHistoneH1hescEzh239875AlnRep1.bam H1-hESC ChipSeq EZH2_(39875) Alignments 1 bam Broad Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeBroadHistone/wgEncodeBroadHistoneH1hescEzh239875AlnRep2.bam H1-hESC ChipSeq EZH2_(39875) Alignments 2 bam Broad Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeBroadHistone/wgEncodeBroadHistoneH1hescEzh239875Pk.broadPeak.gz H1-hESC ChipSeq EZH2_(39875) Peaks broadPeak Broad Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeBroadHistone/wgEncodeBroadHistoneH1hescEzh239875Sig.bigWig H1-hESC ChipSeq EZH2_(39875) Signal bigWig Broad Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeBroadHistone/wgEncodeBroadHistoneH1hescH2azStdAlnRep1.bam H1-hESC ChipSeq H2A.Z Alignments 1 bam Broad Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeBroadHistone/wgEncodeBroadHistoneH1hescH2azStdAlnRep2.bam H1-hESC ChipSeq H2A.Z Alignments 2 bam Broad Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeBroadHistone/wgEncodeBroadHistoneH1hescH2azStdPk.broadPeak.gz H1-hESC ChipSeq H2A.Z Peaks broadPeak Broad Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeBroadHistone/wgEncodeBroadHistoneH1hescH2azStdSig.bigWig H1-hESC ChipSeq H2A.Z Signal bigWig Broad Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeBroadHistone/wgEncodeBroadHistoneH1hescH3k09me3StdAlnRep1.bam H1-hESC ChipSeq H3K9me3 Alignments 1 bam Broad Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeBroadHistone/wgEncodeBroadHistoneH1hescH3k09me3StdAlnRep2.bam H1-hESC ChipSeq H3K9me3 Alignments 2 bam Broad Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeBroadHistone/wgEncodeBroadHistoneH1hescH3k09me3StdPk.broadPeak.gz H1-hESC ChipSeq H3K9me3 Peaks broadPeak Broad Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeBroadHistone/wgEncodeBroadHistoneH1hescH3k09me3StdSig.bigWig H1-hESC ChipSeq H3K9me3 Signal bigWig Broad Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeBroadHistone/wgEncodeBroadHistoneH1hescH3k27acStdAlnRep1.bam H1-hESC ChipSeq H3K27ac Alignments 1 bam Broad Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeBroadHistone/wgEncodeBroadHistoneH1hescH3k27acStdAlnRep2.bam H1-hESC ChipSeq H3K27ac Alignments 2 bam Broad Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeBroadHistone/wgEncodeBroadHistoneH1hescH3k27acStdPk.broadPeak.gz H1-hESC ChipSeq H3K27ac Peaks broadPeak Broad Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeBroadHistone/wgEncodeBroadHistoneH1hescH3k27acStdSig.bigWig H1-hESC ChipSeq H3K27ac Signal bigWig Broad Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeBroadHistone/wgEncodeBroadHistoneH1hescH3k27me3StdAlnRep1.bam H1-hESC ChipSeq H3K27me3 Alignments 1 bam Broad Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeBroadHistone/wgEncodeBroadHistoneH1hescH3k27me3StdAlnRep2.bam H1-hESC ChipSeq H3K27me3 Alignments 2 bam Broad Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeBroadHistone/wgEncodeBroadHistoneH1hescH3k27me3StdPk.broadPeak.gz H1-hESC ChipSeq H3K27me3 Peaks broadPeak Broad Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeBroadHistone/wgEncodeBroadHistoneH1hescH3k27me3StdSig.bigWig H1-hESC ChipSeq H3K27me3 Signal bigWig Broad Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeBroadHistone/wgEncodeBroadHistoneH1hescH3k36me3StdAlnRep1.bam H1-hESC ChipSeq H3K36me3 Alignments 1 bam Broad Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeBroadHistone/wgEncodeBroadHistoneH1hescH3k36me3StdAlnRep2.bam H1-hESC ChipSeq H3K36me3 Alignments 2 bam Broad Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeBroadHistone/wgEncodeBroadHistoneH1hescH3k36me3StdPk.broadPeak.gz H1-hESC ChipSeq H3K36me3 Peaks broadPeak Broad Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeBroadHistone/wgEncodeBroadHistoneH1hescH3k36me3StdSig.bigWig H1-hESC ChipSeq H3K36me3 Signal bigWig Broad Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeBroadHistone/wgEncodeBroadHistoneH1hescH3k4me1StdAlnRep1.bam H1-hESC ChipSeq H3K4me1 Alignments 1 bam Broad Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeBroadHistone/wgEncodeBroadHistoneH1hescH3k4me1StdAlnRep2.bam H1-hESC ChipSeq H3K4me1 Alignments 2 bam Broad Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeBroadHistone/wgEncodeBroadHistoneH1hescH3k4me1StdPk.broadPeak.gz H1-hESC ChipSeq H3K4me1 Peaks broadPeak Broad Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeBroadHistone/wgEncodeBroadHistoneH1hescH3k4me1StdSig.bigWig H1-hESC ChipSeq H3K4me1 Signal bigWig Broad Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeBroadHistone/wgEncodeBroadHistoneH1hescH3k4me2StdAlnRep1.bam H1-hESC ChipSeq H3K4me2 Alignments 1 bam Broad Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeBroadHistone/wgEncodeBroadHistoneH1hescH3k4me2StdAlnRep2.bam H1-hESC ChipSeq H3K4me2 Alignments 2 bam Broad Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeBroadHistone/wgEncodeBroadHistoneH1hescH3k4me2StdPk.broadPeak.gz H1-hESC ChipSeq H3K4me2 Peaks broadPeak Broad Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeBroadHistone/wgEncodeBroadHistoneH1hescH3k4me2StdSig.bigWig H1-hESC ChipSeq H3K4me2 Signal bigWig Broad Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeBroadHistone/wgEncodeBroadHistoneH1hescH3k4me3StdAlnRep1.bam H1-hESC ChipSeq H3K4me3 Alignments 1 bam Broad Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeBroadHistone/wgEncodeBroadHistoneH1hescH3k4me3StdAlnRep2.bam H1-hESC ChipSeq H3K4me3 Alignments 2 bam Broad Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeBroadHistone/wgEncodeBroadHistoneH1hescH3k4me3StdPk.broadPeak.gz H1-hESC ChipSeq H3K4me3 Peaks broadPeak Broad Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeBroadHistone/wgEncodeBroadHistoneH1hescH3k4me3StdSig.bigWig H1-hESC ChipSeq H3K4me3 Signal bigWig Broad Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeBroadHistone/wgEncodeBroadHistoneH1hescH3k79me2StdAlnRep1.bam H1-hESC ChipSeq H3K79me2 Alignments 1 bam Broad Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeBroadHistone/wgEncodeBroadHistoneH1hescH3k79me2StdAlnRep2.bam H1-hESC ChipSeq H3K79me2 Alignments 2 bam Broad Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeBroadHistone/wgEncodeBroadHistoneH1hescH3k79me2StdPk.broadPeak.gz H1-hESC ChipSeq H3K79me2 Peaks broadPeak Broad Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeBroadHistone/wgEncodeBroadHistoneH1hescH3k79me2StdSig.bigWig H1-hESC ChipSeq H3K79me2 Signal bigWig Broad Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeBroadHistone/wgEncodeBroadHistoneH1hescH3k9acStdAlnRep1.bam H1-hESC ChipSeq H3K9ac Alignments 1 bam Broad Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeBroadHistone/wgEncodeBroadHistoneH1hescH3k9acStdAlnRep2.bam H1-hESC ChipSeq H3K9ac Alignments 2 bam Broad Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeBroadHistone/wgEncodeBroadHistoneH1hescH3k9acStdPk.broadPeak.gz H1-hESC ChipSeq H3K9ac Peaks broadPeak Broad Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeBroadHistone/wgEncodeBroadHistoneH1hescH3k9acStdSig.bigWig H1-hESC ChipSeq H3K9ac Signal bigWig Broad Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeBroadHistone/wgEncodeBroadHistoneH1hescH4k20me1StdAlnRep1.bam H1-hESC ChipSeq H4K20me1 Alignments 1 bam Broad Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeBroadHistone/wgEncodeBroadHistoneH1hescH4k20me1StdAlnRep2.bam H1-hESC ChipSeq H4K20me1 Alignments 2 bam Broad Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeBroadHistone/wgEncodeBroadHistoneH1hescH4k20me1StdPk.broadPeak.gz H1-hESC ChipSeq H4K20me1 Peaks broadPeak Broad Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeBroadHistone/wgEncodeBroadHistoneH1hescH4k20me1StdSig.bigWig H1-hESC ChipSeq H4K20me1 Signal bigWig Broad Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeBroadHistone/wgEncodeBroadHistoneH1hescHdac2a300705aAlnRep1.bam H1-hESC ChipSeq HDAC2_(A300-705A) Alignments 1 bam Broad Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeBroadHistone/wgEncodeBroadHistoneH1hescHdac2a300705aPk.broadPeak.gz H1-hESC ChipSeq HDAC2_(A300-705A) Peaks broadPeak Broad Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeBroadHistone/wgEncodeBroadHistoneH1hescHdac2a300705aSig.bigWig H1-hESC ChipSeq HDAC2_(A300-705A) Signal bigWig Broad Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeBroadHistone/wgEncodeBroadHistoneH1hescHdac6a301341aAlnRep1.bam H1-hESC ChipSeq HDAC6_(A301-341A) Alignments 1 bam Broad Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeBroadHistone/wgEncodeBroadHistoneH1hescHdac6a301341aPk.broadPeak.gz H1-hESC ChipSeq HDAC6_(A301-341A) Peaks broadPeak Broad Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeBroadHistone/wgEncodeBroadHistoneH1hescHdac6a301341aSig.bigWig H1-hESC ChipSeq HDAC6_(A301-341A) Signal bigWig Broad Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeBroadHistone/wgEncodeBroadHistoneH1hescJarid1aab26049StdAlnRep1.bam H1-hESC ChipSeq JARID1A_(ab26049) Alignments 1 bam Broad Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeBroadHistone/wgEncodeBroadHistoneH1hescJarid1aab26049StdAlnRep2.bam H1-hESC ChipSeq JARID1A_(ab26049) Alignments 2 bam Broad Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeBroadHistone/wgEncodeBroadHistoneH1hescJarid1aab26049StdPk.broadPeak.gz H1-hESC ChipSeq JARID1A_(ab26049) Peaks broadPeak Broad Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeBroadHistone/wgEncodeBroadHistoneH1hescJarid1aab26049StdSig.bigWig H1-hESC ChipSeq JARID1A_(ab26049) Signal bigWig Broad Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeBroadHistone/wgEncodeBroadHistoneH1hescJmjd2aa300861a1AlnRep1.bam H1-hESC ChipSeq JMJD2A_(A300-861A-1) Alignments 1 bam Broad Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeBroadHistone/wgEncodeBroadHistoneH1hescJmjd2aa300861a1Pk.broadPeak.gz H1-hESC ChipSeq JMJD2A_(A300-861A-1) Peaks broadPeak Broad Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeBroadHistone/wgEncodeBroadHistoneH1hescJmjd2aa300861a1Sig.bigWig H1-hESC ChipSeq JMJD2A_(A300-861A-1) Signal bigWig Broad Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeBroadHistone/wgEncodeBroadHistoneH1hescP300kat3bAlnRep1.bam H1-hESC ChipSeq P300_KAT3B Alignments 1 bam Broad Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeBroadHistone/wgEncodeBroadHistoneH1hescP300kat3bPk.broadPeak.gz H1-hESC ChipSeq P300_KAT3B Peaks broadPeak Broad Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeBroadHistone/wgEncodeBroadHistoneH1hescP300kat3bSig.bigWig H1-hESC ChipSeq P300_KAT3B Signal bigWig Broad Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeBroadHistone/wgEncodeBroadHistoneH1hescPhf8a301772aAlnRep1.bam H1-hESC ChipSeq PHF8_(A301-772A) Alignments 1 bam Broad Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeBroadHistone/wgEncodeBroadHistoneH1hescPhf8a301772aPk.broadPeak.gz H1-hESC ChipSeq PHF8_(A301-772A) Peaks broadPeak Broad Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeBroadHistone/wgEncodeBroadHistoneH1hescPhf8a301772aSig.bigWig H1-hESC ChipSeq PHF8_(A301-772A) Signal bigWig Broad Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeBroadHistone/wgEncodeBroadHistoneH1hescPlu1AlnRep1.bam H1-hESC ChipSeq PLU1 Alignments 1 bam Broad Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeBroadHistone/wgEncodeBroadHistoneH1hescPlu1Pk.broadPeak.gz H1-hESC ChipSeq PLU1 Peaks broadPeak Broad Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeBroadHistone/wgEncodeBroadHistoneH1hescPlu1Sig.bigWig H1-hESC ChipSeq PLU1 Signal bigWig Broad Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeBroadHistone/wgEncodeBroadHistoneH1hescRbbp5a300109aStdAlnRep1.bam H1-hESC ChipSeq RBBP5_(A300-109A) Alignments 1 bam Broad Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeBroadHistone/wgEncodeBroadHistoneH1hescRbbp5a300109aStdAlnRep2.bam H1-hESC ChipSeq RBBP5_(A300-109A) Alignments 2 bam Broad Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeBroadHistone/wgEncodeBroadHistoneH1hescRbbp5a300109aStdPk.broadPeak.gz H1-hESC ChipSeq RBBP5_(A300-109A) Peaks broadPeak Broad Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeBroadHistone/wgEncodeBroadHistoneH1hescRbbp5a300109aStdSig.bigWig H1-hESC ChipSeq RBBP5_(A300-109A) Signal bigWig Broad Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeBroadHistone/wgEncodeBroadHistoneH1hescSap3039731AlnRep1.bam H1-hESC ChipSeq SAP30_(39731) Alignments 1 bam Broad Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeBroadHistone/wgEncodeBroadHistoneH1hescSap3039731Pk.broadPeak.gz H1-hESC ChipSeq SAP30_(39731) Peaks broadPeak Broad Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeBroadHistone/wgEncodeBroadHistoneH1hescSap3039731Sig.bigWig H1-hESC ChipSeq SAP30_(39731) Signal bigWig Broad Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeBroadHistone/wgEncodeBroadHistoneH1hescSirt6AlnRep1.bam H1-hESC ChipSeq SIRT6 Alignments 1 bam Broad Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeBroadHistone/wgEncodeBroadHistoneH1hescSirt6Pk.broadPeak.gz H1-hESC ChipSeq SIRT6 Peaks broadPeak Broad Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeBroadHistone/wgEncodeBroadHistoneH1hescSirt6Sig.bigWig H1-hESC ChipSeq SIRT6 Signal bigWig Broad Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeBroadHistone/wgEncodeBroadHistoneH1hescSuz12051317AlnRep1.bam H1-hESC ChipSeq SUZ12_(05-1317) Alignments 1 bam Broad Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeBroadHistone/wgEncodeBroadHistoneH1hescSuz12051317Pk.broadPeak.gz H1-hESC ChipSeq SUZ12_(05-1317) Peaks broadPeak Broad Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeBroadHistone/wgEncodeBroadHistoneH1hescSuz12051317Sig.bigWig H1-hESC ChipSeq SUZ12_(05-1317) Signal bigWig Broad Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeBroadHistone/wgEncodeBroadHistoneHelas3ControlStdAlnRep1.bam HeLa-S3 ChipSeq Input Alignments 1 bam Broad Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeBroadHistone/wgEncodeBroadHistoneHelas3ControlStdAlnRep2.bam HeLa-S3 ChipSeq Input Alignments 2 bam Broad Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeBroadHistone/wgEncodeBroadHistoneHelas3ControlStdSig.bigWig HeLa-S3 ChipSeq Input Signal bigWig Broad Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeBroadHistone/wgEncodeBroadHistoneHelas3CtcfStdAlnRep1.bam HeLa-S3 ChipSeq CTCF Alignments 1 bam Broad Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeBroadHistone/wgEncodeBroadHistoneHelas3CtcfStdAlnRep2.bam HeLa-S3 ChipSeq CTCF Alignments 2 bam Broad Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeBroadHistone/wgEncodeBroadHistoneHelas3CtcfStdPk.broadPeak.gz HeLa-S3 ChipSeq CTCF Peaks broadPeak Broad Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeBroadHistone/wgEncodeBroadHistoneHelas3CtcfStdSig.bigWig HeLa-S3 ChipSeq CTCF Signal bigWig Broad Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeBroadHistone/wgEncodeBroadHistoneHelas3Ezh239875AlnRep1.bam HeLa-S3 ChipSeq EZH2_(39875) Alignments 1 bam Broad Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeBroadHistone/wgEncodeBroadHistoneHelas3Ezh239875AlnRep2.bam HeLa-S3 ChipSeq EZH2_(39875) Alignments 2 bam Broad Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeBroadHistone/wgEncodeBroadHistoneHelas3Ezh239875Pk.broadPeak.gz HeLa-S3 ChipSeq EZH2_(39875) Peaks broadPeak Broad Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeBroadHistone/wgEncodeBroadHistoneHelas3Ezh239875Sig.bigWig HeLa-S3 ChipSeq EZH2_(39875) Signal bigWig Broad Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeBroadHistone/wgEncodeBroadHistoneHelas3H2azAlnRep1.bam HeLa-S3 ChipSeq H2A.Z Alignments 1 bam Broad Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeBroadHistone/wgEncodeBroadHistoneHelas3H2azAlnRep2.bam HeLa-S3 ChipSeq H2A.Z Alignments 2 bam Broad Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeBroadHistone/wgEncodeBroadHistoneHelas3H2azPk.broadPeak.gz HeLa-S3 ChipSeq H2A.Z Peaks broadPeak Broad Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeBroadHistone/wgEncodeBroadHistoneHelas3H2azSig.bigWig HeLa-S3 ChipSeq H2A.Z Signal bigWig Broad Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeBroadHistone/wgEncodeBroadHistoneHelas3H3k04me1StdAlnRep1.bam HeLa-S3 ChipSeq H3K4me1 Alignments 1 bam Broad Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeBroadHistone/wgEncodeBroadHistoneHelas3H3k04me1StdAlnRep2.bam HeLa-S3 ChipSeq H3K4me1 Alignments 2 bam Broad Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeBroadHistone/wgEncodeBroadHistoneHelas3H3k04me1StdPk.broadPeak.gz HeLa-S3 ChipSeq H3K4me1 Peaks broadPeak Broad Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeBroadHistone/wgEncodeBroadHistoneHelas3H3k04me1StdSig.bigWig HeLa-S3 ChipSeq H3K4me1 Signal bigWig Broad Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeBroadHistone/wgEncodeBroadHistoneHelas3H3k09me3AlnRep1.bam HeLa-S3 ChipSeq H3K9me3 Alignments 1 bam Broad Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeBroadHistone/wgEncodeBroadHistoneHelas3H3k09me3AlnRep2.bam HeLa-S3 ChipSeq H3K9me3 Alignments 2 bam Broad Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeBroadHistone/wgEncodeBroadHistoneHelas3H3k09me3Pk.broadPeak.gz HeLa-S3 ChipSeq H3K9me3 Peaks broadPeak Broad Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeBroadHistone/wgEncodeBroadHistoneHelas3H3k09me3Sig.bigWig HeLa-S3 ChipSeq H3K9me3 Signal bigWig Broad Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeBroadHistone/wgEncodeBroadHistoneHelas3H3k27acStdAlnRep1.bam HeLa-S3 ChipSeq H3K27ac Alignments 1 bam Broad Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeBroadHistone/wgEncodeBroadHistoneHelas3H3k27acStdAlnRep2.bam HeLa-S3 ChipSeq H3K27ac Alignments 2 bam Broad Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeBroadHistone/wgEncodeBroadHistoneHelas3H3k27acStdPk.broadPeak.gz HeLa-S3 ChipSeq H3K27ac Peaks broadPeak Broad Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeBroadHistone/wgEncodeBroadHistoneHelas3H3k27acStdSig.bigWig HeLa-S3 ChipSeq H3K27ac Signal bigWig Broad Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeBroadHistone/wgEncodeBroadHistoneHelas3H3k27me3StdAlnRep1.bam HeLa-S3 ChipSeq H3K27me3 Alignments 1 bam Broad Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeBroadHistone/wgEncodeBroadHistoneHelas3H3k27me3StdAlnRep2.bam HeLa-S3 ChipSeq H3K27me3 Alignments 2 bam Broad Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeBroadHistone/wgEncodeBroadHistoneHelas3H3k27me3StdPk.broadPeak.gz HeLa-S3 ChipSeq H3K27me3 Peaks broadPeak Broad Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeBroadHistone/wgEncodeBroadHistoneHelas3H3k27me3StdSig.bigWig HeLa-S3 ChipSeq H3K27me3 Signal bigWig Broad Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeBroadHistone/wgEncodeBroadHistoneHelas3H3k36me3StdAlnRep1.bam HeLa-S3 ChipSeq H3K36me3 Alignments 1 bam Broad Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeBroadHistone/wgEncodeBroadHistoneHelas3H3k36me3StdAlnRep2.bam HeLa-S3 ChipSeq H3K36me3 Alignments 2 bam Broad Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeBroadHistone/wgEncodeBroadHistoneHelas3H3k36me3StdPk.broadPeak.gz HeLa-S3 ChipSeq H3K36me3 Peaks broadPeak Broad Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeBroadHistone/wgEncodeBroadHistoneHelas3H3k36me3StdSig.bigWig HeLa-S3 ChipSeq H3K36me3 Signal bigWig Broad Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeBroadHistone/wgEncodeBroadHistoneHelas3H3k4me2StdAlnRep1.bam HeLa-S3 ChipSeq H3K4me2 Alignments 1 bam Broad Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeBroadHistone/wgEncodeBroadHistoneHelas3H3k4me2StdAlnRep2.bam HeLa-S3 ChipSeq H3K4me2 Alignments 2 bam Broad Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeBroadHistone/wgEncodeBroadHistoneHelas3H3k4me2StdPk.broadPeak.gz HeLa-S3 ChipSeq H3K4me2 Peaks broadPeak Broad Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeBroadHistone/wgEncodeBroadHistoneHelas3H3k4me2StdSig.bigWig HeLa-S3 ChipSeq H3K4me2 Signal bigWig Broad Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeBroadHistone/wgEncodeBroadHistoneHelas3H3k4me3StdAlnRep1.bam HeLa-S3 ChipSeq H3K4me3 Alignments 1 bam Broad Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeBroadHistone/wgEncodeBroadHistoneHelas3H3k4me3StdAlnRep2.bam HeLa-S3 ChipSeq H3K4me3 Alignments 2 bam Broad Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeBroadHistone/wgEncodeBroadHistoneHelas3H3k4me3StdPk.broadPeak.gz HeLa-S3 ChipSeq H3K4me3 Peaks broadPeak Broad Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeBroadHistone/wgEncodeBroadHistoneHelas3H3k4me3StdSig.bigWig HeLa-S3 ChipSeq H3K4me3 Signal bigWig Broad Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeBroadHistone/wgEncodeBroadHistoneHelas3H3k79me2StdAlnRep1.bam HeLa-S3 ChipSeq H3K79me2 Alignments 1 bam Broad Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeBroadHistone/wgEncodeBroadHistoneHelas3H3k79me2StdAlnRep2.bam HeLa-S3 ChipSeq H3K79me2 Alignments 2 bam Broad Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeBroadHistone/wgEncodeBroadHistoneHelas3H3k79me2StdPk.broadPeak.gz HeLa-S3 ChipSeq H3K79me2 Peaks broadPeak Broad Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeBroadHistone/wgEncodeBroadHistoneHelas3H3k79me2StdSig.bigWig HeLa-S3 ChipSeq H3K79me2 Signal bigWig Broad Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeBroadHistone/wgEncodeBroadHistoneHelas3H3k9acStdAlnRep1.bam HeLa-S3 ChipSeq H3K9ac Alignments 1 bam Broad Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeBroadHistone/wgEncodeBroadHistoneHelas3H3k9acStdAlnRep2.bam HeLa-S3 ChipSeq H3K9ac Alignments 2 bam Broad Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeBroadHistone/wgEncodeBroadHistoneHelas3H3k9acStdPk.broadPeak.gz HeLa-S3 ChipSeq H3K9ac Peaks broadPeak Broad Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeBroadHistone/wgEncodeBroadHistoneHelas3H3k9acStdSig.bigWig HeLa-S3 ChipSeq H3K9ac Signal bigWig Broad Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeBroadHistone/wgEncodeBroadHistoneHelas3H4k20me1StdAlnRep1.bam HeLa-S3 ChipSeq H4K20me1 Alignments 1 bam Broad Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeBroadHistone/wgEncodeBroadHistoneHelas3H4k20me1StdAlnRep2.bam HeLa-S3 ChipSeq H4K20me1 Alignments 2 bam Broad Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeBroadHistone/wgEncodeBroadHistoneHelas3H4k20me1StdPk.broadPeak.gz HeLa-S3 ChipSeq H4K20me1 Peaks broadPeak Broad Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeBroadHistone/wgEncodeBroadHistoneHelas3H4k20me1StdSig.bigWig HeLa-S3 ChipSeq H4K20me1 Signal bigWig Broad Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeBroadHistone/wgEncodeBroadHistoneHelas3Pol2bStdAlnRep1.bam HeLa-S3 ChipSeq Pol2(b) Alignments 1 bam Broad Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeBroadHistone/wgEncodeBroadHistoneHelas3Pol2bStdAlnRep2.bam HeLa-S3 ChipSeq Pol2(b) Alignments 2 bam Broad Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeBroadHistone/wgEncodeBroadHistoneHelas3Pol2bStdPk.broadPeak.gz HeLa-S3 ChipSeq Pol2(b) Peaks broadPeak Broad Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeBroadHistone/wgEncodeBroadHistoneHelas3Pol2bStdSig.bigWig HeLa-S3 ChipSeq Pol2(b) Signal bigWig Broad Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeBroadHistone/wgEncodeBroadHistoneHepg2ControlStdAlnRep1.bam HepG2 ChipSeq Input Alignments 1 bam Broad Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeBroadHistone/wgEncodeBroadHistoneHepg2ControlStdAlnRep2.bam HepG2 ChipSeq Input Alignments 2 bam Broad Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeBroadHistone/wgEncodeBroadHistoneHepg2ControlStdSig.bigWig HepG2 ChipSeq Input Signal bigWig Broad Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeBroadHistone/wgEncodeBroadHistoneHepg2CtcfStdAlnRep1.bam HepG2 ChipSeq CTCF Alignments 1 bam Broad Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeBroadHistone/wgEncodeBroadHistoneHepg2CtcfStdAlnRep2.bam HepG2 ChipSeq CTCF Alignments 2 bam Broad Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeBroadHistone/wgEncodeBroadHistoneHepg2CtcfStdPk.broadPeak.gz HepG2 ChipSeq CTCF Peaks broadPeak Broad Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeBroadHistone/wgEncodeBroadHistoneHepg2CtcfStdSig.bigWig HepG2 ChipSeq CTCF Signal bigWig Broad Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeBroadHistone/wgEncodeBroadHistoneHepg2Ezh239875AlnRep1.bam HepG2 ChipSeq EZH2_(39875) Alignments 1 bam Broad Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeBroadHistone/wgEncodeBroadHistoneHepg2Ezh239875AlnRep2.bam HepG2 ChipSeq EZH2_(39875) Alignments 2 bam Broad Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeBroadHistone/wgEncodeBroadHistoneHepg2Ezh239875Pk.broadPeak.gz HepG2 ChipSeq EZH2_(39875) Peaks broadPeak Broad Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeBroadHistone/wgEncodeBroadHistoneHepg2Ezh239875Sig.bigWig HepG2 ChipSeq EZH2_(39875) Signal bigWig Broad Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeBroadHistone/wgEncodeBroadHistoneHepg2H2azStdAlnRep1.bam HepG2 ChipSeq H2A.Z Alignments 1 bam Broad Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeBroadHistone/wgEncodeBroadHistoneHepg2H2azStdAlnRep2.bam HepG2 ChipSeq H2A.Z Alignments 2 bam Broad Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeBroadHistone/wgEncodeBroadHistoneHepg2H2azStdPk.broadPeak.gz HepG2 ChipSeq H2A.Z Peaks broadPeak Broad Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeBroadHistone/wgEncodeBroadHistoneHepg2H2azStdSig.bigWig HepG2 ChipSeq H2A.Z Signal bigWig Broad Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeBroadHistone/wgEncodeBroadHistoneHepg2H3k04me1StdAlnRep1.bam HepG2 ChipSeq H3K4me1 Alignments 1 bam Broad Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeBroadHistone/wgEncodeBroadHistoneHepg2H3k04me1StdAlnRep2.bam HepG2 ChipSeq H3K4me1 Alignments 2 bam Broad Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeBroadHistone/wgEncodeBroadHistoneHepg2H3k04me1StdPk.broadPeak.gz HepG2 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HepG2 ChipSeq H3K79me2 Alignments 1 bam Broad Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeBroadHistone/wgEncodeBroadHistoneHepg2H3k79me2StdAlnRep2.bam HepG2 ChipSeq H3K79me2 Alignments 2 bam Broad Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeBroadHistone/wgEncodeBroadHistoneHepg2H3k79me2StdPk.broadPeak.gz HepG2 ChipSeq H3K79me2 Peaks broadPeak Broad Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeBroadHistone/wgEncodeBroadHistoneHepg2H3k79me2StdSig.bigWig HepG2 ChipSeq H3K79me2 Signal bigWig Broad Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeBroadHistone/wgEncodeBroadHistoneHepg2H3k9acStdAlnRep1.bam HepG2 ChipSeq H3K9ac Alignments 1 bam Broad Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeBroadHistone/wgEncodeBroadHistoneHepg2H3k9acStdAlnRep2.bam HepG2 ChipSeq H3K9ac Alignments 2 bam Broad Data 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http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeBroadHistone/wgEncodeBroadHistoneHepg2H4k20me1StdSig.bigWig HepG2 ChipSeq H4K20me1 Signal bigWig Broad Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeBroadHistone/wgEncodeBroadHistoneHmecControlStdAlnRep1.bam HMEC ChipSeq Input Alignments 1 bam Broad Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeBroadHistone/wgEncodeBroadHistoneHmecControlStdAlnRep2.bam HMEC ChipSeq Input Alignments 2 bam Broad Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeBroadHistone/wgEncodeBroadHistoneHmecControlStdSig.bigWig HMEC ChipSeq Input Signal bigWig Broad Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeBroadHistone/wgEncodeBroadHistoneHmecCtcfStdAlnRep1.bam HMEC ChipSeq CTCF Alignments 1 bam Broad Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeBroadHistone/wgEncodeBroadHistoneHmecCtcfStdAlnRep2.bam HMEC ChipSeq CTCF Alignments 2 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http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeBroadHistone/wgEncodeBroadHistoneHmecEzh239875Sig.bigWig HMEC ChipSeq EZH2_(39875) Signal bigWig Broad Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeBroadHistone/wgEncodeBroadHistoneHmecH2azAlnRep1.bam HMEC ChipSeq H2A.Z Alignments 1 bam Broad Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeBroadHistone/wgEncodeBroadHistoneHmecH2azAlnRep2.bam HMEC ChipSeq H2A.Z Alignments 2 bam Broad Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeBroadHistone/wgEncodeBroadHistoneHmecH2azPk.broadPeak.gz HMEC ChipSeq H2A.Z Peaks broadPeak Broad Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeBroadHistone/wgEncodeBroadHistoneHmecH2azSig.bigWig HMEC ChipSeq H2A.Z Signal bigWig Broad Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeBroadHistone/wgEncodeBroadHistoneHmecH3k09me3AlnRep1.bam HMEC ChipSeq H3K9me3 Alignments 1 bam Broad Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeBroadHistone/wgEncodeBroadHistoneHmecH3k09me3AlnRep2.bam HMEC ChipSeq H3K9me3 Alignments 2 bam Broad Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeBroadHistone/wgEncodeBroadHistoneHmecH3k09me3Pk.broadPeak.gz HMEC ChipSeq H3K9me3 Peaks broadPeak Broad Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeBroadHistone/wgEncodeBroadHistoneHmecH3k09me3Sig.bigWig HMEC ChipSeq H3K9me3 Signal bigWig Broad Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeBroadHistone/wgEncodeBroadHistoneHmecH3k27acStdAlnRep1.bam HMEC ChipSeq H3K27ac Alignments 1 bam Broad Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeBroadHistone/wgEncodeBroadHistoneHmecH3k27acStdAlnRep2.bam HMEC ChipSeq H3K27ac Alignments 2 bam Broad Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeBroadHistone/wgEncodeBroadHistoneHmecH3k27acStdPk.broadPeak.gz HMEC ChipSeq H3K27ac Peaks broadPeak Broad Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeBroadHistone/wgEncodeBroadHistoneHmecH3k27acStdSig.bigWig HMEC ChipSeq H3K27ac Signal bigWig Broad Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeBroadHistone/wgEncodeBroadHistoneHmecH3k27me3StdAlnRep1.bam HMEC ChipSeq H3K27me3 Alignments 1 bam Broad Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeBroadHistone/wgEncodeBroadHistoneHmecH3k27me3StdAlnRep2.bam HMEC ChipSeq H3K27me3 Alignments 2 bam Broad Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeBroadHistone/wgEncodeBroadHistoneHmecH3k27me3StdPk.broadPeak.gz HMEC ChipSeq H3K27me3 Peaks broadPeak Broad Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeBroadHistone/wgEncodeBroadHistoneHmecH3k27me3StdSig.bigWig HMEC ChipSeq H3K27me3 Signal bigWig Broad Data 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ChipSeq H3K4me1 Alignments 2 bam Broad Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeBroadHistone/wgEncodeBroadHistoneHmecH3k4me1StdPk.broadPeak.gz HMEC ChipSeq H3K4me1 Peaks broadPeak Broad Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeBroadHistone/wgEncodeBroadHistoneHmecH3k4me1StdSig.bigWig HMEC ChipSeq H3K4me1 Signal bigWig Broad Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeBroadHistone/wgEncodeBroadHistoneHmecH3k4me2StdAlnRep1.bam HMEC ChipSeq H3K4me2 Alignments 1 bam Broad Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeBroadHistone/wgEncodeBroadHistoneHmecH3k4me2StdAlnRep2.bam HMEC ChipSeq H3K4me2 Alignments 2 bam Broad Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeBroadHistone/wgEncodeBroadHistoneHmecH3k4me2StdPk.broadPeak.gz HMEC ChipSeq H3K4me2 Peaks broadPeak Broad Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeBroadHistone/wgEncodeBroadHistoneHmecH3k4me2StdSig.bigWig HMEC ChipSeq H3K4me2 Signal bigWig Broad Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeBroadHistone/wgEncodeBroadHistoneHmecH3k4me3StdAlnRep1.bam HMEC ChipSeq H3K4me3 Alignments 1 bam Broad Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeBroadHistone/wgEncodeBroadHistoneHmecH3k4me3StdAlnRep2.bam HMEC ChipSeq H3K4me3 Alignments 2 bam Broad Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeBroadHistone/wgEncodeBroadHistoneHmecH3k4me3StdPk.broadPeak.gz HMEC ChipSeq H3K4me3 Peaks broadPeak Broad Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeBroadHistone/wgEncodeBroadHistoneHmecH3k4me3StdSig.bigWig HMEC ChipSeq H3K4me3 Signal bigWig Broad Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeBroadHistone/wgEncodeBroadHistoneHmecH3k79me2AlnRep1.bam HMEC ChipSeq H3K79me2 Alignments 1 bam Broad Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeBroadHistone/wgEncodeBroadHistoneHmecH3k79me2AlnRep2.bam HMEC ChipSeq H3K79me2 Alignments 2 bam Broad Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeBroadHistone/wgEncodeBroadHistoneHmecH3k79me2Pk.broadPeak.gz HMEC ChipSeq H3K79me2 Peaks broadPeak Broad Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeBroadHistone/wgEncodeBroadHistoneHmecH3k79me2Sig.bigWig HMEC ChipSeq H3K79me2 Signal bigWig Broad Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeBroadHistone/wgEncodeBroadHistoneHmecH3k9acStdAlnRep1.bam HMEC ChipSeq H3K9ac Alignments 1 bam Broad Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeBroadHistone/wgEncodeBroadHistoneHmecH3k9acStdAlnRep2.bam HMEC ChipSeq H3K9ac Alignments 2 bam Broad Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeBroadHistone/wgEncodeBroadHistoneHmecH3k9acStdPk.broadPeak.gz HMEC ChipSeq H3K9ac Peaks broadPeak Broad Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeBroadHistone/wgEncodeBroadHistoneHmecH3k9acStdSig.bigWig HMEC ChipSeq H3K9ac Signal bigWig Broad Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeBroadHistone/wgEncodeBroadHistoneHmecH4k20me1StdAlnRep1.bam HMEC ChipSeq H4K20me1 Alignments 1 bam Broad Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeBroadHistone/wgEncodeBroadHistoneHmecH4k20me1StdAlnRep2.bam HMEC ChipSeq H4K20me1 Alignments 2 bam Broad Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeBroadHistone/wgEncodeBroadHistoneHmecH4k20me1StdPk.broadPeak.gz HMEC ChipSeq H4K20me1 Peaks broadPeak Broad Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeBroadHistone/wgEncodeBroadHistoneHmecH4k20me1StdSig.bigWig HMEC ChipSeq H4K20me1 Signal bigWig Broad Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeBroadHistone/wgEncodeBroadHistoneHsmmControlStdAlnRep1.bam HSMM ChipSeq Input Alignments 1 bam Broad Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeBroadHistone/wgEncodeBroadHistoneHsmmControlStdAlnRep2.bam HSMM ChipSeq Input Alignments 2 bam Broad Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeBroadHistone/wgEncodeBroadHistoneHsmmControlStdSig.bigWig HSMM ChipSeq Input Signal bigWig Broad Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeBroadHistone/wgEncodeBroadHistoneHsmmCtcfStdAlnRep1.bam HSMM ChipSeq CTCF Alignments 1 bam Broad Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeBroadHistone/wgEncodeBroadHistoneHsmmCtcfStdAlnRep2.bam HSMM ChipSeq CTCF Alignments 2 bam Broad Data 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Alignments 3 bam Broad Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeBroadHistone/wgEncodeBroadHistoneHuvecCtcfStdPk.broadPeak.gz HUVEC ChipSeq CTCF Peaks broadPeak Broad Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeBroadHistone/wgEncodeBroadHistoneHuvecCtcfStdSig.bigWig HUVEC ChipSeq CTCF Signal bigWig Broad Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeBroadHistone/wgEncodeBroadHistoneHuvecEzh239875AlnRep1.bam HUVEC ChipSeq EZH2_(39875) Alignments 1 bam Broad Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeBroadHistone/wgEncodeBroadHistoneHuvecEzh239875AlnRep2.bam HUVEC ChipSeq EZH2_(39875) Alignments 2 bam Broad Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeBroadHistone/wgEncodeBroadHistoneHuvecEzh239875Pk.broadPeak.gz HUVEC ChipSeq EZH2_(39875) Peaks broadPeak Broad Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeBroadHistone/wgEncodeBroadHistoneHuvecEzh239875Sig.bigWig HUVEC ChipSeq EZH2_(39875) Signal bigWig Broad Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeBroadHistone/wgEncodeBroadHistoneHuvecH2azAlnRep1.bam HUVEC ChipSeq H2A.Z Alignments 1 bam Broad Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeBroadHistone/wgEncodeBroadHistoneHuvecH2azAlnRep2.bam HUVEC ChipSeq H2A.Z Alignments 2 bam Broad Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeBroadHistone/wgEncodeBroadHistoneHuvecH2azPk.broadPeak.gz HUVEC ChipSeq H2A.Z Peaks broadPeak Broad Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeBroadHistone/wgEncodeBroadHistoneHuvecH2azSig.bigWig HUVEC ChipSeq H2A.Z Signal bigWig Broad Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeBroadHistone/wgEncodeBroadHistoneHuvecH3k09me3AlnRep1.bam HUVEC ChipSeq H3K9me3 Alignments 1 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http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeBroadHistone/wgEncodeBroadHistoneHuvecH3k36me3StdPk.broadPeak.gz HUVEC ChipSeq H3K36me3 Peaks broadPeak Broad Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeBroadHistone/wgEncodeBroadHistoneHuvecH3k36me3StdSig.bigWig HUVEC ChipSeq H3K36me3 Signal bigWig Broad Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeBroadHistone/wgEncodeBroadHistoneHuvecH3k4me1StdAlnRep1.bam HUVEC ChipSeq H3K4me1 Alignments 1 bam Broad Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeBroadHistone/wgEncodeBroadHistoneHuvecH3k4me1StdAlnRep2.bam HUVEC ChipSeq H3K4me1 Alignments 2 bam Broad Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeBroadHistone/wgEncodeBroadHistoneHuvecH3k4me1StdAlnRep3.bam HUVEC ChipSeq H3K4me1 Alignments 3 bam Broad Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeBroadHistone/wgEncodeBroadHistoneHuvecH3k4me1StdPk.broadPeak.gz HUVEC ChipSeq H3K4me1 Peaks broadPeak Broad Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeBroadHistone/wgEncodeBroadHistoneHuvecH3k4me1StdSig.bigWig HUVEC ChipSeq H3K4me1 Signal bigWig Broad Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeBroadHistone/wgEncodeBroadHistoneHuvecH3k4me2StdAlnRep1.bam HUVEC ChipSeq H3K4me2 Alignments 1 bam Broad Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeBroadHistone/wgEncodeBroadHistoneHuvecH3k4me2StdAlnRep2.bam HUVEC ChipSeq H3K4me2 Alignments 2 bam Broad Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeBroadHistone/wgEncodeBroadHistoneHuvecH3k4me2StdPk.broadPeak.gz HUVEC ChipSeq H3K4me2 Peaks broadPeak Broad Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeBroadHistone/wgEncodeBroadHistoneHuvecH3k4me2StdSig.bigWig HUVEC ChipSeq H3K4me2 Signal bigWig Broad Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeBroadHistone/wgEncodeBroadHistoneHuvecH3k4me3StdAlnRep1.bam HUVEC ChipSeq H3K4me3 Alignments 1 bam Broad Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeBroadHistone/wgEncodeBroadHistoneHuvecH3k4me3StdAlnRep2.bam HUVEC ChipSeq H3K4me3 Alignments 2 bam Broad Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeBroadHistone/wgEncodeBroadHistoneHuvecH3k4me3StdAlnRep3.bam HUVEC ChipSeq H3K4me3 Alignments 3 bam Broad Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeBroadHistone/wgEncodeBroadHistoneHuvecH3k4me3StdPk.broadPeak.gz HUVEC ChipSeq H3K4me3 Peaks broadPeak Broad Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeBroadHistone/wgEncodeBroadHistoneHuvecH3k4me3StdSig.bigWig HUVEC ChipSeq H3K4me3 Signal bigWig Broad Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeBroadHistone/wgEncodeBroadHistoneHuvecH3k79me2AlnRep1.bam HUVEC ChipSeq H3K79me2 Alignments 1 bam Broad Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeBroadHistone/wgEncodeBroadHistoneHuvecH3k79me2AlnRep2.bam HUVEC ChipSeq H3K79me2 Alignments 2 bam Broad Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeBroadHistone/wgEncodeBroadHistoneHuvecH3k79me2Pk.broadPeak.gz HUVEC ChipSeq H3K79me2 Peaks broadPeak Broad Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeBroadHistone/wgEncodeBroadHistoneHuvecH3k79me2Sig.bigWig HUVEC ChipSeq H3K79me2 Signal bigWig Broad Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeBroadHistone/wgEncodeBroadHistoneHuvecH3k9acStdAlnRep1.bam HUVEC ChipSeq H3K9ac Alignments 1 bam Broad Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeBroadHistone/wgEncodeBroadHistoneHuvecH3k9acStdAlnRep2.bam HUVEC ChipSeq H3K9ac Alignments 2 bam Broad Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeBroadHistone/wgEncodeBroadHistoneHuvecH3k9acStdAlnRep3.bam HUVEC ChipSeq H3K9ac Alignments 3 bam Broad Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeBroadHistone/wgEncodeBroadHistoneHuvecH3k9acStdPk.broadPeak.gz HUVEC ChipSeq H3K9ac Peaks broadPeak Broad Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeBroadHistone/wgEncodeBroadHistoneHuvecH3k9acStdSig.bigWig HUVEC ChipSeq H3K9ac Signal bigWig Broad Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeBroadHistone/wgEncodeBroadHistoneHuvecH3k9me1StdAlnRep1.bam HUVEC ChipSeq H3K9me1 Alignments 1 bam Broad Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeBroadHistone/wgEncodeBroadHistoneHuvecH3k9me1StdAlnRep2.bam HUVEC ChipSeq H3K9me1 Alignments 2 bam Broad Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeBroadHistone/wgEncodeBroadHistoneHuvecH3k9me1StdAlnRep3.bam HUVEC ChipSeq H3K9me1 Alignments 3 bam Broad Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeBroadHistone/wgEncodeBroadHistoneHuvecH3k9me1StdPk.broadPeak.gz HUVEC ChipSeq H3K9me1 Peaks broadPeak Broad Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeBroadHistone/wgEncodeBroadHistoneHuvecH3k9me1StdSig.bigWig HUVEC ChipSeq H3K9me1 Signal bigWig Broad Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeBroadHistone/wgEncodeBroadHistoneHuvecH4k20me1StdAlnRep1.bam HUVEC ChipSeq H4K20me1 Alignments 1 bam Broad Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeBroadHistone/wgEncodeBroadHistoneHuvecH4k20me1StdAlnRep2.bam HUVEC ChipSeq H4K20me1 Alignments 2 bam Broad Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeBroadHistone/wgEncodeBroadHistoneHuvecH4k20me1StdAlnRep3.bam HUVEC ChipSeq H4K20me1 Alignments 3 bam Broad Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeBroadHistone/wgEncodeBroadHistoneHuvecH4k20me1StdPk.broadPeak.gz HUVEC ChipSeq H4K20me1 Peaks broadPeak Broad Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeBroadHistone/wgEncodeBroadHistoneHuvecH4k20me1StdSig.bigWig HUVEC ChipSeq H4K20me1 Signal bigWig Broad Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeBroadHistone/wgEncodeBroadHistoneHuvecPol2bStdAlnRep1.bam HUVEC ChipSeq Pol2(b) Alignments 1 bam Broad Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeBroadHistone/wgEncodeBroadHistoneHuvecPol2bStdAlnRep2.bam HUVEC ChipSeq Pol2(b) Alignments 2 bam Broad Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeBroadHistone/wgEncodeBroadHistoneHuvecPol2bStdAlnRep3.bam HUVEC ChipSeq Pol2(b) Alignments 3 bam Broad Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeBroadHistone/wgEncodeBroadHistoneHuvecPol2bStdPk.broadPeak.gz HUVEC ChipSeq Pol2(b) Peaks broadPeak Broad Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeBroadHistone/wgEncodeBroadHistoneHuvecPol2bStdSig.bigWig HUVEC ChipSeq Pol2(b) Signal bigWig Broad Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeBroadHistone/wgEncodeBroadHistoneK562Cbpsc369AlnRep1.bam K562 ChipSeq CBP_(sc-369) Alignments 1 bam Broad Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeBroadHistone/wgEncodeBroadHistoneK562Cbpsc369Pk.broadPeak.gz K562 ChipSeq CBP_(sc-369) Peaks broadPeak Broad Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeBroadHistone/wgEncodeBroadHistoneK562Cbpsc369Sig.bigWig K562 ChipSeq CBP_(sc-369) Signal bigWig Broad Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeBroadHistone/wgEncodeBroadHistoneK562Cbx2AlnRep1.bam K562 ChipSeq CBX2 Alignments 1 bam Broad Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeBroadHistone/wgEncodeBroadHistoneK562Cbx2Pk.broadPeak.gz K562 ChipSeq CBX2 Peaks broadPeak Broad Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeBroadHistone/wgEncodeBroadHistoneK562Cbx2Sig.bigWig K562 ChipSeq CBX2 Signal bigWig Broad Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeBroadHistone/wgEncodeBroadHistoneK562Cbx3sc101004AlnRep1.bam K562 ChipSeq CBX3_(SC-101004) Alignments 1 bam Broad Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeBroadHistone/wgEncodeBroadHistoneK562Cbx3sc101004Pk.broadPeak.gz K562 ChipSeq CBX3_(SC-101004) Peaks broadPeak Broad Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeBroadHistone/wgEncodeBroadHistoneK562Cbx3sc101004Sig.bigWig K562 ChipSeq CBX3_(SC-101004) Signal bigWig Broad Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeBroadHistone/wgEncodeBroadHistoneK562Cbx8AlnRep1.bam K562 ChipSeq CBX8 Alignments 1 bam Broad Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeBroadHistone/wgEncodeBroadHistoneK562Cbx8Pk.broadPeak.gz K562 ChipSeq CBX8 Peaks broadPeak Broad Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeBroadHistone/wgEncodeBroadHistoneK562Cbx8Sig.bigWig K562 ChipSeq CBX8 Signal bigWig Broad Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeBroadHistone/wgEncodeBroadHistoneK562Chd1a301218aStdAlnRep1.bam K562 ChipSeq CHD1_(A301-218A) Alignments 1 bam Broad Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeBroadHistone/wgEncodeBroadHistoneK562Chd1a301218aStdAlnRep2.bam K562 ChipSeq CHD1_(A301-218A) Alignments 2 bam Broad Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeBroadHistone/wgEncodeBroadHistoneK562Chd1a301218aStdPk.broadPeak.gz K562 ChipSeq CHD1_(A301-218A) Peaks broadPeak Broad Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeBroadHistone/wgEncodeBroadHistoneK562Chd1a301218aStdSig.bigWig K562 ChipSeq CHD1_(A301-218A) Signal bigWig Broad Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeBroadHistone/wgEncodeBroadHistoneK562Chd4mi2AlnRep1.bam K562 ChipSeq CHD4_Mi2 Alignments 1 bam Broad Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeBroadHistone/wgEncodeBroadHistoneK562Chd4mi2Pk.broadPeak.gz K562 ChipSeq CHD4_Mi2 Peaks broadPeak Broad Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeBroadHistone/wgEncodeBroadHistoneK562Chd4mi2Sig.bigWig K562 ChipSeq CHD4_Mi2 Signal bigWig Broad Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeBroadHistone/wgEncodeBroadHistoneK562Chd7a301223a1AlnRep1.bam K562 ChipSeq CHD7_(A301-223A-1) Alignments 1 bam Broad Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeBroadHistone/wgEncodeBroadHistoneK562Chd7a301223a1Pk.broadPeak.gz K562 ChipSeq CHD7_(A301-223A-1) Peaks broadPeak Broad Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeBroadHistone/wgEncodeBroadHistoneK562Chd7a301223a1Sig.bigWig K562 ChipSeq CHD7_(A301-223A-1) Signal bigWig Broad Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeBroadHistone/wgEncodeBroadHistoneK562ControlStdAlnRep1.bam K562 ChipSeq Input Alignments 1 bam Broad Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeBroadHistone/wgEncodeBroadHistoneK562ControlStdSig.bigWig K562 ChipSeq Input Signal bigWig Broad Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeBroadHistone/wgEncodeBroadHistoneK562CtcfStdAlnRep1.bam K562 ChipSeq CTCF Alignments 1 bam Broad Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeBroadHistone/wgEncodeBroadHistoneK562CtcfStdAlnRep2.bam K562 ChipSeq CTCF Alignments 2 bam Broad Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeBroadHistone/wgEncodeBroadHistoneK562CtcfStdPk.broadPeak.gz K562 ChipSeq CTCF Peaks broadPeak Broad Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeBroadHistone/wgEncodeBroadHistoneK562CtcfStdSig.bigWig K562 ChipSeq CTCF Signal bigWig Broad Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeBroadHistone/wgEncodeBroadHistoneK562Ezh239875StdAlnRep1.bam K562 ChipSeq EZH2_(39875) Alignments 1 bam Broad Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeBroadHistone/wgEncodeBroadHistoneK562Ezh239875StdAlnRep2.bam K562 ChipSeq EZH2_(39875) Alignments 2 bam Broad Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeBroadHistone/wgEncodeBroadHistoneK562Ezh239875StdPk.broadPeak.gz K562 ChipSeq EZH2_(39875) Peaks broadPeak Broad Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeBroadHistone/wgEncodeBroadHistoneK562Ezh239875StdSig.bigWig K562 ChipSeq EZH2_(39875) Signal bigWig Broad Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeBroadHistone/wgEncodeBroadHistoneK562H2azStdAlnRep1.bam K562 ChipSeq H2A.Z Alignments 1 bam Broad Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeBroadHistone/wgEncodeBroadHistoneK562H2azStdAlnRep2.bam K562 ChipSeq H2A.Z Alignments 2 bam Broad Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeBroadHistone/wgEncodeBroadHistoneK562H2azStdPk.broadPeak.gz K562 ChipSeq H2A.Z Peaks broadPeak Broad Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeBroadHistone/wgEncodeBroadHistoneK562H2azStdSig.bigWig K562 ChipSeq H2A.Z Signal bigWig Broad Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeBroadHistone/wgEncodeBroadHistoneK562H3k27acStdAlnRep1.bam K562 ChipSeq H3K27ac Alignments 1 bam Broad Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeBroadHistone/wgEncodeBroadHistoneK562H3k27acStdAlnRep2.bam K562 ChipSeq H3K27ac Alignments 2 bam Broad Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeBroadHistone/wgEncodeBroadHistoneK562H3k27acStdPk.broadPeak.gz K562 ChipSeq H3K27ac Peaks broadPeak Broad Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeBroadHistone/wgEncodeBroadHistoneK562H3k27acStdSig.bigWig K562 ChipSeq H3K27ac Signal bigWig Broad Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeBroadHistone/wgEncodeBroadHistoneK562H3k27me3StdAlnRep1.bam K562 ChipSeq H3K27me3 Alignments 1 bam Broad Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeBroadHistone/wgEncodeBroadHistoneK562H3k27me3StdAlnRep2.bam K562 ChipSeq H3K27me3 Alignments 2 bam Broad Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeBroadHistone/wgEncodeBroadHistoneK562H3k27me3StdPk.broadPeak.gz K562 ChipSeq H3K27me3 Peaks broadPeak Broad Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeBroadHistone/wgEncodeBroadHistoneK562H3k27me3StdSig.bigWig K562 ChipSeq H3K27me3 Signal bigWig Broad Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeBroadHistone/wgEncodeBroadHistoneK562H3k36me3StdAlnRep1.bam K562 ChipSeq H3K36me3 Alignments 1 bam Broad Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeBroadHistone/wgEncodeBroadHistoneK562H3k36me3StdAlnRep2.bam K562 ChipSeq H3K36me3 Alignments 2 bam Broad Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeBroadHistone/wgEncodeBroadHistoneK562H3k36me3StdPk.broadPeak.gz K562 ChipSeq H3K36me3 Peaks broadPeak Broad Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeBroadHistone/wgEncodeBroadHistoneK562H3k36me3StdSig.bigWig K562 ChipSeq H3K36me3 Signal bigWig Broad Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeBroadHistone/wgEncodeBroadHistoneK562H3k4me1StdAlnRep1.bam K562 ChipSeq H3K4me1 Alignments 1 bam Broad Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeBroadHistone/wgEncodeBroadHistoneK562H3k4me1StdAlnRep2.bam K562 ChipSeq H3K4me1 Alignments 2 bam Broad Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeBroadHistone/wgEncodeBroadHistoneK562H3k4me1StdPk.broadPeak.gz K562 ChipSeq H3K4me1 Peaks broadPeak Broad Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeBroadHistone/wgEncodeBroadHistoneK562H3k4me1StdSig.bigWig K562 ChipSeq H3K4me1 Signal bigWig Broad Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeBroadHistone/wgEncodeBroadHistoneK562H3k4me2StdAlnRep1.bam K562 ChipSeq H3K4me2 Alignments 1 bam Broad Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeBroadHistone/wgEncodeBroadHistoneK562H3k4me2StdAlnRep2.bam K562 ChipSeq H3K4me2 Alignments 2 bam Broad Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeBroadHistone/wgEncodeBroadHistoneK562H3k4me2StdPk.broadPeak.gz K562 ChipSeq H3K4me2 Peaks broadPeak Broad Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeBroadHistone/wgEncodeBroadHistoneK562H3k4me2StdSig.bigWig K562 ChipSeq H3K4me2 Signal bigWig Broad Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeBroadHistone/wgEncodeBroadHistoneK562H3k4me3StdAlnRep1.bam K562 ChipSeq H3K4me3 Alignments 1 bam Broad Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeBroadHistone/wgEncodeBroadHistoneK562H3k4me3StdAlnRep2.bam K562 ChipSeq H3K4me3 Alignments 2 bam Broad Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeBroadHistone/wgEncodeBroadHistoneK562H3k4me3StdPk.broadPeak.gz K562 ChipSeq H3K4me3 Peaks broadPeak Broad Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeBroadHistone/wgEncodeBroadHistoneK562H3k4me3StdSig.bigWig K562 ChipSeq H3K4me3 Signal bigWig Broad Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeBroadHistone/wgEncodeBroadHistoneK562H3k79me2StdAlnRep1.bam K562 ChipSeq H3K79me2 Alignments 1 bam Broad Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeBroadHistone/wgEncodeBroadHistoneK562H3k79me2StdAlnRep2.bam K562 ChipSeq H3K79me2 Alignments 2 bam Broad Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeBroadHistone/wgEncodeBroadHistoneK562H3k79me2StdPk.broadPeak.gz K562 ChipSeq H3K79me2 Peaks broadPeak Broad Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeBroadHistone/wgEncodeBroadHistoneK562H3k79me2StdSig.bigWig K562 ChipSeq H3K79me2 Signal bigWig Broad Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeBroadHistone/wgEncodeBroadHistoneK562H3k9acStdAlnRep1.bam K562 ChipSeq H3K9ac Alignments 1 bam Broad Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeBroadHistone/wgEncodeBroadHistoneK562H3k9acStdAlnRep2.bam K562 ChipSeq H3K9ac Alignments 2 bam Broad Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeBroadHistone/wgEncodeBroadHistoneK562H3k9acStdPk.broadPeak.gz K562 ChipSeq H3K9ac Peaks broadPeak Broad Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeBroadHistone/wgEncodeBroadHistoneK562H3k9acStdSig.bigWig K562 ChipSeq H3K9ac Signal bigWig Broad Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeBroadHistone/wgEncodeBroadHistoneK562H3k9me1StdAlnRep1.bam K562 ChipSeq H3K9me1 Alignments 1 bam Broad Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeBroadHistone/wgEncodeBroadHistoneK562H3k9me1StdPk.broadPeak.gz K562 ChipSeq H3K9me1 Peaks broadPeak Broad Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeBroadHistone/wgEncodeBroadHistoneK562H3k9me1StdSig.bigWig K562 ChipSeq H3K9me1 Signal bigWig Broad Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeBroadHistone/wgEncodeBroadHistoneK562H3k9me3StdAlnRep1.bam K562 ChipSeq H3K9me3 Alignments 1 bam Broad Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeBroadHistone/wgEncodeBroadHistoneK562H3k9me3StdAlnRep2.bam K562 ChipSeq H3K9me3 Alignments 2 bam Broad Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeBroadHistone/wgEncodeBroadHistoneK562H3k9me3StdPk.broadPeak.gz K562 ChipSeq H3K9me3 Peaks broadPeak Broad Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeBroadHistone/wgEncodeBroadHistoneK562H3k9me3StdSig.bigWig K562 ChipSeq H3K9me3 Signal bigWig Broad Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeBroadHistone/wgEncodeBroadHistoneK562H4k20me1StdAlnRep1.bam K562 ChipSeq H4K20me1 Alignments 1 bam Broad Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeBroadHistone/wgEncodeBroadHistoneK562H4k20me1StdAlnRep2.bam K562 ChipSeq H4K20me1 Alignments 2 bam Broad Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeBroadHistone/wgEncodeBroadHistoneK562H4k20me1StdPk.broadPeak.gz K562 ChipSeq H4K20me1 Peaks broadPeak Broad Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeBroadHistone/wgEncodeBroadHistoneK562H4k20me1StdSig.bigWig K562 ChipSeq H4K20me1 Signal bigWig Broad Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeBroadHistone/wgEncodeBroadHistoneK562Hdac1sc6298StdAlnRep1.bam K562 ChipSeq HDAC1_(SC-6298) Alignments 1 bam Broad Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeBroadHistone/wgEncodeBroadHistoneK562Hdac1sc6298StdAlnRep2.bam K562 ChipSeq HDAC1_(SC-6298) Alignments 2 bam Broad Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeBroadHistone/wgEncodeBroadHistoneK562Hdac1sc6298StdPk.broadPeak.gz K562 ChipSeq HDAC1_(SC-6298) Peaks broadPeak Broad Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeBroadHistone/wgEncodeBroadHistoneK562Hdac1sc6298StdSig.bigWig K562 ChipSeq HDAC1_(SC-6298) Signal bigWig Broad Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeBroadHistone/wgEncodeBroadHistoneK562Hdac2a300705aStdAlnRep1.bam K562 ChipSeq HDAC2_(A300-705A) Alignments 1 bam Broad Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeBroadHistone/wgEncodeBroadHistoneK562Hdac2a300705aStdAlnRep2.bam K562 ChipSeq HDAC2_(A300-705A) Alignments 2 bam Broad Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeBroadHistone/wgEncodeBroadHistoneK562Hdac2a300705aStdPk.broadPeak.gz K562 ChipSeq HDAC2_(A300-705A) Peaks broadPeak Broad Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeBroadHistone/wgEncodeBroadHistoneK562Hdac2a300705aStdSig.bigWig K562 ChipSeq HDAC2_(A300-705A) Signal bigWig Broad Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeBroadHistone/wgEncodeBroadHistoneK562Hdac6a301341aAlnRep1.bam K562 ChipSeq HDAC6_(A301-341A) Alignments 1 bam Broad Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeBroadHistone/wgEncodeBroadHistoneK562Hdac6a301341aAlnRep2.bam K562 ChipSeq HDAC6_(A301-341A) Alignments 2 bam Broad Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeBroadHistone/wgEncodeBroadHistoneK562Hdac6a301341aPk.broadPeak.gz K562 ChipSeq HDAC6_(A301-341A) Peaks broadPeak Broad Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeBroadHistone/wgEncodeBroadHistoneK562Hdac6a301341aSig.bigWig K562 ChipSeq HDAC6_(A301-341A) Signal bigWig Broad Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeBroadHistone/wgEncodeBroadHistoneK562Lsd1AlnRep1.bam K562 ChipSeq LSD1 Alignments 1 bam Broad Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeBroadHistone/wgEncodeBroadHistoneK562Lsd1Pk.broadPeak.gz K562 ChipSeq LSD1 Peaks broadPeak Broad Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeBroadHistone/wgEncodeBroadHistoneK562Lsd1Sig.bigWig K562 ChipSeq LSD1 Signal bigWig Broad Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeBroadHistone/wgEncodeBroadHistoneK562NcorAlnRep1.bam K562 ChipSeq NCoR Alignments 1 bam Broad Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeBroadHistone/wgEncodeBroadHistoneK562NcorPk.broadPeak.gz K562 ChipSeq NCoR Peaks broadPeak Broad Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeBroadHistone/wgEncodeBroadHistoneK562NcorSig.bigWig K562 ChipSeq NCoR Signal bigWig Broad Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeBroadHistone/wgEncodeBroadHistoneK562Nsd2ab75359AlnRep1.bam K562 ChipSeq NSD2_(ab75359) Alignments 1 bam Broad Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeBroadHistone/wgEncodeBroadHistoneK562Nsd2ab75359Pk.broadPeak.gz K562 ChipSeq NSD2_(ab75359) Peaks broadPeak Broad Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeBroadHistone/wgEncodeBroadHistoneK562Nsd2ab75359Sig.bigWig K562 ChipSeq NSD2_(ab75359) Signal bigWig Broad Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeBroadHistone/wgEncodeBroadHistoneK562P300StdAlnRep1.bam K562 ChipSeq p300 Alignments 1 bam Broad Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeBroadHistone/wgEncodeBroadHistoneK562P300StdAlnRep2.bam K562 ChipSeq p300 Alignments 2 bam Broad Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeBroadHistone/wgEncodeBroadHistoneK562P300StdPk.broadPeak.gz K562 ChipSeq p300 Peaks broadPeak Broad Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeBroadHistone/wgEncodeBroadHistoneK562P300StdSig.bigWig K562 ChipSeq p300 Signal bigWig Broad Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeBroadHistone/wgEncodeBroadHistoneK562PcafAlnRep1.bam K562 ChipSeq PCAF Alignments 1 bam Broad Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeBroadHistone/wgEncodeBroadHistoneK562PcafPk.broadPeak.gz K562 ChipSeq PCAF Peaks broadPeak Broad Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeBroadHistone/wgEncodeBroadHistoneK562PcafSig.bigWig K562 ChipSeq PCAF Signal bigWig Broad Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeBroadHistone/wgEncodeBroadHistoneK562Phf8a301772aStdAlnRep1.bam K562 ChipSeq PHF8_(A301-772A) Alignments 1 bam Broad Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeBroadHistone/wgEncodeBroadHistoneK562Phf8a301772aStdAlnRep2.bam K562 ChipSeq PHF8_(A301-772A) Alignments 2 bam Broad Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeBroadHistone/wgEncodeBroadHistoneK562Phf8a301772aStdPk.broadPeak.gz K562 ChipSeq PHF8_(A301-772A) Peaks broadPeak Broad Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeBroadHistone/wgEncodeBroadHistoneK562Phf8a301772aStdSig.bigWig K562 ChipSeq PHF8_(A301-772A) Signal bigWig Broad Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeBroadHistone/wgEncodeBroadHistoneK562Plu1StdAlnRep1.bam K562 ChipSeq PLU1 Alignments 1 bam Broad Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeBroadHistone/wgEncodeBroadHistoneK562Plu1StdAlnRep2.bam K562 ChipSeq PLU1 Alignments 2 bam Broad Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeBroadHistone/wgEncodeBroadHistoneK562Plu1StdPk.broadPeak.gz K562 ChipSeq PLU1 Peaks broadPeak Broad Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeBroadHistone/wgEncodeBroadHistoneK562Plu1StdSig.bigWig K562 ChipSeq PLU1 Signal bigWig Broad Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeBroadHistone/wgEncodeBroadHistoneK562Pol2bStdAlnRep1.bam K562 ChipSeq Pol2(b) Alignments 1 bam Broad Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeBroadHistone/wgEncodeBroadHistoneK562Pol2bStdAlnRep2.bam K562 ChipSeq Pol2(b) Alignments 2 bam Broad Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeBroadHistone/wgEncodeBroadHistoneK562Pol2bStdPk.broadPeak.gz K562 ChipSeq Pol2(b) Peaks broadPeak Broad Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeBroadHistone/wgEncodeBroadHistoneK562Pol2bStdSig.bigWig K562 ChipSeq Pol2(b) Signal bigWig Broad Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeBroadHistone/wgEncodeBroadHistoneK562Rbbp5a300109aStdAlnRep1.bam K562 ChipSeq RBBP5_(A300-109A) Alignments 1 bam Broad Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeBroadHistone/wgEncodeBroadHistoneK562Rbbp5a300109aStdAlnRep2.bam K562 ChipSeq RBBP5_(A300-109A) Alignments 2 bam Broad Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeBroadHistone/wgEncodeBroadHistoneK562Rbbp5a300109aStdPk.broadPeak.gz K562 ChipSeq RBBP5_(A300-109A) Peaks broadPeak Broad Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeBroadHistone/wgEncodeBroadHistoneK562Rbbp5a300109aStdSig.bigWig K562 ChipSeq RBBP5_(A300-109A) Signal bigWig Broad Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeBroadHistone/wgEncodeBroadHistoneK562RestAlnRep1.bam K562 ChipSeq REST Alignments 1 bam Broad Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeBroadHistone/wgEncodeBroadHistoneK562RestPk.broadPeak.gz K562 ChipSeq REST Peaks broadPeak Broad Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeBroadHistone/wgEncodeBroadHistoneK562RestSig.bigWig K562 ChipSeq REST Signal bigWig Broad Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeBroadHistone/wgEncodeBroadHistoneK562Rnf2AlnRep1.bam K562 ChipSeq RNF2 Alignments 1 bam Broad Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeBroadHistone/wgEncodeBroadHistoneK562Rnf2Pk.broadPeak.gz K562 ChipSeq RNF2 Peaks broadPeak Broad Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeBroadHistone/wgEncodeBroadHistoneK562Rnf2Sig.bigWig K562 ChipSeq RNF2 Signal bigWig Broad Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeBroadHistone/wgEncodeBroadHistoneK562Sap3039731StdAlnRep1.bam K562 ChipSeq SAP30_(39731) Alignments 1 bam Broad Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeBroadHistone/wgEncodeBroadHistoneK562Sap3039731StdAlnRep2.bam K562 ChipSeq SAP30_(39731) Alignments 2 bam Broad Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeBroadHistone/wgEncodeBroadHistoneK562Sap3039731StdPk.broadPeak.gz K562 ChipSeq SAP30_(39731) Peaks broadPeak Broad Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeBroadHistone/wgEncodeBroadHistoneK562Sap3039731StdSig.bigWig K562 ChipSeq SAP30_(39731) Signal bigWig Broad Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeBroadHistone/wgEncodeBroadHistoneK562Setdb1AlnRep1.bam K562 ChipSeq SETDB1 Alignments 1 bam Broad Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeBroadHistone/wgEncodeBroadHistoneK562Setdb1Pk.broadPeak.gz K562 ChipSeq SETDB1 Peaks broadPeak Broad Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeBroadHistone/wgEncodeBroadHistoneK562Setdb1Sig.bigWig K562 ChipSeq SETDB1 Signal bigWig Broad Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeBroadHistone/wgEncodeBroadHistoneK562Sirt6AlnRep1.bam K562 ChipSeq SIRT6 Alignments 1 bam Broad Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeBroadHistone/wgEncodeBroadHistoneK562Sirt6Pk.broadPeak.gz K562 ChipSeq SIRT6 Peaks broadPeak Broad Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeBroadHistone/wgEncodeBroadHistoneK562Sirt6Sig.bigWig K562 ChipSeq SIRT6 Signal bigWig Broad Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeBroadHistone/wgEncodeBroadHistoneK562Suz12051317AlnRep1.bam K562 ChipSeq SUZ12_(05-1317) Alignments 1 bam Broad Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeBroadHistone/wgEncodeBroadHistoneK562Suz12051317Pk.broadPeak.gz K562 ChipSeq SUZ12_(05-1317) Peaks broadPeak Broad Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeBroadHistone/wgEncodeBroadHistoneK562Suz12051317Sig.bigWig K562 ChipSeq SUZ12_(05-1317) Signal bigWig Broad Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeBroadHistone/wgEncodeBroadHistoneMonocd14ro1746ControlAlnRep1.bam Monocytes-CD14+_RO01746 ChipSeq Control Alignments 1 bam Broad Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeBroadHistone/wgEncodeBroadHistoneMonocd14ro1746ControlAlnRep2.bam Monocytes-CD14+_RO01746 ChipSeq Control Alignments 2 bam Broad Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeBroadHistone/wgEncodeBroadHistoneMonocd14ro1746ControlSig.bigWig Monocytes-CD14+_RO01746 ChipSeq Control Signal bigWig Broad Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeBroadHistone/wgEncodeBroadHistoneMonocd14ro1746CtcfAlnRep1.bam Monocytes-CD14+_RO01746 ChipSeq CTCF Alignments 1 bam Broad Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeBroadHistone/wgEncodeBroadHistoneMonocd14ro1746CtcfAlnRep2.bam Monocytes-CD14+_RO01746 ChipSeq CTCF Alignments 2 bam Broad Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeBroadHistone/wgEncodeBroadHistoneMonocd14ro1746CtcfPk.broadPeak.gz Monocytes-CD14+_RO01746 ChipSeq CTCF Peaks broadPeak Broad Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeBroadHistone/wgEncodeBroadHistoneMonocd14ro1746CtcfSig.bigWig Monocytes-CD14+_RO01746 ChipSeq CTCF Signal bigWig Broad Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeBroadHistone/wgEncodeBroadHistoneMonocd14ro1746H2azAlnRep1.bam Monocytes-CD14+_RO01746 ChipSeq H2A.Z Alignments 1 bam Broad Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeBroadHistone/wgEncodeBroadHistoneMonocd14ro1746H2azAlnRep2.bam Monocytes-CD14+_RO01746 ChipSeq H2A.Z Alignments 2 bam Broad Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeBroadHistone/wgEncodeBroadHistoneMonocd14ro1746H2azPk.broadPeak.gz Monocytes-CD14+_RO01746 ChipSeq H2A.Z Peaks broadPeak Broad Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeBroadHistone/wgEncodeBroadHistoneMonocd14ro1746H2azSig.bigWig Monocytes-CD14+_RO01746 ChipSeq H2A.Z Signal bigWig Broad Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeBroadHistone/wgEncodeBroadHistoneMonocd14ro1746H3k04me1AlnRep1.bam Monocytes-CD14+_RO01746 ChipSeq H3K4me1 Alignments 1 bam Broad Data 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Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeBroadHistone/wgEncodeBroadHistoneMonocd14ro1746H3k04me3Sig.bigWig Monocytes-CD14+_RO01746 ChipSeq H3K4me3 Signal bigWig Broad Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeBroadHistone/wgEncodeBroadHistoneMonocd14ro1746H3k09acAlnRep1.bam Monocytes-CD14+_RO01746 ChipSeq H3K9ac Alignments 1 bam Broad Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeBroadHistone/wgEncodeBroadHistoneMonocd14ro1746H3k09acAlnRep2.bam Monocytes-CD14+_RO01746 ChipSeq H3K9ac Alignments 2 bam Broad Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeBroadHistone/wgEncodeBroadHistoneMonocd14ro1746H3k09acPk.broadPeak.gz Monocytes-CD14+_RO01746 ChipSeq H3K9ac Peaks broadPeak Broad Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeBroadHistone/wgEncodeBroadHistoneMonocd14ro1746H3k09acSig.bigWig Monocytes-CD14+_RO01746 ChipSeq H3K9ac Signal bigWig Broad Data 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http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeBroadHistone/wgEncodeBroadHistoneMonocd14ro1746H3k27acAlnRep2.bam Monocytes-CD14+_RO01746 ChipSeq H3K27ac Alignments 2 bam Broad Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeBroadHistone/wgEncodeBroadHistoneMonocd14ro1746H3k27acPk.broadPeak.gz Monocytes-CD14+_RO01746 ChipSeq H3K27ac Peaks broadPeak Broad Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeBroadHistone/wgEncodeBroadHistoneMonocd14ro1746H3k27acSig.bigWig Monocytes-CD14+_RO01746 ChipSeq H3K27ac Signal bigWig Broad Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeBroadHistone/wgEncodeBroadHistoneMonocd14ro1746H3k27me3AlnRep1.bam Monocytes-CD14+_RO01746 ChipSeq H3K27me3 Alignments 1 bam Broad Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeBroadHistone/wgEncodeBroadHistoneMonocd14ro1746H3k27me3AlnRep2.bam Monocytes-CD14+_RO01746 ChipSeq H3K27me3 Alignments 2 bam Broad Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeBroadHistone/wgEncodeBroadHistoneMonocd14ro1746H3k27me3Pk.broadPeak.gz Monocytes-CD14+_RO01746 ChipSeq H3K27me3 Peaks broadPeak Broad Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeBroadHistone/wgEncodeBroadHistoneMonocd14ro1746H3k27me3Sig.bigWig Monocytes-CD14+_RO01746 ChipSeq H3K27me3 Signal bigWig Broad Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeBroadHistone/wgEncodeBroadHistoneMonocd14ro1746H3k36me3AlnRep1.bam Monocytes-CD14+_RO01746 ChipSeq H3K36me3 Alignments 1 bam Broad Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeBroadHistone/wgEncodeBroadHistoneMonocd14ro1746H3k36me3AlnRep2.bam Monocytes-CD14+_RO01746 ChipSeq H3K36me3 Alignments 2 bam Broad Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeBroadHistone/wgEncodeBroadHistoneMonocd14ro1746H3k36me3Pk.broadPeak.gz Monocytes-CD14+_RO01746 ChipSeq H3K36me3 Peaks broadPeak Broad Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeBroadHistone/wgEncodeBroadHistoneMonocd14ro1746H3k36me3Sig.bigWig Monocytes-CD14+_RO01746 ChipSeq H3K36me3 Signal bigWig Broad Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeBroadHistone/wgEncodeBroadHistoneMonocd14ro1746H3k79me2AlnRep1.bam Monocytes-CD14+_RO01746 ChipSeq H3K79me2 Alignments 1 bam Broad Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeBroadHistone/wgEncodeBroadHistoneMonocd14ro1746H3k79me2AlnRep2.bam Monocytes-CD14+_RO01746 ChipSeq H3K79me2 Alignments 2 bam Broad Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeBroadHistone/wgEncodeBroadHistoneMonocd14ro1746H3k79me2Pk.broadPeak.gz Monocytes-CD14+_RO01746 ChipSeq H3K79me2 Peaks broadPeak Broad Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeBroadHistone/wgEncodeBroadHistoneMonocd14ro1746H3k79me2Sig.bigWig Monocytes-CD14+_RO01746 ChipSeq H3K79me2 Signal bigWig Broad Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeBroadHistone/wgEncodeBroadHistoneMonocd14ro1746H4k20me1AlnRep1.bam Monocytes-CD14+_RO01746 ChipSeq H4K20me1 Alignments 1 bam Broad Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeBroadHistone/wgEncodeBroadHistoneMonocd14ro1746H4k20me1AlnRep2.bam Monocytes-CD14+_RO01746 ChipSeq H4K20me1 Alignments 2 bam Broad Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeBroadHistone/wgEncodeBroadHistoneMonocd14ro1746H4k20me1Pk.broadPeak.gz Monocytes-CD14+_RO01746 ChipSeq H4K20me1 Peaks broadPeak Broad Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeBroadHistone/wgEncodeBroadHistoneMonocd14ro1746H4k20me1Sig.bigWig Monocytes-CD14+_RO01746 ChipSeq H4K20me1 Signal bigWig Broad Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeBroadHistone/wgEncodeBroadHistoneNhaControlStdAlnRep1.bam NH-A ChipSeq Input Alignments 1 bam Broad Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeBroadHistone/wgEncodeBroadHistoneNhaControlStdAlnRep2.bam NH-A ChipSeq Input Alignments 2 bam Broad Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeBroadHistone/wgEncodeBroadHistoneNhaControlStdSig.bigWig NH-A ChipSeq Input Signal bigWig Broad Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeBroadHistone/wgEncodeBroadHistoneNhaCtcfStdAlnRep1.bam NH-A ChipSeq CTCF Alignments 1 bam Broad Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeBroadHistone/wgEncodeBroadHistoneNhaCtcfStdAlnRep2.bam NH-A ChipSeq CTCF Alignments 2 bam Broad Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeBroadHistone/wgEncodeBroadHistoneNhaCtcfStdPk.broadPeak.gz NH-A ChipSeq CTCF Peaks broadPeak Broad Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeBroadHistone/wgEncodeBroadHistoneNhaCtcfStdSig.bigWig NH-A ChipSeq CTCF Signal bigWig Broad Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeBroadHistone/wgEncodeBroadHistoneNhaEzh239875AlnRep1.bam NH-A ChipSeq EZH2_(39875) Alignments 1 bam Broad Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeBroadHistone/wgEncodeBroadHistoneNhaEzh239875AlnRep2.bam NH-A ChipSeq EZH2_(39875) Alignments 2 bam Broad Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeBroadHistone/wgEncodeBroadHistoneNhaEzh239875Pk.broadPeak.gz NH-A ChipSeq EZH2_(39875) Peaks broadPeak Broad Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeBroadHistone/wgEncodeBroadHistoneNhaEzh239875Sig.bigWig NH-A ChipSeq EZH2_(39875) Signal bigWig Broad Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeBroadHistone/wgEncodeBroadHistoneNhaH2azAlnRep1.bam NH-A ChipSeq H2A.Z Alignments 1 bam Broad Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeBroadHistone/wgEncodeBroadHistoneNhaH2azAlnRep2.bam NH-A ChipSeq H2A.Z Alignments 2 bam Broad Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeBroadHistone/wgEncodeBroadHistoneNhaH2azPk.broadPeak.gz NH-A ChipSeq H2A.Z Peaks broadPeak Broad Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeBroadHistone/wgEncodeBroadHistoneNhaH2azSig.bigWig NH-A ChipSeq H2A.Z Signal bigWig Broad Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeBroadHistone/wgEncodeBroadHistoneNhaH3k04me2AlnRep1.bam NH-A ChipSeq H3K4me2 Alignments 1 bam Broad Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeBroadHistone/wgEncodeBroadHistoneNhaH3k04me2AlnRep2.bam NH-A ChipSeq H3K4me2 Alignments 2 bam Broad Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeBroadHistone/wgEncodeBroadHistoneNhaH3k04me2Pk.broadPeak.gz NH-A ChipSeq H3K4me2 Peaks broadPeak Broad Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeBroadHistone/wgEncodeBroadHistoneNhaH3k04me2Sig.bigWig NH-A ChipSeq H3K4me2 Signal bigWig Broad Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeBroadHistone/wgEncodeBroadHistoneNhaH3k09acAlnRep1.bam NH-A ChipSeq H3K9ac Alignments 1 bam Broad Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeBroadHistone/wgEncodeBroadHistoneNhaH3k09acAlnRep2.bam NH-A ChipSeq H3K9ac Alignments 2 bam Broad Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeBroadHistone/wgEncodeBroadHistoneNhaH3k09acPk.broadPeak.gz NH-A ChipSeq H3K9ac Peaks broadPeak Broad Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeBroadHistone/wgEncodeBroadHistoneNhaH3k09acSig.bigWig NH-A ChipSeq H3K9ac Signal bigWig Broad Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeBroadHistone/wgEncodeBroadHistoneNhaH3k09me3AlnRep1.bam NH-A ChipSeq H3K9me3 Alignments 1 bam Broad Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeBroadHistone/wgEncodeBroadHistoneNhaH3k09me3AlnRep2.bam NH-A ChipSeq H3K9me3 Alignments 2 bam Broad Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeBroadHistone/wgEncodeBroadHistoneNhaH3k09me3Pk.broadPeak.gz NH-A ChipSeq H3K9me3 Peaks broadPeak Broad Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeBroadHistone/wgEncodeBroadHistoneNhaH3k09me3Sig.bigWig NH-A ChipSeq H3K9me3 Signal bigWig Broad Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeBroadHistone/wgEncodeBroadHistoneNhaH3k27acStdAlnRep1.bam NH-A ChipSeq H3K27ac Alignments 1 bam Broad Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeBroadHistone/wgEncodeBroadHistoneNhaH3k27acStdAlnRep2.bam NH-A ChipSeq H3K27ac Alignments 2 bam Broad Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeBroadHistone/wgEncodeBroadHistoneNhaH3k27acStdPk.broadPeak.gz NH-A ChipSeq H3K27ac Peaks broadPeak Broad Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeBroadHistone/wgEncodeBroadHistoneNhaH3k27acStdSig.bigWig NH-A ChipSeq H3K27ac Signal bigWig Broad Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeBroadHistone/wgEncodeBroadHistoneNhaH3k27me3StdAlnRep1.bam NH-A ChipSeq H3K27me3 Alignments 1 bam Broad Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeBroadHistone/wgEncodeBroadHistoneNhaH3k27me3StdAlnRep2.bam NH-A ChipSeq H3K27me3 Alignments 2 bam Broad Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeBroadHistone/wgEncodeBroadHistoneNhaH3k27me3StdPk.broadPeak.gz NH-A ChipSeq H3K27me3 Peaks broadPeak Broad Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeBroadHistone/wgEncodeBroadHistoneNhaH3k27me3StdSig.bigWig NH-A ChipSeq H3K27me3 Signal bigWig Broad Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeBroadHistone/wgEncodeBroadHistoneNhaH3k36me3StdAlnRep1.bam NH-A ChipSeq H3K36me3 Alignments 1 bam Broad Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeBroadHistone/wgEncodeBroadHistoneNhaH3k36me3StdAlnRep2.bam NH-A ChipSeq H3K36me3 Alignments 2 bam Broad Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeBroadHistone/wgEncodeBroadHistoneNhaH3k36me3StdPk.broadPeak.gz NH-A ChipSeq H3K36me3 Peaks broadPeak Broad Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeBroadHistone/wgEncodeBroadHistoneNhaH3k36me3StdSig.bigWig NH-A ChipSeq H3K36me3 Signal bigWig Broad Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeBroadHistone/wgEncodeBroadHistoneNhaH3k4me1StdAlnRep1.bam NH-A ChipSeq H3K4me1 Alignments 1 bam Broad Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeBroadHistone/wgEncodeBroadHistoneNhaH3k4me1StdAlnRep2.bam NH-A ChipSeq H3K4me1 Alignments 2 bam Broad Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeBroadHistone/wgEncodeBroadHistoneNhaH3k4me1StdPk.broadPeak.gz NH-A ChipSeq H3K4me1 Peaks broadPeak Broad Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeBroadHistone/wgEncodeBroadHistoneNhaH3k4me1StdSig.bigWig NH-A ChipSeq H3K4me1 Signal bigWig Broad Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeBroadHistone/wgEncodeBroadHistoneNhaH3k4me3StdAlnRep1.bam NH-A ChipSeq H3K4me3 Alignments 1 bam Broad Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeBroadHistone/wgEncodeBroadHistoneNhaH3k4me3StdAlnRep2.bam NH-A ChipSeq H3K4me3 Alignments 2 bam Broad Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeBroadHistone/wgEncodeBroadHistoneNhaH3k4me3StdPk.broadPeak.gz NH-A ChipSeq H3K4me3 Peaks broadPeak Broad Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeBroadHistone/wgEncodeBroadHistoneNhaH3k4me3StdSig.bigWig NH-A ChipSeq H3K4me3 Signal bigWig Broad Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeBroadHistone/wgEncodeBroadHistoneNhaH3k79me2AlnRep1.bam NH-A ChipSeq H3K79me2 Alignments 1 bam Broad Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeBroadHistone/wgEncodeBroadHistoneNhaH3k79me2AlnRep2.bam NH-A ChipSeq H3K79me2 Alignments 2 bam Broad Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeBroadHistone/wgEncodeBroadHistoneNhaH3k79me2Pk.broadPeak.gz NH-A ChipSeq H3K79me2 Peaks broadPeak Broad Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeBroadHistone/wgEncodeBroadHistoneNhaH3k79me2Sig.bigWig NH-A ChipSeq H3K79me2 Signal bigWig Broad Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeBroadHistone/wgEncodeBroadHistoneNhaH4k20me1AlnRep1.bam NH-A ChipSeq H4K20me1 Alignments 1 bam Broad Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeBroadHistone/wgEncodeBroadHistoneNhaH4k20me1AlnRep2.bam NH-A ChipSeq H4K20me1 Alignments 2 bam Broad Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeBroadHistone/wgEncodeBroadHistoneNhaH4k20me1Pk.broadPeak.gz NH-A ChipSeq H4K20me1 Peaks broadPeak Broad Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeBroadHistone/wgEncodeBroadHistoneNhaH4k20me1Sig.bigWig NH-A ChipSeq H4K20me1 Signal bigWig Broad Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeBroadHistone/wgEncodeBroadHistoneNhdfadControlStdAlnRep1.bam NHDF-Ad ChipSeq Input Alignments 1 bam Broad Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeBroadHistone/wgEncodeBroadHistoneNhdfadControlStdAlnRep2.bam NHDF-Ad ChipSeq Input Alignments 2 bam Broad Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeBroadHistone/wgEncodeBroadHistoneNhdfadControlStdSig.bigWig NHDF-Ad ChipSeq Input Signal bigWig Broad Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeBroadHistone/wgEncodeBroadHistoneNhdfadCtcfStdAlnRep1.bam NHDF-Ad ChipSeq CTCF Alignments 1 bam Broad Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeBroadHistone/wgEncodeBroadHistoneNhdfadCtcfStdAlnRep2.bam NHDF-Ad ChipSeq CTCF Alignments 2 bam Broad Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeBroadHistone/wgEncodeBroadHistoneNhdfadCtcfStdPk.broadPeak.gz NHDF-Ad ChipSeq CTCF Peaks broadPeak Broad Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeBroadHistone/wgEncodeBroadHistoneNhdfadCtcfStdSig.bigWig NHDF-Ad ChipSeq CTCF Signal bigWig Broad Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeBroadHistone/wgEncodeBroadHistoneNhdfadEzh239875AlnRep1.bam NHDF-Ad ChipSeq 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http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeBroadHistone/wgEncodeBroadHistoneNhdfadH3k36me3StdSig.bigWig NHDF-Ad ChipSeq H3K36me3 Signal bigWig Broad Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeBroadHistone/wgEncodeBroadHistoneNhdfadH3k4me2StdAlnRep1.bam NHDF-Ad ChipSeq H3K4me2 Alignments 1 bam Broad Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeBroadHistone/wgEncodeBroadHistoneNhdfadH3k4me2StdAlnRep2.bam NHDF-Ad ChipSeq H3K4me2 Alignments 2 bam Broad Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeBroadHistone/wgEncodeBroadHistoneNhdfadH3k4me2StdPk.broadPeak.gz NHDF-Ad ChipSeq H3K4me2 Peaks broadPeak Broad Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeBroadHistone/wgEncodeBroadHistoneNhdfadH3k4me2StdSig.bigWig NHDF-Ad ChipSeq H3K4me2 Signal bigWig Broad Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeBroadHistone/wgEncodeBroadHistoneNhdfadH3k4me3StdAlnRep1.bam NHDF-Ad ChipSeq H3K4me3 Alignments 1 bam Broad Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeBroadHistone/wgEncodeBroadHistoneNhdfadH3k4me3StdAlnRep2.bam NHDF-Ad ChipSeq H3K4me3 Alignments 2 bam Broad Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeBroadHistone/wgEncodeBroadHistoneNhdfadH3k4me3StdPk.broadPeak.gz NHDF-Ad ChipSeq H3K4me3 Peaks broadPeak Broad Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeBroadHistone/wgEncodeBroadHistoneNhdfadH3k4me3StdSig.bigWig NHDF-Ad ChipSeq H3K4me3 Signal bigWig Broad Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeBroadHistone/wgEncodeBroadHistoneNhdfadH3k79me2AlnRep1.bam NHDF-Ad ChipSeq H3K79me2 Alignments 1 bam Broad Data 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http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeBroadHistone/wgEncodeBroadHistoneNhekH2azSig.bigWig NHEK ChipSeq H2A.Z Signal bigWig Broad Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeBroadHistone/wgEncodeBroadHistoneNhekH3k09me3AlnRep1.bam NHEK ChipSeq H3K9me3 Alignments 1 bam Broad Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeBroadHistone/wgEncodeBroadHistoneNhekH3k09me3AlnRep2.bam NHEK ChipSeq H3K9me3 Alignments 2 bam Broad Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeBroadHistone/wgEncodeBroadHistoneNhekH3k09me3Pk.broadPeak.gz NHEK ChipSeq H3K9me3 Peaks broadPeak Broad Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeBroadHistone/wgEncodeBroadHistoneNhekH3k09me3Sig.bigWig NHEK ChipSeq H3K9me3 Signal bigWig Broad Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeBroadHistone/wgEncodeBroadHistoneNhekH3k27acStdAlnRep1.bam NHEK ChipSeq H3K27ac Alignments 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http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeBroadHistone/wgEncodeBroadHistoneNhekH3k4me3StdPk.broadPeak.gz NHEK ChipSeq H3K4me3 Peaks broadPeak Broad Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeBroadHistone/wgEncodeBroadHistoneNhekH3k4me3StdSig.bigWig NHEK ChipSeq H3K4me3 Signal bigWig Broad Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeBroadHistone/wgEncodeBroadHistoneNhekH3k79me2AlnRep1.bam NHEK ChipSeq H3K79me2 Alignments 1 bam Broad Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeBroadHistone/wgEncodeBroadHistoneNhekH3k79me2AlnRep2.bam NHEK ChipSeq H3K79me2 Alignments 2 bam Broad Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeBroadHistone/wgEncodeBroadHistoneNhekH3k79me2Pk.broadPeak.gz NHEK ChipSeq H3K79me2 Peaks broadPeak Broad Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeBroadHistone/wgEncodeBroadHistoneNhekH3k79me2Sig.bigWig NHEK ChipSeq H3K79me2 Signal bigWig Broad Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeBroadHistone/wgEncodeBroadHistoneNhekH3k9acStdAlnRep1.bam NHEK ChipSeq H3K9ac Alignments 1 bam Broad Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeBroadHistone/wgEncodeBroadHistoneNhekH3k9acStdAlnRep2.bam NHEK ChipSeq H3K9ac Alignments 2 bam Broad Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeBroadHistone/wgEncodeBroadHistoneNhekH3k9acStdAlnRep3.bam NHEK ChipSeq H3K9ac Alignments 3 bam Broad Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeBroadHistone/wgEncodeBroadHistoneNhekH3k9acStdPk.broadPeak.gz NHEK ChipSeq H3K9ac Peaks broadPeak Broad Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeBroadHistone/wgEncodeBroadHistoneNhekH3k9acStdSig.bigWig NHEK ChipSeq H3K9ac Signal bigWig Broad Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeBroadHistone/wgEncodeBroadHistoneNhekH3k9me1StdAlnRep1.bam NHEK ChipSeq H3K9me1 Alignments 1 bam Broad Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeBroadHistone/wgEncodeBroadHistoneNhekH3k9me1StdAlnRep2.bam NHEK ChipSeq H3K9me1 Alignments 2 bam Broad Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeBroadHistone/wgEncodeBroadHistoneNhekH3k9me1StdAlnRep3.bam NHEK ChipSeq H3K9me1 Alignments 3 bam Broad Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeBroadHistone/wgEncodeBroadHistoneNhekH3k9me1StdPk.broadPeak.gz NHEK ChipSeq H3K9me1 Peaks broadPeak Broad Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeBroadHistone/wgEncodeBroadHistoneNhekH3k9me1StdSig.bigWig NHEK ChipSeq H3K9me1 Signal bigWig Broad Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeBroadHistone/wgEncodeBroadHistoneNhekH4k20me1StdAlnRep1.bam NHEK ChipSeq H4K20me1 Alignments 1 bam Broad Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeBroadHistone/wgEncodeBroadHistoneNhekH4k20me1StdAlnRep2.bam NHEK ChipSeq H4K20me1 Alignments 2 bam Broad Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeBroadHistone/wgEncodeBroadHistoneNhekH4k20me1StdAlnRep3.bam NHEK ChipSeq H4K20me1 Alignments 3 bam Broad Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeBroadHistone/wgEncodeBroadHistoneNhekH4k20me1StdPk.broadPeak.gz NHEK ChipSeq H4K20me1 Peaks broadPeak Broad Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeBroadHistone/wgEncodeBroadHistoneNhekH4k20me1StdSig.bigWig NHEK ChipSeq H4K20me1 Signal bigWig Broad Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeBroadHistone/wgEncodeBroadHistoneNhekPol2bStdAlnRep1.bam NHEK ChipSeq Pol2(b) Alignments 1 bam Broad Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeBroadHistone/wgEncodeBroadHistoneNhekPol2bStdAlnRep2.bam NHEK ChipSeq Pol2(b) Alignments 2 bam Broad Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeBroadHistone/wgEncodeBroadHistoneNhekPol2bStdPk.broadPeak.gz NHEK ChipSeq Pol2(b) Peaks broadPeak Broad Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeBroadHistone/wgEncodeBroadHistoneNhekPol2bStdSig.bigWig NHEK ChipSeq Pol2(b) Signal bigWig Broad Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeBroadHistone/wgEncodeBroadHistoneNhlfControlStdAlnRep1.bam NHLF ChipSeq Input Alignments 1 bam Broad Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeBroadHistone/wgEncodeBroadHistoneNhlfControlStdAlnRep2.bam NHLF ChipSeq Input Alignments 2 bam Broad Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeBroadHistone/wgEncodeBroadHistoneNhlfControlStdSig.bigWig NHLF ChipSeq Input Signal bigWig Broad Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeBroadHistone/wgEncodeBroadHistoneNhlfCtcfStdAlnRep1.bam NHLF ChipSeq CTCF Alignments 1 bam Broad Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeBroadHistone/wgEncodeBroadHistoneNhlfCtcfStdAlnRep2.bam NHLF ChipSeq CTCF Alignments 2 bam Broad Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeBroadHistone/wgEncodeBroadHistoneNhlfCtcfStdPk.broadPeak.gz NHLF ChipSeq CTCF Peaks broadPeak Broad Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeBroadHistone/wgEncodeBroadHistoneNhlfCtcfStdSig.bigWig NHLF ChipSeq CTCF Signal bigWig Broad Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeBroadHistone/wgEncodeBroadHistoneNhlfEzh239875AlnRep1.bam NHLF ChipSeq EZH2_(39875) Alignments 1 bam Broad Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeBroadHistone/wgEncodeBroadHistoneNhlfEzh239875AlnRep2.bam NHLF ChipSeq EZH2_(39875) Alignments 2 bam Broad Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeBroadHistone/wgEncodeBroadHistoneNhlfEzh239875Pk.broadPeak.gz NHLF ChipSeq EZH2_(39875) Peaks broadPeak Broad Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeBroadHistone/wgEncodeBroadHistoneNhlfEzh239875Sig.bigWig NHLF ChipSeq EZH2_(39875) Signal bigWig Broad Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeBroadHistone/wgEncodeBroadHistoneNhlfH2azAlnRep1.bam NHLF ChipSeq H2A.Z Alignments 1 bam Broad Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeBroadHistone/wgEncodeBroadHistoneNhlfH2azAlnRep2.bam NHLF ChipSeq H2A.Z Alignments 2 bam Broad Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeBroadHistone/wgEncodeBroadHistoneNhlfH2azPk.broadPeak.gz NHLF ChipSeq H2A.Z Peaks broadPeak Broad Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeBroadHistone/wgEncodeBroadHistoneNhlfH2azSig.bigWig NHLF ChipSeq H2A.Z Signal bigWig Broad Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeBroadHistone/wgEncodeBroadHistoneNhlfH3k09me3AlnRep1.bam NHLF ChipSeq H3K9me3 Alignments 1 bam Broad Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeBroadHistone/wgEncodeBroadHistoneNhlfH3k09me3AlnRep2.bam NHLF ChipSeq H3K9me3 Alignments 2 bam Broad Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeBroadHistone/wgEncodeBroadHistoneNhlfH3k09me3Pk.broadPeak.gz NHLF ChipSeq H3K9me3 Peaks broadPeak Broad Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeBroadHistone/wgEncodeBroadHistoneNhlfH3k09me3Sig.bigWig NHLF ChipSeq H3K9me3 Signal bigWig Broad Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeBroadHistone/wgEncodeBroadHistoneNhlfH3k27acStdAlnRep1.bam NHLF ChipSeq H3K27ac Alignments 1 bam Broad Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeBroadHistone/wgEncodeBroadHistoneNhlfH3k27acStdAlnRep2.bam NHLF ChipSeq H3K27ac Alignments 2 bam Broad Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeBroadHistone/wgEncodeBroadHistoneNhlfH3k27acStdPk.broadPeak.gz NHLF ChipSeq H3K27ac Peaks broadPeak Broad Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeBroadHistone/wgEncodeBroadHistoneNhlfH3k27acStdSig.bigWig NHLF ChipSeq H3K27ac Signal bigWig Broad Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeBroadHistone/wgEncodeBroadHistoneNhlfH3k27me3StdAlnRep1.bam NHLF ChipSeq H3K27me3 Alignments 1 bam Broad Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeBroadHistone/wgEncodeBroadHistoneNhlfH3k27me3StdAlnRep2.bam NHLF ChipSeq H3K27me3 Alignments 2 bam Broad Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeBroadHistone/wgEncodeBroadHistoneNhlfH3k27me3StdPk.broadPeak.gz NHLF ChipSeq H3K27me3 Peaks broadPeak Broad Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeBroadHistone/wgEncodeBroadHistoneNhlfH3k27me3StdSig.bigWig NHLF ChipSeq H3K27me3 Signal bigWig Broad Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeBroadHistone/wgEncodeBroadHistoneNhlfH3k36me3StdAlnRep1.bam NHLF ChipSeq H3K36me3 Alignments 1 bam Broad Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeBroadHistone/wgEncodeBroadHistoneNhlfH3k36me3StdAlnRep2.bam NHLF ChipSeq H3K36me3 Alignments 2 bam Broad Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeBroadHistone/wgEncodeBroadHistoneNhlfH3k36me3StdPk.broadPeak.gz NHLF ChipSeq H3K36me3 Peaks broadPeak Broad Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeBroadHistone/wgEncodeBroadHistoneNhlfH3k36me3StdSig.bigWig NHLF ChipSeq H3K36me3 Signal bigWig Broad Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeBroadHistone/wgEncodeBroadHistoneNhlfH3k4me1StdAlnRep1.bam NHLF ChipSeq H3K4me1 Alignments 1 bam Broad Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeBroadHistone/wgEncodeBroadHistoneNhlfH3k4me1StdAlnRep2.bam NHLF ChipSeq H3K4me1 Alignments 2 bam Broad Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeBroadHistone/wgEncodeBroadHistoneNhlfH3k4me1StdPk.broadPeak.gz NHLF ChipSeq H3K4me1 Peaks broadPeak Broad Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeBroadHistone/wgEncodeBroadHistoneNhlfH3k4me1StdSig.bigWig NHLF ChipSeq H3K4me1 Signal bigWig Broad Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeBroadHistone/wgEncodeBroadHistoneNhlfH3k4me2StdAlnRep1.bam NHLF ChipSeq H3K4me2 Alignments 1 bam Broad Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeBroadHistone/wgEncodeBroadHistoneNhlfH3k4me2StdAlnRep2.bam NHLF ChipSeq H3K4me2 Alignments 2 bam Broad Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeBroadHistone/wgEncodeBroadHistoneNhlfH3k4me2StdPk.broadPeak.gz NHLF ChipSeq H3K4me2 Peaks broadPeak Broad Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeBroadHistone/wgEncodeBroadHistoneNhlfH3k4me2StdSig.bigWig NHLF ChipSeq H3K4me2 Signal bigWig Broad Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeBroadHistone/wgEncodeBroadHistoneNhlfH3k4me3StdAlnRep1.bam NHLF ChipSeq H3K4me3 Alignments 1 bam Broad Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeBroadHistone/wgEncodeBroadHistoneNhlfH3k4me3StdAlnRep2.bam NHLF ChipSeq H3K4me3 Alignments 2 bam Broad Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeBroadHistone/wgEncodeBroadHistoneNhlfH3k4me3StdPk.broadPeak.gz NHLF ChipSeq H3K4me3 Peaks broadPeak Broad Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeBroadHistone/wgEncodeBroadHistoneNhlfH3k4me3StdSig.bigWig NHLF ChipSeq H3K4me3 Signal bigWig Broad Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeBroadHistone/wgEncodeBroadHistoneNhlfH3k79me2AlnRep1.bam NHLF ChipSeq H3K79me2 Alignments 1 bam Broad Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeBroadHistone/wgEncodeBroadHistoneNhlfH3k79me2AlnRep2.bam NHLF ChipSeq H3K79me2 Alignments 2 bam Broad Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeBroadHistone/wgEncodeBroadHistoneNhlfH3k79me2Pk.broadPeak.gz NHLF ChipSeq H3K79me2 Peaks broadPeak Broad Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeBroadHistone/wgEncodeBroadHistoneNhlfH3k79me2Sig.bigWig NHLF ChipSeq H3K79me2 Signal bigWig Broad Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeBroadHistone/wgEncodeBroadHistoneNhlfH3k9acStdAlnRep1.bam NHLF ChipSeq H3K9ac Alignments 1 bam Broad Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeBroadHistone/wgEncodeBroadHistoneNhlfH3k9acStdAlnRep2.bam NHLF ChipSeq H3K9ac Alignments 2 bam Broad Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeBroadHistone/wgEncodeBroadHistoneNhlfH3k9acStdPk.broadPeak.gz NHLF ChipSeq H3K9ac Peaks broadPeak Broad Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeBroadHistone/wgEncodeBroadHistoneNhlfH3k9acStdSig.bigWig NHLF ChipSeq H3K9ac Signal bigWig Broad Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeBroadHistone/wgEncodeBroadHistoneNhlfH4k20me1StdAlnRep1.bam NHLF ChipSeq H4K20me1 Alignments 1 bam Broad Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeBroadHistone/wgEncodeBroadHistoneNhlfH4k20me1StdAlnRep2.bam NHLF ChipSeq H4K20me1 Alignments 2 bam Broad Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeBroadHistone/wgEncodeBroadHistoneNhlfH4k20me1StdPk.broadPeak.gz NHLF ChipSeq H4K20me1 Peaks broadPeak Broad Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeBroadHistone/wgEncodeBroadHistoneNhlfH4k20me1StdSig.bigWig NHLF ChipSeq H4K20me1 Signal bigWig Broad Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeBroadHistone/wgEncodeBroadHistoneOsteoH3k04me3AlnRep1.bam Osteobl ChipSeq H3K4me3 Alignments 1 bam Broad Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeBroadHistone/wgEncodeBroadHistoneOsteoH3k04me3AlnRep2.bam Osteobl ChipSeq H3K4me3 Alignments 2 bam Broad Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeBroadHistone/wgEncodeBroadHistoneOsteoH3k04me3AlnRep3.bam Osteobl ChipSeq H3K4me3 Alignments 3 bam Broad Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeBroadHistone/wgEncodeBroadHistoneOsteoH3k04me3Pk.broadPeak.gz Osteobl ChipSeq H3K4me3 Peaks broadPeak Broad Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeBroadHistone/wgEncodeBroadHistoneOsteoH3k04me3Sig.bigWig Osteobl ChipSeq H3K4me3 Signal bigWig Broad Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeBroadHistone/wgEncodeBroadHistoneOsteoH3k27me3AlnRep1.bam Osteobl ChipSeq H3K27me3 Alignments 1 bam Broad Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeBroadHistone/wgEncodeBroadHistoneOsteoH3k27me3AlnRep2.bam Osteobl ChipSeq H3K27me3 Alignments 2 bam Broad Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeBroadHistone/wgEncodeBroadHistoneOsteoH3k27me3Pk.broadPeak.gz Osteobl ChipSeq H3K27me3 Peaks broadPeak Broad Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeBroadHistone/wgEncodeBroadHistoneOsteoH3k27me3Sig.bigWig Osteobl ChipSeq H3K27me3 Signal bigWig Broad Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeBroadHistone/wgEncodeBroadHistoneOsteoH3k79me2AlnRep1.bam Osteobl ChipSeq H3K79me2 Alignments 1 bam Broad Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeBroadHistone/wgEncodeBroadHistoneOsteoH3k79me2AlnRep2.bam Osteobl ChipSeq H3K79me2 Alignments 2 bam Broad Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeBroadHistone/wgEncodeBroadHistoneOsteoH3k79me2Pk.broadPeak.gz Osteobl ChipSeq H3K79me2 Peaks broadPeak Broad Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeBroadHistone/wgEncodeBroadHistoneOsteoH3k79me2Sig.bigWig Osteobl ChipSeq H3K79me2 Signal bigWig Broad Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeBroadHistone/wgEncodeBroadHistoneOsteoH4k20me1AlnRep1.bam Osteobl ChipSeq H4K20me1 Alignments 1 bam Broad Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeBroadHistone/wgEncodeBroadHistoneOsteoH4k20me1AlnRep2.bam Osteobl ChipSeq H4K20me1 Alignments 2 bam Broad Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeBroadHistone/wgEncodeBroadHistoneOsteoH4k20me1Pk.broadPeak.gz Osteobl ChipSeq H4K20me1 Peaks broadPeak Broad Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeBroadHistone/wgEncodeBroadHistoneOsteoH4k20me1Sig.bigWig Osteobl ChipSeq H4K20me1 Signal bigWig Broad Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeBroadHistone/wgEncodeBroadHistoneOsteoP300kat3bAlnRep1.bam Osteobl ChipSeq P300_KAT3B Alignments 1 bam Broad Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeBroadHistone/wgEncodeBroadHistoneOsteoP300kat3bAlnRep2.bam Osteobl ChipSeq P300_KAT3B Alignments 2 bam Broad Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeBroadHistone/wgEncodeBroadHistoneOsteoP300kat3bPk.broadPeak.gz Osteobl ChipSeq P300_KAT3B Peaks broadPeak Broad Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeBroadHistone/wgEncodeBroadHistoneOsteoP300kat3bSig.bigWig Osteobl ChipSeq P300_KAT3B Signal bigWig Broad Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeBroadHistone/wgEncodeBroadHistoneOsteoblControlStdAlnRep1.bam Osteobl ChipSeq Input Alignments 1 bam Broad Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeBroadHistone/wgEncodeBroadHistoneOsteoblControlStdAlnRep2.bam Osteobl ChipSeq Input Alignments 2 bam Broad Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeBroadHistone/wgEncodeBroadHistoneOsteoblControlStdSig.bigWig Osteobl ChipSeq Input Signal bigWig Broad Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeBroadHistone/wgEncodeBroadHistoneOsteoblCtcfStdAlnRep1.bam Osteobl ChipSeq CTCF Alignments 1 bam Broad Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeBroadHistone/wgEncodeBroadHistoneOsteoblCtcfStdAlnRep2.bam Osteobl ChipSeq CTCF Alignments 2 bam Broad Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeBroadHistone/wgEncodeBroadHistoneOsteoblCtcfStdPk.broadPeak.gz Osteobl ChipSeq CTCF Peaks broadPeak Broad Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeBroadHistone/wgEncodeBroadHistoneOsteoblCtcfStdSig.bigWig Osteobl ChipSeq CTCF Signal bigWig Broad Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeBroadHistone/wgEncodeBroadHistoneOsteoblH2azStdAlnRep1.bam Osteobl ChipSeq H2A.Z Alignments 1 bam Broad Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeBroadHistone/wgEncodeBroadHistoneOsteoblH2azStdAlnRep2.bam Osteobl ChipSeq H2A.Z Alignments 2 bam Broad Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeBroadHistone/wgEncodeBroadHistoneOsteoblH2azStdPk.broadPeak.gz Osteobl ChipSeq H2A.Z Peaks broadPeak Broad Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeBroadHistone/wgEncodeBroadHistoneOsteoblH2azStdSig.bigWig Osteobl ChipSeq H2A.Z Signal bigWig Broad Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeBroadHistone/wgEncodeBroadHistoneOsteoblH3k27acStdAlnRep1.bam Osteobl ChipSeq H3K27ac Alignments 1 bam Broad Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeBroadHistone/wgEncodeBroadHistoneOsteoblH3k27acStdAlnRep2.bam Osteobl ChipSeq H3K27ac Alignments 2 bam Broad Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeBroadHistone/wgEncodeBroadHistoneOsteoblH3k27acStdPk.broadPeak.gz Osteobl ChipSeq H3K27ac Peaks broadPeak Broad Data 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RnaSeq Splices 3 bam Caltech Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeCaltechRnaSeq/wgEncodeCaltechRnaSeqMcf7R2x75Il200TSSRep1V3.gtf.gz MCF-7 RnaSeq TssGencV3c 1 gtf Caltech Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeCaltechRnaSeq/wgEncodeCaltechRnaSeqMcf7R2x75Il200TSSRep2V3.gtf.gz MCF-7 RnaSeq TssGencV3c 2 gtf Caltech Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeCaltechRnaSeq/wgEncodeCaltechRnaSeqMcf7R2x75Il200TSSRep3V3.gtf.gz MCF-7 RnaSeq TssGencV3c 3 gtf Caltech Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeCaltechRnaSeq/wgEncodeCaltechRnaSeqMcf7R2x75Il200TranscriptDeNovoRep1V3.gtf.gz MCF-7 RnaSeq TranscriptDeNovo 1 gtf Caltech Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeCaltechRnaSeq/wgEncodeCaltechRnaSeqMcf7R2x75Il200TranscriptDeNovoRep2V3.gtf.gz MCF-7 RnaSeq TranscriptDeNovo 2 gtf Caltech Data 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http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeCshlLongRnaSeq/wgEncodeCshlLongRnaSeqMcf7NucleusPapTranscriptGencV10.gtf.gz MCF-7 RnaSeq TranscriptGencV10 gtf CSHL Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeCshlLongRnaSeq/wgEncodeCshlLongRnaSeqMonocd14CellPamAlnRep1.bam Monocytes-CD14+ RnaSeq Alignments 1 bam CSHL Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeCshlLongRnaSeq/wgEncodeCshlLongRnaSeqMonocd14CellPamAlnRep2.bam Monocytes-CD14+ RnaSeq Alignments 2 bam CSHL Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeCshlLongRnaSeq/wgEncodeCshlLongRnaSeqMonocd14CellPamExonsDeNovo.gff.gz Monocytes-CD14+ RnaSeq ExonsDeNovo gff CSHL Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeCshlLongRnaSeq/wgEncodeCshlLongRnaSeqMonocd14CellPamExonsGencV10.gtf.gz Monocytes-CD14+ RnaSeq ExonsGencV10 gtf CSHL Data 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RnaSeq TranscriptDeNovo gtf CSHL Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeCshlLongRnaSeq/wgEncodeCshlLongRnaSeqNhekCellPamTranscriptDeNovoRep5V2.gtf.gz NHEK RnaSeq TranscriptDeNovo 5 gtf CSHL Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeCshlLongRnaSeq/wgEncodeCshlLongRnaSeqNhekCellPamTranscriptDeNovoV2.gtf.gz NHEK RnaSeq TranscriptDeNovo gtf CSHL Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeCshlLongRnaSeq/wgEncodeCshlLongRnaSeqNhekCellPamTranscriptGencV7.gtf.gz NHEK RnaSeq TranscriptGencV7 gtf CSHL Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeCshlLongRnaSeq/wgEncodeCshlLongRnaSeqNhekCellPamTranscriptGencV7Rep5.gtf.gz NHEK RnaSeq TranscriptGencV7 gtf CSHL Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeCshlLongRnaSeq/wgEncodeCshlLongRnaSeqNhekCellPapAlnRep1.bam NHEK RnaSeq Alignments 1 bam CSHL Data 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http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeCshlShortRnaSeq/wgEncodeCshlShortRnaSeqCd20ro01794CellShorttotalTapPlusRep1.bigWig CD20+ RnaSeq PlusSignal 1 bigWig CSHL Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeCshlShortRnaSeq/wgEncodeCshlShortRnaSeqCd34mobilizedCellTapAlnRep1.bam CD34+_Mobilized RnaSeq Alignments 1 bam CSHL Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeCshlShortRnaSeq/wgEncodeCshlShortRnaSeqCd34mobilizedCellTapExonsGencV10.gtf.gz CD34+_Mobilized RnaSeq ExonsGencV10 gtf CSHL Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeCshlShortRnaSeq/wgEncodeCshlShortRnaSeqCd34mobilizedCellTapMinusRep1.bigWig CD34+_Mobilized RnaSeq MinusSignal 1 bigWig CSHL Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeCshlShortRnaSeq/wgEncodeCshlShortRnaSeqCd34mobilizedCellTapPlusRep1.bigWig CD34+_Mobilized RnaSeq PlusSignal 1 bigWig CSHL Data 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http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeCshlShortRnaSeq/wgEncodeCshlShortRnaSeqGm12878ChromatinTapPlusRep3.bigWig GM12878 RnaSeq PlusSignal 3 bigWig CSHL Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeCshlShortRnaSeq/wgEncodeCshlShortRnaSeqGm12878ChromatinTapPlusRep4.bigWig GM12878 RnaSeq PlusSignal 4 bigWig CSHL Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeCshlShortRnaSeq/wgEncodeCshlShortRnaSeqGm12878CytosolShortAln.bam GM12878 RnaSeq Alignments bam CSHL Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeCshlShortRnaSeq/wgEncodeCshlShortRnaSeqGm12878CytosolShortMinusRaw.bigWig GM12878 RnaSeq MinusSignal bigWig CSHL Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeCshlShortRnaSeq/wgEncodeCshlShortRnaSeqGm12878CytosolShortPlusRaw.bigWig GM12878 RnaSeq PlusSignal bigWig CSHL Data 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http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeCshlShortRnaSeq/wgEncodeCshlShortRnaSeqGm12878CytosolShorttotalTapPlusRawRep1.bigWig GM12878 RnaSeq PlusSignal 1 bigWig CSHL Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeCshlShortRnaSeq/wgEncodeCshlShortRnaSeqGm12878CytosolShorttotalTapPlusRawRep2.bigWig GM12878 RnaSeq PlusSignal 2 bigWig CSHL Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeCshlShortRnaSeq/wgEncodeCshlShortRnaSeqGm12878NucleolusTapAlnRep3.bam GM12878 RnaSeq Alignments 3 bam CSHL Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeCshlShortRnaSeq/wgEncodeCshlShortRnaSeqGm12878NucleolusTapAlnRep4.bam GM12878 RnaSeq Alignments 4 bam CSHL Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeCshlShortRnaSeq/wgEncodeCshlShortRnaSeqGm12878NucleolusTapExonsGencV10.gtf.gz GM12878 RnaSeq ExonsGencV10 gtf CSHL Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeCshlShortRnaSeq/wgEncodeCshlShortRnaSeqGm12878NucleolusTapMinusRawRep3.bigWig GM12878 RnaSeq MinusRawSignal 3 bigWig CSHL Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeCshlShortRnaSeq/wgEncodeCshlShortRnaSeqGm12878NucleolusTapMinusRawRep4.bigWig GM12878 RnaSeq MinusRawSignal 4 bigWig CSHL Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeCshlShortRnaSeq/wgEncodeCshlShortRnaSeqGm12878NucleolusTapPlusRawRep3.bigWig GM12878 RnaSeq PlusRawSignal 3 bigWig CSHL Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeCshlShortRnaSeq/wgEncodeCshlShortRnaSeqGm12878NucleolusTapPlusRawRep4.bigWig GM12878 RnaSeq PlusRawSignal 4 bigWig CSHL Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeCshlShortRnaSeq/wgEncodeCshlShortRnaSeqGm12878NucleusShortAln.bam GM12878 RnaSeq Alignments bam CSHL Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeCshlShortRnaSeq/wgEncodeCshlShortRnaSeqGm12878NucleusShortMinusRaw.bigWig GM12878 RnaSeq MinusSignal bigWig CSHL Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeCshlShortRnaSeq/wgEncodeCshlShortRnaSeqGm12878NucleusShortPlusRaw.bigWig GM12878 RnaSeq PlusSignal bigWig CSHL Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeCshlShortRnaSeq/wgEncodeCshlShortRnaSeqGm12878NucleusShorttotalTapAlnRep1.bam GM12878 RnaSeq Alignments 1 bam CSHL Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeCshlShortRnaSeq/wgEncodeCshlShortRnaSeqGm12878NucleusShorttotalTapAlnRep2.bam GM12878 RnaSeq Alignments 2 bam CSHL Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeCshlShortRnaSeq/wgEncodeCshlShortRnaSeqGm12878NucleusShorttotalTapExonsGencV7.gtf.gz GM12878 RnaSeq ExonsGencV7 gtf CSHL Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeCshlShortRnaSeq/wgEncodeCshlShortRnaSeqGm12878NucleusShorttotalTapMinusRawRep1.bigWig GM12878 RnaSeq MinusSignal 1 bigWig CSHL Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeCshlShortRnaSeq/wgEncodeCshlShortRnaSeqGm12878NucleusShorttotalTapMinusRawRep2.bigWig GM12878 RnaSeq MinusSignal 2 bigWig CSHL Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeCshlShortRnaSeq/wgEncodeCshlShortRnaSeqGm12878NucleusShorttotalTapPlusRawRep1.bigWig GM12878 RnaSeq PlusSignal 1 bigWig CSHL Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeCshlShortRnaSeq/wgEncodeCshlShortRnaSeqGm12878NucleusShorttotalTapPlusRawRep2.bigWig GM12878 RnaSeq PlusSignal 2 bigWig CSHL Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeCshlShortRnaSeq/wgEncodeCshlShortRnaSeqH1hescCellShorttotalTapAlnRep1.bam H1-hESC RnaSeq Alignments 1 bam CSHL Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeCshlShortRnaSeq/wgEncodeCshlShortRnaSeqH1hescCellShorttotalTapAlnRep2.bam H1-hESC RnaSeq Alignments 2 bam CSHL Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeCshlShortRnaSeq/wgEncodeCshlShortRnaSeqH1hescCellShorttotalTapExonsGencV7.gtf.gz H1-hESC RnaSeq ExonsGencV7 gtf CSHL Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeCshlShortRnaSeq/wgEncodeCshlShortRnaSeqH1hescCellShorttotalTapMinusRawRep1.bigWig H1-hESC RnaSeq MinusSignal 1 bigWig CSHL Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeCshlShortRnaSeq/wgEncodeCshlShortRnaSeqH1hescCellShorttotalTapMinusRawRep2.bigWig H1-hESC RnaSeq MinusSignal 2 bigWig CSHL Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeCshlShortRnaSeq/wgEncodeCshlShortRnaSeqH1hescCellShorttotalTapPlusRawRep1.bigWig H1-hESC RnaSeq PlusSignal 1 bigWig CSHL Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeCshlShortRnaSeq/wgEncodeCshlShortRnaSeqH1hescCellShorttotalTapPlusRawRep2.bigWig H1-hESC RnaSeq PlusSignal 2 bigWig CSHL Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeCshlShortRnaSeq/wgEncodeCshlShortRnaSeqH1hescCytosolShorttotalTapAlnRep2.bam H1-hESC RnaSeq Alignments 2 bam CSHL Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeCshlShortRnaSeq/wgEncodeCshlShortRnaSeqH1hescCytosolShorttotalTapExonsGencV7.gtf.gz H1-hESC RnaSeq ExonsGencV7 gtf CSHL Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeCshlShortRnaSeq/wgEncodeCshlShortRnaSeqH1hescCytosolShorttotalTapMinusRawRep2.bigWig H1-hESC RnaSeq MinusSignal 2 bigWig CSHL Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeCshlShortRnaSeq/wgEncodeCshlShortRnaSeqH1hescCytosolShorttotalTapPlusRawRep2.bigWig H1-hESC RnaSeq PlusSignal 2 bigWig CSHL Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeCshlShortRnaSeq/wgEncodeCshlShortRnaSeqH1hescNucleusShorttotalTapAlnRep2.bam H1-hESC RnaSeq Alignments 2 bam CSHL Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeCshlShortRnaSeq/wgEncodeCshlShortRnaSeqH1hescNucleusShorttotalTapExonsGencV7.gtf.gz H1-hESC RnaSeq ExonsGencV7 gtf CSHL Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeCshlShortRnaSeq/wgEncodeCshlShortRnaSeqH1hescNucleusShorttotalTapMinusRawRep2.bigWig H1-hESC RnaSeq MinusSignal 2 bigWig CSHL Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeCshlShortRnaSeq/wgEncodeCshlShortRnaSeqH1hescNucleusShorttotalTapPlusRawRep2.bigWig H1-hESC RnaSeq PlusSignal 2 bigWig CSHL Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeCshlShortRnaSeq/wgEncodeCshlShortRnaSeqH1neuronsCellAlnRep1.bam H1-neurons RnaSeq Alignments 1 bam CSHL Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeCshlShortRnaSeq/wgEncodeCshlShortRnaSeqH1neuronsCellAlnRep2.bam H1-neurons RnaSeq Alignments 2 bam CSHL Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeCshlShortRnaSeq/wgEncodeCshlShortRnaSeqH1neuronsCellCiptapAlnRep1.bam H1-neurons RnaSeq Alignments 1 bam CSHL Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeCshlShortRnaSeq/wgEncodeCshlShortRnaSeqH1neuronsCellCiptapAlnRep2.bam H1-neurons RnaSeq Alignments 2 bam CSHL Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeCshlShortRnaSeq/wgEncodeCshlShortRnaSeqH1neuronsCellCiptapExonsGencV10.gtf.gz H1-neurons RnaSeq ExonsGencV10 gtf CSHL Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeCshlShortRnaSeq/wgEncodeCshlShortRnaSeqH1neuronsCellCiptapMinusRawRep1.bigWig H1-neurons RnaSeq MinusRawSignal 1 bigWig CSHL Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeCshlShortRnaSeq/wgEncodeCshlShortRnaSeqH1neuronsCellCiptapMinusRawRep2.bigWig H1-neurons RnaSeq MinusRawSignal 2 bigWig CSHL Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeCshlShortRnaSeq/wgEncodeCshlShortRnaSeqH1neuronsCellCiptapPlusRawRep1.bigWig H1-neurons RnaSeq PlusRawSignal 1 bigWig CSHL Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeCshlShortRnaSeq/wgEncodeCshlShortRnaSeqH1neuronsCellCiptapPlusRawRep2.bigWig H1-neurons RnaSeq PlusRawSignal 2 bigWig CSHL Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeCshlShortRnaSeq/wgEncodeCshlShortRnaSeqH1neuronsCellExonsGencV10.gtf.gz H1-neurons RnaSeq ExonsGencV10 gtf CSHL Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeCshlShortRnaSeq/wgEncodeCshlShortRnaSeqH1neuronsCellMinusRawRep1.bigWig H1-neurons RnaSeq MinusRawSignal 1 bigWig CSHL Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeCshlShortRnaSeq/wgEncodeCshlShortRnaSeqH1neuronsCellMinusRawRep2.bigWig H1-neurons RnaSeq MinusRawSignal 2 bigWig CSHL Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeCshlShortRnaSeq/wgEncodeCshlShortRnaSeqH1neuronsCellPlusRawRep1.bigWig H1-neurons RnaSeq PlusRawSignal 1 bigWig CSHL Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeCshlShortRnaSeq/wgEncodeCshlShortRnaSeqH1neuronsCellPlusRawRep2.bigWig H1-neurons RnaSeq PlusRawSignal 2 bigWig CSHL Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeCshlShortRnaSeq/wgEncodeCshlShortRnaSeqH1neuronsCellTapAlnRep1.bam H1-neurons RnaSeq Alignments 1 bam CSHL Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeCshlShortRnaSeq/wgEncodeCshlShortRnaSeqH1neuronsCellTapAlnRep2.bam H1-neurons RnaSeq Alignments 2 bam CSHL Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeCshlShortRnaSeq/wgEncodeCshlShortRnaSeqH1neuronsCellTapExonsGencV10.gtf.gz H1-neurons RnaSeq ExonsGencV10 gtf CSHL Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeCshlShortRnaSeq/wgEncodeCshlShortRnaSeqH1neuronsCellTapMinusRawRep1.bigWig H1-neurons RnaSeq MinusRawSignal 1 bigWig CSHL Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeCshlShortRnaSeq/wgEncodeCshlShortRnaSeqH1neuronsCellTapMinusRawRep2.bigWig H1-neurons RnaSeq MinusRawSignal 2 bigWig CSHL Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeCshlShortRnaSeq/wgEncodeCshlShortRnaSeqH1neuronsCellTapPlusRawRep1.bigWig H1-neurons RnaSeq PlusRawSignal 1 bigWig CSHL Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeCshlShortRnaSeq/wgEncodeCshlShortRnaSeqH1neuronsCellTapPlusRawRep2.bigWig H1-neurons RnaSeq PlusRawSignal 2 bigWig CSHL Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeCshlShortRnaSeq/wgEncodeCshlShortRnaSeqHaoaf609010111CellTapAlnRep2.bam HAoAF RnaSeq Alignments 2 bam CSHL Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeCshlShortRnaSeq/wgEncodeCshlShortRnaSeqHaoaf609010111CellTapMinusRep2.bigWig HAoAF RnaSeq MinusSignal 2 bigWig CSHL Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeCshlShortRnaSeq/wgEncodeCshlShortRnaSeqHaoaf609010111CellTapPlusRep2.bigWig HAoAF RnaSeq PlusSignal 2 bigWig CSHL Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeCshlShortRnaSeq/wgEncodeCshlShortRnaSeqHaoaf61113019CellTapAlnRep1.bam HAoAF RnaSeq Alignments 1 bam CSHL Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeCshlShortRnaSeq/wgEncodeCshlShortRnaSeqHaoaf61113019CellTapMinusRep1.bigWig HAoAF RnaSeq MinusSignal 1 bigWig CSHL Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeCshlShortRnaSeq/wgEncodeCshlShortRnaSeqHaoaf61113019CellTapPlusRep1.bigWig HAoAF RnaSeq PlusSignal 1 bigWig CSHL Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeCshlShortRnaSeq/wgEncodeCshlShortRnaSeqHaoafCellTapExonsGencV10.gtf.gz HAoAF RnaSeq ExonsGencV10 gtf CSHL Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeCshlShortRnaSeq/wgEncodeCshlShortRnaSeqHaoec70717061CellTapAlnRep1.bam HAoEC RnaSeq Alignments 1 bam CSHL Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeCshlShortRnaSeq/wgEncodeCshlShortRnaSeqHaoec70717061CellTapMinusRep1.bigWig HAoEC RnaSeq MinusSignal 1 bigWig CSHL Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeCshlShortRnaSeq/wgEncodeCshlShortRnaSeqHaoec70717061CellTapPlusRep1.bigWig HAoEC RnaSeq PlusSignal 1 bigWig CSHL Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeCshlShortRnaSeq/wgEncodeCshlShortRnaSeqHaoec80611021CellTapAlnRep2.bam HAoEC RnaSeq Alignments 2 bam CSHL Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeCshlShortRnaSeq/wgEncodeCshlShortRnaSeqHaoec80611021CellTapMinusRep2.bigWig HAoEC RnaSeq MinusSignal 2 bigWig CSHL Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeCshlShortRnaSeq/wgEncodeCshlShortRnaSeqHaoec80611021CellTapPlusRep2.bigWig HAoEC RnaSeq PlusSignal 2 bigWig CSHL Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeCshlShortRnaSeq/wgEncodeCshlShortRnaSeqHaoecCellTapExonsGencV10.gtf.gz HAoEC RnaSeq ExonsGencV10 gtf CSHL Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeCshlShortRnaSeq/wgEncodeCshlShortRnaSeqHch00113082pCellShorttotalTapAlnRep1.bam HCH RnaSeq Alignments 1 bam CSHL Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeCshlShortRnaSeq/wgEncodeCshlShortRnaSeqHch00113082pCellShorttotalTapMinusRep1.bigWig HCH RnaSeq MinusSignal 1 bigWig CSHL Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeCshlShortRnaSeq/wgEncodeCshlShortRnaSeqHch00113082pCellShorttotalTapPlusRep1.bigWig HCH RnaSeq PlusSignal 1 bigWig CSHL Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeCshlShortRnaSeq/wgEncodeCshlShortRnaSeqHch81008082CellShorttotalTapAlnRep2.bam HCH RnaSeq Alignments 2 bam CSHL Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeCshlShortRnaSeq/wgEncodeCshlShortRnaSeqHch81008082CellShorttotalTapMinusRep2.bigWig HCH RnaSeq MinusSignal 2 bigWig CSHL Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeCshlShortRnaSeq/wgEncodeCshlShortRnaSeqHch81008082CellShorttotalTapPlusRep2.bigWig HCH RnaSeq PlusSignal 2 bigWig CSHL Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeCshlShortRnaSeq/wgEncodeCshlShortRnaSeqHchCellTapExonsGencV10.gtf.gz HCH RnaSeq ExonsGencV10 gtf CSHL Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeCshlShortRnaSeq/wgEncodeCshlShortRnaSeqHelas3CellShorttotalTapAlnRep1.bam HeLa-S3 RnaSeq Alignments 1 bam CSHL Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeCshlShortRnaSeq/wgEncodeCshlShortRnaSeqHelas3CellShorttotalTapAlnRep2.bam HeLa-S3 RnaSeq Alignments 2 bam CSHL Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeCshlShortRnaSeq/wgEncodeCshlShortRnaSeqHelas3CellShorttotalTapExonsGencV7.gtf.gz HeLa-S3 RnaSeq ExonsGencV7 gtf CSHL Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeCshlShortRnaSeq/wgEncodeCshlShortRnaSeqHelas3CellShorttotalTapMinusRawRep1.bigWig HeLa-S3 RnaSeq MinusSignal 1 bigWig CSHL Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeCshlShortRnaSeq/wgEncodeCshlShortRnaSeqHelas3CellShorttotalTapMinusRawRep2.bigWig HeLa-S3 RnaSeq MinusSignal 2 bigWig CSHL Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeCshlShortRnaSeq/wgEncodeCshlShortRnaSeqHelas3CellShorttotalTapPlusRawRep1.bigWig HeLa-S3 RnaSeq PlusSignal 1 bigWig CSHL Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeCshlShortRnaSeq/wgEncodeCshlShortRnaSeqHelas3CellShorttotalTapPlusRawRep2.bigWig HeLa-S3 RnaSeq PlusSignal 2 bigWig CSHL Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeCshlShortRnaSeq/wgEncodeCshlShortRnaSeqHelas3CytosolShorttotalTapAlnRep1.bam HeLa-S3 RnaSeq Alignments 1 bam CSHL Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeCshlShortRnaSeq/wgEncodeCshlShortRnaSeqHelas3CytosolShorttotalTapAlnRep2.bam HeLa-S3 RnaSeq Alignments 2 bam CSHL Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeCshlShortRnaSeq/wgEncodeCshlShortRnaSeqHelas3CytosolShorttotalTapExonsGencV7.gtf.gz HeLa-S3 RnaSeq ExonsGencV7 gtf CSHL Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeCshlShortRnaSeq/wgEncodeCshlShortRnaSeqHelas3CytosolShorttotalTapMinusRawRep1.bigWig HeLa-S3 RnaSeq MinusSignal 1 bigWig CSHL Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeCshlShortRnaSeq/wgEncodeCshlShortRnaSeqHelas3CytosolShorttotalTapMinusRawRep2.bigWig HeLa-S3 RnaSeq MinusSignal 2 bigWig CSHL Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeCshlShortRnaSeq/wgEncodeCshlShortRnaSeqHelas3CytosolShorttotalTapPlusRawRep1.bigWig HeLa-S3 RnaSeq PlusSignal 1 bigWig CSHL Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeCshlShortRnaSeq/wgEncodeCshlShortRnaSeqHelas3CytosolShorttotalTapPlusRawRep2.bigWig HeLa-S3 RnaSeq PlusSignal 2 bigWig CSHL Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeCshlShortRnaSeq/wgEncodeCshlShortRnaSeqHelas3NucleusShorttotalTapAlnRep1.bam HeLa-S3 RnaSeq Alignments 1 bam CSHL Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeCshlShortRnaSeq/wgEncodeCshlShortRnaSeqHelas3NucleusShorttotalTapAlnRep2.bam HeLa-S3 RnaSeq Alignments 2 bam CSHL Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeCshlShortRnaSeq/wgEncodeCshlShortRnaSeqHelas3NucleusShorttotalTapExonsGencV7.gtf.gz HeLa-S3 RnaSeq ExonsGencV7 gtf CSHL Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeCshlShortRnaSeq/wgEncodeCshlShortRnaSeqHelas3NucleusShorttotalTapMinusRawRep1.bigWig HeLa-S3 RnaSeq MinusSignal 1 bigWig CSHL Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeCshlShortRnaSeq/wgEncodeCshlShortRnaSeqHelas3NucleusShorttotalTapMinusRawRep2.bigWig HeLa-S3 RnaSeq MinusSignal 2 bigWig CSHL Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeCshlShortRnaSeq/wgEncodeCshlShortRnaSeqHelas3NucleusShorttotalTapPlusRawRep1.bigWig HeLa-S3 RnaSeq PlusSignal 1 bigWig CSHL Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeCshlShortRnaSeq/wgEncodeCshlShortRnaSeqHelas3NucleusShorttotalTapPlusRawRep2.bigWig HeLa-S3 RnaSeq PlusSignal 2 bigWig CSHL Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeCshlShortRnaSeq/wgEncodeCshlShortRnaSeqHepg2CellShorttotalTapAlnRep1.bam HepG2 RnaSeq Alignments 1 bam CSHL Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeCshlShortRnaSeq/wgEncodeCshlShortRnaSeqHepg2CellShorttotalTapAlnRep2.bam HepG2 RnaSeq Alignments 2 bam CSHL Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeCshlShortRnaSeq/wgEncodeCshlShortRnaSeqHepg2CellShorttotalTapExonsGencV7.gtf.gz HepG2 RnaSeq ExonsGencV7 gtf CSHL Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeCshlShortRnaSeq/wgEncodeCshlShortRnaSeqHepg2CellShorttotalTapMinusRawRep1.bigWig HepG2 RnaSeq MinusSignal 1 bigWig CSHL Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeCshlShortRnaSeq/wgEncodeCshlShortRnaSeqHepg2CellShorttotalTapMinusRawRep2.bigWig HepG2 RnaSeq MinusSignal 2 bigWig CSHL Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeCshlShortRnaSeq/wgEncodeCshlShortRnaSeqHepg2CellShorttotalTapPlusRawRep1.bigWig HepG2 RnaSeq PlusSignal 1 bigWig CSHL Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeCshlShortRnaSeq/wgEncodeCshlShortRnaSeqHepg2CellShorttotalTapPlusRawRep2.bigWig HepG2 RnaSeq PlusSignal 2 bigWig CSHL Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeCshlShortRnaSeq/wgEncodeCshlShortRnaSeqHepg2CytosolShorttotalTapAlnRep1.bam HepG2 RnaSeq Alignments 1 bam CSHL Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeCshlShortRnaSeq/wgEncodeCshlShortRnaSeqHepg2CytosolShorttotalTapAlnRep2.bam HepG2 RnaSeq Alignments 2 bam CSHL Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeCshlShortRnaSeq/wgEncodeCshlShortRnaSeqHepg2CytosolShorttotalTapExonsGencV7.gtf.gz HepG2 RnaSeq ExonsGencV7 gtf CSHL Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeCshlShortRnaSeq/wgEncodeCshlShortRnaSeqHepg2CytosolShorttotalTapMinusRawRep1.bigWig HepG2 RnaSeq MinusSignal 1 bigWig CSHL Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeCshlShortRnaSeq/wgEncodeCshlShortRnaSeqHepg2CytosolShorttotalTapMinusRawRep2.bigWig HepG2 RnaSeq MinusSignal 2 bigWig CSHL Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeCshlShortRnaSeq/wgEncodeCshlShortRnaSeqHepg2CytosolShorttotalTapPlusRawRep1.bigWig HepG2 RnaSeq PlusSignal 1 bigWig CSHL Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeCshlShortRnaSeq/wgEncodeCshlShortRnaSeqHepg2CytosolShorttotalTapPlusRawRep2.bigWig HepG2 RnaSeq PlusSignal 2 bigWig CSHL Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeCshlShortRnaSeq/wgEncodeCshlShortRnaSeqHepg2NucleusShorttotalTapAlnRep1.bam HepG2 RnaSeq Alignments 1 bam CSHL Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeCshlShortRnaSeq/wgEncodeCshlShortRnaSeqHepg2NucleusShorttotalTapAlnRep2.bam HepG2 RnaSeq Alignments 2 bam CSHL Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeCshlShortRnaSeq/wgEncodeCshlShortRnaSeqHepg2NucleusShorttotalTapExonsGencV7.gtf.gz HepG2 RnaSeq ExonsGencV7 gtf CSHL Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeCshlShortRnaSeq/wgEncodeCshlShortRnaSeqHepg2NucleusShorttotalTapMinusRawRep1.bigWig HepG2 RnaSeq MinusSignal 1 bigWig CSHL Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeCshlShortRnaSeq/wgEncodeCshlShortRnaSeqHepg2NucleusShorttotalTapMinusRawRep2.bigWig HepG2 RnaSeq MinusSignal 2 bigWig CSHL Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeCshlShortRnaSeq/wgEncodeCshlShortRnaSeqHepg2NucleusShorttotalTapPlusRawRep1.bigWig HepG2 RnaSeq PlusSignal 1 bigWig CSHL Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeCshlShortRnaSeq/wgEncodeCshlShortRnaSeqHepg2NucleusShorttotalTapPlusRawRep2.bigWig HepG2 RnaSeq PlusSignal 2 bigWig CSHL Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeCshlShortRnaSeq/wgEncodeCshlShortRnaSeqHfdpc01005032CellTapAlnRep2.bam HFDPC RnaSeq Alignments 2 bam CSHL Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeCshlShortRnaSeq/wgEncodeCshlShortRnaSeqHfdpc01005032CellTapMinusRep2.bigWig HFDPC RnaSeq MinusSignal 2 bigWig CSHL Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeCshlShortRnaSeq/wgEncodeCshlShortRnaSeqHfdpc01005032CellTapPlusRep2.bigWig HFDPC RnaSeq PlusSignal 2 bigWig CSHL Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeCshlShortRnaSeq/wgEncodeCshlShortRnaSeqHfdpc01027033CellTapAlnRep1.bam HFDPC RnaSeq Alignments 1 bam CSHL Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeCshlShortRnaSeq/wgEncodeCshlShortRnaSeqHfdpc01027033CellTapMinusRep1.bigWig HFDPC RnaSeq MinusSignal 1 bigWig CSHL Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeCshlShortRnaSeq/wgEncodeCshlShortRnaSeqHfdpc01027033CellTapPlusRep1.bigWig HFDPC RnaSeq PlusSignal 1 bigWig CSHL Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeCshlShortRnaSeq/wgEncodeCshlShortRnaSeqHfdpcCellTapExonsGencV10.gtf.gz HFDPC RnaSeq ExonsGencV10 gtf CSHL Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeCshlShortRnaSeq/wgEncodeCshlShortRnaSeqHmepcCellTapAlnRep1.bam HMEpC RnaSeq Alignments 1 bam CSHL Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeCshlShortRnaSeq/wgEncodeCshlShortRnaSeqHmepcCellTapExonsGencV10.gtf.gz HMEpC RnaSeq ExonsGencV10 gtf CSHL Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeCshlShortRnaSeq/wgEncodeCshlShortRnaSeqHmepcCellTapMinusRep1.bigWig HMEpC RnaSeq MinusSignal 1 bigWig CSHL Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeCshlShortRnaSeq/wgEncodeCshlShortRnaSeqHmepcCellTapPlusRep1.bigWig HMEpC RnaSeq PlusSignal 1 bigWig CSHL Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeCshlShortRnaSeq/wgEncodeCshlShortRnaSeqHmscat010260412CellTapAlnRep1.bam hMSC-AT RnaSeq Alignments 1 bam CSHL Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeCshlShortRnaSeq/wgEncodeCshlShortRnaSeqHmscat010260412CellTapMinusRep1.bigWig hMSC-AT RnaSeq MinusSignal 1 bigWig CSHL Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeCshlShortRnaSeq/wgEncodeCshlShortRnaSeqHmscat010260412CellTapPlusRep1.bigWig hMSC-AT RnaSeq PlusSignal 1 bigWig CSHL Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeCshlShortRnaSeq/wgEncodeCshlShortRnaSeqHmscat906160112CellTapAlnRep2.bam hMSC-AT RnaSeq Alignments 2 bam CSHL Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeCshlShortRnaSeq/wgEncodeCshlShortRnaSeqHmscat906160112CellTapMinusRep2.bigWig hMSC-AT RnaSeq MinusSignal 2 bigWig CSHL Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeCshlShortRnaSeq/wgEncodeCshlShortRnaSeqHmscat906160112CellTapPlusRep2.bigWig hMSC-AT RnaSeq PlusSignal 2 bigWig CSHL Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeCshlShortRnaSeq/wgEncodeCshlShortRnaSeqHmscatCellTapExonsGencV10.gtf.gz hMSC-AT RnaSeq ExonsGencV10 gtf CSHL Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeCshlShortRnaSeq/wgEncodeCshlShortRnaSeqHmscbmCellTapAlnRep1.bam hMSC-BM RnaSeq Alignments 1 bam CSHL Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeCshlShortRnaSeq/wgEncodeCshlShortRnaSeqHmscbmCellTapAlnRep2.bam hMSC-BM RnaSeq Alignments 2 bam CSHL Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeCshlShortRnaSeq/wgEncodeCshlShortRnaSeqHmscbmCellTapExonsGencV10.gtf.gz hMSC-BM RnaSeq ExonsGencV10 gtf CSHL Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeCshlShortRnaSeq/wgEncodeCshlShortRnaSeqHmscbmCellTapMinusRawRep1.bigWig hMSC-BM RnaSeq MinusRawSignal 1 bigWig CSHL Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeCshlShortRnaSeq/wgEncodeCshlShortRnaSeqHmscbmCellTapMinusRawRep2.bigWig hMSC-BM RnaSeq MinusRawSignal 2 bigWig CSHL Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeCshlShortRnaSeq/wgEncodeCshlShortRnaSeqHmscbmCellTapPlusRawRep1.bigWig hMSC-BM RnaSeq PlusRawSignal 1 bigWig CSHL Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeCshlShortRnaSeq/wgEncodeCshlShortRnaSeqHmscbmCellTapPlusRawRep2.bigWig hMSC-BM RnaSeq PlusRawSignal 2 bigWig CSHL Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeCshlShortRnaSeq/wgEncodeCshlShortRnaSeqHmscucCellTapAlnRep1.bam hMSC-UC RnaSeq Alignments 1 bam CSHL Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeCshlShortRnaSeq/wgEncodeCshlShortRnaSeqHmscucCellTapAlnRep2.bam hMSC-UC RnaSeq Alignments 2 bam CSHL Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeCshlShortRnaSeq/wgEncodeCshlShortRnaSeqHmscucCellTapExonsGencV10.gtf.gz hMSC-UC RnaSeq ExonsGencV10 gtf CSHL Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeCshlShortRnaSeq/wgEncodeCshlShortRnaSeqHmscucCellTapMinusRep1.bigWig hMSC-UC RnaSeq MinusSignal 1 bigWig CSHL Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeCshlShortRnaSeq/wgEncodeCshlShortRnaSeqHmscucCellTapMinusRep2.bigWig hMSC-UC RnaSeq MinusSignal 2 bigWig CSHL Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeCshlShortRnaSeq/wgEncodeCshlShortRnaSeqHmscucCellTapPlusRep1.bigWig hMSC-UC RnaSeq PlusSignal 1 bigWig CSHL Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeCshlShortRnaSeq/wgEncodeCshlShortRnaSeqHmscucCellTapPlusRep2.bigWig hMSC-UC RnaSeq PlusSignal 2 bigWig CSHL Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeCshlShortRnaSeq/wgEncodeCshlShortRnaSeqHob00902021CellShorttotalTapAlnRep2.bam HOB RnaSeq Alignments 2 bam CSHL Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeCshlShortRnaSeq/wgEncodeCshlShortRnaSeqHob00902021CellShorttotalTapMinusRep2.bigWig HOB RnaSeq MinusSignal 2 bigWig CSHL Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeCshlShortRnaSeq/wgEncodeCshlShortRnaSeqHob00902021CellShorttotalTapPlusRep2.bigWig HOB RnaSeq PlusSignal 2 bigWig CSHL Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeCshlShortRnaSeq/wgEncodeCshlShortRnaSeqHobCellTapAlnRep1.bam HOB RnaSeq Alignments 1 bam CSHL Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeCshlShortRnaSeq/wgEncodeCshlShortRnaSeqHobCellTapExonsGencV10.gtf.gz HOB RnaSeq ExonsGencV10 gtf CSHL Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeCshlShortRnaSeq/wgEncodeCshlShortRnaSeqHobCellTapMinusRawRep1.bigWig HOB RnaSeq MinusRawSignal 1 bigWig CSHL Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeCshlShortRnaSeq/wgEncodeCshlShortRnaSeqHobCellTapPlusRawRep1.bigWig HOB RnaSeq PlusRawSignal 1 bigWig CSHL Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeCshlShortRnaSeq/wgEncodeCshlShortRnaSeqHpcplCellTapAlnRep1.bam HPC-PL RnaSeq Alignments 1 bam CSHL Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeCshlShortRnaSeq/wgEncodeCshlShortRnaSeqHpcplCellTapAlnRep2.bam HPC-PL RnaSeq Alignments 2 bam CSHL Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeCshlShortRnaSeq/wgEncodeCshlShortRnaSeqHpcplCellTapExonsGencV10.gtf.gz HPC-PL RnaSeq ExonsGencV10 gtf CSHL Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeCshlShortRnaSeq/wgEncodeCshlShortRnaSeqHpcplCellTapMinusRep1.bigWig HPC-PL RnaSeq MinusSignal 1 bigWig CSHL Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeCshlShortRnaSeq/wgEncodeCshlShortRnaSeqHpcplCellTapMinusRep2.bigWig HPC-PL RnaSeq MinusSignal 2 bigWig CSHL Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeCshlShortRnaSeq/wgEncodeCshlShortRnaSeqHpcplCellTapPlusRep1.bigWig HPC-PL RnaSeq PlusSignal 1 bigWig CSHL Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeCshlShortRnaSeq/wgEncodeCshlShortRnaSeqHpcplCellTapPlusRep2.bigWig HPC-PL RnaSeq PlusSignal 2 bigWig CSHL Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeCshlShortRnaSeq/wgEncodeCshlShortRnaSeqHpiepcCellTapAlnRep1.bam HPIEpC RnaSeq Alignments 1 bam CSHL Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeCshlShortRnaSeq/wgEncodeCshlShortRnaSeqHpiepcCellTapAlnRep2.bam HPIEpC RnaSeq Alignments 2 bam CSHL Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeCshlShortRnaSeq/wgEncodeCshlShortRnaSeqHpiepcCellTapExonsGencV10.gtf.gz HPIEpC RnaSeq ExonsGencV10 gtf CSHL Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeCshlShortRnaSeq/wgEncodeCshlShortRnaSeqHpiepcCellTapMinusRep1.bigWig HPIEpC RnaSeq MinusSignal 1 bigWig CSHL Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeCshlShortRnaSeq/wgEncodeCshlShortRnaSeqHpiepcCellTapMinusRep2.bigWig HPIEpC RnaSeq MinusSignal 2 bigWig CSHL Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeCshlShortRnaSeq/wgEncodeCshlShortRnaSeqHpiepcCellTapPlusRep1.bigWig HPIEpC RnaSeq PlusSignal 1 bigWig CSHL Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeCshlShortRnaSeq/wgEncodeCshlShortRnaSeqHpiepcCellTapPlusRep2.bigWig HPIEpC RnaSeq PlusSignal 2 bigWig CSHL Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeCshlShortRnaSeq/wgEncodeCshlShortRnaSeqHsavecCellTapAlnRep1.bam HSaVEC RnaSeq Alignments 1 bam CSHL Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeCshlShortRnaSeq/wgEncodeCshlShortRnaSeqHsavecCellTapAlnRep2.bam HSaVEC RnaSeq Alignments 2 bam CSHL Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeCshlShortRnaSeq/wgEncodeCshlShortRnaSeqHsavecCellTapExonsGencV10.gtf.gz HSaVEC RnaSeq ExonsGencV10 gtf CSHL Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeCshlShortRnaSeq/wgEncodeCshlShortRnaSeqHsavecCellTapMinusRep1.bigWig HSaVEC RnaSeq MinusSignal 1 bigWig CSHL Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeCshlShortRnaSeq/wgEncodeCshlShortRnaSeqHsavecCellTapMinusRep2.bigWig HSaVEC RnaSeq MinusSignal 2 bigWig CSHL Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeCshlShortRnaSeq/wgEncodeCshlShortRnaSeqHsavecCellTapPlusRep1.bigWig HSaVEC RnaSeq PlusSignal 1 bigWig CSHL Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeCshlShortRnaSeq/wgEncodeCshlShortRnaSeqHsavecCellTapPlusRep2.bigWig HSaVEC RnaSeq PlusSignal 2 bigWig CSHL Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeCshlShortRnaSeq/wgEncodeCshlShortRnaSeqHuvecNucleusShorttotalTapAlnRep3.bam HUVEC RnaSeq Alignments 3 bam CSHL Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeCshlShortRnaSeq/wgEncodeCshlShortRnaSeqHuvecNucleusShorttotalTapAlnRep4.bam HUVEC RnaSeq Alignments 4 bam CSHL Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeCshlShortRnaSeq/wgEncodeCshlShortRnaSeqHuvecNucleusShorttotalTapExonsGencV7.gtf.gz HUVEC RnaSeq ExonsGencV7 gtf CSHL Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeCshlShortRnaSeq/wgEncodeCshlShortRnaSeqHuvecNucleusShorttotalTapMinusRawRep3.bigWig HUVEC RnaSeq MinusSignal 3 bigWig CSHL Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeCshlShortRnaSeq/wgEncodeCshlShortRnaSeqHuvecNucleusShorttotalTapMinusRawRep4.bigWig HUVEC RnaSeq MinusSignal 4 bigWig CSHL Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeCshlShortRnaSeq/wgEncodeCshlShortRnaSeqHuvecNucleusShorttotalTapPlusRawRep3.bigWig HUVEC RnaSeq PlusSignal 3 bigWig CSHL Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeCshlShortRnaSeq/wgEncodeCshlShortRnaSeqHuvecNucleusShorttotalTapPlusRawRep4.bigWig HUVEC RnaSeq PlusSignal 4 bigWig CSHL Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeCshlShortRnaSeq/wgEncodeCshlShortRnaSeqHvmf60912033CellShorttotalTapAlnRep1.bam HVMF RnaSeq Alignments 1 bam CSHL Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeCshlShortRnaSeq/wgEncodeCshlShortRnaSeqHvmf60912033CellShorttotalTapMinusRep1.bigWig HVMF RnaSeq MinusSignal 1 bigWig CSHL Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeCshlShortRnaSeq/wgEncodeCshlShortRnaSeqHvmf60912033CellShorttotalTapPlusRep1.bigWig HVMF RnaSeq PlusSignal 1 bigWig CSHL Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeCshlShortRnaSeq/wgEncodeCshlShortRnaSeqHvmf61004013CellShorttotalTapAlnRep2.bam HVMF RnaSeq Alignments 2 bam CSHL Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeCshlShortRnaSeq/wgEncodeCshlShortRnaSeqHvmf61004013CellShorttotalTapMinusRep2.bigWig HVMF RnaSeq MinusSignal 2 bigWig CSHL Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeCshlShortRnaSeq/wgEncodeCshlShortRnaSeqHvmf61004013CellShorttotalTapPlusRep2.bigWig HVMF RnaSeq PlusSignal 2 bigWig CSHL Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeCshlShortRnaSeq/wgEncodeCshlShortRnaSeqHvmfCellTapExonsGencV10.gtf.gz HVMF RnaSeq ExonsGencV10 gtf CSHL Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeCshlShortRnaSeq/wgEncodeCshlShortRnaSeqHwpCellTapAlnRep1.bam HWP RnaSeq Alignments 1 bam CSHL Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeCshlShortRnaSeq/wgEncodeCshlShortRnaSeqHwpCellTapAlnRep2.bam HWP RnaSeq Alignments 2 bam CSHL Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeCshlShortRnaSeq/wgEncodeCshlShortRnaSeqHwpCellTapExonsGencV10.gtf.gz HWP RnaSeq ExonsGencV10 gtf CSHL Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeCshlShortRnaSeq/wgEncodeCshlShortRnaSeqHwpCellTapMinusRep1.bigWig HWP RnaSeq MinusSignal 1 bigWig CSHL Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeCshlShortRnaSeq/wgEncodeCshlShortRnaSeqHwpCellTapMinusRep2.bigWig HWP RnaSeq MinusSignal 2 bigWig CSHL Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeCshlShortRnaSeq/wgEncodeCshlShortRnaSeqHwpCellTapPlusRep1.bigWig HWP RnaSeq PlusSignal 1 bigWig CSHL Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeCshlShortRnaSeq/wgEncodeCshlShortRnaSeqHwpCellTapPlusRep2.bigWig HWP RnaSeq PlusSignal 2 bigWig CSHL Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeCshlShortRnaSeq/wgEncodeCshlShortRnaSeqImr90CellCiptapExonsGencV10.gtf.gz IMR90 RnaSeq ExonsGencV10 gtf CSHL Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeCshlShortRnaSeq/wgEncodeCshlShortRnaSeqImr90CellExonsGencV10.gtf.gz IMR90 RnaSeq ExonsGencV10 gtf CSHL Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeCshlShortRnaSeq/wgEncodeCshlShortRnaSeqImr90CellShorttotalAlnRep1.bam IMR90 RnaSeq Alignments 1 bam CSHL Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeCshlShortRnaSeq/wgEncodeCshlShortRnaSeqImr90CellShorttotalAlnRep2.bam IMR90 RnaSeq Alignments 2 bam CSHL Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeCshlShortRnaSeq/wgEncodeCshlShortRnaSeqImr90CellShorttotalCiptapAlnRep1.bam IMR90 RnaSeq Alignments 1 bam CSHL Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeCshlShortRnaSeq/wgEncodeCshlShortRnaSeqImr90CellShorttotalCiptapAlnRep2.bam IMR90 RnaSeq Alignments 2 bam CSHL Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeCshlShortRnaSeq/wgEncodeCshlShortRnaSeqImr90CellShorttotalCiptapMinusRep1.bigWig IMR90 RnaSeq MinusSignal 1 bigWig CSHL Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeCshlShortRnaSeq/wgEncodeCshlShortRnaSeqImr90CellShorttotalCiptapMinusRep2.bigWig IMR90 RnaSeq MinusSignal 2 bigWig CSHL Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeCshlShortRnaSeq/wgEncodeCshlShortRnaSeqImr90CellShorttotalCiptapPlusRep1.bigWig IMR90 RnaSeq PlusSignal 1 bigWig CSHL Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeCshlShortRnaSeq/wgEncodeCshlShortRnaSeqImr90CellShorttotalCiptapPlusRep2.bigWig IMR90 RnaSeq PlusSignal 2 bigWig CSHL Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeCshlShortRnaSeq/wgEncodeCshlShortRnaSeqImr90CellShorttotalMinusRep1.bigWig IMR90 RnaSeq MinusSignal 1 bigWig CSHL Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeCshlShortRnaSeq/wgEncodeCshlShortRnaSeqImr90CellShorttotalMinusRep2.bigWig IMR90 RnaSeq MinusSignal 2 bigWig CSHL Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeCshlShortRnaSeq/wgEncodeCshlShortRnaSeqImr90CellShorttotalPlusRep1.bigWig IMR90 RnaSeq PlusSignal 1 bigWig CSHL Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeCshlShortRnaSeq/wgEncodeCshlShortRnaSeqImr90CellShorttotalPlusRep2.bigWig IMR90 RnaSeq PlusSignal 2 bigWig CSHL Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeCshlShortRnaSeq/wgEncodeCshlShortRnaSeqImr90CellShorttotalTapAlnRep1.bam IMR90 RnaSeq Alignments 1 bam CSHL Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeCshlShortRnaSeq/wgEncodeCshlShortRnaSeqImr90CellShorttotalTapAlnRep2.bam IMR90 RnaSeq Alignments 2 bam CSHL Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeCshlShortRnaSeq/wgEncodeCshlShortRnaSeqImr90CellShorttotalTapMinusRep1.bigWig IMR90 RnaSeq MinusSignal 1 bigWig CSHL Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeCshlShortRnaSeq/wgEncodeCshlShortRnaSeqImr90CellShorttotalTapMinusRep2.bigWig IMR90 RnaSeq MinusSignal 2 bigWig CSHL Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeCshlShortRnaSeq/wgEncodeCshlShortRnaSeqImr90CellShorttotalTapPlusRep1.bigWig IMR90 RnaSeq PlusSignal 1 bigWig CSHL Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeCshlShortRnaSeq/wgEncodeCshlShortRnaSeqImr90CellShorttotalTapPlusRep2.bigWig IMR90 RnaSeq PlusSignal 2 bigWig CSHL Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeCshlShortRnaSeq/wgEncodeCshlShortRnaSeqImr90CellTapExonsGencV10.gtf.gz IMR90 RnaSeq ExonsGencV10 gtf CSHL Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeCshlShortRnaSeq/wgEncodeCshlShortRnaSeqImr90CytosolCiptapExonsGencV10.gtf.gz IMR90 RnaSeq ExonsGencV10 gtf CSHL Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeCshlShortRnaSeq/wgEncodeCshlShortRnaSeqImr90CytosolExonsGencV10.gtf.gz IMR90 RnaSeq ExonsGencV10 gtf CSHL Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeCshlShortRnaSeq/wgEncodeCshlShortRnaSeqImr90CytosolShorttotalAlnRep1.bam IMR90 RnaSeq Alignments 1 bam CSHL Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeCshlShortRnaSeq/wgEncodeCshlShortRnaSeqImr90CytosolShorttotalAlnRep2.bam IMR90 RnaSeq Alignments 2 bam CSHL Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeCshlShortRnaSeq/wgEncodeCshlShortRnaSeqImr90CytosolShorttotalCiptapAlnRep1.bam IMR90 RnaSeq Alignments 1 bam CSHL Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeCshlShortRnaSeq/wgEncodeCshlShortRnaSeqImr90CytosolShorttotalCiptapAlnRep2.bam IMR90 RnaSeq Alignments 2 bam CSHL Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeCshlShortRnaSeq/wgEncodeCshlShortRnaSeqImr90CytosolShorttotalCiptapMinusRep1.bigWig IMR90 RnaSeq MinusSignal 1 bigWig CSHL Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeCshlShortRnaSeq/wgEncodeCshlShortRnaSeqImr90CytosolShorttotalCiptapMinusRep2.bigWig IMR90 RnaSeq MinusSignal 2 bigWig CSHL Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeCshlShortRnaSeq/wgEncodeCshlShortRnaSeqImr90CytosolShorttotalCiptapPlusRep1.bigWig IMR90 RnaSeq PlusSignal 1 bigWig CSHL Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeCshlShortRnaSeq/wgEncodeCshlShortRnaSeqImr90CytosolShorttotalCiptapPlusRep2.bigWig IMR90 RnaSeq PlusSignal 2 bigWig CSHL Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeCshlShortRnaSeq/wgEncodeCshlShortRnaSeqImr90CytosolShorttotalMinusRep1.bigWig IMR90 RnaSeq MinusSignal 1 bigWig CSHL Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeCshlShortRnaSeq/wgEncodeCshlShortRnaSeqImr90CytosolShorttotalMinusRep2.bigWig IMR90 RnaSeq MinusSignal 2 bigWig CSHL Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeCshlShortRnaSeq/wgEncodeCshlShortRnaSeqImr90CytosolShorttotalPlusRep1.bigWig IMR90 RnaSeq PlusSignal 1 bigWig CSHL Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeCshlShortRnaSeq/wgEncodeCshlShortRnaSeqImr90CytosolShorttotalPlusRep2.bigWig IMR90 RnaSeq PlusSignal 2 bigWig CSHL Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeCshlShortRnaSeq/wgEncodeCshlShortRnaSeqImr90CytosolShorttotalTapAlnRep1.bam IMR90 RnaSeq Alignments 1 bam CSHL Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeCshlShortRnaSeq/wgEncodeCshlShortRnaSeqImr90CytosolShorttotalTapAlnRep2.bam IMR90 RnaSeq Alignments 2 bam CSHL Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeCshlShortRnaSeq/wgEncodeCshlShortRnaSeqImr90CytosolShorttotalTapMinusRep1.bigWig IMR90 RnaSeq MinusSignal 1 bigWig CSHL Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeCshlShortRnaSeq/wgEncodeCshlShortRnaSeqImr90CytosolShorttotalTapMinusRep2.bigWig IMR90 RnaSeq MinusSignal 2 bigWig CSHL Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeCshlShortRnaSeq/wgEncodeCshlShortRnaSeqImr90CytosolShorttotalTapPlusRep1.bigWig IMR90 RnaSeq PlusSignal 1 bigWig CSHL Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeCshlShortRnaSeq/wgEncodeCshlShortRnaSeqImr90CytosolShorttotalTapPlusRep2.bigWig IMR90 RnaSeq PlusSignal 2 bigWig CSHL Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeCshlShortRnaSeq/wgEncodeCshlShortRnaSeqImr90CytosolTapExonsGencV10.gtf.gz IMR90 RnaSeq ExonsGencV10 gtf CSHL Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeCshlShortRnaSeq/wgEncodeCshlShortRnaSeqImr90NucleusCiptapExonsGencV10.gtf.gz IMR90 RnaSeq ExonsGencV10 gtf CSHL Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeCshlShortRnaSeq/wgEncodeCshlShortRnaSeqImr90NucleusExonsGencV10.gtf.gz IMR90 RnaSeq ExonsGencV10 gtf CSHL Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeCshlShortRnaSeq/wgEncodeCshlShortRnaSeqImr90NucleusShorttotalAlnRep1.bam IMR90 RnaSeq Alignments 1 bam CSHL Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeCshlShortRnaSeq/wgEncodeCshlShortRnaSeqImr90NucleusShorttotalAlnRep2.bam IMR90 RnaSeq Alignments 2 bam CSHL Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeCshlShortRnaSeq/wgEncodeCshlShortRnaSeqImr90NucleusShorttotalCiptapAlnRep1.bam IMR90 RnaSeq Alignments 1 bam CSHL Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeCshlShortRnaSeq/wgEncodeCshlShortRnaSeqImr90NucleusShorttotalCiptapAlnRep2.bam IMR90 RnaSeq Alignments 2 bam CSHL Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeCshlShortRnaSeq/wgEncodeCshlShortRnaSeqImr90NucleusShorttotalCiptapMinusRep1.bigWig IMR90 RnaSeq MinusSignal 1 bigWig CSHL Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeCshlShortRnaSeq/wgEncodeCshlShortRnaSeqImr90NucleusShorttotalCiptapMinusRep2.bigWig IMR90 RnaSeq MinusSignal 2 bigWig CSHL Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeCshlShortRnaSeq/wgEncodeCshlShortRnaSeqImr90NucleusShorttotalCiptapPlusRep1.bigWig IMR90 RnaSeq PlusSignal 1 bigWig CSHL Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeCshlShortRnaSeq/wgEncodeCshlShortRnaSeqImr90NucleusShorttotalCiptapPlusRep2.bigWig IMR90 RnaSeq PlusSignal 2 bigWig CSHL Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeCshlShortRnaSeq/wgEncodeCshlShortRnaSeqImr90NucleusShorttotalMinusRep1.bigWig IMR90 RnaSeq MinusSignal 1 bigWig CSHL Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeCshlShortRnaSeq/wgEncodeCshlShortRnaSeqImr90NucleusShorttotalMinusRep2.bigWig IMR90 RnaSeq MinusSignal 2 bigWig CSHL Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeCshlShortRnaSeq/wgEncodeCshlShortRnaSeqImr90NucleusShorttotalPlusRep1.bigWig IMR90 RnaSeq PlusSignal 1 bigWig CSHL Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeCshlShortRnaSeq/wgEncodeCshlShortRnaSeqImr90NucleusShorttotalPlusRep2.bigWig IMR90 RnaSeq PlusSignal 2 bigWig CSHL Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeCshlShortRnaSeq/wgEncodeCshlShortRnaSeqImr90NucleusShorttotalTapAlnRep1.bam IMR90 RnaSeq Alignments 1 bam CSHL Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeCshlShortRnaSeq/wgEncodeCshlShortRnaSeqImr90NucleusShorttotalTapAlnRep2.bam IMR90 RnaSeq Alignments 2 bam CSHL Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeCshlShortRnaSeq/wgEncodeCshlShortRnaSeqImr90NucleusShorttotalTapMinusRep1.bigWig IMR90 RnaSeq MinusSignal 1 bigWig CSHL Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeCshlShortRnaSeq/wgEncodeCshlShortRnaSeqImr90NucleusShorttotalTapMinusRep2.bigWig IMR90 RnaSeq MinusSignal 2 bigWig CSHL Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeCshlShortRnaSeq/wgEncodeCshlShortRnaSeqImr90NucleusShorttotalTapPlusRep1.bigWig IMR90 RnaSeq PlusSignal 1 bigWig CSHL Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeCshlShortRnaSeq/wgEncodeCshlShortRnaSeqImr90NucleusShorttotalTapPlusRep2.bigWig IMR90 RnaSeq PlusSignal 2 bigWig CSHL Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeCshlShortRnaSeq/wgEncodeCshlShortRnaSeqImr90NucleusTapExonsGencV10.gtf.gz IMR90 RnaSeq ExonsGencV10 gtf CSHL Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeCshlShortRnaSeq/wgEncodeCshlShortRnaSeqK562CellShortAln.bam K562 RnaSeq Alignments bam CSHL Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeCshlShortRnaSeq/wgEncodeCshlShortRnaSeqK562CellShortMinusRaw.bigWig K562 RnaSeq MinusSignal bigWig CSHL Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeCshlShortRnaSeq/wgEncodeCshlShortRnaSeqK562CellShortPlusRaw.bigWig K562 RnaSeq PlusSignal bigWig CSHL Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeCshlShortRnaSeq/wgEncodeCshlShortRnaSeqK562CellShorttotalTapAlnRep1.bam K562 RnaSeq Alignments 1 bam CSHL Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeCshlShortRnaSeq/wgEncodeCshlShortRnaSeqK562CellShorttotalTapAlnRep2.bam K562 RnaSeq Alignments 2 bam CSHL Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeCshlShortRnaSeq/wgEncodeCshlShortRnaSeqK562CellShorttotalTapExonsGencV7.gtf.gz K562 RnaSeq ExonsGencV7 gtf CSHL Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeCshlShortRnaSeq/wgEncodeCshlShortRnaSeqK562CellShorttotalTapMinusRawRep1.bigWig K562 RnaSeq MinusSignal 1 bigWig CSHL Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeCshlShortRnaSeq/wgEncodeCshlShortRnaSeqK562CellShorttotalTapMinusRawRep2.bigWig K562 RnaSeq MinusSignal 2 bigWig CSHL Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeCshlShortRnaSeq/wgEncodeCshlShortRnaSeqK562CellShorttotalTapPlusRawRep1.bigWig K562 RnaSeq PlusSignal 1 bigWig CSHL Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeCshlShortRnaSeq/wgEncodeCshlShortRnaSeqK562CellShorttotalTapPlusRawRep2.bigWig K562 RnaSeq PlusSignal 2 bigWig CSHL Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeCshlShortRnaSeq/wgEncodeCshlShortRnaSeqK562ChromatinShortAln.bam K562 RnaSeq Alignments bam CSHL Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeCshlShortRnaSeq/wgEncodeCshlShortRnaSeqK562ChromatinShortMinusRaw.bigWig K562 RnaSeq MinusSignal bigWig CSHL Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeCshlShortRnaSeq/wgEncodeCshlShortRnaSeqK562ChromatinShortPlusRaw.bigWig K562 RnaSeq PlusSignal bigWig CSHL Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeCshlShortRnaSeq/wgEncodeCshlShortRnaSeqK562ChromatinShorttotalTapAlnRep3.bam K562 RnaSeq Alignments 3 bam CSHL Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeCshlShortRnaSeq/wgEncodeCshlShortRnaSeqK562ChromatinShorttotalTapAlnRep4.bam K562 RnaSeq Alignments 4 bam CSHL Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeCshlShortRnaSeq/wgEncodeCshlShortRnaSeqK562ChromatinShorttotalTapExonsGencV7.gtf.gz K562 RnaSeq ExonsGencV7 gtf CSHL Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeCshlShortRnaSeq/wgEncodeCshlShortRnaSeqK562ChromatinShorttotalTapMinusRawRep3.bigWig K562 RnaSeq MinusSignal 3 bigWig CSHL Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeCshlShortRnaSeq/wgEncodeCshlShortRnaSeqK562ChromatinShorttotalTapMinusRawRep4.bigWig K562 RnaSeq MinusSignal 4 bigWig CSHL Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeCshlShortRnaSeq/wgEncodeCshlShortRnaSeqK562ChromatinShorttotalTapPlusRawRep3.bigWig K562 RnaSeq PlusSignal 3 bigWig CSHL Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeCshlShortRnaSeq/wgEncodeCshlShortRnaSeqK562ChromatinShorttotalTapPlusRawRep4.bigWig K562 RnaSeq PlusSignal 4 bigWig CSHL Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeCshlShortRnaSeq/wgEncodeCshlShortRnaSeqK562CytosolShortAln.bam K562 RnaSeq Alignments bam CSHL Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeCshlShortRnaSeq/wgEncodeCshlShortRnaSeqK562CytosolShortMinusRaw.bigWig K562 RnaSeq MinusSignal bigWig CSHL Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeCshlShortRnaSeq/wgEncodeCshlShortRnaSeqK562CytosolShortPlusRaw.bigWig K562 RnaSeq PlusSignal bigWig CSHL Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeCshlShortRnaSeq/wgEncodeCshlShortRnaSeqK562CytosolShorttotalTapAlnRep1.bam K562 RnaSeq Alignments 1 bam CSHL Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeCshlShortRnaSeq/wgEncodeCshlShortRnaSeqK562CytosolShorttotalTapAlnRep2.bam K562 RnaSeq Alignments 2 bam CSHL Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeCshlShortRnaSeq/wgEncodeCshlShortRnaSeqK562CytosolShorttotalTapExonsGencV7.gtf.gz K562 RnaSeq ExonsGencV7 gtf CSHL Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeCshlShortRnaSeq/wgEncodeCshlShortRnaSeqK562CytosolShorttotalTapMinusRawRep1.bigWig K562 RnaSeq MinusSignal 1 bigWig CSHL Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeCshlShortRnaSeq/wgEncodeCshlShortRnaSeqK562CytosolShorttotalTapMinusRawRep2.bigWig K562 RnaSeq MinusSignal 2 bigWig CSHL Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeCshlShortRnaSeq/wgEncodeCshlShortRnaSeqK562CytosolShorttotalTapPlusRawRep1.bigWig K562 RnaSeq PlusSignal 1 bigWig CSHL Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeCshlShortRnaSeq/wgEncodeCshlShortRnaSeqK562CytosolShorttotalTapPlusRawRep2.bigWig K562 RnaSeq PlusSignal 2 bigWig CSHL Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeCshlShortRnaSeq/wgEncodeCshlShortRnaSeqK562NucleolusShortAln.bam K562 RnaSeq Alignments bam CSHL Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeCshlShortRnaSeq/wgEncodeCshlShortRnaSeqK562NucleolusShortMinusRaw.bigWig K562 RnaSeq MinusSignal bigWig CSHL Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeCshlShortRnaSeq/wgEncodeCshlShortRnaSeqK562NucleolusShortPlusRaw.bigWig K562 RnaSeq PlusSignal bigWig CSHL Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeCshlShortRnaSeq/wgEncodeCshlShortRnaSeqK562NucleolusShorttotalTapAlnRep3.bam K562 RnaSeq Alignments 3 bam CSHL Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeCshlShortRnaSeq/wgEncodeCshlShortRnaSeqK562NucleolusShorttotalTapAlnRep4.bam K562 RnaSeq Alignments 4 bam CSHL Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeCshlShortRnaSeq/wgEncodeCshlShortRnaSeqK562NucleolusShorttotalTapExonsGencV7.gtf.gz K562 RnaSeq ExonsGencV7 gtf CSHL Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeCshlShortRnaSeq/wgEncodeCshlShortRnaSeqK562NucleolusShorttotalTapMinusRawRep3.bigWig K562 RnaSeq MinusSignal 3 bigWig CSHL Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeCshlShortRnaSeq/wgEncodeCshlShortRnaSeqK562NucleolusShorttotalTapMinusRawRep4.bigWig K562 RnaSeq MinusSignal 4 bigWig CSHL Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeCshlShortRnaSeq/wgEncodeCshlShortRnaSeqK562NucleolusShorttotalTapPlusRawRep3.bigWig K562 RnaSeq PlusSignal 3 bigWig CSHL Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeCshlShortRnaSeq/wgEncodeCshlShortRnaSeqK562NucleolusShorttotalTapPlusRawRep4.bigWig K562 RnaSeq PlusSignal 4 bigWig CSHL Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeCshlShortRnaSeq/wgEncodeCshlShortRnaSeqK562NucleoplasmShortAln.bam K562 RnaSeq Alignments bam CSHL Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeCshlShortRnaSeq/wgEncodeCshlShortRnaSeqK562NucleoplasmShortMinusRaw.bigWig K562 RnaSeq MinusSignal bigWig CSHL Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeCshlShortRnaSeq/wgEncodeCshlShortRnaSeqK562NucleoplasmShortPlusRaw.bigWig K562 RnaSeq PlusSignal bigWig CSHL Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeCshlShortRnaSeq/wgEncodeCshlShortRnaSeqK562NucleoplasmShorttotalTapAlnRep3.bam K562 RnaSeq Alignments 3 bam CSHL Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeCshlShortRnaSeq/wgEncodeCshlShortRnaSeqK562NucleoplasmShorttotalTapAlnRep4.bam K562 RnaSeq Alignments 4 bam CSHL Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeCshlShortRnaSeq/wgEncodeCshlShortRnaSeqK562NucleoplasmShorttotalTapExonsGencV7.gtf.gz K562 RnaSeq ExonsGencV7 gtf CSHL Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeCshlShortRnaSeq/wgEncodeCshlShortRnaSeqK562NucleoplasmShorttotalTapMinusRawRep3.bigWig K562 RnaSeq MinusSignal 3 bigWig CSHL Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeCshlShortRnaSeq/wgEncodeCshlShortRnaSeqK562NucleoplasmShorttotalTapMinusRawRep4.bigWig K562 RnaSeq MinusSignal 4 bigWig CSHL Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeCshlShortRnaSeq/wgEncodeCshlShortRnaSeqK562NucleoplasmShorttotalTapPlusRawRep3.bigWig K562 RnaSeq PlusSignal 3 bigWig CSHL Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeCshlShortRnaSeq/wgEncodeCshlShortRnaSeqK562NucleoplasmShorttotalTapPlusRawRep4.bigWig K562 RnaSeq PlusSignal 4 bigWig CSHL Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeCshlShortRnaSeq/wgEncodeCshlShortRnaSeqK562NucleusShortAln.bam K562 RnaSeq Alignments bam CSHL Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeCshlShortRnaSeq/wgEncodeCshlShortRnaSeqK562NucleusShortMinusRaw.bigWig K562 RnaSeq MinusSignal bigWig CSHL Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeCshlShortRnaSeq/wgEncodeCshlShortRnaSeqK562NucleusShortPlusRaw.bigWig K562 RnaSeq PlusSignal bigWig CSHL Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeCshlShortRnaSeq/wgEncodeCshlShortRnaSeqK562NucleusShorttotalTapAlnRep1.bam K562 RnaSeq Alignments 1 bam CSHL Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeCshlShortRnaSeq/wgEncodeCshlShortRnaSeqK562NucleusShorttotalTapAlnRep2.bam K562 RnaSeq Alignments 2 bam CSHL Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeCshlShortRnaSeq/wgEncodeCshlShortRnaSeqK562NucleusShorttotalTapExonsGencV7.gtf.gz K562 RnaSeq ExonsGencV7 gtf CSHL Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeCshlShortRnaSeq/wgEncodeCshlShortRnaSeqK562NucleusShorttotalTapMinusRawRep1.bigWig K562 RnaSeq MinusSignal 1 bigWig CSHL Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeCshlShortRnaSeq/wgEncodeCshlShortRnaSeqK562NucleusShorttotalTapMinusRawRep2.bigWig K562 RnaSeq MinusSignal 2 bigWig CSHL Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeCshlShortRnaSeq/wgEncodeCshlShortRnaSeqK562NucleusShorttotalTapPlusRawRep1.bigWig K562 RnaSeq PlusSignal 1 bigWig CSHL Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeCshlShortRnaSeq/wgEncodeCshlShortRnaSeqK562NucleusShorttotalTapPlusRawRep2.bigWig K562 RnaSeq PlusSignal 2 bigWig CSHL Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeCshlShortRnaSeq/wgEncodeCshlShortRnaSeqK562PolysomeShortAln.bam K562 RnaSeq Alignments bam CSHL Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeCshlShortRnaSeq/wgEncodeCshlShortRnaSeqK562PolysomeShortMinusRaw.bigWig K562 RnaSeq MinusSignal bigWig CSHL Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeCshlShortRnaSeq/wgEncodeCshlShortRnaSeqK562PolysomeShortPlusRaw.bigWig K562 RnaSeq PlusSignal bigWig CSHL Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeCshlShortRnaSeq/wgEncodeCshlShortRnaSeqMcf7CellCiptapExonsGencV10.gtf.gz MCF-7 RnaSeq ExonsGencV10 gtf CSHL Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeCshlShortRnaSeq/wgEncodeCshlShortRnaSeqMcf7CellExonsGencV10.gtf.gz MCF-7 RnaSeq ExonsGencV10 gtf CSHL Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeCshlShortRnaSeq/wgEncodeCshlShortRnaSeqMcf7CellShorttotalAlnRep3.bam MCF-7 RnaSeq Alignments 3 bam CSHL Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeCshlShortRnaSeq/wgEncodeCshlShortRnaSeqMcf7CellShorttotalAlnRep4.bam MCF-7 RnaSeq Alignments 4 bam CSHL Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeCshlShortRnaSeq/wgEncodeCshlShortRnaSeqMcf7CellShorttotalCiptapAlnRep3.bam MCF-7 RnaSeq Alignments 3 bam CSHL Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeCshlShortRnaSeq/wgEncodeCshlShortRnaSeqMcf7CellShorttotalCiptapAlnRep4.bam MCF-7 RnaSeq Alignments 4 bam CSHL Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeCshlShortRnaSeq/wgEncodeCshlShortRnaSeqMcf7CellShorttotalCiptapMinusRep3.bigWig MCF-7 RnaSeq MinusSignal 3 bigWig CSHL Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeCshlShortRnaSeq/wgEncodeCshlShortRnaSeqMcf7CellShorttotalCiptapMinusRep4.bigWig MCF-7 RnaSeq MinusSignal 4 bigWig CSHL Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeCshlShortRnaSeq/wgEncodeCshlShortRnaSeqMcf7CellShorttotalCiptapPlusRep3.bigWig MCF-7 RnaSeq PlusSignal 3 bigWig CSHL Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeCshlShortRnaSeq/wgEncodeCshlShortRnaSeqMcf7CellShorttotalCiptapPlusRep4.bigWig MCF-7 RnaSeq PlusSignal 4 bigWig CSHL Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeCshlShortRnaSeq/wgEncodeCshlShortRnaSeqMcf7CellShorttotalExonsGencV7.gtf.gz MCF-7 RnaSeq ExonsGencV7 gtf CSHL Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeCshlShortRnaSeq/wgEncodeCshlShortRnaSeqMcf7CellShorttotalMinusRep3.bigWig MCF-7 RnaSeq MinusSignal 3 bigWig CSHL Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeCshlShortRnaSeq/wgEncodeCshlShortRnaSeqMcf7CellShorttotalMinusRep4.bigWig MCF-7 RnaSeq MinusSignal 4 bigWig CSHL Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeCshlShortRnaSeq/wgEncodeCshlShortRnaSeqMcf7CellShorttotalPlusRep3.bigWig MCF-7 RnaSeq PlusSignal 3 bigWig CSHL Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeCshlShortRnaSeq/wgEncodeCshlShortRnaSeqMcf7CellShorttotalPlusRep4.bigWig MCF-7 RnaSeq PlusSignal 4 bigWig CSHL Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeCshlShortRnaSeq/wgEncodeCshlShortRnaSeqMcf7CellShorttotalTapAlnRep1.bam MCF-7 RnaSeq Alignments 1 bam CSHL Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeCshlShortRnaSeq/wgEncodeCshlShortRnaSeqMcf7CellShorttotalTapAlnRep1V2.bam MCF-7 RnaSeq Alignments 1 bam CSHL Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeCshlShortRnaSeq/wgEncodeCshlShortRnaSeqMcf7CellShorttotalTapAlnRep2.bam MCF-7 RnaSeq Alignments 2 bam CSHL Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeCshlShortRnaSeq/wgEncodeCshlShortRnaSeqMcf7CellShorttotalTapAlnRep2V2.bam MCF-7 RnaSeq Alignments 2 bam CSHL Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeCshlShortRnaSeq/wgEncodeCshlShortRnaSeqMcf7CellShorttotalTapMinusRawRep1.bigWig MCF-7 RnaSeq MinusSignal 1 bigWig CSHL Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeCshlShortRnaSeq/wgEncodeCshlShortRnaSeqMcf7CellShorttotalTapMinusRawRep2.bigWig MCF-7 RnaSeq MinusSignal 2 bigWig CSHL Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeCshlShortRnaSeq/wgEncodeCshlShortRnaSeqMcf7CellShorttotalTapMinusRep1V2.bigWig MCF-7 RnaSeq MinusSignal 1 bigWig CSHL Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeCshlShortRnaSeq/wgEncodeCshlShortRnaSeqMcf7CellShorttotalTapMinusRep2V2.bigWig MCF-7 RnaSeq MinusSignal 2 bigWig CSHL Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeCshlShortRnaSeq/wgEncodeCshlShortRnaSeqMcf7CellShorttotalTapPlusRawRep1.bigWig MCF-7 RnaSeq PlusSignal 1 bigWig CSHL Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeCshlShortRnaSeq/wgEncodeCshlShortRnaSeqMcf7CellShorttotalTapPlusRawRep2.bigWig MCF-7 RnaSeq PlusSignal 2 bigWig CSHL Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeCshlShortRnaSeq/wgEncodeCshlShortRnaSeqMcf7CellShorttotalTapPlusRep1V2.bigWig MCF-7 RnaSeq PlusSignal 1 bigWig CSHL Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeCshlShortRnaSeq/wgEncodeCshlShortRnaSeqMcf7CellShorttotalTapPlusRep2V2.bigWig MCF-7 RnaSeq PlusSignal 2 bigWig CSHL Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeCshlShortRnaSeq/wgEncodeCshlShortRnaSeqMcf7CellTapExonsGencV10.gtf.gz MCF-7 RnaSeq ExonsGencV10 gtf CSHL Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeCshlShortRnaSeq/wgEncodeCshlShortRnaSeqMcf7CellTapExonsGencV10V2.gtf.gz MCF-7 RnaSeq ExonsGencV10 gtf CSHL Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeCshlShortRnaSeq/wgEncodeCshlShortRnaSeqMcf7CytosolExonsGencV10.gtf.gz MCF-7 RnaSeq ExonsGencV10 gtf CSHL Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeCshlShortRnaSeq/wgEncodeCshlShortRnaSeqMcf7CytosolShorttotalAlnRep3.bam MCF-7 RnaSeq Alignments 3 bam CSHL Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeCshlShortRnaSeq/wgEncodeCshlShortRnaSeqMcf7CytosolShorttotalAlnRep4.bam MCF-7 RnaSeq Alignments 4 bam CSHL Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeCshlShortRnaSeq/wgEncodeCshlShortRnaSeqMcf7CytosolShorttotalMinusRep3.bigWig MCF-7 RnaSeq MinusSignal 3 bigWig CSHL Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeCshlShortRnaSeq/wgEncodeCshlShortRnaSeqMcf7CytosolShorttotalMinusRep4.bigWig MCF-7 RnaSeq MinusSignal 4 bigWig CSHL Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeCshlShortRnaSeq/wgEncodeCshlShortRnaSeqMcf7CytosolShorttotalPlusRep3.bigWig MCF-7 RnaSeq PlusSignal 3 bigWig CSHL Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeCshlShortRnaSeq/wgEncodeCshlShortRnaSeqMcf7CytosolShorttotalPlusRep4.bigWig MCF-7 RnaSeq PlusSignal 4 bigWig CSHL Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeCshlShortRnaSeq/wgEncodeCshlShortRnaSeqMcf7CytosolShorttotalTapAlnRep3.bam MCF-7 RnaSeq Alignments 3 bam CSHL Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeCshlShortRnaSeq/wgEncodeCshlShortRnaSeqMcf7CytosolShorttotalTapAlnRep4.bam MCF-7 RnaSeq Alignments 4 bam CSHL Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeCshlShortRnaSeq/wgEncodeCshlShortRnaSeqMcf7CytosolShorttotalTapMinusRep3.bigWig MCF-7 RnaSeq MinusSignal 3 bigWig CSHL Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeCshlShortRnaSeq/wgEncodeCshlShortRnaSeqMcf7CytosolShorttotalTapMinusRep4.bigWig MCF-7 RnaSeq MinusSignal 4 bigWig CSHL Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeCshlShortRnaSeq/wgEncodeCshlShortRnaSeqMcf7CytosolShorttotalTapPlusRep3.bigWig MCF-7 RnaSeq PlusSignal 3 bigWig CSHL Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeCshlShortRnaSeq/wgEncodeCshlShortRnaSeqMcf7CytosolShorttotalTapPlusRep4.bigWig MCF-7 RnaSeq PlusSignal 4 bigWig CSHL Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeCshlShortRnaSeq/wgEncodeCshlShortRnaSeqMcf7CytosolTapExonsGencV10.gtf.gz MCF-7 RnaSeq ExonsGencV10 gtf CSHL Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeCshlShortRnaSeq/wgEncodeCshlShortRnaSeqMcf7NucleusExonsGencV10.gtf.gz MCF-7 RnaSeq ExonsGencV10 gtf CSHL Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeCshlShortRnaSeq/wgEncodeCshlShortRnaSeqMcf7NucleusShorttotalAlnRep3.bam MCF-7 RnaSeq Alignments 3 bam CSHL Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeCshlShortRnaSeq/wgEncodeCshlShortRnaSeqMcf7NucleusShorttotalAlnRep4.bam MCF-7 RnaSeq Alignments 4 bam CSHL Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeCshlShortRnaSeq/wgEncodeCshlShortRnaSeqMcf7NucleusShorttotalMinusRep3.bigWig MCF-7 RnaSeq MinusSignal 3 bigWig CSHL Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeCshlShortRnaSeq/wgEncodeCshlShortRnaSeqMcf7NucleusShorttotalMinusRep4.bigWig MCF-7 RnaSeq MinusSignal 4 bigWig CSHL Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeCshlShortRnaSeq/wgEncodeCshlShortRnaSeqMcf7NucleusShorttotalPlusRep3.bigWig MCF-7 RnaSeq PlusSignal 3 bigWig CSHL Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeCshlShortRnaSeq/wgEncodeCshlShortRnaSeqMcf7NucleusShorttotalPlusRep4.bigWig MCF-7 RnaSeq PlusSignal 4 bigWig CSHL Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeCshlShortRnaSeq/wgEncodeCshlShortRnaSeqMcf7NucleusShorttotalTapAlnRep3.bam MCF-7 RnaSeq Alignments 3 bam CSHL Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeCshlShortRnaSeq/wgEncodeCshlShortRnaSeqMcf7NucleusShorttotalTapAlnRep4.bam MCF-7 RnaSeq Alignments 4 bam CSHL Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeCshlShortRnaSeq/wgEncodeCshlShortRnaSeqMcf7NucleusShorttotalTapMinusRep3.bigWig MCF-7 RnaSeq MinusSignal 3 bigWig CSHL Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeCshlShortRnaSeq/wgEncodeCshlShortRnaSeqMcf7NucleusShorttotalTapMinusRep4.bigWig MCF-7 RnaSeq MinusSignal 4 bigWig CSHL Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeCshlShortRnaSeq/wgEncodeCshlShortRnaSeqMcf7NucleusShorttotalTapPlusRep3.bigWig MCF-7 RnaSeq PlusSignal 3 bigWig CSHL Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeCshlShortRnaSeq/wgEncodeCshlShortRnaSeqMcf7NucleusShorttotalTapPlusRep4.bigWig MCF-7 RnaSeq PlusSignal 4 bigWig CSHL Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeCshlShortRnaSeq/wgEncodeCshlShortRnaSeqMcf7NucleusTapExonsGencV10.gtf.gz MCF-7 RnaSeq ExonsGencV10 gtf CSHL Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeCshlShortRnaSeq/wgEncodeCshlShortRnaSeqMonocd14CellTapAlnRep1.bam Monocytes-CD14+ RnaSeq Alignments 1 bam CSHL Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeCshlShortRnaSeq/wgEncodeCshlShortRnaSeqMonocd14CellTapAlnRep2.bam Monocytes-CD14+ RnaSeq Alignments 2 bam CSHL Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeCshlShortRnaSeq/wgEncodeCshlShortRnaSeqMonocd14CellTapExonsGencV10.gtf.gz Monocytes-CD14+ RnaSeq ExonsGencV10 gtf CSHL Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeCshlShortRnaSeq/wgEncodeCshlShortRnaSeqMonocd14CellTapMinusRep1.bigWig Monocytes-CD14+ RnaSeq MinusSignal 1 bigWig CSHL Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeCshlShortRnaSeq/wgEncodeCshlShortRnaSeqMonocd14CellTapMinusRep2.bigWig Monocytes-CD14+ RnaSeq MinusSignal 2 bigWig CSHL Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeCshlShortRnaSeq/wgEncodeCshlShortRnaSeqMonocd14CellTapPlusRep1.bigWig Monocytes-CD14+ RnaSeq PlusSignal 1 bigWig CSHL Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeCshlShortRnaSeq/wgEncodeCshlShortRnaSeqMonocd14CellTapPlusRep2.bigWig Monocytes-CD14+ RnaSeq PlusSignal 2 bigWig CSHL Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeCshlShortRnaSeq/wgEncodeCshlShortRnaSeqNhdf00608013CellShorttotalTapAlnRep2.bam NHDF RnaSeq Alignments 2 bam CSHL Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeCshlShortRnaSeq/wgEncodeCshlShortRnaSeqNhdf00608013CellShorttotalTapMinusRep2.bigWig NHDF RnaSeq MinusSignal 2 bigWig CSHL Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeCshlShortRnaSeq/wgEncodeCshlShortRnaSeqNhdf00608013CellShorttotalTapPlusRep2.bigWig NHDF RnaSeq PlusSignal 2 bigWig CSHL Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeCshlShortRnaSeq/wgEncodeCshlShortRnaSeqNhdf70717012CellShorttotalTapAlnRep1.bam NHDF RnaSeq Alignments 1 bam CSHL Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeCshlShortRnaSeq/wgEncodeCshlShortRnaSeqNhdf70717012CellShorttotalTapMinusRep1.bigWig NHDF RnaSeq MinusSignal 1 bigWig CSHL Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeCshlShortRnaSeq/wgEncodeCshlShortRnaSeqNhdf70717012CellShorttotalTapPlusRep1.bigWig NHDF RnaSeq PlusSignal 1 bigWig CSHL Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeCshlShortRnaSeq/wgEncodeCshlShortRnaSeqNhdfCellTapExonsGencV10.gtf.gz NHDF RnaSeq ExonsGencV10 gtf CSHL Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeCshlShortRnaSeq/wgEncodeCshlShortRnaSeqNhekCellShorttotalTapAlnRep1.bam NHEK RnaSeq Alignments 1 bam CSHL Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeCshlShortRnaSeq/wgEncodeCshlShortRnaSeqNhekCellShorttotalTapAlnRep2.bam NHEK RnaSeq Alignments 2 bam CSHL Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeCshlShortRnaSeq/wgEncodeCshlShortRnaSeqNhekCellShorttotalTapExonsGencV7.gtf.gz NHEK RnaSeq ExonsGencV7 gtf CSHL Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeCshlShortRnaSeq/wgEncodeCshlShortRnaSeqNhekCellShorttotalTapMinusRawRep1.bigWig NHEK RnaSeq MinusSignal 1 bigWig CSHL Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeCshlShortRnaSeq/wgEncodeCshlShortRnaSeqNhekCellShorttotalTapMinusRawRep2.bigWig NHEK RnaSeq MinusSignal 2 bigWig CSHL Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeCshlShortRnaSeq/wgEncodeCshlShortRnaSeqNhekCellShorttotalTapPlusRawRep1.bigWig NHEK RnaSeq PlusSignal 1 bigWig CSHL Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeCshlShortRnaSeq/wgEncodeCshlShortRnaSeqNhekCellShorttotalTapPlusRawRep2.bigWig NHEK RnaSeq PlusSignal 2 bigWig CSHL Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeCshlShortRnaSeq/wgEncodeCshlShortRnaSeqNhekCytosolShorttotalTapAlnRep3.bam NHEK RnaSeq Alignments 3 bam CSHL Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeCshlShortRnaSeq/wgEncodeCshlShortRnaSeqNhekCytosolShorttotalTapAlnRep4.bam NHEK RnaSeq Alignments 4 bam CSHL Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeCshlShortRnaSeq/wgEncodeCshlShortRnaSeqNhekCytosolShorttotalTapExonsGencV7.gtf.gz NHEK RnaSeq ExonsGencV7 gtf CSHL Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeCshlShortRnaSeq/wgEncodeCshlShortRnaSeqNhekCytosolShorttotalTapMinusRawRep3.bigWig NHEK RnaSeq MinusSignal 3 bigWig CSHL Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeCshlShortRnaSeq/wgEncodeCshlShortRnaSeqNhekCytosolShorttotalTapMinusRawRep4.bigWig NHEK RnaSeq MinusSignal 4 bigWig CSHL Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeCshlShortRnaSeq/wgEncodeCshlShortRnaSeqNhekCytosolShorttotalTapPlusRawRep3.bigWig NHEK RnaSeq PlusSignal 3 bigWig CSHL Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeCshlShortRnaSeq/wgEncodeCshlShortRnaSeqNhekCytosolShorttotalTapPlusRawRep4.bigWig NHEK RnaSeq PlusSignal 4 bigWig CSHL Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeCshlShortRnaSeq/wgEncodeCshlShortRnaSeqNhekNucleusShorttotalTapAlnRep3.bam NHEK RnaSeq Alignments 3 bam CSHL Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeCshlShortRnaSeq/wgEncodeCshlShortRnaSeqNhekNucleusShorttotalTapAlnRep4.bam NHEK RnaSeq Alignments 4 bam CSHL Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeCshlShortRnaSeq/wgEncodeCshlShortRnaSeqNhekNucleusShorttotalTapExonsGencV7.gtf.gz NHEK RnaSeq ExonsGencV7 gtf CSHL Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeCshlShortRnaSeq/wgEncodeCshlShortRnaSeqNhekNucleusShorttotalTapMinusRawRep3.bigWig NHEK RnaSeq MinusSignal 3 bigWig CSHL Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeCshlShortRnaSeq/wgEncodeCshlShortRnaSeqNhekNucleusShorttotalTapMinusRawRep4.bigWig NHEK RnaSeq MinusSignal 4 bigWig CSHL Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeCshlShortRnaSeq/wgEncodeCshlShortRnaSeqNhekNucleusShorttotalTapPlusRawRep3.bigWig NHEK RnaSeq PlusSignal 3 bigWig CSHL Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeCshlShortRnaSeq/wgEncodeCshlShortRnaSeqNhekNucleusShorttotalTapPlusRawRep4.bigWig NHEK RnaSeq PlusSignal 4 bigWig CSHL Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeCshlShortRnaSeq/wgEncodeCshlShortRnaSeqNhekNucleusTapExonsGencV10.gtf.gz NHEK RnaSeq ExonsGencV10 gtf CSHL Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeCshlShortRnaSeq/wgEncodeCshlShortRnaSeqNhemfm2CellTapAlnRep1.bam NHEM.f_M2 RnaSeq Alignments 1 bam CSHL Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeCshlShortRnaSeq/wgEncodeCshlShortRnaSeqNhemfm2CellTapAlnRep2.bam NHEM.f_M2 RnaSeq Alignments 2 bam CSHL Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeCshlShortRnaSeq/wgEncodeCshlShortRnaSeqNhemfm2CellTapExonsGencV10.gtf.gz NHEM.f_M2 RnaSeq ExonsGencV10 gtf CSHL Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeCshlShortRnaSeq/wgEncodeCshlShortRnaSeqNhemfm2CellTapMinusRep1.bigWig NHEM.f_M2 RnaSeq MinusSignal 1 bigWig CSHL Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeCshlShortRnaSeq/wgEncodeCshlShortRnaSeqNhemfm2CellTapMinusRep2.bigWig NHEM.f_M2 RnaSeq MinusSignal 2 bigWig CSHL Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeCshlShortRnaSeq/wgEncodeCshlShortRnaSeqNhemfm2CellTapPlusRep1.bigWig NHEM.f_M2 RnaSeq PlusSignal 1 bigWig CSHL Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeCshlShortRnaSeq/wgEncodeCshlShortRnaSeqNhemfm2CellTapPlusRep2.bigWig NHEM.f_M2 RnaSeq PlusSignal 2 bigWig CSHL Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeCshlShortRnaSeq/wgEncodeCshlShortRnaSeqNhemm2CellTapAlnRep1.bam NHEM_M2 RnaSeq Alignments 1 bam CSHL Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeCshlShortRnaSeq/wgEncodeCshlShortRnaSeqNhemm2CellTapAlnRep2.bam NHEM_M2 RnaSeq Alignments 2 bam CSHL Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeCshlShortRnaSeq/wgEncodeCshlShortRnaSeqNhemm2CellTapExonsGencV10.gtf.gz NHEM_M2 RnaSeq ExonsGencV10 gtf CSHL Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeCshlShortRnaSeq/wgEncodeCshlShortRnaSeqNhemm2CellTapMinusRep1.bigWig NHEM_M2 RnaSeq MinusSignal 1 bigWig CSHL Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeCshlShortRnaSeq/wgEncodeCshlShortRnaSeqNhemm2CellTapMinusRep2.bigWig NHEM_M2 RnaSeq MinusSignal 2 bigWig CSHL Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeCshlShortRnaSeq/wgEncodeCshlShortRnaSeqNhemm2CellTapPlusRep1.bigWig NHEM_M2 RnaSeq PlusSignal 1 bigWig CSHL Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeCshlShortRnaSeq/wgEncodeCshlShortRnaSeqNhemm2CellTapPlusRep2.bigWig NHEM_M2 RnaSeq PlusSignal 2 bigWig CSHL Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeCshlShortRnaSeq/wgEncodeCshlShortRnaSeqProstateCellTotalAln.bam prostate RnaSeq Alignments bam CSHL Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeCshlShortRnaSeq/wgEncodeCshlShortRnaSeqProstateCellTotalMinusRaw.bigWig prostate RnaSeq MinusSignal bigWig CSHL Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeCshlShortRnaSeq/wgEncodeCshlShortRnaSeqProstateCellTotalPlusRaw.bigWig prostate RnaSeq PlusSignal bigWig CSHL Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeCshlShortRnaSeq/wgEncodeCshlShortRnaSeqSkmc812190217CellTapAlnRep2.bam SkMC RnaSeq Alignments 2 bam CSHL Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeCshlShortRnaSeq/wgEncodeCshlShortRnaSeqSkmc812190217CellTapMinusRep2.bigWig SkMC RnaSeq MinusSignal 2 bigWig CSHL Data 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http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeCshlShortRnaSeq/wgEncodeCshlShortRnaSeqSknshCellCiptapExonsGencV10.gtf.gz SK-N-SH RnaSeq ExonsGencV10 gtf CSHL Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeCshlShortRnaSeq/wgEncodeCshlShortRnaSeqSknshCellExonsGencV10.gtf.gz SK-N-SH RnaSeq ExonsGencV10 gtf CSHL Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeCshlShortRnaSeq/wgEncodeCshlShortRnaSeqSknshCellShorttotalAlnRep3.bam SK-N-SH RnaSeq Alignments 3 bam CSHL Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeCshlShortRnaSeq/wgEncodeCshlShortRnaSeqSknshCellShorttotalAlnRep4.bam SK-N-SH RnaSeq Alignments 4 bam CSHL Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeCshlShortRnaSeq/wgEncodeCshlShortRnaSeqSknshCellShorttotalCiptapAlnRep3.bam SK-N-SH RnaSeq Alignments 3 bam CSHL Data 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http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeGisRnaPet/wgEncodeGisRnaPetMcf7NucleusPapPlusRawRep3.bigWig MCF-7 RnaPet PlusRawSignal 3 bigWig GIS Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeGisRnaPet/wgEncodeGisRnaPetMcf7NucleusPapPlusRawRep4.bigWig MCF-7 RnaPet PlusRawSignal 4 bigWig GIS Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeGisRnaPet/wgEncodeGisRnaPetNhekCytosolPapAlnRep1.bam NHEK RnaPet Alignments 1 bam GIS Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeGisRnaPet/wgEncodeGisRnaPetNhekCytosolPapClustersRep1.bed.gz NHEK RnaPet Clusters 1 bed GIS Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeGisRnaPet/wgEncodeGisRnaPetNhekCytosolPapMinusRawRep1.bigWig NHEK RnaPet MinusRawSignal 1 bigWig GIS Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeGisRnaPet/wgEncodeGisRnaPetNhekCytosolPapPlusRawRep1.bigWig NHEK RnaPet PlusRawSignal 1 bigWig GIS Data 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http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeGisRnaPet/wgEncodeGisRnaPetProstateCellPapMinusRawSigRep1.bigWig prostate RnaPet MinusRawSignal 1 bigWig GIS Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeGisRnaPet/wgEncodeGisRnaPetProstateCellPapPlusRawSigRep1.bigWig prostate RnaPet PlusRawSignal 1 bigWig GIS Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeGisRnaPet/wgEncodeGisRnaPetSknshCellPapAlnRep3.bam SK-N-SH RnaPet Alignments 3 bam GIS Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeGisRnaPet/wgEncodeGisRnaPetSknshCellPapAlnRep4.bam SK-N-SH RnaPet Alignments 4 bam GIS Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeGisRnaPet/wgEncodeGisRnaPetSknshCellPapMinusRawRep3.bigWig SK-N-SH RnaPet MinusRawSignal 3 bigWig GIS Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeGisRnaPet/wgEncodeGisRnaPetSknshCellPapMinusRawRep4.bigWig SK-N-SH RnaPet MinusRawSignal 4 bigWig GIS Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeGisRnaPet/wgEncodeGisRnaPetSknshCellPapPlusRawRep3.bigWig SK-N-SH RnaPet PlusRawSignal 3 bigWig GIS Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeGisRnaPet/wgEncodeGisRnaPetSknshCellPapPlusRawRep4.bigWig SK-N-SH RnaPet PlusRawSignal 4 bigWig GIS Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeGisRnaPet/wgEncodeGisRnaPetSknshCytosolPapAlnRep3.bam SK-N-SH RnaPet Alignments 3 bam GIS Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeGisRnaPet/wgEncodeGisRnaPetSknshCytosolPapAlnRep4.bam SK-N-SH RnaPet Alignments 4 bam GIS Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeGisRnaPet/wgEncodeGisRnaPetSknshCytosolPapMinusRawRep3.bigWig SK-N-SH RnaPet MinusRawSignal 3 bigWig GIS Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeGisRnaPet/wgEncodeGisRnaPetSknshCytosolPapMinusRawRep4.bigWig SK-N-SH RnaPet MinusRawSignal 4 bigWig GIS Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeGisRnaPet/wgEncodeGisRnaPetSknshCytosolPapPlusRawRep3.bigWig SK-N-SH RnaPet PlusRawSignal 3 bigWig GIS Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeGisRnaPet/wgEncodeGisRnaPetSknshCytosolPapPlusRawRep4.bigWig SK-N-SH RnaPet PlusRawSignal 4 bigWig GIS Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeGisRnaPet/wgEncodeGisRnaPetSknshNucleusPapAlnRep3.bam SK-N-SH RnaPet Alignments 3 bam GIS Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeGisRnaPet/wgEncodeGisRnaPetSknshNucleusPapAlnRep4.bam SK-N-SH RnaPet Alignments 4 bam GIS Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeGisRnaPet/wgEncodeGisRnaPetSknshNucleusPapMinusRawRep3.bigWig SK-N-SH RnaPet MinusRawSignal 3 bigWig GIS Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeGisRnaPet/wgEncodeGisRnaPetSknshNucleusPapMinusRawRep4.bigWig SK-N-SH RnaPet MinusRawSignal 4 bigWig GIS Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeGisRnaPet/wgEncodeGisRnaPetSknshNucleusPapPlusRawRep3.bigWig SK-N-SH RnaPet PlusRawSignal 3 bigWig GIS Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeGisRnaPet/wgEncodeGisRnaPetSknshNucleusPapPlusRawRep4.bigWig SK-N-SH RnaPet PlusRawSignal 4 bigWig GIS Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeGisRnaSeq/wgEncodeGisRnaSeqGm12878CytosolPapAlnRep1.bam GM12878 RnaSeq Alignments 1 bam GIS Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeGisRnaSeq/wgEncodeGisRnaSeqGm12878CytosolPapMinusRawRep1.bigWig GM12878 RnaSeq MinusRawSignal 1 bigWig GIS Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeGisRnaSeq/wgEncodeGisRnaSeqGm12878CytosolPapPlusRawRep1.bigWig GM12878 RnaSeq PlusRawSignal 1 bigWig GIS Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeGisRnaSeq/wgEncodeGisRnaSeqH1hescCellPapAlnRep1.bam H1-hESC RnaSeq Alignments 1 bam GIS Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeGisRnaSeq/wgEncodeGisRnaSeqH1hescCellPapMinusRawRep1.bigWig H1-hESC RnaSeq MinusRawSignal 1 bigWig GIS Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeGisRnaSeq/wgEncodeGisRnaSeqH1hescCellPapPlusRawRep1.bigWig H1-hESC RnaSeq PlusRawSignal 1 bigWig GIS Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeGisRnaSeq/wgEncodeGisRnaSeqK562CytosolPapAlnRep1.bam K562 RnaSeq Alignments 1 bam GIS Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeGisRnaSeq/wgEncodeGisRnaSeqK562CytosolPapAlnRep2.bam K562 RnaSeq Alignments 2 bam GIS Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeGisRnaSeq/wgEncodeGisRnaSeqK562CytosolPapMinusRawRep1.bigWig K562 RnaSeq MinusRawSignal 1 bigWig GIS Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeGisRnaSeq/wgEncodeGisRnaSeqK562CytosolPapMinusRawRep2.bigWig K562 RnaSeq MinusRawSignal 2 bigWig GIS Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeGisRnaSeq/wgEncodeGisRnaSeqK562CytosolPapPlusRawRep1.bigWig K562 RnaSeq PlusRawSignal 1 bigWig GIS Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeGisRnaSeq/wgEncodeGisRnaSeqK562CytosolPapPlusRawRep2.bigWig K562 RnaSeq PlusRawSignal 2 bigWig GIS Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeHaibMethyl450/wgEncodeHaibMethyl450A549Etoh02SitesRep1.bed.gz A549 MethylArray Sites 1 bed HudsonAlpha Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeHaibMethyl450/wgEncodeHaibMethyl450Ag04449SitesRep1.bed.gz AG04449 MethylArray Sites 1 bed HudsonAlpha Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeHaibMethyl450/wgEncodeHaibMethyl450Ag04450SitesRep1.bed.gz AG04450 MethylArray 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http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeHaibMethyl450/wgEncodeHaibMethyl450BjSitesRep1.bed.gz BJ MethylArray Sites 1 bed HudsonAlpha Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeHaibMethyl450/wgEncodeHaibMethyl450Caco2SitesRep1.bed.gz Caco-2 MethylArray Sites 1 bed HudsonAlpha Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeHaibMethyl450/wgEncodeHaibMethyl450CmkSitesRep1.bed.gz CMK MethylArray Sites 1 bed HudsonAlpha Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeHaibMethyl450/wgEncodeHaibMethyl450Ecc1SitesRep1.bed.gz ECC-1 MethylArray Sites 1 bed HudsonAlpha Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeHaibMethyl450/wgEncodeHaibMethyl450Gm06990SitesRep1.bed.gz GM06990 MethylArray Sites 1 bed HudsonAlpha Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeHaibMethyl450/wgEncodeHaibMethyl450Gm12878SitesRep1.bed.gz GM12878 MethylArray Sites 1 bed HudsonAlpha Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeHaibMethyl450/wgEncodeHaibMethyl450Gm12891SitesRep1.bed.gz GM12891 MethylArray Sites 1 bed HudsonAlpha Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeHaibMethyl450/wgEncodeHaibMethyl450Gm12892SitesRep1.bed.gz GM12892 MethylArray Sites 1 bed HudsonAlpha Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeHaibMethyl450/wgEncodeHaibMethyl450Gm19239SitesRep1.bed.gz GM19239 MethylArray Sites 1 bed HudsonAlpha Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeHaibMethyl450/wgEncodeHaibMethyl450H1hescSitesRep1.bed.gz H1-hESC MethylArray Sites 1 bed HudsonAlpha Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeHaibMethyl450/wgEncodeHaibMethyl450HaeSitesRep1.bed.gz HAEpiC MethylArray Sites 1 bed HudsonAlpha Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeHaibMethyl450/wgEncodeHaibMethyl450HcfSitesRep1.bed.gz HCF MethylArray Sites 1 bed HudsonAlpha Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeHaibMethyl450/wgEncodeHaibMethyl450HcmSitesRep1.bed.gz HCM MethylArray Sites 1 bed HudsonAlpha Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeHaibMethyl450/wgEncodeHaibMethyl450HcpeSitesRep1.bed.gz HCPEpiC MethylArray Sites 1 bed HudsonAlpha Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeHaibMethyl450/wgEncodeHaibMethyl450Hct116HaibSitesRep1.bed.gz HCT-116 MethylArray Sites 1 bed HudsonAlpha Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeHaibMethyl450/wgEncodeHaibMethyl450Hct116StanfordSitesRep1.bed.gz HCT-116 MethylArray Sites 1 bed HudsonAlpha Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeHaibMethyl450/wgEncodeHaibMethyl450HeeSitesRep1.bed.gz HEEpiC MethylArray Sites 1 bed HudsonAlpha Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeHaibMethyl450/wgEncodeHaibMethyl450Hek293SitesRep1.bed.gz HEK293 MethylArray Sites 1 bed HudsonAlpha Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeHaibMethyl450/wgEncodeHaibMethyl450Helas3SitesRep1.bed.gz HeLa-S3 MethylArray Sites 1 bed HudsonAlpha Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeHaibMethyl450/wgEncodeHaibMethyl450HepatoSitesRep1.bed.gz Hepatocytes MethylArray Sites 1 bed HudsonAlpha Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeHaibMethyl450/wgEncodeHaibMethyl450Hepg2SitesRep1.bed.gz HepG2 MethylArray Sites 1 bed HudsonAlpha Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeHaibMethyl450/wgEncodeHaibMethyl450HipeSitesRep1.bed.gz HIPEpiC MethylArray Sites 1 bed HudsonAlpha Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeHaibMethyl450/wgEncodeHaibMethyl450Hl60SitesRep1.bed.gz HL-60 MethylArray 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HRPEpiC MethylArray Sites 1 bed HudsonAlpha Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeHaibMethyl450/wgEncodeHaibMethyl450HuvecSitesRep1.bed.gz HUVEC MethylArray Sites 1 bed HudsonAlpha Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeHaibMethyl450/wgEncodeHaibMethyl450Imr90SitesRep1.bed.gz IMR90 MethylArray Sites 1 bed HudsonAlpha Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeHaibMethyl450/wgEncodeHaibMethyl450JurkatSitesRep1.bed.gz Jurkat MethylArray Sites 1 bed HudsonAlpha Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeHaibMethyl450/wgEncodeHaibMethyl450K562SitesRep1.bed.gz K562 MethylArray Sites 1 bed HudsonAlpha Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeHaibMethyl450/wgEncodeHaibMethyl450LncapSitesRep1.bed.gz LNCaP MethylArray Sites 1 bed HudsonAlpha Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeHaibMethyl450/wgEncodeHaibMethyl450Mcf10aesSitesRep1.bed.gz MCF10A-Er-Src MethylArray Sites 1 bed HudsonAlpha Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeHaibMethyl450/wgEncodeHaibMethyl450Mcf10aesTamSitesRep1.bed.gz MCF10A-Er-Src MethylArray Sites 1 bed HudsonAlpha Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeHaibMethyl450/wgEncodeHaibMethyl450Mcf7SitesRep1.bed.gz MCF-7 MethylArray Sites 1 bed HudsonAlpha Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeHaibMethyl450/wgEncodeHaibMethyl450Nb4SitesRep1.bed.gz NB4 MethylArray Sites 1 bed HudsonAlpha Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeHaibMethyl450/wgEncodeHaibMethyl450NhaSitesRep1.bed.gz NH-A MethylArray Sites 1 bed HudsonAlpha Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeHaibMethyl450/wgEncodeHaibMethyl450NhbeSitesRep1.bed.gz NHBE MethylArray 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HudsonAlpha Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeHaibTfbs/wgEncodeHaibTfbsEcc1Foxa1sc6553V0416102Dm002p1hRawRep2.bigWig ECC-1 ChipSeq FOXA1_(SC-6553) RawSignal 2 bigWig HudsonAlpha Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeHaibTfbs/wgEncodeHaibTfbsEcc1Foxm1sc502V0422111AlnRep1.bam ECC-1 ChipSeq FOXM1_(SC-502) Alignments 1 bam HudsonAlpha Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeHaibTfbs/wgEncodeHaibTfbsEcc1Foxm1sc502V0422111AlnRep2.bam ECC-1 ChipSeq FOXM1_(SC-502) Alignments 2 bam HudsonAlpha Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeHaibTfbs/wgEncodeHaibTfbsEcc1Foxm1sc502V0422111PkRep1.broadPeak.gz ECC-1 ChipSeq FOXM1_(SC-502) Peaks 1 broadPeak HudsonAlpha Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeHaibTfbs/wgEncodeHaibTfbsEcc1Foxm1sc502V0422111PkRep2.broadPeak.gz ECC-1 ChipSeq FOXM1_(SC-502) Peaks 2 broadPeak HudsonAlpha Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeHaibTfbs/wgEncodeHaibTfbsEcc1Foxm1sc502V0422111RawRep1.bigWig ECC-1 ChipSeq FOXM1_(SC-502) RawSignal 1 bigWig HudsonAlpha Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeHaibTfbs/wgEncodeHaibTfbsEcc1Foxm1sc502V0422111RawRep2.bigWig ECC-1 ChipSeq FOXM1_(SC-502) RawSignal 2 bigWig HudsonAlpha Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeHaibTfbs/wgEncodeHaibTfbsEcc1GrV0416102Dex100nmAlnRep1.bam ECC-1 ChipSeq GR Alignments 1 bam HudsonAlpha Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeHaibTfbs/wgEncodeHaibTfbsEcc1GrV0416102Dex100nmAlnRep2.bam ECC-1 ChipSeq GR Alignments 2 bam HudsonAlpha Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeHaibTfbs/wgEncodeHaibTfbsEcc1GrV0416102Dex100nmPkRep1.broadPeak.gz ECC-1 ChipSeq GR Peaks 1 broadPeak HudsonAlpha Data 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ChipSeq TAF1 Peaks 1 broadPeak HudsonAlpha Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeHaibTfbs/wgEncodeHaibTfbsEcc1Taf1V0422111PkRep2.broadPeak.gz ECC-1 ChipSeq TAF1 Peaks 2 broadPeak HudsonAlpha Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeHaibTfbs/wgEncodeHaibTfbsEcc1Taf1V0422111RawRep1.bigWig ECC-1 ChipSeq TAF1 RawSignal 1 bigWig HudsonAlpha Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeHaibTfbs/wgEncodeHaibTfbsEcc1Taf1V0422111RawRep2.bigWig ECC-1 ChipSeq TAF1 RawSignal 2 bigWig HudsonAlpha Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeHaibTfbs/wgEncodeHaibTfbsEcc1Tcf12V0422111AlnRep1.bam ECC-1 ChipSeq TCF12 Alignments 1 bam HudsonAlpha Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeHaibTfbs/wgEncodeHaibTfbsEcc1Tcf12V0422111AlnRep2.bam ECC-1 ChipSeq TCF12 Alignments 2 bam HudsonAlpha Data 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http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeHaibTfbs/wgEncodeHaibTfbsGm12878Atf3Pcr1xAlnRep2.bam GM12878 ChipSeq ATF3 Alignments 2 bam HudsonAlpha Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeHaibTfbs/wgEncodeHaibTfbsGm12878Atf3Pcr1xPkRep1.broadPeak.gz GM12878 ChipSeq ATF3 Peaks 1 broadPeak HudsonAlpha Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeHaibTfbs/wgEncodeHaibTfbsGm12878Atf3Pcr1xPkRep2.broadPeak.gz GM12878 ChipSeq ATF3 Peaks 2 broadPeak HudsonAlpha Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeHaibTfbs/wgEncodeHaibTfbsGm12878Atf3Pcr1xRawRep1.bigWig GM12878 ChipSeq ATF3 RawSignal 1 bigWig HudsonAlpha Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeHaibTfbs/wgEncodeHaibTfbsGm12878Atf3Pcr1xRawRep2.bigWig GM12878 ChipSeq ATF3 RawSignal 2 bigWig HudsonAlpha Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeHaibTfbs/wgEncodeHaibTfbsGm12878BatfPcr1xAlnRep1.bam GM12878 ChipSeq BATF Alignments 1 bam HudsonAlpha Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeHaibTfbs/wgEncodeHaibTfbsGm12878BatfPcr1xAlnRep2.bam GM12878 ChipSeq BATF Alignments 2 bam HudsonAlpha Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeHaibTfbs/wgEncodeHaibTfbsGm12878BatfPcr1xPkRep1.broadPeak.gz GM12878 ChipSeq BATF Peaks 1 broadPeak HudsonAlpha Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeHaibTfbs/wgEncodeHaibTfbsGm12878BatfPcr1xPkRep2.broadPeak.gz GM12878 ChipSeq BATF Peaks 2 broadPeak HudsonAlpha Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeHaibTfbs/wgEncodeHaibTfbsGm12878BatfPcr1xRawRep1.bigWig GM12878 ChipSeq BATF RawSignal 1 bigWig HudsonAlpha Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeHaibTfbs/wgEncodeHaibTfbsGm12878BatfPcr1xRawRep2.bigWig GM12878 ChipSeq BATF RawSignal 2 bigWig HudsonAlpha Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeHaibTfbs/wgEncodeHaibTfbsGm12878Bcl11aPcr1xAlnRep1.bam GM12878 ChipSeq BCL11A Alignments 1 bam HudsonAlpha Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeHaibTfbs/wgEncodeHaibTfbsGm12878Bcl11aPcr1xAlnRep2.bam GM12878 ChipSeq BCL11A Alignments 2 bam HudsonAlpha Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeHaibTfbs/wgEncodeHaibTfbsGm12878Bcl11aPcr1xPkRep1.broadPeak.gz GM12878 ChipSeq BCL11A Peaks 1 broadPeak HudsonAlpha Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeHaibTfbs/wgEncodeHaibTfbsGm12878Bcl11aPcr1xPkRep2.broadPeak.gz GM12878 ChipSeq BCL11A Peaks 2 broadPeak HudsonAlpha Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeHaibTfbs/wgEncodeHaibTfbsGm12878Bcl11aPcr1xRawRep1.bigWig GM12878 ChipSeq BCL11A RawSignal 1 bigWig HudsonAlpha Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeHaibTfbs/wgEncodeHaibTfbsGm12878Bcl11aPcr1xRawRep2.bigWig GM12878 ChipSeq BCL11A RawSignal 2 bigWig HudsonAlpha Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeHaibTfbs/wgEncodeHaibTfbsGm12878Bcl3V0416101AlnRep1.bam GM12878 ChipSeq BCL3 Alignments 1 bam HudsonAlpha Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeHaibTfbs/wgEncodeHaibTfbsGm12878Bcl3V0416101AlnRep2.bam GM12878 ChipSeq BCL3 Alignments 2 bam HudsonAlpha Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeHaibTfbs/wgEncodeHaibTfbsGm12878Bcl3V0416101PkRep1.broadPeak.gz GM12878 ChipSeq BCL3 Peaks 1 broadPeak HudsonAlpha Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeHaibTfbs/wgEncodeHaibTfbsGm12878Bcl3V0416101PkRep2.broadPeak.gz GM12878 ChipSeq BCL3 Peaks 2 broadPeak HudsonAlpha Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeHaibTfbs/wgEncodeHaibTfbsGm12878Bcl3V0416101RawRep1.bigWig GM12878 ChipSeq BCL3 RawSignal 1 bigWig HudsonAlpha Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeHaibTfbs/wgEncodeHaibTfbsGm12878Bcl3V0416101RawRep2.bigWig GM12878 ChipSeq BCL3 RawSignal 2 bigWig HudsonAlpha Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeHaibTfbs/wgEncodeHaibTfbsGm12878Bclaf101388V0416101AlnRep1.bam GM12878 ChipSeq BCLAF1_(SC-101388) Alignments 1 bam HudsonAlpha Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeHaibTfbs/wgEncodeHaibTfbsGm12878Bclaf101388V0416101AlnRep2.bam GM12878 ChipSeq BCLAF1_(SC-101388) Alignments 2 bam HudsonAlpha Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeHaibTfbs/wgEncodeHaibTfbsGm12878Bclaf101388V0416101PkRep1.broadPeak.gz GM12878 ChipSeq BCLAF1_(SC-101388) Peaks 1 broadPeak HudsonAlpha Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeHaibTfbs/wgEncodeHaibTfbsGm12878Bclaf101388V0416101PkRep2.broadPeak.gz GM12878 ChipSeq BCLAF1_(SC-101388) Peaks 2 broadPeak HudsonAlpha Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeHaibTfbs/wgEncodeHaibTfbsGm12878Bclaf101388V0416101RawRep1.bigWig GM12878 ChipSeq BCLAF1_(SC-101388) RawSignal 1 bigWig HudsonAlpha Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeHaibTfbs/wgEncodeHaibTfbsGm12878Bclaf101388V0416101RawRep2.bigWig GM12878 ChipSeq BCLAF1_(SC-101388) RawSignal 2 bigWig HudsonAlpha Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeHaibTfbs/wgEncodeHaibTfbsGm12878Cebpbsc150V0422111AlnRep1.bam GM12878 ChipSeq CEBPB_(SC-150) Alignments 1 bam HudsonAlpha Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeHaibTfbs/wgEncodeHaibTfbsGm12878Cebpbsc150V0422111AlnRep2.bam GM12878 ChipSeq CEBPB_(SC-150) Alignments 2 bam HudsonAlpha Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeHaibTfbs/wgEncodeHaibTfbsGm12878Cebpbsc150V0422111PkRep1.broadPeak.gz GM12878 ChipSeq CEBPB_(SC-150) Peaks 1 broadPeak HudsonAlpha Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeHaibTfbs/wgEncodeHaibTfbsGm12878Cebpbsc150V0422111PkRep2.broadPeak.gz GM12878 ChipSeq CEBPB_(SC-150) Peaks 2 broadPeak HudsonAlpha Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeHaibTfbs/wgEncodeHaibTfbsGm12878Cebpbsc150V0422111RawRep1.bigWig GM12878 ChipSeq CEBPB_(SC-150) RawSignal 1 bigWig HudsonAlpha Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeHaibTfbs/wgEncodeHaibTfbsGm12878Cebpbsc150V0422111RawRep2.bigWig GM12878 ChipSeq CEBPB_(SC-150) RawSignal 2 bigWig HudsonAlpha Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeHaibTfbs/wgEncodeHaibTfbsGm12878Creb1sc240V0422111AlnRep1.bam GM12878 ChipSeq CREB1_(SC-240) Alignments 1 bam HudsonAlpha Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeHaibTfbs/wgEncodeHaibTfbsGm12878Creb1sc240V0422111AlnRep2.bam GM12878 ChipSeq CREB1_(SC-240) Alignments 2 bam HudsonAlpha Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeHaibTfbs/wgEncodeHaibTfbsGm12878Creb1sc240V0422111PkRep1.broadPeak.gz GM12878 ChipSeq CREB1_(SC-240) Peaks 1 broadPeak HudsonAlpha Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeHaibTfbs/wgEncodeHaibTfbsGm12878Creb1sc240V0422111PkRep2.broadPeak.gz GM12878 ChipSeq CREB1_(SC-240) Peaks 2 broadPeak HudsonAlpha Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeHaibTfbs/wgEncodeHaibTfbsGm12878Creb1sc240V0422111RawRep1.bigWig GM12878 ChipSeq CREB1_(SC-240) RawSignal 1 bigWig HudsonAlpha Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeHaibTfbs/wgEncodeHaibTfbsGm12878Creb1sc240V0422111RawRep2.bigWig GM12878 ChipSeq CREB1_(SC-240) RawSignal 2 bigWig HudsonAlpha Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeHaibTfbs/wgEncodeHaibTfbsGm12878Ebf1sc137065Pcr1xAlnRep1.bam GM12878 ChipSeq EBF1_(SC-137065) Alignments 1 bam HudsonAlpha Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeHaibTfbs/wgEncodeHaibTfbsGm12878Ebf1sc137065Pcr1xAlnRep2.bam GM12878 ChipSeq EBF1_(SC-137065) Alignments 2 bam HudsonAlpha Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeHaibTfbs/wgEncodeHaibTfbsGm12878Ebf1sc137065Pcr1xRawRep1.bigWig GM12878 ChipSeq EBF1_(SC-137065) RawSignal 1 bigWig HudsonAlpha Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeHaibTfbs/wgEncodeHaibTfbsGm12878Ebf1sc137065Pcr1xRawRep2.bigWig GM12878 ChipSeq EBF1_(SC-137065) RawSignal 2 bigWig HudsonAlpha Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeHaibTfbs/wgEncodeHaibTfbsGm12878Ebfsc137065Pcr1xPkRep1.broadPeak.gz GM12878 ChipSeq EBF1_(SC-137065) Peaks 1 broadPeak HudsonAlpha Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeHaibTfbs/wgEncodeHaibTfbsGm12878Ebfsc137065Pcr1xPkRep2.broadPeak.gz GM12878 ChipSeq EBF1_(SC-137065) Peaks 2 broadPeak HudsonAlpha Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeHaibTfbs/wgEncodeHaibTfbsGm12878Egr1Pcr2xAlnRep3.bam GM12878 ChipSeq Egr-1 Alignments 3 bam HudsonAlpha Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeHaibTfbs/wgEncodeHaibTfbsGm12878Egr1Pcr2xPkRep3.broadPeak.gz GM12878 ChipSeq Egr-1 Peaks 3 broadPeak HudsonAlpha Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeHaibTfbs/wgEncodeHaibTfbsGm12878Egr1Pcr2xRawRep3.bigWig GM12878 ChipSeq Egr-1 RawSignal 3 bigWig HudsonAlpha Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeHaibTfbs/wgEncodeHaibTfbsGm12878Egr1V0416101AlnRep1.bam GM12878 ChipSeq Egr-1 Alignments 1 bam HudsonAlpha Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeHaibTfbs/wgEncodeHaibTfbsGm12878Egr1V0416101AlnRep2.bam GM12878 ChipSeq Egr-1 Alignments 2 bam HudsonAlpha Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeHaibTfbs/wgEncodeHaibTfbsGm12878Egr1V0416101PkRep1.broadPeak.gz GM12878 ChipSeq Egr-1 Peaks 1 broadPeak HudsonAlpha Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeHaibTfbs/wgEncodeHaibTfbsGm12878Egr1V0416101PkRep2.broadPeak.gz GM12878 ChipSeq Egr-1 Peaks 2 broadPeak HudsonAlpha Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeHaibTfbs/wgEncodeHaibTfbsGm12878Egr1V0416101RawRep1.bigWig GM12878 ChipSeq Egr-1 RawSignal 1 bigWig HudsonAlpha Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeHaibTfbs/wgEncodeHaibTfbsGm12878Egr1V0416101RawRep2.bigWig GM12878 ChipSeq Egr-1 RawSignal 2 bigWig HudsonAlpha Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeHaibTfbs/wgEncodeHaibTfbsGm12878Elf1sc631V0416101AlnRep1.bam GM12878 ChipSeq ELF1_(SC-631) Alignments 1 bam HudsonAlpha Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeHaibTfbs/wgEncodeHaibTfbsGm12878Elf1sc631V0416101AlnRep2.bam GM12878 ChipSeq ELF1_(SC-631) Alignments 2 bam HudsonAlpha Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeHaibTfbs/wgEncodeHaibTfbsGm12878Elf1sc631V0416101PkRep1.broadPeak.gz GM12878 ChipSeq ELF1_(SC-631) Peaks 1 broadPeak HudsonAlpha Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeHaibTfbs/wgEncodeHaibTfbsGm12878Elf1sc631V0416101PkRep2.broadPeak.gz GM12878 ChipSeq ELF1_(SC-631) Peaks 2 broadPeak HudsonAlpha Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeHaibTfbs/wgEncodeHaibTfbsGm12878Elf1sc631V0416101RawRep1.bigWig GM12878 ChipSeq ELF1_(SC-631) RawSignal 1 bigWig HudsonAlpha Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeHaibTfbs/wgEncodeHaibTfbsGm12878Elf1sc631V0416101RawRep2.bigWig GM12878 ChipSeq ELF1_(SC-631) RawSignal 2 bigWig HudsonAlpha Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeHaibTfbs/wgEncodeHaibTfbsGm12878Ets1Pcr1xAlnRep1.bam GM12878 ChipSeq ETS1 Alignments 1 bam HudsonAlpha Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeHaibTfbs/wgEncodeHaibTfbsGm12878Ets1Pcr1xAlnRep2.bam GM12878 ChipSeq ETS1 Alignments 2 bam HudsonAlpha Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeHaibTfbs/wgEncodeHaibTfbsGm12878Ets1Pcr1xPkRep1.broadPeak.gz GM12878 ChipSeq ETS1 Peaks 1 broadPeak HudsonAlpha Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeHaibTfbs/wgEncodeHaibTfbsGm12878Ets1Pcr1xPkRep1V2.broadPeak.gz GM12878 ChipSeq ETS1 Peaks 1 broadPeak HudsonAlpha Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeHaibTfbs/wgEncodeHaibTfbsGm12878Ets1Pcr1xPkRep2.broadPeak.gz GM12878 ChipSeq ETS1 Peaks 2 broadPeak HudsonAlpha Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeHaibTfbs/wgEncodeHaibTfbsGm12878Ets1Pcr1xPkRep2V2.broadPeak.gz GM12878 ChipSeq ETS1 Peaks 2 broadPeak HudsonAlpha Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeHaibTfbs/wgEncodeHaibTfbsGm12878Ets1Pcr1xRawRep1.bigWig GM12878 ChipSeq ETS1 RawSignal 1 bigWig HudsonAlpha Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeHaibTfbs/wgEncodeHaibTfbsGm12878Ets1Pcr1xRawRep2.bigWig GM12878 ChipSeq ETS1 RawSignal 2 bigWig HudsonAlpha Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeHaibTfbs/wgEncodeHaibTfbsGm12878Foxm1sc502V0422111AlnRep1.bam GM12878 ChipSeq FOXM1_(SC-502) Alignments 1 bam HudsonAlpha Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeHaibTfbs/wgEncodeHaibTfbsGm12878Foxm1sc502V0422111AlnRep2.bam GM12878 ChipSeq FOXM1_(SC-502) Alignments 2 bam HudsonAlpha Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeHaibTfbs/wgEncodeHaibTfbsGm12878Foxm1sc502V0422111PkRep1.broadPeak.gz GM12878 ChipSeq FOXM1_(SC-502) Peaks 1 broadPeak HudsonAlpha Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeHaibTfbs/wgEncodeHaibTfbsGm12878Foxm1sc502V0422111PkRep2.broadPeak.gz GM12878 ChipSeq FOXM1_(SC-502) Peaks 2 broadPeak HudsonAlpha Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeHaibTfbs/wgEncodeHaibTfbsGm12878Foxm1sc502V0422111RawRep1.bigWig GM12878 ChipSeq FOXM1_(SC-502) RawSignal 1 bigWig HudsonAlpha Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeHaibTfbs/wgEncodeHaibTfbsGm12878Foxm1sc502V0422111RawRep2.bigWig GM12878 ChipSeq FOXM1_(SC-502) RawSignal 2 bigWig HudsonAlpha Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeHaibTfbs/wgEncodeHaibTfbsGm12878GabpPcr2xAlnRep1.bam GM12878 ChipSeq GABP Alignments 1 bam HudsonAlpha Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeHaibTfbs/wgEncodeHaibTfbsGm12878GabpPcr2xAlnRep2.bam GM12878 ChipSeq GABP Alignments 2 bam HudsonAlpha Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeHaibTfbs/wgEncodeHaibTfbsGm12878GabpPcr2xPkRep1.broadPeak.gz GM12878 ChipSeq GABP Peaks 1 broadPeak HudsonAlpha Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeHaibTfbs/wgEncodeHaibTfbsGm12878GabpPcr2xPkRep2.broadPeak.gz GM12878 ChipSeq GABP Peaks 2 broadPeak HudsonAlpha Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeHaibTfbs/wgEncodeHaibTfbsGm12878GabpPcr2xRawRep1.bigWig GM12878 ChipSeq GABP RawSignal 1 bigWig HudsonAlpha Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeHaibTfbs/wgEncodeHaibTfbsGm12878GabpPcr2xRawRep2.bigWig GM12878 ChipSeq GABP RawSignal 2 bigWig HudsonAlpha Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeHaibTfbs/wgEncodeHaibTfbsGm12878Irf4sc6059Pcr1xAlnRep1.bam GM12878 ChipSeq IRF4_(SC-6059) Alignments 1 bam HudsonAlpha Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeHaibTfbs/wgEncodeHaibTfbsGm12878Irf4sc6059Pcr1xAlnRep2.bam GM12878 ChipSeq IRF4_(SC-6059) Alignments 2 bam HudsonAlpha Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeHaibTfbs/wgEncodeHaibTfbsGm12878Irf4sc6059Pcr1xPkRep1.broadPeak.gz GM12878 ChipSeq IRF4_(SC-6059) Peaks 1 broadPeak HudsonAlpha Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeHaibTfbs/wgEncodeHaibTfbsGm12878Irf4sc6059Pcr1xPkRep2.broadPeak.gz GM12878 ChipSeq IRF4_(SC-6059) Peaks 2 broadPeak HudsonAlpha Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeHaibTfbs/wgEncodeHaibTfbsGm12878Irf4sc6059Pcr1xRawRep1.bigWig GM12878 ChipSeq IRF4_(SC-6059) RawSignal 1 bigWig HudsonAlpha Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeHaibTfbs/wgEncodeHaibTfbsGm12878Irf4sc6059Pcr1xRawRep2.bigWig GM12878 ChipSeq IRF4_(SC-6059) RawSignal 2 bigWig HudsonAlpha Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeHaibTfbs/wgEncodeHaibTfbsGm12878Mef2aPcr1xAlnRep1.bam GM12878 ChipSeq MEF2A Alignments 1 bam HudsonAlpha Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeHaibTfbs/wgEncodeHaibTfbsGm12878Mef2aPcr1xAlnRep2.bam GM12878 ChipSeq MEF2A Alignments 2 bam HudsonAlpha Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeHaibTfbs/wgEncodeHaibTfbsGm12878Mef2aPcr1xPkRep1.broadPeak.gz GM12878 ChipSeq MEF2A Peaks 1 broadPeak HudsonAlpha Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeHaibTfbs/wgEncodeHaibTfbsGm12878Mef2aPcr1xPkRep2.broadPeak.gz GM12878 ChipSeq MEF2A Peaks 2 broadPeak HudsonAlpha Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeHaibTfbs/wgEncodeHaibTfbsGm12878Mef2aPcr1xRawRep1.bigWig GM12878 ChipSeq MEF2A RawSignal 1 bigWig HudsonAlpha Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeHaibTfbs/wgEncodeHaibTfbsGm12878Mef2aPcr1xRawRep2.bigWig GM12878 ChipSeq MEF2A RawSignal 2 bigWig HudsonAlpha Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeHaibTfbs/wgEncodeHaibTfbsGm12878Mef2csc13268V0416101AlnRep1.bam GM12878 ChipSeq MEF2C_(SC-13268) Alignments 1 bam HudsonAlpha Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeHaibTfbs/wgEncodeHaibTfbsGm12878Mef2csc13268V0416101AlnRep2.bam GM12878 ChipSeq MEF2C_(SC-13268) Alignments 2 bam HudsonAlpha Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeHaibTfbs/wgEncodeHaibTfbsGm12878Mef2csc13268V0416101PkRep1.broadPeak.gz GM12878 ChipSeq MEF2C_(SC-13268) Peaks 1 broadPeak HudsonAlpha Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeHaibTfbs/wgEncodeHaibTfbsGm12878Mef2csc13268V0416101PkRep2.broadPeak.gz GM12878 ChipSeq MEF2C_(SC-13268) Peaks 2 broadPeak HudsonAlpha Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeHaibTfbs/wgEncodeHaibTfbsGm12878Mef2csc13268V0416101RawRep1.bigWig GM12878 ChipSeq MEF2C_(SC-13268) RawSignal 1 bigWig HudsonAlpha Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeHaibTfbs/wgEncodeHaibTfbsGm12878Mef2csc13268V0416101RawRep2.bigWig GM12878 ChipSeq MEF2C_(SC-13268) RawSignal 2 bigWig 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HudsonAlpha Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeHaibTfbs/wgEncodeHaibTfbsGm12878Mta3sc81325V0422111RawRep2.bigWig GM12878 ChipSeq MTA3_(SC-81325) RawSignal 2 bigWig HudsonAlpha Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeHaibTfbs/wgEncodeHaibTfbsGm12878Nfatc1sc17834V0422111AlnRep1.bam GM12878 ChipSeq NFATC1_(SC-17834) Alignments 1 bam HudsonAlpha Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeHaibTfbs/wgEncodeHaibTfbsGm12878Nfatc1sc17834V0422111AlnRep2.bam GM12878 ChipSeq NFATC1_(SC-17834) Alignments 2 bam HudsonAlpha Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeHaibTfbs/wgEncodeHaibTfbsGm12878Nfatc1sc17834V0422111PkRep1.broadPeak.gz GM12878 ChipSeq NFATC1_(SC-17834) Peaks 1 broadPeak HudsonAlpha Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeHaibTfbs/wgEncodeHaibTfbsGm12878Nfatc1sc17834V0422111PkRep2.broadPeak.gz GM12878 ChipSeq NFATC1_(SC-17834) Peaks 2 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http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeHaibTfbs/wgEncodeHaibTfbsGm12878RxraPcr1xRawRep1.bigWig GM12878 ChipSeq RXRA RawSignal 1 bigWig HudsonAlpha Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeHaibTfbs/wgEncodeHaibTfbsGm12878RxraPcr1xRawRep2.bigWig GM12878 ChipSeq RXRA RawSignal 2 bigWig HudsonAlpha Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeHaibTfbs/wgEncodeHaibTfbsGm12878Six5Pcr1xAlnRep1.bam GM12878 ChipSeq SIX5 Alignments 1 bam HudsonAlpha Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeHaibTfbs/wgEncodeHaibTfbsGm12878Six5Pcr1xAlnRep2.bam GM12878 ChipSeq SIX5 Alignments 2 bam HudsonAlpha Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeHaibTfbs/wgEncodeHaibTfbsGm12878Six5Pcr1xPkRep1.broadPeak.gz GM12878 ChipSeq SIX5 Peaks 1 broadPeak HudsonAlpha Data 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GM12878 ChipSeq SRF Alignments 2 bam HudsonAlpha Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeHaibTfbs/wgEncodeHaibTfbsGm12878SrfPcr2xPkRep1.broadPeak.gz GM12878 ChipSeq SRF Peaks 1 broadPeak HudsonAlpha Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeHaibTfbs/wgEncodeHaibTfbsGm12878SrfPcr2xPkRep2.broadPeak.gz GM12878 ChipSeq SRF Peaks 2 broadPeak HudsonAlpha Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeHaibTfbs/wgEncodeHaibTfbsGm12878SrfPcr2xRawRep1.bigWig GM12878 ChipSeq SRF RawSignal 1 bigWig HudsonAlpha Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeHaibTfbs/wgEncodeHaibTfbsGm12878SrfPcr2xRawRep2.bigWig GM12878 ChipSeq SRF RawSignal 2 bigWig HudsonAlpha Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeHaibTfbs/wgEncodeHaibTfbsGm12878SrfV0416101AlnRep1.bam GM12878 ChipSeq SRF Alignments 1 bam HudsonAlpha Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeHaibTfbs/wgEncodeHaibTfbsGm12878SrfV0416101AlnRep2.bam GM12878 ChipSeq SRF Alignments 2 bam HudsonAlpha Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeHaibTfbs/wgEncodeHaibTfbsGm12878SrfV0416101PkRep1.broadPeak.gz GM12878 ChipSeq SRF Peaks 1 broadPeak HudsonAlpha Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeHaibTfbs/wgEncodeHaibTfbsGm12878SrfV0416101PkRep2.broadPeak.gz GM12878 ChipSeq SRF Peaks 2 broadPeak HudsonAlpha Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeHaibTfbs/wgEncodeHaibTfbsGm12878SrfV0416101RawRep1.bigWig GM12878 ChipSeq SRF RawSignal 1 bigWig HudsonAlpha Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeHaibTfbs/wgEncodeHaibTfbsGm12878SrfV0416101RawRep2.bigWig GM12878 ChipSeq SRF RawSignal 2 bigWig HudsonAlpha Data 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HudsonAlpha Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeHaibTfbs/wgEncodeHaibTfbsGm12878Stat5asc74442V0422111RawRep2.bigWig GM12878 ChipSeq STAT5A_(SC-74442) RawSignal 2 bigWig HudsonAlpha Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeHaibTfbs/wgEncodeHaibTfbsGm12878Taf1Pcr1xAlnRep1.bam GM12878 ChipSeq TAF1 Alignments 1 bam HudsonAlpha Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeHaibTfbs/wgEncodeHaibTfbsGm12878Taf1Pcr1xAlnRep2.bam GM12878 ChipSeq TAF1 Alignments 2 bam HudsonAlpha Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeHaibTfbs/wgEncodeHaibTfbsGm12878Taf1Pcr1xPkRep1.broadPeak.gz GM12878 ChipSeq TAF1 Peaks 1 broadPeak HudsonAlpha Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeHaibTfbs/wgEncodeHaibTfbsGm12878Taf1Pcr1xPkRep2.broadPeak.gz GM12878 ChipSeq TAF1 Peaks 2 broadPeak HudsonAlpha Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeHaibTfbs/wgEncodeHaibTfbsGm12878Taf1Pcr1xRawRep1.bigWig GM12878 ChipSeq TAF1 RawSignal 1 bigWig HudsonAlpha Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeHaibTfbs/wgEncodeHaibTfbsGm12878Taf1Pcr1xRawRep2.bigWig GM12878 ChipSeq TAF1 RawSignal 2 bigWig HudsonAlpha Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeHaibTfbs/wgEncodeHaibTfbsGm12878Tcf12Pcr1xAlnRep1.bam GM12878 ChipSeq TCF12 Alignments 1 bam HudsonAlpha Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeHaibTfbs/wgEncodeHaibTfbsGm12878Tcf12Pcr1xAlnRep2.bam GM12878 ChipSeq TCF12 Alignments 2 bam HudsonAlpha Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeHaibTfbs/wgEncodeHaibTfbsGm12878Tcf12Pcr1xPkRep1.broadPeak.gz GM12878 ChipSeq TCF12 Peaks 1 broadPeak HudsonAlpha Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeHaibTfbs/wgEncodeHaibTfbsGm12878Tcf12Pcr1xPkRep2.broadPeak.gz GM12878 ChipSeq TCF12 Peaks 2 broadPeak HudsonAlpha Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeHaibTfbs/wgEncodeHaibTfbsGm12878Tcf12Pcr1xRawRep1.bigWig GM12878 ChipSeq TCF12 RawSignal 1 bigWig HudsonAlpha Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeHaibTfbs/wgEncodeHaibTfbsGm12878Tcf12Pcr1xRawRep2.bigWig GM12878 ChipSeq TCF12 RawSignal 2 bigWig HudsonAlpha Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeHaibTfbs/wgEncodeHaibTfbsGm12878Tcf3Pcr1xAlnRep1.bam GM12878 ChipSeq TCF3_(SC-349) Alignments 1 bam HudsonAlpha Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeHaibTfbs/wgEncodeHaibTfbsGm12878Tcf3Pcr1xAlnRep2.bam GM12878 ChipSeq TCF3_(SC-349) Alignments 2 bam HudsonAlpha Data 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http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeHaibTfbs/wgEncodeHaibTfbsGm12891Pou2f2Pcr1xRawRep1.bigWig GM12891 ChipSeq POU2F2 RawSignal 1 bigWig HudsonAlpha Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeHaibTfbs/wgEncodeHaibTfbsGm12891Pou2f2Pcr1xRawRep2.bigWig GM12891 ChipSeq POU2F2 RawSignal 2 bigWig HudsonAlpha Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeHaibTfbs/wgEncodeHaibTfbsGm12891Pu1Pcr1xAlnRep1.bam GM12891 ChipSeq PU.1 Alignments 1 bam HudsonAlpha Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeHaibTfbs/wgEncodeHaibTfbsGm12891Pu1Pcr1xAlnRep2.bam GM12891 ChipSeq PU.1 Alignments 2 bam HudsonAlpha Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeHaibTfbs/wgEncodeHaibTfbsGm12891Pu1Pcr1xPkRep1.broadPeak.gz GM12891 ChipSeq PU.1 Peaks 1 broadPeak HudsonAlpha Data 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http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeHaibTfbs/wgEncodeHaibTfbsGm12891RxlchV0416101AlnRep1.bam GM12891 ChipSeq RevXlinkChromatin Alignments 1 bam HudsonAlpha Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeHaibTfbs/wgEncodeHaibTfbsGm12891RxlchV0416101RawRep1.bigWig GM12891 ChipSeq RevXlinkChromatin RawSignal 1 bigWig HudsonAlpha Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeHaibTfbs/wgEncodeHaibTfbsGm12891Taf1Pcr1xAlnRep1.bam GM12891 ChipSeq TAF1 Alignments 1 bam HudsonAlpha Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeHaibTfbs/wgEncodeHaibTfbsGm12891Taf1Pcr1xAlnRep2.bam GM12891 ChipSeq TAF1 Alignments 2 bam HudsonAlpha Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeHaibTfbs/wgEncodeHaibTfbsGm12891Taf1Pcr1xPkRep1.broadPeak.gz GM12891 ChipSeq TAF1 Peaks 1 broadPeak HudsonAlpha Data 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http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeHaibTfbs/wgEncodeHaibTfbsGm12892Pax5c20V0416101AlnRep2.bam GM12892 ChipSeq PAX5-C20 Alignments 2 bam HudsonAlpha Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeHaibTfbs/wgEncodeHaibTfbsGm12892Pax5c20V0416101PkRep1.broadPeak.gz GM12892 ChipSeq PAX5-C20 Peaks 1 broadPeak HudsonAlpha Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeHaibTfbs/wgEncodeHaibTfbsGm12892Pax5c20V0416101PkRep2.broadPeak.gz GM12892 ChipSeq PAX5-C20 Peaks 2 broadPeak HudsonAlpha Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeHaibTfbs/wgEncodeHaibTfbsGm12892Pax5c20V0416101RawRep1.bigWig GM12892 ChipSeq PAX5-C20 RawSignal 1 bigWig HudsonAlpha Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeHaibTfbs/wgEncodeHaibTfbsGm12892Pax5c20V0416101RawRep2.bigWig GM12892 ChipSeq PAX5-C20 RawSignal 2 bigWig HudsonAlpha Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeHaibTfbs/wgEncodeHaibTfbsGm12892Pol24h8V0416102AlnRep1.bam GM12892 ChipSeq Pol2-4H8 Alignments 1 bam HudsonAlpha Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeHaibTfbs/wgEncodeHaibTfbsGm12892Pol24h8V0416102AlnRep2.bam GM12892 ChipSeq Pol2-4H8 Alignments 2 bam HudsonAlpha Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeHaibTfbs/wgEncodeHaibTfbsGm12892Pol24h8V0416102PkRep1.broadPeak.gz GM12892 ChipSeq Pol2-4H8 Peaks 1 broadPeak HudsonAlpha Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeHaibTfbs/wgEncodeHaibTfbsGm12892Pol24h8V0416102PkRep2.broadPeak.gz GM12892 ChipSeq Pol2-4H8 Peaks 2 broadPeak HudsonAlpha Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeHaibTfbs/wgEncodeHaibTfbsGm12892Pol24h8V0416102RawRep1.bigWig GM12892 ChipSeq Pol2-4H8 RawSignal 1 bigWig HudsonAlpha Data 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http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeHaibTfbs/wgEncodeHaibTfbsH1hescE2f6V0422111RawRep2.bigWig H1-hESC ChipSeq E2F6 RawSignal 2 bigWig HudsonAlpha Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeHaibTfbs/wgEncodeHaibTfbsH1hescEgr1V0416102AlnRep1.bam H1-hESC ChipSeq Egr-1 Alignments 1 bam HudsonAlpha Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeHaibTfbs/wgEncodeHaibTfbsH1hescEgr1V0416102AlnRep2.bam H1-hESC ChipSeq Egr-1 Alignments 2 bam HudsonAlpha Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeHaibTfbs/wgEncodeHaibTfbsH1hescEgr1V0416102PkRep1.broadPeak.gz H1-hESC ChipSeq Egr-1 Peaks 1 broadPeak HudsonAlpha Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeHaibTfbs/wgEncodeHaibTfbsH1hescEgr1V0416102PkRep2.broadPeak.gz H1-hESC ChipSeq Egr-1 Peaks 2 broadPeak HudsonAlpha Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeHaibTfbs/wgEncodeHaibTfbsH1hescEgr1V0416102RawRep1.bigWig H1-hESC ChipSeq Egr-1 RawSignal 1 bigWig HudsonAlpha Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeHaibTfbs/wgEncodeHaibTfbsH1hescEgr1V0416102RawRep2.bigWig H1-hESC ChipSeq Egr-1 RawSignal 2 bigWig HudsonAlpha Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeHaibTfbs/wgEncodeHaibTfbsH1hescFosl1sc183V0416102AlnRep1.bam H1-hESC ChipSeq FOSL1_(SC-183) Alignments 1 bam HudsonAlpha Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeHaibTfbs/wgEncodeHaibTfbsH1hescFosl1sc183V0416102AlnRep2.bam H1-hESC ChipSeq FOSL1_(SC-183) Alignments 2 bam HudsonAlpha Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeHaibTfbs/wgEncodeHaibTfbsH1hescFosl1sc183V0416102PkRep1.broadPeak.gz H1-hESC ChipSeq FOSL1_(SC-183) Peaks 1 broadPeak HudsonAlpha Data 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http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeHaibTfbs/wgEncodeHaibTfbsH1hescHdac2sc6296V0416102AlnRep2.bam H1-hESC ChipSeq HDAC2_(SC-6296) Alignments 2 bam HudsonAlpha Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeHaibTfbs/wgEncodeHaibTfbsH1hescHdac2sc6296V0416102PkRep1.broadPeak.gz H1-hESC ChipSeq HDAC2_(SC-6296) Peaks 1 broadPeak HudsonAlpha Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeHaibTfbs/wgEncodeHaibTfbsH1hescHdac2sc6296V0416102PkRep2.broadPeak.gz H1-hESC ChipSeq HDAC2_(SC-6296) Peaks 2 broadPeak HudsonAlpha Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeHaibTfbs/wgEncodeHaibTfbsH1hescHdac2sc6296V0416102RawRep1.bigWig H1-hESC ChipSeq HDAC2_(SC-6296) RawSignal 1 bigWig HudsonAlpha Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeHaibTfbs/wgEncodeHaibTfbsH1hescHdac2sc6296V0416102RawRep2.bigWig H1-hESC ChipSeq HDAC2_(SC-6296) RawSignal 2 bigWig HudsonAlpha Data 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http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeHaibTfbs/wgEncodeHaibTfbsH1hescJundV0416102RawRep2.bigWig H1-hESC ChipSeq JunD RawSignal 2 bigWig HudsonAlpha Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeHaibTfbs/wgEncodeHaibTfbsH1hescMaxV0422111AlnRep1.bam H1-hESC ChipSeq Max Alignments 1 bam HudsonAlpha Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeHaibTfbs/wgEncodeHaibTfbsH1hescMaxV0422111AlnRep2.bam H1-hESC ChipSeq Max Alignments 2 bam HudsonAlpha Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeHaibTfbs/wgEncodeHaibTfbsH1hescMaxV0422111PkRep1.broadPeak.gz H1-hESC ChipSeq Max Peaks 1 broadPeak HudsonAlpha Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeHaibTfbs/wgEncodeHaibTfbsH1hescMaxV0422111PkRep2.broadPeak.gz H1-hESC ChipSeq Max Peaks 2 broadPeak HudsonAlpha Data 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Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeHaibTfbs/wgEncodeHaibTfbsH1hescTcf12Pcr1xAlnRep1.bam H1-hESC ChipSeq TCF12 Alignments 1 bam HudsonAlpha Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeHaibTfbs/wgEncodeHaibTfbsH1hescTcf12Pcr1xAlnRep2.bam H1-hESC ChipSeq TCF12 Alignments 2 bam HudsonAlpha Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeHaibTfbs/wgEncodeHaibTfbsH1hescTcf12Pcr1xPkRep1.broadPeak.gz H1-hESC ChipSeq TCF12 Peaks 1 broadPeak HudsonAlpha Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeHaibTfbs/wgEncodeHaibTfbsH1hescTcf12Pcr1xPkRep2.broadPeak.gz H1-hESC ChipSeq TCF12 Peaks 2 broadPeak HudsonAlpha Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeHaibTfbs/wgEncodeHaibTfbsH1hescTcf12Pcr1xRawRep1.bigWig H1-hESC ChipSeq TCF12 RawSignal 1 bigWig HudsonAlpha Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeHaibTfbs/wgEncodeHaibTfbsH1hescTcf12Pcr1xRawRep2.bigWig H1-hESC ChipSeq TCF12 RawSignal 2 bigWig HudsonAlpha Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeHaibTfbs/wgEncodeHaibTfbsH1hescTead4sc101184V0422111AlnRep1.bam H1-hESC ChipSeq TEAD4_(SC-101184) Alignments 1 bam HudsonAlpha Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeHaibTfbs/wgEncodeHaibTfbsH1hescTead4sc101184V0422111AlnRep2.bam H1-hESC ChipSeq TEAD4_(SC-101184) Alignments 2 bam HudsonAlpha Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeHaibTfbs/wgEncodeHaibTfbsH1hescTead4sc101184V0422111PkRep1.broadPeak.gz H1-hESC ChipSeq TEAD4_(SC-101184) Peaks 1 broadPeak HudsonAlpha Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeHaibTfbs/wgEncodeHaibTfbsH1hescTead4sc101184V0422111PkRep2.broadPeak.gz H1-hESC ChipSeq TEAD4_(SC-101184) Peaks 2 broadPeak HudsonAlpha Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeHaibTfbs/wgEncodeHaibTfbsH1hescTead4sc101184V0422111RawRep1.bigWig H1-hESC ChipSeq TEAD4_(SC-101184) RawSignal 1 bigWig HudsonAlpha Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeHaibTfbs/wgEncodeHaibTfbsH1hescTead4sc101184V0422111RawRep2.bigWig H1-hESC ChipSeq TEAD4_(SC-101184) RawSignal 2 bigWig HudsonAlpha Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeHaibTfbs/wgEncodeHaibTfbsH1hescUsf1Pcr1xAlnRep1.bam H1-hESC ChipSeq USF-1 Alignments 1 bam HudsonAlpha Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeHaibTfbs/wgEncodeHaibTfbsH1hescUsf1Pcr1xAlnRep2.bam H1-hESC ChipSeq USF-1 Alignments 2 bam HudsonAlpha Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeHaibTfbs/wgEncodeHaibTfbsH1hescUsf1Pcr1xPkRep1.broadPeak.gz H1-hESC ChipSeq USF-1 Peaks 1 broadPeak HudsonAlpha Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeHaibTfbs/wgEncodeHaibTfbsH1hescUsf1Pcr1xPkRep2.broadPeak.gz H1-hESC ChipSeq USF-1 Peaks 2 broadPeak HudsonAlpha Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeHaibTfbs/wgEncodeHaibTfbsH1hescUsf1Pcr1xRawRep1.bigWig H1-hESC ChipSeq USF-1 RawSignal 1 bigWig HudsonAlpha Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeHaibTfbs/wgEncodeHaibTfbsH1hescUsf1Pcr1xRawRep2.bigWig H1-hESC ChipSeq USF-1 RawSignal 2 bigWig HudsonAlpha Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeHaibTfbs/wgEncodeHaibTfbsH1hescYy1sc281V0416102AlnRep1.bam H1-hESC ChipSeq YY1_(SC-281) Alignments 1 bam HudsonAlpha Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeHaibTfbs/wgEncodeHaibTfbsH1hescYy1sc281V0416102AlnRep2.bam H1-hESC ChipSeq YY1_(SC-281) Alignments 2 bam HudsonAlpha Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeHaibTfbs/wgEncodeHaibTfbsH1hescYy1sc281V0416102PkRep1.broadPeak.gz H1-hESC ChipSeq YY1_(SC-281) Peaks 1 broadPeak HudsonAlpha Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeHaibTfbs/wgEncodeHaibTfbsH1hescYy1sc281V0416102PkRep2.broadPeak.gz H1-hESC ChipSeq YY1_(SC-281) Peaks 2 broadPeak HudsonAlpha Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeHaibTfbs/wgEncodeHaibTfbsH1hescYy1sc281V0416102RawRep1.bigWig H1-hESC ChipSeq YY1_(SC-281) RawSignal 1 bigWig HudsonAlpha Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeHaibTfbs/wgEncodeHaibTfbsH1hescYy1sc281V0416102RawRep2.bigWig H1-hESC ChipSeq YY1_(SC-281) RawSignal 2 bigWig HudsonAlpha Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeHaibTfbs/wgEncodeHaibTfbsH1neuronsNrsfV0422111AlnRep1.bam H1-neurons ChipSeq NRSF Alignments 1 bam HudsonAlpha Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeHaibTfbs/wgEncodeHaibTfbsH1neuronsNrsfV0422111AlnRep2.bam H1-neurons ChipSeq NRSF Alignments 2 bam HudsonAlpha Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeHaibTfbs/wgEncodeHaibTfbsH1neuronsNrsfV0422111PkRep1.broadPeak.gz H1-neurons ChipSeq NRSF Peaks 1 broadPeak HudsonAlpha Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeHaibTfbs/wgEncodeHaibTfbsH1neuronsNrsfV0422111PkRep2.broadPeak.gz H1-neurons ChipSeq NRSF Peaks 2 broadPeak HudsonAlpha Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeHaibTfbs/wgEncodeHaibTfbsH1neuronsNrsfV0422111RawRep1.bigWig H1-neurons ChipSeq NRSF RawSignal 1 bigWig HudsonAlpha Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeHaibTfbs/wgEncodeHaibTfbsH1neuronsNrsfV0422111RawRep2.bigWig H1-neurons ChipSeq NRSF RawSignal 2 bigWig HudsonAlpha Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeHaibTfbs/wgEncodeHaibTfbsH1neuronsPol24h8V0422111AlnRep1.bam H1-neurons ChipSeq Pol2-4H8 Alignments 1 bam HudsonAlpha Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeHaibTfbs/wgEncodeHaibTfbsH1neuronsPol24h8V0422111AlnRep2.bam H1-neurons ChipSeq Pol2-4H8 Alignments 2 bam HudsonAlpha Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeHaibTfbs/wgEncodeHaibTfbsH1neuronsPol24h8V0422111PkRep1.broadPeak.gz H1-neurons ChipSeq Pol2-4H8 Peaks 1 broadPeak HudsonAlpha Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeHaibTfbs/wgEncodeHaibTfbsH1neuronsPol24h8V0422111PkRep2.broadPeak.gz H1-neurons ChipSeq Pol2-4H8 Peaks 2 broadPeak HudsonAlpha Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeHaibTfbs/wgEncodeHaibTfbsH1neuronsPol24h8V0422111RawRep1.bigWig H1-neurons ChipSeq Pol2-4H8 RawSignal 1 bigWig HudsonAlpha Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeHaibTfbs/wgEncodeHaibTfbsH1neuronsPol24h8V0422111RawRep2.bigWig H1-neurons ChipSeq Pol2-4H8 RawSignal 2 bigWig HudsonAlpha Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeHaibTfbs/wgEncodeHaibTfbsH1neuronsRxlchV0422111AlnRep1.bam H1-neurons ChipSeq RevXlinkChromatin Alignments 1 bam HudsonAlpha Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeHaibTfbs/wgEncodeHaibTfbsH1neuronsRxlchV0422111AlnRep2.bam H1-neurons ChipSeq RevXlinkChromatin Alignments 2 bam HudsonAlpha Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeHaibTfbs/wgEncodeHaibTfbsH1neuronsRxlchV0422111RawRep1.bigWig H1-neurons ChipSeq RevXlinkChromatin RawSignal 1 bigWig HudsonAlpha Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeHaibTfbs/wgEncodeHaibTfbsH1neuronsRxlchV0422111RawRep2.bigWig H1-neurons ChipSeq RevXlinkChromatin RawSignal 2 bigWig HudsonAlpha Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeHaibTfbs/wgEncodeHaibTfbsH1neuronsTaf1V0422111AlnRep1.bam H1-neurons ChipSeq TAF1 Alignments 1 bam HudsonAlpha Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeHaibTfbs/wgEncodeHaibTfbsH1neuronsTaf1V0422111AlnRep2.bam H1-neurons ChipSeq TAF1 Alignments 2 bam HudsonAlpha Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeHaibTfbs/wgEncodeHaibTfbsH1neuronsTaf1V0422111PkRep1.broadPeak.gz H1-neurons ChipSeq TAF1 Peaks 1 broadPeak HudsonAlpha Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeHaibTfbs/wgEncodeHaibTfbsH1neuronsTaf1V0422111PkRep2.broadPeak.gz H1-neurons ChipSeq TAF1 Peaks 2 broadPeak HudsonAlpha Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeHaibTfbs/wgEncodeHaibTfbsH1neuronsTaf1V0422111RawRep1.bigWig H1-neurons ChipSeq TAF1 RawSignal 1 bigWig HudsonAlpha Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeHaibTfbs/wgEncodeHaibTfbsH1neuronsTaf1V0422111RawRep2.bigWig H1-neurons ChipSeq TAF1 RawSignal 2 bigWig HudsonAlpha Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeHaibTfbs/wgEncodeHaibTfbsHct116Atf3V0422111AlnRep1.bam HCT-116 ChipSeq ATF3 Alignments 1 bam HudsonAlpha Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeHaibTfbs/wgEncodeHaibTfbsHct116Atf3V0422111AlnRep2.bam HCT-116 ChipSeq ATF3 Alignments 2 bam HudsonAlpha Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeHaibTfbs/wgEncodeHaibTfbsHct116Atf3V0422111PkRep1.broadPeak.gz HCT-116 ChipSeq ATF3 Peaks 1 broadPeak HudsonAlpha Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeHaibTfbs/wgEncodeHaibTfbsHct116Atf3V0422111PkRep2.broadPeak.gz HCT-116 ChipSeq ATF3 Peaks 2 broadPeak HudsonAlpha Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeHaibTfbs/wgEncodeHaibTfbsHct116Atf3V0422111RawRep1.bigWig HCT-116 ChipSeq ATF3 RawSignal 1 bigWig HudsonAlpha Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeHaibTfbs/wgEncodeHaibTfbsHct116Atf3V0422111RawRep2.bigWig HCT-116 ChipSeq ATF3 RawSignal 2 bigWig HudsonAlpha Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeHaibTfbs/wgEncodeHaibTfbsHct116Cbx3sc101004V0422111AlnRep1.bam HCT-116 ChipSeq CBX3_(SC-101004) Alignments 1 bam HudsonAlpha Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeHaibTfbs/wgEncodeHaibTfbsHct116Cbx3sc101004V0422111AlnRep2.bam HCT-116 ChipSeq CBX3_(SC-101004) Alignments 2 bam HudsonAlpha Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeHaibTfbs/wgEncodeHaibTfbsHct116Cbx3sc101004V0422111PkRep1.broadPeak.gz HCT-116 ChipSeq CBX3_(SC-101004) Peaks 1 broadPeak HudsonAlpha Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeHaibTfbs/wgEncodeHaibTfbsHct116Cbx3sc101004V0422111PkRep2.broadPeak.gz HCT-116 ChipSeq CBX3_(SC-101004) Peaks 2 broadPeak HudsonAlpha Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeHaibTfbs/wgEncodeHaibTfbsHct116Cbx3sc101004V0422111RawRep1.bigWig HCT-116 ChipSeq CBX3_(SC-101004) RawSignal 1 bigWig HudsonAlpha Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeHaibTfbs/wgEncodeHaibTfbsHct116Cbx3sc101004V0422111RawRep2.bigWig HCT-116 ChipSeq CBX3_(SC-101004) RawSignal 2 bigWig HudsonAlpha Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeHaibTfbs/wgEncodeHaibTfbsHct116Cebpbsc150V0422111AlnRep1.bam HCT-116 ChipSeq CEBPB_(SC-150) Alignments 1 bam HudsonAlpha Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeHaibTfbs/wgEncodeHaibTfbsHct116Cebpbsc150V0422111AlnRep2.bam HCT-116 ChipSeq CEBPB_(SC-150) Alignments 2 bam HudsonAlpha Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeHaibTfbs/wgEncodeHaibTfbsHct116Cebpbsc150V0422111PkRep1.broadPeak.gz HCT-116 ChipSeq CEBPB_(SC-150) Peaks 1 broadPeak HudsonAlpha Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeHaibTfbs/wgEncodeHaibTfbsHct116Cebpbsc150V0422111PkRep2.broadPeak.gz HCT-116 ChipSeq CEBPB_(SC-150) Peaks 2 broadPeak HudsonAlpha Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeHaibTfbs/wgEncodeHaibTfbsHct116Cebpbsc150V0422111RawRep1.bigWig HCT-116 ChipSeq CEBPB_(SC-150) RawSignal 1 bigWig HudsonAlpha Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeHaibTfbs/wgEncodeHaibTfbsHct116Cebpbsc150V0422111RawRep2.bigWig HCT-116 ChipSeq CEBPB_(SC-150) RawSignal 2 bigWig HudsonAlpha Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeHaibTfbs/wgEncodeHaibTfbsHct116CtcfcV0422111AlnRep1.bam HCT-116 ChipSeq CTCF_(SC-5916) Alignments 1 bam HudsonAlpha Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeHaibTfbs/wgEncodeHaibTfbsHct116CtcfcV0422111AlnRep2.bam HCT-116 ChipSeq CTCF_(SC-5916) Alignments 2 bam HudsonAlpha Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeHaibTfbs/wgEncodeHaibTfbsHct116CtcfcV0422111PkRep1.broadPeak.gz HCT-116 ChipSeq CTCF_(SC-5916) Peaks 1 broadPeak HudsonAlpha Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeHaibTfbs/wgEncodeHaibTfbsHct116CtcfcV0422111PkRep2.broadPeak.gz HCT-116 ChipSeq CTCF_(SC-5916) Peaks 2 broadPeak HudsonAlpha Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeHaibTfbs/wgEncodeHaibTfbsHct116CtcfcV0422111RawRep1.bigWig HCT-116 ChipSeq CTCF_(SC-5916) RawSignal 1 bigWig HudsonAlpha Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeHaibTfbs/wgEncodeHaibTfbsHct116CtcfcV0422111RawRep2.bigWig HCT-116 ChipSeq CTCF_(SC-5916) RawSignal 2 bigWig HudsonAlpha Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeHaibTfbs/wgEncodeHaibTfbsHct116Egr1V0422111AlnRep1.bam HCT-116 ChipSeq Egr-1 Alignments 1 bam HudsonAlpha Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeHaibTfbs/wgEncodeHaibTfbsHct116Egr1V0422111AlnRep2.bam HCT-116 ChipSeq Egr-1 Alignments 2 bam HudsonAlpha Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeHaibTfbs/wgEncodeHaibTfbsHct116Egr1V0422111PkRep1.broadPeak.gz HCT-116 ChipSeq Egr-1 Peaks 1 broadPeak HudsonAlpha Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeHaibTfbs/wgEncodeHaibTfbsHct116Egr1V0422111PkRep2.broadPeak.gz HCT-116 ChipSeq Egr-1 Peaks 2 broadPeak HudsonAlpha Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeHaibTfbs/wgEncodeHaibTfbsHct116Egr1V0422111RawRep1.bigWig HCT-116 ChipSeq Egr-1 RawSignal 1 bigWig HudsonAlpha Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeHaibTfbs/wgEncodeHaibTfbsHct116Egr1V0422111RawRep2.bigWig HCT-116 ChipSeq Egr-1 RawSignal 2 bigWig HudsonAlpha Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeHaibTfbs/wgEncodeHaibTfbsHct116Elf1V0422111AlnRep1.bam HCT-116 ChipSeq ELF1_(SC-631) Alignments 1 bam HudsonAlpha Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeHaibTfbs/wgEncodeHaibTfbsHct116Elf1V0422111AlnRep2.bam HCT-116 ChipSeq ELF1_(SC-631) Alignments 2 bam HudsonAlpha Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeHaibTfbs/wgEncodeHaibTfbsHct116Elf1V0422111PkRep1.broadPeak.gz HCT-116 ChipSeq ELF1_(SC-631) Peaks 1 broadPeak HudsonAlpha Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeHaibTfbs/wgEncodeHaibTfbsHct116Elf1V0422111PkRep2.broadPeak.gz HCT-116 ChipSeq ELF1_(SC-631) Peaks 2 broadPeak HudsonAlpha Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeHaibTfbs/wgEncodeHaibTfbsHct116Elf1V0422111RawRep1.bigWig HCT-116 ChipSeq ELF1_(SC-631) RawSignal 1 bigWig HudsonAlpha Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeHaibTfbs/wgEncodeHaibTfbsHct116Elf1V0422111RawRep2.bigWig HCT-116 ChipSeq ELF1_(SC-631) RawSignal 2 bigWig HudsonAlpha Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeHaibTfbs/wgEncodeHaibTfbsHct116Fosl1V0422111AlnRep1.bam HCT-116 ChipSeq FOSL1_(SC-183) Alignments 1 bam HudsonAlpha Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeHaibTfbs/wgEncodeHaibTfbsHct116Fosl1V0422111AlnRep2.bam HCT-116 ChipSeq FOSL1_(SC-183) Alignments 2 bam HudsonAlpha Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeHaibTfbs/wgEncodeHaibTfbsHct116Fosl1V0422111PkRep1.broadPeak.gz HCT-116 ChipSeq FOSL1_(SC-183) Peaks 1 broadPeak HudsonAlpha Data 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http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeHaibTfbs/wgEncodeHaibTfbsHct116Zbtb33V0416101RawRep2.bigWig HCT-116 ChipSeq ZBTB33 RawSignal 2 bigWig HudsonAlpha Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeHaibTfbs/wgEncodeHaibTfbsHelas3GabpPcr1xAlnRep1.bam HeLa-S3 ChipSeq GABP Alignments 1 bam HudsonAlpha Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeHaibTfbs/wgEncodeHaibTfbsHelas3GabpPcr1xAlnRep2.bam HeLa-S3 ChipSeq GABP Alignments 2 bam HudsonAlpha Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeHaibTfbs/wgEncodeHaibTfbsHelas3GabpPcr1xPkRep1.broadPeak.gz HeLa-S3 ChipSeq GABP Peaks 1 broadPeak HudsonAlpha Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeHaibTfbs/wgEncodeHaibTfbsHelas3GabpPcr1xPkRep2.broadPeak.gz HeLa-S3 ChipSeq GABP Peaks 2 broadPeak HudsonAlpha Data 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http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeHaibTfbs/wgEncodeHaibTfbsHelas3NrsfPcr1xPkRep2.broadPeak.gz HeLa-S3 ChipSeq NRSF Peaks 2 broadPeak HudsonAlpha Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeHaibTfbs/wgEncodeHaibTfbsHelas3NrsfPcr1xRawRep1.bigWig HeLa-S3 ChipSeq NRSF RawSignal 1 bigWig HudsonAlpha Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeHaibTfbs/wgEncodeHaibTfbsHelas3NrsfPcr1xRawRep2.bigWig HeLa-S3 ChipSeq NRSF RawSignal 2 bigWig HudsonAlpha Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeHaibTfbs/wgEncodeHaibTfbsHelas3Pol2Pcr1xAlnRep1.bam HeLa-S3 ChipSeq Pol2 Alignments 1 bam HudsonAlpha Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeHaibTfbs/wgEncodeHaibTfbsHelas3Pol2Pcr1xAlnRep2.bam HeLa-S3 ChipSeq Pol2 Alignments 2 bam HudsonAlpha Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeHaibTfbs/wgEncodeHaibTfbsHelas3Pol2Pcr1xPkRep1.broadPeak.gz HeLa-S3 ChipSeq Pol2 Peaks 1 broadPeak HudsonAlpha Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeHaibTfbs/wgEncodeHaibTfbsHelas3Pol2Pcr1xPkRep2.broadPeak.gz HeLa-S3 ChipSeq Pol2 Peaks 2 broadPeak HudsonAlpha Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeHaibTfbs/wgEncodeHaibTfbsHelas3Pol2Pcr1xRawRep1.bigWig HeLa-S3 ChipSeq Pol2 RawSignal 1 bigWig HudsonAlpha Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeHaibTfbs/wgEncodeHaibTfbsHelas3Pol2Pcr1xRawRep2.bigWig HeLa-S3 ChipSeq Pol2 RawSignal 2 bigWig HudsonAlpha Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeHaibTfbs/wgEncodeHaibTfbsHelas3RxlchPcr1xAlnRep1.bam HeLa-S3 ChipSeq RevXlinkChromatin Alignments 1 bam HudsonAlpha Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeHaibTfbs/wgEncodeHaibTfbsHelas3RxlchPcr1xRawRep1.bigWig HeLa-S3 ChipSeq RevXlinkChromatin RawSignal 1 bigWig HudsonAlpha Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeHaibTfbs/wgEncodeHaibTfbsHelas3Taf1Pcr1xAlnRep1.bam HeLa-S3 ChipSeq TAF1 Alignments 1 bam HudsonAlpha Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeHaibTfbs/wgEncodeHaibTfbsHelas3Taf1Pcr1xAlnRep2.bam HeLa-S3 ChipSeq TAF1 Alignments 2 bam HudsonAlpha Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeHaibTfbs/wgEncodeHaibTfbsHelas3Taf1Pcr1xPkRep1.broadPeak.gz HeLa-S3 ChipSeq TAF1 Peaks 1 broadPeak HudsonAlpha Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeHaibTfbs/wgEncodeHaibTfbsHelas3Taf1Pcr1xPkRep2.broadPeak.gz HeLa-S3 ChipSeq TAF1 Peaks 2 broadPeak HudsonAlpha Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeHaibTfbs/wgEncodeHaibTfbsHelas3Taf1Pcr1xRawRep1.bigWig HeLa-S3 ChipSeq TAF1 RawSignal 1 bigWig HudsonAlpha Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeHaibTfbs/wgEncodeHaibTfbsHelas3Taf1Pcr1xRawRep2.bigWig HeLa-S3 ChipSeq TAF1 RawSignal 2 bigWig HudsonAlpha Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeHaibTfbs/wgEncodeHaibTfbsHepg2Atf3V0416101AlnRep1.bam HepG2 ChipSeq ATF3 Alignments 1 bam HudsonAlpha Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeHaibTfbs/wgEncodeHaibTfbsHepg2Atf3V0416101AlnRep2.bam HepG2 ChipSeq ATF3 Alignments 2 bam HudsonAlpha Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeHaibTfbs/wgEncodeHaibTfbsHepg2Atf3V0416101PkRep1.broadPeak.gz HepG2 ChipSeq ATF3 Peaks 1 broadPeak HudsonAlpha Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeHaibTfbs/wgEncodeHaibTfbsHepg2Atf3V0416101PkRep2.broadPeak.gz HepG2 ChipSeq ATF3 Peaks 2 broadPeak HudsonAlpha Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeHaibTfbs/wgEncodeHaibTfbsHepg2Atf3V0416101RawRep1.bigWig HepG2 ChipSeq ATF3 RawSignal 1 bigWig HudsonAlpha Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeHaibTfbs/wgEncodeHaibTfbsHepg2Atf3V0416101RawRep2.bigWig HepG2 ChipSeq ATF3 RawSignal 2 bigWig HudsonAlpha Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeHaibTfbs/wgEncodeHaibTfbsHepg2Bhlhe40V0416101AlnRep1.bam HepG2 ChipSeq BHLHE40 Alignments 1 bam HudsonAlpha Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeHaibTfbs/wgEncodeHaibTfbsHepg2Bhlhe40V0416101AlnRep2.bam HepG2 ChipSeq BHLHE40 Alignments 2 bam HudsonAlpha Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeHaibTfbs/wgEncodeHaibTfbsHepg2Bhlhe40V0416101PkRep1.broadPeak.gz HepG2 ChipSeq BHLHE40 Peaks 1 broadPeak HudsonAlpha Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeHaibTfbs/wgEncodeHaibTfbsHepg2Bhlhe40V0416101PkRep2.broadPeak.gz HepG2 ChipSeq BHLHE40 Peaks 2 broadPeak HudsonAlpha Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeHaibTfbs/wgEncodeHaibTfbsHepg2Bhlhe40V0416101RawRep1.bigWig HepG2 ChipSeq BHLHE40 RawSignal 1 bigWig HudsonAlpha Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeHaibTfbs/wgEncodeHaibTfbsHepg2Bhlhe40V0416101RawRep2.bigWig HepG2 ChipSeq BHLHE40 RawSignal 2 bigWig HudsonAlpha Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeHaibTfbs/wgEncodeHaibTfbsHepg2Cebpbsc150V0416101AlnRep1.bam HepG2 ChipSeq CEBPB_(SC-150) Alignments 1 bam HudsonAlpha Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeHaibTfbs/wgEncodeHaibTfbsHepg2Cebpbsc150V0416101AlnRep2.bam HepG2 ChipSeq CEBPB_(SC-150) Alignments 2 bam HudsonAlpha Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeHaibTfbs/wgEncodeHaibTfbsHepg2Cebpbsc150V0416101PkRep1.broadPeak.gz HepG2 ChipSeq CEBPB_(SC-150) Peaks 1 broadPeak HudsonAlpha Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeHaibTfbs/wgEncodeHaibTfbsHepg2Cebpbsc150V0416101PkRep2.broadPeak.gz HepG2 ChipSeq CEBPB_(SC-150) Peaks 2 broadPeak HudsonAlpha Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeHaibTfbs/wgEncodeHaibTfbsHepg2Cebpbsc150V0416101RawRep1.bigWig HepG2 ChipSeq CEBPB_(SC-150) RawSignal 1 bigWig HudsonAlpha Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeHaibTfbs/wgEncodeHaibTfbsHepg2Cebpbsc150V0416101RawRep2.bigWig HepG2 ChipSeq CEBPB_(SC-150) RawSignal 2 bigWig HudsonAlpha Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeHaibTfbs/wgEncodeHaibTfbsHepg2Cebpdsc636V0416101AlnRep1.bam HepG2 ChipSeq CEBPD_(SC-636) Alignments 1 bam HudsonAlpha Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeHaibTfbs/wgEncodeHaibTfbsHepg2Cebpdsc636V0416101AlnRep2.bam HepG2 ChipSeq CEBPD_(SC-636) Alignments 2 bam HudsonAlpha Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeHaibTfbs/wgEncodeHaibTfbsHepg2Cebpdsc636V0416101PkRep1.broadPeak.gz HepG2 ChipSeq CEBPD_(SC-636) Peaks 1 broadPeak HudsonAlpha Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeHaibTfbs/wgEncodeHaibTfbsHepg2Cebpdsc636V0416101PkRep2.broadPeak.gz HepG2 ChipSeq CEBPD_(SC-636) Peaks 2 broadPeak HudsonAlpha Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeHaibTfbs/wgEncodeHaibTfbsHepg2Cebpdsc636V0416101RawRep1.bigWig HepG2 ChipSeq CEBPD_(SC-636) RawSignal 1 bigWig HudsonAlpha Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeHaibTfbs/wgEncodeHaibTfbsHepg2Cebpdsc636V0416101RawRep2.bigWig HepG2 ChipSeq CEBPD_(SC-636) RawSignal 2 bigWig HudsonAlpha Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeHaibTfbs/wgEncodeHaibTfbsHepg2Creb1sc240V0422111AlnRep1.bam HepG2 ChipSeq CREB1_(SC-240) Alignments 1 bam HudsonAlpha Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeHaibTfbs/wgEncodeHaibTfbsHepg2Creb1sc240V0422111AlnRep2.bam HepG2 ChipSeq CREB1_(SC-240) Alignments 2 bam HudsonAlpha Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeHaibTfbs/wgEncodeHaibTfbsHepg2Creb1sc240V0422111PkRep1.broadPeak.gz HepG2 ChipSeq CREB1_(SC-240) Peaks 1 broadPeak HudsonAlpha Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeHaibTfbs/wgEncodeHaibTfbsHepg2Creb1sc240V0422111PkRep2.broadPeak.gz HepG2 ChipSeq CREB1_(SC-240) Peaks 2 broadPeak HudsonAlpha Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeHaibTfbs/wgEncodeHaibTfbsHepg2Creb1sc240V0422111RawRep1.bigWig HepG2 ChipSeq CREB1_(SC-240) RawSignal 1 bigWig HudsonAlpha Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeHaibTfbs/wgEncodeHaibTfbsHepg2Creb1sc240V0422111RawRep2.bigWig HepG2 ChipSeq CREB1_(SC-240) RawSignal 2 bigWig HudsonAlpha Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeHaibTfbs/wgEncodeHaibTfbsHepg2Ctcfsc5916V0416101AlnRep1.bam HepG2 ChipSeq CTCF_(SC-5916) Alignments 1 bam HudsonAlpha Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeHaibTfbs/wgEncodeHaibTfbsHepg2Ctcfsc5916V0416101AlnRep2.bam HepG2 ChipSeq CTCF_(SC-5916) Alignments 2 bam HudsonAlpha Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeHaibTfbs/wgEncodeHaibTfbsHepg2Ctcfsc5916V0416101PkRep1.broadPeak.gz HepG2 ChipSeq CTCF_(SC-5916) Peaks 1 broadPeak HudsonAlpha Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeHaibTfbs/wgEncodeHaibTfbsHepg2Ctcfsc5916V0416101PkRep2.broadPeak.gz HepG2 ChipSeq CTCF_(SC-5916) Peaks 2 broadPeak HudsonAlpha Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeHaibTfbs/wgEncodeHaibTfbsHepg2Ctcfsc5916V0416101RawRep1.bigWig HepG2 ChipSeq CTCF_(SC-5916) RawSignal 1 bigWig HudsonAlpha Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeHaibTfbs/wgEncodeHaibTfbsHepg2Ctcfsc5916V0416101RawRep2.bigWig HepG2 ChipSeq CTCF_(SC-5916) RawSignal 2 bigWig HudsonAlpha Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeHaibTfbs/wgEncodeHaibTfbsHepg2Elf1sc631V0416101AlnRep1.bam HepG2 ChipSeq ELF1_(SC-631) Alignments 1 bam HudsonAlpha Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeHaibTfbs/wgEncodeHaibTfbsHepg2Elf1sc631V0416101AlnRep2.bam HepG2 ChipSeq ELF1_(SC-631) Alignments 2 bam HudsonAlpha Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeHaibTfbs/wgEncodeHaibTfbsHepg2Elf1sc631V0416101PkRep1.broadPeak.gz HepG2 ChipSeq ELF1_(SC-631) Peaks 1 broadPeak HudsonAlpha Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeHaibTfbs/wgEncodeHaibTfbsHepg2Elf1sc631V0416101PkRep2.broadPeak.gz HepG2 ChipSeq ELF1_(SC-631) Peaks 2 broadPeak HudsonAlpha Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeHaibTfbs/wgEncodeHaibTfbsHepg2Elf1sc631V0416101RawRep1.bigWig HepG2 ChipSeq ELF1_(SC-631) RawSignal 1 bigWig HudsonAlpha Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeHaibTfbs/wgEncodeHaibTfbsHepg2Elf1sc631V0416101RawRep2.bigWig HepG2 ChipSeq ELF1_(SC-631) RawSignal 2 bigWig HudsonAlpha Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeHaibTfbs/wgEncodeHaibTfbsHepg2Fosl2V0416101AlnRep1.bam HepG2 ChipSeq FOSL2 Alignments 1 bam HudsonAlpha Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeHaibTfbs/wgEncodeHaibTfbsHepg2Fosl2V0416101AlnRep2.bam HepG2 ChipSeq FOSL2 Alignments 2 bam HudsonAlpha Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeHaibTfbs/wgEncodeHaibTfbsHepg2Fosl2V0416101PkRep1.broadPeak.gz HepG2 ChipSeq FOSL2 Peaks 1 broadPeak HudsonAlpha Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeHaibTfbs/wgEncodeHaibTfbsHepg2Fosl2V0416101PkRep2.broadPeak.gz HepG2 ChipSeq FOSL2 Peaks 2 broadPeak HudsonAlpha Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeHaibTfbs/wgEncodeHaibTfbsHepg2Fosl2V0416101RawRep1.bigWig HepG2 ChipSeq FOSL2 RawSignal 1 bigWig HudsonAlpha Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeHaibTfbs/wgEncodeHaibTfbsHepg2Fosl2V0416101RawRep2.bigWig HepG2 ChipSeq FOSL2 RawSignal 2 bigWig HudsonAlpha Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeHaibTfbs/wgEncodeHaibTfbsHepg2Foxa1sc101058V0416101AlnRep1.bam HepG2 ChipSeq FOXA1_(SC-101058) Alignments 1 bam HudsonAlpha Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeHaibTfbs/wgEncodeHaibTfbsHepg2Foxa1sc101058V0416101AlnRep2.bam HepG2 ChipSeq FOXA1_(SC-101058) Alignments 2 bam HudsonAlpha Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeHaibTfbs/wgEncodeHaibTfbsHepg2Foxa1sc101058V0416101PkRep1.broadPeak.gz HepG2 ChipSeq FOXA1_(SC-101058) Peaks 1 broadPeak HudsonAlpha Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeHaibTfbs/wgEncodeHaibTfbsHepg2Foxa1sc101058V0416101PkRep2.broadPeak.gz HepG2 ChipSeq FOXA1_(SC-101058) Peaks 2 broadPeak HudsonAlpha Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeHaibTfbs/wgEncodeHaibTfbsHepg2Foxa1sc101058V0416101RawRep1.bigWig HepG2 ChipSeq FOXA1_(SC-101058) RawSignal 1 bigWig HudsonAlpha Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeHaibTfbs/wgEncodeHaibTfbsHepg2Foxa1sc101058V0416101RawRep2.bigWig HepG2 ChipSeq FOXA1_(SC-101058) RawSignal 2 bigWig HudsonAlpha Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeHaibTfbs/wgEncodeHaibTfbsHepg2Foxa1sc6553V0416101AlnRep1.bam HepG2 ChipSeq FOXA1_(SC-6553) Alignments 1 bam HudsonAlpha Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeHaibTfbs/wgEncodeHaibTfbsHepg2Foxa1sc6553V0416101AlnRep2.bam HepG2 ChipSeq FOXA1_(SC-6553) Alignments 2 bam HudsonAlpha Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeHaibTfbs/wgEncodeHaibTfbsHepg2Foxa1sc6553V0416101PkRep1.broadPeak.gz HepG2 ChipSeq FOXA1_(SC-6553) Peaks 1 broadPeak HudsonAlpha Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeHaibTfbs/wgEncodeHaibTfbsHepg2Foxa1sc6553V0416101PkRep2.broadPeak.gz HepG2 ChipSeq FOXA1_(SC-6553) Peaks 2 broadPeak HudsonAlpha Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeHaibTfbs/wgEncodeHaibTfbsHepg2Foxa1sc6553V0416101RawRep1.bigWig HepG2 ChipSeq FOXA1_(SC-6553) RawSignal 1 bigWig HudsonAlpha Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeHaibTfbs/wgEncodeHaibTfbsHepg2Foxa1sc6553V0416101RawRep2.bigWig HepG2 ChipSeq FOXA1_(SC-6553) RawSignal 2 bigWig HudsonAlpha Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeHaibTfbs/wgEncodeHaibTfbsHepg2Foxa2sc6554V0416101AlnRep1.bam HepG2 ChipSeq FOXA2_(SC-6554) Alignments 1 bam HudsonAlpha Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeHaibTfbs/wgEncodeHaibTfbsHepg2Foxa2sc6554V0416101AlnRep2.bam HepG2 ChipSeq FOXA2_(SC-6554) Alignments 2 bam HudsonAlpha Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeHaibTfbs/wgEncodeHaibTfbsHepg2Foxa2sc6554V0416101PkRep1.broadPeak.gz HepG2 ChipSeq FOXA2_(SC-6554) Peaks 1 broadPeak HudsonAlpha Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeHaibTfbs/wgEncodeHaibTfbsHepg2Foxa2sc6554V0416101PkRep2.broadPeak.gz HepG2 ChipSeq FOXA2_(SC-6554) Peaks 2 broadPeak HudsonAlpha Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeHaibTfbs/wgEncodeHaibTfbsHepg2Foxa2sc6554V0416101RawRep1.bigWig HepG2 ChipSeq FOXA2_(SC-6554) RawSignal 1 bigWig HudsonAlpha Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeHaibTfbs/wgEncodeHaibTfbsHepg2Foxa2sc6554V0416101RawRep2.bigWig HepG2 ChipSeq FOXA2_(SC-6554) RawSignal 2 bigWig HudsonAlpha Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeHaibTfbs/wgEncodeHaibTfbsHepg2GabpPcr2xAlnRep1.bam HepG2 ChipSeq GABP Alignments 1 bam HudsonAlpha Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeHaibTfbs/wgEncodeHaibTfbsHepg2GabpPcr2xAlnRep2.bam HepG2 ChipSeq GABP Alignments 2 bam HudsonAlpha Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeHaibTfbs/wgEncodeHaibTfbsHepg2GabpPcr2xPkRep1.broadPeak.gz HepG2 ChipSeq GABP Peaks 1 broadPeak HudsonAlpha Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeHaibTfbs/wgEncodeHaibTfbsHepg2GabpPcr2xPkRep2.broadPeak.gz HepG2 ChipSeq GABP Peaks 2 broadPeak HudsonAlpha Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeHaibTfbs/wgEncodeHaibTfbsHepg2GabpPcr2xRawRep1.bigWig HepG2 ChipSeq GABP RawSignal 1 bigWig HudsonAlpha Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeHaibTfbs/wgEncodeHaibTfbsHepg2GabpPcr2xRawRep2.bigWig HepG2 ChipSeq GABP RawSignal 2 bigWig HudsonAlpha Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeHaibTfbs/wgEncodeHaibTfbsHepg2Hdac2sc6296V0416101AlnRep1.bam HepG2 ChipSeq HDAC2_(SC-6296) Alignments 1 bam HudsonAlpha Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeHaibTfbs/wgEncodeHaibTfbsHepg2Hdac2sc6296V0416101AlnRep2.bam HepG2 ChipSeq HDAC2_(SC-6296) Alignments 2 bam HudsonAlpha Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeHaibTfbs/wgEncodeHaibTfbsHepg2Hdac2sc6296V0416101PkRep1.broadPeak.gz HepG2 ChipSeq HDAC2_(SC-6296) Peaks 1 broadPeak HudsonAlpha Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeHaibTfbs/wgEncodeHaibTfbsHepg2Hdac2sc6296V0416101PkRep2.broadPeak.gz HepG2 ChipSeq HDAC2_(SC-6296) Peaks 2 broadPeak HudsonAlpha Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeHaibTfbs/wgEncodeHaibTfbsHepg2Hdac2sc6296V0416101RawRep1.bigWig HepG2 ChipSeq HDAC2_(SC-6296) RawSignal 1 bigWig HudsonAlpha Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeHaibTfbs/wgEncodeHaibTfbsHepg2Hdac2sc6296V0416101RawRep2.bigWig HepG2 ChipSeq HDAC2_(SC-6296) RawSignal 2 bigWig HudsonAlpha Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeHaibTfbs/wgEncodeHaibTfbsHepg2Hey1V0416101AlnRep1.bam HepG2 ChipSeq HEY1 Alignments 1 bam HudsonAlpha Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeHaibTfbs/wgEncodeHaibTfbsHepg2Hey1V0416101AlnRep2.bam HepG2 ChipSeq HEY1 Alignments 2 bam HudsonAlpha Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeHaibTfbs/wgEncodeHaibTfbsHepg2Hey1V0416101PkRep1.broadPeak.gz HepG2 ChipSeq HEY1 Peaks 1 broadPeak HudsonAlpha Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeHaibTfbs/wgEncodeHaibTfbsHepg2Hey1V0416101PkRep2.broadPeak.gz HepG2 ChipSeq HEY1 Peaks 2 broadPeak HudsonAlpha Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeHaibTfbs/wgEncodeHaibTfbsHepg2Hey1V0416101RawRep1.bigWig HepG2 ChipSeq HEY1 RawSignal 1 bigWig HudsonAlpha Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeHaibTfbs/wgEncodeHaibTfbsHepg2Hey1V0416101RawRep2.bigWig HepG2 ChipSeq HEY1 RawSignal 2 bigWig HudsonAlpha Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeHaibTfbs/wgEncodeHaibTfbsHepg2Hnf4asc8987V0416101AlnRep1.bam HepG2 ChipSeq HNF4A_(SC-8987) Alignments 1 bam HudsonAlpha Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeHaibTfbs/wgEncodeHaibTfbsHepg2Hnf4asc8987V0416101AlnRep2.bam HepG2 ChipSeq HNF4A_(SC-8987) Alignments 2 bam HudsonAlpha Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeHaibTfbs/wgEncodeHaibTfbsHepg2Hnf4asc8987V0416101PkRep1.broadPeak.gz HepG2 ChipSeq HNF4A_(SC-8987) Peaks 1 broadPeak HudsonAlpha Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeHaibTfbs/wgEncodeHaibTfbsHepg2Hnf4asc8987V0416101PkRep2.broadPeak.gz HepG2 ChipSeq HNF4A_(SC-8987) Peaks 2 broadPeak HudsonAlpha Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeHaibTfbs/wgEncodeHaibTfbsHepg2Hnf4asc8987V0416101RawRep1.bigWig HepG2 ChipSeq HNF4A_(SC-8987) RawSignal 1 bigWig HudsonAlpha Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeHaibTfbs/wgEncodeHaibTfbsHepg2Hnf4asc8987V0416101RawRep2.bigWig HepG2 ChipSeq HNF4A_(SC-8987) RawSignal 2 bigWig HudsonAlpha Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeHaibTfbs/wgEncodeHaibTfbsHepg2Hnf4gsc6558V0416101AlnRep1.bam HepG2 ChipSeq HNF4G_(SC-6558) Alignments 1 bam HudsonAlpha Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeHaibTfbs/wgEncodeHaibTfbsHepg2Hnf4gsc6558V0416101AlnRep2.bam HepG2 ChipSeq HNF4G_(SC-6558) Alignments 2 bam HudsonAlpha Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeHaibTfbs/wgEncodeHaibTfbsHepg2Hnf4gsc6558V0416101PkRep1.broadPeak.gz HepG2 ChipSeq HNF4G_(SC-6558) Peaks 1 broadPeak HudsonAlpha Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeHaibTfbs/wgEncodeHaibTfbsHepg2Hnf4gsc6558V0416101PkRep2.broadPeak.gz HepG2 ChipSeq HNF4G_(SC-6558) Peaks 2 broadPeak HudsonAlpha Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeHaibTfbs/wgEncodeHaibTfbsHepg2Hnf4gsc6558V0416101RawRep1.bigWig HepG2 ChipSeq HNF4G_(SC-6558) RawSignal 1 bigWig HudsonAlpha Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeHaibTfbs/wgEncodeHaibTfbsHepg2Hnf4gsc6558V0416101RawRep2.bigWig HepG2 ChipSeq HNF4G_(SC-6558) RawSignal 2 bigWig HudsonAlpha Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeHaibTfbs/wgEncodeHaibTfbsHepg2JundPcr1xAlnRep1.bam HepG2 ChipSeq JunD Alignments 1 bam HudsonAlpha Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeHaibTfbs/wgEncodeHaibTfbsHepg2JundPcr1xAlnRep2.bam HepG2 ChipSeq JunD Alignments 2 bam HudsonAlpha Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeHaibTfbs/wgEncodeHaibTfbsHepg2JundPcr1xPkRep1.broadPeak.gz HepG2 ChipSeq JunD Peaks 1 broadPeak HudsonAlpha Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeHaibTfbs/wgEncodeHaibTfbsHepg2JundPcr1xPkRep2.broadPeak.gz HepG2 ChipSeq JunD Peaks 2 broadPeak HudsonAlpha Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeHaibTfbs/wgEncodeHaibTfbsHepg2JundPcr1xRawRep1.bigWig HepG2 ChipSeq JunD RawSignal 1 bigWig HudsonAlpha Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeHaibTfbs/wgEncodeHaibTfbsHepg2JundPcr1xRawRep2.bigWig HepG2 ChipSeq JunD RawSignal 2 bigWig HudsonAlpha Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeHaibTfbs/wgEncodeHaibTfbsHepg2MaxV0422111AlnRep1.bam HepG2 ChipSeq Max Alignments 1 bam HudsonAlpha Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeHaibTfbs/wgEncodeHaibTfbsHepg2MaxV0422111AlnRep2.bam HepG2 ChipSeq Max Alignments 2 bam HudsonAlpha Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeHaibTfbs/wgEncodeHaibTfbsHepg2MaxV0422111PkRep1.broadPeak.gz HepG2 ChipSeq Max Peaks 1 broadPeak HudsonAlpha Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeHaibTfbs/wgEncodeHaibTfbsHepg2MaxV0422111PkRep2.broadPeak.gz HepG2 ChipSeq Max Peaks 2 broadPeak HudsonAlpha Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeHaibTfbs/wgEncodeHaibTfbsHepg2MaxV0422111RawRep1.bigWig HepG2 ChipSeq Max RawSignal 1 bigWig HudsonAlpha Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeHaibTfbs/wgEncodeHaibTfbsHepg2MaxV0422111RawRep2.bigWig HepG2 ChipSeq Max RawSignal 2 bigWig HudsonAlpha Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeHaibTfbs/wgEncodeHaibTfbsHepg2Mbd4sc271530V0422111AlnRep1.bam HepG2 ChipSeq MBD4_(SC-271530) Alignments 1 bam HudsonAlpha Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeHaibTfbs/wgEncodeHaibTfbsHepg2Mbd4sc271530V0422111AlnRep2.bam HepG2 ChipSeq MBD4_(SC-271530) Alignments 2 bam HudsonAlpha Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeHaibTfbs/wgEncodeHaibTfbsHepg2Mbd4sc271530V0422111PkRep1.broadPeak.gz HepG2 ChipSeq MBD4_(SC-271530) Peaks 1 broadPeak HudsonAlpha Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeHaibTfbs/wgEncodeHaibTfbsHepg2Mbd4sc271530V0422111PkRep2.broadPeak.gz HepG2 ChipSeq MBD4_(SC-271530) Peaks 2 broadPeak HudsonAlpha Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeHaibTfbs/wgEncodeHaibTfbsHepg2Mbd4sc271530V0422111RawRep1.bigWig HepG2 ChipSeq MBD4_(SC-271530) RawSignal 1 bigWig HudsonAlpha Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeHaibTfbs/wgEncodeHaibTfbsHepg2Mbd4sc271530V0422111RawRep2.bigWig HepG2 ChipSeq MBD4_(SC-271530) RawSignal 2 bigWig HudsonAlpha Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeHaibTfbs/wgEncodeHaibTfbsHepg2Mybl2sc81192V0422111AlnRep1.bam HepG2 ChipSeq MYBL2_(SC-81192) Alignments 1 bam HudsonAlpha Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeHaibTfbs/wgEncodeHaibTfbsHepg2Mybl2sc81192V0422111AlnRep2.bam HepG2 ChipSeq MYBL2_(SC-81192) Alignments 2 bam HudsonAlpha Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeHaibTfbs/wgEncodeHaibTfbsHepg2Mybl2sc81192V0422111PkRep1.broadPeak.gz HepG2 ChipSeq MYBL2_(SC-81192) Peaks 1 broadPeak HudsonAlpha Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeHaibTfbs/wgEncodeHaibTfbsHepg2Mybl2sc81192V0422111PkRep2.broadPeak.gz HepG2 ChipSeq MYBL2_(SC-81192) Peaks 2 broadPeak HudsonAlpha Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeHaibTfbs/wgEncodeHaibTfbsHepg2Mybl2sc81192V0422111RawRep1.bigWig HepG2 ChipSeq MYBL2_(SC-81192) RawSignal 1 bigWig HudsonAlpha Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeHaibTfbs/wgEncodeHaibTfbsHepg2Mybl2sc81192V0422111RawRep2.bigWig HepG2 ChipSeq MYBL2_(SC-81192) RawSignal 2 bigWig HudsonAlpha Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeHaibTfbs/wgEncodeHaibTfbsHepg2Nficsc81335V0422111AlnRep1.bam HepG2 ChipSeq NFIC_(SC-81335) Alignments 1 bam HudsonAlpha Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeHaibTfbs/wgEncodeHaibTfbsHepg2Nficsc81335V0422111AlnRep2.bam HepG2 ChipSeq NFIC_(SC-81335) Alignments 2 bam HudsonAlpha Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeHaibTfbs/wgEncodeHaibTfbsHepg2Nficsc81335V0422111PkRep1.broadPeak.gz HepG2 ChipSeq NFIC_(SC-81335) Peaks 1 broadPeak HudsonAlpha Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeHaibTfbs/wgEncodeHaibTfbsHepg2Nficsc81335V0422111PkRep2.broadPeak.gz HepG2 ChipSeq NFIC_(SC-81335) Peaks 2 broadPeak HudsonAlpha Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeHaibTfbs/wgEncodeHaibTfbsHepg2Nficsc81335V0422111RawRep1.bigWig HepG2 ChipSeq NFIC_(SC-81335) RawSignal 1 bigWig HudsonAlpha Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeHaibTfbs/wgEncodeHaibTfbsHepg2Nficsc81335V0422111RawRep2.bigWig HepG2 ChipSeq NFIC_(SC-81335) RawSignal 2 bigWig HudsonAlpha Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeHaibTfbs/wgEncodeHaibTfbsHepg2Nr2f2sc271940V0422111AlnRep1.bam HepG2 ChipSeq NR2F2_(SC-271940) Alignments 1 bam HudsonAlpha Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeHaibTfbs/wgEncodeHaibTfbsHepg2Nr2f2sc271940V0422111AlnRep2.bam HepG2 ChipSeq NR2F2_(SC-271940) Alignments 2 bam HudsonAlpha Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeHaibTfbs/wgEncodeHaibTfbsHepg2Nr2f2sc271940V0422111PkRep1.broadPeak.gz HepG2 ChipSeq NR2F2_(SC-271940) Peaks 1 broadPeak HudsonAlpha Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeHaibTfbs/wgEncodeHaibTfbsHepg2Nr2f2sc271940V0422111PkRep2.broadPeak.gz HepG2 ChipSeq NR2F2_(SC-271940) Peaks 2 broadPeak HudsonAlpha Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeHaibTfbs/wgEncodeHaibTfbsHepg2Nr2f2sc271940V0422111RawRep1.bigWig HepG2 ChipSeq NR2F2_(SC-271940) RawSignal 1 bigWig HudsonAlpha Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeHaibTfbs/wgEncodeHaibTfbsHepg2Nr2f2sc271940V0422111RawRep2.bigWig HepG2 ChipSeq NR2F2_(SC-271940) RawSignal 2 bigWig HudsonAlpha Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeHaibTfbs/wgEncodeHaibTfbsHepg2NrsfPcr2xAlnRep1.bam HepG2 ChipSeq NRSF Alignments 1 bam HudsonAlpha Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeHaibTfbs/wgEncodeHaibTfbsHepg2NrsfPcr2xAlnRep2.bam HepG2 ChipSeq NRSF Alignments 2 bam HudsonAlpha Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeHaibTfbs/wgEncodeHaibTfbsHepg2NrsfPcr2xPkRep1.broadPeak.gz HepG2 ChipSeq NRSF Peaks 1 broadPeak HudsonAlpha Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeHaibTfbs/wgEncodeHaibTfbsHepg2NrsfPcr2xPkRep2.broadPeak.gz HepG2 ChipSeq NRSF Peaks 2 broadPeak HudsonAlpha Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeHaibTfbs/wgEncodeHaibTfbsHepg2NrsfPcr2xRawRep1.bigWig HepG2 ChipSeq NRSF RawSignal 1 bigWig HudsonAlpha Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeHaibTfbs/wgEncodeHaibTfbsHepg2NrsfPcr2xRawRep2.bigWig HepG2 ChipSeq NRSF RawSignal 2 bigWig HudsonAlpha Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeHaibTfbs/wgEncodeHaibTfbsHepg2NrsfV0416101AlnRep1.bam HepG2 ChipSeq NRSF Alignments 1 bam HudsonAlpha Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeHaibTfbs/wgEncodeHaibTfbsHepg2NrsfV0416101AlnRep2V2.bam HepG2 ChipSeq NRSF Alignments 2 bam HudsonAlpha Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeHaibTfbs/wgEncodeHaibTfbsHepg2NrsfV0416101PkRep1.broadPeak.gz HepG2 ChipSeq NRSF Peaks 1 broadPeak HudsonAlpha Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeHaibTfbs/wgEncodeHaibTfbsHepg2NrsfV0416101PkRep2.broadPeak.gz HepG2 ChipSeq NRSF Peaks 2 broadPeak HudsonAlpha Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeHaibTfbs/wgEncodeHaibTfbsHepg2NrsfV0416101RawRep1.bigWig HepG2 ChipSeq NRSF RawSignal 1 bigWig HudsonAlpha Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeHaibTfbs/wgEncodeHaibTfbsHepg2NrsfV0416101RawRep2.bigWig HepG2 ChipSeq NRSF RawSignal 2 bigWig HudsonAlpha Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeHaibTfbs/wgEncodeHaibTfbsHepg2P300V0416101AlnRep1.bam HepG2 ChipSeq p300 Alignments 1 bam HudsonAlpha Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeHaibTfbs/wgEncodeHaibTfbsHepg2P300V0416101AlnRep2.bam HepG2 ChipSeq p300 Alignments 2 bam HudsonAlpha Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeHaibTfbs/wgEncodeHaibTfbsHepg2P300V0416101PkRep1.broadPeak.gz HepG2 ChipSeq p300 Peaks 1 broadPeak HudsonAlpha Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeHaibTfbs/wgEncodeHaibTfbsHepg2P300V0416101PkRep2.broadPeak.gz HepG2 ChipSeq p300 Peaks 2 broadPeak HudsonAlpha Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeHaibTfbs/wgEncodeHaibTfbsHepg2P300V0416101RawRep1.bigWig HepG2 ChipSeq p300 RawSignal 1 bigWig HudsonAlpha Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeHaibTfbs/wgEncodeHaibTfbsHepg2P300V0416101RawRep2.bigWig HepG2 ChipSeq p300 RawSignal 2 bigWig HudsonAlpha Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeHaibTfbs/wgEncodeHaibTfbsHepg2Pol24h8V0416102AlnRep1.bam HepG2 ChipSeq Pol2-4H8 Alignments 1 bam HudsonAlpha Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeHaibTfbs/wgEncodeHaibTfbsHepg2Pol24h8V0416102AlnRep2V2.bam HepG2 ChipSeq Pol2-4H8 Alignments 2 bam HudsonAlpha Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeHaibTfbs/wgEncodeHaibTfbsHepg2Pol24h8V0416102PkRep1.broadPeak.gz HepG2 ChipSeq Pol2-4H8 Peaks 1 broadPeak HudsonAlpha Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeHaibTfbs/wgEncodeHaibTfbsHepg2Pol24h8V0416102PkRep2.broadPeak.gz HepG2 ChipSeq Pol2-4H8 Peaks 2 broadPeak HudsonAlpha Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeHaibTfbs/wgEncodeHaibTfbsHepg2Pol24h8V0416102RawRep1.bigWig HepG2 ChipSeq Pol2-4H8 RawSignal 1 bigWig HudsonAlpha Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeHaibTfbs/wgEncodeHaibTfbsHepg2Pol24h8V0416102RawRep2.bigWig HepG2 ChipSeq Pol2-4H8 RawSignal 2 bigWig HudsonAlpha Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeHaibTfbs/wgEncodeHaibTfbsHepg2Pol2Pcr2xAlnRep1.bam HepG2 ChipSeq Pol2 Alignments 1 bam HudsonAlpha Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeHaibTfbs/wgEncodeHaibTfbsHepg2Pol2Pcr2xAlnRep2.bam HepG2 ChipSeq Pol2 Alignments 2 bam HudsonAlpha Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeHaibTfbs/wgEncodeHaibTfbsHepg2Pol2Pcr2xPkRep1.broadPeak.gz HepG2 ChipSeq Pol2 Peaks 1 broadPeak HudsonAlpha Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeHaibTfbs/wgEncodeHaibTfbsHepg2Pol2Pcr2xPkRep2.broadPeak.gz HepG2 ChipSeq Pol2 Peaks 2 broadPeak HudsonAlpha Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeHaibTfbs/wgEncodeHaibTfbsHepg2Pol2Pcr2xRawRep1.bigWig HepG2 ChipSeq Pol2 RawSignal 1 bigWig HudsonAlpha Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeHaibTfbs/wgEncodeHaibTfbsHepg2Pol2Pcr2xRawRep2.bigWig HepG2 ChipSeq Pol2 RawSignal 2 bigWig HudsonAlpha Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeHaibTfbs/wgEncodeHaibTfbsHepg2Rad21V0416101AlnRep1.bam HepG2 ChipSeq Rad21 Alignments 1 bam HudsonAlpha Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeHaibTfbs/wgEncodeHaibTfbsHepg2Rad21V0416101AlnRep2.bam HepG2 ChipSeq Rad21 Alignments 2 bam HudsonAlpha Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeHaibTfbs/wgEncodeHaibTfbsHepg2Rad21V0416101PkRep1.broadPeak.gz HepG2 ChipSeq Rad21 Peaks 1 broadPeak HudsonAlpha Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeHaibTfbs/wgEncodeHaibTfbsHepg2Rad21V0416101PkRep2.broadPeak.gz HepG2 ChipSeq Rad21 Peaks 2 broadPeak HudsonAlpha Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeHaibTfbs/wgEncodeHaibTfbsHepg2Rad21V0416101RawRep1.bigWig HepG2 ChipSeq Rad21 RawSignal 1 bigWig HudsonAlpha Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeHaibTfbs/wgEncodeHaibTfbsHepg2Rad21V0416101RawRep2.bigWig HepG2 ChipSeq Rad21 RawSignal 2 bigWig HudsonAlpha Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeHaibTfbs/wgEncodeHaibTfbsHepg2RxlchPcr1xAlnRep1.bam HepG2 ChipSeq RevXlinkChromatin Alignments 1 bam HudsonAlpha Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeHaibTfbs/wgEncodeHaibTfbsHepg2RxlchPcr1xAlnRep2.bam HepG2 ChipSeq RevXlinkChromatin Alignments 2 bam HudsonAlpha Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeHaibTfbs/wgEncodeHaibTfbsHepg2RxlchPcr1xAlnRep3.bam HepG2 ChipSeq RevXlinkChromatin Alignments 3 bam HudsonAlpha Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeHaibTfbs/wgEncodeHaibTfbsHepg2RxlchPcr1xAlnRep4.bam HepG2 ChipSeq RevXlinkChromatin Alignments 4 bam HudsonAlpha Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeHaibTfbs/wgEncodeHaibTfbsHepg2RxlchPcr1xRawRep1.bigWig HepG2 ChipSeq RevXlinkChromatin RawSignal 1 bigWig HudsonAlpha Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeHaibTfbs/wgEncodeHaibTfbsHepg2RxlchPcr1xRawRep2.bigWig HepG2 ChipSeq RevXlinkChromatin RawSignal 2 bigWig HudsonAlpha Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeHaibTfbs/wgEncodeHaibTfbsHepg2RxlchPcr1xRawRep3.bigWig HepG2 ChipSeq RevXlinkChromatin RawSignal 3 bigWig HudsonAlpha Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeHaibTfbs/wgEncodeHaibTfbsHepg2RxlchPcr1xRawRep4.bigWig HepG2 ChipSeq RevXlinkChromatin RawSignal 4 bigWig HudsonAlpha Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeHaibTfbs/wgEncodeHaibTfbsHepg2RxlchPcr2xAlnRep1.bam HepG2 ChipSeq RevXlinkChromatin Alignments 1 bam HudsonAlpha Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeHaibTfbs/wgEncodeHaibTfbsHepg2RxlchPcr2xAlnRep2.bam HepG2 ChipSeq RevXlinkChromatin Alignments 2 bam HudsonAlpha Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeHaibTfbs/wgEncodeHaibTfbsHepg2RxlchPcr2xRawRep1.bigWig HepG2 ChipSeq RevXlinkChromatin RawSignal 1 bigWig HudsonAlpha Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeHaibTfbs/wgEncodeHaibTfbsHepg2RxlchPcr2xRawRep2.bigWig HepG2 ChipSeq RevXlinkChromatin RawSignal 2 bigWig HudsonAlpha Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeHaibTfbs/wgEncodeHaibTfbsHepg2RxlchV0416101AlnRep1.bam HepG2 ChipSeq RevXlinkChromatin Alignments 1 bam HudsonAlpha Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeHaibTfbs/wgEncodeHaibTfbsHepg2RxlchV0416101AlnRep2.bam HepG2 ChipSeq RevXlinkChromatin Alignments 2 bam HudsonAlpha Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeHaibTfbs/wgEncodeHaibTfbsHepg2RxlchV0416101RawRep1.bigWig HepG2 ChipSeq RevXlinkChromatin RawSignal 1 bigWig HudsonAlpha Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeHaibTfbs/wgEncodeHaibTfbsHepg2RxlchV0416101RawRep2.bigWig HepG2 ChipSeq RevXlinkChromatin RawSignal 2 bigWig HudsonAlpha Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeHaibTfbs/wgEncodeHaibTfbsHepg2RxlchV0422111AlnRep1V2.bam HepG2 ChipSeq RevXlinkChromatin Alignments 1 bam HudsonAlpha Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeHaibTfbs/wgEncodeHaibTfbsHepg2RxlchV0422111AlnRep2.bam HepG2 ChipSeq RevXlinkChromatin Alignments 2 bam HudsonAlpha Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeHaibTfbs/wgEncodeHaibTfbsHepg2RxlchV0422111AlnRep3.bam HepG2 ChipSeq RevXlinkChromatin Alignments 3 bam HudsonAlpha Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeHaibTfbs/wgEncodeHaibTfbsHepg2RxlchV0422111RawRep1.bigWig HepG2 ChipSeq RevXlinkChromatin RawSignal 1 bigWig HudsonAlpha Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeHaibTfbs/wgEncodeHaibTfbsHepg2RxlchV0422111RawRep2.bigWig HepG2 ChipSeq RevXlinkChromatin RawSignal 2 bigWig HudsonAlpha Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeHaibTfbs/wgEncodeHaibTfbsHepg2RxlchV0422111RawRep3.bigWig HepG2 ChipSeq RevXlinkChromatin RawSignal 3 bigWig HudsonAlpha Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeHaibTfbs/wgEncodeHaibTfbsHepg2RxraPcr1xAlnRep1.bam HepG2 ChipSeq RXRA Alignments 1 bam HudsonAlpha Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeHaibTfbs/wgEncodeHaibTfbsHepg2RxraPcr1xAlnRep2.bam HepG2 ChipSeq RXRA Alignments 2 bam HudsonAlpha Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeHaibTfbs/wgEncodeHaibTfbsHepg2RxraPcr1xPkRep1.broadPeak.gz HepG2 ChipSeq RXRA Peaks 1 broadPeak HudsonAlpha Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeHaibTfbs/wgEncodeHaibTfbsHepg2RxraPcr1xPkRep2.broadPeak.gz HepG2 ChipSeq RXRA Peaks 2 broadPeak HudsonAlpha Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeHaibTfbs/wgEncodeHaibTfbsHepg2RxraPcr1xRawRep1.bigWig HepG2 ChipSeq RXRA RawSignal 1 bigWig HudsonAlpha Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeHaibTfbs/wgEncodeHaibTfbsHepg2RxraPcr1xRawRep2.bigWig HepG2 ChipSeq RXRA RawSignal 2 bigWig HudsonAlpha Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeHaibTfbs/wgEncodeHaibTfbsHepg2Sin3ak20Pcr1xAlnRep1.bam HepG2 ChipSeq Sin3Ak-20 Alignments 1 bam HudsonAlpha Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeHaibTfbs/wgEncodeHaibTfbsHepg2Sin3ak20Pcr1xAlnRep2.bam HepG2 ChipSeq Sin3Ak-20 Alignments 2 bam HudsonAlpha Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeHaibTfbs/wgEncodeHaibTfbsHepg2Sin3ak20Pcr1xPkRep1.broadPeak.gz HepG2 ChipSeq Sin3Ak-20 Peaks 1 broadPeak HudsonAlpha Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeHaibTfbs/wgEncodeHaibTfbsHepg2Sin3ak20Pcr1xPkRep2.broadPeak.gz HepG2 ChipSeq Sin3Ak-20 Peaks 2 broadPeak HudsonAlpha Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeHaibTfbs/wgEncodeHaibTfbsHepg2Sin3ak20Pcr1xRawRep1.bigWig HepG2 ChipSeq Sin3Ak-20 RawSignal 1 bigWig HudsonAlpha Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeHaibTfbs/wgEncodeHaibTfbsHepg2Sin3ak20Pcr1xRawRep2.bigWig HepG2 ChipSeq Sin3Ak-20 RawSignal 2 bigWig HudsonAlpha Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeHaibTfbs/wgEncodeHaibTfbsHepg2Sp1Pcr1xAlnRep1.bam HepG2 ChipSeq SP1 Alignments 1 bam HudsonAlpha Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeHaibTfbs/wgEncodeHaibTfbsHepg2Sp1Pcr1xAlnRep2.bam HepG2 ChipSeq SP1 Alignments 2 bam HudsonAlpha Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeHaibTfbs/wgEncodeHaibTfbsHepg2Sp1Pcr1xPkRep1.broadPeak.gz HepG2 ChipSeq SP1 Peaks 1 broadPeak HudsonAlpha Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeHaibTfbs/wgEncodeHaibTfbsHepg2Sp1Pcr1xPkRep2.broadPeak.gz HepG2 ChipSeq SP1 Peaks 2 broadPeak HudsonAlpha Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeHaibTfbs/wgEncodeHaibTfbsHepg2Sp1Pcr1xRawRep1.bigWig HepG2 ChipSeq SP1 RawSignal 1 bigWig HudsonAlpha Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeHaibTfbs/wgEncodeHaibTfbsHepg2Sp1Pcr1xRawRep2.bigWig HepG2 ChipSeq SP1 RawSignal 2 bigWig HudsonAlpha Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeHaibTfbs/wgEncodeHaibTfbsHepg2Sp2V0422111AlnRep1.bam HepG2 ChipSeq SP2_(SC-643) Alignments 1 bam HudsonAlpha Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeHaibTfbs/wgEncodeHaibTfbsHepg2Sp2V0422111AlnRep2.bam HepG2 ChipSeq SP2_(SC-643) Alignments 2 bam HudsonAlpha Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeHaibTfbs/wgEncodeHaibTfbsHepg2Sp2V0422111PkRep1.broadPeak.gz HepG2 ChipSeq SP2_(SC-643) Peaks 1 broadPeak HudsonAlpha Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeHaibTfbs/wgEncodeHaibTfbsHepg2Sp2V0422111PkRep2.broadPeak.gz HepG2 ChipSeq SP2_(SC-643) Peaks 2 broadPeak HudsonAlpha Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeHaibTfbs/wgEncodeHaibTfbsHepg2Sp2V0422111RawRep1.bigWig HepG2 ChipSeq SP2_(SC-643) RawSignal 1 bigWig HudsonAlpha Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeHaibTfbs/wgEncodeHaibTfbsHepg2Sp2V0422111RawRep2.bigWig HepG2 ChipSeq SP2_(SC-643) RawSignal 2 bigWig HudsonAlpha Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeHaibTfbs/wgEncodeHaibTfbsHepg2SrfV0416101AlnRep1.bam HepG2 ChipSeq SRF Alignments 1 bam HudsonAlpha Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeHaibTfbs/wgEncodeHaibTfbsHepg2SrfV0416101AlnRep2.bam HepG2 ChipSeq SRF Alignments 2 bam HudsonAlpha Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeHaibTfbs/wgEncodeHaibTfbsHepg2SrfV0416101PkRep1.broadPeak.gz HepG2 ChipSeq SRF Peaks 1 broadPeak HudsonAlpha Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeHaibTfbs/wgEncodeHaibTfbsHepg2SrfV0416101PkRep2.broadPeak.gz HepG2 ChipSeq SRF Peaks 2 broadPeak HudsonAlpha Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeHaibTfbs/wgEncodeHaibTfbsHepg2SrfV0416101RawRep1.bigWig HepG2 ChipSeq SRF RawSignal 1 bigWig HudsonAlpha Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeHaibTfbs/wgEncodeHaibTfbsHepg2SrfV0416101RawRep2.bigWig HepG2 ChipSeq SRF RawSignal 2 bigWig HudsonAlpha Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeHaibTfbs/wgEncodeHaibTfbsHepg2Taf1Pcr2xAlnRep1.bam HepG2 ChipSeq TAF1 Alignments 1 bam HudsonAlpha Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeHaibTfbs/wgEncodeHaibTfbsHepg2Taf1Pcr2xAlnRep2.bam HepG2 ChipSeq TAF1 Alignments 2 bam HudsonAlpha Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeHaibTfbs/wgEncodeHaibTfbsHepg2Taf1Pcr2xPkRep1.broadPeak.gz HepG2 ChipSeq TAF1 Peaks 1 broadPeak HudsonAlpha Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeHaibTfbs/wgEncodeHaibTfbsHepg2Taf1Pcr2xPkRep2.broadPeak.gz HepG2 ChipSeq TAF1 Peaks 2 broadPeak HudsonAlpha Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeHaibTfbs/wgEncodeHaibTfbsHepg2Taf1Pcr2xRawRep1.bigWig HepG2 ChipSeq TAF1 RawSignal 1 bigWig HudsonAlpha Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeHaibTfbs/wgEncodeHaibTfbsHepg2Taf1Pcr2xRawRep2.bigWig HepG2 ChipSeq TAF1 RawSignal 2 bigWig HudsonAlpha Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeHaibTfbs/wgEncodeHaibTfbsHepg2Tcf12Pcr1xAlnRep1.bam HepG2 ChipSeq TCF12 Alignments 1 bam HudsonAlpha Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeHaibTfbs/wgEncodeHaibTfbsHepg2Tcf12Pcr1xAlnRep2.bam HepG2 ChipSeq TCF12 Alignments 2 bam HudsonAlpha Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeHaibTfbs/wgEncodeHaibTfbsHepg2Tcf12Pcr1xPkRep1.broadPeak.gz HepG2 ChipSeq TCF12 Peaks 1 broadPeak HudsonAlpha Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeHaibTfbs/wgEncodeHaibTfbsHepg2Tcf12Pcr1xPkRep2.broadPeak.gz HepG2 ChipSeq TCF12 Peaks 2 broadPeak HudsonAlpha Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeHaibTfbs/wgEncodeHaibTfbsHepg2Tcf12Pcr1xRawRep1.bigWig HepG2 ChipSeq TCF12 RawSignal 1 bigWig HudsonAlpha Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeHaibTfbs/wgEncodeHaibTfbsHepg2Tcf12Pcr1xRawRep2.bigWig HepG2 ChipSeq TCF12 RawSignal 2 bigWig HudsonAlpha Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeHaibTfbs/wgEncodeHaibTfbsHepg2Tead4sc101184V0422111AlnRep1.bam HepG2 ChipSeq TEAD4_(SC-101184) Alignments 1 bam HudsonAlpha Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeHaibTfbs/wgEncodeHaibTfbsHepg2Tead4sc101184V0422111AlnRep2.bam HepG2 ChipSeq TEAD4_(SC-101184) Alignments 2 bam HudsonAlpha Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeHaibTfbs/wgEncodeHaibTfbsHepg2Tead4sc101184V0422111PkRep1.broadPeak.gz HepG2 ChipSeq TEAD4_(SC-101184) Peaks 1 broadPeak HudsonAlpha Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeHaibTfbs/wgEncodeHaibTfbsHepg2Tead4sc101184V0422111PkRep2.broadPeak.gz HepG2 ChipSeq TEAD4_(SC-101184) Peaks 2 broadPeak HudsonAlpha Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeHaibTfbs/wgEncodeHaibTfbsHepg2Tead4sc101184V0422111RawRep1.bigWig HepG2 ChipSeq TEAD4_(SC-101184) RawSignal 1 bigWig HudsonAlpha Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeHaibTfbs/wgEncodeHaibTfbsHepg2Tead4sc101184V0422111RawRep2.bigWig HepG2 ChipSeq TEAD4_(SC-101184) RawSignal 2 bigWig HudsonAlpha Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeHaibTfbs/wgEncodeHaibTfbsHepg2Usf1Pcr1xAlnRep1.bam HepG2 ChipSeq USF-1 Alignments 1 bam HudsonAlpha Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeHaibTfbs/wgEncodeHaibTfbsHepg2Usf1Pcr1xAlnRep2.bam HepG2 ChipSeq USF-1 Alignments 2 bam HudsonAlpha Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeHaibTfbs/wgEncodeHaibTfbsHepg2Usf1Pcr1xPkRep1.broadPeak.gz HepG2 ChipSeq USF-1 Peaks 1 broadPeak HudsonAlpha Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeHaibTfbs/wgEncodeHaibTfbsHepg2Usf1Pcr1xPkRep2.broadPeak.gz HepG2 ChipSeq USF-1 Peaks 2 broadPeak HudsonAlpha Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeHaibTfbs/wgEncodeHaibTfbsHepg2Usf1Pcr1xRawRep1.bigWig HepG2 ChipSeq USF-1 RawSignal 1 bigWig HudsonAlpha Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeHaibTfbs/wgEncodeHaibTfbsHepg2Usf1Pcr1xRawRep2.bigWig HepG2 ChipSeq USF-1 RawSignal 2 bigWig HudsonAlpha Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeHaibTfbs/wgEncodeHaibTfbsHepg2Yy1sc281V0416101AlnRep1.bam HepG2 ChipSeq YY1_(SC-281) Alignments 1 bam HudsonAlpha Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeHaibTfbs/wgEncodeHaibTfbsHepg2Yy1sc281V0416101AlnRep2.bam HepG2 ChipSeq YY1_(SC-281) Alignments 2 bam HudsonAlpha Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeHaibTfbs/wgEncodeHaibTfbsHepg2Yy1sc281V0416101PkRep1.broadPeak.gz HepG2 ChipSeq YY1_(SC-281) Peaks 1 broadPeak HudsonAlpha Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeHaibTfbs/wgEncodeHaibTfbsHepg2Yy1sc281V0416101PkRep2.broadPeak.gz HepG2 ChipSeq YY1_(SC-281) Peaks 2 broadPeak HudsonAlpha Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeHaibTfbs/wgEncodeHaibTfbsHepg2Yy1sc281V0416101RawRep1.bigWig HepG2 ChipSeq YY1_(SC-281) RawSignal 1 bigWig HudsonAlpha Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeHaibTfbs/wgEncodeHaibTfbsHepg2Yy1sc281V0416101RawRep2.bigWig HepG2 ChipSeq YY1_(SC-281) RawSignal 2 bigWig HudsonAlpha Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeHaibTfbs/wgEncodeHaibTfbsHepg2Zbtb33Pcr1xAlnRep1.bam HepG2 ChipSeq ZBTB33 Alignments 1 bam HudsonAlpha Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeHaibTfbs/wgEncodeHaibTfbsHepg2Zbtb33Pcr1xAlnRep2.bam HepG2 ChipSeq ZBTB33 Alignments 2 bam HudsonAlpha Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeHaibTfbs/wgEncodeHaibTfbsHepg2Zbtb33Pcr1xPkRep1.broadPeak.gz HepG2 ChipSeq ZBTB33 Peaks 1 broadPeak HudsonAlpha Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeHaibTfbs/wgEncodeHaibTfbsHepg2Zbtb33Pcr1xPkRep2.broadPeak.gz HepG2 ChipSeq ZBTB33 Peaks 2 broadPeak HudsonAlpha Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeHaibTfbs/wgEncodeHaibTfbsHepg2Zbtb33Pcr1xRawRep1.bigWig HepG2 ChipSeq ZBTB33 RawSignal 1 bigWig HudsonAlpha Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeHaibTfbs/wgEncodeHaibTfbsHepg2Zbtb33Pcr1xRawRep2.bigWig HepG2 ChipSeq ZBTB33 RawSignal 2 bigWig HudsonAlpha Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeHaibTfbs/wgEncodeHaibTfbsHepg2Zbtb33V0416101AlnRep1.bam HepG2 ChipSeq ZBTB33 Alignments 1 bam HudsonAlpha Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeHaibTfbs/wgEncodeHaibTfbsHepg2Zbtb33V0416101AlnRep2.bam HepG2 ChipSeq ZBTB33 Alignments 2 bam HudsonAlpha Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeHaibTfbs/wgEncodeHaibTfbsHepg2Zbtb33V0416101PkRep1.broadPeak.gz HepG2 ChipSeq ZBTB33 Peaks 1 broadPeak HudsonAlpha Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeHaibTfbs/wgEncodeHaibTfbsHepg2Zbtb33V0416101PkRep2.broadPeak.gz HepG2 ChipSeq ZBTB33 Peaks 2 broadPeak HudsonAlpha Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeHaibTfbs/wgEncodeHaibTfbsHepg2Zbtb33V0416101RawRep1.bigWig HepG2 ChipSeq ZBTB33 RawSignal 1 bigWig HudsonAlpha Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeHaibTfbs/wgEncodeHaibTfbsHepg2Zbtb33V0416101RawRep2.bigWig HepG2 ChipSeq ZBTB33 RawSignal 2 bigWig HudsonAlpha Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeHaibTfbs/wgEncodeHaibTfbsHepg2Zbtb7aV0416101AlnRep1.bam HepG2 ChipSeq ZBTB7A_(SC-34508) Alignments 1 bam HudsonAlpha Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeHaibTfbs/wgEncodeHaibTfbsHepg2Zbtb7aV0416101AlnRep2.bam HepG2 ChipSeq ZBTB7A_(SC-34508) Alignments 2 bam HudsonAlpha Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeHaibTfbs/wgEncodeHaibTfbsHepg2Zbtb7aV0416101PkRep1.broadPeak.gz HepG2 ChipSeq ZBTB7A_(SC-34508) Peaks 1 broadPeak HudsonAlpha Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeHaibTfbs/wgEncodeHaibTfbsHepg2Zbtb7aV0416101PkRep2.broadPeak.gz HepG2 ChipSeq ZBTB7A_(SC-34508) Peaks 2 broadPeak HudsonAlpha Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeHaibTfbs/wgEncodeHaibTfbsHepg2Zbtb7aV0416101RawRep1.bigWig HepG2 ChipSeq ZBTB7A_(SC-34508) RawSignal 1 bigWig HudsonAlpha Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeHaibTfbs/wgEncodeHaibTfbsHepg2Zbtb7aV0416101RawRep2.bigWig HepG2 ChipSeq ZBTB7A_(SC-34508) RawSignal 2 bigWig HudsonAlpha Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeHaibTfbs/wgEncodeHaibTfbsHepg2Zeb1V0422111AlnRep1.bam HepG2 ChipSeq ZEB1_(SC-25388) Alignments 1 bam HudsonAlpha Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeHaibTfbs/wgEncodeHaibTfbsHepg2Zeb1V0422111AlnRep2.bam HepG2 ChipSeq ZEB1_(SC-25388) Alignments 2 bam HudsonAlpha Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeHaibTfbs/wgEncodeHaibTfbsHepg2Zeb1V0422111PkRep1.broadPeak.gz HepG2 ChipSeq ZEB1_(SC-25388) Peaks 1 broadPeak HudsonAlpha Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeHaibTfbs/wgEncodeHaibTfbsHepg2Zeb1V0422111PkRep2.broadPeak.gz HepG2 ChipSeq ZEB1_(SC-25388) Peaks 2 broadPeak HudsonAlpha Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeHaibTfbs/wgEncodeHaibTfbsHepg2Zeb1V0422111RawRep1.bigWig HepG2 ChipSeq ZEB1_(SC-25388) RawSignal 1 bigWig HudsonAlpha Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeHaibTfbs/wgEncodeHaibTfbsHepg2Zeb1V0422111RawRep2.bigWig HepG2 ChipSeq ZEB1_(SC-25388) RawSignal 2 bigWig HudsonAlpha Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeHaibTfbs/wgEncodeHaibTfbsHl60GabpV0422111AlnRep1.bam HL-60 ChipSeq GABP Alignments 1 bam HudsonAlpha Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeHaibTfbs/wgEncodeHaibTfbsHl60GabpV0422111AlnRep2.bam HL-60 ChipSeq GABP Alignments 2 bam HudsonAlpha Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeHaibTfbs/wgEncodeHaibTfbsHl60GabpV0422111PkRep1.broadPeak.gz HL-60 ChipSeq GABP Peaks 1 broadPeak HudsonAlpha Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeHaibTfbs/wgEncodeHaibTfbsHl60GabpV0422111PkRep2.broadPeak.gz HL-60 ChipSeq GABP Peaks 2 broadPeak HudsonAlpha Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeHaibTfbs/wgEncodeHaibTfbsHl60GabpV0422111RawRep1.bigWig HL-60 ChipSeq GABP RawSignal 1 bigWig HudsonAlpha Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeHaibTfbs/wgEncodeHaibTfbsHl60GabpV0422111RawRep2.bigWig HL-60 ChipSeq GABP RawSignal 2 bigWig HudsonAlpha Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeHaibTfbs/wgEncodeHaibTfbsHl60NrsfV0422111AlnRep1.bam HL-60 ChipSeq NRSF Alignments 1 bam HudsonAlpha Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeHaibTfbs/wgEncodeHaibTfbsHl60NrsfV0422111AlnRep2.bam HL-60 ChipSeq NRSF Alignments 2 bam HudsonAlpha Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeHaibTfbs/wgEncodeHaibTfbsHl60NrsfV0422111PkRep1.broadPeak.gz HL-60 ChipSeq NRSF Peaks 1 broadPeak HudsonAlpha Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeHaibTfbs/wgEncodeHaibTfbsHl60NrsfV0422111PkRep2.broadPeak.gz HL-60 ChipSeq NRSF Peaks 2 broadPeak HudsonAlpha Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeHaibTfbs/wgEncodeHaibTfbsHl60NrsfV0422111RawRep1.bigWig HL-60 ChipSeq NRSF RawSignal 1 bigWig HudsonAlpha Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeHaibTfbs/wgEncodeHaibTfbsHl60NrsfV0422111RawRep2.bigWig HL-60 ChipSeq NRSF RawSignal 2 bigWig HudsonAlpha Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeHaibTfbs/wgEncodeHaibTfbsHl60Pol24h8V0422111AlnRep1.bam HL-60 ChipSeq Pol2-4H8 Alignments 1 bam HudsonAlpha Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeHaibTfbs/wgEncodeHaibTfbsHl60Pol24h8V0422111AlnRep2.bam HL-60 ChipSeq Pol2-4H8 Alignments 2 bam HudsonAlpha Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeHaibTfbs/wgEncodeHaibTfbsHl60Pol24h8V0422111PkRep1.broadPeak.gz HL-60 ChipSeq Pol2-4H8 Peaks 1 broadPeak HudsonAlpha Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeHaibTfbs/wgEncodeHaibTfbsHl60Pol24h8V0422111PkRep2.broadPeak.gz HL-60 ChipSeq Pol2-4H8 Peaks 2 broadPeak HudsonAlpha Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeHaibTfbs/wgEncodeHaibTfbsHl60Pol24h8V0422111RawRep1.bigWig HL-60 ChipSeq Pol2-4H8 RawSignal 1 bigWig HudsonAlpha Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeHaibTfbs/wgEncodeHaibTfbsHl60Pol24h8V0422111RawRep2.bigWig HL-60 ChipSeq Pol2-4H8 RawSignal 2 bigWig HudsonAlpha Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeHaibTfbs/wgEncodeHaibTfbsHl60Pu1V0422111AlnRep1.bam HL-60 ChipSeq PU.1 Alignments 1 bam HudsonAlpha Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeHaibTfbs/wgEncodeHaibTfbsHl60Pu1V0422111AlnRep2.bam HL-60 ChipSeq PU.1 Alignments 2 bam HudsonAlpha Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeHaibTfbs/wgEncodeHaibTfbsHl60Pu1V0422111PkRep1.broadPeak.gz HL-60 ChipSeq PU.1 Peaks 1 broadPeak HudsonAlpha Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeHaibTfbs/wgEncodeHaibTfbsHl60Pu1V0422111PkRep2.broadPeak.gz HL-60 ChipSeq PU.1 Peaks 2 broadPeak HudsonAlpha Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeHaibTfbs/wgEncodeHaibTfbsHl60Pu1V0422111RawRep1.bigWig HL-60 ChipSeq PU.1 RawSignal 1 bigWig HudsonAlpha Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeHaibTfbs/wgEncodeHaibTfbsHl60Pu1V0422111RawRep2.bigWig HL-60 ChipSeq PU.1 RawSignal 2 bigWig HudsonAlpha Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeHaibTfbs/wgEncodeHaibTfbsHl60RxlchV0422111AlnRep1.bam HL-60 ChipSeq RevXlinkChromatin Alignments 1 bam HudsonAlpha Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeHaibTfbs/wgEncodeHaibTfbsHl60RxlchV0422111AlnRep2.bam HL-60 ChipSeq RevXlinkChromatin Alignments 2 bam HudsonAlpha Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeHaibTfbs/wgEncodeHaibTfbsHl60RxlchV0422111RawRep1.bigWig HL-60 ChipSeq RevXlinkChromatin RawSignal 1 bigWig HudsonAlpha Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeHaibTfbs/wgEncodeHaibTfbsHl60RxlchV0422111RawRep2.bigWig HL-60 ChipSeq RevXlinkChromatin RawSignal 2 bigWig HudsonAlpha Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeHaibTfbs/wgEncodeHaibTfbsHuvecPol24h8V0416101AlnRep1.bam HUVEC ChipSeq Pol2-4H8 Alignments 1 bam HudsonAlpha Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeHaibTfbs/wgEncodeHaibTfbsHuvecPol24h8V0416101AlnRep2.bam HUVEC ChipSeq Pol2-4H8 Alignments 2 bam HudsonAlpha Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeHaibTfbs/wgEncodeHaibTfbsHuvecPol24h8V0416101PkRep1.broadPeak.gz HUVEC ChipSeq Pol2-4H8 Peaks 1 broadPeak HudsonAlpha Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeHaibTfbs/wgEncodeHaibTfbsHuvecPol24h8V0416101PkRep2.broadPeak.gz HUVEC ChipSeq Pol2-4H8 Peaks 2 broadPeak HudsonAlpha Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeHaibTfbs/wgEncodeHaibTfbsHuvecPol24h8V0416101RawRep1.bigWig HUVEC ChipSeq Pol2-4H8 RawSignal 1 bigWig HudsonAlpha Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeHaibTfbs/wgEncodeHaibTfbsHuvecPol24h8V0416101RawRep2.bigWig HUVEC ChipSeq Pol2-4H8 RawSignal 2 bigWig HudsonAlpha Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeHaibTfbs/wgEncodeHaibTfbsHuvecPol2Pcr1xAlnRep1.bam HUVEC ChipSeq Pol2 Alignments 1 bam HudsonAlpha Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeHaibTfbs/wgEncodeHaibTfbsHuvecPol2Pcr1xAlnRep2.bam HUVEC ChipSeq Pol2 Alignments 2 bam HudsonAlpha Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeHaibTfbs/wgEncodeHaibTfbsHuvecPol2Pcr1xPkRep1.broadPeak.gz HUVEC ChipSeq Pol2 Peaks 1 broadPeak HudsonAlpha Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeHaibTfbs/wgEncodeHaibTfbsHuvecPol2Pcr1xPkRep2.broadPeak.gz HUVEC ChipSeq Pol2 Peaks 2 broadPeak HudsonAlpha Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeHaibTfbs/wgEncodeHaibTfbsHuvecPol2Pcr1xRawRep1.bigWig HUVEC ChipSeq Pol2 RawSignal 1 bigWig HudsonAlpha Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeHaibTfbs/wgEncodeHaibTfbsHuvecPol2Pcr1xRawRep2.bigWig HUVEC ChipSeq Pol2 RawSignal 2 bigWig HudsonAlpha Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeHaibTfbs/wgEncodeHaibTfbsHuvecRxlchPcr1xAlnRep1.bam HUVEC ChipSeq RevXlinkChromatin Alignments 1 bam HudsonAlpha Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeHaibTfbs/wgEncodeHaibTfbsHuvecRxlchPcr1xRawRep1.bigWig HUVEC ChipSeq RevXlinkChromatin RawSignal 1 bigWig HudsonAlpha Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeHaibTfbs/wgEncodeHaibTfbsK562Atf3V0416101AlnRep1.bam K562 ChipSeq ATF3 Alignments 1 bam HudsonAlpha Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeHaibTfbs/wgEncodeHaibTfbsK562Atf3V0416101AlnRep2.bam K562 ChipSeq ATF3 Alignments 2 bam HudsonAlpha Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeHaibTfbs/wgEncodeHaibTfbsK562Atf3V0416101PkRep1.broadPeak.gz K562 ChipSeq ATF3 Peaks 1 broadPeak HudsonAlpha Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeHaibTfbs/wgEncodeHaibTfbsK562Atf3V0416101PkRep2.broadPeak.gz K562 ChipSeq ATF3 Peaks 2 broadPeak HudsonAlpha Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeHaibTfbs/wgEncodeHaibTfbsK562Atf3V0416101RawRep1.bigWig K562 ChipSeq ATF3 RawSignal 1 bigWig HudsonAlpha Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeHaibTfbs/wgEncodeHaibTfbsK562Atf3V0416101RawRep2.bigWig K562 ChipSeq ATF3 RawSignal 2 bigWig HudsonAlpha Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeHaibTfbs/wgEncodeHaibTfbsK562Bcl3Pcr1xAlnRep1.bam K562 ChipSeq BCL3 Alignments 1 bam HudsonAlpha Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeHaibTfbs/wgEncodeHaibTfbsK562Bcl3Pcr1xAlnRep2.bam K562 ChipSeq BCL3 Alignments 2 bam HudsonAlpha Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeHaibTfbs/wgEncodeHaibTfbsK562Bcl3Pcr1xPkRep1.broadPeak.gz K562 ChipSeq BCL3 Peaks 1 broadPeak HudsonAlpha Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeHaibTfbs/wgEncodeHaibTfbsK562Bcl3Pcr1xPkRep2.broadPeak.gz K562 ChipSeq BCL3 Peaks 2 broadPeak HudsonAlpha Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeHaibTfbs/wgEncodeHaibTfbsK562Bcl3Pcr1xRawRep1.bigWig K562 ChipSeq BCL3 RawSignal 1 bigWig HudsonAlpha Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeHaibTfbs/wgEncodeHaibTfbsK562Bcl3Pcr1xRawRep2.bigWig K562 ChipSeq BCL3 RawSignal 2 bigWig HudsonAlpha Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeHaibTfbs/wgEncodeHaibTfbsK562Bclaf101388Pcr1xAlnRep1.bam K562 ChipSeq BCLAF1_(SC-101388) Alignments 1 bam HudsonAlpha Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeHaibTfbs/wgEncodeHaibTfbsK562Bclaf101388Pcr1xAlnRep2.bam K562 ChipSeq BCLAF1_(SC-101388) Alignments 2 bam HudsonAlpha Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeHaibTfbs/wgEncodeHaibTfbsK562Bclaf101388Pcr1xPkRep1.broadPeak.gz K562 ChipSeq BCLAF1_(SC-101388) Peaks 1 broadPeak HudsonAlpha Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeHaibTfbs/wgEncodeHaibTfbsK562Bclaf101388Pcr1xPkRep2.broadPeak.gz K562 ChipSeq BCLAF1_(SC-101388) Peaks 2 broadPeak HudsonAlpha Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeHaibTfbs/wgEncodeHaibTfbsK562Bclaf101388Pcr1xRawRep1.bigWig K562 ChipSeq BCLAF1_(SC-101388) RawSignal 1 bigWig HudsonAlpha Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeHaibTfbs/wgEncodeHaibTfbsK562Bclaf101388Pcr1xRawRep2.bigWig K562 ChipSeq BCLAF1_(SC-101388) RawSignal 2 bigWig HudsonAlpha Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeHaibTfbs/wgEncodeHaibTfbsK562Cbx3sc101004V0422111AlnRep1.bam K562 ChipSeq CBX3_(SC-101004) Alignments 1 bam HudsonAlpha Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeHaibTfbs/wgEncodeHaibTfbsK562Cbx3sc101004V0422111AlnRep2.bam K562 ChipSeq CBX3_(SC-101004) Alignments 2 bam HudsonAlpha Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeHaibTfbs/wgEncodeHaibTfbsK562Cbx3sc101004V0422111PkRep1.broadPeak.gz K562 ChipSeq CBX3_(SC-101004) Peaks 1 broadPeak HudsonAlpha Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeHaibTfbs/wgEncodeHaibTfbsK562Cbx3sc101004V0422111PkRep2.broadPeak.gz K562 ChipSeq CBX3_(SC-101004) Peaks 2 broadPeak HudsonAlpha Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeHaibTfbs/wgEncodeHaibTfbsK562Cbx3sc101004V0422111RawRep1.bigWig K562 ChipSeq CBX3_(SC-101004) RawSignal 1 bigWig HudsonAlpha Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeHaibTfbs/wgEncodeHaibTfbsK562Cbx3sc101004V0422111RawRep2.bigWig K562 ChipSeq CBX3_(SC-101004) RawSignal 2 bigWig HudsonAlpha Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeHaibTfbs/wgEncodeHaibTfbsK562Cebpbsc150V0422111AlnRep1.bam K562 ChipSeq CEBPB_(SC-150) Alignments 1 bam HudsonAlpha Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeHaibTfbs/wgEncodeHaibTfbsK562Cebpbsc150V0422111AlnRep2.bam K562 ChipSeq CEBPB_(SC-150) Alignments 2 bam HudsonAlpha Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeHaibTfbs/wgEncodeHaibTfbsK562Cebpbsc150V0422111PkRep1.broadPeak.gz K562 ChipSeq CEBPB_(SC-150) Peaks 1 broadPeak HudsonAlpha Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeHaibTfbs/wgEncodeHaibTfbsK562Cebpbsc150V0422111PkRep2.broadPeak.gz K562 ChipSeq CEBPB_(SC-150) Peaks 2 broadPeak HudsonAlpha Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeHaibTfbs/wgEncodeHaibTfbsK562Cebpbsc150V0422111RawRep1.bigWig K562 ChipSeq CEBPB_(SC-150) RawSignal 1 bigWig HudsonAlpha Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeHaibTfbs/wgEncodeHaibTfbsK562Cebpbsc150V0422111RawRep2.bigWig K562 ChipSeq CEBPB_(SC-150) RawSignal 2 bigWig HudsonAlpha Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeHaibTfbs/wgEncodeHaibTfbsK562Cebpdsc636V0422111AlnRep1.bam K562 ChipSeq CEBPD_(SC-636) Alignments 1 bam HudsonAlpha Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeHaibTfbs/wgEncodeHaibTfbsK562Cebpdsc636V0422111AlnRep2.bam K562 ChipSeq CEBPD_(SC-636) Alignments 2 bam HudsonAlpha Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeHaibTfbs/wgEncodeHaibTfbsK562Cebpdsc636V0422111PkRep1.broadPeak.gz K562 ChipSeq CEBPD_(SC-636) Peaks 1 broadPeak HudsonAlpha Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeHaibTfbs/wgEncodeHaibTfbsK562Cebpdsc636V0422111PkRep2.broadPeak.gz K562 ChipSeq CEBPD_(SC-636) Peaks 2 broadPeak HudsonAlpha Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeHaibTfbs/wgEncodeHaibTfbsK562Cebpdsc636V0422111RawRep1.bigWig K562 ChipSeq CEBPD_(SC-636) RawSignal 1 bigWig HudsonAlpha Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeHaibTfbs/wgEncodeHaibTfbsK562Cebpdsc636V0422111RawRep2.bigWig K562 ChipSeq CEBPD_(SC-636) RawSignal 2 bigWig HudsonAlpha Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeHaibTfbs/wgEncodeHaibTfbsK562Creb1sc240V0422111AlnRep1.bam K562 ChipSeq CREB1_(SC-240) Alignments 1 bam HudsonAlpha Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeHaibTfbs/wgEncodeHaibTfbsK562Creb1sc240V0422111AlnRep2.bam K562 ChipSeq CREB1_(SC-240) Alignments 2 bam HudsonAlpha Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeHaibTfbs/wgEncodeHaibTfbsK562Creb1sc240V0422111PkRep1.broadPeak.gz K562 ChipSeq CREB1_(SC-240) Peaks 1 broadPeak HudsonAlpha Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeHaibTfbs/wgEncodeHaibTfbsK562Creb1sc240V0422111PkRep2.broadPeak.gz K562 ChipSeq CREB1_(SC-240) Peaks 2 broadPeak HudsonAlpha Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeHaibTfbs/wgEncodeHaibTfbsK562Creb1sc240V0422111RawRep1.bigWig K562 ChipSeq CREB1_(SC-240) RawSignal 1 bigWig HudsonAlpha Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeHaibTfbs/wgEncodeHaibTfbsK562Creb1sc240V0422111RawRep2.bigWig K562 ChipSeq CREB1_(SC-240) RawSignal 2 bigWig HudsonAlpha Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeHaibTfbs/wgEncodeHaibTfbsK562CtcfcPcr1xAlnRep1.bam K562 ChipSeq CTCF_(SC-5916) Alignments 1 bam HudsonAlpha Data 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http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeHaibTfbs/wgEncodeHaibTfbsK562CtcfcPcr1xRawRep1.bigWig K562 ChipSeq CTCF_(SC-5916) RawSignal 1 bigWig HudsonAlpha Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeHaibTfbs/wgEncodeHaibTfbsK562CtcfcPcr1xRawRep1V2.bigWig K562 ChipSeq CTCF_(SC-5916) RawSignal 1 bigWig HudsonAlpha Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeHaibTfbs/wgEncodeHaibTfbsK562CtcfcPcr1xRawRep2.bigWig K562 ChipSeq CTCF_(SC-5916) RawSignal 2 bigWig HudsonAlpha Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeHaibTfbs/wgEncodeHaibTfbsK562Ctcflsc98982V0416101AlnRep1.bam K562 ChipSeq CTCFL_(SC-98982) Alignments 1 bam HudsonAlpha Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeHaibTfbs/wgEncodeHaibTfbsK562Ctcflsc98982V0416101AlnRep2.bam K562 ChipSeq CTCFL_(SC-98982) Alignments 2 bam HudsonAlpha Data 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http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeHaibTfbs/wgEncodeHaibTfbsK562E2f6V0416102AlnRep2.bam K562 ChipSeq E2F6 Alignments 2 bam HudsonAlpha Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeHaibTfbs/wgEncodeHaibTfbsK562E2f6V0416102PkRep1.broadPeak.gz K562 ChipSeq E2F6 Peaks 1 broadPeak HudsonAlpha Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeHaibTfbs/wgEncodeHaibTfbsK562E2f6V0416102PkRep2.broadPeak.gz K562 ChipSeq E2F6 Peaks 2 broadPeak HudsonAlpha Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeHaibTfbs/wgEncodeHaibTfbsK562E2f6V0416102RawRep1.bigWig K562 ChipSeq E2F6 RawSignal 1 bigWig HudsonAlpha Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeHaibTfbs/wgEncodeHaibTfbsK562E2f6V0416102RawRep2.bigWig K562 ChipSeq E2F6 RawSignal 2 bigWig HudsonAlpha Data 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http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeHaibTfbs/wgEncodeHaibTfbsK562E2f6sc22823V0416102RawRep2.bigWig K562 ChipSeq E2F6 RawSignal 2 bigWig HudsonAlpha Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeHaibTfbs/wgEncodeHaibTfbsK562Egr1V0416101AlnRep1.bam K562 ChipSeq Egr-1 Alignments 1 bam HudsonAlpha Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeHaibTfbs/wgEncodeHaibTfbsK562Egr1V0416101AlnRep2.bam K562 ChipSeq Egr-1 Alignments 2 bam HudsonAlpha Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeHaibTfbs/wgEncodeHaibTfbsK562Egr1V0416101PkRep1.broadPeak.gz K562 ChipSeq Egr-1 Peaks 1 broadPeak HudsonAlpha Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeHaibTfbs/wgEncodeHaibTfbsK562Egr1V0416101PkRep2.broadPeak.gz K562 ChipSeq Egr-1 Peaks 2 broadPeak HudsonAlpha Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeHaibTfbs/wgEncodeHaibTfbsK562Egr1V0416101RawRep1.bigWig K562 ChipSeq Egr-1 RawSignal 1 bigWig HudsonAlpha Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeHaibTfbs/wgEncodeHaibTfbsK562Egr1V0416101RawRep2.bigWig K562 ChipSeq Egr-1 RawSignal 2 bigWig HudsonAlpha Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeHaibTfbs/wgEncodeHaibTfbsK562Elf1sc631V0416102AlnRep1.bam K562 ChipSeq ELF1_(SC-631) Alignments 1 bam HudsonAlpha Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeHaibTfbs/wgEncodeHaibTfbsK562Elf1sc631V0416102AlnRep2.bam K562 ChipSeq ELF1_(SC-631) Alignments 2 bam HudsonAlpha Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeHaibTfbs/wgEncodeHaibTfbsK562Elf1sc631V0416102PkRep1.broadPeak.gz K562 ChipSeq ELF1_(SC-631) Peaks 1 broadPeak HudsonAlpha Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeHaibTfbs/wgEncodeHaibTfbsK562Elf1sc631V0416102PkRep2.broadPeak.gz K562 ChipSeq ELF1_(SC-631) Peaks 2 broadPeak HudsonAlpha Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeHaibTfbs/wgEncodeHaibTfbsK562Elf1sc631V0416102RawRep1.bigWig K562 ChipSeq ELF1_(SC-631) RawSignal 1 bigWig HudsonAlpha Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeHaibTfbs/wgEncodeHaibTfbsK562Elf1sc631V0416102RawRep2.bigWig K562 ChipSeq ELF1_(SC-631) RawSignal 2 bigWig HudsonAlpha Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeHaibTfbs/wgEncodeHaibTfbsK562Ets1V0416101AlnRep1.bam K562 ChipSeq ETS1 Alignments 1 bam HudsonAlpha Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeHaibTfbs/wgEncodeHaibTfbsK562Ets1V0416101AlnRep2.bam K562 ChipSeq ETS1 Alignments 2 bam HudsonAlpha Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeHaibTfbs/wgEncodeHaibTfbsK562Ets1V0416101PkRep1.broadPeak.gz K562 ChipSeq ETS1 Peaks 1 broadPeak HudsonAlpha Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeHaibTfbs/wgEncodeHaibTfbsK562Ets1V0416101PkRep2.broadPeak.gz K562 ChipSeq ETS1 Peaks 2 broadPeak HudsonAlpha Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeHaibTfbs/wgEncodeHaibTfbsK562Ets1V0416101RawRep1.bigWig K562 ChipSeq ETS1 RawSignal 1 bigWig HudsonAlpha Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeHaibTfbs/wgEncodeHaibTfbsK562Ets1V0416101RawRep2.bigWig K562 ChipSeq ETS1 RawSignal 2 bigWig HudsonAlpha Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeHaibTfbs/wgEncodeHaibTfbsK562Fosl1sc183V0416101AlnRep1.bam K562 ChipSeq FOSL1_(SC-183) Alignments 1 bam HudsonAlpha Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeHaibTfbs/wgEncodeHaibTfbsK562Fosl1sc183V0416101AlnRep2.bam K562 ChipSeq FOSL1_(SC-183) Alignments 2 bam HudsonAlpha Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeHaibTfbs/wgEncodeHaibTfbsK562Fosl1sc183V0416101PkRep1.broadPeak.gz K562 ChipSeq FOSL1_(SC-183) Peaks 1 broadPeak HudsonAlpha Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeHaibTfbs/wgEncodeHaibTfbsK562Fosl1sc183V0416101PkRep2.broadPeak.gz K562 ChipSeq FOSL1_(SC-183) Peaks 2 broadPeak HudsonAlpha Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeHaibTfbs/wgEncodeHaibTfbsK562Fosl1sc183V0416101RawRep1.bigWig K562 ChipSeq FOSL1_(SC-183) RawSignal 1 bigWig HudsonAlpha Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeHaibTfbs/wgEncodeHaibTfbsK562Fosl1sc183V0416101RawRep2.bigWig K562 ChipSeq FOSL1_(SC-183) RawSignal 2 bigWig HudsonAlpha Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeHaibTfbs/wgEncodeHaibTfbsK562GabpV0416101AlnRep1.bam K562 ChipSeq GABP Alignments 1 bam HudsonAlpha Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeHaibTfbs/wgEncodeHaibTfbsK562GabpV0416101AlnRep2.bam K562 ChipSeq GABP Alignments 2 bam HudsonAlpha Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeHaibTfbs/wgEncodeHaibTfbsK562GabpV0416101PkRep1.broadPeak.gz K562 ChipSeq GABP Peaks 1 broadPeak HudsonAlpha Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeHaibTfbs/wgEncodeHaibTfbsK562GabpV0416101PkRep2.broadPeak.gz K562 ChipSeq GABP Peaks 2 broadPeak HudsonAlpha Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeHaibTfbs/wgEncodeHaibTfbsK562GabpV0416101RawRep1.bigWig K562 ChipSeq GABP RawSignal 1 bigWig HudsonAlpha Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeHaibTfbs/wgEncodeHaibTfbsK562GabpV0416101RawRep2.bigWig K562 ChipSeq GABP RawSignal 2 bigWig HudsonAlpha Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeHaibTfbs/wgEncodeHaibTfbsK562Gata2sc267Pcr1xAlnRep1.bam K562 ChipSeq GATA2_(SC-267) Alignments 1 bam HudsonAlpha Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeHaibTfbs/wgEncodeHaibTfbsK562Gata2sc267Pcr1xAlnRep2.bam K562 ChipSeq GATA2_(SC-267) Alignments 2 bam HudsonAlpha Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeHaibTfbs/wgEncodeHaibTfbsK562Gata2sc267Pcr1xPkRep1.broadPeak.gz K562 ChipSeq GATA2_(SC-267) Peaks 1 broadPeak HudsonAlpha Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeHaibTfbs/wgEncodeHaibTfbsK562Gata2sc267Pcr1xPkRep2.broadPeak.gz K562 ChipSeq GATA2_(SC-267) Peaks 2 broadPeak HudsonAlpha Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeHaibTfbs/wgEncodeHaibTfbsK562Gata2sc267Pcr1xRawRep1.bigWig K562 ChipSeq GATA2_(SC-267) RawSignal 1 bigWig HudsonAlpha Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeHaibTfbs/wgEncodeHaibTfbsK562Gata2sc267Pcr1xRawRep2.bigWig K562 ChipSeq GATA2_(SC-267) RawSignal 2 bigWig HudsonAlpha Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeHaibTfbs/wgEncodeHaibTfbsK562Hdac2sc6296V0416102AlnRep1.bam K562 ChipSeq HDAC2_(SC-6296) Alignments 1 bam HudsonAlpha Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeHaibTfbs/wgEncodeHaibTfbsK562Hdac2sc6296V0416102AlnRep2.bam K562 ChipSeq HDAC2_(SC-6296) Alignments 2 bam HudsonAlpha Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeHaibTfbs/wgEncodeHaibTfbsK562Hdac2sc6296V0416102PkRep1.broadPeak.gz K562 ChipSeq HDAC2_(SC-6296) Peaks 1 broadPeak HudsonAlpha Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeHaibTfbs/wgEncodeHaibTfbsK562Hdac2sc6296V0416102PkRep2.broadPeak.gz K562 ChipSeq HDAC2_(SC-6296) Peaks 2 broadPeak HudsonAlpha Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeHaibTfbs/wgEncodeHaibTfbsK562Hdac2sc6296V0416102RawRep1.bigWig K562 ChipSeq HDAC2_(SC-6296) RawSignal 1 bigWig HudsonAlpha Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeHaibTfbs/wgEncodeHaibTfbsK562Hdac2sc6296V0416102RawRep2.bigWig K562 ChipSeq HDAC2_(SC-6296) RawSignal 2 bigWig HudsonAlpha Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeHaibTfbs/wgEncodeHaibTfbsK562Hey1Pcr1xAlnRep1.bam K562 ChipSeq HEY1 Alignments 1 bam HudsonAlpha Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeHaibTfbs/wgEncodeHaibTfbsK562Hey1Pcr1xAlnRep2.bam K562 ChipSeq HEY1 Alignments 2 bam HudsonAlpha Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeHaibTfbs/wgEncodeHaibTfbsK562Hey1Pcr1xPkRep1.broadPeak.gz K562 ChipSeq HEY1 Peaks 1 broadPeak HudsonAlpha Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeHaibTfbs/wgEncodeHaibTfbsK562Hey1Pcr1xPkRep2.broadPeak.gz K562 ChipSeq HEY1 Peaks 2 broadPeak HudsonAlpha Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeHaibTfbs/wgEncodeHaibTfbsK562Hey1Pcr1xRawRep1.bigWig K562 ChipSeq HEY1 RawSignal 1 bigWig HudsonAlpha Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeHaibTfbs/wgEncodeHaibTfbsK562Hey1Pcr1xRawRep2.bigWig K562 ChipSeq HEY1 RawSignal 2 bigWig HudsonAlpha Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeHaibTfbs/wgEncodeHaibTfbsK562MaxV0416102AlnRep1.bam K562 ChipSeq Max Alignments 1 bam HudsonAlpha Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeHaibTfbs/wgEncodeHaibTfbsK562MaxV0416102AlnRep2.bam K562 ChipSeq Max Alignments 2 bam HudsonAlpha Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeHaibTfbs/wgEncodeHaibTfbsK562MaxV0416102PkRep1.broadPeak.gz K562 ChipSeq Max Peaks 1 broadPeak HudsonAlpha Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeHaibTfbs/wgEncodeHaibTfbsK562MaxV0416102PkRep2.broadPeak.gz K562 ChipSeq Max Peaks 2 broadPeak HudsonAlpha Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeHaibTfbs/wgEncodeHaibTfbsK562MaxV0416102RawRep1.bigWig K562 ChipSeq Max RawSignal 1 bigWig HudsonAlpha Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeHaibTfbs/wgEncodeHaibTfbsK562MaxV0416102RawRep2.bigWig K562 ChipSeq Max RawSignal 2 bigWig HudsonAlpha Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeHaibTfbs/wgEncodeHaibTfbsK562Mef2aV0416101AlnRep1.bam K562 ChipSeq MEF2A Alignments 1 bam HudsonAlpha Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeHaibTfbs/wgEncodeHaibTfbsK562Mef2aV0416101AlnRep2.bam K562 ChipSeq MEF2A Alignments 2 bam HudsonAlpha Data 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http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeHaibTfbs/wgEncodeHaibTfbsK562Taf1V0416101AlnRep2.bam K562 ChipSeq TAF1 Alignments 2 bam HudsonAlpha Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeHaibTfbs/wgEncodeHaibTfbsK562Taf1V0416101PkRep1.broadPeak.gz K562 ChipSeq TAF1 Peaks 1 broadPeak HudsonAlpha Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeHaibTfbs/wgEncodeHaibTfbsK562Taf1V0416101PkRep2.broadPeak.gz K562 ChipSeq TAF1 Peaks 2 broadPeak HudsonAlpha Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeHaibTfbs/wgEncodeHaibTfbsK562Taf1V0416101RawRep1.bigWig K562 ChipSeq TAF1 RawSignal 1 bigWig HudsonAlpha Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeHaibTfbs/wgEncodeHaibTfbsK562Taf1V0416101RawRep2.bigWig K562 ChipSeq TAF1 RawSignal 2 bigWig HudsonAlpha Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeHaibTfbs/wgEncodeHaibTfbsK562Taf7sc101167V0416101AlnRep1.bam K562 ChipSeq TAF7_(SC-101167) Alignments 1 bam HudsonAlpha Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeHaibTfbs/wgEncodeHaibTfbsK562Taf7sc101167V0416101AlnRep2.bam K562 ChipSeq TAF7_(SC-101167) Alignments 2 bam HudsonAlpha Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeHaibTfbs/wgEncodeHaibTfbsK562Taf7sc101167V0416101PkRep1.broadPeak.gz K562 ChipSeq TAF7_(SC-101167) Peaks 1 broadPeak HudsonAlpha Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeHaibTfbs/wgEncodeHaibTfbsK562Taf7sc101167V0416101PkRep2.broadPeak.gz K562 ChipSeq TAF7_(SC-101167) Peaks 2 broadPeak HudsonAlpha Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeHaibTfbs/wgEncodeHaibTfbsK562Taf7sc101167V0416101RawRep1.bigWig K562 ChipSeq TAF7_(SC-101167) RawSignal 1 bigWig HudsonAlpha Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeHaibTfbs/wgEncodeHaibTfbsK562Taf7sc101167V0416101RawRep2.bigWig K562 ChipSeq TAF7_(SC-101167) RawSignal 2 bigWig HudsonAlpha Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeHaibTfbs/wgEncodeHaibTfbsK562Tead4sc101184V0422111AlnRep1.bam K562 ChipSeq TEAD4_(SC-101184) Alignments 1 bam HudsonAlpha Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeHaibTfbs/wgEncodeHaibTfbsK562Tead4sc101184V0422111AlnRep2.bam K562 ChipSeq TEAD4_(SC-101184) Alignments 2 bam HudsonAlpha Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeHaibTfbs/wgEncodeHaibTfbsK562Tead4sc101184V0422111PkRep1.broadPeak.gz K562 ChipSeq TEAD4_(SC-101184) Peaks 1 broadPeak HudsonAlpha Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeHaibTfbs/wgEncodeHaibTfbsK562Tead4sc101184V0422111PkRep2.broadPeak.gz K562 ChipSeq TEAD4_(SC-101184) Peaks 2 broadPeak HudsonAlpha Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeHaibTfbs/wgEncodeHaibTfbsK562Tead4sc101184V0422111RawRep1.bigWig K562 ChipSeq TEAD4_(SC-101184) RawSignal 1 bigWig HudsonAlpha Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeHaibTfbs/wgEncodeHaibTfbsK562Tead4sc101184V0422111RawRep2.bigWig K562 ChipSeq TEAD4_(SC-101184) RawSignal 2 bigWig HudsonAlpha Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeHaibTfbs/wgEncodeHaibTfbsK562Thap1sc98174V0416101AlnRep1.bam K562 ChipSeq THAP1_(SC-98174) Alignments 1 bam HudsonAlpha Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeHaibTfbs/wgEncodeHaibTfbsK562Thap1sc98174V0416101AlnRep2.bam K562 ChipSeq THAP1_(SC-98174) Alignments 2 bam HudsonAlpha Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeHaibTfbs/wgEncodeHaibTfbsK562Thap1sc98174V0416101PkRep1.broadPeak.gz K562 ChipSeq THAP1_(SC-98174) Peaks 1 broadPeak HudsonAlpha Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeHaibTfbs/wgEncodeHaibTfbsK562Thap1sc98174V0416101PkRep2.broadPeak.gz K562 ChipSeq THAP1_(SC-98174) Peaks 2 broadPeak HudsonAlpha Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeHaibTfbs/wgEncodeHaibTfbsK562Thap1sc98174V0416101RawRep1.bigWig K562 ChipSeq THAP1_(SC-98174) RawSignal 1 bigWig HudsonAlpha Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeHaibTfbs/wgEncodeHaibTfbsK562Thap1sc98174V0416101RawRep2.bigWig K562 ChipSeq THAP1_(SC-98174) RawSignal 2 bigWig HudsonAlpha Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeHaibTfbs/wgEncodeHaibTfbsK562Trim28sc81411V0422111AlnRep1.bam K562 ChipSeq TRIM28_(SC-81411) Alignments 1 bam HudsonAlpha Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeHaibTfbs/wgEncodeHaibTfbsK562Trim28sc81411V0422111AlnRep2.bam K562 ChipSeq TRIM28_(SC-81411) Alignments 2 bam HudsonAlpha Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeHaibTfbs/wgEncodeHaibTfbsK562Trim28sc81411V0422111PkRep1.broadPeak.gz K562 ChipSeq TRIM28_(SC-81411) Peaks 1 broadPeak HudsonAlpha Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeHaibTfbs/wgEncodeHaibTfbsK562Trim28sc81411V0422111PkRep2.broadPeak.gz K562 ChipSeq TRIM28_(SC-81411) Peaks 2 broadPeak HudsonAlpha Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeHaibTfbs/wgEncodeHaibTfbsK562Trim28sc81411V0422111RawRep1.bigWig K562 ChipSeq TRIM28_(SC-81411) RawSignal 1 bigWig HudsonAlpha Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeHaibTfbs/wgEncodeHaibTfbsK562Trim28sc81411V0422111RawRep2.bigWig K562 ChipSeq TRIM28_(SC-81411) RawSignal 2 bigWig HudsonAlpha Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeHaibTfbs/wgEncodeHaibTfbsK562Usf1V0416101AlnRep1.bam K562 ChipSeq USF-1 Alignments 1 bam HudsonAlpha Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeHaibTfbs/wgEncodeHaibTfbsK562Usf1V0416101AlnRep2.bam K562 ChipSeq USF-1 Alignments 2 bam HudsonAlpha Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeHaibTfbs/wgEncodeHaibTfbsK562Usf1V0416101PkRep1.broadPeak.gz K562 ChipSeq USF-1 Peaks 1 broadPeak HudsonAlpha Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeHaibTfbs/wgEncodeHaibTfbsK562Usf1V0416101PkRep2.broadPeak.gz K562 ChipSeq USF-1 Peaks 2 broadPeak HudsonAlpha Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeHaibTfbs/wgEncodeHaibTfbsK562Usf1V0416101RawRep1.bigWig K562 ChipSeq USF-1 RawSignal 1 bigWig HudsonAlpha Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeHaibTfbs/wgEncodeHaibTfbsK562Usf1V0416101RawRep2.bigWig K562 ChipSeq USF-1 RawSignal 2 bigWig HudsonAlpha Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeHaibTfbs/wgEncodeHaibTfbsK562Yy1V0416101AlnRep1.bam K562 ChipSeq YY1_(SC-281) Alignments 1 bam HudsonAlpha Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeHaibTfbs/wgEncodeHaibTfbsK562Yy1V0416101AlnRep2.bam K562 ChipSeq YY1_(SC-281) Alignments 2 bam HudsonAlpha Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeHaibTfbs/wgEncodeHaibTfbsK562Yy1V0416101PkRep1.broadPeak.gz K562 ChipSeq YY1_(SC-281) Peaks 1 broadPeak HudsonAlpha Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeHaibTfbs/wgEncodeHaibTfbsK562Yy1V0416101PkRep2.broadPeak.gz K562 ChipSeq YY1_(SC-281) Peaks 2 broadPeak HudsonAlpha Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeHaibTfbs/wgEncodeHaibTfbsK562Yy1V0416101RawRep1.bigWig K562 ChipSeq YY1_(SC-281) RawSignal 1 bigWig HudsonAlpha Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeHaibTfbs/wgEncodeHaibTfbsK562Yy1V0416101RawRep2.bigWig K562 ChipSeq YY1_(SC-281) RawSignal 2 bigWig HudsonAlpha Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeHaibTfbs/wgEncodeHaibTfbsK562Yy1V0416102AlnRep1.bam K562 ChipSeq YY1 Alignments 1 bam HudsonAlpha Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeHaibTfbs/wgEncodeHaibTfbsK562Yy1V0416102AlnRep2.bam K562 ChipSeq YY1 Alignments 2 bam HudsonAlpha Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeHaibTfbs/wgEncodeHaibTfbsK562Yy1V0416102PkRep1.broadPeak.gz K562 ChipSeq YY1 Peaks 1 broadPeak HudsonAlpha Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeHaibTfbs/wgEncodeHaibTfbsK562Yy1V0416102PkRep2.broadPeak.gz K562 ChipSeq YY1 Peaks 2 broadPeak HudsonAlpha Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeHaibTfbs/wgEncodeHaibTfbsK562Yy1V0416102RawRep1.bigWig K562 ChipSeq YY1 RawSignal 1 bigWig HudsonAlpha Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeHaibTfbs/wgEncodeHaibTfbsK562Yy1V0416102RawRep2.bigWig K562 ChipSeq YY1 RawSignal 2 bigWig HudsonAlpha Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeHaibTfbs/wgEncodeHaibTfbsK562Yy1sc281V0416101AlnRep1.bam K562 ChipSeq YY1_(SC-281) Alignments 1 bam HudsonAlpha Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeHaibTfbs/wgEncodeHaibTfbsK562Yy1sc281V0416101AlnRep2.bam K562 ChipSeq YY1_(SC-281) Alignments 2 bam HudsonAlpha Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeHaibTfbs/wgEncodeHaibTfbsK562Yy1sc281V0416101PkRep1.broadPeak.gz K562 ChipSeq YY1_(SC-281) Peaks 1 broadPeak HudsonAlpha Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeHaibTfbs/wgEncodeHaibTfbsK562Yy1sc281V0416101PkRep2.broadPeak.gz K562 ChipSeq YY1_(SC-281) Peaks 2 broadPeak HudsonAlpha Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeHaibTfbs/wgEncodeHaibTfbsK562Yy1sc281V0416101RawRep1.bigWig K562 ChipSeq YY1_(SC-281) RawSignal 1 bigWig HudsonAlpha Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeHaibTfbs/wgEncodeHaibTfbsK562Yy1sc281V0416101RawRep2.bigWig K562 ChipSeq YY1_(SC-281) RawSignal 2 bigWig HudsonAlpha Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeHaibTfbs/wgEncodeHaibTfbsK562Zbtb33Pcr1xAlnRep1.bam K562 ChipSeq ZBTB33 Alignments 1 bam HudsonAlpha Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeHaibTfbs/wgEncodeHaibTfbsK562Zbtb33Pcr1xAlnRep2.bam K562 ChipSeq ZBTB33 Alignments 2 bam HudsonAlpha Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeHaibTfbs/wgEncodeHaibTfbsK562Zbtb33Pcr1xPkRep1.broadPeak.gz K562 ChipSeq ZBTB33 Peaks 1 broadPeak HudsonAlpha Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeHaibTfbs/wgEncodeHaibTfbsK562Zbtb33Pcr1xPkRep2.broadPeak.gz K562 ChipSeq ZBTB33 Peaks 2 broadPeak HudsonAlpha Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeHaibTfbs/wgEncodeHaibTfbsK562Zbtb33Pcr1xRawRep1.bigWig K562 ChipSeq ZBTB33 RawSignal 1 bigWig HudsonAlpha Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeHaibTfbs/wgEncodeHaibTfbsK562Zbtb33Pcr1xRawRep2.bigWig K562 ChipSeq ZBTB33 RawSignal 2 bigWig HudsonAlpha Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeHaibTfbs/wgEncodeHaibTfbsK562Zbtb7asc34508V0416101AlnRep1.bam K562 ChipSeq ZBTB7A_(SC-34508) Alignments 1 bam HudsonAlpha Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeHaibTfbs/wgEncodeHaibTfbsK562Zbtb7asc34508V0416101AlnRep2.bam K562 ChipSeq ZBTB7A_(SC-34508) Alignments 2 bam HudsonAlpha Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeHaibTfbs/wgEncodeHaibTfbsK562Zbtb7asc34508V0416101PkRep1.broadPeak.gz K562 ChipSeq ZBTB7A_(SC-34508) Peaks 1 broadPeak HudsonAlpha Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeHaibTfbs/wgEncodeHaibTfbsK562Zbtb7asc34508V0416101PkRep2.broadPeak.gz K562 ChipSeq ZBTB7A_(SC-34508) Peaks 2 broadPeak HudsonAlpha Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeHaibTfbs/wgEncodeHaibTfbsK562Zbtb7asc34508V0416101RawRep1.bigWig K562 ChipSeq ZBTB7A_(SC-34508) RawSignal 1 bigWig HudsonAlpha Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeHaibTfbs/wgEncodeHaibTfbsK562Zbtb7asc34508V0416101RawRep2.bigWig K562 ChipSeq ZBTB7A_(SC-34508) RawSignal 2 bigWig HudsonAlpha Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeHaibTfbs/wgEncodeHaibTfbsMcf7Cebpbsc150V0422111AlnRep1.bam MCF-7 ChipSeq CEBPB_(SC-150) Alignments 1 bam HudsonAlpha Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeHaibTfbs/wgEncodeHaibTfbsMcf7Cebpbsc150V0422111AlnRep2.bam MCF-7 ChipSeq CEBPB_(SC-150) Alignments 2 bam HudsonAlpha Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeHaibTfbs/wgEncodeHaibTfbsMcf7Cebpbsc150V0422111PkRep1.broadPeak.gz MCF-7 ChipSeq CEBPB_(SC-150) Peaks 1 broadPeak HudsonAlpha Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeHaibTfbs/wgEncodeHaibTfbsMcf7Cebpbsc150V0422111PkRep2.broadPeak.gz MCF-7 ChipSeq CEBPB_(SC-150) Peaks 2 broadPeak HudsonAlpha Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeHaibTfbs/wgEncodeHaibTfbsMcf7Cebpbsc150V0422111RawRep1.bigWig MCF-7 ChipSeq CEBPB_(SC-150) RawSignal 1 bigWig HudsonAlpha Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeHaibTfbs/wgEncodeHaibTfbsMcf7Cebpbsc150V0422111RawRep2.bigWig MCF-7 ChipSeq CEBPB_(SC-150) RawSignal 2 bigWig HudsonAlpha Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeHaibTfbs/wgEncodeHaibTfbsMcf7CtcfcV0422111AlnRep1.bam MCF-7 ChipSeq CTCF_(SC-5916) Alignments 1 bam HudsonAlpha Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeHaibTfbs/wgEncodeHaibTfbsMcf7CtcfcV0422111AlnRep2.bam MCF-7 ChipSeq CTCF_(SC-5916) Alignments 2 bam HudsonAlpha Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeHaibTfbs/wgEncodeHaibTfbsMcf7CtcfcV0422111PkRep1.broadPeak.gz MCF-7 ChipSeq CTCF_(SC-5916) Peaks 1 broadPeak HudsonAlpha Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeHaibTfbs/wgEncodeHaibTfbsMcf7CtcfcV0422111PkRep2.broadPeak.gz MCF-7 ChipSeq CTCF_(SC-5916) Peaks 2 broadPeak HudsonAlpha Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeHaibTfbs/wgEncodeHaibTfbsMcf7CtcfcV0422111RawRep1.bigWig MCF-7 ChipSeq CTCF_(SC-5916) RawSignal 1 bigWig HudsonAlpha Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeHaibTfbs/wgEncodeHaibTfbsMcf7CtcfcV0422111RawRep2.bigWig MCF-7 ChipSeq CTCF_(SC-5916) RawSignal 2 bigWig HudsonAlpha Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeHaibTfbs/wgEncodeHaibTfbsMcf7Egr1V0422111AlnRep1.bam MCF-7 ChipSeq Egr-1 Alignments 1 bam HudsonAlpha Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeHaibTfbs/wgEncodeHaibTfbsMcf7Egr1V0422111AlnRep2.bam MCF-7 ChipSeq Egr-1 Alignments 2 bam HudsonAlpha Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeHaibTfbs/wgEncodeHaibTfbsMcf7Egr1V0422111PkRep1.broadPeak.gz MCF-7 ChipSeq Egr-1 Peaks 1 broadPeak HudsonAlpha Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeHaibTfbs/wgEncodeHaibTfbsMcf7Egr1V0422111PkRep2.broadPeak.gz MCF-7 ChipSeq Egr-1 Peaks 2 broadPeak HudsonAlpha Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeHaibTfbs/wgEncodeHaibTfbsMcf7Egr1V0422111RawRep1.bigWig MCF-7 ChipSeq Egr-1 RawSignal 1 bigWig HudsonAlpha Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeHaibTfbs/wgEncodeHaibTfbsMcf7Egr1V0422111RawRep2.bigWig MCF-7 ChipSeq Egr-1 RawSignal 2 bigWig HudsonAlpha Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeHaibTfbs/wgEncodeHaibTfbsMcf7Elf1V0422111AlnRep1.bam MCF-7 ChipSeq ELF1_(SC-631) Alignments 1 bam HudsonAlpha Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeHaibTfbs/wgEncodeHaibTfbsMcf7Elf1V0422111AlnRep2.bam MCF-7 ChipSeq ELF1_(SC-631) Alignments 2 bam HudsonAlpha Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeHaibTfbs/wgEncodeHaibTfbsMcf7Elf1V0422111PkRep1.broadPeak.gz MCF-7 ChipSeq ELF1_(SC-631) Peaks 1 broadPeak HudsonAlpha Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeHaibTfbs/wgEncodeHaibTfbsMcf7Elf1V0422111PkRep2.broadPeak.gz MCF-7 ChipSeq ELF1_(SC-631) Peaks 2 broadPeak HudsonAlpha Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeHaibTfbs/wgEncodeHaibTfbsMcf7Elf1V0422111RawRep1.bigWig MCF-7 ChipSeq ELF1_(SC-631) RawSignal 1 bigWig HudsonAlpha Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeHaibTfbs/wgEncodeHaibTfbsMcf7Elf1V0422111RawRep2.bigWig MCF-7 ChipSeq ELF1_(SC-631) RawSignal 2 bigWig HudsonAlpha Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeHaibTfbs/wgEncodeHaibTfbsMcf7Fosl2V0422111AlnRep1.bam MCF-7 ChipSeq FOSL2 Alignments 1 bam HudsonAlpha Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeHaibTfbs/wgEncodeHaibTfbsMcf7Fosl2V0422111AlnRep2.bam MCF-7 ChipSeq FOSL2 Alignments 2 bam HudsonAlpha Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeHaibTfbs/wgEncodeHaibTfbsMcf7Fosl2V0422111PkRep1.broadPeak.gz MCF-7 ChipSeq FOSL2 Peaks 1 broadPeak HudsonAlpha Data 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http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeHaibTfbs/wgEncodeHaibTfbsMcf7GabpV0422111AlnRep2.bam MCF-7 ChipSeq GABP Alignments 2 bam HudsonAlpha Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeHaibTfbs/wgEncodeHaibTfbsMcf7GabpV0422111PkRep1.broadPeak.gz MCF-7 ChipSeq GABP Peaks 1 broadPeak HudsonAlpha Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeHaibTfbs/wgEncodeHaibTfbsMcf7GabpV0422111PkRep2.broadPeak.gz MCF-7 ChipSeq GABP Peaks 2 broadPeak HudsonAlpha Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeHaibTfbs/wgEncodeHaibTfbsMcf7GabpV0422111RawRep1.bigWig MCF-7 ChipSeq GABP RawSignal 1 bigWig HudsonAlpha Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeHaibTfbs/wgEncodeHaibTfbsMcf7GabpV0422111RawRep2.bigWig MCF-7 ChipSeq GABP RawSignal 2 bigWig HudsonAlpha Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeHaibTfbs/wgEncodeHaibTfbsMcf7Gata3V0422111AlnRep1.bam MCF-7 ChipSeq GATA3_(SC-268) Alignments 1 bam HudsonAlpha Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeHaibTfbs/wgEncodeHaibTfbsMcf7Gata3V0422111AlnRep2.bam MCF-7 ChipSeq GATA3_(SC-268) Alignments 2 bam HudsonAlpha Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeHaibTfbs/wgEncodeHaibTfbsMcf7Gata3V0422111PkRep1.broadPeak.gz MCF-7 ChipSeq GATA3_(SC-268) Peaks 1 broadPeak HudsonAlpha Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeHaibTfbs/wgEncodeHaibTfbsMcf7Gata3V0422111PkRep2.broadPeak.gz MCF-7 ChipSeq GATA3_(SC-268) Peaks 2 broadPeak HudsonAlpha Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeHaibTfbs/wgEncodeHaibTfbsMcf7Gata3V0422111RawRep1.bigWig MCF-7 ChipSeq GATA3_(SC-268) RawSignal 1 bigWig HudsonAlpha Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeHaibTfbs/wgEncodeHaibTfbsMcf7Gata3V0422111RawRep2.bigWig MCF-7 ChipSeq GATA3_(SC-268) RawSignal 2 bigWig HudsonAlpha Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeHaibTfbs/wgEncodeHaibTfbsMcf7Hdac2sc6296V0422111AlnRep1.bam MCF-7 ChipSeq HDAC2_(SC-6296) Alignments 1 bam HudsonAlpha Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeHaibTfbs/wgEncodeHaibTfbsMcf7Hdac2sc6296V0422111AlnRep2.bam MCF-7 ChipSeq HDAC2_(SC-6296) Alignments 2 bam HudsonAlpha Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeHaibTfbs/wgEncodeHaibTfbsMcf7Hdac2sc6296V0422111PkRep1.broadPeak.gz MCF-7 ChipSeq HDAC2_(SC-6296) Peaks 1 broadPeak HudsonAlpha Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeHaibTfbs/wgEncodeHaibTfbsMcf7Hdac2sc6296V0422111PkRep2.broadPeak.gz MCF-7 ChipSeq HDAC2_(SC-6296) Peaks 2 broadPeak HudsonAlpha Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeHaibTfbs/wgEncodeHaibTfbsMcf7Hdac2sc6296V0422111RawRep1.bigWig MCF-7 ChipSeq HDAC2_(SC-6296) RawSignal 1 bigWig HudsonAlpha Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeHaibTfbs/wgEncodeHaibTfbsMcf7Hdac2sc6296V0422111RawRep2.bigWig MCF-7 ChipSeq HDAC2_(SC-6296) RawSignal 2 bigWig HudsonAlpha Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeHaibTfbs/wgEncodeHaibTfbsMcf7JundV0422111AlnRep1.bam MCF-7 ChipSeq JunD Alignments 1 bam HudsonAlpha Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeHaibTfbs/wgEncodeHaibTfbsMcf7JundV0422111AlnRep2.bam MCF-7 ChipSeq JunD Alignments 2 bam HudsonAlpha Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeHaibTfbs/wgEncodeHaibTfbsMcf7JundV0422111PkRep1.broadPeak.gz MCF-7 ChipSeq JunD Peaks 1 broadPeak HudsonAlpha Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeHaibTfbs/wgEncodeHaibTfbsMcf7JundV0422111PkRep2.broadPeak.gz MCF-7 ChipSeq JunD Peaks 2 broadPeak HudsonAlpha Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeHaibTfbs/wgEncodeHaibTfbsMcf7JundV0422111RawRep1.bigWig MCF-7 ChipSeq JunD RawSignal 1 bigWig HudsonAlpha Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeHaibTfbs/wgEncodeHaibTfbsMcf7JundV0422111RawRep2.bigWig MCF-7 ChipSeq JunD RawSignal 2 bigWig HudsonAlpha Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeHaibTfbs/wgEncodeHaibTfbsMcf7MaxV0422111AlnRep1.bam MCF-7 ChipSeq Max Alignments 1 bam HudsonAlpha Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeHaibTfbs/wgEncodeHaibTfbsMcf7MaxV0422111AlnRep2.bam MCF-7 ChipSeq Max Alignments 2 bam HudsonAlpha Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeHaibTfbs/wgEncodeHaibTfbsMcf7MaxV0422111PkRep1.broadPeak.gz MCF-7 ChipSeq Max Peaks 1 broadPeak HudsonAlpha Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeHaibTfbs/wgEncodeHaibTfbsMcf7MaxV0422111PkRep2.broadPeak.gz MCF-7 ChipSeq Max Peaks 2 broadPeak HudsonAlpha Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeHaibTfbs/wgEncodeHaibTfbsMcf7MaxV0422111RawRep1.bigWig MCF-7 ChipSeq Max RawSignal 1 bigWig HudsonAlpha Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeHaibTfbs/wgEncodeHaibTfbsMcf7MaxV0422111RawRep2.bigWig MCF-7 ChipSeq Max RawSignal 2 bigWig HudsonAlpha Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeHaibTfbs/wgEncodeHaibTfbsMcf7Nr2f2sc271940V0422111AlnRep1.bam MCF-7 ChipSeq NR2F2_(SC-271940) Alignments 1 bam HudsonAlpha Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeHaibTfbs/wgEncodeHaibTfbsMcf7Nr2f2sc271940V0422111AlnRep2.bam MCF-7 ChipSeq NR2F2_(SC-271940) Alignments 2 bam HudsonAlpha Data 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MCF-7 ChipSeq p300 Alignments 1 bam HudsonAlpha Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeHaibTfbs/wgEncodeHaibTfbsMcf7P300V0422111AlnRep2.bam MCF-7 ChipSeq p300 Alignments 2 bam HudsonAlpha Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeHaibTfbs/wgEncodeHaibTfbsMcf7P300V0422111PkRep1.broadPeak.gz MCF-7 ChipSeq p300 Peaks 1 broadPeak HudsonAlpha Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeHaibTfbs/wgEncodeHaibTfbsMcf7P300V0422111PkRep2.broadPeak.gz MCF-7 ChipSeq p300 Peaks 2 broadPeak HudsonAlpha Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeHaibTfbs/wgEncodeHaibTfbsMcf7P300V0422111RawRep1.bigWig MCF-7 ChipSeq p300 RawSignal 1 bigWig HudsonAlpha Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeHaibTfbs/wgEncodeHaibTfbsMcf7P300V0422111RawRep2.bigWig MCF-7 ChipSeq p300 RawSignal 2 bigWig HudsonAlpha Data 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http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeHaibTfbs/wgEncodeHaibTfbsMcf7Rad21V0422111RawRep1.bigWig MCF-7 ChipSeq Rad21 RawSignal 1 bigWig HudsonAlpha Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeHaibTfbs/wgEncodeHaibTfbsMcf7Rad21V0422111RawRep2.bigWig MCF-7 ChipSeq Rad21 RawSignal 2 bigWig HudsonAlpha Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeHaibTfbs/wgEncodeHaibTfbsMcf7RxlchV0422111AlnRep1.bam MCF-7 ChipSeq RevXlinkChromatin Alignments 1 bam HudsonAlpha Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeHaibTfbs/wgEncodeHaibTfbsMcf7RxlchV0422111AlnRep2.bam MCF-7 ChipSeq RevXlinkChromatin Alignments 2 bam HudsonAlpha Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeHaibTfbs/wgEncodeHaibTfbsMcf7RxlchV0422111AlnRep3.bam MCF-7 ChipSeq RevXlinkChromatin Alignments 3 bam HudsonAlpha Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeHaibTfbs/wgEncodeHaibTfbsMcf7RxlchV0422111AlnRep4.bam MCF-7 ChipSeq RevXlinkChromatin Alignments 4 bam HudsonAlpha Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeHaibTfbs/wgEncodeHaibTfbsMcf7RxlchV0422111RawRep1.bigWig MCF-7 ChipSeq RevXlinkChromatin RawSignal 1 bigWig HudsonAlpha Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeHaibTfbs/wgEncodeHaibTfbsMcf7RxlchV0422111RawRep2.bigWig MCF-7 ChipSeq RevXlinkChromatin RawSignal 2 bigWig HudsonAlpha Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeHaibTfbs/wgEncodeHaibTfbsMcf7RxlchV0422111RawRep3.bigWig MCF-7 ChipSeq RevXlinkChromatin RawSignal 3 bigWig HudsonAlpha Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeHaibTfbs/wgEncodeHaibTfbsMcf7RxlchV0422111RawRep4.bigWig MCF-7 ChipSeq RevXlinkChromatin RawSignal 4 bigWig HudsonAlpha Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeHaibTfbs/wgEncodeHaibTfbsMcf7Sin3ak20V0422111AlnRep1.bam MCF-7 ChipSeq Sin3Ak-20 Alignments 1 bam HudsonAlpha Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeHaibTfbs/wgEncodeHaibTfbsMcf7Sin3ak20V0422111AlnRep2.bam MCF-7 ChipSeq Sin3Ak-20 Alignments 2 bam HudsonAlpha Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeHaibTfbs/wgEncodeHaibTfbsMcf7Sin3ak20V0422111PkRep1.broadPeak.gz MCF-7 ChipSeq Sin3Ak-20 Peaks 1 broadPeak HudsonAlpha Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeHaibTfbs/wgEncodeHaibTfbsMcf7Sin3ak20V0422111PkRep2.broadPeak.gz MCF-7 ChipSeq Sin3Ak-20 Peaks 2 broadPeak HudsonAlpha Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeHaibTfbs/wgEncodeHaibTfbsMcf7Sin3ak20V0422111RawRep1.bigWig MCF-7 ChipSeq Sin3Ak-20 RawSignal 1 bigWig HudsonAlpha Data 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http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeOpenChromChip/wgEncodeOpenChromChipGm12878CtcfSig.bigWig GM12878 ChipSeq CTCF Signal bigWig UT-A Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeOpenChromChip/wgEncodeOpenChromChipGm12878InputAln.bam GM12878 ChipSeq Input Alignments bam UT-A Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeOpenChromChip/wgEncodeOpenChromChipGm12878InputSig.bigWig GM12878 ChipSeq Input Signal bigWig UT-A Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeOpenChromChip/wgEncodeOpenChromChipGm12878Pol2AlnRep1.bam GM12878 ChipSeq Pol2 Alignments 1 bam UT-A Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeOpenChromChip/wgEncodeOpenChromChipGm12878Pol2AlnRep2.bam GM12878 ChipSeq Pol2 Alignments 2 bam UT-A Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeOpenChromChip/wgEncodeOpenChromChipGm12878Pol2BaseOverlapSignal.bigWig GM12878 ChipSeq Pol2 Base_Overlap_Signal bigWig UT-A Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeOpenChromChip/wgEncodeOpenChromChipGm12878Pol2Pk.narrowPeak.gz GM12878 ChipSeq Pol2 Peaks narrowPeak UT-A Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeOpenChromChip/wgEncodeOpenChromChipGm12878Pol2Sig.bigWig GM12878 ChipSeq Pol2 Signal bigWig UT-A Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeOpenChromChip/wgEncodeOpenChromChipGm12891CtcfAlnRep1.bam GM12891 ChipSeq CTCF Alignments 1 bam UT-A Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeOpenChromChip/wgEncodeOpenChromChipGm12891CtcfAlnRep2.bam GM12891 ChipSeq CTCF Alignments 2 bam UT-A Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeOpenChromChip/wgEncodeOpenChromChipGm12891CtcfBaseOverlapSignal.bigWig GM12891 ChipSeq CTCF Base_Overlap_Signal bigWig UT-A Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeOpenChromChip/wgEncodeOpenChromChipGm12891CtcfPk.narrowPeak.gz GM12891 ChipSeq CTCF Peaks narrowPeak UT-A Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeOpenChromChip/wgEncodeOpenChromChipGm12891CtcfSig.bigWig GM12891 ChipSeq CTCF Signal bigWig UT-A Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeOpenChromChip/wgEncodeOpenChromChipGm12892CtcfAlnRep1.bam GM12892 ChipSeq CTCF Alignments 1 bam UT-A Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeOpenChromChip/wgEncodeOpenChromChipGm12892CtcfAlnRep2.bam GM12892 ChipSeq CTCF Alignments 2 bam UT-A Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeOpenChromChip/wgEncodeOpenChromChipGm12892CtcfBaseOverlapSignal.bigWig GM12892 ChipSeq CTCF Base_Overlap_Signal bigWig UT-A Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeOpenChromChip/wgEncodeOpenChromChipGm12892CtcfPk.narrowPeak.gz GM12892 ChipSeq CTCF Peaks narrowPeak UT-A Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeOpenChromChip/wgEncodeOpenChromChipGm12892CtcfSig.bigWig GM12892 ChipSeq CTCF Signal bigWig UT-A Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeOpenChromChip/wgEncodeOpenChromChipGm13976CtcfAlnRep1.bam GM13976 ChipSeq CTCF Alignments 1 bam UT-A Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeOpenChromChip/wgEncodeOpenChromChipGm13976CtcfAlnRep2.bam GM13976 ChipSeq CTCF Alignments 2 bam UT-A Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeOpenChromChip/wgEncodeOpenChromChipGm13976CtcfBaseOverlapSignalRep1.bigWig GM13976 ChipSeq CTCF Base_Overlap_Signal 1 bigWig UT-A Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeOpenChromChip/wgEncodeOpenChromChipGm13976CtcfPkRep1.narrowPeak.gz GM13976 ChipSeq CTCF Peaks 1 narrowPeak UT-A Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeOpenChromChip/wgEncodeOpenChromChipGm13976CtcfSigRep1.bigWig GM13976 ChipSeq CTCF Signal 1 bigWig UT-A Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeOpenChromChip/wgEncodeOpenChromChipGm13976InputAln.bam GM13976 ChipSeq Input Alignments bam UT-A Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeOpenChromChip/wgEncodeOpenChromChipGm13976InputSig.bigWig GM13976 ChipSeq Input Signal bigWig UT-A Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeOpenChromChip/wgEncodeOpenChromChipGm13977CtcfAlnRep1.bam GM13977 ChipSeq CTCF Alignments 1 bam UT-A Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeOpenChromChip/wgEncodeOpenChromChipGm13977CtcfAlnRep2.bam GM13977 ChipSeq CTCF Alignments 2 bam UT-A Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeOpenChromChip/wgEncodeOpenChromChipGm13977CtcfBaseOverlapSignalRep1.bigWig GM13977 ChipSeq CTCF Base_Overlap_Signal 1 bigWig UT-A Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeOpenChromChip/wgEncodeOpenChromChipGm13977CtcfPkRep1.narrowPeak.gz GM13977 ChipSeq CTCF Peaks 1 narrowPeak UT-A Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeOpenChromChip/wgEncodeOpenChromChipGm13977CtcfSigRep1.bigWig GM13977 ChipSeq CTCF Signal 1 bigWig UT-A Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeOpenChromChip/wgEncodeOpenChromChipGm13977InputAln.bam GM13977 ChipSeq Input Alignments bam UT-A Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeOpenChromChip/wgEncodeOpenChromChipGm13977InputSig.bigWig GM13977 ChipSeq Input Signal bigWig UT-A Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeOpenChromChip/wgEncodeOpenChromChipGm19238CtcfAlnRep1.bam GM19238 ChipSeq CTCF Alignments 1 bam UT-A Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeOpenChromChip/wgEncodeOpenChromChipGm19238CtcfAlnRep2.bam GM19238 ChipSeq CTCF Alignments 2 bam UT-A Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeOpenChromChip/wgEncodeOpenChromChipGm19238CtcfBaseOverlapSignal.bigWig GM19238 ChipSeq CTCF Base_Overlap_Signal bigWig UT-A Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeOpenChromChip/wgEncodeOpenChromChipGm19238CtcfPk.narrowPeak.gz GM19238 ChipSeq CTCF Peaks narrowPeak UT-A Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeOpenChromChip/wgEncodeOpenChromChipGm19238CtcfSig.bigWig GM19238 ChipSeq CTCF Signal bigWig UT-A Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeOpenChromChip/wgEncodeOpenChromChipGm19239CtcfAlnRep1.bam GM19239 ChipSeq CTCF Alignments 1 bam UT-A Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeOpenChromChip/wgEncodeOpenChromChipGm19239CtcfAlnRep2.bam GM19239 ChipSeq CTCF Alignments 2 bam UT-A Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeOpenChromChip/wgEncodeOpenChromChipGm19239CtcfBaseOverlapSignal.bigWig GM19239 ChipSeq CTCF Base_Overlap_Signal bigWig UT-A Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeOpenChromChip/wgEncodeOpenChromChipGm19239CtcfPk.narrowPeak.gz GM19239 ChipSeq CTCF Peaks narrowPeak UT-A Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeOpenChromChip/wgEncodeOpenChromChipGm19239CtcfSig.bigWig GM19239 ChipSeq CTCF Signal bigWig UT-A Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeOpenChromChip/wgEncodeOpenChromChipGm19240CtcfAlnRep1.bam GM19240 ChipSeq CTCF Alignments 1 bam UT-A Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeOpenChromChip/wgEncodeOpenChromChipGm19240CtcfAlnRep2.bam GM19240 ChipSeq CTCF Alignments 2 bam UT-A Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeOpenChromChip/wgEncodeOpenChromChipGm19240CtcfBaseOverlapSignal.bigWig GM19240 ChipSeq CTCF Base_Overlap_Signal bigWig UT-A Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeOpenChromChip/wgEncodeOpenChromChipGm19240CtcfPk.narrowPeak.gz GM19240 ChipSeq CTCF Peaks narrowPeak UT-A Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeOpenChromChip/wgEncodeOpenChromChipGm19240CtcfSig.bigWig GM19240 ChipSeq CTCF Signal bigWig UT-A Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeOpenChromChip/wgEncodeOpenChromChipGm20000CtcfAlnRep1.bam GM20000 ChipSeq CTCF Alignments 1 bam UT-A Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeOpenChromChip/wgEncodeOpenChromChipGm20000CtcfAlnRep2.bam GM20000 ChipSeq CTCF Alignments 2 bam UT-A Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeOpenChromChip/wgEncodeOpenChromChipGm20000CtcfBaseOverlapSignalRep1.bigWig GM20000 ChipSeq CTCF Base_Overlap_Signal 1 bigWig UT-A Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeOpenChromChip/wgEncodeOpenChromChipGm20000CtcfPkRep1.narrowPeak.gz GM20000 ChipSeq CTCF Peaks 1 narrowPeak UT-A Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeOpenChromChip/wgEncodeOpenChromChipGm20000CtcfSigRep1.bigWig GM20000 ChipSeq CTCF Signal 1 bigWig UT-A Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeOpenChromChip/wgEncodeOpenChromChipGm20000InputAln.bam GM20000 ChipSeq Input Alignments bam UT-A Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeOpenChromChip/wgEncodeOpenChromChipGm20000InputSig.bigWig GM20000 ChipSeq Input Signal bigWig UT-A Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeOpenChromChip/wgEncodeOpenChromChipH1hescCmycAlnRep1.bam H1-hESC ChipSeq c-Myc Alignments 1 bam UT-A Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeOpenChromChip/wgEncodeOpenChromChipH1hescCmycBaseOverlapSignal.bigWig H1-hESC ChipSeq c-Myc Base_Overlap_Signal bigWig UT-A Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeOpenChromChip/wgEncodeOpenChromChipH1hescCmycPk.narrowPeak.gz H1-hESC ChipSeq c-Myc Peaks narrowPeak UT-A Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeOpenChromChip/wgEncodeOpenChromChipH1hescCmycSig.bigWig H1-hESC ChipSeq c-Myc Signal bigWig UT-A Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeOpenChromChip/wgEncodeOpenChromChipH1hescCtcfAlnRep1.bam H1-hESC ChipSeq CTCF Alignments 1 bam UT-A Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeOpenChromChip/wgEncodeOpenChromChipH1hescCtcfBaseOverlapSignal.bigWig H1-hESC ChipSeq CTCF Base_Overlap_Signal bigWig UT-A Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeOpenChromChip/wgEncodeOpenChromChipH1hescCtcfPk.narrowPeak.gz H1-hESC ChipSeq CTCF Peaks narrowPeak UT-A Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeOpenChromChip/wgEncodeOpenChromChipH1hescCtcfSig.bigWig H1-hESC ChipSeq CTCF Signal bigWig UT-A Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeOpenChromChip/wgEncodeOpenChromChipH1hescPol2AlnRep1.bam H1-hESC ChipSeq Pol2 Alignments 1 bam UT-A Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeOpenChromChip/wgEncodeOpenChromChipH1hescPol2BaseOverlapSignal.bigWig H1-hESC ChipSeq Pol2 Base_Overlap_Signal bigWig UT-A Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeOpenChromChip/wgEncodeOpenChromChipH1hescPol2Pk.narrowPeak.gz H1-hESC ChipSeq Pol2 Peaks narrowPeak UT-A Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeOpenChromChip/wgEncodeOpenChromChipH1hescPol2Sig.bigWig H1-hESC ChipSeq Pol2 Signal bigWig UT-A Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeOpenChromChip/wgEncodeOpenChromChipHeartocInputAln.bam Heart_OC ChipSeq Input Alignments bam UT-A Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeOpenChromChip/wgEncodeOpenChromChipHeartocInputSig.bigWig Heart_OC ChipSeq Input Signal bigWig UT-A Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeOpenChromChip/wgEncodeOpenChromChipHelas3CmycAlnRep1.bam HeLa-S3 ChipSeq c-Myc Alignments 1 bam UT-A Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeOpenChromChip/wgEncodeOpenChromChipHelas3CmycAlnRep2.bam HeLa-S3 ChipSeq c-Myc Alignments 2 bam UT-A Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeOpenChromChip/wgEncodeOpenChromChipHelas3CmycBaseOverlapSignal.bigWig HeLa-S3 ChipSeq c-Myc Base_Overlap_Signal bigWig UT-A Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeOpenChromChip/wgEncodeOpenChromChipHelas3CmycPk.narrowPeak.gz HeLa-S3 ChipSeq c-Myc Peaks narrowPeak UT-A Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeOpenChromChip/wgEncodeOpenChromChipHelas3CmycSig.bigWig HeLa-S3 ChipSeq c-Myc Signal bigWig UT-A Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeOpenChromChip/wgEncodeOpenChromChipHelas3CtcfAlnRep1.bam HeLa-S3 ChipSeq CTCF Alignments 1 bam UT-A Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeOpenChromChip/wgEncodeOpenChromChipHelas3CtcfAlnRep2.bam HeLa-S3 ChipSeq CTCF Alignments 2 bam UT-A Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeOpenChromChip/wgEncodeOpenChromChipHelas3CtcfBaseOverlapSignal.bigWig HeLa-S3 ChipSeq CTCF Base_Overlap_Signal bigWig UT-A Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeOpenChromChip/wgEncodeOpenChromChipHelas3CtcfPk.narrowPeak.gz HeLa-S3 ChipSeq CTCF Peaks narrowPeak UT-A Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeOpenChromChip/wgEncodeOpenChromChipHelas3CtcfSig.bigWig HeLa-S3 ChipSeq CTCF Signal bigWig UT-A Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeOpenChromChip/wgEncodeOpenChromChipHelas3InputAln.bam HeLa-S3 ChipSeq Input Alignments bam UT-A Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeOpenChromChip/wgEncodeOpenChromChipHelas3InputSig.bigWig HeLa-S3 ChipSeq Input Signal bigWig UT-A Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeOpenChromChip/wgEncodeOpenChromChipHelas3Pol2AlnRep1.bam HeLa-S3 ChipSeq Pol2 Alignments 1 bam UT-A Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeOpenChromChip/wgEncodeOpenChromChipHelas3Pol2AlnRep2.bam HeLa-S3 ChipSeq Pol2 Alignments 2 bam UT-A Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeOpenChromChip/wgEncodeOpenChromChipHelas3Pol2BaseOverlapSignal.bigWig HeLa-S3 ChipSeq Pol2 Base_Overlap_Signal bigWig UT-A Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeOpenChromChip/wgEncodeOpenChromChipHelas3Pol2Pk.narrowPeak.gz HeLa-S3 ChipSeq Pol2 Peaks narrowPeak UT-A Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeOpenChromChip/wgEncodeOpenChromChipHelas3Pol2Sig.bigWig HeLa-S3 ChipSeq Pol2 Signal bigWig UT-A Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeOpenChromChip/wgEncodeOpenChromChipHepg2CmycAlnRep1.bam HepG2 ChipSeq c-Myc Alignments 1 bam UT-A Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeOpenChromChip/wgEncodeOpenChromChipHepg2CmycAlnRep2.bam HepG2 ChipSeq c-Myc Alignments 2 bam UT-A Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeOpenChromChip/wgEncodeOpenChromChipHepg2CmycAlnRep3.bam HepG2 ChipSeq c-Myc Alignments 3 bam UT-A Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeOpenChromChip/wgEncodeOpenChromChipHepg2CmycBaseOverlapSignal.bigWig HepG2 ChipSeq c-Myc Base_Overlap_Signal bigWig UT-A Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeOpenChromChip/wgEncodeOpenChromChipHepg2CmycPk.narrowPeak.gz HepG2 ChipSeq c-Myc Peaks narrowPeak UT-A Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeOpenChromChip/wgEncodeOpenChromChipHepg2CmycSig.bigWig HepG2 ChipSeq c-Myc Signal bigWig UT-A Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeOpenChromChip/wgEncodeOpenChromChipHepg2CtcfAlnRep1.bam HepG2 ChipSeq CTCF Alignments 1 bam UT-A Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeOpenChromChip/wgEncodeOpenChromChipHepg2CtcfAlnRep2.bam HepG2 ChipSeq CTCF Alignments 2 bam UT-A Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeOpenChromChip/wgEncodeOpenChromChipHepg2CtcfBaseOverlapSignal.bigWig HepG2 ChipSeq CTCF Base_Overlap_Signal bigWig UT-A Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeOpenChromChip/wgEncodeOpenChromChipHepg2CtcfPk.narrowPeak.gz HepG2 ChipSeq CTCF Peaks narrowPeak UT-A Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeOpenChromChip/wgEncodeOpenChromChipHepg2CtcfSig.bigWig HepG2 ChipSeq CTCF Signal bigWig UT-A Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeOpenChromChip/wgEncodeOpenChromChipHepg2InputAln.bam HepG2 ChipSeq Input Alignments bam UT-A Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeOpenChromChip/wgEncodeOpenChromChipHepg2InputSig.bigWig HepG2 ChipSeq Input Signal bigWig UT-A Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeOpenChromChip/wgEncodeOpenChromChipHepg2Pol2AlnRep1.bam HepG2 ChipSeq Pol2 Alignments 1 bam UT-A Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeOpenChromChip/wgEncodeOpenChromChipHepg2Pol2AlnRep2.bam HepG2 ChipSeq Pol2 Alignments 2 bam UT-A Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeOpenChromChip/wgEncodeOpenChromChipHepg2Pol2AlnRep3.bam HepG2 ChipSeq Pol2 Alignments 3 bam UT-A Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeOpenChromChip/wgEncodeOpenChromChipHepg2Pol2BaseOverlapSignal.bigWig HepG2 ChipSeq Pol2 Base_Overlap_Signal bigWig UT-A Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeOpenChromChip/wgEncodeOpenChromChipHepg2Pol2Pk.narrowPeak.gz HepG2 ChipSeq Pol2 Peaks narrowPeak UT-A Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeOpenChromChip/wgEncodeOpenChromChipHepg2Pol2Sig.bigWig HepG2 ChipSeq Pol2 Signal bigWig UT-A Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeOpenChromChip/wgEncodeOpenChromChipHuvecCmycAlnRep1.bam HUVEC ChipSeq c-Myc Alignments 1 bam UT-A Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeOpenChromChip/wgEncodeOpenChromChipHuvecCmycBaseOverlapSignal.bigWig HUVEC ChipSeq c-Myc Base_Overlap_Signal bigWig UT-A Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeOpenChromChip/wgEncodeOpenChromChipHuvecCmycPk.narrowPeak.gz HUVEC ChipSeq c-Myc Peaks narrowPeak UT-A Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeOpenChromChip/wgEncodeOpenChromChipHuvecCmycSig.bigWig HUVEC ChipSeq c-Myc Signal bigWig UT-A Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeOpenChromChip/wgEncodeOpenChromChipHuvecCtcfAlnRep1.bam HUVEC ChipSeq CTCF Alignments 1 bam UT-A Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeOpenChromChip/wgEncodeOpenChromChipHuvecCtcfAlnRep2.bam HUVEC ChipSeq CTCF Alignments 2 bam UT-A Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeOpenChromChip/wgEncodeOpenChromChipHuvecCtcfBaseOverlapSignal.bigWig HUVEC ChipSeq CTCF Base_Overlap_Signal bigWig UT-A Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeOpenChromChip/wgEncodeOpenChromChipHuvecCtcfPk.narrowPeak.gz HUVEC ChipSeq CTCF Peaks narrowPeak UT-A Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeOpenChromChip/wgEncodeOpenChromChipHuvecCtcfSig.bigWig HUVEC ChipSeq CTCF Signal bigWig UT-A Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeOpenChromChip/wgEncodeOpenChromChipHuvecInputAln.bam HUVEC ChipSeq Input Alignments bam UT-A Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeOpenChromChip/wgEncodeOpenChromChipHuvecInputSig.bigWig HUVEC ChipSeq Input Signal bigWig UT-A Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeOpenChromChip/wgEncodeOpenChromChipHuvecPol2AlnRep1.bam HUVEC ChipSeq Pol2 Alignments 1 bam UT-A Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeOpenChromChip/wgEncodeOpenChromChipHuvecPol2AlnRep2.bam HUVEC ChipSeq Pol2 Alignments 2 bam UT-A Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeOpenChromChip/wgEncodeOpenChromChipHuvecPol2BaseOverlapSignal.bigWig HUVEC ChipSeq Pol2 Base_Overlap_Signal bigWig UT-A Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeOpenChromChip/wgEncodeOpenChromChipHuvecPol2Pk.narrowPeak.gz HUVEC ChipSeq Pol2 Peaks narrowPeak UT-A Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeOpenChromChip/wgEncodeOpenChromChipHuvecPol2Sig.bigWig HUVEC ChipSeq Pol2 Signal bigWig UT-A Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeOpenChromChip/wgEncodeOpenChromChipK562CmycAlnRep1.bam K562 ChipSeq c-Myc Alignments 1 bam UT-A Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeOpenChromChip/wgEncodeOpenChromChipK562CmycAlnRep2.bam K562 ChipSeq c-Myc Alignments 2 bam UT-A Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeOpenChromChip/wgEncodeOpenChromChipK562CmycAlnRep3.bam K562 ChipSeq c-Myc Alignments 3 bam UT-A Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeOpenChromChip/wgEncodeOpenChromChipK562CmycBaseOverlapSignal.bigWig K562 ChipSeq c-Myc Base_Overlap_Signal bigWig UT-A Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeOpenChromChip/wgEncodeOpenChromChipK562CmycPk.narrowPeak.gz K562 ChipSeq c-Myc Peaks narrowPeak UT-A Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeOpenChromChip/wgEncodeOpenChromChipK562CmycSig.bigWig K562 ChipSeq c-Myc Signal bigWig UT-A Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeOpenChromChip/wgEncodeOpenChromChipK562CtcfAlnRep1.bam K562 ChipSeq CTCF Alignments 1 bam UT-A Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeOpenChromChip/wgEncodeOpenChromChipK562CtcfAlnRep2.bam K562 ChipSeq CTCF Alignments 2 bam UT-A Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeOpenChromChip/wgEncodeOpenChromChipK562CtcfAlnRep3.bam K562 ChipSeq CTCF Alignments 3 bam UT-A Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeOpenChromChip/wgEncodeOpenChromChipK562CtcfBaseOverlapSignal.bigWig K562 ChipSeq CTCF Base_Overlap_Signal bigWig UT-A Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeOpenChromChip/wgEncodeOpenChromChipK562CtcfPk.narrowPeak.gz K562 ChipSeq CTCF Peaks narrowPeak UT-A Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeOpenChromChip/wgEncodeOpenChromChipK562CtcfSig.bigWig K562 ChipSeq CTCF Signal bigWig UT-A Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeOpenChromChip/wgEncodeOpenChromChipK562InputAln.bam K562 ChipSeq Input Alignments bam UT-A Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeOpenChromChip/wgEncodeOpenChromChipK562InputSig.bigWig K562 ChipSeq Input Signal bigWig UT-A Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeOpenChromChip/wgEncodeOpenChromChipK562Pol2AlnRep1.bam K562 ChipSeq Pol2 Alignments 1 bam UT-A Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeOpenChromChip/wgEncodeOpenChromChipK562Pol2AlnRep2.bam K562 ChipSeq Pol2 Alignments 2 bam UT-A Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeOpenChromChip/wgEncodeOpenChromChipK562Pol2BaseOverlapSignal.bigWig K562 ChipSeq Pol2 Base_Overlap_Signal bigWig UT-A Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeOpenChromChip/wgEncodeOpenChromChipK562Pol2Pk.narrowPeak.gz K562 ChipSeq Pol2 Peaks narrowPeak UT-A Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeOpenChromChip/wgEncodeOpenChromChipK562Pol2Sig.bigWig K562 ChipSeq Pol2 Signal bigWig UT-A Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeOpenChromChip/wgEncodeOpenChromChipKidneyocCtcfAlnRep1.bam Kidney_OC ChipSeq CTCF Alignments 1 bam UT-A Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeOpenChromChip/wgEncodeOpenChromChipKidneyocCtcfAlnRep2.bam Kidney_OC ChipSeq CTCF Alignments 2 bam UT-A Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeOpenChromChip/wgEncodeOpenChromChipKidneyocCtcfAlnRep3.bam Kidney_OC ChipSeq CTCF Alignments 3 bam UT-A Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeOpenChromChip/wgEncodeOpenChromChipKidneyocCtcfBaseOverlapSignalRep1.bigWig Kidney_OC ChipSeq CTCF Base_Overlap_Signal 1 bigWig UT-A Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeOpenChromChip/wgEncodeOpenChromChipKidneyocCtcfPkRep1.narrowPeak.gz Kidney_OC ChipSeq CTCF Peaks 1 narrowPeak UT-A Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeOpenChromChip/wgEncodeOpenChromChipKidneyocCtcfSigRep1.bigWig Kidney_OC ChipSeq CTCF Signal 1 bigWig UT-A Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeOpenChromChip/wgEncodeOpenChromChipKidneyocInputAln.bam Kidney_OC ChipSeq Input Alignments bam UT-A Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeOpenChromChip/wgEncodeOpenChromChipKidneyocInputSig.bigWig Kidney_OC ChipSeq Input Signal bigWig UT-A Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeOpenChromChip/wgEncodeOpenChromChipLncapCtcfAlnRep1.bam LNCaP ChipSeq CTCF Alignments 1 bam UT-A Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeOpenChromChip/wgEncodeOpenChromChipLncapCtcfAlnRep2.bam LNCaP ChipSeq CTCF Alignments 2 bam UT-A Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeOpenChromChip/wgEncodeOpenChromChipLncapCtcfAndroAlnRep1.bam LNCaP ChipSeq CTCF Alignments 1 bam UT-A Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeOpenChromChip/wgEncodeOpenChromChipLncapCtcfAndroAlnRep2.bam LNCaP ChipSeq CTCF Alignments 2 bam UT-A Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeOpenChromChip/wgEncodeOpenChromChipLncapCtcfAndroBaseOverlapSignalRep1.bigWig LNCaP ChipSeq CTCF Base_Overlap_Signal 1 bigWig UT-A Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeOpenChromChip/wgEncodeOpenChromChipLncapCtcfAndroPkRep1.narrowPeak.gz LNCaP ChipSeq CTCF Peaks 1 narrowPeak UT-A Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeOpenChromChip/wgEncodeOpenChromChipLncapCtcfAndroSigRep1.bigWig LNCaP ChipSeq CTCF Signal 1 bigWig UT-A Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeOpenChromChip/wgEncodeOpenChromChipLncapCtcfBaseOverlapSignalRep1.bigWig LNCaP ChipSeq CTCF Base_Overlap_Signal 1 bigWig UT-A Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeOpenChromChip/wgEncodeOpenChromChipLncapCtcfPkRep1.narrowPeak.gz LNCaP ChipSeq CTCF Peaks 1 narrowPeak UT-A Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeOpenChromChip/wgEncodeOpenChromChipLncapCtcfSigRep1.bigWig LNCaP ChipSeq CTCF Signal 1 bigWig UT-A Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeOpenChromChip/wgEncodeOpenChromChipLncapInputAln.bam LNCaP ChipSeq Input Alignments bam UT-A Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeOpenChromChip/wgEncodeOpenChromChipLncapInputSig.bigWig LNCaP ChipSeq Input Signal bigWig UT-A Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeOpenChromChip/wgEncodeOpenChromChipLungocCtcfAlnRep1.bam Lung_OC ChipSeq CTCF Alignments 1 bam UT-A Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeOpenChromChip/wgEncodeOpenChromChipLungocCtcfAlnRep2.bam Lung_OC ChipSeq CTCF Alignments 2 bam UT-A Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeOpenChromChip/wgEncodeOpenChromChipLungocCtcfBaseOverlapSignalRep1.bigWig Lung_OC ChipSeq CTCF Base_Overlap_Signal 1 bigWig UT-A Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeOpenChromChip/wgEncodeOpenChromChipLungocCtcfPkRep1.narrowPeak.gz Lung_OC ChipSeq CTCF Peaks 1 narrowPeak UT-A Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeOpenChromChip/wgEncodeOpenChromChipLungocCtcfSigRep1.bigWig Lung_OC ChipSeq CTCF Signal 1 bigWig UT-A Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeOpenChromChip/wgEncodeOpenChromChipLungocInputAln.bam Lung_OC ChipSeq Input Alignments bam UT-A Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeOpenChromChip/wgEncodeOpenChromChipLungocInputSig.bigWig Lung_OC ChipSeq Input Signal bigWig UT-A Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeOpenChromChip/wgEncodeOpenChromChipMcf7CmycEstroAlnRep1.bam MCF-7 ChipSeq c-Myc Alignments 1 bam UT-A Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeOpenChromChip/wgEncodeOpenChromChipMcf7CmycEstroAlnRep2.bam MCF-7 ChipSeq c-Myc Alignments 2 bam UT-A Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeOpenChromChip/wgEncodeOpenChromChipMcf7CmycEstroBaseOverlapSignal.bigWig MCF-7 ChipSeq c-Myc Base_Overlap_Signal bigWig UT-A Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeOpenChromChip/wgEncodeOpenChromChipMcf7CmycEstroPkRep1.narrowPeak.gz MCF-7 ChipSeq c-Myc Peaks 1 narrowPeak UT-A Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeOpenChromChip/wgEncodeOpenChromChipMcf7CmycEstroSig.bigWig MCF-7 ChipSeq c-Myc Signal bigWig UT-A Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeOpenChromChip/wgEncodeOpenChromChipMcf7CmycSerumstimAlnRep1.bam MCF-7 ChipSeq c-Myc Alignments 1 bam UT-A Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeOpenChromChip/wgEncodeOpenChromChipMcf7CmycSerumstimAlnRep2.bam MCF-7 ChipSeq c-Myc Alignments 2 bam UT-A Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeOpenChromChip/wgEncodeOpenChromChipMcf7CmycSerumstimBaseOverlapSignal.bigWig MCF-7 ChipSeq c-Myc Base_Overlap_Signal bigWig UT-A Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeOpenChromChip/wgEncodeOpenChromChipMcf7CmycSerumstimPkRep1.narrowPeak.gz MCF-7 ChipSeq c-Myc Peaks 1 narrowPeak UT-A Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeOpenChromChip/wgEncodeOpenChromChipMcf7CmycSerumstimSig.bigWig MCF-7 ChipSeq c-Myc Signal bigWig UT-A Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeOpenChromChip/wgEncodeOpenChromChipMcf7CmycSerumstvdAlnRep1.bam MCF-7 ChipSeq c-Myc Alignments 1 bam UT-A Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeOpenChromChip/wgEncodeOpenChromChipMcf7CmycSerumstvdAlnRep2.bam MCF-7 ChipSeq c-Myc Alignments 2 bam UT-A Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeOpenChromChip/wgEncodeOpenChromChipMcf7CmycSerumstvdBaseOverlapSignal.bigWig MCF-7 ChipSeq c-Myc Base_Overlap_Signal bigWig UT-A Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeOpenChromChip/wgEncodeOpenChromChipMcf7CmycSerumstvdPkRep1.narrowPeak.gz MCF-7 ChipSeq c-Myc Peaks 1 narrowPeak UT-A Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeOpenChromChip/wgEncodeOpenChromChipMcf7CmycSerumstvdSig.bigWig MCF-7 ChipSeq c-Myc Signal bigWig UT-A Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeOpenChromChip/wgEncodeOpenChromChipMcf7CmycVehAlnRep1.bam MCF-7 ChipSeq c-Myc Alignments 1 bam UT-A Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeOpenChromChip/wgEncodeOpenChromChipMcf7CmycVehAlnRep2.bam MCF-7 ChipSeq c-Myc Alignments 2 bam UT-A Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeOpenChromChip/wgEncodeOpenChromChipMcf7CmycVehBaseOverlapSignal.bigWig MCF-7 ChipSeq c-Myc Base_Overlap_Signal bigWig UT-A Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeOpenChromChip/wgEncodeOpenChromChipMcf7CmycVehPkRep1.narrowPeak.gz MCF-7 ChipSeq c-Myc Peaks narrowPeak UT-A Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeOpenChromChip/wgEncodeOpenChromChipMcf7CmycVehSig.bigWig MCF-7 ChipSeq c-Myc Signal bigWig UT-A Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeOpenChromChip/wgEncodeOpenChromChipMcf7CtcfAlnRep1.bam MCF-7 ChipSeq CTCF Alignments 1 bam UT-A Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeOpenChromChip/wgEncodeOpenChromChipMcf7CtcfAlnRep2.bam MCF-7 ChipSeq CTCF Alignments 2 bam UT-A Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeOpenChromChip/wgEncodeOpenChromChipMcf7CtcfBaseOverlapSignal.bigWig MCF-7 ChipSeq CTCF Base_Overlap_Signal bigWig UT-A Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeOpenChromChip/wgEncodeOpenChromChipMcf7CtcfEstroAlnRep1.bam MCF-7 ChipSeq CTCF Alignments 1 bam UT-A Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeOpenChromChip/wgEncodeOpenChromChipMcf7CtcfEstroAlnRep2.bam MCF-7 ChipSeq CTCF Alignments 2 bam UT-A Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeOpenChromChip/wgEncodeOpenChromChipMcf7CtcfEstroBaseOverlapSignal.bigWig MCF-7 ChipSeq CTCF Base_Overlap_Signal bigWig UT-A Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeOpenChromChip/wgEncodeOpenChromChipMcf7CtcfEstroPkRep1.narrowPeak.gz MCF-7 ChipSeq CTCF Peaks narrowPeak UT-A Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeOpenChromChip/wgEncodeOpenChromChipMcf7CtcfEstroSig.bigWig MCF-7 ChipSeq CTCF Signal bigWig UT-A Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeOpenChromChip/wgEncodeOpenChromChipMcf7CtcfPk.narrowPeak.gz MCF-7 ChipSeq CTCF Peaks narrowPeak UT-A Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeOpenChromChip/wgEncodeOpenChromChipMcf7CtcfSerumstimAlnRep1.bam MCF-7 ChipSeq CTCF Alignments 1 bam UT-A Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeOpenChromChip/wgEncodeOpenChromChipMcf7CtcfSerumstimAlnRep2.bam MCF-7 ChipSeq CTCF Alignments 2 bam UT-A Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeOpenChromChip/wgEncodeOpenChromChipMcf7CtcfSerumstimBaseOverlapSignal.bigWig MCF-7 ChipSeq CTCF Base_Overlap_Signal bigWig UT-A Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeOpenChromChip/wgEncodeOpenChromChipMcf7CtcfSerumstimPkRep1.narrowPeak.gz MCF-7 ChipSeq CTCF Peaks 1 narrowPeak UT-A Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeOpenChromChip/wgEncodeOpenChromChipMcf7CtcfSerumstimSig.bigWig MCF-7 ChipSeq CTCF Signal bigWig UT-A Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeOpenChromChip/wgEncodeOpenChromChipMcf7CtcfSerumstvdAlnRep1.bam MCF-7 ChipSeq CTCF Alignments 1 bam UT-A Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeOpenChromChip/wgEncodeOpenChromChipMcf7CtcfSerumstvdAlnRep2.bam MCF-7 ChipSeq CTCF Alignments 2 bam UT-A Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeOpenChromChip/wgEncodeOpenChromChipMcf7CtcfSerumstvdBaseOverlapSignal.bigWig MCF-7 ChipSeq CTCF Base_Overlap_Signal bigWig UT-A Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeOpenChromChip/wgEncodeOpenChromChipMcf7CtcfSerumstvdPkRep1.narrowPeak.gz MCF-7 ChipSeq CTCF Peaks 1 narrowPeak UT-A Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeOpenChromChip/wgEncodeOpenChromChipMcf7CtcfSerumstvdSig.bigWig MCF-7 ChipSeq CTCF Signal bigWig UT-A Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeOpenChromChip/wgEncodeOpenChromChipMcf7CtcfSig.bigWig MCF-7 ChipSeq CTCF Signal bigWig UT-A Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeOpenChromChip/wgEncodeOpenChromChipMcf7CtcfVehAlnRep1.bam MCF-7 ChipSeq CTCF Alignments 1 bam UT-A Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeOpenChromChip/wgEncodeOpenChromChipMcf7CtcfVehAlnRep2.bam MCF-7 ChipSeq CTCF Alignments 2 bam UT-A Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeOpenChromChip/wgEncodeOpenChromChipMcf7CtcfVehBaseOverlapSignal.bigWig MCF-7 ChipSeq CTCF Base_Overlap_Signal bigWig UT-A Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeOpenChromChip/wgEncodeOpenChromChipMcf7CtcfVehPkRep1.narrowPeak.gz MCF-7 ChipSeq CTCF Peaks narrowPeak UT-A Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeOpenChromChip/wgEncodeOpenChromChipMcf7CtcfVehSig.bigWig MCF-7 ChipSeq CTCF Signal bigWig UT-A Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeOpenChromChip/wgEncodeOpenChromChipMcf7InputAln.bam MCF-7 ChipSeq Input Alignments bam UT-A Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeOpenChromChip/wgEncodeOpenChromChipMcf7InputSig.bigWig MCF-7 ChipSeq Input Signal bigWig UT-A Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeOpenChromChip/wgEncodeOpenChromChipMcf7Pol2AlnRep1.bam MCF-7 ChipSeq Pol2 Alignments 1 bam UT-A Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeOpenChromChip/wgEncodeOpenChromChipMcf7Pol2AlnRep2.bam MCF-7 ChipSeq Pol2 Alignments 2 bam UT-A Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeOpenChromChip/wgEncodeOpenChromChipMcf7Pol2BaseOverlapSignal.bigWig MCF-7 ChipSeq Pol2 Base_Overlap_Signal bigWig UT-A Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeOpenChromChip/wgEncodeOpenChromChipMcf7Pol2PkRep1.narrowPeak.gz MCF-7 ChipSeq Pol2 Peaks narrowPeak UT-A Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeOpenChromChip/wgEncodeOpenChromChipMcf7Pol2SerumstimAlnRep1.bam MCF-7 ChipSeq Pol2 Alignments 1 bam UT-A Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeOpenChromChip/wgEncodeOpenChromChipMcf7Pol2SerumstimAlnRep2.bam MCF-7 ChipSeq Pol2 Alignments 2 bam UT-A Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeOpenChromChip/wgEncodeOpenChromChipMcf7Pol2SerumstimBaseOverlapSignal.bigWig MCF-7 ChipSeq Pol2 Base_Overlap_Signal bigWig UT-A Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeOpenChromChip/wgEncodeOpenChromChipMcf7Pol2SerumstimPkRep1.narrowPeak.gz MCF-7 ChipSeq Pol2 Peaks 1 narrowPeak UT-A Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeOpenChromChip/wgEncodeOpenChromChipMcf7Pol2SerumstimSig.bigWig MCF-7 ChipSeq Pol2 Signal bigWig UT-A Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeOpenChromChip/wgEncodeOpenChromChipMcf7Pol2SerumstvdAlnRep1.bam MCF-7 ChipSeq Pol2 Alignments 1 bam UT-A Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeOpenChromChip/wgEncodeOpenChromChipMcf7Pol2SerumstvdAlnRep2.bam MCF-7 ChipSeq Pol2 Alignments 2 bam UT-A Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeOpenChromChip/wgEncodeOpenChromChipMcf7Pol2SerumstvdBaseOverlapSignal.bigWig MCF-7 ChipSeq Pol2 Base_Overlap_Signal bigWig UT-A Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeOpenChromChip/wgEncodeOpenChromChipMcf7Pol2SerumstvdPkRep1.narrowPeak.gz MCF-7 ChipSeq Pol2 Peaks 1 narrowPeak UT-A Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeOpenChromChip/wgEncodeOpenChromChipMcf7Pol2SerumstvdSig.bigWig MCF-7 ChipSeq Pol2 Signal bigWig UT-A Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeOpenChromChip/wgEncodeOpenChromChipMcf7Pol2Sig.bigWig MCF-7 ChipSeq Pol2 Signal bigWig UT-A Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeOpenChromChip/wgEncodeOpenChromChipMedulloCtcfAlnRep1.bam Medullo ChipSeq CTCF Alignments 1 bam UT-A Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeOpenChromChip/wgEncodeOpenChromChipMedulloCtcfAlnRep2.bam Medullo ChipSeq CTCF Alignments 2 bam UT-A Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeOpenChromChip/wgEncodeOpenChromChipMedulloCtcfBaseOverlapSignal.bigWig Medullo ChipSeq CTCF Base_Overlap_Signal bigWig UT-A Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeOpenChromChip/wgEncodeOpenChromChipMedulloCtcfPkRep1.narrowPeak.gz Medullo ChipSeq CTCF Peaks 1 narrowPeak UT-A Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeOpenChromChip/wgEncodeOpenChromChipMedulloCtcfSig.bigWig Medullo ChipSeq CTCF Signal bigWig UT-A Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeOpenChromChip/wgEncodeOpenChromChipMedulloInputAln.bam Medullo ChipSeq Input Alignments bam UT-A Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeOpenChromChip/wgEncodeOpenChromChipMedulloInputSig.bigWig Medullo ChipSeq Input Signal bigWig UT-A Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeOpenChromChip/wgEncodeOpenChromChipMonocd14InputAln.bam Monocytes-CD14+_RO01746 ChipSeq Input Alignments bam UT-A Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeOpenChromChip/wgEncodeOpenChromChipMonocd14InputSig.bigWig Monocytes-CD14+_RO01746 ChipSeq Input Signal bigWig UT-A Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeOpenChromChip/wgEncodeOpenChromChipMonocd14ro1746InputAln.bam Monocytes-CD14+_RO01746 ChipSeq Input Alignments bam UT-A Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeOpenChromChip/wgEncodeOpenChromChipMonocd14ro1746InputSig.bigWig Monocytes-CD14+_RO01746 ChipSeq Input Signal bigWig UT-A Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeOpenChromChip/wgEncodeOpenChromChipNhekCtcfAlnRep1.bam NHEK ChipSeq CTCF Alignments 1 bam UT-A Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeOpenChromChip/wgEncodeOpenChromChipNhekCtcfAlnRep2.bam NHEK ChipSeq CTCF Alignments 2 bam UT-A Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeOpenChromChip/wgEncodeOpenChromChipNhekCtcfBaseOverlapSignal.bigWig NHEK ChipSeq CTCF Base_Overlap_Signal bigWig UT-A Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeOpenChromChip/wgEncodeOpenChromChipNhekCtcfPk.narrowPeak.gz NHEK ChipSeq CTCF Peaks narrowPeak UT-A Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeOpenChromChip/wgEncodeOpenChromChipNhekCtcfSig.bigWig NHEK ChipSeq CTCF Signal bigWig UT-A Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeOpenChromChip/wgEncodeOpenChromChipPancreasocCtcfAlnRep1.bam Pancreas_OC ChipSeq CTCF Alignments 1 bam UT-A Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeOpenChromChip/wgEncodeOpenChromChipPancreasocCtcfAlnRep2.bam Pancreas_OC ChipSeq CTCF Alignments 2 bam UT-A Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeOpenChromChip/wgEncodeOpenChromChipPancreasocCtcfBaseOverlapSignalRep1.bigWig Pancreas_OC ChipSeq CTCF Base_Overlap_Signal 1 bigWig UT-A Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeOpenChromChip/wgEncodeOpenChromChipPancreasocCtcfPkRep1.narrowPeak.gz Pancreas_OC ChipSeq CTCF Peaks 1 narrowPeak UT-A Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeOpenChromChip/wgEncodeOpenChromChipPancreasocCtcfSigRep1.bigWig Pancreas_OC ChipSeq CTCF Signal 1 bigWig UT-A Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeOpenChromChip/wgEncodeOpenChromChipPancreasocInputAln.bam Pancreas_OC ChipSeq Input Alignments bam UT-A Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeOpenChromChip/wgEncodeOpenChromChipPancreasocInputSig.bigWig Pancreas_OC ChipSeq Input Signal bigWig UT-A Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeOpenChromChip/wgEncodeOpenChromChipProgfibCtcfAlnRep1.bam ProgFib ChipSeq CTCF Alignments 1 bam UT-A Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeOpenChromChip/wgEncodeOpenChromChipProgfibCtcfAlnRep2.bam ProgFib ChipSeq CTCF Alignments 2 bam UT-A Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeOpenChromChip/wgEncodeOpenChromChipProgfibCtcfBaseOverlapSignal.bigWig ProgFib ChipSeq CTCF Base_Overlap_Signal bigWig UT-A Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeOpenChromChip/wgEncodeOpenChromChipProgfibCtcfPkRep1.narrowPeak.gz ProgFib ChipSeq CTCF Peaks 1 narrowPeak UT-A Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeOpenChromChip/wgEncodeOpenChromChipProgfibCtcfSig.bigWig ProgFib ChipSeq CTCF Signal bigWig UT-A Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeOpenChromChip/wgEncodeOpenChromChipProgfibInputAln.bam ProgFib ChipSeq Input Alignments bam UT-A Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeOpenChromChip/wgEncodeOpenChromChipProgfibInputSig.bigWig ProgFib ChipSeq Input Signal bigWig UT-A Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeOpenChromChip/wgEncodeOpenChromChipProgfibPol2AlnRep1.bam ProgFib ChipSeq Pol2 Alignments 1 bam UT-A Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeOpenChromChip/wgEncodeOpenChromChipProgfibPol2AlnRep2.bam ProgFib ChipSeq Pol2 Alignments 2 bam UT-A Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeOpenChromChip/wgEncodeOpenChromChipProgfibPol2BaseOverlapSignal.bigWig ProgFib ChipSeq Pol2 Base_Overlap_Signal bigWig UT-A Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeOpenChromChip/wgEncodeOpenChromChipProgfibPol2PkRep1.narrowPeak.gz ProgFib ChipSeq Pol2 Peaks 1 narrowPeak UT-A Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeOpenChromChip/wgEncodeOpenChromChipProgfibPol2Sig.bigWig ProgFib ChipSeq Pol2 Signal bigWig UT-A Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeOpenChromChip/wgEncodeOpenChromChipSpleenocCtcfAlnRep1.bam Spleen_OC ChipSeq CTCF Alignments 1 bam UT-A Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeOpenChromChip/wgEncodeOpenChromChipSpleenocCtcfAlnRep2.bam Spleen_OC ChipSeq CTCF Alignments 2 bam UT-A Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeOpenChromChip/wgEncodeOpenChromChipSpleenocCtcfBaseOverlapSignalRep1.bigWig Spleen_OC ChipSeq CTCF Base_Overlap_Signal 1 bigWig UT-A Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeOpenChromChip/wgEncodeOpenChromChipSpleenocCtcfPkRep1.narrowPeak.gz Spleen_OC ChipSeq CTCF Peaks 1 narrowPeak UT-A Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeOpenChromChip/wgEncodeOpenChromChipSpleenocCtcfSigRep1.bigWig Spleen_OC ChipSeq CTCF Signal 1 bigWig UT-A Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeOpenChromChip/wgEncodeOpenChromChipSpleenocInputAln.bam Spleen_OC ChipSeq Input Alignments bam UT-A Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeOpenChromChip/wgEncodeOpenChromChipSpleenocInputSig.bigWig Spleen_OC ChipSeq Input Signal bigWig UT-A Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeOpenChromDnase/wgEncodeOpenChromDnase8988tAlnRep1.bam 8988T DnaseSeq Alignments 1 bam Duke Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeOpenChromDnase/wgEncodeOpenChromDnase8988tAlnRep2.bam 8988T DnaseSeq Alignments 2 bam Duke Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeOpenChromDnase/wgEncodeOpenChromDnase8988tBaseOverlapSignal.bigWig 8988T DnaseSeq Base_Overlap_Signal bigWig Duke Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeOpenChromDnase/wgEncodeOpenChromDnase8988tPk.narrowPeak.gz 8988T DnaseSeq Peaks narrowPeak Duke Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeOpenChromDnase/wgEncodeOpenChromDnase8988tSig.bigWig 8988T DnaseSeq Signal bigWig Duke Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeOpenChromDnase/wgEncodeOpenChromDnaseA549AlnRep1.bam A549 DnaseSeq Alignments 1 bam Duke Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeOpenChromDnase/wgEncodeOpenChromDnaseA549AlnRep2.bam A549 DnaseSeq Alignments 2 bam Duke Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeOpenChromDnase/wgEncodeOpenChromDnaseA549BaseOverlapSignal.bigWig A549 DnaseSeq Base_Overlap_Signal bigWig Duke Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeOpenChromDnase/wgEncodeOpenChromDnaseA549Pk.narrowPeak.gz A549 DnaseSeq Peaks narrowPeak Duke Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeOpenChromDnase/wgEncodeOpenChromDnaseA549Sig.bigWig A549 DnaseSeq Signal bigWig Duke Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeOpenChromDnase/wgEncodeOpenChromDnaseAdultcd4th0AlnRep1.bam Adult_CD4_Th0 DnaseSeq Alignments 1 bam Duke Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeOpenChromDnase/wgEncodeOpenChromDnaseAdultcd4th0AlnRep2.bam Adult_CD4_Th0 DnaseSeq Alignments 2 bam Duke Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeOpenChromDnase/wgEncodeOpenChromDnaseAdultcd4th0BaseOverlapSignal.bigWig Adult_CD4_Th0 DnaseSeq Base_Overlap_Signal bigWig Duke Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeOpenChromDnase/wgEncodeOpenChromDnaseAdultcd4th0Pk.narrowPeak.gz Adult_CD4_Th0 DnaseSeq Peaks narrowPeak Duke Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeOpenChromDnase/wgEncodeOpenChromDnaseAdultcd4th0Sig.bigWig Adult_CD4_Th0 DnaseSeq Signal bigWig Duke Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeOpenChromDnase/wgEncodeOpenChromDnaseAdultcd4th1AlnRep1.bam Adult_CD4_Th1 DnaseSeq Alignments 1 bam Duke Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeOpenChromDnase/wgEncodeOpenChromDnaseAdultcd4th1AlnRep2.bam Adult_CD4_Th1 DnaseSeq Alignments 2 bam Duke Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeOpenChromDnase/wgEncodeOpenChromDnaseAdultcd4th1BaseOverlapSignal.bigWig Adult_CD4_Th1 DnaseSeq Base_Overlap_Signal bigWig Duke Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeOpenChromDnase/wgEncodeOpenChromDnaseAdultcd4th1Pk.narrowPeak.gz Adult_CD4_Th1 DnaseSeq Peaks narrowPeak Duke Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeOpenChromDnase/wgEncodeOpenChromDnaseAdultcd4th1Sig.bigWig Adult_CD4_Th1 DnaseSeq Signal bigWig Duke Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeOpenChromDnase/wgEncodeOpenChromDnaseAosmcSerumfreeAlnRep1.bam AoSMC DnaseSeq Alignments 1 bam Duke Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeOpenChromDnase/wgEncodeOpenChromDnaseAosmcSerumfreeAlnRep2.bam AoSMC DnaseSeq Alignments 2 bam Duke Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeOpenChromDnase/wgEncodeOpenChromDnaseAosmcSerumfreeBaseOverlapSignal.bigWig AoSMC DnaseSeq Base_Overlap_Signal bigWig Duke Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeOpenChromDnase/wgEncodeOpenChromDnaseAosmcSerumfreePk.narrowPeak.gz AoSMC DnaseSeq Peaks narrowPeak Duke Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeOpenChromDnase/wgEncodeOpenChromDnaseAosmcSerumfreeSig.bigWig AoSMC DnaseSeq Signal bigWig Duke Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeOpenChromDnase/wgEncodeOpenChromDnaseCd20ro01794AlnRep1.bam CD20+_RO01794 DnaseSeq Alignments 1 bam Duke Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeOpenChromDnase/wgEncodeOpenChromDnaseCd20ro01794AlnRep2.bam CD20+_RO01794 DnaseSeq Alignments 2 bam Duke Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeOpenChromDnase/wgEncodeOpenChromDnaseCd20ro01794BaseOverlapSignal.bigWig CD20+_RO01794 DnaseSeq Base_Overlap_Signal bigWig Duke Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeOpenChromDnase/wgEncodeOpenChromDnaseCd20ro01794Pk.narrowPeak.gz CD20+_RO01794 DnaseSeq Peaks narrowPeak Duke Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeOpenChromDnase/wgEncodeOpenChromDnaseCd20ro01794Sig.bigWig CD20+_RO01794 DnaseSeq Signal bigWig Duke Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeOpenChromDnase/wgEncodeOpenChromDnaseCerebellumocAlnRep1.bam Cerebellum_OC DnaseSeq Alignments 1 bam Duke Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeOpenChromDnase/wgEncodeOpenChromDnaseCerebellumocAlnRep2.bam Cerebellum_OC DnaseSeq Alignments 2 bam Duke Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeOpenChromDnase/wgEncodeOpenChromDnaseCerebellumocBaseOverlapSignal.bigWig Cerebellum_OC DnaseSeq Base_Overlap_Signal bigWig Duke Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeOpenChromDnase/wgEncodeOpenChromDnaseCerebellumocPk.narrowPeak.gz Cerebellum_OC DnaseSeq Peaks narrowPeak Duke Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeOpenChromDnase/wgEncodeOpenChromDnaseCerebellumocSig.bigWig Cerebellum_OC DnaseSeq Signal bigWig Duke Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeOpenChromDnase/wgEncodeOpenChromDnaseCerebrumfrontalocAlnRep1.bam Cerebrum_frontal_OC DnaseSeq Alignments 1 bam Duke Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeOpenChromDnase/wgEncodeOpenChromDnaseCerebrumfrontalocAlnRep2.bam Cerebrum_frontal_OC DnaseSeq Alignments 2 bam Duke Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeOpenChromDnase/wgEncodeOpenChromDnaseCerebrumfrontalocBaseOverlapSignal.bigWig Cerebrum_frontal_OC DnaseSeq Base_Overlap_Signal bigWig Duke Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeOpenChromDnase/wgEncodeOpenChromDnaseCerebrumfrontalocPk.narrowPeak.gz Cerebrum_frontal_OC DnaseSeq Peaks narrowPeak Duke Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeOpenChromDnase/wgEncodeOpenChromDnaseCerebrumfrontalocSig.bigWig Cerebrum_frontal_OC DnaseSeq Signal bigWig Duke Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeOpenChromDnase/wgEncodeOpenChromDnaseChorionAlnRep1.bam Chorion DnaseSeq Alignments 1 bam Duke Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeOpenChromDnase/wgEncodeOpenChromDnaseChorionAlnRep2.bam Chorion DnaseSeq Alignments 2 bam Duke Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeOpenChromDnase/wgEncodeOpenChromDnaseChorionBaseOverlapSignal.bigWig Chorion DnaseSeq Base_Overlap_Signal bigWig Duke Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeOpenChromDnase/wgEncodeOpenChromDnaseChorionPk.narrowPeak.gz Chorion DnaseSeq Peaks narrowPeak Duke Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeOpenChromDnase/wgEncodeOpenChromDnaseChorionSig.bigWig Chorion DnaseSeq Signal bigWig Duke Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeOpenChromDnase/wgEncodeOpenChromDnaseCllAlnRep1.bam CLL DnaseSeq Alignments 1 bam Duke Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeOpenChromDnase/wgEncodeOpenChromDnaseCllAlnRep2.bam CLL DnaseSeq Alignments 2 bam Duke Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeOpenChromDnase/wgEncodeOpenChromDnaseCllAlnRep3.bam CLL DnaseSeq Alignments 3 bam Duke Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeOpenChromDnase/wgEncodeOpenChromDnaseCllBaseOverlapSignal.bigWig CLL DnaseSeq Base_Overlap_Signal bigWig Duke Data 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Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeOpenChromDnase/wgEncodeOpenChromDnaseFibroblgm03348LenticonPk.narrowPeak.gz Fibrobl_GM03348 DnaseSeq Peaks narrowPeak Duke Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeOpenChromDnase/wgEncodeOpenChromDnaseFibroblgm03348LenticonSig.bigWig Fibrobl_GM03348 DnaseSeq Signal bigWig Duke Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeOpenChromDnase/wgEncodeOpenChromDnaseFibroblgm03348LentimyodAlnRep1.bam Fibrobl_GM03348 DnaseSeq Alignments 1 bam Duke Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeOpenChromDnase/wgEncodeOpenChromDnaseFibroblgm03348LentimyodAlnRep2.bam Fibrobl_GM03348 DnaseSeq Alignments 2 bam Duke Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeOpenChromDnase/wgEncodeOpenChromDnaseFibroblgm03348LentimyodBaseOverlapSignal.bigWig Fibrobl_GM03348 DnaseSeq Base_Overlap_Signal bigWig Duke Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeOpenChromDnase/wgEncodeOpenChromDnaseFibroblgm03348LentimyodPk.narrowPeak.gz Fibrobl_GM03348 DnaseSeq Peaks narrowPeak Duke Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeOpenChromDnase/wgEncodeOpenChromDnaseFibroblgm03348LentimyodSig.bigWig Fibrobl_GM03348 DnaseSeq Signal bigWig Duke Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeOpenChromDnase/wgEncodeOpenChromDnaseFibroblgm03348Pk.narrowPeak.gz Fibrobl_GM03348 DnaseSeq Peaks narrowPeak Duke Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeOpenChromDnase/wgEncodeOpenChromDnaseFibroblgm03348Sig.bigWig Fibrobl_GM03348 DnaseSeq Signal bigWig Duke Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeOpenChromDnase/wgEncodeOpenChromDnaseFibropAlnRep1.bam FibroP DnaseSeq Alignments 1 bam Duke Data 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http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeOpenChromDnase/wgEncodeOpenChromDnaseFibropag08396AlnRep1.bam FibroP_AG08396 DnaseSeq Alignments 1 bam Duke Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeOpenChromDnase/wgEncodeOpenChromDnaseFibropag08396AlnRep2.bam FibroP_AG08396 DnaseSeq Alignments 2 bam Duke Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeOpenChromDnase/wgEncodeOpenChromDnaseFibropag08396AlnRep3.bam FibroP_AG08396 DnaseSeq Alignments 3 bam Duke Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeOpenChromDnase/wgEncodeOpenChromDnaseFibropag08396BaseOverlapSignal.bigWig FibroP_AG08396 DnaseSeq Base_Overlap_Signal bigWig Duke Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeOpenChromDnase/wgEncodeOpenChromDnaseFibropag08396Pk.narrowPeak.gz FibroP_AG08396 DnaseSeq Peaks narrowPeak Duke Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeOpenChromDnase/wgEncodeOpenChromDnaseFibropag08396Sig.bigWig FibroP_AG08396 DnaseSeq Signal bigWig Duke Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeOpenChromDnase/wgEncodeOpenChromDnaseFibropag20443AlnRep1.bam FibroP_AG20443 DnaseSeq Alignments 1 bam Duke Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeOpenChromDnase/wgEncodeOpenChromDnaseFibropag20443AlnRep2.bam FibroP_AG20443 DnaseSeq Alignments 2 bam Duke Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeOpenChromDnase/wgEncodeOpenChromDnaseFibropag20443AlnRep3.bam FibroP_AG20443 DnaseSeq Alignments 3 bam Duke Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeOpenChromDnase/wgEncodeOpenChromDnaseFibropag20443BaseOverlapSignal.bigWig FibroP_AG20443 DnaseSeq Base_Overlap_Signal bigWig Duke Data 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http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeOpenChromDnase/wgEncodeOpenChromDnasePhteAlnRep1.bam pHTE DnaseSeq Alignments 1 bam Duke Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeOpenChromDnase/wgEncodeOpenChromDnasePhteAlnRep2.bam pHTE DnaseSeq Alignments 2 bam Duke Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeOpenChromDnase/wgEncodeOpenChromDnasePhteBaseOverlapSignal.bigWig pHTE DnaseSeq Base_Overlap_Signal bigWig Duke Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeOpenChromDnase/wgEncodeOpenChromDnasePhtePk.narrowPeak.gz pHTE DnaseSeq Peaks narrowPeak Duke Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeOpenChromDnase/wgEncodeOpenChromDnasePhteSig.bigWig pHTE DnaseSeq Signal bigWig Duke Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeOpenChromDnase/wgEncodeOpenChromDnaseProgfibAlnRep1.bam ProgFib DnaseSeq Alignments 1 bam Duke Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeOpenChromDnase/wgEncodeOpenChromDnaseProgfibAlnRep2.bam ProgFib DnaseSeq Alignments 2 bam Duke Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeOpenChromDnase/wgEncodeOpenChromDnaseProgfibBaseOverlapSignal.bigWig ProgFib DnaseSeq Base_Overlap_Signal bigWig Duke Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeOpenChromDnase/wgEncodeOpenChromDnaseProgfibPk.narrowPeak.gz ProgFib DnaseSeq Peaks narrowPeak Duke Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeOpenChromDnase/wgEncodeOpenChromDnaseProgfibSig.bigWig ProgFib DnaseSeq Signal bigWig Duke Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeOpenChromDnase/wgEncodeOpenChromDnasePsoasmuscleocAlnRep1.bam Psoas_muscle_OC DnaseSeq Alignments 1 bam Duke Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeOpenChromDnase/wgEncodeOpenChromDnasePsoasmuscleocAlnRep2.bam Psoas_muscle_OC DnaseSeq Alignments 2 bam Duke Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeOpenChromDnase/wgEncodeOpenChromDnasePsoasmuscleocBaseOverlapSignal.bigWig Psoas_muscle_OC DnaseSeq Base_Overlap_Signal bigWig Duke Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeOpenChromDnase/wgEncodeOpenChromDnasePsoasmuscleocPk.narrowPeak.gz Psoas_muscle_OC DnaseSeq Peaks narrowPeak Duke Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeOpenChromDnase/wgEncodeOpenChromDnasePsoasmuscleocSig.bigWig Psoas_muscle_OC DnaseSeq Signal bigWig Duke Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeOpenChromDnase/wgEncodeOpenChromDnaseRwpe1AlnRep1.bam RWPE1 DnaseSeq Alignments 1 bam Duke Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeOpenChromDnase/wgEncodeOpenChromDnaseRwpe1AlnRep2.bam RWPE1 DnaseSeq Alignments 2 bam Duke Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeOpenChromDnase/wgEncodeOpenChromDnaseRwpe1BaseOverlapSignal.bigWig RWPE1 DnaseSeq Base_Overlap_Signal bigWig Duke Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeOpenChromDnase/wgEncodeOpenChromDnaseRwpe1Pk.narrowPeak.gz RWPE1 DnaseSeq Peaks narrowPeak Duke Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeOpenChromDnase/wgEncodeOpenChromDnaseRwpe1Sig.bigWig RWPE1 DnaseSeq Signal bigWig Duke Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeOpenChromDnase/wgEncodeOpenChromDnaseSknshAlnRep1.bam SK-N-SH DnaseSeq Alignments 1 bam Duke Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeOpenChromDnase/wgEncodeOpenChromDnaseSknshAlnRep2.bam SK-N-SH DnaseSeq Alignments 2 bam Duke Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeOpenChromDnase/wgEncodeOpenChromDnaseSknshBaseOverlapSignal.bigWig SK-N-SH DnaseSeq Base_Overlap_Signal bigWig Duke Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeOpenChromDnase/wgEncodeOpenChromDnaseSknshPk.narrowPeak.gz SK-N-SH DnaseSeq Peaks narrowPeak Duke Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeOpenChromDnase/wgEncodeOpenChromDnaseSknshSig.bigWig SK-N-SH DnaseSeq Signal bigWig Duke Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeOpenChromDnase/wgEncodeOpenChromDnaseStellateAlnRep1.bam Stellate DnaseSeq Alignments 1 bam Duke Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeOpenChromDnase/wgEncodeOpenChromDnaseStellateAlnRep2.bam Stellate DnaseSeq Alignments 2 bam Duke Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeOpenChromDnase/wgEncodeOpenChromDnaseStellateBaseOverlapSignal.bigWig Stellate DnaseSeq Base_Overlap_Signal bigWig Duke Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeOpenChromDnase/wgEncodeOpenChromDnaseStellatePk.narrowPeak.gz Stellate DnaseSeq Peaks narrowPeak Duke Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeOpenChromDnase/wgEncodeOpenChromDnaseStellateSig.bigWig Stellate DnaseSeq Signal bigWig Duke Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeOpenChromDnase/wgEncodeOpenChromDnaseT47dAlnRep1.bam T-47D DnaseSeq Alignments 1 bam Duke Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeOpenChromDnase/wgEncodeOpenChromDnaseT47dAlnRep2.bam T-47D DnaseSeq Alignments 2 bam Duke Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeOpenChromDnase/wgEncodeOpenChromDnaseT47dBaseOverlapSignal.bigWig T-47D DnaseSeq Base_Overlap_Signal bigWig Duke Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeOpenChromDnase/wgEncodeOpenChromDnaseT47dEst10nm30mAlnRep1.bam T-47D DnaseSeq Alignments 1 bam Duke Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeOpenChromDnase/wgEncodeOpenChromDnaseT47dEst10nm30mAlnRep2.bam T-47D DnaseSeq Alignments 2 bam Duke Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeOpenChromDnase/wgEncodeOpenChromDnaseT47dEst10nm30mBaseOverlapSignal.bigWig T-47D DnaseSeq Base_Overlap_Signal bigWig Duke Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeOpenChromDnase/wgEncodeOpenChromDnaseT47dEst10nm30mPk.narrowPeak.gz T-47D DnaseSeq Peaks narrowPeak Duke Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeOpenChromDnase/wgEncodeOpenChromDnaseT47dEst10nm30mSig.bigWig T-47D DnaseSeq Signal bigWig Duke Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeOpenChromDnase/wgEncodeOpenChromDnaseT47dPk.narrowPeak.gz T-47D DnaseSeq Peaks narrowPeak Duke Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeOpenChromDnase/wgEncodeOpenChromDnaseT47dSig.bigWig T-47D DnaseSeq Signal bigWig Duke Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeOpenChromDnase/wgEncodeOpenChromDnaseUrothelAlnRep1V2.bam Urothelia DnaseSeq Alignments 1 bam Duke Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeOpenChromDnase/wgEncodeOpenChromDnaseUrothelAlnRep2V2.bam Urothelia DnaseSeq Alignments 2 bam Duke Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeOpenChromDnase/wgEncodeOpenChromDnaseUrothelBaseOverlapSignalV2.bigWig Urothelia DnaseSeq Base_Overlap_Signal bigWig Duke Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeOpenChromDnase/wgEncodeOpenChromDnaseUrothelPkV2.narrowPeak.gz Urothelia DnaseSeq Peaks narrowPeak Duke Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeOpenChromDnase/wgEncodeOpenChromDnaseUrothelSigV2.bigWig Urothelia DnaseSeq Signal bigWig Duke Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeOpenChromDnase/wgEncodeOpenChromDnaseUrothelUt189AlnRep1V2.bam Urothelia DnaseSeq Alignments 1 bam Duke Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeOpenChromDnase/wgEncodeOpenChromDnaseUrothelUt189AlnRep2V2.bam Urothelia DnaseSeq Alignments 2 bam Duke Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeOpenChromDnase/wgEncodeOpenChromDnaseUrothelUt189BaseOverlapSignalV2.bigWig Urothelia DnaseSeq Base_Overlap_Signal bigWig Duke Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeOpenChromDnase/wgEncodeOpenChromDnaseUrothelUt189PkV2.narrowPeak.gz Urothelia DnaseSeq Peaks narrowPeak Duke Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeOpenChromDnase/wgEncodeOpenChromDnaseUrothelUt189SigV2.bigWig Urothelia DnaseSeq Signal bigWig Duke Data 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Alignments 1 bam Duke Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeOpenChromDnase/wgEncodeOpenChromDnaseUrotsaUt189AlnRep2.bam Urothelia DnaseSeq Alignments 2 bam Duke Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeOpenChromDnase/wgEncodeOpenChromDnaseUrotsaUt189BaseOverlapSignal.bigWig Urothelia DnaseSeq Base_Overlap_Signal bigWig Duke Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeOpenChromDnase/wgEncodeOpenChromDnaseUrotsaUt189Pk.narrowPeak.gz Urothelia DnaseSeq Peaks narrowPeak Duke Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeOpenChromDnase/wgEncodeOpenChromDnaseUrotsaUt189Sig.bigWig Urothelia DnaseSeq Signal bigWig Duke Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeOpenChromFaire/wgEncodeOpenChromFaireA549AlnRep1.bam A549 FaireSeq Alignments 1 bam UNC Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeOpenChromFaire/wgEncodeOpenChromFaireA549AlnRep2.bam A549 FaireSeq Alignments 2 bam UNC Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeOpenChromFaire/wgEncodeOpenChromFaireA549BaseOverlapSignal.bigWig A549 FaireSeq Base_Overlap_Signal bigWig UNC Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeOpenChromFaire/wgEncodeOpenChromFaireA549Pk.narrowPeak.gz A549 FaireSeq Peaks narrowPeak UNC Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeOpenChromFaire/wgEncodeOpenChromFaireA549Sig.bigWig A549 FaireSeq Signal bigWig UNC Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeOpenChromFaire/wgEncodeOpenChromFaireAstrocyAlnRep1.bam Astrocy FaireSeq Alignments 1 bam UNC Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeOpenChromFaire/wgEncodeOpenChromFaireAstrocyAlnRep2.bam Astrocy FaireSeq Alignments 2 bam UNC Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeOpenChromFaire/wgEncodeOpenChromFaireAstrocyBaseOverlapSignal.bigWig Astrocy FaireSeq Base_Overlap_Signal bigWig UNC Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeOpenChromFaire/wgEncodeOpenChromFaireAstrocyPk.narrowPeak.gz Astrocy FaireSeq Peaks narrowPeak UNC Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeOpenChromFaire/wgEncodeOpenChromFaireAstrocySig.bigWig Astrocy FaireSeq Signal bigWig UNC Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeOpenChromFaire/wgEncodeOpenChromFaireColonocAlnRep1.bam Colon_OC FaireSeq Alignments 1 bam UNC Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeOpenChromFaire/wgEncodeOpenChromFaireColonocAlnRep2.bam Colon_OC FaireSeq Alignments 2 bam UNC Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeOpenChromFaire/wgEncodeOpenChromFaireColonocBaseOverlapSignal.bigWig Colon_OC FaireSeq Base_Overlap_Signal bigWig UNC Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeOpenChromFaire/wgEncodeOpenChromFaireColonocPk.narrowPeak.gz Colon_OC FaireSeq Peaks narrowPeak UNC Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeOpenChromFaire/wgEncodeOpenChromFaireColonocSig.bigWig Colon_OC FaireSeq Signal bigWig UNC Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeOpenChromFaire/wgEncodeOpenChromFaireEndometriumocAlnRep1.bam Endometrium_OC FaireSeq Alignments 1 bam UNC Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeOpenChromFaire/wgEncodeOpenChromFaireEndometriumocAlnRep2.bam Endometrium_OC FaireSeq Alignments 2 bam UNC Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeOpenChromFaire/wgEncodeOpenChromFaireEndometriumocBaseOverlapSignal.bigWig Endometrium_OC FaireSeq Base_Overlap_Signal bigWig UNC Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeOpenChromFaire/wgEncodeOpenChromFaireEndometriumocPk.narrowPeak.gz Endometrium_OC FaireSeq Peaks narrowPeak UNC Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeOpenChromFaire/wgEncodeOpenChromFaireEndometriumocSig.bigWig Endometrium_OC FaireSeq Signal bigWig UNC Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeOpenChromFaire/wgEncodeOpenChromFaireFrontalcortexocAlnRep1.bam Frontal_cortex_OC FaireSeq Alignments 1 bam UNC Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeOpenChromFaire/wgEncodeOpenChromFaireFrontalcortexocAlnRep2.bam Frontal_cortex_OC FaireSeq Alignments 2 bam UNC Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeOpenChromFaire/wgEncodeOpenChromFaireFrontalcortexocBaseOverlapSignal.bigWig Frontal_cortex_OC FaireSeq Base_Overlap_Signal bigWig UNC Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeOpenChromFaire/wgEncodeOpenChromFaireFrontalcortexocPk.narrowPeak.gz Frontal_cortex_OC FaireSeq Peaks narrowPeak UNC Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeOpenChromFaire/wgEncodeOpenChromFaireFrontalcortexocSig.bigWig Frontal_cortex_OC FaireSeq Signal bigWig UNC Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeOpenChromFaire/wgEncodeOpenChromFaireGlioblaAlnRep1.bam Gliobla FaireSeq Alignments 1 bam UNC Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeOpenChromFaire/wgEncodeOpenChromFaireGlioblaAlnRep2.bam Gliobla FaireSeq Alignments 2 bam UNC Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeOpenChromFaire/wgEncodeOpenChromFaireGlioblaAlnRep3.bam Gliobla FaireSeq Alignments 3 bam UNC Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeOpenChromFaire/wgEncodeOpenChromFaireGlioblaBaseOverlapSignal.bigWig Gliobla FaireSeq Base_Overlap_Signal bigWig UNC Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeOpenChromFaire/wgEncodeOpenChromFaireGlioblaPk.narrowPeak.gz Gliobla FaireSeq Peaks narrowPeak UNC Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeOpenChromFaire/wgEncodeOpenChromFaireGlioblaSig.bigWig Gliobla FaireSeq Signal bigWig UNC Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeOpenChromFaire/wgEncodeOpenChromFaireGm12878AlnRep1.bam GM12878 FaireSeq Alignments 1 bam UNC Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeOpenChromFaire/wgEncodeOpenChromFaireGm12878AlnRep2.bam GM12878 FaireSeq Alignments 2 bam UNC Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeOpenChromFaire/wgEncodeOpenChromFaireGm12878AlnRep3.bam GM12878 FaireSeq Alignments 3 bam UNC Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeOpenChromFaire/wgEncodeOpenChromFaireGm12878BaseOverlapSignal.bigWig 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Cage MinusSignal 1 bigWig RIKEN Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeRikenCage/wgEncodeRikenCageHuvecNucleusPamPlusRawRep1.bigWig HUVEC Cage PlusSignal 1 bigWig RIKEN Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeRikenCage/wgEncodeRikenCageHuvecNucleusPapAlnRep3.bam HUVEC Cage Alignments 3 bam RIKEN Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeRikenCage/wgEncodeRikenCageHuvecNucleusPapAlnRep4.bam HUVEC Cage Alignments 4 bam RIKEN Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeRikenCage/wgEncodeRikenCageHuvecNucleusPapMinusClustersRep3.bigWig HUVEC Cage MinusSignal 3 bigWig RIKEN Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeRikenCage/wgEncodeRikenCageHuvecNucleusPapMinusClustersRep4.bigWig HUVEC Cage MinusSignal 4 bigWig RIKEN Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeRikenCage/wgEncodeRikenCageHuvecNucleusPapMinusSignalRep3.bigWig HUVEC Cage MinusSignal 3 bigWig RIKEN Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeRikenCage/wgEncodeRikenCageHuvecNucleusPapMinusSignalRep4.bigWig HUVEC Cage MinusSignal 4 bigWig RIKEN Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeRikenCage/wgEncodeRikenCageHuvecNucleusPapPlusClustersRep3.bigWig HUVEC Cage PlusSignal 3 bigWig RIKEN Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeRikenCage/wgEncodeRikenCageHuvecNucleusPapPlusClustersRep4.bigWig HUVEC Cage PlusSignal 4 bigWig RIKEN Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeRikenCage/wgEncodeRikenCageHuvecNucleusPapPlusSignalRep3.bigWig HUVEC Cage PlusSignal 3 bigWig RIKEN Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeRikenCage/wgEncodeRikenCageHuvecNucleusPapPlusSignalRep4.bigWig HUVEC Cage PlusSignal 4 bigWig RIKEN Data 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narrowPeak Stanford Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeSydhTfbs/wgEncodeSydhTfbsA549CmycIggrabSig.bigWig A549 ChipSeq c-Myc Signal bigWig Stanford Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeSydhTfbs/wgEncodeSydhTfbsA549CtcfbIggrabAlnRep1.bam A549 ChipSeq CTCF_(SC-15914) Alignments 1 bam Stanford Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeSydhTfbs/wgEncodeSydhTfbsA549CtcfbIggrabAlnRep2.bam A549 ChipSeq CTCF_(SC-15914) Alignments 2 bam Stanford Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeSydhTfbs/wgEncodeSydhTfbsA549CtcfbIggrabPk.narrowPeak.gz A549 ChipSeq CTCF_(SC-15914) Peaks narrowPeak Stanford Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeSydhTfbs/wgEncodeSydhTfbsA549CtcfbIggrabSig.bigWig A549 ChipSeq CTCF_(SC-15914) Signal bigWig Stanford Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeSydhTfbs/wgEncodeSydhTfbsA549InputIggrabAlnRep1.bam A549 ChipSeq Input Alignments 1 bam Stanford Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeSydhTfbs/wgEncodeSydhTfbsA549InputIggrabSig.bigWig A549 ChipSeq Input Signal bigWig Stanford Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeSydhTfbs/wgEncodeSydhTfbsA549MaxIggrabAlnRep1.bam A549 ChipSeq Max Alignments 1 bam Stanford Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeSydhTfbs/wgEncodeSydhTfbsA549MaxIggrabAlnRep2.bam A549 ChipSeq Max Alignments 2 bam Stanford Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeSydhTfbs/wgEncodeSydhTfbsA549MaxIggrabPk.narrowPeak.gz A549 ChipSeq Max Peaks narrowPeak Stanford Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeSydhTfbs/wgEncodeSydhTfbsA549MaxIggrabSig.bigWig A549 ChipSeq Max Signal bigWig Stanford Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeSydhTfbs/wgEncodeSydhTfbsA549Pol2s2IggrabAlnRep1.bam A549 ChipSeq Pol2(phosphoS2) Alignments 1 bam Stanford Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeSydhTfbs/wgEncodeSydhTfbsA549Pol2s2IggrabAlnRep2.bam A549 ChipSeq Pol2(phosphoS2) Alignments 2 bam Stanford Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeSydhTfbs/wgEncodeSydhTfbsA549Pol2s2IggrabPk.narrowPeak.gz A549 ChipSeq Pol2(phosphoS2) Peaks narrowPeak Stanford Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeSydhTfbs/wgEncodeSydhTfbsA549Pol2s2IggrabSig.bigWig A549 ChipSeq Pol2(phosphoS2) Signal bigWig Stanford Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeSydhTfbs/wgEncodeSydhTfbsA549Rad21IggrabAlnRep1.bam A549 ChipSeq Rad21 Alignments 1 bam Stanford Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeSydhTfbs/wgEncodeSydhTfbsA549Rad21IggrabAlnRep2.bam A549 ChipSeq Rad21 Alignments 2 bam Stanford Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeSydhTfbs/wgEncodeSydhTfbsA549Rad21IggrabPk.narrowPeak.gz A549 ChipSeq Rad21 Peaks narrowPeak Stanford Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeSydhTfbs/wgEncodeSydhTfbsA549Rad21IggrabSig.bigWig A549 ChipSeq Rad21 Signal bigWig Stanford Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeSydhTfbs/wgEncodeSydhTfbsGm08714InputUcdAlnRep1.bam GM08714 ChipSeq Input Alignments 1 bam USC Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeSydhTfbs/wgEncodeSydhTfbsGm08714InputUcdSig.bigWig GM08714 ChipSeq Input Signal bigWig USC Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeSydhTfbs/wgEncodeSydhTfbsGm08714Znf274UcdAlnRep1.bam GM08714 ChipSeq ZNF274 Alignments 1 bam USC Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeSydhTfbs/wgEncodeSydhTfbsGm08714Znf274UcdAlnRep2.bam GM08714 ChipSeq ZNF274 Alignments 2 bam USC Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeSydhTfbs/wgEncodeSydhTfbsGm08714Znf274UcdPk.narrowPeak.gz GM08714 ChipSeq ZNF274 Peaks narrowPeak USC Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeSydhTfbs/wgEncodeSydhTfbsGm08714Znf274UcdSig.bigWig GM08714 ChipSeq ZNF274 Signal bigWig USC Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeSydhTfbs/wgEncodeSydhTfbsGm10847InputIggmusAlnRep1.bam GM10847 ChipSeq Input Alignments 1 bam Stanford Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeSydhTfbs/wgEncodeSydhTfbsGm10847InputIggmusAlnRep2.bam GM10847 ChipSeq Input Alignments 2 bam Stanford Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeSydhTfbs/wgEncodeSydhTfbsGm10847InputIggmusSig.bigWig GM10847 ChipSeq Input Signal bigWig Stanford Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeSydhTfbs/wgEncodeSydhTfbsGm10847InputTnfaIggrabAlnRep1.bam GM10847 ChipSeq Input Alignments 1 bam Stanford Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeSydhTfbs/wgEncodeSydhTfbsGm10847InputTnfaIggrabAlnRep2.bam GM10847 ChipSeq Input Alignments 2 bam Stanford Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeSydhTfbs/wgEncodeSydhTfbsGm10847InputTnfaIggrabSig.bigWig GM10847 ChipSeq Input Signal bigWig Stanford Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeSydhTfbs/wgEncodeSydhTfbsGm10847NfkbTnfaIggrabAlnRep1.bam GM10847 ChipSeq NFKB Alignments 1 bam Stanford Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeSydhTfbs/wgEncodeSydhTfbsGm10847NfkbTnfaIggrabAlnRep2.bam GM10847 ChipSeq NFKB Alignments 2 bam Stanford Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeSydhTfbs/wgEncodeSydhTfbsGm10847NfkbTnfaIggrabAlnRep3.bam GM10847 ChipSeq NFKB Alignments 3 bam Stanford Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeSydhTfbs/wgEncodeSydhTfbsGm10847NfkbTnfaIggrabAlnRep4.bam GM10847 ChipSeq NFKB Alignments 4 bam Stanford Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeSydhTfbs/wgEncodeSydhTfbsGm10847NfkbTnfaIggrabAlnRep5.bam GM10847 ChipSeq NFKB Alignments 5 bam Stanford Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeSydhTfbs/wgEncodeSydhTfbsGm10847NfkbTnfaIggrabPk.narrowPeak.gz GM10847 ChipSeq NFKB Peaks narrowPeak Stanford Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeSydhTfbs/wgEncodeSydhTfbsGm10847NfkbTnfaIggrabSig.bigWig GM10847 ChipSeq NFKB Signal bigWig Stanford Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeSydhTfbs/wgEncodeSydhTfbsGm10847Pol2IggmusAlnRep1.bam GM10847 ChipSeq Pol2 Alignments 1 bam Stanford Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeSydhTfbs/wgEncodeSydhTfbsGm10847Pol2IggmusAlnRep2.bam GM10847 ChipSeq Pol2 Alignments 2 bam Stanford Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeSydhTfbs/wgEncodeSydhTfbsGm10847Pol2IggmusPk.narrowPeak.gz GM10847 ChipSeq Pol2 Peaks narrowPeak Stanford Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeSydhTfbs/wgEncodeSydhTfbsGm10847Pol2IggmusSig.bigWig GM10847 ChipSeq Pol2 Signal bigWig Stanford Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeSydhTfbs/wgEncodeSydhTfbsGm12878Bhlhe40cIggmusAlnRep1.bam GM12878 ChipSeq BHLHE40_(NB100-1800) Alignments 1 bam Stanford Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeSydhTfbs/wgEncodeSydhTfbsGm12878Bhlhe40cIggmusAlnRep2.bam GM12878 ChipSeq BHLHE40_(NB100-1800) Alignments 2 bam Stanford Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeSydhTfbs/wgEncodeSydhTfbsGm12878Bhlhe40cIggmusPk.narrowPeak.gz GM12878 ChipSeq BHLHE40_(NB100-1800) Peaks narrowPeak Stanford Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeSydhTfbs/wgEncodeSydhTfbsGm12878Bhlhe40cIggmusSig.bigWig GM12878 ChipSeq BHLHE40_(NB100-1800) Signal bigWig Stanford Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeSydhTfbs/wgEncodeSydhTfbsGm12878Brca1a300IggmusAlnRep1.bam GM12878 ChipSeq BRCA1_(A300-000A) Alignments 1 bam Stanford Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeSydhTfbs/wgEncodeSydhTfbsGm12878Brca1a300IggmusAlnRep2.bam GM12878 ChipSeq BRCA1_(A300-000A) Alignments 2 bam Stanford Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeSydhTfbs/wgEncodeSydhTfbsGm12878Brca1a300IggmusPk.narrowPeak.gz GM12878 ChipSeq BRCA1_(A300-000A) Peaks narrowPeak Stanford Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeSydhTfbs/wgEncodeSydhTfbsGm12878Brca1a300IggmusSig.bigWig GM12878 ChipSeq BRCA1_(A300-000A) Signal bigWig Stanford Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeSydhTfbs/wgEncodeSydhTfbsGm12878Cdpsc6327IggmusAlnRep1.bam GM12878 ChipSeq CDP_(sc-6327) Alignments 1 bam Stanford Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeSydhTfbs/wgEncodeSydhTfbsGm12878Cdpsc6327IggmusAlnRep2.bam GM12878 ChipSeq CDP_(sc-6327) Alignments 2 bam Stanford Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeSydhTfbs/wgEncodeSydhTfbsGm12878Cdpsc6327IggmusPk.narrowPeak.gz GM12878 ChipSeq CDP_(sc-6327) Peaks narrowPeak Stanford Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeSydhTfbs/wgEncodeSydhTfbsGm12878Cdpsc6327IggmusSig.bigWig GM12878 ChipSeq CDP_(sc-6327) Signal bigWig Stanford Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeSydhTfbs/wgEncodeSydhTfbsGm12878CfosStdAlnRep1.bam GM12878 ChipSeq c-Fos Alignments 1 bam Yale Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeSydhTfbs/wgEncodeSydhTfbsGm12878CfosStdAlnRep2.bam GM12878 ChipSeq c-Fos Alignments 2 bam Yale Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeSydhTfbs/wgEncodeSydhTfbsGm12878CfosStdAlnRep3.bam GM12878 ChipSeq c-Fos Alignments 3 bam Yale Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeSydhTfbs/wgEncodeSydhTfbsGm12878CfosStdPk.narrowPeak.gz GM12878 ChipSeq c-Fos Peaks narrowPeak Yale Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeSydhTfbs/wgEncodeSydhTfbsGm12878CfosStdSig.bigWig GM12878 ChipSeq c-Fos Signal bigWig Yale Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeSydhTfbs/wgEncodeSydhTfbsGm12878Chd1a301218aIggmusAlnRep1.bam GM12878 ChipSeq CHD1_(A301-218A) Alignments 1 bam Stanford Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeSydhTfbs/wgEncodeSydhTfbsGm12878Chd1a301218aIggmusAlnRep2.bam GM12878 ChipSeq CHD1_(A301-218A) Alignments 2 bam Stanford Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeSydhTfbs/wgEncodeSydhTfbsGm12878Chd1a301218aIggmusPk.narrowPeak.gz GM12878 ChipSeq CHD1_(A301-218A) Peaks narrowPeak Stanford Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeSydhTfbs/wgEncodeSydhTfbsGm12878Chd1a301218aIggmusSig.bigWig GM12878 ChipSeq CHD1_(A301-218A) Signal bigWig Stanford Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeSydhTfbs/wgEncodeSydhTfbsGm12878Chd2ab68301IggmusAlnRep1.bam GM12878 ChipSeq CHD2_(AB68301) Alignments 1 bam Stanford Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeSydhTfbs/wgEncodeSydhTfbsGm12878Chd2ab68301IggmusAlnRep2.bam GM12878 ChipSeq CHD2_(AB68301) Alignments 2 bam Stanford Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeSydhTfbs/wgEncodeSydhTfbsGm12878Chd2ab68301IggmusPk.narrowPeak.gz GM12878 ChipSeq CHD2_(AB68301) Peaks narrowPeak Stanford Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeSydhTfbs/wgEncodeSydhTfbsGm12878Chd2ab68301IggmusSig.bigWig GM12878 ChipSeq CHD2_(AB68301) Signal bigWig Stanford Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeSydhTfbs/wgEncodeSydhTfbsGm12878Corestsc30189IggmusAlnRep1.bam GM12878 ChipSeq COREST_(sc-30189) Alignments 1 bam Stanford Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeSydhTfbs/wgEncodeSydhTfbsGm12878Corestsc30189IggmusAlnRep2.bam GM12878 ChipSeq COREST_(sc-30189) Alignments 2 bam Stanford Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeSydhTfbs/wgEncodeSydhTfbsGm12878Corestsc30189IggmusPk.narrowPeak.gz GM12878 ChipSeq COREST_(sc-30189) Peaks narrowPeak Stanford Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeSydhTfbs/wgEncodeSydhTfbsGm12878Corestsc30189IggmusSig.bigWig GM12878 ChipSeq COREST_(sc-30189) Signal bigWig Stanford Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeSydhTfbs/wgEncodeSydhTfbsGm12878Ctcfsc15914c20StdAlnRep1.bam GM12878 ChipSeq CTCF_(SC-15914) Alignments 1 bam Stanford Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeSydhTfbs/wgEncodeSydhTfbsGm12878Ctcfsc15914c20StdAlnRep2.bam GM12878 ChipSeq CTCF_(SC-15914) Alignments 2 bam Stanford Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeSydhTfbs/wgEncodeSydhTfbsGm12878Ctcfsc15914c20StdPk.narrowPeak.gz GM12878 ChipSeq CTCF_(SC-15914) Peaks narrowPeak Stanford Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeSydhTfbs/wgEncodeSydhTfbsGm12878Ctcfsc15914c20StdSig.bigWig GM12878 ChipSeq CTCF_(SC-15914) Signal bigWig Stanford Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeSydhTfbs/wgEncodeSydhTfbsGm12878E2f4IggmusAlnRep1.bam GM12878 ChipSeq E2F4 Alignments 1 bam Stanford Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeSydhTfbs/wgEncodeSydhTfbsGm12878E2f4IggmusAlnRep2.bam GM12878 ChipSeq E2F4 Alignments 2 bam Stanford Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeSydhTfbs/wgEncodeSydhTfbsGm12878E2f4IggmusPk.narrowPeak.gz GM12878 ChipSeq E2F4 Peaks narrowPeak Stanford Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeSydhTfbs/wgEncodeSydhTfbsGm12878E2f4IggmusSig.bigWig GM12878 ChipSeq E2F4 Signal bigWig Stanford Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeSydhTfbs/wgEncodeSydhTfbsGm12878Ebf1sc137065StdAlnRep1.bam GM12878 ChipSeq EBF1_(SC-137065) Alignments 1 bam Stanford Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeSydhTfbs/wgEncodeSydhTfbsGm12878Ebf1sc137065StdAlnRep2.bam GM12878 ChipSeq EBF1_(SC-137065) Alignments 2 bam Stanford Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeSydhTfbs/wgEncodeSydhTfbsGm12878Ebf1sc137065StdPk.narrowPeak.gz GM12878 ChipSeq EBF1_(SC-137065) Peaks narrowPeak Stanford Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeSydhTfbs/wgEncodeSydhTfbsGm12878Ebf1sc137065StdSig.bigWig GM12878 ChipSeq EBF1_(SC-137065) Signal bigWig Stanford Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeSydhTfbs/wgEncodeSydhTfbsGm12878Elk112771IggmusAlnRep1.bam GM12878 ChipSeq ELK1_(1277-1) Alignments 1 bam Stanford Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeSydhTfbs/wgEncodeSydhTfbsGm12878Elk112771IggmusAlnRep2.bam GM12878 ChipSeq ELK1_(1277-1) Alignments 2 bam Stanford Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeSydhTfbs/wgEncodeSydhTfbsGm12878Elk112771IggmusPk.narrowPeak.gz GM12878 ChipSeq ELK1_(1277-1) Peaks narrowPeak Stanford Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeSydhTfbs/wgEncodeSydhTfbsGm12878Elk112771IggmusSig.bigWig GM12878 ChipSeq ELK1_(1277-1) Signal bigWig Stanford Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeSydhTfbs/wgEncodeSydhTfbsGm12878ErraIggrabAlnRep1.bam GM12878 ChipSeq ERRA Alignments 1 bam Stanford Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeSydhTfbs/wgEncodeSydhTfbsGm12878ErraIggrabAlnRep2.bam GM12878 ChipSeq ERRA Alignments 2 bam Stanford Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeSydhTfbs/wgEncodeSydhTfbsGm12878ErraIggrabPk.narrowPeak.gz GM12878 ChipSeq ERRA Peaks narrowPeak Stanford Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeSydhTfbs/wgEncodeSydhTfbsGm12878ErraIggrabSig.bigWig GM12878 ChipSeq ERRA Signal bigWig Stanford Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeSydhTfbs/wgEncodeSydhTfbsGm12878Gcn5StdAlnRep1.bam GM12878 ChipSeq GCN5 Alignments 1 bam Harvard Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeSydhTfbs/wgEncodeSydhTfbsGm12878Gcn5StdAlnRep2.bam GM12878 ChipSeq GCN5 Alignments 2 bam Harvard Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeSydhTfbs/wgEncodeSydhTfbsGm12878Gcn5StdPk.narrowPeak.gz GM12878 ChipSeq GCN5 Peaks narrowPeak Harvard Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeSydhTfbs/wgEncodeSydhTfbsGm12878Gcn5StdSig.bigWig GM12878 ChipSeq GCN5 Signal bigWig Harvard Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeSydhTfbs/wgEncodeSydhTfbsGm12878Ikzf1iknuclaStdAlnRep1.bam GM12878 ChipSeq IKZF1_(IkN)_(UCLA) Alignments 1 bam USC Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeSydhTfbs/wgEncodeSydhTfbsGm12878Ikzf1iknuclaStdAlnRep2.bam GM12878 ChipSeq IKZF1_(IkN)_(UCLA) Alignments 2 bam USC Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeSydhTfbs/wgEncodeSydhTfbsGm12878Ikzf1iknuclaStdPk.narrowPeak.gz GM12878 ChipSeq IKZF1_(IkN)_(UCLA) Peaks narrowPeak USC Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeSydhTfbs/wgEncodeSydhTfbsGm12878Ikzf1iknuclaStdSig.bigWig GM12878 ChipSeq IKZF1_(IkN)_(UCLA) Signal bigWig USC Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeSydhTfbs/wgEncodeSydhTfbsGm12878InputIggmusAlnRep1.bam GM12878 ChipSeq Input Alignments 1 bam Stanford Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeSydhTfbs/wgEncodeSydhTfbsGm12878InputIggmusAlnRep2.bam GM12878 ChipSeq Input Alignments 2 bam Stanford Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeSydhTfbs/wgEncodeSydhTfbsGm12878InputIggmusSig.bigWig GM12878 ChipSeq Input Signal bigWig Stanford Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeSydhTfbs/wgEncodeSydhTfbsGm12878InputIggrabAlnRep1.bam GM12878 ChipSeq Input Alignments 1 bam Stanford Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeSydhTfbs/wgEncodeSydhTfbsGm12878InputIggrabSig.bigWig GM12878 ChipSeq Input Signal bigWig Stanford Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeSydhTfbs/wgEncodeSydhTfbsGm12878InputStdAlnRep1.bam GM12878 ChipSeq Input Alignments 1 bam Yale Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeSydhTfbs/wgEncodeSydhTfbsGm12878InputStdSig.bigWig GM12878 ChipSeq Input Signal bigWig Yale Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeSydhTfbs/wgEncodeSydhTfbsGm12878InputTnfaIggrabAlnRep1.bam GM12878 ChipSeq Input Alignments 1 bam Stanford Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeSydhTfbs/wgEncodeSydhTfbsGm12878InputTnfaIggrabAlnRep2.bam GM12878 ChipSeq Input Alignments 2 bam Stanford Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeSydhTfbs/wgEncodeSydhTfbsGm12878InputTnfaIggrabSig.bigWig GM12878 ChipSeq Input Signal bigWig Stanford Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeSydhTfbs/wgEncodeSydhTfbsGm12878Irf3IggmusAlnRep1.bam GM12878 ChipSeq IRF3 Alignments 1 bam Stanford Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeSydhTfbs/wgEncodeSydhTfbsGm12878Irf3IggmusAlnRep2.bam GM12878 ChipSeq IRF3 Alignments 2 bam Stanford Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeSydhTfbs/wgEncodeSydhTfbsGm12878Irf3IggmusPk.narrowPeak.gz GM12878 ChipSeq IRF3 Peaks narrowPeak Stanford Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeSydhTfbs/wgEncodeSydhTfbsGm12878Irf3IggmusSig.bigWig GM12878 ChipSeq IRF3 Signal bigWig Stanford Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeSydhTfbs/wgEncodeSydhTfbsGm12878JundIggrabAlnRep1.bam GM12878 ChipSeq JunD Alignments 1 bam Stanford Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeSydhTfbs/wgEncodeSydhTfbsGm12878JundIggrabAlnRep2.bam GM12878 ChipSeq JunD Alignments 2 bam Stanford Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeSydhTfbs/wgEncodeSydhTfbsGm12878JundIggrabPk.narrowPeak.gz GM12878 ChipSeq JunD Peaks narrowPeak Stanford Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeSydhTfbs/wgEncodeSydhTfbsGm12878JundIggrabSig.bigWig GM12878 ChipSeq JunD Signal bigWig Stanford Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeSydhTfbs/wgEncodeSydhTfbsGm12878JundStdAlnRep1.bam GM12878 ChipSeq JunD Alignments 1 bam Yale Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeSydhTfbs/wgEncodeSydhTfbsGm12878JundStdAlnRep2.bam GM12878 ChipSeq JunD Alignments 2 bam Yale Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeSydhTfbs/wgEncodeSydhTfbsGm12878JundStdPk.narrowPeak.gz GM12878 ChipSeq JunD Peaks narrowPeak Yale Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeSydhTfbs/wgEncodeSydhTfbsGm12878JundStdSig.bigWig GM12878 ChipSeq JunD Signal bigWig Yale Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeSydhTfbs/wgEncodeSydhTfbsGm12878MafkIggmusAlnRep1.bam GM12878 ChipSeq MafK_(ab50322) Alignments 1 bam Stanford Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeSydhTfbs/wgEncodeSydhTfbsGm12878MafkIggmusAlnRep2.bam GM12878 ChipSeq MafK_(ab50322) Alignments 2 bam Stanford Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeSydhTfbs/wgEncodeSydhTfbsGm12878MafkIggmusPk.narrowPeak.gz GM12878 ChipSeq MafK_(ab50322) Peaks narrowPeak Stanford Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeSydhTfbs/wgEncodeSydhTfbsGm12878MafkIggmusSig.bigWig GM12878 ChipSeq MafK_(ab50322) Signal bigWig Stanford Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeSydhTfbs/wgEncodeSydhTfbsGm12878MaxIggmusAlnRep1.bam GM12878 ChipSeq Max Alignments 1 bam Stanford Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeSydhTfbs/wgEncodeSydhTfbsGm12878MaxIggmusAlnRep2.bam GM12878 ChipSeq Max Alignments 2 bam Stanford Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeSydhTfbs/wgEncodeSydhTfbsGm12878MaxIggmusPk.narrowPeak.gz GM12878 ChipSeq Max Peaks narrowPeak Stanford Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeSydhTfbs/wgEncodeSydhTfbsGm12878MaxIggmusSig.bigWig GM12878 ChipSeq Max Signal bigWig Stanford Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeSydhTfbs/wgEncodeSydhTfbsGm12878MaxStdAlnRep1.bam GM12878 ChipSeq Max Alignments 1 bam Yale Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeSydhTfbs/wgEncodeSydhTfbsGm12878MaxStdAlnRep2.bam GM12878 ChipSeq Max Alignments 2 bam Yale Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeSydhTfbs/wgEncodeSydhTfbsGm12878MaxStdPk.narrowPeak.gz GM12878 ChipSeq Max Peaks narrowPeak Yale Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeSydhTfbs/wgEncodeSydhTfbsGm12878MaxStdSig.bigWig GM12878 ChipSeq Max Signal bigWig Yale Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeSydhTfbs/wgEncodeSydhTfbsGm12878Mazab85725IggmusAlnRep1.bam GM12878 ChipSeq MAZ_(ab85725) Alignments 1 bam Stanford Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeSydhTfbs/wgEncodeSydhTfbsGm12878Mazab85725IggmusAlnRep2.bam GM12878 ChipSeq MAZ_(ab85725) Alignments 2 bam Stanford Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeSydhTfbs/wgEncodeSydhTfbsGm12878Mazab85725IggmusPk.narrowPeak.gz GM12878 ChipSeq MAZ_(ab85725) Peaks narrowPeak Stanford Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeSydhTfbs/wgEncodeSydhTfbsGm12878Mazab85725IggmusSig.bigWig GM12878 ChipSeq MAZ_(ab85725) Signal bigWig Stanford Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeSydhTfbs/wgEncodeSydhTfbsGm12878Mxi1IggmusAlnRep1.bam GM12878 ChipSeq Mxi1_(AF4185) Alignments 1 bam Stanford Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeSydhTfbs/wgEncodeSydhTfbsGm12878Mxi1IggmusAlnRep2.bam GM12878 ChipSeq Mxi1_(AF4185) Alignments 2 bam Stanford Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeSydhTfbs/wgEncodeSydhTfbsGm12878Mxi1IggmusPk.narrowPeak.gz GM12878 ChipSeq Mxi1_(AF4185) Peaks narrowPeak Stanford Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeSydhTfbs/wgEncodeSydhTfbsGm12878Mxi1IggmusSig.bigWig GM12878 ChipSeq Mxi1_(AF4185) Signal bigWig Stanford Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeSydhTfbs/wgEncodeSydhTfbsGm12878Nfe2sc22827StdAlnRep1.bam GM12878 ChipSeq NF-E2_(SC-22827) Alignments 1 bam Stanford Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeSydhTfbs/wgEncodeSydhTfbsGm12878Nfe2sc22827StdAlnRep2.bam GM12878 ChipSeq NF-E2_(SC-22827) Alignments 2 bam Stanford Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeSydhTfbs/wgEncodeSydhTfbsGm12878Nfe2sc22827StdPk.narrowPeak.gz GM12878 ChipSeq NF-E2_(SC-22827) Peaks narrowPeak Stanford Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeSydhTfbs/wgEncodeSydhTfbsGm12878Nfe2sc22827StdSig.bigWig GM12878 ChipSeq NF-E2_(SC-22827) Signal bigWig Stanford Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeSydhTfbs/wgEncodeSydhTfbsGm12878NfkbTnfaIggrabAlnRep1.bam GM12878 ChipSeq NFKB Alignments 1 bam Stanford Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeSydhTfbs/wgEncodeSydhTfbsGm12878NfkbTnfaIggrabAlnRep2.bam GM12878 ChipSeq NFKB Alignments 2 bam Stanford Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeSydhTfbs/wgEncodeSydhTfbsGm12878NfkbTnfaIggrabAlnRep3.bam GM12878 ChipSeq NFKB Alignments 3 bam Stanford Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeSydhTfbs/wgEncodeSydhTfbsGm12878NfkbTnfaIggrabAlnRep4.bam GM12878 ChipSeq NFKB Alignments 4 bam Stanford Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeSydhTfbs/wgEncodeSydhTfbsGm12878NfkbTnfaIggrabPk.narrowPeak.gz GM12878 ChipSeq NFKB Peaks narrowPeak Stanford Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeSydhTfbs/wgEncodeSydhTfbsGm12878NfkbTnfaIggrabSig.bigWig GM12878 ChipSeq NFKB Signal bigWig Stanford Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeSydhTfbs/wgEncodeSydhTfbsGm12878NfyaIggmusAlnRep1.bam GM12878 ChipSeq NF-YA Alignments 1 bam Harvard Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeSydhTfbs/wgEncodeSydhTfbsGm12878NfyaIggmusAlnRep2.bam GM12878 ChipSeq NF-YA Alignments 2 bam Harvard Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeSydhTfbs/wgEncodeSydhTfbsGm12878NfyaIggmusPk.narrowPeak.gz GM12878 ChipSeq NF-YA Peaks narrowPeak Harvard Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeSydhTfbs/wgEncodeSydhTfbsGm12878NfyaIggmusSig.bigWig GM12878 ChipSeq NF-YA Signal bigWig Harvard Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeSydhTfbs/wgEncodeSydhTfbsGm12878NfybIggmusAlnRep1.bam GM12878 ChipSeq NF-YB Alignments 1 bam Harvard Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeSydhTfbs/wgEncodeSydhTfbsGm12878NfybIggmusAlnRep2.bam GM12878 ChipSeq NF-YB Alignments 2 bam Harvard Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeSydhTfbs/wgEncodeSydhTfbsGm12878NfybIggmusPk.narrowPeak.gz GM12878 ChipSeq NF-YB Peaks narrowPeak Harvard Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeSydhTfbs/wgEncodeSydhTfbsGm12878NfybIggmusSig.bigWig GM12878 ChipSeq NF-YB Signal bigWig Harvard Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeSydhTfbs/wgEncodeSydhTfbsGm12878Nrf1IggmusAlnRep1.bam GM12878 ChipSeq Nrf1 Alignments 1 bam Stanford Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeSydhTfbs/wgEncodeSydhTfbsGm12878Nrf1IggmusAlnRep2.bam GM12878 ChipSeq Nrf1 Alignments 2 bam Stanford Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeSydhTfbs/wgEncodeSydhTfbsGm12878Nrf1IggmusPk.narrowPeak.gz GM12878 ChipSeq Nrf1 Peaks narrowPeak Stanford Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeSydhTfbs/wgEncodeSydhTfbsGm12878Nrf1IggmusSig.bigWig GM12878 ChipSeq Nrf1 Signal bigWig Stanford Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeSydhTfbs/wgEncodeSydhTfbsGm12878P300IggmusAlnRep1.bam GM12878 ChipSeq p300 Alignments 1 bam Stanford Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeSydhTfbs/wgEncodeSydhTfbsGm12878P300IggmusAlnRep2.bam GM12878 ChipSeq p300 Alignments 2 bam Stanford Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeSydhTfbs/wgEncodeSydhTfbsGm12878P300IggmusPk.narrowPeak.gz GM12878 ChipSeq p300 Peaks narrowPeak Stanford Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeSydhTfbs/wgEncodeSydhTfbsGm12878P300IggmusSig.bigWig GM12878 ChipSeq p300 Signal bigWig Stanford Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeSydhTfbs/wgEncodeSydhTfbsGm12878P300bStdAlnRep1.bam GM12878 ChipSeq p300_(SC-584) Alignments 1 bam Stanford Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeSydhTfbs/wgEncodeSydhTfbsGm12878P300bStdAlnRep2.bam GM12878 ChipSeq p300_(SC-584) Alignments 2 bam Stanford Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeSydhTfbs/wgEncodeSydhTfbsGm12878P300bStdPk.narrowPeak.gz GM12878 ChipSeq p300_(SC-584) Peaks narrowPeak Stanford Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeSydhTfbs/wgEncodeSydhTfbsGm12878P300bStdSig.bigWig GM12878 ChipSeq p300_(SC-584) Signal bigWig Stanford Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeSydhTfbs/wgEncodeSydhTfbsGm12878P300sc584IggmusAlnRep1.bam GM12878 ChipSeq p300_(SC-584) Alignments 1 bam Stanford Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeSydhTfbs/wgEncodeSydhTfbsGm12878P300sc584IggmusAlnRep2.bam GM12878 ChipSeq p300_(SC-584) Alignments 2 bam Stanford Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeSydhTfbs/wgEncodeSydhTfbsGm12878P300sc584IggmusPk.narrowPeak.gz GM12878 ChipSeq p300_(SC-584) Peaks narrowPeak Stanford Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeSydhTfbs/wgEncodeSydhTfbsGm12878P300sc584IggmusSig.bigWig GM12878 ChipSeq p300_(SC-584) Signal bigWig Stanford Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeSydhTfbs/wgEncodeSydhTfbsGm12878Pol2IggmusAlnRep1.bam GM12878 ChipSeq Pol2 Alignments 1 bam Stanford Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeSydhTfbs/wgEncodeSydhTfbsGm12878Pol2IggmusAlnRep2.bam GM12878 ChipSeq Pol2 Alignments 2 bam Stanford Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeSydhTfbs/wgEncodeSydhTfbsGm12878Pol2IggmusAlnRep3.bam GM12878 ChipSeq Pol2 Alignments 3 bam Stanford Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeSydhTfbs/wgEncodeSydhTfbsGm12878Pol2IggmusAlnRep4.bam GM12878 ChipSeq Pol2 Alignments 4 bam Stanford Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeSydhTfbs/wgEncodeSydhTfbsGm12878Pol2IggmusAlnRep5.bam GM12878 ChipSeq Pol2 Alignments 5 bam Stanford Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeSydhTfbs/wgEncodeSydhTfbsGm12878Pol2IggmusAlnRep6.bam GM12878 ChipSeq Pol2 Alignments 6 bam Stanford Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeSydhTfbs/wgEncodeSydhTfbsGm12878Pol2IggmusAlnRep7.bam GM12878 ChipSeq Pol2 Alignments 7 bam Stanford Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeSydhTfbs/wgEncodeSydhTfbsGm12878Pol2IggmusPk.narrowPeak.gz GM12878 ChipSeq Pol2 Peaks narrowPeak Stanford Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeSydhTfbs/wgEncodeSydhTfbsGm12878Pol2IggmusSig.bigWig GM12878 ChipSeq Pol2 Signal bigWig Stanford Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeSydhTfbs/wgEncodeSydhTfbsGm12878Pol2StdAlnRep1.bam GM12878 ChipSeq Pol2 Alignments 1 bam Yale Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeSydhTfbs/wgEncodeSydhTfbsGm12878Pol2StdAlnRep2.bam GM12878 ChipSeq Pol2 Alignments 2 bam Yale Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeSydhTfbs/wgEncodeSydhTfbsGm12878Pol2StdPk.narrowPeak.gz GM12878 ChipSeq Pol2 Peaks narrowPeak Yale Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeSydhTfbs/wgEncodeSydhTfbsGm12878Pol2StdSig.bigWig GM12878 ChipSeq Pol2 Signal bigWig Yale Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeSydhTfbs/wgEncodeSydhTfbsGm12878Pol2s2IggmusAlnRep1.bam GM12878 ChipSeq Pol2(phosphoS2) Alignments 1 bam Stanford Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeSydhTfbs/wgEncodeSydhTfbsGm12878Pol2s2IggmusAlnRep2.bam GM12878 ChipSeq Pol2(phosphoS2) Alignments 2 bam Stanford Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeSydhTfbs/wgEncodeSydhTfbsGm12878Pol2s2IggmusPk.narrowPeak.gz GM12878 ChipSeq Pol2(phosphoS2) Peaks narrowPeak Stanford Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeSydhTfbs/wgEncodeSydhTfbsGm12878Pol2s2IggmusSig.bigWig GM12878 ChipSeq Pol2(phosphoS2) Signal bigWig Stanford Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeSydhTfbs/wgEncodeSydhTfbsGm12878Pol3StdAlnRep1.bam GM12878 ChipSeq Pol3 Alignments 1 bam Yale Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeSydhTfbs/wgEncodeSydhTfbsGm12878Pol3StdAlnRep2.bam GM12878 ChipSeq Pol3 Alignments 2 bam Yale Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeSydhTfbs/wgEncodeSydhTfbsGm12878Pol3StdPk.narrowPeak.gz GM12878 ChipSeq Pol3 Peaks narrowPeak Yale Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeSydhTfbs/wgEncodeSydhTfbsGm12878Pol3StdSig.bigWig GM12878 ChipSeq Pol3 Signal bigWig Yale Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeSydhTfbs/wgEncodeSydhTfbsGm12878Rad21IggrabAlnRep1.bam GM12878 ChipSeq Rad21 Alignments 1 bam Stanford Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeSydhTfbs/wgEncodeSydhTfbsGm12878Rad21IggrabAlnRep2.bam GM12878 ChipSeq Rad21 Alignments 2 bam Stanford Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeSydhTfbs/wgEncodeSydhTfbsGm12878Rad21IggrabPk.narrowPeak.gz GM12878 ChipSeq Rad21 Peaks narrowPeak Stanford Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeSydhTfbs/wgEncodeSydhTfbsGm12878Rad21IggrabSig.bigWig GM12878 ChipSeq Rad21 Signal bigWig Stanford Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeSydhTfbs/wgEncodeSydhTfbsGm12878Rfx5200401194IggmusAlnRep1.bam GM12878 ChipSeq RFX5_(200-401-194) Alignments 1 bam Stanford Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeSydhTfbs/wgEncodeSydhTfbsGm12878Rfx5200401194IggmusAlnRep2.bam GM12878 ChipSeq RFX5_(200-401-194) Alignments 2 bam Stanford Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeSydhTfbs/wgEncodeSydhTfbsGm12878Rfx5200401194IggmusPk.narrowPeak.gz GM12878 ChipSeq RFX5_(200-401-194) Peaks narrowPeak Stanford Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeSydhTfbs/wgEncodeSydhTfbsGm12878Rfx5200401194IggmusSig.bigWig GM12878 ChipSeq RFX5_(200-401-194) Signal bigWig Stanford Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeSydhTfbs/wgEncodeSydhTfbsGm12878Sin3anb6001263IggmusAlnRep1.bam GM12878 ChipSeq SIN3A_(NB600-1263) Alignments 1 bam Stanford Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeSydhTfbs/wgEncodeSydhTfbsGm12878Sin3anb6001263IggmusAlnRep2.bam GM12878 ChipSeq SIN3A_(NB600-1263) Alignments 2 bam Stanford Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeSydhTfbs/wgEncodeSydhTfbsGm12878Sin3anb6001263IggmusPk.narrowPeak.gz GM12878 ChipSeq SIN3A_(NB600-1263) Peaks narrowPeak Stanford Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeSydhTfbs/wgEncodeSydhTfbsGm12878Sin3anb6001263IggmusSig.bigWig GM12878 ChipSeq SIN3A_(NB600-1263) Signal bigWig Stanford Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeSydhTfbs/wgEncodeSydhTfbsGm12878Smc3ab9263IggmusAlnRep1.bam GM12878 ChipSeq SMC3_(ab9263) Alignments 1 bam Stanford Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeSydhTfbs/wgEncodeSydhTfbsGm12878Smc3ab9263IggmusAlnRep2.bam GM12878 ChipSeq SMC3_(ab9263) Alignments 2 bam Stanford Data 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GM12878 ChipSeq SPT20 Signal bigWig Harvard Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeSydhTfbs/wgEncodeSydhTfbsGm12878Srebp1IggrabAlnRep1.bam GM12878 ChipSeq SREBP1 Alignments 1 bam Stanford Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeSydhTfbs/wgEncodeSydhTfbsGm12878Srebp1IggrabAlnRep2.bam GM12878 ChipSeq SREBP1 Alignments 2 bam Stanford Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeSydhTfbs/wgEncodeSydhTfbsGm12878Srebp1IggrabPk.narrowPeak.gz GM12878 ChipSeq SREBP1 Peaks narrowPeak Stanford Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeSydhTfbs/wgEncodeSydhTfbsGm12878Srebp1IggrabSig.bigWig GM12878 ChipSeq SREBP1 Signal bigWig Stanford Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeSydhTfbs/wgEncodeSydhTfbsGm12878Srebp2IggrabAlnRep1.bam GM12878 ChipSeq SREBP2 Alignments 1 bam Stanford Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeSydhTfbs/wgEncodeSydhTfbsGm12878Srebp2IggrabAlnRep2.bam GM12878 ChipSeq SREBP2 Alignments 2 bam Stanford Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeSydhTfbs/wgEncodeSydhTfbsGm12878Srebp2IggrabPk.narrowPeak.gz GM12878 ChipSeq SREBP2 Peaks narrowPeak Stanford Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeSydhTfbs/wgEncodeSydhTfbsGm12878Srebp2IggrabSig.bigWig GM12878 ChipSeq SREBP2 Signal bigWig Stanford Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeSydhTfbs/wgEncodeSydhTfbsGm12878Stat1StdAlnRep1.bam GM12878 ChipSeq STAT1 Alignments 1 bam Stanford Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeSydhTfbs/wgEncodeSydhTfbsGm12878Stat1StdAlnRep2.bam GM12878 ChipSeq STAT1 Alignments 2 bam Stanford Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeSydhTfbs/wgEncodeSydhTfbsGm12878Stat1StdPk.narrowPeak.gz GM12878 ChipSeq STAT1 Peaks narrowPeak Stanford Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeSydhTfbs/wgEncodeSydhTfbsGm12878Stat1StdSig.bigWig GM12878 ChipSeq STAT1 Signal bigWig Stanford Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeSydhTfbs/wgEncodeSydhTfbsGm12878Stat3IggmusAlnRep1.bam GM12878 ChipSeq STAT3 Alignments 1 bam Stanford Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeSydhTfbs/wgEncodeSydhTfbsGm12878Stat3IggmusAlnRep2.bam GM12878 ChipSeq STAT3 Alignments 2 bam Stanford Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeSydhTfbs/wgEncodeSydhTfbsGm12878Stat3IggmusPk.narrowPeak.gz GM12878 ChipSeq STAT3 Peaks narrowPeak Stanford Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeSydhTfbs/wgEncodeSydhTfbsGm12878Stat3IggmusSig.bigWig GM12878 ChipSeq STAT3 Signal bigWig Stanford Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeSydhTfbs/wgEncodeSydhTfbsGm12878Tblr1ab24550IggmusAlnRep1.bam GM12878 ChipSeq TBLR1_(ab24550) Alignments 1 bam Stanford Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeSydhTfbs/wgEncodeSydhTfbsGm12878Tblr1ab24550IggmusAlnRep1V2.bam GM12878 ChipSeq TBLR1_(ab24550) Alignments 1 bam Stanford Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeSydhTfbs/wgEncodeSydhTfbsGm12878Tblr1ab24550IggmusAlnRep2.bam GM12878 ChipSeq TBLR1_(ab24550) Alignments 2 bam Stanford Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeSydhTfbs/wgEncodeSydhTfbsGm12878Tblr1ab24550IggmusPk.narrowPeak.gz GM12878 ChipSeq TBLR1_(ab24550) Peaks narrowPeak Stanford Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeSydhTfbs/wgEncodeSydhTfbsGm12878Tblr1ab24550IggmusSig.bigWig GM12878 ChipSeq TBLR1_(ab24550) Signal bigWig Stanford Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeSydhTfbs/wgEncodeSydhTfbsGm12878TbpIggmusAlnRep1.bam GM12878 ChipSeq TBP Alignments 1 bam Stanford Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeSydhTfbs/wgEncodeSydhTfbsGm12878TbpIggmusAlnRep2.bam GM12878 ChipSeq TBP Alignments 2 bam Stanford Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeSydhTfbs/wgEncodeSydhTfbsGm12878TbpIggmusPk.narrowPeak.gz GM12878 ChipSeq TBP Peaks narrowPeak Stanford Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeSydhTfbs/wgEncodeSydhTfbsGm12878TbpIggmusSig.bigWig GM12878 ChipSeq TBP Signal bigWig Stanford Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeSydhTfbs/wgEncodeSydhTfbsGm12878Tr4StdAlnRep1.bam GM12878 ChipSeq TR4 Alignments 1 bam USC Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeSydhTfbs/wgEncodeSydhTfbsGm12878Tr4StdAlnRep2.bam GM12878 ChipSeq TR4 Alignments 2 bam USC Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeSydhTfbs/wgEncodeSydhTfbsGm12878Tr4StdPk.narrowPeak.gz GM12878 ChipSeq TR4 Peaks narrowPeak USC Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeSydhTfbs/wgEncodeSydhTfbsGm12878Tr4StdSig.bigWig GM12878 ChipSeq TR4 Signal bigWig USC Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeSydhTfbs/wgEncodeSydhTfbsGm12878Usf2IggmusAlnRep1.bam GM12878 ChipSeq USF2 Alignments 1 bam Stanford Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeSydhTfbs/wgEncodeSydhTfbsGm12878Usf2IggmusAlnRep2.bam GM12878 ChipSeq USF2 Alignments 2 bam Stanford Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeSydhTfbs/wgEncodeSydhTfbsGm12878Usf2IggmusPk.narrowPeak.gz GM12878 ChipSeq USF2 Peaks narrowPeak Stanford Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeSydhTfbs/wgEncodeSydhTfbsGm12878Usf2IggmusSig.bigWig GM12878 ChipSeq USF2 Signal bigWig Stanford Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeSydhTfbs/wgEncodeSydhTfbsGm12878WhipIggmusAlnRep1.bam GM12878 ChipSeq WHIP Alignments 1 bam Stanford Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeSydhTfbs/wgEncodeSydhTfbsGm12878WhipIggmusAlnRep2.bam GM12878 ChipSeq WHIP Alignments 2 bam Stanford Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeSydhTfbs/wgEncodeSydhTfbsGm12878WhipIggmusPk.narrowPeak.gz GM12878 ChipSeq WHIP Peaks narrowPeak Stanford Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeSydhTfbs/wgEncodeSydhTfbsGm12878WhipIggmusSig.bigWig GM12878 ChipSeq WHIP Signal bigWig Stanford Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeSydhTfbs/wgEncodeSydhTfbsGm12878Yy1StdAlnRep1.bam GM12878 ChipSeq YY1 Alignments 1 bam USC Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeSydhTfbs/wgEncodeSydhTfbsGm12878Yy1StdAlnRep2.bam GM12878 ChipSeq YY1 Alignments 2 bam USC Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeSydhTfbs/wgEncodeSydhTfbsGm12878Yy1StdPk.narrowPeak.gz GM12878 ChipSeq YY1 Peaks narrowPeak USC Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeSydhTfbs/wgEncodeSydhTfbsGm12878Yy1StdSig.bigWig GM12878 ChipSeq YY1 Signal bigWig USC Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeSydhTfbs/wgEncodeSydhTfbsGm12878Znf143166181apStdAlnRep1.bam GM12878 ChipSeq Znf143_(16618-1-AP) Alignments 1 bam Stanford Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeSydhTfbs/wgEncodeSydhTfbsGm12878Znf143166181apStdAlnRep2.bam GM12878 ChipSeq Znf143_(16618-1-AP) Alignments 2 bam Stanford Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeSydhTfbs/wgEncodeSydhTfbsGm12878Znf143166181apStdPk.narrowPeak.gz GM12878 ChipSeq Znf143_(16618-1-AP) Peaks narrowPeak Stanford Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeSydhTfbs/wgEncodeSydhTfbsGm12878Znf143166181apStdSig.bigWig GM12878 ChipSeq Znf143_(16618-1-AP) Signal bigWig Stanford Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeSydhTfbs/wgEncodeSydhTfbsGm12878Znf274StdAlnRep1.bam GM12878 ChipSeq ZNF274 Alignments 1 bam USC Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeSydhTfbs/wgEncodeSydhTfbsGm12878Znf274StdAlnRep1V2.bam GM12878 ChipSeq ZNF274 Alignments 1 bam Stanford Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeSydhTfbs/wgEncodeSydhTfbsGm12878Znf274StdAlnRep2.bam GM12878 ChipSeq ZNF274 Alignments 2 bam USC Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeSydhTfbs/wgEncodeSydhTfbsGm12878Znf274StdAlnRep2V2.bam GM12878 ChipSeq ZNF274 Alignments 2 bam Stanford Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeSydhTfbs/wgEncodeSydhTfbsGm12878Znf274StdPk.narrowPeak.gz GM12878 ChipSeq ZNF274 Peaks narrowPeak USC Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeSydhTfbs/wgEncodeSydhTfbsGm12878Znf274StdSig.bigWig GM12878 ChipSeq ZNF274 Signal bigWig USC Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeSydhTfbs/wgEncodeSydhTfbsGm12878Znf384hpa004051IggmusAlnRep1.bam GM12878 ChipSeq ZNF384_(HPA004051) Alignments 1 bam Stanford Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeSydhTfbs/wgEncodeSydhTfbsGm12878Znf384hpa004051IggmusAlnRep2.bam GM12878 ChipSeq ZNF384_(HPA004051) Alignments 2 bam Stanford Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeSydhTfbs/wgEncodeSydhTfbsGm12878Znf384hpa004051IggmusPk.narrowPeak.gz GM12878 ChipSeq ZNF384_(HPA004051) Peaks narrowPeak Stanford Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeSydhTfbs/wgEncodeSydhTfbsGm12878Znf384hpa004051IggmusSig.bigWig GM12878 ChipSeq ZNF384_(HPA004051) Signal bigWig Stanford Data 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ChipSeq Input Signal bigWig Stanford Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeSydhTfbs/wgEncodeSydhTfbsGm19099NfkbTnfaIggrabAlnRep1.bam GM19099 ChipSeq NFKB Alignments 1 bam Stanford Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeSydhTfbs/wgEncodeSydhTfbsGm19099NfkbTnfaIggrabAlnRep2.bam GM19099 ChipSeq NFKB Alignments 2 bam Stanford Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeSydhTfbs/wgEncodeSydhTfbsGm19099NfkbTnfaIggrabAlnRep3.bam GM19099 ChipSeq NFKB Alignments 3 bam Stanford Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeSydhTfbs/wgEncodeSydhTfbsGm19099NfkbTnfaIggrabPk.narrowPeak.gz GM19099 ChipSeq NFKB Peaks narrowPeak Stanford Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeSydhTfbs/wgEncodeSydhTfbsGm19099NfkbTnfaIggrabSig.bigWig GM19099 ChipSeq NFKB Signal bigWig Stanford Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeSydhTfbs/wgEncodeSydhTfbsGm19099Pol2IggmusAlnRep1.bam GM19099 ChipSeq Pol2 Alignments 1 bam Stanford Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeSydhTfbs/wgEncodeSydhTfbsGm19099Pol2IggmusAlnRep2.bam GM19099 ChipSeq Pol2 Alignments 2 bam Stanford Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeSydhTfbs/wgEncodeSydhTfbsGm19099Pol2IggmusAlnRep3.bam GM19099 ChipSeq Pol2 Alignments 3 bam Stanford Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeSydhTfbs/wgEncodeSydhTfbsGm19099Pol2IggmusPk.narrowPeak.gz GM19099 ChipSeq Pol2 Peaks narrowPeak Stanford Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeSydhTfbs/wgEncodeSydhTfbsGm19099Pol2IggmusSig.bigWig GM19099 ChipSeq Pol2 Signal bigWig Stanford Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeSydhTfbs/wgEncodeSydhTfbsGm19193InputIggmusAlnRep1.bam GM19193 ChipSeq Input Alignments 1 bam Stanford Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeSydhTfbs/wgEncodeSydhTfbsGm19193InputIggmusAlnRep2.bam GM19193 ChipSeq Input Alignments 2 bam Stanford Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeSydhTfbs/wgEncodeSydhTfbsGm19193InputIggmusSig.bigWig GM19193 ChipSeq Input Signal bigWig Stanford Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeSydhTfbs/wgEncodeSydhTfbsGm19193InputTnfaIggrabAlnRep1.bam GM19193 ChipSeq Input Alignments 1 bam Stanford Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeSydhTfbs/wgEncodeSydhTfbsGm19193InputTnfaIggrabAlnRep2.bam GM19193 ChipSeq Input Alignments 2 bam Stanford Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeSydhTfbs/wgEncodeSydhTfbsGm19193InputTnfaIggrabSig.bigWig GM19193 ChipSeq Input Signal bigWig Stanford Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeSydhTfbs/wgEncodeSydhTfbsGm19193NfkbTnfaIggrabAlnRep1.bam GM19193 ChipSeq NFKB Alignments 1 bam Stanford Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeSydhTfbs/wgEncodeSydhTfbsGm19193NfkbTnfaIggrabAlnRep2.bam GM19193 ChipSeq NFKB Alignments 2 bam Stanford Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeSydhTfbs/wgEncodeSydhTfbsGm19193NfkbTnfaIggrabAlnRep3.bam GM19193 ChipSeq NFKB Alignments 3 bam Stanford Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeSydhTfbs/wgEncodeSydhTfbsGm19193NfkbTnfaIggrabPk.narrowPeak.gz GM19193 ChipSeq NFKB Peaks narrowPeak Stanford Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeSydhTfbs/wgEncodeSydhTfbsGm19193NfkbTnfaIggrabSig.bigWig GM19193 ChipSeq NFKB Signal bigWig Stanford Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeSydhTfbs/wgEncodeSydhTfbsGm19193Pol2IggmusAlnRep1.bam GM19193 ChipSeq Pol2 Alignments 1 bam Stanford Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeSydhTfbs/wgEncodeSydhTfbsGm19193Pol2IggmusAlnRep2.bam GM19193 ChipSeq Pol2 Alignments 2 bam Stanford Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeSydhTfbs/wgEncodeSydhTfbsGm19193Pol2IggmusAlnRep3.bam GM19193 ChipSeq Pol2 Alignments 3 bam Stanford Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeSydhTfbs/wgEncodeSydhTfbsGm19193Pol2IggmusAlnRep4.bam GM19193 ChipSeq Pol2 Alignments 4 bam Stanford Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeSydhTfbs/wgEncodeSydhTfbsGm19193Pol2IggmusPk.narrowPeak.gz GM19193 ChipSeq Pol2 Peaks narrowPeak Stanford Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeSydhTfbs/wgEncodeSydhTfbsGm19193Pol2IggmusSig.bigWig GM19193 ChipSeq Pol2 Signal bigWig Stanford Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeSydhTfbs/wgEncodeSydhTfbsH1hescBach1sc14700IggrabAlnRep1.bam H1-hESC ChipSeq Bach1_(sc-14700) Alignments 1 bam Stanford Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeSydhTfbs/wgEncodeSydhTfbsH1hescBach1sc14700IggrabAlnRep2.bam H1-hESC ChipSeq Bach1_(sc-14700) Alignments 2 bam Stanford Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeSydhTfbs/wgEncodeSydhTfbsH1hescBach1sc14700IggrabPk.narrowPeak.gz H1-hESC ChipSeq Bach1_(sc-14700) Peaks narrowPeak Stanford Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeSydhTfbs/wgEncodeSydhTfbsH1hescBach1sc14700IggrabSig.bigWig H1-hESC ChipSeq Bach1_(sc-14700) Signal bigWig Stanford Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeSydhTfbs/wgEncodeSydhTfbsH1hescBrca1IggrabAlnRep1.bam H1-hESC ChipSeq BRCA1_(A300-000A) Alignments 1 bam Stanford Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeSydhTfbs/wgEncodeSydhTfbsH1hescBrca1IggrabAlnRep2.bam H1-hESC ChipSeq BRCA1_(A300-000A) Alignments 2 bam Stanford Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeSydhTfbs/wgEncodeSydhTfbsH1hescBrca1IggrabPk.narrowPeak.gz H1-hESC ChipSeq BRCA1_(A300-000A) Peaks narrowPeak Stanford Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeSydhTfbs/wgEncodeSydhTfbsH1hescBrca1IggrabSig.bigWig H1-hESC ChipSeq BRCA1_(A300-000A) Signal bigWig Stanford Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeSydhTfbs/wgEncodeSydhTfbsH1hescCebpbIggrabAlnRep1.bam H1-hESC ChipSeq CEBPB Alignments 1 bam Stanford Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeSydhTfbs/wgEncodeSydhTfbsH1hescCebpbIggrabAlnRep2.bam H1-hESC ChipSeq CEBPB Alignments 2 bam Stanford Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeSydhTfbs/wgEncodeSydhTfbsH1hescCebpbIggrabPk.narrowPeak.gz H1-hESC ChipSeq CEBPB Peaks narrowPeak Stanford Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeSydhTfbs/wgEncodeSydhTfbsH1hescCebpbIggrabSig.bigWig H1-hESC ChipSeq CEBPB Signal bigWig Stanford Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeSydhTfbs/wgEncodeSydhTfbsH1hescChd1a301218aIggrabAlnRep1.bam H1-hESC ChipSeq CHD1_(A301-218A) Alignments 1 bam Stanford Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeSydhTfbs/wgEncodeSydhTfbsH1hescChd1a301218aIggrabAlnRep2.bam H1-hESC ChipSeq CHD1_(A301-218A) Alignments 2 bam Stanford Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeSydhTfbs/wgEncodeSydhTfbsH1hescChd1a301218aIggrabPk.narrowPeak.gz H1-hESC ChipSeq CHD1_(A301-218A) Peaks narrowPeak Stanford Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeSydhTfbs/wgEncodeSydhTfbsH1hescChd1a301218aIggrabSig.bigWig H1-hESC ChipSeq CHD1_(A301-218A) Signal bigWig Stanford Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeSydhTfbs/wgEncodeSydhTfbsH1hescChd2IggrabAlnRep1.bam H1-hESC ChipSeq CHD2_(AB68301) Alignments 1 bam Stanford Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeSydhTfbs/wgEncodeSydhTfbsH1hescChd2IggrabAlnRep2.bam H1-hESC ChipSeq CHD2_(AB68301) Alignments 2 bam Stanford Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeSydhTfbs/wgEncodeSydhTfbsH1hescChd2IggrabPk.narrowPeak.gz H1-hESC ChipSeq CHD2_(AB68301) Peaks narrowPeak Stanford Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeSydhTfbs/wgEncodeSydhTfbsH1hescChd2IggrabSig.bigWig H1-hESC ChipSeq CHD2_(AB68301) Signal bigWig Stanford Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeSydhTfbs/wgEncodeSydhTfbsH1hescCjunIggrabAlnRep1.bam H1-hESC ChipSeq c-Jun Alignments 1 bam Stanford Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeSydhTfbs/wgEncodeSydhTfbsH1hescCjunIggrabAlnRep2.bam H1-hESC ChipSeq c-Jun Alignments 2 bam Stanford Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeSydhTfbs/wgEncodeSydhTfbsH1hescCjunIggrabPk.narrowPeak.gz H1-hESC ChipSeq c-Jun Peaks narrowPeak Stanford Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeSydhTfbs/wgEncodeSydhTfbsH1hescCjunIggrabSig.bigWig H1-hESC ChipSeq c-Jun Signal bigWig Stanford Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeSydhTfbs/wgEncodeSydhTfbsH1hescCmycIggrabAlnRep1.bam H1-hESC ChipSeq c-Myc Alignments 1 bam Stanford Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeSydhTfbs/wgEncodeSydhTfbsH1hescCmycIggrabAlnRep2.bam H1-hESC ChipSeq c-Myc Alignments 2 bam Stanford Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeSydhTfbs/wgEncodeSydhTfbsH1hescCmycIggrabPk.narrowPeak.gz H1-hESC ChipSeq c-Myc Peaks narrowPeak Stanford Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeSydhTfbs/wgEncodeSydhTfbsH1hescCmycIggrabSig.bigWig H1-hESC ChipSeq c-Myc Signal bigWig Stanford Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeSydhTfbs/wgEncodeSydhTfbsH1hescCtbp2UcdAlnRep1.bam H1-hESC ChipSeq CtBP2 Alignments 1 bam USC Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeSydhTfbs/wgEncodeSydhTfbsH1hescCtbp2UcdAlnRep2.bam H1-hESC ChipSeq CtBP2 Alignments 2 bam USC Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeSydhTfbs/wgEncodeSydhTfbsH1hescCtbp2UcdPk.narrowPeak.gz H1-hESC ChipSeq CtBP2 Peaks narrowPeak USC Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeSydhTfbs/wgEncodeSydhTfbsH1hescCtbp2UcdSig.bigWig H1-hESC ChipSeq CtBP2 Signal bigWig USC Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeSydhTfbs/wgEncodeSydhTfbsH1hescGtf2f1IggrabAlnRep1.bam H1-hESC ChipSeq GTF2F1_(AB28179) Alignments 1 bam Stanford Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeSydhTfbs/wgEncodeSydhTfbsH1hescGtf2f1IggrabAlnRep2.bam H1-hESC ChipSeq GTF2F1_(AB28179) Alignments 2 bam Stanford Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeSydhTfbs/wgEncodeSydhTfbsH1hescGtf2f1IggrabPk.narrowPeak.gz H1-hESC ChipSeq GTF2F1_(AB28179) Peaks narrowPeak Stanford Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeSydhTfbs/wgEncodeSydhTfbsH1hescGtf2f1IggrabSig.bigWig H1-hESC ChipSeq GTF2F1_(AB28179) Signal bigWig Stanford Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeSydhTfbs/wgEncodeSydhTfbsH1hescInputIggrabAln.bam H1-hESC ChipSeq Input Alignments bam Stanford Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeSydhTfbs/wgEncodeSydhTfbsH1hescInputIggrabSig.bigWig H1-hESC ChipSeq Input Signal bigWig Stanford Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeSydhTfbs/wgEncodeSydhTfbsH1hescInputUcdAln.bam H1-hESC ChipSeq Input Alignments bam USC Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeSydhTfbs/wgEncodeSydhTfbsH1hescInputUcdSig.bigWig H1-hESC ChipSeq Input Signal bigWig USC Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeSydhTfbs/wgEncodeSydhTfbsH1hescJundIggrabAlnRep1.bam H1-hESC ChipSeq JunD Alignments 1 bam Stanford Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeSydhTfbs/wgEncodeSydhTfbsH1hescJundIggrabAlnRep2.bam H1-hESC ChipSeq JunD Alignments 2 bam Stanford Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeSydhTfbs/wgEncodeSydhTfbsH1hescJundIggrabPk.narrowPeak.gz H1-hESC ChipSeq JunD Peaks narrowPeak Stanford Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeSydhTfbs/wgEncodeSydhTfbsH1hescJundIggrabSig.bigWig H1-hESC ChipSeq JunD Signal bigWig Stanford Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeSydhTfbs/wgEncodeSydhTfbsH1hescMafkIggrabAlnRep1.bam H1-hESC ChipSeq MafK_(ab50322) Alignments 1 bam Stanford Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeSydhTfbs/wgEncodeSydhTfbsH1hescMafkIggrabAlnRep2.bam H1-hESC ChipSeq MafK_(ab50322) Alignments 2 bam Stanford Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeSydhTfbs/wgEncodeSydhTfbsH1hescMafkIggrabPk.narrowPeak.gz H1-hESC ChipSeq MafK_(ab50322) Peaks narrowPeak Stanford Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeSydhTfbs/wgEncodeSydhTfbsH1hescMafkIggrabSig.bigWig H1-hESC ChipSeq MafK_(ab50322) Signal bigWig Stanford Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeSydhTfbs/wgEncodeSydhTfbsH1hescMaxUcdAlnRep1.bam H1-hESC ChipSeq Max Alignments 1 bam USC Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeSydhTfbs/wgEncodeSydhTfbsH1hescMaxUcdAlnRep1V2.bam H1-hESC ChipSeq Max Alignments 1 bam Stanford Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeSydhTfbs/wgEncodeSydhTfbsH1hescMaxUcdAlnRep2.bam H1-hESC ChipSeq Max Alignments 2 bam USC Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeSydhTfbs/wgEncodeSydhTfbsH1hescMaxUcdAlnRep2V2.bam H1-hESC ChipSeq Max Alignments 2 bam Stanford Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeSydhTfbs/wgEncodeSydhTfbsH1hescMaxUcdPk.narrowPeak.gz H1-hESC ChipSeq Max Peaks narrowPeak USC Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeSydhTfbs/wgEncodeSydhTfbsH1hescMaxUcdSig.bigWig H1-hESC ChipSeq Max Signal bigWig USC Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeSydhTfbs/wgEncodeSydhTfbsH1hescMxi1IggrabAlnRep1.bam H1-hESC ChipSeq Mxi1_(AF4185) Alignments 1 bam Stanford Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeSydhTfbs/wgEncodeSydhTfbsH1hescMxi1IggrabAlnRep2.bam H1-hESC ChipSeq Mxi1_(AF4185) Alignments 2 bam Stanford Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeSydhTfbs/wgEncodeSydhTfbsH1hescMxi1IggrabPk.narrowPeak.gz H1-hESC ChipSeq Mxi1_(AF4185) Peaks narrowPeak Stanford Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeSydhTfbs/wgEncodeSydhTfbsH1hescMxi1IggrabSig.bigWig H1-hESC ChipSeq Mxi1_(AF4185) Signal bigWig Stanford Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeSydhTfbs/wgEncodeSydhTfbsH1hescNrf1IggrabAlnRep1.bam H1-hESC ChipSeq Nrf1 Alignments 1 bam Stanford Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeSydhTfbs/wgEncodeSydhTfbsH1hescNrf1IggrabAlnRep2.bam H1-hESC ChipSeq Nrf1 Alignments 2 bam Stanford Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeSydhTfbs/wgEncodeSydhTfbsH1hescNrf1IggrabPk.narrowPeak.gz H1-hESC ChipSeq Nrf1 Peaks narrowPeak Stanford Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeSydhTfbs/wgEncodeSydhTfbsH1hescNrf1IggrabSig.bigWig H1-hESC ChipSeq Nrf1 Signal bigWig Stanford Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeSydhTfbs/wgEncodeSydhTfbsH1hescRad21IggrabAlnRep1.bam H1-hESC ChipSeq Rad21 Alignments 1 bam Stanford Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeSydhTfbs/wgEncodeSydhTfbsH1hescRad21IggrabAlnRep2.bam H1-hESC ChipSeq Rad21 Alignments 2 bam Stanford Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeSydhTfbs/wgEncodeSydhTfbsH1hescRad21IggrabPk.narrowPeak.gz H1-hESC ChipSeq Rad21 Peaks narrowPeak Stanford Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeSydhTfbs/wgEncodeSydhTfbsH1hescRad21IggrabSig.bigWig H1-hESC ChipSeq Rad21 Signal bigWig Stanford Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeSydhTfbs/wgEncodeSydhTfbsH1hescRfx5200401194IggrabAlnRep1.bam H1-hESC ChipSeq RFX5_(200-401-194) Alignments 1 bam Stanford Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeSydhTfbs/wgEncodeSydhTfbsH1hescRfx5200401194IggrabAlnRep2.bam H1-hESC ChipSeq RFX5_(200-401-194) Alignments 2 bam Stanford Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeSydhTfbs/wgEncodeSydhTfbsH1hescRfx5200401194IggrabPk.narrowPeak.gz H1-hESC ChipSeq RFX5_(200-401-194) Peaks narrowPeak Stanford Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeSydhTfbs/wgEncodeSydhTfbsH1hescRfx5200401194IggrabSig.bigWig H1-hESC ChipSeq RFX5_(200-401-194) Signal bigWig Stanford Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeSydhTfbs/wgEncodeSydhTfbsH1hescSin3anb6001263IggrabAlnRep1.bam H1-hESC ChipSeq SIN3A_(NB600-1263) Alignments 1 bam Stanford Data 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Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeSydhTfbs/wgEncodeSydhTfbsH1hescUsf2IggrabAlnRep1.bam H1-hESC ChipSeq USF2 Alignments 1 bam Stanford Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeSydhTfbs/wgEncodeSydhTfbsH1hescUsf2IggrabAlnRep2.bam H1-hESC ChipSeq USF2 Alignments 2 bam Stanford Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeSydhTfbs/wgEncodeSydhTfbsH1hescUsf2IggrabPk.narrowPeak.gz H1-hESC ChipSeq USF2 Peaks narrowPeak Stanford Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeSydhTfbs/wgEncodeSydhTfbsH1hescUsf2IggrabSig.bigWig H1-hESC ChipSeq USF2 Signal bigWig Stanford Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeSydhTfbs/wgEncodeSydhTfbsH1hescZnf143IggrabAlnRep1.bam H1-hESC ChipSeq Znf143_(16618-1-AP) Alignments 1 bam Stanford Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeSydhTfbs/wgEncodeSydhTfbsH1hescZnf143IggrabAlnRep2.bam H1-hESC ChipSeq Znf143_(16618-1-AP) Alignments 2 bam Stanford Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeSydhTfbs/wgEncodeSydhTfbsH1hescZnf143IggrabPk.narrowPeak.gz H1-hESC ChipSeq Znf143_(16618-1-AP) Peaks narrowPeak Stanford Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeSydhTfbs/wgEncodeSydhTfbsH1hescZnf143IggrabSig.bigWig H1-hESC ChipSeq Znf143_(16618-1-AP) Signal bigWig Stanford Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeSydhTfbs/wgEncodeSydhTfbsH1hescZnf274m01UcdAlnRep1.bam H1-hESC ChipSeq ZNF274_(M01) Alignments 1 bam USC Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeSydhTfbs/wgEncodeSydhTfbsH1hescZnf274m01UcdAlnRep2.bam H1-hESC ChipSeq ZNF274_(M01) Alignments 2 bam USC Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeSydhTfbs/wgEncodeSydhTfbsH1hescZnf274m01UcdPk.narrowPeak.gz H1-hESC ChipSeq ZNF274_(M01) Peaks narrowPeak USC Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeSydhTfbs/wgEncodeSydhTfbsH1hescZnf274m01UcdSig.bigWig H1-hESC ChipSeq ZNF274_(M01) Signal bigWig USC Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeSydhTfbs/wgEncodeSydhTfbsHct116InputUcdAlnRep1.bam HCT-116 ChipSeq Input Alignments 1 bam USC Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeSydhTfbs/wgEncodeSydhTfbsHct116InputUcdSig.bigWig HCT-116 ChipSeq Input Signal bigWig USC Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeSydhTfbs/wgEncodeSydhTfbsHct116Pol2UcdAlnRep1.bam HCT-116 ChipSeq Pol2 Alignments 1 bam USC Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeSydhTfbs/wgEncodeSydhTfbsHct116Pol2UcdAlnRep2.bam HCT-116 ChipSeq Pol2 Alignments 2 bam USC Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeSydhTfbs/wgEncodeSydhTfbsHct116Pol2UcdPk.narrowPeak.gz HCT-116 ChipSeq Pol2 Peaks narrowPeak USC Data 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http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeSydhTfbs/wgEncodeSydhTfbsHek293Tcf7l2UcdPk.narrowPeak.gz HEK293 ChipSeq TCF7L2 Peaks narrowPeak USC Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeSydhTfbs/wgEncodeSydhTfbsHek293Tcf7l2UcdSig.bigWig HEK293 ChipSeq TCF7L2 Signal bigWig USC Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeSydhTfbs/wgEncodeSydhTfbsHek293tInputUcdAln.bam HEK293-T-REx ChipSeq Input Alignments bam USC Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeSydhTfbs/wgEncodeSydhTfbsHek293tInputUcdSig.bigWig HEK293-T-REx ChipSeq Input Signal bigWig USC Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeSydhTfbs/wgEncodeSydhTfbsHek293tZnf263UcdAlnRep1.bam HEK293-T-REx ChipSeq ZNF263 Alignments 1 bam USC Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeSydhTfbs/wgEncodeSydhTfbsHek293tZnf263UcdAlnRep2.bam HEK293-T-REx ChipSeq ZNF263 Alignments 2 bam USC Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeSydhTfbs/wgEncodeSydhTfbsHek293tZnf263UcdPk.narrowPeak.gz HEK293-T-REx ChipSeq ZNF263 Peaks narrowPeak USC Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeSydhTfbs/wgEncodeSydhTfbsHek293tZnf263UcdSig.bigWig HEK293-T-REx ChipSeq ZNF263 Signal bigWig USC Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeSydhTfbs/wgEncodeSydhTfbsHelas3Ap2alphaStdAlnRep1.bam HeLa-S3 ChipSeq AP-2alpha Alignments 1 bam USC Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeSydhTfbs/wgEncodeSydhTfbsHelas3Ap2alphaStdAlnRep2.bam HeLa-S3 ChipSeq AP-2alpha Alignments 2 bam USC Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeSydhTfbs/wgEncodeSydhTfbsHelas3Ap2alphaStdPk.narrowPeak.gz HeLa-S3 ChipSeq AP-2alpha Peaks narrowPeak USC Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeSydhTfbs/wgEncodeSydhTfbsHelas3Ap2alphaStdSig.bigWig HeLa-S3 ChipSeq AP-2alpha Signal bigWig USC Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeSydhTfbs/wgEncodeSydhTfbsHelas3Ap2gammaStdAlnRep1.bam HeLa-S3 ChipSeq AP-2gamma Alignments 1 bam USC Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeSydhTfbs/wgEncodeSydhTfbsHelas3Ap2gammaStdAlnRep2.bam HeLa-S3 ChipSeq AP-2gamma Alignments 2 bam USC Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeSydhTfbs/wgEncodeSydhTfbsHelas3Ap2gammaStdPk.narrowPeak.gz HeLa-S3 ChipSeq AP-2gamma Peaks narrowPeak USC Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeSydhTfbs/wgEncodeSydhTfbsHelas3Ap2gammaStdSig.bigWig HeLa-S3 ChipSeq AP-2gamma Signal bigWig USC Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeSydhTfbs/wgEncodeSydhTfbsHelas3Baf155IggmusAlnRep1.bam HeLa-S3 ChipSeq BAF155 Alignments 1 bam Stanford Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeSydhTfbs/wgEncodeSydhTfbsHelas3Baf155IggmusAlnRep2.bam HeLa-S3 ChipSeq BAF155 Alignments 2 bam Stanford Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeSydhTfbs/wgEncodeSydhTfbsHelas3Baf155IggmusAlnRep3.bam HeLa-S3 ChipSeq BAF155 Alignments 3 bam Stanford Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeSydhTfbs/wgEncodeSydhTfbsHelas3Baf155IggmusPk.narrowPeak.gz HeLa-S3 ChipSeq BAF155 Peaks narrowPeak Stanford Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeSydhTfbs/wgEncodeSydhTfbsHelas3Baf155IggmusSig.bigWig HeLa-S3 ChipSeq BAF155 Signal bigWig Stanford Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeSydhTfbs/wgEncodeSydhTfbsHelas3Baf170IggmusAlnRep1.bam HeLa-S3 ChipSeq BAF170 Alignments 1 bam Stanford Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeSydhTfbs/wgEncodeSydhTfbsHelas3Baf170IggmusAlnRep2.bam HeLa-S3 ChipSeq BAF170 Alignments 2 bam Stanford Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeSydhTfbs/wgEncodeSydhTfbsHelas3Baf170IggmusAlnRep3.bam HeLa-S3 ChipSeq BAF170 Alignments 3 bam Stanford Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeSydhTfbs/wgEncodeSydhTfbsHelas3Baf170IggmusPk.narrowPeak.gz HeLa-S3 ChipSeq BAF170 Peaks narrowPeak Stanford Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeSydhTfbs/wgEncodeSydhTfbsHelas3Baf170IggmusSig.bigWig HeLa-S3 ChipSeq BAF170 Signal bigWig Stanford Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeSydhTfbs/wgEncodeSydhTfbsHelas3Bdp1StdAlnRep1.bam HeLa-S3 ChipSeq BDP1 Alignments 1 bam Harvard Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeSydhTfbs/wgEncodeSydhTfbsHelas3Bdp1StdAlnRep2.bam HeLa-S3 ChipSeq BDP1 Alignments 2 bam Harvard Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeSydhTfbs/wgEncodeSydhTfbsHelas3Bdp1StdPk.narrowPeak.gz HeLa-S3 ChipSeq BDP1 Peaks narrowPeak Harvard Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeSydhTfbs/wgEncodeSydhTfbsHelas3Bdp1StdSig.bigWig HeLa-S3 ChipSeq BDP1 Signal bigWig Harvard Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeSydhTfbs/wgEncodeSydhTfbsHelas3Brca1a300IggrabAlnRep1.bam HeLa-S3 ChipSeq BRCA1_(A300-000A) Alignments 1 bam Stanford Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeSydhTfbs/wgEncodeSydhTfbsHelas3Brca1a300IggrabAlnRep2.bam HeLa-S3 ChipSeq BRCA1_(A300-000A) Alignments 2 bam Stanford Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeSydhTfbs/wgEncodeSydhTfbsHelas3Brca1a300IggrabPk.narrowPeak.gz HeLa-S3 ChipSeq BRCA1_(A300-000A) Peaks narrowPeak Stanford Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeSydhTfbs/wgEncodeSydhTfbsHelas3Brca1a300IggrabSig.bigWig HeLa-S3 ChipSeq BRCA1_(A300-000A) Signal bigWig Stanford Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeSydhTfbs/wgEncodeSydhTfbsHelas3Brf1StdAlnRep1.bam HeLa-S3 ChipSeq BRF1 Alignments 1 bam Harvard Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeSydhTfbs/wgEncodeSydhTfbsHelas3Brf1StdAlnRep2.bam HeLa-S3 ChipSeq BRF1 Alignments 2 bam Harvard Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeSydhTfbs/wgEncodeSydhTfbsHelas3Brf1StdPk.narrowPeak.gz HeLa-S3 ChipSeq BRF1 Peaks narrowPeak Harvard Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeSydhTfbs/wgEncodeSydhTfbsHelas3Brf1StdSig.bigWig HeLa-S3 ChipSeq BRF1 Signal bigWig Harvard Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeSydhTfbs/wgEncodeSydhTfbsHelas3Brf2StdAlnRep1.bam HeLa-S3 ChipSeq BRF2 Alignments 1 bam Harvard Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeSydhTfbs/wgEncodeSydhTfbsHelas3Brf2StdAlnRep2.bam HeLa-S3 ChipSeq BRF2 Alignments 2 bam Harvard Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeSydhTfbs/wgEncodeSydhTfbsHelas3Brf2StdPk.narrowPeak.gz HeLa-S3 ChipSeq BRF2 Peaks narrowPeak Harvard Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeSydhTfbs/wgEncodeSydhTfbsHelas3Brf2StdSig.bigWig HeLa-S3 ChipSeq BRF2 Signal bigWig Harvard Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeSydhTfbs/wgEncodeSydhTfbsHelas3Brg1IggmusAlnRep1.bam HeLa-S3 ChipSeq Brg1 Alignments 1 bam Yale Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeSydhTfbs/wgEncodeSydhTfbsHelas3Brg1IggmusAlnRep2.bam HeLa-S3 ChipSeq Brg1 Alignments 2 bam Yale Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeSydhTfbs/wgEncodeSydhTfbsHelas3Brg1IggmusAlnRep3.bam HeLa-S3 ChipSeq Brg1 Alignments 3 bam Yale Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeSydhTfbs/wgEncodeSydhTfbsHelas3Brg1IggmusPk.narrowPeak.gz HeLa-S3 ChipSeq Brg1 Peaks narrowPeak Yale Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeSydhTfbs/wgEncodeSydhTfbsHelas3Brg1IggmusSig.bigWig HeLa-S3 ChipSeq Brg1 Signal bigWig Yale Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeSydhTfbs/wgEncodeSydhTfbsHelas3CebpbIggrabAlnRep1.bam HeLa-S3 ChipSeq CEBPB Alignments 1 bam Stanford Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeSydhTfbs/wgEncodeSydhTfbsHelas3CebpbIggrabAlnRep2.bam HeLa-S3 ChipSeq CEBPB Alignments 2 bam Stanford Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeSydhTfbs/wgEncodeSydhTfbsHelas3CebpbIggrabPk.narrowPeak.gz HeLa-S3 ChipSeq CEBPB Peaks narrowPeak Stanford Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeSydhTfbs/wgEncodeSydhTfbsHelas3CebpbIggrabSig.bigWig HeLa-S3 ChipSeq CEBPB Signal bigWig Stanford Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeSydhTfbs/wgEncodeSydhTfbsHelas3CfosStdAlnRep1.bam HeLa-S3 ChipSeq c-Fos Alignments 1 bam Yale Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeSydhTfbs/wgEncodeSydhTfbsHelas3CfosStdAlnRep2.bam HeLa-S3 ChipSeq c-Fos Alignments 2 bam Yale Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeSydhTfbs/wgEncodeSydhTfbsHelas3CfosStdPk.narrowPeak.gz HeLa-S3 ChipSeq c-Fos Peaks narrowPeak Yale Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeSydhTfbs/wgEncodeSydhTfbsHelas3CfosStdSig.bigWig HeLa-S3 ChipSeq c-Fos Signal bigWig Yale Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeSydhTfbs/wgEncodeSydhTfbsHelas3Chd2IggrabAlnRep1.bam HeLa-S3 ChipSeq CHD2_(AB68301) Alignments 1 bam Stanford Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeSydhTfbs/wgEncodeSydhTfbsHelas3Chd2IggrabAlnRep2.bam HeLa-S3 ChipSeq CHD2_(AB68301) Alignments 2 bam Stanford Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeSydhTfbs/wgEncodeSydhTfbsHelas3Chd2IggrabPk.narrowPeak.gz HeLa-S3 ChipSeq CHD2_(AB68301) Peaks narrowPeak Stanford Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeSydhTfbs/wgEncodeSydhTfbsHelas3Chd2IggrabSig.bigWig HeLa-S3 ChipSeq CHD2_(AB68301) Signal bigWig Stanford Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeSydhTfbs/wgEncodeSydhTfbsHelas3CjunIggrabAlnRep1.bam HeLa-S3 ChipSeq c-Jun Alignments 1 bam Stanford Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeSydhTfbs/wgEncodeSydhTfbsHelas3CjunIggrabAlnRep2.bam HeLa-S3 ChipSeq c-Jun Alignments 2 bam Stanford Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeSydhTfbs/wgEncodeSydhTfbsHelas3CjunIggrabPk.narrowPeak.gz HeLa-S3 ChipSeq c-Jun Peaks narrowPeak Stanford Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeSydhTfbs/wgEncodeSydhTfbsHelas3CjunIggrabSig.bigWig HeLa-S3 ChipSeq c-Jun Signal bigWig Stanford Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeSydhTfbs/wgEncodeSydhTfbsHelas3CmycStdAlnRep1.bam HeLa-S3 ChipSeq c-Myc Alignments 1 bam Yale Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeSydhTfbs/wgEncodeSydhTfbsHelas3CmycStdAlnRep2.bam HeLa-S3 ChipSeq c-Myc Alignments 2 bam Yale Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeSydhTfbs/wgEncodeSydhTfbsHelas3CmycStdPk.narrowPeak.gz HeLa-S3 ChipSeq c-Myc Peaks narrowPeak Yale Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeSydhTfbs/wgEncodeSydhTfbsHelas3CmycStdSig.bigWig HeLa-S3 ChipSeq c-Myc Signal bigWig Yale Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeSydhTfbs/wgEncodeSydhTfbsHelas3Corestsc30189IggrabAlnRep1.bam HeLa-S3 ChipSeq COREST_(sc-30189) Alignments 1 bam Stanford Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeSydhTfbs/wgEncodeSydhTfbsHelas3Corestsc30189IggrabAlnRep2.bam HeLa-S3 ChipSeq COREST_(sc-30189) Alignments 2 bam Stanford Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeSydhTfbs/wgEncodeSydhTfbsHelas3Corestsc30189IggrabPk.narrowPeak.gz HeLa-S3 ChipSeq COREST_(sc-30189) Peaks narrowPeak Stanford Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeSydhTfbs/wgEncodeSydhTfbsHelas3Corestsc30189IggrabSig.bigWig HeLa-S3 ChipSeq COREST_(sc-30189) Signal bigWig Stanford Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeSydhTfbs/wgEncodeSydhTfbsHelas3E2f1StdAlnRep1.bam HeLa-S3 ChipSeq E2F1 Alignments 1 bam USC Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeSydhTfbs/wgEncodeSydhTfbsHelas3E2f1StdAlnRep2.bam HeLa-S3 ChipSeq E2F1 Alignments 2 bam USC Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeSydhTfbs/wgEncodeSydhTfbsHelas3E2f1StdPk.narrowPeak.gz HeLa-S3 ChipSeq E2F1 Peaks narrowPeak USC Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeSydhTfbs/wgEncodeSydhTfbsHelas3E2f1StdSig.bigWig HeLa-S3 ChipSeq E2F1 Signal bigWig USC Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeSydhTfbs/wgEncodeSydhTfbsHelas3E2f4StdAlnRep1.bam HeLa-S3 ChipSeq E2F4 Alignments 1 bam USC Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeSydhTfbs/wgEncodeSydhTfbsHelas3E2f4StdAlnRep2.bam HeLa-S3 ChipSeq E2F4 Alignments 2 bam USC Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeSydhTfbs/wgEncodeSydhTfbsHelas3E2f4StdPk.narrowPeak.gz HeLa-S3 ChipSeq E2F4 Peaks narrowPeak USC Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeSydhTfbs/wgEncodeSydhTfbsHelas3E2f4StdSig.bigWig HeLa-S3 ChipSeq E2F4 Signal bigWig USC Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeSydhTfbs/wgEncodeSydhTfbsHelas3E2f6StdAlnRep1.bam HeLa-S3 ChipSeq E2F6 Alignments 1 bam USC Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeSydhTfbs/wgEncodeSydhTfbsHelas3E2f6StdAlnRep2.bam HeLa-S3 ChipSeq E2F6 Alignments 2 bam USC Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeSydhTfbs/wgEncodeSydhTfbsHelas3E2f6StdPk.narrowPeak.gz HeLa-S3 ChipSeq E2F6 Peaks narrowPeak USC Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeSydhTfbs/wgEncodeSydhTfbsHelas3E2f6StdSig.bigWig HeLa-S3 ChipSeq E2F6 Signal bigWig USC Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeSydhTfbs/wgEncodeSydhTfbsHelas3Elk112771IggrabAlnRep1.bam HeLa-S3 ChipSeq ELK1_(1277-1) Alignments 1 bam Stanford Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeSydhTfbs/wgEncodeSydhTfbsHelas3Elk112771IggrabAlnRep2.bam HeLa-S3 ChipSeq ELK1_(1277-1) Alignments 2 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ChipSeq ELK4 Signal bigWig USC Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeSydhTfbs/wgEncodeSydhTfbsHelas3Gcn5StdAlnRep1.bam HeLa-S3 ChipSeq GCN5 Alignments 1 bam Stanford Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeSydhTfbs/wgEncodeSydhTfbsHelas3Gcn5StdAlnRep2.bam HeLa-S3 ChipSeq GCN5 Alignments 2 bam Stanford Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeSydhTfbs/wgEncodeSydhTfbsHelas3Gcn5StdPk.narrowPeak.gz HeLa-S3 ChipSeq GCN5 Peaks narrowPeak Stanford Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeSydhTfbs/wgEncodeSydhTfbsHelas3Gcn5StdSig.bigWig HeLa-S3 ChipSeq GCN5 Signal bigWig Stanford Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeSydhTfbs/wgEncodeSydhTfbsHelas3Gtf2f1ab28179IggrabAlnRep1.bam HeLa-S3 ChipSeq GTF2F1_(AB28179) Alignments 1 bam Stanford Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeSydhTfbs/wgEncodeSydhTfbsHelas3Gtf2f1ab28179IggrabAlnRep2.bam HeLa-S3 ChipSeq GTF2F1_(AB28179) Alignments 2 bam Stanford Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeSydhTfbs/wgEncodeSydhTfbsHelas3Gtf2f1ab28179IggrabPk.narrowPeak.gz HeLa-S3 ChipSeq GTF2F1_(AB28179) Peaks narrowPeak Stanford Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeSydhTfbs/wgEncodeSydhTfbsHelas3Gtf2f1ab28179IggrabSig.bigWig HeLa-S3 ChipSeq GTF2F1_(AB28179) Signal bigWig Stanford Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeSydhTfbs/wgEncodeSydhTfbsHelas3Hae2f1StdAlnRep1.bam HeLa-S3 ChipSeq HA-E2F1 Alignments 1 bam USC Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeSydhTfbs/wgEncodeSydhTfbsHelas3Hae2f1StdAlnRep2.bam HeLa-S3 ChipSeq HA-E2F1 Alignments 2 bam USC Data 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HeLa-S3 ChipSeq Ini1 Signal bigWig Stanford Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeSydhTfbs/wgEncodeSydhTfbsHelas3InputIfng30StdAlnRep1.bam HeLa-S3 ChipSeq Input Alignments 1 bam Yale Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeSydhTfbs/wgEncodeSydhTfbsHelas3InputIfng30StdSig.bigWig HeLa-S3 ChipSeq Input Signal bigWig Yale Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeSydhTfbs/wgEncodeSydhTfbsHelas3InputIggmusAlnRep1.bam HeLa-S3 ChipSeq Input Alignments 1 bam Yale Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeSydhTfbs/wgEncodeSydhTfbsHelas3InputIggmusAlnRep2.bam HeLa-S3 ChipSeq Input Alignments 2 bam Yale Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeSydhTfbs/wgEncodeSydhTfbsHelas3InputIggmusSig.bigWig HeLa-S3 ChipSeq Input Signal bigWig Yale Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeSydhTfbs/wgEncodeSydhTfbsHelas3InputIggrabAlnRep1.bam HeLa-S3 ChipSeq Input Alignments 1 bam Stanford Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeSydhTfbs/wgEncodeSydhTfbsHelas3InputIggrabSig.bigWig HeLa-S3 ChipSeq Input Signal bigWig Stanford Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeSydhTfbs/wgEncodeSydhTfbsHelas3InputLargefragmentAlnRep1.bam HeLa-S3 ChipSeq Input Alignments 1 bam Yale Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeSydhTfbs/wgEncodeSydhTfbsHelas3InputLargefragmentAlnRep2.bam HeLa-S3 ChipSeq Input Alignments 2 bam Yale Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeSydhTfbs/wgEncodeSydhTfbsHelas3InputLargefragmentSig.bigWig HeLa-S3 ChipSeq Input Signal bigWig Yale Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeSydhTfbs/wgEncodeSydhTfbsHelas3InputMnaseAlnRep1.bam HeLa-S3 ChipSeq Input Alignments 1 bam Yale Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeSydhTfbs/wgEncodeSydhTfbsHelas3InputMnaseAlnRep2.bam HeLa-S3 ChipSeq Input Alignments 2 bam Yale Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeSydhTfbs/wgEncodeSydhTfbsHelas3InputMnaseSig.bigWig HeLa-S3 ChipSeq Input Signal bigWig Yale Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeSydhTfbs/wgEncodeSydhTfbsHelas3InputNakeddnaAlnRep1.bam HeLa-S3 ChipSeq Input Alignments 1 bam Yale Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeSydhTfbs/wgEncodeSydhTfbsHelas3InputNakeddnaAlnRep2.bam HeLa-S3 ChipSeq Input Alignments 2 bam Yale Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeSydhTfbs/wgEncodeSydhTfbsHelas3InputNakeddnaAlnRep3.bam HeLa-S3 ChipSeq Input Alignments 3 bam Yale Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeSydhTfbs/wgEncodeSydhTfbsHelas3InputNakeddnaSig.bigWig HeLa-S3 ChipSeq Input Signal bigWig Yale Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeSydhTfbs/wgEncodeSydhTfbsHelas3InputStdAlnRep1.bam HeLa-S3 ChipSeq Input Alignments 1 bam Yale Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeSydhTfbs/wgEncodeSydhTfbsHelas3InputStdSig.bigWig HeLa-S3 ChipSeq Input Signal bigWig Yale Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeSydhTfbs/wgEncodeSydhTfbsHelas3InputUcdAln.bam HeLa-S3 ChipSeq Input Alignments bam USC Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeSydhTfbs/wgEncodeSydhTfbsHelas3InputUcdSig.bigWig HeLa-S3 ChipSeq Input Signal bigWig USC Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeSydhTfbs/wgEncodeSydhTfbsHelas3Irf3IggrabAlnRep1.bam HeLa-S3 ChipSeq IRF3 Alignments 1 bam Stanford Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeSydhTfbs/wgEncodeSydhTfbsHelas3Irf3IggrabAlnRep2.bam HeLa-S3 ChipSeq IRF3 Alignments 2 bam Stanford Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeSydhTfbs/wgEncodeSydhTfbsHelas3Irf3IggrabPk.narrowPeak.gz HeLa-S3 ChipSeq IRF3 Peaks narrowPeak Stanford Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeSydhTfbs/wgEncodeSydhTfbsHelas3Irf3IggrabSig.bigWig HeLa-S3 ChipSeq IRF3 Signal bigWig Stanford Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeSydhTfbs/wgEncodeSydhTfbsHelas3JundIggrabAlnRep1.bam HeLa-S3 ChipSeq JunD Alignments 1 bam Stanford Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeSydhTfbs/wgEncodeSydhTfbsHelas3JundIggrabAlnRep2.bam HeLa-S3 ChipSeq JunD Alignments 2 bam Stanford Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeSydhTfbs/wgEncodeSydhTfbsHelas3JundIggrabPk.narrowPeak.gz HeLa-S3 ChipSeq JunD Peaks narrowPeak Stanford Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeSydhTfbs/wgEncodeSydhTfbsHelas3JundIggrabSig.bigWig HeLa-S3 ChipSeq JunD Signal bigWig Stanford Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeSydhTfbs/wgEncodeSydhTfbsHelas3MafkIggrabAlnRep1.bam HeLa-S3 ChipSeq MafK_(ab50322) Alignments 1 bam Stanford Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeSydhTfbs/wgEncodeSydhTfbsHelas3MafkIggrabAlnRep2.bam HeLa-S3 ChipSeq MafK_(ab50322) Alignments 2 bam Stanford Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeSydhTfbs/wgEncodeSydhTfbsHelas3MafkIggrabPk.narrowPeak.gz HeLa-S3 ChipSeq MafK_(ab50322) Peaks narrowPeak Stanford Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeSydhTfbs/wgEncodeSydhTfbsHelas3MafkIggrabSig.bigWig HeLa-S3 ChipSeq MafK_(ab50322) Signal bigWig Stanford Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeSydhTfbs/wgEncodeSydhTfbsHelas3MaxIggrabAlnRep1.bam HeLa-S3 ChipSeq Max Alignments 1 bam Stanford Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeSydhTfbs/wgEncodeSydhTfbsHelas3MaxIggrabAlnRep2.bam HeLa-S3 ChipSeq Max Alignments 2 bam Stanford Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeSydhTfbs/wgEncodeSydhTfbsHelas3MaxIggrabPk.narrowPeak.gz HeLa-S3 ChipSeq Max Peaks narrowPeak Stanford Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeSydhTfbs/wgEncodeSydhTfbsHelas3MaxIggrabSig.bigWig HeLa-S3 ChipSeq Max Signal bigWig Stanford Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeSydhTfbs/wgEncodeSydhTfbsHelas3MaxStdAlnRep1.bam HeLa-S3 ChipSeq Max Alignments 1 bam Yale Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeSydhTfbs/wgEncodeSydhTfbsHelas3MaxStdAlnRep2.bam HeLa-S3 ChipSeq Max Alignments 2 bam Yale Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeSydhTfbs/wgEncodeSydhTfbsHelas3MaxStdPk.narrowPeak.gz HeLa-S3 ChipSeq Max Peaks narrowPeak Yale Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeSydhTfbs/wgEncodeSydhTfbsHelas3MaxStdSig.bigWig HeLa-S3 ChipSeq Max Signal bigWig Yale Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeSydhTfbs/wgEncodeSydhTfbsHelas3Mazab85725IggrabAlnRep1.bam HeLa-S3 ChipSeq MAZ_(ab85725) Alignments 1 bam Stanford Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeSydhTfbs/wgEncodeSydhTfbsHelas3Mazab85725IggrabAlnRep2.bam HeLa-S3 ChipSeq MAZ_(ab85725) Alignments 2 bam Stanford Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeSydhTfbs/wgEncodeSydhTfbsHelas3Mazab85725IggrabPk.narrowPeak.gz HeLa-S3 ChipSeq MAZ_(ab85725) Peaks narrowPeak Stanford Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeSydhTfbs/wgEncodeSydhTfbsHelas3Mazab85725IggrabSig.bigWig HeLa-S3 ChipSeq MAZ_(ab85725) Signal bigWig Stanford Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeSydhTfbs/wgEncodeSydhTfbsHelas3Mxi1af4185IggrabAlnRep1.bam HeLa-S3 ChipSeq Mxi1_(AF4185) Alignments 1 bam Stanford Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeSydhTfbs/wgEncodeSydhTfbsHelas3Mxi1af4185IggrabAlnRep2.bam HeLa-S3 ChipSeq Mxi1_(AF4185) Alignments 2 bam Stanford Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeSydhTfbs/wgEncodeSydhTfbsHelas3Mxi1af4185IggrabPk.narrowPeak.gz HeLa-S3 ChipSeq Mxi1_(AF4185) Peaks narrowPeak Stanford Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeSydhTfbs/wgEncodeSydhTfbsHelas3Mxi1af4185IggrabSig.bigWig HeLa-S3 ChipSeq Mxi1_(AF4185) Signal bigWig Stanford Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeSydhTfbs/wgEncodeSydhTfbsHelas3NfyaIggrabAlnRep1.bam HeLa-S3 ChipSeq NF-YA Alignments 1 bam Harvard Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeSydhTfbs/wgEncodeSydhTfbsHelas3NfyaIggrabAlnRep2.bam HeLa-S3 ChipSeq NF-YA Alignments 2 bam Harvard Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeSydhTfbs/wgEncodeSydhTfbsHelas3NfyaIggrabPk.narrowPeak.gz HeLa-S3 ChipSeq NF-YA Peaks narrowPeak Harvard Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeSydhTfbs/wgEncodeSydhTfbsHelas3NfyaIggrabSig.bigWig HeLa-S3 ChipSeq NF-YA Signal bigWig Harvard Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeSydhTfbs/wgEncodeSydhTfbsHelas3NfybIggrabAlnRep1.bam HeLa-S3 ChipSeq NF-YB Alignments 1 bam Harvard Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeSydhTfbs/wgEncodeSydhTfbsHelas3NfybIggrabAlnRep2.bam HeLa-S3 ChipSeq NF-YB Alignments 2 bam Harvard Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeSydhTfbs/wgEncodeSydhTfbsHelas3NfybIggrabPk.narrowPeak.gz HeLa-S3 ChipSeq NF-YB Peaks narrowPeak Harvard Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeSydhTfbs/wgEncodeSydhTfbsHelas3NfybIggrabSig.bigWig HeLa-S3 ChipSeq NF-YB Signal bigWig Harvard Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeSydhTfbs/wgEncodeSydhTfbsHelas3Nrf1IggmusAlnRep1.bam HeLa-S3 ChipSeq Nrf1 Alignments 1 bam Stanford Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeSydhTfbs/wgEncodeSydhTfbsHelas3Nrf1IggmusAlnRep2.bam HeLa-S3 ChipSeq Nrf1 Alignments 2 bam Stanford Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeSydhTfbs/wgEncodeSydhTfbsHelas3Nrf1IggmusPk.narrowPeak.gz HeLa-S3 ChipSeq Nrf1 Peaks narrowPeak Stanford Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeSydhTfbs/wgEncodeSydhTfbsHelas3Nrf1IggmusSig.bigWig HeLa-S3 ChipSeq Nrf1 Signal bigWig Stanford Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeSydhTfbs/wgEncodeSydhTfbsHelas3P300sc584sc584IggrabAlnRep1.bam HeLa-S3 ChipSeq p300_(SC-584) Alignments 1 bam Stanford Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeSydhTfbs/wgEncodeSydhTfbsHelas3P300sc584sc584IggrabAlnRep2.bam HeLa-S3 ChipSeq p300_(SC-584) Alignments 2 bam Stanford Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeSydhTfbs/wgEncodeSydhTfbsHelas3P300sc584sc584IggrabPk.narrowPeak.gz HeLa-S3 ChipSeq p300_(SC-584) Peaks narrowPeak Stanford Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeSydhTfbs/wgEncodeSydhTfbsHelas3P300sc584sc584IggrabSig.bigWig HeLa-S3 ChipSeq p300_(SC-584) Signal bigWig Stanford Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeSydhTfbs/wgEncodeSydhTfbsHelas3Pol2StdAlnRep1.bam HeLa-S3 ChipSeq Pol2 Alignments 1 bam Yale Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeSydhTfbs/wgEncodeSydhTfbsHelas3Pol2StdAlnRep2.bam HeLa-S3 ChipSeq Pol2 Alignments 2 bam Yale Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeSydhTfbs/wgEncodeSydhTfbsHelas3Pol2StdAlnRep3.bam HeLa-S3 ChipSeq Pol2 Alignments 3 bam Yale Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeSydhTfbs/wgEncodeSydhTfbsHelas3Pol2StdPk.narrowPeak.gz HeLa-S3 ChipSeq Pol2 Peaks narrowPeak Yale Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeSydhTfbs/wgEncodeSydhTfbsHelas3Pol2StdSig.bigWig HeLa-S3 ChipSeq Pol2 Signal bigWig Yale Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeSydhTfbs/wgEncodeSydhTfbsHelas3Pol2s2IggrabAlnRep1.bam HeLa-S3 ChipSeq Pol2(phosphoS2) Alignments 1 bam Stanford Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeSydhTfbs/wgEncodeSydhTfbsHelas3Pol2s2IggrabAlnRep2.bam HeLa-S3 ChipSeq Pol2(phosphoS2) Alignments 2 bam Stanford Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeSydhTfbs/wgEncodeSydhTfbsHelas3Pol2s2IggrabPk.narrowPeak.gz HeLa-S3 ChipSeq Pol2(phosphoS2) Peaks narrowPeak Stanford Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeSydhTfbs/wgEncodeSydhTfbsHelas3Pol2s2IggrabSig.bigWig HeLa-S3 ChipSeq Pol2(phosphoS2) Signal bigWig Stanford Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeSydhTfbs/wgEncodeSydhTfbsHelas3Prdm19115IggrabAlnRep1.bam HeLa-S3 ChipSeq PRDM1_(9115) Alignments 1 bam Stanford Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeSydhTfbs/wgEncodeSydhTfbsHelas3Prdm19115IggrabAlnRep2.bam HeLa-S3 ChipSeq PRDM1_(9115) Alignments 2 bam Stanford Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeSydhTfbs/wgEncodeSydhTfbsHelas3Prdm19115IggrabPk.narrowPeak.gz HeLa-S3 ChipSeq PRDM1_(9115) Peaks narrowPeak Stanford Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeSydhTfbs/wgEncodeSydhTfbsHelas3Prdm19115IggrabSig.bigWig HeLa-S3 ChipSeq PRDM1_(9115) Signal bigWig Stanford Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeSydhTfbs/wgEncodeSydhTfbsHelas3Rad21IggrabAlnRep1.bam HeLa-S3 ChipSeq Rad21 Alignments 1 bam Stanford Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeSydhTfbs/wgEncodeSydhTfbsHelas3Rad21IggrabAlnRep2.bam HeLa-S3 ChipSeq Rad21 Alignments 2 bam Stanford Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeSydhTfbs/wgEncodeSydhTfbsHelas3Rad21IggrabPk.narrowPeak.gz HeLa-S3 ChipSeq Rad21 Peaks narrowPeak Stanford Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeSydhTfbs/wgEncodeSydhTfbsHelas3Rad21IggrabSig.bigWig HeLa-S3 ChipSeq Rad21 Signal bigWig Stanford Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeSydhTfbs/wgEncodeSydhTfbsHelas3Rfx5200401194IggrabAlnRep1.bam HeLa-S3 ChipSeq RFX5_(200-401-194) Alignments 1 bam Stanford Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeSydhTfbs/wgEncodeSydhTfbsHelas3Rfx5200401194IggrabAlnRep2.bam HeLa-S3 ChipSeq RFX5_(200-401-194) Alignments 2 bam Stanford Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeSydhTfbs/wgEncodeSydhTfbsHelas3Rfx5200401194IggrabPk.narrowPeak.gz HeLa-S3 ChipSeq RFX5_(200-401-194) Peaks narrowPeak Stanford Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeSydhTfbs/wgEncodeSydhTfbsHelas3Rfx5200401194IggrabSig.bigWig HeLa-S3 ChipSeq RFX5_(200-401-194) Signal bigWig Stanford Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeSydhTfbs/wgEncodeSydhTfbsHelas3Rpc155StdAlnRep1.bam HeLa-S3 ChipSeq RPC155 Alignments 1 bam Harvard Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeSydhTfbs/wgEncodeSydhTfbsHelas3Rpc155StdAlnRep2.bam HeLa-S3 ChipSeq RPC155 Alignments 2 bam Harvard Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeSydhTfbs/wgEncodeSydhTfbsHelas3Rpc155StdPk.narrowPeak.gz HeLa-S3 ChipSeq RPC155 Peaks narrowPeak Harvard Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeSydhTfbs/wgEncodeSydhTfbsHelas3Rpc155StdSig.bigWig HeLa-S3 ChipSeq RPC155 Signal bigWig Harvard Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeSydhTfbs/wgEncodeSydhTfbsHelas3Smc3ab9263IggrabAlnRep1.bam HeLa-S3 ChipSeq SMC3_(ab9263) Alignments 1 bam Stanford Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeSydhTfbs/wgEncodeSydhTfbsHelas3Smc3ab9263IggrabAlnRep2.bam HeLa-S3 ChipSeq SMC3_(ab9263) Alignments 2 bam Stanford Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeSydhTfbs/wgEncodeSydhTfbsHelas3Smc3ab9263IggrabPk.narrowPeak.gz HeLa-S3 ChipSeq SMC3_(ab9263) Peaks narrowPeak Stanford Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeSydhTfbs/wgEncodeSydhTfbsHelas3Smc3ab9263IggrabSig.bigWig HeLa-S3 ChipSeq SMC3_(ab9263) Signal bigWig Stanford Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeSydhTfbs/wgEncodeSydhTfbsHelas3Spt20StdAlnRep1.bam HeLa-S3 ChipSeq SPT20 Alignments 1 bam Stanford Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeSydhTfbs/wgEncodeSydhTfbsHelas3Spt20StdAlnRep2.bam HeLa-S3 ChipSeq SPT20 Alignments 2 bam Stanford Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeSydhTfbs/wgEncodeSydhTfbsHelas3Spt20StdPk.narrowPeak.gz HeLa-S3 ChipSeq SPT20 Peaks narrowPeak Stanford Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeSydhTfbs/wgEncodeSydhTfbsHelas3Spt20StdSig.bigWig HeLa-S3 ChipSeq SPT20 Signal bigWig Stanford Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeSydhTfbs/wgEncodeSydhTfbsHelas3Stat1Ifng30StdAlnRep1.bam HeLa-S3 ChipSeq STAT1 Alignments 1 bam Yale Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeSydhTfbs/wgEncodeSydhTfbsHelas3Stat1Ifng30StdAlnRep2.bam HeLa-S3 ChipSeq STAT1 Alignments 2 bam Yale Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeSydhTfbs/wgEncodeSydhTfbsHelas3Stat1Ifng30StdPk.narrowPeak.gz HeLa-S3 ChipSeq STAT1 Peaks narrowPeak Yale Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeSydhTfbs/wgEncodeSydhTfbsHelas3Stat1Ifng30StdSig.bigWig HeLa-S3 ChipSeq STAT1 Signal bigWig Yale Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeSydhTfbs/wgEncodeSydhTfbsHelas3Stat3IggrabAlnRep1.bam HeLa-S3 ChipSeq STAT3 Alignments 1 bam Stanford Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeSydhTfbs/wgEncodeSydhTfbsHelas3Stat3IggrabAlnRep2.bam HeLa-S3 ChipSeq STAT3 Alignments 2 bam Stanford Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeSydhTfbs/wgEncodeSydhTfbsHelas3Stat3IggrabPk.narrowPeak.gz HeLa-S3 ChipSeq STAT3 Peaks narrowPeak Stanford Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeSydhTfbs/wgEncodeSydhTfbsHelas3Stat3IggrabSig.bigWig HeLa-S3 ChipSeq STAT3 Signal bigWig Stanford Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeSydhTfbs/wgEncodeSydhTfbsHelas3TbpIggrabAlnRep1.bam HeLa-S3 ChipSeq TBP Alignments 1 bam Stanford Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeSydhTfbs/wgEncodeSydhTfbsHelas3TbpIggrabAlnRep2.bam HeLa-S3 ChipSeq TBP Alignments 2 bam Stanford Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeSydhTfbs/wgEncodeSydhTfbsHelas3TbpIggrabPk.narrowPeak.gz HeLa-S3 ChipSeq TBP Peaks narrowPeak Stanford Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeSydhTfbs/wgEncodeSydhTfbsHelas3TbpIggrabSig.bigWig HeLa-S3 ChipSeq TBP Signal bigWig Stanford Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeSydhTfbs/wgEncodeSydhTfbsHelas3Tcf7l2UcdAlnRep1.bam HeLa-S3 ChipSeq TCF7L2 Alignments 1 bam USC Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeSydhTfbs/wgEncodeSydhTfbsHelas3Tcf7l2UcdAlnRep2.bam HeLa-S3 ChipSeq TCF7L2 Alignments 2 bam USC Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeSydhTfbs/wgEncodeSydhTfbsHelas3Tcf7l2UcdPk.narrowPeak.gz HeLa-S3 ChipSeq TCF7L2 Peaks narrowPeak USC Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeSydhTfbs/wgEncodeSydhTfbsHelas3Tcf7l2UcdSig.bigWig HeLa-S3 ChipSeq TCF7L2 Signal bigWig USC Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeSydhTfbs/wgEncodeSydhTfbsHelas3Tcf7l2c9b92565UcdAlnRep1.bam HeLa-S3 ChipSeq TCF7L2_C9B9_(2565) Alignments 1 bam USC Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeSydhTfbs/wgEncodeSydhTfbsHelas3Tcf7l2c9b92565UcdAlnRep2.bam HeLa-S3 ChipSeq TCF7L2_C9B9_(2565) Alignments 2 bam USC Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeSydhTfbs/wgEncodeSydhTfbsHelas3Tcf7l2c9b92565UcdPk.narrowPeak.gz HeLa-S3 ChipSeq TCF7L2_C9B9_(2565) Peaks narrowPeak USC Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeSydhTfbs/wgEncodeSydhTfbsHelas3Tcf7l2c9b92565UcdSig.bigWig HeLa-S3 ChipSeq TCF7L2_C9B9_(2565) Signal bigWig USC Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeSydhTfbs/wgEncodeSydhTfbsHelas3Tf3c110StdAlnRep1.bam HeLa-S3 ChipSeq TFIIIC-110 Alignments 1 bam Harvard Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeSydhTfbs/wgEncodeSydhTfbsHelas3Tf3c110StdAlnRep2.bam HeLa-S3 ChipSeq TFIIIC-110 Alignments 2 bam Harvard Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeSydhTfbs/wgEncodeSydhTfbsHelas3Tf3c110StdPk.narrowPeak.gz HeLa-S3 ChipSeq TFIIIC-110 Peaks narrowPeak Harvard Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeSydhTfbs/wgEncodeSydhTfbsHelas3Tf3c110StdSig.bigWig HeLa-S3 ChipSeq TFIIIC-110 Signal bigWig Harvard Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeSydhTfbs/wgEncodeSydhTfbsHelas3Tr4StdAlnRep1.bam HeLa-S3 ChipSeq TR4 Alignments 1 bam USC Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeSydhTfbs/wgEncodeSydhTfbsHelas3Tr4StdAlnRep2.bam HeLa-S3 ChipSeq TR4 Alignments 2 bam USC Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeSydhTfbs/wgEncodeSydhTfbsHelas3Tr4StdPk.narrowPeak.gz HeLa-S3 ChipSeq TR4 Peaks narrowPeak USC Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeSydhTfbs/wgEncodeSydhTfbsHelas3Tr4StdSig.bigWig HeLa-S3 ChipSeq TR4 Signal bigWig USC Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeSydhTfbs/wgEncodeSydhTfbsHelas3Usf2IggmusAlnRep1.bam HeLa-S3 ChipSeq USF2 Alignments 1 bam Stanford Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeSydhTfbs/wgEncodeSydhTfbsHelas3Usf2IggmusAlnRep2.bam HeLa-S3 ChipSeq USF2 Alignments 2 bam Stanford Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeSydhTfbs/wgEncodeSydhTfbsHelas3Usf2IggmusPk.narrowPeak.gz HeLa-S3 ChipSeq USF2 Peaks narrowPeak Stanford Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeSydhTfbs/wgEncodeSydhTfbsHelas3Usf2IggmusSig.bigWig HeLa-S3 ChipSeq USF2 Signal bigWig Stanford Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeSydhTfbs/wgEncodeSydhTfbsHelas3Zkscan1hpa006672IggrabAlnRep1.bam HeLa-S3 ChipSeq ZKSCAN1_(HPA006672) Alignments 1 bam Stanford Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeSydhTfbs/wgEncodeSydhTfbsHelas3Zkscan1hpa006672IggrabAlnRep2.bam HeLa-S3 ChipSeq ZKSCAN1_(HPA006672) Alignments 2 bam Stanford Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeSydhTfbs/wgEncodeSydhTfbsHelas3Zkscan1hpa006672IggrabPk.narrowPeak.gz HeLa-S3 ChipSeq ZKSCAN1_(HPA006672) Peaks narrowPeak Stanford Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeSydhTfbs/wgEncodeSydhTfbsHelas3Zkscan1hpa006672IggrabSig.bigWig HeLa-S3 ChipSeq ZKSCAN1_(HPA006672) Signal bigWig Stanford Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeSydhTfbs/wgEncodeSydhTfbsHelas3Znf143IggrabAlnRep1.bam HeLa-S3 ChipSeq Znf143_(16618-1-AP) Alignments 1 bam Stanford Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeSydhTfbs/wgEncodeSydhTfbsHelas3Znf143IggrabAlnRep2.bam HeLa-S3 ChipSeq Znf143_(16618-1-AP) Alignments 2 bam Stanford Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeSydhTfbs/wgEncodeSydhTfbsHelas3Znf143IggrabPk.narrowPeak.gz HeLa-S3 ChipSeq Znf143_(16618-1-AP) Peaks narrowPeak Stanford Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeSydhTfbs/wgEncodeSydhTfbsHelas3Znf143IggrabSig.bigWig HeLa-S3 ChipSeq Znf143_(16618-1-AP) Signal bigWig Stanford Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeSydhTfbs/wgEncodeSydhTfbsHelas3Znf274UcdAlnRep1.bam HeLa-S3 ChipSeq ZNF274 Alignments 1 bam USC Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeSydhTfbs/wgEncodeSydhTfbsHelas3Znf274UcdAlnRep2.bam HeLa-S3 ChipSeq ZNF274 Alignments 2 bam USC Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeSydhTfbs/wgEncodeSydhTfbsHelas3Znf274UcdPk.narrowPeak.gz HeLa-S3 ChipSeq ZNF274 Peaks narrowPeak USC Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeSydhTfbs/wgEncodeSydhTfbsHelas3Znf274UcdSig.bigWig HeLa-S3 ChipSeq ZNF274 Signal bigWig USC Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeSydhTfbs/wgEncodeSydhTfbsHelas3Zzz3StdAlnRep1.bam HeLa-S3 ChipSeq ZZZ3 Alignments 1 bam Harvard Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeSydhTfbs/wgEncodeSydhTfbsHelas3Zzz3StdAlnRep2.bam HeLa-S3 ChipSeq ZZZ3 Alignments 2 bam Harvard Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeSydhTfbs/wgEncodeSydhTfbsHelas3Zzz3StdPk.narrowPeak.gz HeLa-S3 ChipSeq ZZZ3 Peaks narrowPeak Harvard Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeSydhTfbs/wgEncodeSydhTfbsHelas3Zzz3StdSig.bigWig HeLa-S3 ChipSeq ZZZ3 Signal bigWig Harvard Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeSydhTfbs/wgEncodeSydhTfbsHepg2Arid3anb100279IggrabAlnRep1.bam HepG2 ChipSeq ARID3A_(NB100-279) Alignments 1 bam Stanford Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeSydhTfbs/wgEncodeSydhTfbsHepg2Arid3anb100279IggrabAlnRep2.bam HepG2 ChipSeq ARID3A_(NB100-279) Alignments 2 bam Stanford Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeSydhTfbs/wgEncodeSydhTfbsHepg2Arid3anb100279IggrabPk.narrowPeak.gz HepG2 ChipSeq ARID3A_(NB100-279) Peaks narrowPeak Stanford Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeSydhTfbs/wgEncodeSydhTfbsHepg2Arid3anb100279IggrabSig.bigWig HepG2 ChipSeq ARID3A_(NB100-279) Signal bigWig Stanford Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeSydhTfbs/wgEncodeSydhTfbsHepg2Bhlhe40cIggrabAlnRep1.bam HepG2 ChipSeq BHLHE40_(NB100-1800) Alignments 1 bam Stanford Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeSydhTfbs/wgEncodeSydhTfbsHepg2Bhlhe40cIggrabAlnRep2.bam HepG2 ChipSeq BHLHE40_(NB100-1800) Alignments 2 bam Stanford Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeSydhTfbs/wgEncodeSydhTfbsHepg2Bhlhe40cIggrabPk.narrowPeak.gz HepG2 ChipSeq BHLHE40_(NB100-1800) Peaks narrowPeak Stanford Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeSydhTfbs/wgEncodeSydhTfbsHepg2Bhlhe40cIggrabSig.bigWig HepG2 ChipSeq BHLHE40_(NB100-1800) Signal bigWig Stanford Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeSydhTfbs/wgEncodeSydhTfbsHepg2Brca1a300IggrabAlnRep1.bam HepG2 ChipSeq BRCA1_(A300-000A) Alignments 1 bam Stanford Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeSydhTfbs/wgEncodeSydhTfbsHepg2Brca1a300IggrabAlnRep2.bam HepG2 ChipSeq BRCA1_(A300-000A) Alignments 2 bam Stanford Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeSydhTfbs/wgEncodeSydhTfbsHepg2Brca1a300IggrabPk.narrowPeak.gz HepG2 ChipSeq BRCA1_(A300-000A) Peaks narrowPeak Stanford Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeSydhTfbs/wgEncodeSydhTfbsHepg2Brca1a300IggrabSig.bigWig HepG2 ChipSeq BRCA1_(A300-000A) Signal bigWig Stanford Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeSydhTfbs/wgEncodeSydhTfbsHepg2CebpbForsklnStdAlnRep1.bam HepG2 ChipSeq CEBPB Alignments 1 bam Stanford Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeSydhTfbs/wgEncodeSydhTfbsHepg2CebpbForsklnStdAlnRep2.bam HepG2 ChipSeq CEBPB Alignments 2 bam Stanford Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeSydhTfbs/wgEncodeSydhTfbsHepg2CebpbForsklnStdPk.narrowPeak.gz HepG2 ChipSeq CEBPB Peaks narrowPeak Stanford Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeSydhTfbs/wgEncodeSydhTfbsHepg2CebpbForsklnStdSig.bigWig HepG2 ChipSeq CEBPB Signal bigWig Stanford Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeSydhTfbs/wgEncodeSydhTfbsHepg2CebpbIggrabAlnRep1.bam HepG2 ChipSeq CEBPB Alignments 1 bam Stanford Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeSydhTfbs/wgEncodeSydhTfbsHepg2CebpbIggrabAlnRep2.bam HepG2 ChipSeq CEBPB Alignments 2 bam Stanford Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeSydhTfbs/wgEncodeSydhTfbsHepg2CebpbIggrabPk.narrowPeak.gz HepG2 ChipSeq CEBPB Peaks narrowPeak Stanford Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeSydhTfbs/wgEncodeSydhTfbsHepg2CebpbIggrabSig.bigWig HepG2 ChipSeq CEBPB Signal bigWig Stanford Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeSydhTfbs/wgEncodeSydhTfbsHepg2CebpzIggrabAlnRep1.bam HepG2 ChipSeq CEBPZ Alignments 1 bam Stanford Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeSydhTfbs/wgEncodeSydhTfbsHepg2CebpzIggrabAlnRep2.bam HepG2 ChipSeq CEBPZ Alignments 2 bam Stanford Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeSydhTfbs/wgEncodeSydhTfbsHepg2CebpzIggrabPk.narrowPeak.gz HepG2 ChipSeq CEBPZ Peaks narrowPeak Stanford Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeSydhTfbs/wgEncodeSydhTfbsHepg2CebpzIggrabSig.bigWig HepG2 ChipSeq CEBPZ Signal bigWig Stanford Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeSydhTfbs/wgEncodeSydhTfbsHepg2Chd2ab68301IggrabAlnRep1.bam HepG2 ChipSeq CHD2_(AB68301) Alignments 1 bam Stanford Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeSydhTfbs/wgEncodeSydhTfbsHepg2Chd2ab68301IggrabAlnRep2.bam HepG2 ChipSeq CHD2_(AB68301) Alignments 2 bam Stanford Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeSydhTfbs/wgEncodeSydhTfbsHepg2Chd2ab68301IggrabPk.narrowPeak.gz HepG2 ChipSeq CHD2_(AB68301) Peaks narrowPeak Stanford Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeSydhTfbs/wgEncodeSydhTfbsHepg2Chd2ab68301IggrabSig.bigWig HepG2 ChipSeq CHD2_(AB68301) Signal bigWig Stanford Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeSydhTfbs/wgEncodeSydhTfbsHepg2CjunIggrabAlnRep1.bam HepG2 ChipSeq c-Jun Alignments 1 bam Stanford Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeSydhTfbs/wgEncodeSydhTfbsHepg2CjunIggrabAlnRep2.bam HepG2 ChipSeq c-Jun Alignments 2 bam Stanford Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeSydhTfbs/wgEncodeSydhTfbsHepg2CjunIggrabPk.narrowPeak.gz HepG2 ChipSeq c-Jun Peaks narrowPeak Stanford Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeSydhTfbs/wgEncodeSydhTfbsHepg2CjunIggrabSig.bigWig HepG2 ChipSeq c-Jun Signal bigWig Stanford Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeSydhTfbs/wgEncodeSydhTfbsHepg2Corestsc30189IggrabAlnRep1.bam HepG2 ChipSeq COREST_(sc-30189) Alignments 1 bam Stanford Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeSydhTfbs/wgEncodeSydhTfbsHepg2Corestsc30189IggrabAlnRep2.bam HepG2 ChipSeq COREST_(sc-30189) Alignments 2 bam Stanford Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeSydhTfbs/wgEncodeSydhTfbsHepg2Corestsc30189IggrabPk.narrowPeak.gz HepG2 ChipSeq COREST_(sc-30189) Peaks narrowPeak Stanford Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeSydhTfbs/wgEncodeSydhTfbsHepg2Corestsc30189IggrabSig.bigWig HepG2 ChipSeq COREST_(sc-30189) Signal bigWig Stanford Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeSydhTfbs/wgEncodeSydhTfbsHepg2ErraForsklnStdAlnRep1.bam HepG2 ChipSeq ERRA Alignments 1 bam Stanford Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeSydhTfbs/wgEncodeSydhTfbsHepg2ErraForsklnStdAlnRep2.bam HepG2 ChipSeq ERRA Alignments 2 bam Stanford Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeSydhTfbs/wgEncodeSydhTfbsHepg2ErraForsklnStdPk.narrowPeak.gz HepG2 ChipSeq ERRA Peaks narrowPeak Stanford Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeSydhTfbs/wgEncodeSydhTfbsHepg2ErraForsklnStdSig.bigWig HepG2 ChipSeq ERRA Signal bigWig Stanford Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeSydhTfbs/wgEncodeSydhTfbsHepg2Grp20ForsklnStdAlnRep1.bam HepG2 ChipSeq GRp20 Alignments 1 bam Stanford Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeSydhTfbs/wgEncodeSydhTfbsHepg2Grp20ForsklnStdAlnRep2.bam HepG2 ChipSeq GRp20 Alignments 2 bam Stanford Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeSydhTfbs/wgEncodeSydhTfbsHepg2Grp20ForsklnStdPk.narrowPeak.gz HepG2 ChipSeq GRp20 Peaks narrowPeak Stanford Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeSydhTfbs/wgEncodeSydhTfbsHepg2Grp20ForsklnStdSig.bigWig HepG2 ChipSeq GRp20 Signal bigWig Stanford Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeSydhTfbs/wgEncodeSydhTfbsHepg2Hnf4aForsklnStdAlnRep1.bam HepG2 ChipSeq HNF4A Alignments 1 bam Stanford Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeSydhTfbs/wgEncodeSydhTfbsHepg2Hnf4aForsklnStdAlnRep2.bam HepG2 ChipSeq HNF4A Alignments 2 bam Stanford Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeSydhTfbs/wgEncodeSydhTfbsHepg2Hnf4aForsklnStdPk.narrowPeak.gz HepG2 ChipSeq HNF4A Peaks narrowPeak Stanford Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeSydhTfbs/wgEncodeSydhTfbsHepg2Hnf4aForsklnStdSig.bigWig HepG2 ChipSeq HNF4A Signal bigWig Stanford Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeSydhTfbs/wgEncodeSydhTfbsHepg2Hsf1ForsklnStdAlnRep1.bam HepG2 ChipSeq HSF1 Alignments 1 bam Stanford Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeSydhTfbs/wgEncodeSydhTfbsHepg2Hsf1ForsklnStdAlnRep2.bam HepG2 ChipSeq HSF1 Alignments 2 bam Stanford Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeSydhTfbs/wgEncodeSydhTfbsHepg2Hsf1ForsklnStdPk.narrowPeak.gz HepG2 ChipSeq HSF1 Peaks narrowPeak Stanford Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeSydhTfbs/wgEncodeSydhTfbsHepg2Hsf1ForsklnStdSig.bigWig HepG2 ChipSeq HSF1 Signal bigWig Stanford Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeSydhTfbs/wgEncodeSydhTfbsHepg2InputForsklnStdAlnRep1.bam HepG2 ChipSeq Input Alignments 1 bam Stanford Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeSydhTfbs/wgEncodeSydhTfbsHepg2InputForsklnStdAlnRep2.bam HepG2 ChipSeq Input Alignments 2 bam Stanford Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeSydhTfbs/wgEncodeSydhTfbsHepg2InputForsklnStdSig.bigWig HepG2 ChipSeq Input Signal bigWig Stanford Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeSydhTfbs/wgEncodeSydhTfbsHepg2InputIgggoatAlnRep1.bam HepG2 ChipSeq Input Alignments 1 bam Stanford Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeSydhTfbs/wgEncodeSydhTfbsHepg2InputIgggoatSig.bigWig HepG2 ChipSeq Input Signal bigWig Stanford Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeSydhTfbs/wgEncodeSydhTfbsHepg2InputIggrabAln.bam HepG2 ChipSeq Input Alignments bam Stanford Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeSydhTfbs/wgEncodeSydhTfbsHepg2InputIggrabSig.bigWig HepG2 ChipSeq Input Signal bigWig Stanford Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeSydhTfbs/wgEncodeSydhTfbsHepg2InputInslnStdAlnRep1.bam HepG2 ChipSeq Input Alignments 1 bam Stanford Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeSydhTfbs/wgEncodeSydhTfbsHepg2InputInslnStdAlnRep2.bam HepG2 ChipSeq Input Alignments 2 bam Stanford Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeSydhTfbs/wgEncodeSydhTfbsHepg2InputInslnStdSig.bigWig HepG2 ChipSeq Input Signal bigWig Stanford Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeSydhTfbs/wgEncodeSydhTfbsHepg2InputPravastStdAlnRep1.bam HepG2 ChipSeq Input Alignments 1 bam Yale Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeSydhTfbs/wgEncodeSydhTfbsHepg2InputPravastStdAlnRep2.bam HepG2 ChipSeq Input Alignments 2 bam Yale Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeSydhTfbs/wgEncodeSydhTfbsHepg2InputPravastStdAlnRep3.bam HepG2 ChipSeq Input Alignments 3 bam Yale Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeSydhTfbs/wgEncodeSydhTfbsHepg2InputPravastStdSig.bigWig HepG2 ChipSeq Input Signal bigWig Yale Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeSydhTfbs/wgEncodeSydhTfbsHepg2InputUcdAlnRep1.bam HepG2 ChipSeq Input Alignments 1 bam USC Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeSydhTfbs/wgEncodeSydhTfbsHepg2InputUcdSig.bigWig HepG2 ChipSeq Input Signal bigWig USC Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeSydhTfbs/wgEncodeSydhTfbsHepg2Irf3IggrabAlnRep1.bam HepG2 ChipSeq IRF3 Alignments 1 bam Stanford Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeSydhTfbs/wgEncodeSydhTfbsHepg2Irf3IggrabAlnRep2.bam HepG2 ChipSeq IRF3 Alignments 2 bam Stanford Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeSydhTfbs/wgEncodeSydhTfbsHepg2Irf3IggrabPk.narrowPeak.gz HepG2 ChipSeq IRF3 Peaks narrowPeak Stanford Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeSydhTfbs/wgEncodeSydhTfbsHepg2Irf3IggrabSig.bigWig HepG2 ChipSeq IRF3 Signal bigWig Stanford Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeSydhTfbs/wgEncodeSydhTfbsHepg2JundIggrabAlnRep1.bam HepG2 ChipSeq JunD Alignments 1 bam Stanford Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeSydhTfbs/wgEncodeSydhTfbsHepg2JundIggrabAlnRep2.bam HepG2 ChipSeq JunD Alignments 2 bam Stanford Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeSydhTfbs/wgEncodeSydhTfbsHepg2JundIggrabPk.narrowPeak.gz HepG2 ChipSeq JunD Peaks narrowPeak Stanford Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeSydhTfbs/wgEncodeSydhTfbsHepg2JundIggrabSig.bigWig HepG2 ChipSeq JunD Signal bigWig Stanford Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeSydhTfbs/wgEncodeSydhTfbsHepg2Maffm8194IggrabAlnRep1.bam HepG2 ChipSeq MafF_(M8194) Alignments 1 bam Stanford Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeSydhTfbs/wgEncodeSydhTfbsHepg2Maffm8194IggrabAlnRep2.bam HepG2 ChipSeq MafF_(M8194) Alignments 2 bam Stanford Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeSydhTfbs/wgEncodeSydhTfbsHepg2Maffm8194IggrabPk.narrowPeak.gz HepG2 ChipSeq MafF_(M8194) Peaks narrowPeak Stanford Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeSydhTfbs/wgEncodeSydhTfbsHepg2Maffm8194IggrabSig.bigWig HepG2 ChipSeq MafF_(M8194) Signal bigWig Stanford Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeSydhTfbs/wgEncodeSydhTfbsHepg2Mafkab50322IggrabAlnRep1.bam HepG2 ChipSeq MafK_(ab50322) Alignments 1 bam Stanford Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeSydhTfbs/wgEncodeSydhTfbsHepg2Mafkab50322IggrabAlnRep2.bam HepG2 ChipSeq MafK_(ab50322) Alignments 2 bam Stanford Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeSydhTfbs/wgEncodeSydhTfbsHepg2Mafkab50322IggrabPk.narrowPeak.gz HepG2 ChipSeq MafK_(ab50322) Peaks narrowPeak Stanford Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeSydhTfbs/wgEncodeSydhTfbsHepg2Mafkab50322IggrabSig.bigWig HepG2 ChipSeq MafK_(ab50322) Signal bigWig Stanford Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeSydhTfbs/wgEncodeSydhTfbsHepg2Mafksc477IggrabAlnRep1.bam HepG2 ChipSeq MafK_(SC-477) Alignments 1 bam Stanford Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeSydhTfbs/wgEncodeSydhTfbsHepg2Mafksc477IggrabAlnRep2.bam HepG2 ChipSeq MafK_(SC-477) Alignments 2 bam Stanford Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeSydhTfbs/wgEncodeSydhTfbsHepg2Mafksc477IggrabPk.narrowPeak.gz HepG2 ChipSeq MafK_(SC-477) Peaks narrowPeak Stanford Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeSydhTfbs/wgEncodeSydhTfbsHepg2Mafksc477IggrabSig.bigWig HepG2 ChipSeq MafK_(SC-477) Signal bigWig Stanford Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeSydhTfbs/wgEncodeSydhTfbsHepg2MaxIggrabAlnRep1.bam HepG2 ChipSeq Max Alignments 1 bam Stanford Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeSydhTfbs/wgEncodeSydhTfbsHepg2MaxIggrabAlnRep2.bam HepG2 ChipSeq Max Alignments 2 bam Stanford Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeSydhTfbs/wgEncodeSydhTfbsHepg2MaxIggrabPk.narrowPeak.gz HepG2 ChipSeq Max Peaks narrowPeak Stanford Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeSydhTfbs/wgEncodeSydhTfbsHepg2MaxIggrabSig.bigWig HepG2 ChipSeq Max Signal bigWig Stanford Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeSydhTfbs/wgEncodeSydhTfbsHepg2Mazab85725IggrabAlnRep1.bam HepG2 ChipSeq MAZ_(ab85725) Alignments 1 bam Stanford Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeSydhTfbs/wgEncodeSydhTfbsHepg2Mazab85725IggrabAlnRep2.bam HepG2 ChipSeq MAZ_(ab85725) Alignments 2 bam Stanford Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeSydhTfbs/wgEncodeSydhTfbsHepg2Mazab85725IggrabPk.narrowPeak.gz HepG2 ChipSeq MAZ_(ab85725) Peaks narrowPeak Stanford Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeSydhTfbs/wgEncodeSydhTfbsHepg2Mazab85725IggrabSig.bigWig HepG2 ChipSeq MAZ_(ab85725) Signal bigWig Stanford Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeSydhTfbs/wgEncodeSydhTfbsHepg2Mxi1StdAlnRep1.bam HepG2 ChipSeq Mxi1_(AF4185) Alignments 1 bam Stanford Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeSydhTfbs/wgEncodeSydhTfbsHepg2Mxi1StdAlnRep2.bam HepG2 ChipSeq Mxi1_(AF4185) Alignments 2 bam Stanford Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeSydhTfbs/wgEncodeSydhTfbsHepg2Mxi1StdAlnRep3.bam HepG2 ChipSeq Mxi1_(AF4185) Alignments 3 bam Stanford Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeSydhTfbs/wgEncodeSydhTfbsHepg2Mxi1StdPk.narrowPeak.gz HepG2 ChipSeq Mxi1_(AF4185) Peaks narrowPeak Stanford Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeSydhTfbs/wgEncodeSydhTfbsHepg2Mxi1StdSig.bigWig HepG2 ChipSeq Mxi1_(AF4185) Signal bigWig Stanford Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeSydhTfbs/wgEncodeSydhTfbsHepg2Nrf1IggrabAlnRep1.bam HepG2 ChipSeq Nrf1 Alignments 1 bam Stanford Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeSydhTfbs/wgEncodeSydhTfbsHepg2Nrf1IggrabAlnRep2.bam HepG2 ChipSeq Nrf1 Alignments 2 bam Stanford Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeSydhTfbs/wgEncodeSydhTfbsHepg2Nrf1IggrabPk.narrowPeak.gz HepG2 ChipSeq Nrf1 Peaks narrowPeak Stanford Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeSydhTfbs/wgEncodeSydhTfbsHepg2Nrf1IggrabSig.bigWig HepG2 ChipSeq Nrf1 Signal bigWig Stanford Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeSydhTfbs/wgEncodeSydhTfbsHepg2P300sc582IggrabAlnRep1.bam HepG2 ChipSeq p300_(SC-584) Alignments 1 bam Stanford Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeSydhTfbs/wgEncodeSydhTfbsHepg2P300sc582IggrabAlnRep2.bam HepG2 ChipSeq p300_(SC-584) Alignments 2 bam Stanford Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeSydhTfbs/wgEncodeSydhTfbsHepg2P300sc582IggrabPk.narrowPeak.gz HepG2 ChipSeq p300_(SC-584) Peaks narrowPeak Stanford Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeSydhTfbs/wgEncodeSydhTfbsHepg2P300sc582IggrabSig.bigWig HepG2 ChipSeq p300_(SC-584) Signal bigWig Stanford Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeSydhTfbs/wgEncodeSydhTfbsHepg2Pgc1aForsklnStdAlnRep1.bam HepG2 ChipSeq PGC1A Alignments 1 bam Stanford Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeSydhTfbs/wgEncodeSydhTfbsHepg2Pgc1aForsklnStdAlnRep2.bam HepG2 ChipSeq PGC1A Alignments 2 bam Stanford Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeSydhTfbs/wgEncodeSydhTfbsHepg2Pgc1aForsklnStdPk.narrowPeak.gz HepG2 ChipSeq PGC1A Peaks narrowPeak Stanford Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeSydhTfbs/wgEncodeSydhTfbsHepg2Pgc1aForsklnStdSig.bigWig HepG2 ChipSeq PGC1A Signal bigWig Stanford Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeSydhTfbs/wgEncodeSydhTfbsHepg2Pol2ForsklnStdAlnRep1.bam HepG2 ChipSeq Pol2 Alignments 1 bam Stanford Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeSydhTfbs/wgEncodeSydhTfbsHepg2Pol2ForsklnStdAlnRep2.bam HepG2 ChipSeq Pol2 Alignments 2 bam Stanford Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeSydhTfbs/wgEncodeSydhTfbsHepg2Pol2ForsklnStdPk.narrowPeak.gz HepG2 ChipSeq Pol2 Peaks narrowPeak Stanford Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeSydhTfbs/wgEncodeSydhTfbsHepg2Pol2ForsklnStdSig.bigWig HepG2 ChipSeq Pol2 Signal bigWig Stanford Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeSydhTfbs/wgEncodeSydhTfbsHepg2Pol2IggrabAlnRep1.bam HepG2 ChipSeq Pol2 Alignments 1 bam Stanford Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeSydhTfbs/wgEncodeSydhTfbsHepg2Pol2IggrabAlnRep2.bam HepG2 ChipSeq Pol2 Alignments 2 bam Stanford Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeSydhTfbs/wgEncodeSydhTfbsHepg2Pol2IggrabPk.narrowPeak.gz HepG2 ChipSeq Pol2 Peaks narrowPeak Stanford Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeSydhTfbs/wgEncodeSydhTfbsHepg2Pol2IggrabSig.bigWig HepG2 ChipSeq Pol2 Signal bigWig Stanford Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeSydhTfbs/wgEncodeSydhTfbsHepg2Pol2PravastStdAlnRep1.bam HepG2 ChipSeq Pol2 Alignments 1 bam Yale Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeSydhTfbs/wgEncodeSydhTfbsHepg2Pol2PravastStdAlnRep2.bam HepG2 ChipSeq Pol2 Alignments 2 bam Yale Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeSydhTfbs/wgEncodeSydhTfbsHepg2Pol2PravastStdAlnRep3.bam HepG2 ChipSeq Pol2 Alignments 3 bam Yale Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeSydhTfbs/wgEncodeSydhTfbsHepg2Pol2PravastStdPk.narrowPeak.gz HepG2 ChipSeq Pol2 Peaks narrowPeak Yale Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeSydhTfbs/wgEncodeSydhTfbsHepg2Pol2PravastStdSig.bigWig HepG2 ChipSeq Pol2 Signal bigWig Yale Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeSydhTfbs/wgEncodeSydhTfbsHepg2Pol2s2IggrabAlnRep1.bam HepG2 ChipSeq Pol2(phosphoS2) Alignments 1 bam Stanford Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeSydhTfbs/wgEncodeSydhTfbsHepg2Pol2s2IggrabAlnRep2.bam HepG2 ChipSeq Pol2(phosphoS2) Alignments 2 bam Stanford Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeSydhTfbs/wgEncodeSydhTfbsHepg2Pol2s2IggrabPk.narrowPeak.gz HepG2 ChipSeq Pol2(phosphoS2) Peaks narrowPeak Stanford Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeSydhTfbs/wgEncodeSydhTfbsHepg2Pol2s2IggrabSig.bigWig HepG2 ChipSeq Pol2(phosphoS2) Signal bigWig Stanford Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeSydhTfbs/wgEncodeSydhTfbsHepg2Rad21IggrabAlnRep1.bam HepG2 ChipSeq Rad21 Alignments 1 bam Stanford Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeSydhTfbs/wgEncodeSydhTfbsHepg2Rad21IggrabAlnRep2.bam HepG2 ChipSeq Rad21 Alignments 2 bam Stanford Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeSydhTfbs/wgEncodeSydhTfbsHepg2Rad21IggrabPk.narrowPeak.gz HepG2 ChipSeq Rad21 Peaks narrowPeak Stanford Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeSydhTfbs/wgEncodeSydhTfbsHepg2Rad21IggrabSig.bigWig HepG2 ChipSeq Rad21 Signal bigWig Stanford Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeSydhTfbs/wgEncodeSydhTfbsHepg2Rfx5200401194IggrabAlnRep1.bam HepG2 ChipSeq RFX5_(200-401-194) Alignments 1 bam Stanford Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeSydhTfbs/wgEncodeSydhTfbsHepg2Rfx5200401194IggrabAlnRep2.bam HepG2 ChipSeq RFX5_(200-401-194) Alignments 2 bam Stanford Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeSydhTfbs/wgEncodeSydhTfbsHepg2Rfx5200401194IggrabPk.narrowPeak.gz HepG2 ChipSeq RFX5_(200-401-194) Peaks narrowPeak Stanford Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeSydhTfbs/wgEncodeSydhTfbsHepg2Rfx5200401194IggrabSig.bigWig HepG2 ChipSeq RFX5_(200-401-194) Signal bigWig Stanford Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeSydhTfbs/wgEncodeSydhTfbsHepg2Smc3ab9263IggrabAlnRep1.bam HepG2 ChipSeq SMC3_(ab9263) Alignments 1 bam Stanford Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeSydhTfbs/wgEncodeSydhTfbsHepg2Smc3ab9263IggrabAlnRep2.bam HepG2 ChipSeq SMC3_(ab9263) Alignments 2 bam Stanford Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeSydhTfbs/wgEncodeSydhTfbsHepg2Smc3ab9263IggrabPk.narrowPeak.gz HepG2 ChipSeq SMC3_(ab9263) Peaks narrowPeak Stanford Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeSydhTfbs/wgEncodeSydhTfbsHepg2Smc3ab9263IggrabSig.bigWig HepG2 ChipSeq SMC3_(ab9263) Signal bigWig Stanford Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeSydhTfbs/wgEncodeSydhTfbsHepg2Srebp1InslnStdAlnRep1.bam HepG2 ChipSeq SREBP1 Alignments 1 bam Stanford Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeSydhTfbs/wgEncodeSydhTfbsHepg2Srebp1InslnStdAlnRep2.bam HepG2 ChipSeq SREBP1 Alignments 2 bam Stanford Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeSydhTfbs/wgEncodeSydhTfbsHepg2Srebp1InslnStdAlnRep3.bam HepG2 ChipSeq SREBP1 Alignments 3 bam Stanford Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeSydhTfbs/wgEncodeSydhTfbsHepg2Srebp1InslnStdPk.narrowPeak.gz HepG2 ChipSeq SREBP1 Peaks narrowPeak Stanford Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeSydhTfbs/wgEncodeSydhTfbsHepg2Srebp1InslnStdSig.bigWig HepG2 ChipSeq SREBP1 Signal bigWig Stanford Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeSydhTfbs/wgEncodeSydhTfbsHepg2Srebp1PravastStdAlnRep1.bam HepG2 ChipSeq SREBP1 Alignments 1 bam Yale Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeSydhTfbs/wgEncodeSydhTfbsHepg2Srebp1PravastStdAlnRep2.bam HepG2 ChipSeq SREBP1 Alignments 2 bam Yale Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeSydhTfbs/wgEncodeSydhTfbsHepg2Srebp1PravastStdAlnRep3.bam HepG2 ChipSeq SREBP1 Alignments 3 bam Yale Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeSydhTfbs/wgEncodeSydhTfbsHepg2Srebp1PravastStdPk.narrowPeak.gz HepG2 ChipSeq SREBP1 Peaks narrowPeak Yale Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeSydhTfbs/wgEncodeSydhTfbsHepg2Srebp1PravastStdSig.bigWig HepG2 ChipSeq SREBP1 Signal bigWig Yale Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeSydhTfbs/wgEncodeSydhTfbsHepg2Srebp2PravastStdAlnRep1.bam HepG2 ChipSeq SREBP2 Alignments 1 bam Yale Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeSydhTfbs/wgEncodeSydhTfbsHepg2Srebp2PravastStdAlnRep2.bam HepG2 ChipSeq SREBP2 Alignments 2 bam Yale Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeSydhTfbs/wgEncodeSydhTfbsHepg2Srebp2PravastStdAlnRep3.bam HepG2 ChipSeq SREBP2 Alignments 3 bam Yale Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeSydhTfbs/wgEncodeSydhTfbsHepg2Srebp2PravastStdPk.narrowPeak.gz HepG2 ChipSeq SREBP2 Peaks narrowPeak Yale Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeSydhTfbs/wgEncodeSydhTfbsHepg2Srebp2PravastStdSig.bigWig HepG2 ChipSeq SREBP2 Signal bigWig Yale Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeSydhTfbs/wgEncodeSydhTfbsHepg2TbpIggrabAlnRep1.bam HepG2 ChipSeq TBP Alignments 1 bam Stanford Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeSydhTfbs/wgEncodeSydhTfbsHepg2TbpIggrabAlnRep2.bam HepG2 ChipSeq TBP Alignments 2 bam Stanford Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeSydhTfbs/wgEncodeSydhTfbsHepg2TbpIggrabPk.narrowPeak.gz HepG2 ChipSeq TBP Peaks narrowPeak Stanford Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeSydhTfbs/wgEncodeSydhTfbsHepg2TbpIggrabSig.bigWig HepG2 ChipSeq TBP Signal bigWig Stanford Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeSydhTfbs/wgEncodeSydhTfbsHepg2Tcf7l2UcdAlnRep1.bam HepG2 ChipSeq TCF7L2 Alignments 1 bam USC Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeSydhTfbs/wgEncodeSydhTfbsHepg2Tcf7l2UcdAlnRep2.bam HepG2 ChipSeq TCF7L2 Alignments 2 bam USC Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeSydhTfbs/wgEncodeSydhTfbsHepg2Tcf7l2UcdPk.narrowPeak.gz HepG2 ChipSeq TCF7L2 Peaks narrowPeak USC Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeSydhTfbs/wgEncodeSydhTfbsHepg2Tcf7l2UcdSig.bigWig HepG2 ChipSeq TCF7L2 Signal bigWig USC Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeSydhTfbs/wgEncodeSydhTfbsHepg2Tr4UcdAlnRep1.bam HepG2 ChipSeq TR4 Alignments 1 bam USC Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeSydhTfbs/wgEncodeSydhTfbsHepg2Tr4UcdAlnRep2.bam HepG2 ChipSeq TR4 Alignments 2 bam USC Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeSydhTfbs/wgEncodeSydhTfbsHepg2Tr4UcdPk.narrowPeak.gz HepG2 ChipSeq TR4 Peaks narrowPeak USC Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeSydhTfbs/wgEncodeSydhTfbsHepg2Tr4UcdSig.bigWig HepG2 ChipSeq TR4 Signal bigWig USC Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeSydhTfbs/wgEncodeSydhTfbsHepg2Usf2IggrabAlnRep1.bam HepG2 ChipSeq USF2 Alignments 1 bam Stanford Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeSydhTfbs/wgEncodeSydhTfbsHepg2Usf2IggrabAlnRep2.bam HepG2 ChipSeq USF2 Alignments 2 bam Stanford Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeSydhTfbs/wgEncodeSydhTfbsHepg2Usf2IggrabPk.narrowPeak.gz HepG2 ChipSeq USF2 Peaks narrowPeak Stanford Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeSydhTfbs/wgEncodeSydhTfbsHepg2Usf2IggrabSig.bigWig HepG2 ChipSeq USF2 Signal bigWig Stanford Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeSydhTfbs/wgEncodeSydhTfbsHepg2Znf274UcdAlnRep1.bam HepG2 ChipSeq ZNF274 Alignments 1 bam USC Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeSydhTfbs/wgEncodeSydhTfbsHepg2Znf274UcdAlnRep2.bam HepG2 ChipSeq ZNF274 Alignments 2 bam USC Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeSydhTfbs/wgEncodeSydhTfbsHepg2Znf274UcdPk.narrowPeak.gz HepG2 ChipSeq ZNF274 Peaks narrowPeak USC Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeSydhTfbs/wgEncodeSydhTfbsHepg2Znf274UcdSig.bigWig HepG2 ChipSeq ZNF274 Signal bigWig USC Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeSydhTfbs/wgEncodeSydhTfbsHuvecCfosUcdAlnRep1.bam HUVEC ChipSeq c-Fos Alignments 1 bam USC Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeSydhTfbs/wgEncodeSydhTfbsHuvecCfosUcdAlnRep2.bam HUVEC ChipSeq c-Fos Alignments 2 bam USC Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeSydhTfbs/wgEncodeSydhTfbsHuvecCfosUcdPk.narrowPeak.gz HUVEC ChipSeq c-Fos Peaks narrowPeak USC Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeSydhTfbs/wgEncodeSydhTfbsHuvecCfosUcdSig.bigWig HUVEC ChipSeq c-Fos Signal bigWig USC Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeSydhTfbs/wgEncodeSydhTfbsHuvecCjunStdAlnRep1.bam HUVEC ChipSeq c-Jun Alignments 1 bam Stanford Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeSydhTfbs/wgEncodeSydhTfbsHuvecCjunStdAlnRep2.bam HUVEC ChipSeq c-Jun Alignments 2 bam Stanford Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeSydhTfbs/wgEncodeSydhTfbsHuvecCjunStdPk.narrowPeak.gz HUVEC ChipSeq c-Jun Peaks narrowPeak Stanford Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeSydhTfbs/wgEncodeSydhTfbsHuvecCjunStdSig.bigWig HUVEC ChipSeq c-Jun Signal bigWig Stanford Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeSydhTfbs/wgEncodeSydhTfbsHuvecGata2UcdAlnRep1.bam HUVEC ChipSeq GATA-2 Alignments 1 bam USC Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeSydhTfbs/wgEncodeSydhTfbsHuvecGata2UcdAlnRep1V2.bam HUVEC ChipSeq GATA-2 Alignments 1 bam Stanford Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeSydhTfbs/wgEncodeSydhTfbsHuvecGata2UcdAlnRep2.bam HUVEC ChipSeq GATA-2 Alignments 2 bam USC Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeSydhTfbs/wgEncodeSydhTfbsHuvecGata2UcdAlnRep2V2.bam HUVEC ChipSeq GATA-2 Alignments 2 bam Stanford Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeSydhTfbs/wgEncodeSydhTfbsHuvecGata2UcdPk.narrowPeak.gz HUVEC ChipSeq GATA-2 Peaks narrowPeak USC Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeSydhTfbs/wgEncodeSydhTfbsHuvecGata2UcdSig.bigWig HUVEC ChipSeq GATA-2 Signal bigWig USC Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeSydhTfbs/wgEncodeSydhTfbsHuvecInputStdAlnRep1.bam HUVEC ChipSeq Input Alignments 1 bam Yale Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeSydhTfbs/wgEncodeSydhTfbsHuvecInputStdAlnRep2.bam HUVEC ChipSeq Input Alignments 2 bam Yale Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeSydhTfbs/wgEncodeSydhTfbsHuvecInputStdSig.bigWig HUVEC ChipSeq Input Signal bigWig Yale Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeSydhTfbs/wgEncodeSydhTfbsHuvecInputUcdAlnRep1.bam HUVEC ChipSeq Input Alignments 1 bam USC Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeSydhTfbs/wgEncodeSydhTfbsHuvecInputUcdSig.bigWig HUVEC ChipSeq Input Signal bigWig USC Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeSydhTfbs/wgEncodeSydhTfbsHuvecMaxStdAlnRep1.bam HUVEC ChipSeq Max Alignments 1 bam Stanford Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeSydhTfbs/wgEncodeSydhTfbsHuvecMaxStdAlnRep2.bam HUVEC ChipSeq Max Alignments 2 bam Stanford Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeSydhTfbs/wgEncodeSydhTfbsHuvecMaxStdPk.narrowPeak.gz HUVEC ChipSeq Max Peaks narrowPeak Stanford Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeSydhTfbs/wgEncodeSydhTfbsHuvecMaxStdSig.bigWig HUVEC ChipSeq Max Signal bigWig Stanford Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeSydhTfbs/wgEncodeSydhTfbsHuvecPol2StdAlnRep1.bam HUVEC ChipSeq Pol2 Alignments 1 bam Stanford Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeSydhTfbs/wgEncodeSydhTfbsHuvecPol2StdAlnRep2.bam HUVEC ChipSeq Pol2 Alignments 2 bam Stanford Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeSydhTfbs/wgEncodeSydhTfbsHuvecPol2StdAlnRep3.bam HUVEC ChipSeq Pol2 Alignments 3 bam Stanford Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeSydhTfbs/wgEncodeSydhTfbsHuvecPol2StdPk.narrowPeak.gz HUVEC ChipSeq Pol2 Peaks narrowPeak Stanford Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeSydhTfbs/wgEncodeSydhTfbsHuvecPol2StdSig.bigWig HUVEC ChipSeq Pol2 Signal bigWig Stanford Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeSydhTfbs/wgEncodeSydhTfbsImr90CebpbIggrabAlnRep1.bam IMR90 ChipSeq CEBPB Alignments 1 bam Stanford Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeSydhTfbs/wgEncodeSydhTfbsImr90CebpbIggrabAlnRep2.bam IMR90 ChipSeq CEBPB Alignments 2 bam Stanford Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeSydhTfbs/wgEncodeSydhTfbsImr90CebpbIggrabPk.narrowPeak.gz IMR90 ChipSeq CEBPB Peaks narrowPeak Stanford Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeSydhTfbs/wgEncodeSydhTfbsImr90CebpbIggrabSig.bigWig IMR90 ChipSeq CEBPB Signal bigWig Stanford Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeSydhTfbs/wgEncodeSydhTfbsImr90Chd1nb10060411IggrabAlnRep1.bam IMR90 ChipSeq CHD1_(NB100-60411) Alignments 1 bam Stanford Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeSydhTfbs/wgEncodeSydhTfbsImr90Chd1nb10060411IggrabAlnRep2.bam IMR90 ChipSeq CHD1_(NB100-60411) Alignments 2 bam Stanford Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeSydhTfbs/wgEncodeSydhTfbsImr90Chd1nb10060411IggrabPk.narrowPeak.gz IMR90 ChipSeq CHD1_(NB100-60411) Peaks narrowPeak Stanford Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeSydhTfbs/wgEncodeSydhTfbsImr90Chd1nb10060411IggrabSig.bigWig IMR90 ChipSeq CHD1_(NB100-60411) Signal bigWig Stanford Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeSydhTfbs/wgEncodeSydhTfbsImr90Corestsc30189IggrabAlnRep1.bam IMR90 ChipSeq COREST_(sc-30189) Alignments 1 bam Stanford Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeSydhTfbs/wgEncodeSydhTfbsImr90Corestsc30189IggrabAlnRep2.bam IMR90 ChipSeq COREST_(sc-30189) Alignments 2 bam Stanford Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeSydhTfbs/wgEncodeSydhTfbsImr90Corestsc30189IggrabPk.narrowPeak.gz IMR90 ChipSeq COREST_(sc-30189) Peaks narrowPeak Stanford Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeSydhTfbs/wgEncodeSydhTfbsImr90Corestsc30189IggrabSig.bigWig IMR90 ChipSeq COREST_(sc-30189) Signal bigWig Stanford Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeSydhTfbs/wgEncodeSydhTfbsImr90CtcfbIggrabAlnRep1.bam IMR90 ChipSeq CTCF_(SC-15914) Alignments 1 bam Stanford Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeSydhTfbs/wgEncodeSydhTfbsImr90CtcfbIggrabAlnRep2.bam IMR90 ChipSeq CTCF_(SC-15914) Alignments 2 bam Stanford Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeSydhTfbs/wgEncodeSydhTfbsImr90CtcfbIggrabPk.narrowPeak.gz IMR90 ChipSeq CTCF_(SC-15914) Peaks narrowPeak Stanford Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeSydhTfbs/wgEncodeSydhTfbsImr90CtcfbIggrabSig.bigWig IMR90 ChipSeq CTCF_(SC-15914) Signal bigWig Stanford Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeSydhTfbs/wgEncodeSydhTfbsImr90InputIggrabAlnRep1.bam IMR90 ChipSeq Input Alignments 1 bam Stanford Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeSydhTfbs/wgEncodeSydhTfbsImr90InputIggrabSig.bigWig IMR90 ChipSeq Input Signal bigWig Stanford Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeSydhTfbs/wgEncodeSydhTfbsImr90MafkIggrabAlnRep1.bam IMR90 ChipSeq MafK_(ab50322) Alignments 1 bam Stanford Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeSydhTfbs/wgEncodeSydhTfbsImr90MafkIggrabAlnRep2.bam IMR90 ChipSeq MafK_(ab50322) Alignments 2 bam Stanford Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeSydhTfbs/wgEncodeSydhTfbsImr90MafkIggrabPk.narrowPeak.gz IMR90 ChipSeq MafK_(ab50322) Peaks narrowPeak Stanford Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeSydhTfbs/wgEncodeSydhTfbsImr90MafkIggrabSig.bigWig IMR90 ChipSeq MafK_(ab50322) Signal bigWig Stanford Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeSydhTfbs/wgEncodeSydhTfbsImr90Mazab85725IggrabAlnRep1.bam IMR90 ChipSeq MAZ_(ab85725) Alignments 1 bam Stanford Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeSydhTfbs/wgEncodeSydhTfbsImr90Mazab85725IggrabAlnRep2.bam IMR90 ChipSeq MAZ_(ab85725) Alignments 2 bam Stanford Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeSydhTfbs/wgEncodeSydhTfbsImr90Mazab85725IggrabPk.narrowPeak.gz IMR90 ChipSeq MAZ_(ab85725) Peaks narrowPeak Stanford Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeSydhTfbs/wgEncodeSydhTfbsImr90Mazab85725IggrabSig.bigWig IMR90 ChipSeq MAZ_(ab85725) Signal bigWig Stanford Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeSydhTfbs/wgEncodeSydhTfbsImr90Mxi1IggrabAlnRep1.bam IMR90 ChipSeq Mxi1_(AF4185) Alignments 1 bam Stanford Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeSydhTfbs/wgEncodeSydhTfbsImr90Mxi1IggrabAlnRep2.bam IMR90 ChipSeq Mxi1_(AF4185) Alignments 2 bam Stanford Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeSydhTfbs/wgEncodeSydhTfbsImr90Mxi1IggrabPk.narrowPeak.gz IMR90 ChipSeq Mxi1_(AF4185) Peaks narrowPeak Stanford Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeSydhTfbs/wgEncodeSydhTfbsImr90Mxi1IggrabSig.bigWig IMR90 ChipSeq Mxi1_(AF4185) Signal bigWig Stanford Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeSydhTfbs/wgEncodeSydhTfbsImr90Pol2IggrabAlnRep1.bam IMR90 ChipSeq Pol2 Alignments 1 bam Stanford Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeSydhTfbs/wgEncodeSydhTfbsImr90Pol2IggrabAlnRep2.bam IMR90 ChipSeq Pol2 Alignments 2 bam Stanford Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeSydhTfbs/wgEncodeSydhTfbsImr90Pol2IggrabPk.narrowPeak.gz IMR90 ChipSeq Pol2 Peaks narrowPeak Stanford Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeSydhTfbs/wgEncodeSydhTfbsImr90Pol2IggrabSig.bigWig IMR90 ChipSeq Pol2 Signal bigWig Stanford Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeSydhTfbs/wgEncodeSydhTfbsImr90Rad21IggrabAlnRep1.bam IMR90 ChipSeq Rad21 Alignments 1 bam Stanford Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeSydhTfbs/wgEncodeSydhTfbsImr90Rad21IggrabAlnRep2.bam IMR90 ChipSeq Rad21 Alignments 2 bam Stanford Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeSydhTfbs/wgEncodeSydhTfbsImr90Rad21IggrabPk.narrowPeak.gz IMR90 ChipSeq Rad21 Peaks narrowPeak Stanford Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeSydhTfbs/wgEncodeSydhTfbsImr90Rad21IggrabSig.bigWig IMR90 ChipSeq Rad21 Signal bigWig Stanford Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeSydhTfbs/wgEncodeSydhTfbsImr90Rfx5IggrabAlnRep1.bam IMR90 ChipSeq RFX5_(200-401-194) Alignments 1 bam Stanford Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeSydhTfbs/wgEncodeSydhTfbsImr90Rfx5IggrabAlnRep2.bam IMR90 ChipSeq RFX5_(200-401-194) Alignments 2 bam Stanford Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeSydhTfbs/wgEncodeSydhTfbsImr90Rfx5IggrabPk.narrowPeak.gz IMR90 ChipSeq RFX5_(200-401-194) Peaks narrowPeak Stanford Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeSydhTfbs/wgEncodeSydhTfbsImr90Rfx5IggrabSig.bigWig IMR90 ChipSeq RFX5_(200-401-194) Signal bigWig Stanford Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeSydhTfbs/wgEncodeSydhTfbsK562Arid3asc8821IggrabAlnRep1.bam K562 ChipSeq ARID3A_(sc-8821) Alignments 1 bam Stanford Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeSydhTfbs/wgEncodeSydhTfbsK562Arid3asc8821IggrabAlnRep2.bam K562 ChipSeq ARID3A_(sc-8821) Alignments 2 bam Stanford Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeSydhTfbs/wgEncodeSydhTfbsK562Arid3asc8821IggrabPk.narrowPeak.gz K562 ChipSeq ARID3A_(sc-8821) Peaks narrowPeak Stanford Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeSydhTfbs/wgEncodeSydhTfbsK562Arid3asc8821IggrabSig.bigWig K562 ChipSeq ARID3A_(sc-8821) Signal bigWig Stanford Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeSydhTfbs/wgEncodeSydhTfbsK562Atf106325StdAlnRep1.bam K562 ChipSeq ATF1_(06-325) Alignments 1 bam Harvard Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeSydhTfbs/wgEncodeSydhTfbsK562Atf106325StdAlnRep2.bam K562 ChipSeq ATF1_(06-325) Alignments 2 bam Harvard Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeSydhTfbs/wgEncodeSydhTfbsK562Atf106325StdPk.narrowPeak.gz K562 ChipSeq ATF1_(06-325) Peaks narrowPeak Harvard Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeSydhTfbs/wgEncodeSydhTfbsK562Atf106325StdSig.bigWig K562 ChipSeq ATF1_(06-325) Signal bigWig Harvard Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeSydhTfbs/wgEncodeSydhTfbsK562Atf3StdAlnRep1.bam K562 ChipSeq ATF3 Alignments 1 bam Harvard Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeSydhTfbs/wgEncodeSydhTfbsK562Atf3StdAlnRep2.bam K562 ChipSeq ATF3 Alignments 2 bam Harvard Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeSydhTfbs/wgEncodeSydhTfbsK562Atf3StdPk.narrowPeak.gz K562 ChipSeq ATF3 Peaks narrowPeak Harvard Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeSydhTfbs/wgEncodeSydhTfbsK562Atf3StdSig.bigWig K562 ChipSeq ATF3 Signal bigWig Harvard Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeSydhTfbs/wgEncodeSydhTfbsK562Bach1sc14700IggrabAlnRep1.bam K562 ChipSeq Bach1_(sc-14700) Alignments 1 bam Stanford Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeSydhTfbs/wgEncodeSydhTfbsK562Bach1sc14700IggrabAlnRep2.bam K562 ChipSeq Bach1_(sc-14700) Alignments 2 bam Stanford Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeSydhTfbs/wgEncodeSydhTfbsK562Bach1sc14700IggrabPk.narrowPeak.gz K562 ChipSeq Bach1_(sc-14700) Peaks narrowPeak Stanford Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeSydhTfbs/wgEncodeSydhTfbsK562Bach1sc14700IggrabSig.bigWig K562 ChipSeq Bach1_(sc-14700) Signal bigWig Stanford Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeSydhTfbs/wgEncodeSydhTfbsK562Bdp1StdAlnRep1.bam K562 ChipSeq BDP1 Alignments 1 bam Harvard Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeSydhTfbs/wgEncodeSydhTfbsK562Bdp1StdAlnRep2.bam K562 ChipSeq BDP1 Alignments 2 bam Harvard Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeSydhTfbs/wgEncodeSydhTfbsK562Bdp1StdAlnRep3.bam K562 ChipSeq BDP1 Alignments 3 bam Harvard Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeSydhTfbs/wgEncodeSydhTfbsK562Bdp1StdPk.narrowPeak.gz K562 ChipSeq BDP1 Peaks narrowPeak Harvard Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeSydhTfbs/wgEncodeSydhTfbsK562Bdp1StdSig.bigWig K562 ChipSeq BDP1 Signal bigWig Harvard Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeSydhTfbs/wgEncodeSydhTfbsK562Bhlhe40nb100IggrabAlnRep1.bam K562 ChipSeq BHLHE40_(NB100-1800) Alignments 1 bam Stanford Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeSydhTfbs/wgEncodeSydhTfbsK562Bhlhe40nb100IggrabAlnRep2.bam K562 ChipSeq BHLHE40_(NB100-1800) Alignments 2 bam Stanford Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeSydhTfbs/wgEncodeSydhTfbsK562Bhlhe40nb100IggrabPk.narrowPeak.gz K562 ChipSeq BHLHE40_(NB100-1800) Peaks narrowPeak Stanford Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeSydhTfbs/wgEncodeSydhTfbsK562Bhlhe40nb100IggrabSig.bigWig K562 ChipSeq BHLHE40_(NB100-1800) Signal bigWig Stanford Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeSydhTfbs/wgEncodeSydhTfbsK562Brf1StdAlnRep1.bam K562 ChipSeq BRF1 Alignments 1 bam Harvard Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeSydhTfbs/wgEncodeSydhTfbsK562Brf1StdAlnRep2.bam K562 ChipSeq BRF1 Alignments 2 bam Harvard Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeSydhTfbs/wgEncodeSydhTfbsK562Brf1StdAlnRep3.bam K562 ChipSeq BRF1 Alignments 3 bam Harvard Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeSydhTfbs/wgEncodeSydhTfbsK562Brf1StdPk.narrowPeak.gz K562 ChipSeq BRF1 Peaks narrowPeak Harvard Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeSydhTfbs/wgEncodeSydhTfbsK562Brf1StdSig.bigWig K562 ChipSeq BRF1 Signal bigWig Harvard Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeSydhTfbs/wgEncodeSydhTfbsK562Brf2StdAlnRep1.bam K562 ChipSeq BRF2 Alignments 1 bam Harvard Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeSydhTfbs/wgEncodeSydhTfbsK562Brf2StdAlnRep2.bam K562 ChipSeq BRF2 Alignments 2 bam Harvard Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeSydhTfbs/wgEncodeSydhTfbsK562Brf2StdAlnRep3.bam K562 ChipSeq BRF2 Alignments 3 bam Harvard Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeSydhTfbs/wgEncodeSydhTfbsK562Brf2StdPk.narrowPeak.gz K562 ChipSeq BRF2 Peaks narrowPeak Harvard Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeSydhTfbs/wgEncodeSydhTfbsK562Brf2StdSig.bigWig K562 ChipSeq BRF2 Signal bigWig Harvard Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeSydhTfbs/wgEncodeSydhTfbsK562Brg1IggmusAlnRep1.bam K562 ChipSeq Brg1 Alignments 1 bam Stanford Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeSydhTfbs/wgEncodeSydhTfbsK562Brg1IggmusAlnRep2.bam K562 ChipSeq Brg1 Alignments 2 bam Stanford Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeSydhTfbs/wgEncodeSydhTfbsK562Brg1IggmusPk.narrowPeak.gz K562 ChipSeq Brg1 Peaks narrowPeak Stanford Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeSydhTfbs/wgEncodeSydhTfbsK562Brg1IggmusSig.bigWig K562 ChipSeq Brg1 Signal bigWig Stanford Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeSydhTfbs/wgEncodeSydhTfbsK562Ccnt2StdAlnRep1.bam K562 ChipSeq CCNT2 Alignments 1 bam Harvard Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeSydhTfbs/wgEncodeSydhTfbsK562Ccnt2StdAlnRep2.bam K562 ChipSeq CCNT2 Alignments 2 bam Harvard Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeSydhTfbs/wgEncodeSydhTfbsK562Ccnt2StdPk.narrowPeak.gz K562 ChipSeq CCNT2 Peaks narrowPeak Harvard Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeSydhTfbs/wgEncodeSydhTfbsK562Ccnt2StdSig.bigWig K562 ChipSeq CCNT2 Signal bigWig Harvard Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeSydhTfbs/wgEncodeSydhTfbsK562Cdpsc6327IggrabAlnRep1.bam K562 ChipSeq CDP_(sc-6327) Alignments 1 bam Stanford Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeSydhTfbs/wgEncodeSydhTfbsK562Cdpsc6327IggrabAlnRep2.bam K562 ChipSeq CDP_(sc-6327) Alignments 2 bam Stanford Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeSydhTfbs/wgEncodeSydhTfbsK562Cdpsc6327IggrabPk.narrowPeak.gz K562 ChipSeq CDP_(sc-6327) Peaks narrowPeak Stanford Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeSydhTfbs/wgEncodeSydhTfbsK562Cdpsc6327IggrabSig.bigWig K562 ChipSeq CDP_(sc-6327) Signal bigWig Stanford Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeSydhTfbs/wgEncodeSydhTfbsK562CebpbIggrabAlnRep1.bam K562 ChipSeq CEBPB Alignments 1 bam Stanford Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeSydhTfbs/wgEncodeSydhTfbsK562CebpbIggrabAlnRep2.bam K562 ChipSeq CEBPB Alignments 2 bam Stanford Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeSydhTfbs/wgEncodeSydhTfbsK562CebpbIggrabPk.narrowPeak.gz K562 ChipSeq CEBPB Peaks narrowPeak Stanford Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeSydhTfbs/wgEncodeSydhTfbsK562CebpbIggrabSig.bigWig K562 ChipSeq CEBPB Signal bigWig Stanford Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeSydhTfbs/wgEncodeSydhTfbsK562CfosStdAlnRep1.bam K562 ChipSeq c-Fos Alignments 1 bam Yale Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeSydhTfbs/wgEncodeSydhTfbsK562CfosStdAlnRep2.bam K562 ChipSeq c-Fos Alignments 2 bam Yale Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeSydhTfbs/wgEncodeSydhTfbsK562CfosStdAlnRep3.bam K562 ChipSeq c-Fos Alignments 3 bam Yale Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeSydhTfbs/wgEncodeSydhTfbsK562CfosStdPk.narrowPeak.gz K562 ChipSeq c-Fos Peaks narrowPeak Yale Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeSydhTfbs/wgEncodeSydhTfbsK562CfosStdSig.bigWig K562 ChipSeq c-Fos Signal bigWig Yale Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeSydhTfbs/wgEncodeSydhTfbsK562Chd2ab68301IggrabAlnRep1.bam K562 ChipSeq CHD2_(AB68301) Alignments 1 bam Stanford Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeSydhTfbs/wgEncodeSydhTfbsK562Chd2ab68301IggrabAlnRep2.bam K562 ChipSeq CHD2_(AB68301) Alignments 2 bam Stanford Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeSydhTfbs/wgEncodeSydhTfbsK562Chd2ab68301IggrabPk.narrowPeak.gz K562 ChipSeq CHD2_(AB68301) Peaks narrowPeak Stanford Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeSydhTfbs/wgEncodeSydhTfbsK562Chd2ab68301IggrabSig.bigWig K562 ChipSeq CHD2_(AB68301) Signal bigWig Stanford Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeSydhTfbs/wgEncodeSydhTfbsK562CjunIfna30StdAlnRep1.bam K562 ChipSeq c-Jun Alignments 1 bam Stanford Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeSydhTfbs/wgEncodeSydhTfbsK562CjunIfna30StdAlnRep2.bam K562 ChipSeq c-Jun Alignments 2 bam Stanford Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeSydhTfbs/wgEncodeSydhTfbsK562CjunIfna30StdPk.narrowPeak.gz K562 ChipSeq c-Jun Peaks narrowPeak Stanford Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeSydhTfbs/wgEncodeSydhTfbsK562CjunIfna30StdSig.bigWig K562 ChipSeq c-Jun Signal bigWig Stanford Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeSydhTfbs/wgEncodeSydhTfbsK562CjunIfna6hStdAlnRep1.bam K562 ChipSeq c-Jun Alignments 1 bam Yale Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeSydhTfbs/wgEncodeSydhTfbsK562CjunIfna6hStdAlnRep2.bam K562 ChipSeq c-Jun Alignments 2 bam Yale Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeSydhTfbs/wgEncodeSydhTfbsK562CjunIfna6hStdPk.narrowPeak.gz K562 ChipSeq c-Jun Peaks narrowPeak Yale Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeSydhTfbs/wgEncodeSydhTfbsK562CjunIfna6hStdSig.bigWig K562 ChipSeq c-Jun Signal bigWig Yale Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeSydhTfbs/wgEncodeSydhTfbsK562CjunIfng30StdAlnRep1.bam K562 ChipSeq c-Jun Alignments 1 bam Yale Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeSydhTfbs/wgEncodeSydhTfbsK562CjunIfng30StdAlnRep2.bam K562 ChipSeq c-Jun Alignments 2 bam Yale Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeSydhTfbs/wgEncodeSydhTfbsK562CjunIfng30StdPk.narrowPeak.gz K562 ChipSeq c-Jun Peaks narrowPeak Yale Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeSydhTfbs/wgEncodeSydhTfbsK562CjunIfng30StdSig.bigWig K562 ChipSeq c-Jun Signal bigWig Yale Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeSydhTfbs/wgEncodeSydhTfbsK562CjunIfng6hStdAlnRep1.bam K562 ChipSeq c-Jun Alignments 1 bam Yale Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeSydhTfbs/wgEncodeSydhTfbsK562CjunIfng6hStdAlnRep2.bam K562 ChipSeq c-Jun Alignments 2 bam Yale Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeSydhTfbs/wgEncodeSydhTfbsK562CjunIfng6hStdPk.narrowPeak.gz K562 ChipSeq c-Jun Peaks narrowPeak Yale Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeSydhTfbs/wgEncodeSydhTfbsK562CjunIfng6hStdSig.bigWig K562 ChipSeq c-Jun Signal bigWig Yale Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeSydhTfbs/wgEncodeSydhTfbsK562CjunIggrabAlnRep1.bam K562 ChipSeq c-Jun Alignments 1 bam Stanford Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeSydhTfbs/wgEncodeSydhTfbsK562CjunIggrabAlnRep2.bam K562 ChipSeq c-Jun Alignments 2 bam Stanford Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeSydhTfbs/wgEncodeSydhTfbsK562CjunIggrabPk.narrowPeak.gz K562 ChipSeq c-Jun Peaks narrowPeak Stanford Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeSydhTfbs/wgEncodeSydhTfbsK562CjunIggrabSig.bigWig K562 ChipSeq c-Jun Signal bigWig Stanford Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeSydhTfbs/wgEncodeSydhTfbsK562CjunStdAlnRep1.bam K562 ChipSeq c-Jun Alignments 1 bam Yale Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeSydhTfbs/wgEncodeSydhTfbsK562CjunStdAlnRep2.bam K562 ChipSeq c-Jun Alignments 2 bam Yale Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeSydhTfbs/wgEncodeSydhTfbsK562CjunStdPk.narrowPeak.gz K562 ChipSeq c-Jun Peaks narrowPeak Yale Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeSydhTfbs/wgEncodeSydhTfbsK562CjunStdSig.bigWig K562 ChipSeq c-Jun Signal bigWig Yale Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeSydhTfbs/wgEncodeSydhTfbsK562CmycIfna30StdAlnRep1.bam K562 ChipSeq c-Myc Alignments 1 bam Yale Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeSydhTfbs/wgEncodeSydhTfbsK562CmycIfna30StdAlnRep2.bam K562 ChipSeq c-Myc Alignments 2 bam Yale Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeSydhTfbs/wgEncodeSydhTfbsK562CmycIfna30StdPk.narrowPeak.gz K562 ChipSeq c-Myc Peaks narrowPeak Yale Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeSydhTfbs/wgEncodeSydhTfbsK562CmycIfna30StdSig.bigWig K562 ChipSeq c-Myc Signal bigWig Yale Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeSydhTfbs/wgEncodeSydhTfbsK562CmycIfna6hStdAlnRep1.bam K562 ChipSeq c-Myc Alignments 1 bam Yale Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeSydhTfbs/wgEncodeSydhTfbsK562CmycIfna6hStdAlnRep2.bam K562 ChipSeq c-Myc Alignments 2 bam Yale Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeSydhTfbs/wgEncodeSydhTfbsK562CmycIfna6hStdPk.narrowPeak.gz K562 ChipSeq c-Myc Peaks narrowPeak Yale Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeSydhTfbs/wgEncodeSydhTfbsK562CmycIfna6hStdSig.bigWig K562 ChipSeq c-Myc Signal bigWig Yale Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeSydhTfbs/wgEncodeSydhTfbsK562CmycIfng30StdAlnRep1.bam K562 ChipSeq c-Myc Alignments 1 bam Stanford Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeSydhTfbs/wgEncodeSydhTfbsK562CmycIfng30StdAlnRep2.bam K562 ChipSeq c-Myc Alignments 2 bam Stanford Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeSydhTfbs/wgEncodeSydhTfbsK562CmycIfng30StdPk.narrowPeak.gz K562 ChipSeq c-Myc Peaks narrowPeak Stanford Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeSydhTfbs/wgEncodeSydhTfbsK562CmycIfng30StdSig.bigWig K562 ChipSeq c-Myc Signal bigWig Stanford Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeSydhTfbs/wgEncodeSydhTfbsK562CmycIfng6hStdAlnRep1.bam K562 ChipSeq c-Myc Alignments 1 bam Yale Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeSydhTfbs/wgEncodeSydhTfbsK562CmycIfng6hStdAlnRep2.bam K562 ChipSeq c-Myc Alignments 2 bam Yale Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeSydhTfbs/wgEncodeSydhTfbsK562CmycIfng6hStdPk.narrowPeak.gz K562 ChipSeq c-Myc Peaks narrowPeak Yale Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeSydhTfbs/wgEncodeSydhTfbsK562CmycIfng6hStdSig.bigWig K562 ChipSeq c-Myc Signal bigWig Yale Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeSydhTfbs/wgEncodeSydhTfbsK562CmycIggrabAlnRep1.bam K562 ChipSeq c-Myc Alignments 1 bam Stanford Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeSydhTfbs/wgEncodeSydhTfbsK562CmycIggrabAlnRep2.bam K562 ChipSeq c-Myc Alignments 2 bam Stanford Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeSydhTfbs/wgEncodeSydhTfbsK562CmycIggrabPk.narrowPeak.gz K562 ChipSeq c-Myc Peaks narrowPeak Stanford Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeSydhTfbs/wgEncodeSydhTfbsK562CmycIggrabSig.bigWig K562 ChipSeq c-Myc Signal bigWig Stanford Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeSydhTfbs/wgEncodeSydhTfbsK562CmycStdAlnRep1.bam K562 ChipSeq c-Myc Alignments 1 bam Yale Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeSydhTfbs/wgEncodeSydhTfbsK562CmycStdAlnRep2.bam K562 ChipSeq c-Myc Alignments 2 bam Yale Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeSydhTfbs/wgEncodeSydhTfbsK562CmycStdPk.narrowPeak.gz K562 ChipSeq c-Myc Peaks narrowPeak Yale Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeSydhTfbs/wgEncodeSydhTfbsK562CmycStdSig.bigWig K562 ChipSeq c-Myc Signal bigWig Yale Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeSydhTfbs/wgEncodeSydhTfbsK562Corestab24166IggrabAlnRep1.bam K562 ChipSeq COREST_(ab24166) Alignments 1 bam Stanford Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeSydhTfbs/wgEncodeSydhTfbsK562Corestab24166IggrabAlnRep2.bam K562 ChipSeq COREST_(ab24166) Alignments 2 bam Stanford Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeSydhTfbs/wgEncodeSydhTfbsK562Corestab24166IggrabPk.narrowPeak.gz K562 ChipSeq COREST_(ab24166) Peaks narrowPeak Stanford Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeSydhTfbs/wgEncodeSydhTfbsK562Corestab24166IggrabSig.bigWig K562 ChipSeq COREST_(ab24166) Signal bigWig Stanford Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeSydhTfbs/wgEncodeSydhTfbsK562Corestsc30189IggrabAlnRep1.bam K562 ChipSeq COREST_(sc-30189) Alignments 1 bam Stanford Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeSydhTfbs/wgEncodeSydhTfbsK562Corestsc30189IggrabAlnRep2.bam K562 ChipSeq COREST_(sc-30189) Alignments 2 bam Stanford Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeSydhTfbs/wgEncodeSydhTfbsK562Corestsc30189IggrabPk.narrowPeak.gz K562 ChipSeq COREST_(sc-30189) Peaks narrowPeak Stanford Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeSydhTfbs/wgEncodeSydhTfbsK562Corestsc30189IggrabSig.bigWig K562 ChipSeq COREST_(sc-30189) Signal bigWig Stanford Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeSydhTfbs/wgEncodeSydhTfbsK562CtcfbIggrabAlnRep1.bam K562 ChipSeq CTCF_(SC-15914) Alignments 1 bam Stanford Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeSydhTfbs/wgEncodeSydhTfbsK562CtcfbIggrabAlnRep2.bam K562 ChipSeq CTCF_(SC-15914) Alignments 2 bam Stanford Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeSydhTfbs/wgEncodeSydhTfbsK562CtcfbIggrabPk.narrowPeak.gz K562 ChipSeq CTCF_(SC-15914) Peaks narrowPeak Stanford Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeSydhTfbs/wgEncodeSydhTfbsK562CtcfbIggrabSig.bigWig K562 ChipSeq CTCF_(SC-15914) Signal bigWig Stanford Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeSydhTfbs/wgEncodeSydhTfbsK562E2f4UcdAlnRep1.bam K562 ChipSeq E2F4 Alignments 1 bam USC Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeSydhTfbs/wgEncodeSydhTfbsK562E2f4UcdAlnRep2.bam K562 ChipSeq E2F4 Alignments 2 bam USC Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeSydhTfbs/wgEncodeSydhTfbsK562E2f4UcdPk.narrowPeak.gz K562 ChipSeq E2F4 Peaks narrowPeak USC Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeSydhTfbs/wgEncodeSydhTfbsK562E2f4UcdSig.bigWig K562 ChipSeq E2F4 Signal bigWig USC Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeSydhTfbs/wgEncodeSydhTfbsK562E2f6UcdAlnRep1.bam K562 ChipSeq E2F6 Alignments 1 bam USC Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeSydhTfbs/wgEncodeSydhTfbsK562E2f6UcdAlnRep2.bam K562 ChipSeq E2F6 Alignments 2 bam USC Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeSydhTfbs/wgEncodeSydhTfbsK562E2f6UcdPk.narrowPeak.gz K562 ChipSeq E2F6 Peaks narrowPeak USC Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeSydhTfbs/wgEncodeSydhTfbsK562E2f6UcdSig.bigWig K562 ChipSeq E2F6 Signal bigWig USC Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeSydhTfbs/wgEncodeSydhTfbsK562Elk112771IggrabAlnRep1.bam K562 ChipSeq ELK1_(1277-1) Alignments 1 bam Stanford Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeSydhTfbs/wgEncodeSydhTfbsK562Elk112771IggrabAlnRep2.bam K562 ChipSeq ELK1_(1277-1) Alignments 2 bam Stanford Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeSydhTfbs/wgEncodeSydhTfbsK562Elk112771IggrabPk.narrowPeak.gz K562 ChipSeq ELK1_(1277-1) Peaks narrowPeak Stanford Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeSydhTfbs/wgEncodeSydhTfbsK562Elk112771IggrabSig.bigWig K562 ChipSeq ELK1_(1277-1) Signal bigWig Stanford Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeSydhTfbs/wgEncodeSydhTfbsK562Gata1UcdAlnRep1.bam K562 ChipSeq GATA-1 Alignments 1 bam USC Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeSydhTfbs/wgEncodeSydhTfbsK562Gata1UcdAlnRep2.bam K562 ChipSeq GATA-1 Alignments 2 bam USC Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeSydhTfbs/wgEncodeSydhTfbsK562Gata1UcdPk.narrowPeak.gz K562 ChipSeq GATA-1 Peaks narrowPeak USC Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeSydhTfbs/wgEncodeSydhTfbsK562Gata1UcdSig.bigWig K562 ChipSeq GATA-1 Signal bigWig USC Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeSydhTfbs/wgEncodeSydhTfbsK562Gata1bIggmusAlnRep1.bam K562 ChipSeq GATA1_(SC-266) Alignments 1 bam Stanford Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeSydhTfbs/wgEncodeSydhTfbsK562Gata1bIggmusAlnRep2.bam K562 ChipSeq GATA1_(SC-266) Alignments 2 bam Stanford Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeSydhTfbs/wgEncodeSydhTfbsK562Gata1bIggmusPk.narrowPeak.gz K562 ChipSeq GATA1_(SC-266) Peaks narrowPeak Stanford Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeSydhTfbs/wgEncodeSydhTfbsK562Gata1bIggmusSig.bigWig K562 ChipSeq GATA1_(SC-266) Signal bigWig Stanford Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeSydhTfbs/wgEncodeSydhTfbsK562Gata2UcdAlnRep1.bam K562 ChipSeq GATA-2 Alignments 1 bam USC Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeSydhTfbs/wgEncodeSydhTfbsK562Gata2UcdAlnRep2.bam K562 ChipSeq GATA-2 Alignments 2 bam USC Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeSydhTfbs/wgEncodeSydhTfbsK562Gata2UcdPk.narrowPeak.gz K562 ChipSeq GATA-2 Peaks narrowPeak USC Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeSydhTfbs/wgEncodeSydhTfbsK562Gata2UcdSig.bigWig K562 ChipSeq GATA-2 Signal bigWig USC Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeSydhTfbs/wgEncodeSydhTfbsK562Gtf2bStdAlnRep1.bam K562 ChipSeq GTF2B Alignments 1 bam Harvard Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeSydhTfbs/wgEncodeSydhTfbsK562Gtf2bStdAlnRep2.bam K562 ChipSeq GTF2B Alignments 2 bam Harvard Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeSydhTfbs/wgEncodeSydhTfbsK562Gtf2bStdPk.narrowPeak.gz K562 ChipSeq GTF2B Peaks narrowPeak Harvard Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeSydhTfbs/wgEncodeSydhTfbsK562Gtf2bStdSig.bigWig K562 ChipSeq GTF2B Signal bigWig Harvard Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeSydhTfbs/wgEncodeSydhTfbsK562Gtf2f1ab28179IggrabAlnRep1.bam K562 ChipSeq GTF2F1_(AB28179) Alignments 1 bam Stanford Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeSydhTfbs/wgEncodeSydhTfbsK562Gtf2f1ab28179IggrabAlnRep2.bam K562 ChipSeq GTF2F1_(AB28179) Alignments 2 bam Stanford Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeSydhTfbs/wgEncodeSydhTfbsK562Gtf2f1ab28179IggrabPk.narrowPeak.gz K562 ChipSeq GTF2F1_(AB28179) Peaks narrowPeak Stanford Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeSydhTfbs/wgEncodeSydhTfbsK562Gtf2f1ab28179IggrabSig.bigWig K562 ChipSeq GTF2F1_(AB28179) Signal bigWig Stanford Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeSydhTfbs/wgEncodeSydhTfbsK562Hcfc1nb10068209IggrabAlnRep1.bam K562 ChipSeq HCFC1_(NB100-68209) Alignments 1 bam Stanford Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeSydhTfbs/wgEncodeSydhTfbsK562Hcfc1nb10068209IggrabAlnRep2.bam K562 ChipSeq HCFC1_(NB100-68209) Alignments 2 bam Stanford Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeSydhTfbs/wgEncodeSydhTfbsK562Hcfc1nb10068209IggrabPk.narrowPeak.gz K562 ChipSeq HCFC1_(NB100-68209) Peaks narrowPeak Stanford Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeSydhTfbs/wgEncodeSydhTfbsK562Hcfc1nb10068209IggrabSig.bigWig K562 ChipSeq HCFC1_(NB100-68209) Signal bigWig Stanford Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeSydhTfbs/wgEncodeSydhTfbsK562Hmgn3StdAlnRep1.bam K562 ChipSeq HMGN3 Alignments 1 bam Harvard Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeSydhTfbs/wgEncodeSydhTfbsK562Hmgn3StdAlnRep2.bam K562 ChipSeq HMGN3 Alignments 2 bam Harvard Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeSydhTfbs/wgEncodeSydhTfbsK562Hmgn3StdPk.narrowPeak.gz K562 ChipSeq HMGN3 Peaks narrowPeak Harvard Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeSydhTfbs/wgEncodeSydhTfbsK562Hmgn3StdSig.bigWig K562 ChipSeq HMGN3 Signal bigWig Harvard Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeSydhTfbs/wgEncodeSydhTfbsK562Ini1IggmusAlnRep1.bam K562 ChipSeq Ini1 Alignments 1 bam Stanford Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeSydhTfbs/wgEncodeSydhTfbsK562Ini1IggmusAlnRep2.bam K562 ChipSeq Ini1 Alignments 2 bam Stanford Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeSydhTfbs/wgEncodeSydhTfbsK562Ini1IggmusPk.narrowPeak.gz K562 ChipSeq Ini1 Peaks narrowPeak Stanford Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeSydhTfbs/wgEncodeSydhTfbsK562Ini1IggmusSig.bigWig K562 ChipSeq Ini1 Signal bigWig Stanford Data 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http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeSydhTfbs/wgEncodeSydhTfbsK562InputIggrabSig.bigWig K562 ChipSeq Input Signal bigWig Stanford Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeSydhTfbs/wgEncodeSydhTfbsK562InputStdAlnRep1.bam K562 ChipSeq Input Alignments 1 bam Yale Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeSydhTfbs/wgEncodeSydhTfbsK562InputStdAlnRep2.bam K562 ChipSeq Input Alignments 2 bam Yale Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeSydhTfbs/wgEncodeSydhTfbsK562InputStdSig.bigWig K562 ChipSeq Input Signal bigWig Yale Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeSydhTfbs/wgEncodeSydhTfbsK562InputUcdAlnRep1.bam K562 ChipSeq Input Alignments 1 bam USC Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeSydhTfbs/wgEncodeSydhTfbsK562InputUcdSig.bigWig K562 ChipSeq Input Signal bigWig USC Data 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Stanford Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeSydhTfbs/wgEncodeSydhTfbsK562Irf1Ifna6hStdPk.narrowPeak.gz K562 ChipSeq IRF1 Peaks narrowPeak Stanford Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeSydhTfbs/wgEncodeSydhTfbsK562Irf1Ifna6hStdSig.bigWig K562 ChipSeq IRF1 Signal bigWig Stanford Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeSydhTfbs/wgEncodeSydhTfbsK562Irf1Ifng30StdAlnRep1.bam K562 ChipSeq IRF1 Alignments 1 bam Stanford Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeSydhTfbs/wgEncodeSydhTfbsK562Irf1Ifng30StdAlnRep2.bam K562 ChipSeq IRF1 Alignments 2 bam Stanford Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeSydhTfbs/wgEncodeSydhTfbsK562Irf1Ifng30StdPk.narrowPeak.gz K562 ChipSeq IRF1 Peaks narrowPeak Stanford Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeSydhTfbs/wgEncodeSydhTfbsK562Irf1Ifng30StdSig.bigWig K562 ChipSeq IRF1 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http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeSydhTfbs/wgEncodeSydhTfbsK562MaffIggrabAlnRep1.bam K562 ChipSeq MafF_(M8194) Alignments 1 bam Stanford Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeSydhTfbs/wgEncodeSydhTfbsK562MaffIggrabAlnRep2.bam K562 ChipSeq MafF_(M8194) Alignments 2 bam Stanford Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeSydhTfbs/wgEncodeSydhTfbsK562MaffIggrabPk.narrowPeak.gz K562 ChipSeq MafF_(M8194) Peaks narrowPeak Stanford Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeSydhTfbs/wgEncodeSydhTfbsK562MaffIggrabSig.bigWig K562 ChipSeq MafF_(M8194) Signal bigWig Stanford Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeSydhTfbs/wgEncodeSydhTfbsK562Mafkab50322IggrabAlnRep1.bam K562 ChipSeq MafK_(ab50322) Alignments 1 bam Stanford Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeSydhTfbs/wgEncodeSydhTfbsK562Mafkab50322IggrabAlnRep2.bam K562 ChipSeq MafK_(ab50322) Alignments 2 bam Stanford Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeSydhTfbs/wgEncodeSydhTfbsK562Mafkab50322IggrabPk.narrowPeak.gz K562 ChipSeq MafK_(ab50322) Peaks narrowPeak Stanford Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeSydhTfbs/wgEncodeSydhTfbsK562Mafkab50322IggrabSig.bigWig K562 ChipSeq MafK_(ab50322) Signal bigWig Stanford Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeSydhTfbs/wgEncodeSydhTfbsK562MaxIggrabAlnRep1.bam K562 ChipSeq Max Alignments 1 bam Stanford Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeSydhTfbs/wgEncodeSydhTfbsK562MaxIggrabAlnRep2.bam K562 ChipSeq Max Alignments 2 bam Stanford Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeSydhTfbs/wgEncodeSydhTfbsK562MaxIggrabPk.narrowPeak.gz K562 ChipSeq Max Peaks narrowPeak Stanford Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeSydhTfbs/wgEncodeSydhTfbsK562MaxIggrabSig.bigWig K562 ChipSeq Max Signal bigWig Stanford Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeSydhTfbs/wgEncodeSydhTfbsK562MaxStdAlnRep1.bam K562 ChipSeq Max Alignments 1 bam Yale Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeSydhTfbs/wgEncodeSydhTfbsK562MaxStdAlnRep2.bam K562 ChipSeq Max Alignments 2 bam Yale Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeSydhTfbs/wgEncodeSydhTfbsK562MaxStdPk.narrowPeak.gz K562 ChipSeq Max Peaks narrowPeak Yale Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeSydhTfbs/wgEncodeSydhTfbsK562MaxStdSig.bigWig K562 ChipSeq Max Signal bigWig Yale Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeSydhTfbs/wgEncodeSydhTfbsK562Mazab85725IggrabAlnRep1.bam K562 ChipSeq MAZ_(ab85725) Alignments 1 bam Stanford Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeSydhTfbs/wgEncodeSydhTfbsK562Mazab85725IggrabAlnRep2.bam K562 ChipSeq MAZ_(ab85725) Alignments 2 bam Stanford Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeSydhTfbs/wgEncodeSydhTfbsK562Mazab85725IggrabPk.narrowPeak.gz K562 ChipSeq MAZ_(ab85725) Peaks narrowPeak Stanford Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeSydhTfbs/wgEncodeSydhTfbsK562Mazab85725IggrabSig.bigWig K562 ChipSeq MAZ_(ab85725) Signal bigWig Stanford Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeSydhTfbs/wgEncodeSydhTfbsK562Mxi1af4185IggrabAlnRep1.bam K562 ChipSeq Mxi1_(AF4185) Alignments 1 bam Stanford Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeSydhTfbs/wgEncodeSydhTfbsK562Mxi1af4185IggrabAlnRep2.bam K562 ChipSeq Mxi1_(AF4185) Alignments 2 bam Stanford Data 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Harvard Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeSydhTfbs/wgEncodeSydhTfbsK562Nfe2StdAlnRep1.bam K562 ChipSeq NF-E2 Alignments 1 bam Yale Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeSydhTfbs/wgEncodeSydhTfbsK562Nfe2StdAlnRep2.bam K562 ChipSeq NF-E2 Alignments 2 bam Yale Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeSydhTfbs/wgEncodeSydhTfbsK562Nfe2StdPk.narrowPeak.gz K562 ChipSeq NF-E2 Peaks narrowPeak Yale Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeSydhTfbs/wgEncodeSydhTfbsK562Nfe2StdSig.bigWig K562 ChipSeq NF-E2 Signal bigWig Yale Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeSydhTfbs/wgEncodeSydhTfbsK562NfyaStdAlnRep1.bam K562 ChipSeq NF-YA Alignments 1 bam Stanford Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeSydhTfbs/wgEncodeSydhTfbsK562NfyaStdAlnRep2.bam K562 ChipSeq NF-YA Alignments 2 bam Stanford Data 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http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeSydhTfbs/wgEncodeSydhTfbsK562Nrf1IggrabAlnRep1.bam K562 ChipSeq Nrf1 Alignments 1 bam Stanford Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeSydhTfbs/wgEncodeSydhTfbsK562Nrf1IggrabAlnRep2.bam K562 ChipSeq Nrf1 Alignments 2 bam Stanford Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeSydhTfbs/wgEncodeSydhTfbsK562Nrf1IggrabPk.narrowPeak.gz K562 ChipSeq Nrf1 Peaks narrowPeak Stanford Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeSydhTfbs/wgEncodeSydhTfbsK562Nrf1IggrabSig.bigWig K562 ChipSeq Nrf1 Signal bigWig Stanford Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeSydhTfbs/wgEncodeSydhTfbsK562P300IggrabAlnRep1.bam K562 ChipSeq p300 Alignments 1 bam Stanford Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeSydhTfbs/wgEncodeSydhTfbsK562P300IggrabAlnRep2.bam K562 ChipSeq p300 Alignments 2 bam Stanford Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeSydhTfbs/wgEncodeSydhTfbsK562P300IggrabPk.narrowPeak.gz K562 ChipSeq p300 Peaks narrowPeak Stanford Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeSydhTfbs/wgEncodeSydhTfbsK562P300IggrabSig.bigWig K562 ChipSeq p300 Signal bigWig Stanford Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeSydhTfbs/wgEncodeSydhTfbsK562P300sc584sc48343IggrabAlnRep1.bam K562 ChipSeq p300_(SC-48343) Alignments 1 bam Stanford Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeSydhTfbs/wgEncodeSydhTfbsK562P300sc584sc48343IggrabAlnRep2.bam K562 ChipSeq p300_(SC-48343) Alignments 2 bam Stanford Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeSydhTfbs/wgEncodeSydhTfbsK562P300sc584sc48343IggrabPk.narrowPeak.gz K562 ChipSeq p300_(SC-48343) Peaks narrowPeak Stanford Data 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Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeSydhTfbs/wgEncodeSydhTfbsK562Pol2Ifna6hStdAlnRep2.bam K562 ChipSeq Pol2 Alignments 2 bam Yale Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeSydhTfbs/wgEncodeSydhTfbsK562Pol2Ifna6hStdPk.narrowPeak.gz K562 ChipSeq Pol2 Peaks narrowPeak Yale Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeSydhTfbs/wgEncodeSydhTfbsK562Pol2Ifna6hStdSig.bigWig K562 ChipSeq Pol2 Signal bigWig Yale Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeSydhTfbs/wgEncodeSydhTfbsK562Pol2Ifng30StdAlnRep1.bam K562 ChipSeq Pol2 Alignments 1 bam Stanford Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeSydhTfbs/wgEncodeSydhTfbsK562Pol2Ifng30StdAlnRep2.bam K562 ChipSeq Pol2 Alignments 2 bam Stanford Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeSydhTfbs/wgEncodeSydhTfbsK562Pol2Ifng30StdPk.narrowPeak.gz K562 ChipSeq Pol2 Peaks narrowPeak Stanford Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeSydhTfbs/wgEncodeSydhTfbsK562Pol2Ifng30StdSig.bigWig K562 ChipSeq Pol2 Signal bigWig Stanford Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeSydhTfbs/wgEncodeSydhTfbsK562Pol2Ifng6hStdAlnRep1.bam K562 ChipSeq Pol2 Alignments 1 bam Yale Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeSydhTfbs/wgEncodeSydhTfbsK562Pol2Ifng6hStdAlnRep2.bam K562 ChipSeq Pol2 Alignments 2 bam Yale Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeSydhTfbs/wgEncodeSydhTfbsK562Pol2Ifng6hStdPk.narrowPeak.gz K562 ChipSeq Pol2 Peaks narrowPeak Yale Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeSydhTfbs/wgEncodeSydhTfbsK562Pol2Ifng6hStdSig.bigWig K562 ChipSeq Pol2 Signal bigWig Yale Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeSydhTfbs/wgEncodeSydhTfbsK562Pol2IggmusAlnRep1.bam K562 ChipSeq Pol2 Alignments 1 bam Stanford Data 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http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeSydhTfbs/wgEncodeSydhTfbsK562Pol2StdSig.bigWig K562 ChipSeq Pol2 Signal bigWig Yale Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeSydhTfbs/wgEncodeSydhTfbsK562Pol2s2IggrabAlnRep1.bam K562 ChipSeq Pol2(phosphoS2) Alignments 1 bam Stanford Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeSydhTfbs/wgEncodeSydhTfbsK562Pol2s2IggrabAlnRep2.bam K562 ChipSeq Pol2(phosphoS2) Alignments 2 bam Stanford Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeSydhTfbs/wgEncodeSydhTfbsK562Pol2s2IggrabPk.narrowPeak.gz K562 ChipSeq Pol2(phosphoS2) Peaks narrowPeak Stanford Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeSydhTfbs/wgEncodeSydhTfbsK562Pol2s2IggrabSig.bigWig K562 ChipSeq Pol2(phosphoS2) Signal bigWig Stanford Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeSydhTfbs/wgEncodeSydhTfbsK562Pol2s2StdAlnRep1.bam K562 ChipSeq Pol2(phosphoS2) Alignments 1 bam Stanford Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeSydhTfbs/wgEncodeSydhTfbsK562Pol2s2StdAlnRep2.bam K562 ChipSeq Pol2(phosphoS2) Alignments 2 bam Stanford Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeSydhTfbs/wgEncodeSydhTfbsK562Pol2s2StdPk.narrowPeak.gz K562 ChipSeq Pol2(phosphoS2) Peaks narrowPeak Stanford Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeSydhTfbs/wgEncodeSydhTfbsK562Pol2s2StdSig.bigWig K562 ChipSeq Pol2(phosphoS2) Signal bigWig Stanford Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeSydhTfbs/wgEncodeSydhTfbsK562Pol3StdAlnRep1.bam K562 ChipSeq Pol3 Alignments 1 bam Stanford Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeSydhTfbs/wgEncodeSydhTfbsK562Pol3StdAlnRep2.bam K562 ChipSeq Pol3 Alignments 2 bam Stanford Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeSydhTfbs/wgEncodeSydhTfbsK562Pol3StdPk.narrowPeak.gz K562 ChipSeq Pol3 Peaks narrowPeak Stanford Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeSydhTfbs/wgEncodeSydhTfbsK562Pol3StdSig.bigWig K562 ChipSeq Pol3 Signal bigWig Stanford Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeSydhTfbs/wgEncodeSydhTfbsK562Rad21StdAlnRep1.bam K562 ChipSeq Rad21 Alignments 1 bam Yale Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeSydhTfbs/wgEncodeSydhTfbsK562Rad21StdAlnRep2.bam K562 ChipSeq Rad21 Alignments 2 bam Yale Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeSydhTfbs/wgEncodeSydhTfbsK562Rad21StdPk.narrowPeak.gz K562 ChipSeq Rad21 Peaks narrowPeak Yale Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeSydhTfbs/wgEncodeSydhTfbsK562Rad21StdSig.bigWig K562 ChipSeq Rad21 Signal bigWig Yale Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeSydhTfbs/wgEncodeSydhTfbsK562Rfx5IggrabAlnRep1.bam K562 ChipSeq RFX5_(200-401-194) Alignments 1 bam Stanford Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeSydhTfbs/wgEncodeSydhTfbsK562Rfx5IggrabAlnRep2.bam K562 ChipSeq RFX5_(200-401-194) Alignments 2 bam Stanford Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeSydhTfbs/wgEncodeSydhTfbsK562Rfx5IggrabPk.narrowPeak.gz K562 ChipSeq RFX5_(200-401-194) Peaks narrowPeak Stanford Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeSydhTfbs/wgEncodeSydhTfbsK562Rfx5IggrabSig.bigWig K562 ChipSeq RFX5_(200-401-194) Signal bigWig Stanford Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeSydhTfbs/wgEncodeSydhTfbsK562Rpc155StdAlnRep1.bam K562 ChipSeq RPC155 Alignments 1 bam Harvard Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeSydhTfbs/wgEncodeSydhTfbsK562Rpc155StdAlnRep2.bam K562 ChipSeq RPC155 Alignments 2 bam Harvard Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeSydhTfbs/wgEncodeSydhTfbsK562Rpc155StdPk.narrowPeak.gz K562 ChipSeq RPC155 Peaks narrowPeak Harvard Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeSydhTfbs/wgEncodeSydhTfbsK562Rpc155StdSig.bigWig K562 ChipSeq RPC155 Signal bigWig Harvard Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeSydhTfbs/wgEncodeSydhTfbsK562Setdb1MnasedUcdAlnRep1.bam K562 ChipSeq SETDB1 Alignments 1 bam USC Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeSydhTfbs/wgEncodeSydhTfbsK562Setdb1MnasedUcdAlnRep2.bam K562 ChipSeq SETDB1 Alignments 2 bam USC Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeSydhTfbs/wgEncodeSydhTfbsK562Setdb1MnasedUcdPk.narrowPeak.gz K562 ChipSeq SETDB1 Peaks narrowPeak USC Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeSydhTfbs/wgEncodeSydhTfbsK562Setdb1MnasedUcdSig.bigWig K562 ChipSeq SETDB1 Signal bigWig USC Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeSydhTfbs/wgEncodeSydhTfbsK562Setdb1UcdAlnRep1.bam K562 ChipSeq SETDB1 Alignments 1 bam USC Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeSydhTfbs/wgEncodeSydhTfbsK562Setdb1UcdAlnRep2.bam K562 ChipSeq SETDB1 Alignments 2 bam USC Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeSydhTfbs/wgEncodeSydhTfbsK562Setdb1UcdPk.narrowPeak.gz K562 ChipSeq SETDB1 Peaks narrowPeak USC Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeSydhTfbs/wgEncodeSydhTfbsK562Setdb1UcdSig.bigWig K562 ChipSeq SETDB1 Signal bigWig USC Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeSydhTfbs/wgEncodeSydhTfbsK562Sirt6StdAlnRep1.bam K562 ChipSeq SIRT6 Alignments 1 bam Harvard Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeSydhTfbs/wgEncodeSydhTfbsK562Sirt6StdAlnRep2.bam K562 ChipSeq SIRT6 Alignments 2 bam Harvard Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeSydhTfbs/wgEncodeSydhTfbsK562Sirt6StdPk.narrowPeak.gz K562 ChipSeq SIRT6 Peaks narrowPeak Harvard Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeSydhTfbs/wgEncodeSydhTfbsK562Sirt6StdSig.bigWig K562 ChipSeq SIRT6 Signal bigWig Harvard Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeSydhTfbs/wgEncodeSydhTfbsK562Smc3ab9263IggrabAlnRep1.bam K562 ChipSeq SMC3_(ab9263) Alignments 1 bam Stanford Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeSydhTfbs/wgEncodeSydhTfbsK562Smc3ab9263IggrabAlnRep2.bam K562 ChipSeq SMC3_(ab9263) Alignments 2 bam Stanford Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeSydhTfbs/wgEncodeSydhTfbsK562Smc3ab9263IggrabPk.narrowPeak.gz K562 ChipSeq SMC3_(ab9263) Peaks narrowPeak Stanford Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeSydhTfbs/wgEncodeSydhTfbsK562Smc3ab9263IggrabSig.bigWig K562 ChipSeq SMC3_(ab9263) Signal bigWig Stanford Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeSydhTfbs/wgEncodeSydhTfbsK562Stat1Ifna30StdAlnRep1.bam K562 ChipSeq STAT1 Alignments 1 bam Yale Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeSydhTfbs/wgEncodeSydhTfbsK562Stat1Ifna30StdAlnRep2.bam K562 ChipSeq STAT1 Alignments 2 bam Yale Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeSydhTfbs/wgEncodeSydhTfbsK562Stat1Ifna30StdPk.narrowPeak.gz K562 ChipSeq STAT1 Peaks narrowPeak Yale Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeSydhTfbs/wgEncodeSydhTfbsK562Stat1Ifna30StdSig.bigWig K562 ChipSeq STAT1 Signal bigWig Yale Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeSydhTfbs/wgEncodeSydhTfbsK562Stat1Ifna6hStdAlnRep1.bam K562 ChipSeq STAT1 Alignments 1 bam Yale Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeSydhTfbs/wgEncodeSydhTfbsK562Stat1Ifna6hStdAlnRep2.bam K562 ChipSeq STAT1 Alignments 2 bam Yale Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeSydhTfbs/wgEncodeSydhTfbsK562Stat1Ifna6hStdPk.narrowPeak.gz K562 ChipSeq STAT1 Peaks narrowPeak Yale Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeSydhTfbs/wgEncodeSydhTfbsK562Stat1Ifna6hStdSig.bigWig K562 ChipSeq STAT1 Signal bigWig Yale Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeSydhTfbs/wgEncodeSydhTfbsK562Stat1Ifng30StdAlnRep1.bam K562 ChipSeq STAT1 Alignments 1 bam Stanford Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeSydhTfbs/wgEncodeSydhTfbsK562Stat1Ifng30StdAlnRep2.bam K562 ChipSeq STAT1 Alignments 2 bam Stanford Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeSydhTfbs/wgEncodeSydhTfbsK562Stat1Ifng30StdPk.narrowPeak.gz K562 ChipSeq STAT1 Peaks narrowPeak Stanford Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeSydhTfbs/wgEncodeSydhTfbsK562Stat1Ifng30StdSig.bigWig K562 ChipSeq STAT1 Signal bigWig Stanford Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeSydhTfbs/wgEncodeSydhTfbsK562Stat1Ifng6hStdAlnRep1.bam K562 ChipSeq STAT1 Alignments 1 bam Stanford Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeSydhTfbs/wgEncodeSydhTfbsK562Stat1Ifng6hStdAlnRep2.bam K562 ChipSeq STAT1 Alignments 2 bam Stanford Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeSydhTfbs/wgEncodeSydhTfbsK562Stat1Ifng6hStdPk.narrowPeak.gz K562 ChipSeq STAT1 Peaks narrowPeak Stanford Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeSydhTfbs/wgEncodeSydhTfbsK562Stat1Ifng6hStdSig.bigWig K562 ChipSeq STAT1 Signal bigWig Stanford Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeSydhTfbs/wgEncodeSydhTfbsK562Stat2Ifna30StdAlnRep1.bam K562 ChipSeq STAT2 Alignments 1 bam Yale Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeSydhTfbs/wgEncodeSydhTfbsK562Stat2Ifna30StdAlnRep2.bam K562 ChipSeq STAT2 Alignments 2 bam Yale Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeSydhTfbs/wgEncodeSydhTfbsK562Stat2Ifna30StdPk.narrowPeak.gz K562 ChipSeq STAT2 Peaks narrowPeak Yale Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeSydhTfbs/wgEncodeSydhTfbsK562Stat2Ifna30StdSig.bigWig K562 ChipSeq STAT2 Signal bigWig Yale Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeSydhTfbs/wgEncodeSydhTfbsK562Stat2Ifna6hStdAlnRep1.bam K562 ChipSeq STAT2 Alignments 1 bam Yale Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeSydhTfbs/wgEncodeSydhTfbsK562Stat2Ifna6hStdAlnRep2.bam K562 ChipSeq STAT2 Alignments 2 bam Yale Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeSydhTfbs/wgEncodeSydhTfbsK562Stat2Ifna6hStdPk.narrowPeak.gz K562 ChipSeq STAT2 Peaks narrowPeak Yale Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeSydhTfbs/wgEncodeSydhTfbsK562Stat2Ifna6hStdSig.bigWig K562 ChipSeq STAT2 Signal bigWig Yale Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeSydhTfbs/wgEncodeSydhTfbsK562Tal1sc12984IggmusAlnRep1.bam K562 ChipSeq TAL1_(SC-12984) Alignments 1 bam Stanford Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeSydhTfbs/wgEncodeSydhTfbsK562Tal1sc12984IggmusAlnRep2.bam K562 ChipSeq TAL1_(SC-12984) Alignments 2 bam Stanford Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeSydhTfbs/wgEncodeSydhTfbsK562Tal1sc12984IggmusPk.narrowPeak.gz K562 ChipSeq TAL1_(SC-12984) Peaks narrowPeak Stanford Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeSydhTfbs/wgEncodeSydhTfbsK562Tal1sc12984IggmusSig.bigWig K562 ChipSeq TAL1_(SC-12984) Signal bigWig Stanford Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeSydhTfbs/wgEncodeSydhTfbsK562Tblr1ab24550IggrabAlnRep1.bam K562 ChipSeq TBLR1_(ab24550) Alignments 1 bam Stanford Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeSydhTfbs/wgEncodeSydhTfbsK562Tblr1ab24550IggrabAlnRep2.bam K562 ChipSeq TBLR1_(ab24550) Alignments 2 bam Stanford Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeSydhTfbs/wgEncodeSydhTfbsK562Tblr1ab24550IggrabPk.narrowPeak.gz K562 ChipSeq TBLR1_(ab24550) Peaks narrowPeak Stanford Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeSydhTfbs/wgEncodeSydhTfbsK562Tblr1ab24550IggrabSig.bigWig K562 ChipSeq TBLR1_(ab24550) Signal bigWig Stanford Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeSydhTfbs/wgEncodeSydhTfbsK562Tblr1nb600270IggrabAlnRep1.bam K562 ChipSeq TBLR1_(NB600-270) Alignments 1 bam Stanford Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeSydhTfbs/wgEncodeSydhTfbsK562Tblr1nb600270IggrabAlnRep2.bam K562 ChipSeq TBLR1_(NB600-270) Alignments 2 bam Stanford Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeSydhTfbs/wgEncodeSydhTfbsK562Tblr1nb600270IggrabPk.narrowPeak.gz K562 ChipSeq TBLR1_(NB600-270) Peaks narrowPeak Stanford Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeSydhTfbs/wgEncodeSydhTfbsK562Tblr1nb600270IggrabSig.bigWig K562 ChipSeq TBLR1_(NB600-270) Signal bigWig Stanford Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeSydhTfbs/wgEncodeSydhTfbsK562TbpIggmusAlnRep1.bam K562 ChipSeq TBP Alignments 1 bam Stanford Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeSydhTfbs/wgEncodeSydhTfbsK562TbpIggmusAlnRep2.bam K562 ChipSeq TBP Alignments 2 bam Stanford Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeSydhTfbs/wgEncodeSydhTfbsK562TbpIggmusPk.narrowPeak.gz K562 ChipSeq TBP Peaks narrowPeak Stanford Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeSydhTfbs/wgEncodeSydhTfbsK562TbpIggmusSig.bigWig K562 ChipSeq TBP Signal bigWig Stanford Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeSydhTfbs/wgEncodeSydhTfbsK562Tf3c110StdAlnRep1.bam K562 ChipSeq TFIIIC-110 Alignments 1 bam Harvard Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeSydhTfbs/wgEncodeSydhTfbsK562Tf3c110StdAlnRep2.bam K562 ChipSeq TFIIIC-110 Alignments 2 bam Harvard Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeSydhTfbs/wgEncodeSydhTfbsK562Tf3c110StdAlnRep3.bam K562 ChipSeq TFIIIC-110 Alignments 3 bam Harvard Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeSydhTfbs/wgEncodeSydhTfbsK562Tf3c110StdPk.narrowPeak.gz K562 ChipSeq TFIIIC-110 Peaks narrowPeak Harvard Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeSydhTfbs/wgEncodeSydhTfbsK562Tf3c110StdSig.bigWig K562 ChipSeq TFIIIC-110 Signal bigWig Harvard Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeSydhTfbs/wgEncodeSydhTfbsK562Tr4UcdAlnRep1.bam K562 ChipSeq TR4 Alignments 1 bam USC Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeSydhTfbs/wgEncodeSydhTfbsK562Tr4UcdAlnRep2.bam K562 ChipSeq TR4 Alignments 2 bam USC Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeSydhTfbs/wgEncodeSydhTfbsK562Tr4UcdPk.narrowPeak.gz K562 ChipSeq TR4 Peaks narrowPeak USC Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeSydhTfbs/wgEncodeSydhTfbsK562Tr4UcdSig.bigWig K562 ChipSeq TR4 Signal bigWig USC Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeSydhTfbs/wgEncodeSydhTfbsK562Ubfsc13125IggmusAlnRep1.bam K562 ChipSeq UBF_(sc-13125) Alignments 1 bam Stanford Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeSydhTfbs/wgEncodeSydhTfbsK562Ubfsc13125IggmusAlnRep2.bam K562 ChipSeq UBF_(sc-13125) Alignments 2 bam Stanford Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeSydhTfbs/wgEncodeSydhTfbsK562Ubfsc13125IggmusPk.narrowPeak.gz K562 ChipSeq UBF_(sc-13125) Peaks narrowPeak Stanford Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeSydhTfbs/wgEncodeSydhTfbsK562Ubfsc13125IggmusSig.bigWig K562 ChipSeq UBF_(sc-13125) Signal bigWig Stanford Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeSydhTfbs/wgEncodeSydhTfbsK562Ubtfsab1404509IggmusAlnRep1.bam K562 ChipSeq UBTF_(SAB1404509) Alignments 1 bam Stanford Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeSydhTfbs/wgEncodeSydhTfbsK562Ubtfsab1404509IggmusAlnRep2.bam K562 ChipSeq UBTF_(SAB1404509) Alignments 2 bam Stanford Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeSydhTfbs/wgEncodeSydhTfbsK562Ubtfsab1404509IggmusPk.narrowPeak.gz K562 ChipSeq UBTF_(SAB1404509) Peaks narrowPeak Stanford Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeSydhTfbs/wgEncodeSydhTfbsK562Ubtfsab1404509IggmusSig.bigWig K562 ChipSeq UBTF_(SAB1404509) Signal bigWig Stanford Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeSydhTfbs/wgEncodeSydhTfbsK562Usf2IggrabAlnRep1.bam K562 ChipSeq USF2 Alignments 1 bam Stanford Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeSydhTfbs/wgEncodeSydhTfbsK562Usf2IggrabAlnRep2.bam K562 ChipSeq USF2 Alignments 2 bam Stanford Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeSydhTfbs/wgEncodeSydhTfbsK562Usf2IggrabPk.narrowPeak.gz K562 ChipSeq USF2 Peaks narrowPeak Stanford Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeSydhTfbs/wgEncodeSydhTfbsK562Usf2IggrabSig.bigWig K562 ChipSeq USF2 Signal bigWig Stanford Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeSydhTfbs/wgEncodeSydhTfbsK562Xrcc4StdAlnRep1.bam K562 ChipSeq XRCC4 Alignments 1 bam Yale Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeSydhTfbs/wgEncodeSydhTfbsK562Xrcc4StdAlnRep2.bam K562 ChipSeq XRCC4 Alignments 2 bam Yale Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeSydhTfbs/wgEncodeSydhTfbsK562Xrcc4StdPk.narrowPeak.gz K562 ChipSeq XRCC4 Peaks narrowPeak Yale Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeSydhTfbs/wgEncodeSydhTfbsK562Xrcc4StdSig.bigWig K562 ChipSeq XRCC4 Signal bigWig Yale Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeSydhTfbs/wgEncodeSydhTfbsK562Yy1UcdAlnRep1.bam K562 ChipSeq YY1 Alignments 1 bam USC Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeSydhTfbs/wgEncodeSydhTfbsK562Yy1UcdAlnRep2.bam K562 ChipSeq YY1 Alignments 2 bam USC Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeSydhTfbs/wgEncodeSydhTfbsK562Yy1UcdPk.narrowPeak.gz K562 ChipSeq YY1 Peaks narrowPeak USC Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeSydhTfbs/wgEncodeSydhTfbsK562Yy1UcdSig.bigWig K562 ChipSeq YY1 Signal bigWig USC Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeSydhTfbs/wgEncodeSydhTfbsK562Zc3h11anb10074650IggrabAlnRep1.bam K562 ChipSeq ZC3H11A_(NB100-74650) Alignments 1 bam Stanford Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeSydhTfbs/wgEncodeSydhTfbsK562Zc3h11anb10074650IggrabAlnRep2.bam K562 ChipSeq ZC3H11A_(NB100-74650) Alignments 2 bam Stanford Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeSydhTfbs/wgEncodeSydhTfbsK562Zc3h11anb10074650IggrabPk.narrowPeak.gz K562 ChipSeq ZC3H11A_(NB100-74650) Peaks narrowPeak Stanford Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeSydhTfbs/wgEncodeSydhTfbsK562Zc3h11anb10074650IggrabSig.bigWig K562 ChipSeq ZC3H11A_(NB100-74650) Signal bigWig Stanford Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeSydhTfbs/wgEncodeSydhTfbsK562Znf143IggrabAlnRep1.bam K562 ChipSeq Znf143_(16618-1-AP) Alignments 1 bam Stanford Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeSydhTfbs/wgEncodeSydhTfbsK562Znf143IggrabAlnRep2.bam K562 ChipSeq Znf143_(16618-1-AP) Alignments 2 bam Stanford Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeSydhTfbs/wgEncodeSydhTfbsK562Znf143IggrabPk.narrowPeak.gz K562 ChipSeq Znf143_(16618-1-AP) Peaks narrowPeak Stanford Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeSydhTfbs/wgEncodeSydhTfbsK562Znf143IggrabSig.bigWig K562 ChipSeq Znf143_(16618-1-AP) Signal bigWig Stanford Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeSydhTfbs/wgEncodeSydhTfbsK562Znf263UcdAlnRep1.bam K562 ChipSeq ZNF263 Alignments 1 bam USC Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeSydhTfbs/wgEncodeSydhTfbsK562Znf263UcdAlnRep2.bam K562 ChipSeq ZNF263 Alignments 2 bam USC Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeSydhTfbs/wgEncodeSydhTfbsK562Znf263UcdPk.narrowPeak.gz K562 ChipSeq ZNF263 Peaks narrowPeak USC Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeSydhTfbs/wgEncodeSydhTfbsK562Znf263UcdSig.bigWig K562 ChipSeq ZNF263 Signal bigWig USC Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeSydhTfbs/wgEncodeSydhTfbsK562Znf274UcdAlnRep1.bam K562 ChipSeq ZNF274 Alignments 1 bam USC Data 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http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeSydhTfbs/wgEncodeSydhTfbsNt2d1Znf274UcdSig.bigWig NT2-D1 ChipSeq ZNF274 Signal bigWig USC Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeSydhTfbs/wgEncodeSydhTfbsPanc1InputUcdAlnRep1.bam PANC-1 ChipSeq Input Alignments 1 bam USC Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeSydhTfbs/wgEncodeSydhTfbsPanc1InputUcdSig.bigWig PANC-1 ChipSeq Input Signal bigWig USC Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeSydhTfbs/wgEncodeSydhTfbsPanc1Tcf7l2UcdAlnRep1.bam PANC-1 ChipSeq TCF7L2 Alignments 1 bam USC Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeSydhTfbs/wgEncodeSydhTfbsPanc1Tcf7l2UcdAlnRep2.bam PANC-1 ChipSeq TCF7L2 Alignments 2 bam USC Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeSydhTfbs/wgEncodeSydhTfbsPanc1Tcf7l2UcdPk.narrowPeak.gz PANC-1 ChipSeq TCF7L2 Peaks narrowPeak USC Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeSydhTfbs/wgEncodeSydhTfbsPanc1Tcf7l2UcdSig.bigWig PANC-1 ChipSeq TCF7L2 Signal bigWig USC Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeSydhTfbs/wgEncodeSydhTfbsPbdeGata1UcdAlnRep1.bam PBDE ChipSeq GATA-1 Alignments 1 bam USC Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeSydhTfbs/wgEncodeSydhTfbsPbdeGata1UcdAlnRep2.bam PBDE ChipSeq GATA-1 Alignments 2 bam USC Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeSydhTfbs/wgEncodeSydhTfbsPbdeGata1UcdPk.narrowPeak.gz PBDE ChipSeq GATA-1 Peaks narrowPeak USC Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeSydhTfbs/wgEncodeSydhTfbsPbdeGata1UcdSig.bigWig PBDE ChipSeq GATA-1 Signal bigWig USC Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeSydhTfbs/wgEncodeSydhTfbsPbdeInputUcdAln.bam PBDE ChipSeq Input Alignments bam USC Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeSydhTfbs/wgEncodeSydhTfbsPbdeInputUcdSig.bigWig PBDE ChipSeq Input Signal bigWig USC Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeSydhTfbs/wgEncodeSydhTfbsPbdePol2UcdAlnRep1.bam PBDE ChipSeq Pol2 Alignments 1 bam USC Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeSydhTfbs/wgEncodeSydhTfbsPbdePol2UcdAlnRep2.bam PBDE ChipSeq Pol2 Alignments 2 bam USC Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeSydhTfbs/wgEncodeSydhTfbsPbdePol2UcdPk.narrowPeak.gz PBDE ChipSeq Pol2 Peaks narrowPeak USC Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeSydhTfbs/wgEncodeSydhTfbsPbdePol2UcdSig.bigWig PBDE ChipSeq Pol2 Signal bigWig USC Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeSydhTfbs/wgEncodeSydhTfbsPbdefetalGata1UcdAlnRep1.bam PBDEFetal ChipSeq GATA-1 Alignments 1 bam USC Data 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http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeSydhTfbs/wgEncodeSydhTfbsRajiInputUcdSig.bigWig Raji ChipSeq Input Signal bigWig USC Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeSydhTfbs/wgEncodeSydhTfbsRajiPol2UcdAlnRep1.bam Raji ChipSeq Pol2 Alignments 1 bam USC Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeSydhTfbs/wgEncodeSydhTfbsRajiPol2UcdAlnRep1V2.bam Raji ChipSeq Pol2 Alignments 1 bam Stanford Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeSydhTfbs/wgEncodeSydhTfbsRajiPol2UcdAlnRep2.bam Raji ChipSeq Pol2 Alignments 2 bam USC Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeSydhTfbs/wgEncodeSydhTfbsRajiPol2UcdAlnRep2V2.bam Raji ChipSeq Pol2 Alignments 2 bam Stanford Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeSydhTfbs/wgEncodeSydhTfbsRajiPol2UcdPk.narrowPeak.gz Raji ChipSeq Pol2 Peaks narrowPeak USC Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeSydhTfbs/wgEncodeSydhTfbsRajiPol2UcdSig.bigWig Raji ChipSeq Pol2 Signal bigWig USC Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeSydhTfbs/wgEncodeSydhTfbsShsy5yGata2UcdAlnRep1.bam SH-SY5Y ChipSeq GATA-2 Alignments 1 bam USC Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeSydhTfbs/wgEncodeSydhTfbsShsy5yGata2UcdAlnRep2.bam SH-SY5Y ChipSeq GATA-2 Alignments 2 bam USC Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeSydhTfbs/wgEncodeSydhTfbsShsy5yGata2UcdPk.narrowPeak.gz SH-SY5Y ChipSeq GATA-2 Peaks narrowPeak USC Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeSydhTfbs/wgEncodeSydhTfbsShsy5yGata2UcdSig.bigWig SH-SY5Y ChipSeq GATA-2 Signal bigWig USC Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeSydhTfbs/wgEncodeSydhTfbsShsy5yGata3sc269sc269UcdAlnRep1.bam SH-SY5Y ChipSeq GATA3_(SC-269) Alignments 1 bam USC Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeSydhTfbs/wgEncodeSydhTfbsShsy5yGata3sc269sc269UcdAlnRep2.bam SH-SY5Y ChipSeq GATA3_(SC-269) Alignments 2 bam USC Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeSydhTfbs/wgEncodeSydhTfbsShsy5yGata3sc269sc269UcdPk.narrowPeak.gz SH-SY5Y ChipSeq GATA3_(SC-269) Peaks narrowPeak USC Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeSydhTfbs/wgEncodeSydhTfbsShsy5yGata3sc269sc269UcdSig.bigWig SH-SY5Y ChipSeq GATA3_(SC-269) Signal bigWig USC Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeSydhTfbs/wgEncodeSydhTfbsShsy5yInputUcdAln.bam SH-SY5Y ChipSeq Input Alignments bam USC Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeSydhTfbs/wgEncodeSydhTfbsShsy5yInputUcdSig.bigWig SH-SY5Y ChipSeq Input Signal bigWig USC Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeSydhTfbs/wgEncodeSydhTfbsSknshCtcfbIggrabAlnRep1.bam SK-N-SH ChipSeq CTCF_(SC-15914) Alignments 1 bam Stanford Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeSydhTfbs/wgEncodeSydhTfbsSknshCtcfbIggrabAlnRep2.bam SK-N-SH ChipSeq CTCF_(SC-15914) Alignments 2 bam Stanford Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeSydhTfbs/wgEncodeSydhTfbsSknshCtcfbIggrabPk.narrowPeak.gz SK-N-SH ChipSeq CTCF_(SC-15914) Peaks narrowPeak Stanford Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeSydhTfbs/wgEncodeSydhTfbsSknshCtcfbIggrabSig.bigWig SK-N-SH ChipSeq CTCF_(SC-15914) Signal bigWig Stanford Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeSydhTfbs/wgEncodeSydhTfbsSknshInputIggrabAlnRep1.bam SK-N-SH ChipSeq Input Alignments 1 bam Stanford Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeSydhTfbs/wgEncodeSydhTfbsSknshInputIggrabSig.bigWig SK-N-SH ChipSeq Input Signal bigWig Stanford Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeSydhTfbs/wgEncodeSydhTfbsSknshJundIggrabAlnRep1.bam SK-N-SH ChipSeq JunD Alignments 1 bam Stanford Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeSydhTfbs/wgEncodeSydhTfbsSknshJundIggrabAlnRep2.bam SK-N-SH ChipSeq JunD Alignments 2 bam Stanford Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeSydhTfbs/wgEncodeSydhTfbsSknshJundIggrabPk.narrowPeak.gz SK-N-SH ChipSeq JunD Peaks narrowPeak Stanford Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeSydhTfbs/wgEncodeSydhTfbsSknshJundIggrabSig.bigWig SK-N-SH ChipSeq JunD Signal bigWig Stanford Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeSydhTfbs/wgEncodeSydhTfbsSknshMxi1IggrabAlnRep1.bam SK-N-SH ChipSeq Mxi1_(AF4185) Alignments 1 bam Stanford Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeSydhTfbs/wgEncodeSydhTfbsSknshMxi1IggrabAlnRep2.bam SK-N-SH ChipSeq Mxi1_(AF4185) Alignments 2 bam Stanford Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeSydhTfbs/wgEncodeSydhTfbsSknshMxi1IggrabPk.narrowPeak.gz SK-N-SH ChipSeq Mxi1_(AF4185) Peaks narrowPeak Stanford Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeSydhTfbs/wgEncodeSydhTfbsSknshMxi1IggrabSig.bigWig SK-N-SH ChipSeq Mxi1_(AF4185) Signal bigWig Stanford Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeSydhTfbs/wgEncodeSydhTfbsSknshNrf1IggrabAlnRep1.bam SK-N-SH ChipSeq Nrf1 Alignments 1 bam Stanford Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeSydhTfbs/wgEncodeSydhTfbsSknshNrf1IggrabAlnRep2.bam SK-N-SH ChipSeq Nrf1 Alignments 2 bam Stanford Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeSydhTfbs/wgEncodeSydhTfbsSknshNrf1IggrabPk.narrowPeak.gz SK-N-SH ChipSeq Nrf1 Peaks narrowPeak Stanford Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeSydhTfbs/wgEncodeSydhTfbsSknshNrf1IggrabSig.bigWig SK-N-SH ChipSeq Nrf1 Signal bigWig Stanford Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeSydhTfbs/wgEncodeSydhTfbsSknshP300bIggrabAlnRep1.bam SK-N-SH ChipSeq p300_(SC-584) Alignments 1 bam Stanford Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeSydhTfbs/wgEncodeSydhTfbsSknshP300bIggrabAlnRep2.bam SK-N-SH ChipSeq p300_(SC-584) Alignments 2 bam Stanford Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeSydhTfbs/wgEncodeSydhTfbsSknshP300bIggrabPk.narrowPeak.gz SK-N-SH ChipSeq p300_(SC-584) Peaks narrowPeak Stanford Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeSydhTfbs/wgEncodeSydhTfbsSknshP300bIggrabSig.bigWig SK-N-SH ChipSeq p300_(SC-584) Signal bigWig Stanford Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeSydhTfbs/wgEncodeSydhTfbsSknshRad21IggrabAlnRep1.bam SK-N-SH ChipSeq Rad21 Alignments 1 bam Stanford Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeSydhTfbs/wgEncodeSydhTfbsSknshRad21IggrabAlnRep2.bam SK-N-SH ChipSeq Rad21 Alignments 2 bam Stanford Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeSydhTfbs/wgEncodeSydhTfbsSknshRad21IggrabPk.narrowPeak.gz SK-N-SH ChipSeq Rad21 Peaks narrowPeak Stanford Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeSydhTfbs/wgEncodeSydhTfbsSknshRad21IggrabSig.bigWig SK-N-SH ChipSeq Rad21 Signal bigWig Stanford Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeSydhTfbs/wgEncodeSydhTfbsSknshRfx5IggrabAlnRep1.bam SK-N-SH ChipSeq RFX5_(200-401-194) Alignments 1 bam Stanford Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeSydhTfbs/wgEncodeSydhTfbsSknshRfx5IggrabAlnRep2.bam SK-N-SH ChipSeq RFX5_(200-401-194) Alignments 2 bam Stanford Data 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http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeUwDnase/wgEncodeUwDnaseMcf7Estctrl0hAlnRep2.bam MCF-7 DnaseSeq Alignments 2 bam UW Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeUwDnase/wgEncodeUwDnaseMcf7Estctrl0hHotspotsRep1.broadPeak.gz MCF-7 DnaseSeq Hotspots 1 broadPeak UW Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeUwDnase/wgEncodeUwDnaseMcf7Estctrl0hHotspotsRep2.broadPeak.gz MCF-7 DnaseSeq Hotspots 2 broadPeak UW Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeUwDnase/wgEncodeUwDnaseMcf7Estctrl0hPkRep1.narrowPeak.gz MCF-7 DnaseSeq Peaks 1 narrowPeak UW Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeUwDnase/wgEncodeUwDnaseMcf7Estctrl0hPkRep2.narrowPeak.gz MCF-7 DnaseSeq Peaks 2 narrowPeak UW Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeUwDnase/wgEncodeUwDnaseMcf7Estctrl0hRawRep1.bigWig MCF-7 DnaseSeq RawSignal 1 bigWig UW Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeUwDnase/wgEncodeUwDnaseMcf7Estctrl0hRawRep2.bigWig MCF-7 DnaseSeq RawSignal 2 bigWig UW Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeUwDnase/wgEncodeUwDnaseMcf7HotspotsRep1.broadPeak.gz MCF-7 DnaseSeq Hotspots 1 broadPeak UW Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeUwDnase/wgEncodeUwDnaseMcf7HotspotsRep2.broadPeak.gz MCF-7 DnaseSeq Hotspots 2 broadPeak UW Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeUwDnase/wgEncodeUwDnaseMcf7PkRep1.narrowPeak.gz MCF-7 DnaseSeq Peaks 1 narrowPeak UW Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeUwDnase/wgEncodeUwDnaseMcf7PkRep2.narrowPeak.gz MCF-7 DnaseSeq Peaks 2 narrowPeak UW Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeUwDnase/wgEncodeUwDnaseMcf7RawRep1.bigWig MCF-7 DnaseSeq RawSignal 1 bigWig UW Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeUwDnase/wgEncodeUwDnaseMcf7RawRep2.bigWig MCF-7 DnaseSeq RawSignal 2 bigWig UW Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeUwDnase/wgEncodeUwDnaseMonocd14AlnRep1.bam Monocytes-CD14+_RO01746 DnaseSeq Alignments 1 bam UW Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeUwDnase/wgEncodeUwDnaseMonocd14HotspotsRep1.broadPeak.gz Monocytes-CD14+_RO01746 DnaseSeq Hotspots 1 broadPeak UW Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeUwDnase/wgEncodeUwDnaseMonocd14PkRep1.narrowPeak.gz Monocytes-CD14+_RO01746 DnaseSeq Peaks 1 narrowPeak UW Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeUwDnase/wgEncodeUwDnaseMonocd14RawRep1.bigWig Monocytes-CD14+_RO01746 DnaseSeq RawSignal 1 bigWig UW Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeUwDnase/wgEncodeUwDnaseMonocd14ro1746AlnRep1.bam Monocytes-CD14+_RO01746 DnaseSeq Alignments 1 bam UW Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeUwDnase/wgEncodeUwDnaseMonocd14ro1746AlnRep1V2.bam Monocytes-CD14+_RO01746 DnaseSeq Alignments 1 bam UW Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeUwDnase/wgEncodeUwDnaseMonocd14ro1746AlnRep2.bam Monocytes-CD14+_RO01746 DnaseSeq Alignments 2 bam UW Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeUwDnase/wgEncodeUwDnaseMonocd14ro1746HotspotsRep1.broadPeak.gz Monocytes-CD14+_RO01746 DnaseSeq Hotspots 1 broadPeak UW Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeUwDnase/wgEncodeUwDnaseMonocd14ro1746HotspotsRep1V2.broadPeak.gz Monocytes-CD14+_RO01746 DnaseSeq Hotspots 1 broadPeak UW Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeUwDnase/wgEncodeUwDnaseMonocd14ro1746HotspotsRep2.broadPeak.gz Monocytes-CD14+_RO01746 DnaseSeq Hotspots 2 broadPeak UW Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeUwDnase/wgEncodeUwDnaseMonocd14ro1746PkRep1.narrowPeak.gz Monocytes-CD14+_RO01746 DnaseSeq Peaks 1 narrowPeak UW Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeUwDnase/wgEncodeUwDnaseMonocd14ro1746PkRep1V2.narrowPeak.gz Monocytes-CD14+_RO01746 DnaseSeq Peaks 1 narrowPeak UW Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeUwDnase/wgEncodeUwDnaseMonocd14ro1746PkRep2.narrowPeak.gz Monocytes-CD14+_RO01746 DnaseSeq Peaks 2 narrowPeak UW Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeUwDnase/wgEncodeUwDnaseMonocd14ro1746RawRep1.bigWig Monocytes-CD14+_RO01746 DnaseSeq RawSignal 1 bigWig UW Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeUwDnase/wgEncodeUwDnaseMonocd14ro1746RawRep1V2.bigWig Monocytes-CD14+_RO01746 DnaseSeq RawSignal 1 bigWig UW Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeUwDnase/wgEncodeUwDnaseMonocd14ro1746RawRep2.bigWig Monocytes-CD14+_RO01746 DnaseSeq RawSignal 2 bigWig UW Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeUwDnase/wgEncodeUwDnaseMscAlnRep1.bam bone_marrow_MSC DnaseSeq Alignments 1 bam UW Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeUwDnase/wgEncodeUwDnaseMscAlnRep2.bam bone_marrow_MSC DnaseSeq Alignments 2 bam UW Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeUwDnase/wgEncodeUwDnaseMscHotspotsRep1.broadPeak.gz bone_marrow_MSC DnaseSeq Hotspots 1 broadPeak UW Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeUwDnase/wgEncodeUwDnaseMscHotspotsRep2.broadPeak.gz bone_marrow_MSC DnaseSeq Hotspots 2 broadPeak UW Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeUwDnase/wgEncodeUwDnaseMscPkRep1.narrowPeak.gz bone_marrow_MSC DnaseSeq Peaks 1 narrowPeak UW Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeUwDnase/wgEncodeUwDnaseMscPkRep2.narrowPeak.gz bone_marrow_MSC DnaseSeq Peaks 2 narrowPeak UW Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeUwDnase/wgEncodeUwDnaseMscRawRep1.bigWig bone_marrow_MSC DnaseSeq RawSignal 1 bigWig UW Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeUwDnase/wgEncodeUwDnaseMscRawRep2.bigWig bone_marrow_MSC DnaseSeq RawSignal 2 bigWig UW Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeUwDnase/wgEncodeUwDnaseNb4AlnRep1.bam NB4 DnaseSeq Alignments 1 bam UW Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeUwDnase/wgEncodeUwDnaseNb4AlnRep2.bam NB4 DnaseSeq Alignments 2 bam UW Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeUwDnase/wgEncodeUwDnaseNb4HotspotsRep1.broadPeak.gz NB4 DnaseSeq Hotspots 1 broadPeak UW Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeUwDnase/wgEncodeUwDnaseNb4HotspotsRep2.broadPeak.gz NB4 DnaseSeq Hotspots 2 broadPeak UW Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeUwDnase/wgEncodeUwDnaseNb4PkRep1.narrowPeak.gz NB4 DnaseSeq Peaks 1 narrowPeak UW Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeUwDnase/wgEncodeUwDnaseNb4PkRep2.narrowPeak.gz NB4 DnaseSeq Peaks 2 narrowPeak UW Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeUwDnase/wgEncodeUwDnaseNb4RawRep1.bigWig NB4 DnaseSeq RawSignal 1 bigWig UW Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeUwDnase/wgEncodeUwDnaseNb4RawRep2.bigWig NB4 DnaseSeq RawSignal 2 bigWig UW Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeUwDnase/wgEncodeUwDnaseNhaAlnRep1.bam NH-A DnaseSeq Alignments 1 bam UW Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeUwDnase/wgEncodeUwDnaseNhaAlnRep2.bam NH-A DnaseSeq Alignments 2 bam UW Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeUwDnase/wgEncodeUwDnaseNhaHotspotsRep1.broadPeak.gz NH-A DnaseSeq Hotspots 1 broadPeak UW Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeUwDnase/wgEncodeUwDnaseNhaHotspotsRep2.broadPeak.gz NH-A DnaseSeq Hotspots 2 broadPeak UW Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeUwDnase/wgEncodeUwDnaseNhaPkRep1.narrowPeak.gz NH-A DnaseSeq Peaks 1 narrowPeak UW Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeUwDnase/wgEncodeUwDnaseNhaPkRep2.narrowPeak.gz NH-A DnaseSeq Peaks 2 narrowPeak UW Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeUwDnase/wgEncodeUwDnaseNhaRawRep1.bigWig NH-A DnaseSeq RawSignal 1 bigWig UW Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeUwDnase/wgEncodeUwDnaseNhaRawRep2.bigWig NH-A DnaseSeq RawSignal 2 bigWig UW Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeUwDnase/wgEncodeUwDnaseNhberaAlnRep1.bam NHBE_RA DnaseSeq Alignments 1 bam UW Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeUwDnase/wgEncodeUwDnaseNhberaAlnRep2.bam NHBE_RA DnaseSeq Alignments 2 bam UW Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeUwDnase/wgEncodeUwDnaseNhberaHotspotsRep1.broadPeak.gz NHBE_RA DnaseSeq Hotspots 1 broadPeak UW Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeUwDnase/wgEncodeUwDnaseNhberaHotspotsRep2.broadPeak.gz NHBE_RA DnaseSeq Hotspots 2 broadPeak UW Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeUwDnase/wgEncodeUwDnaseNhberaPkRep1.narrowPeak.gz NHBE_RA DnaseSeq Peaks 1 narrowPeak UW Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeUwDnase/wgEncodeUwDnaseNhberaPkRep2.narrowPeak.gz NHBE_RA DnaseSeq Peaks 2 narrowPeak UW Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeUwDnase/wgEncodeUwDnaseNhberaRawRep1.bigWig NHBE_RA DnaseSeq RawSignal 1 bigWig UW Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeUwDnase/wgEncodeUwDnaseNhberaRawRep2.bigWig NHBE_RA DnaseSeq RawSignal 2 bigWig UW Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeUwDnase/wgEncodeUwDnaseNhdfadAlnRep1.bam NHDF-Ad DnaseSeq Alignments 1 bam UW Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeUwDnase/wgEncodeUwDnaseNhdfadAlnRep2.bam NHDF-Ad DnaseSeq Alignments 2 bam UW Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeUwDnase/wgEncodeUwDnaseNhdfadHotspotsRep1.broadPeak.gz NHDF-Ad DnaseSeq Hotspots 1 broadPeak UW Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeUwDnase/wgEncodeUwDnaseNhdfadHotspotsRep2.broadPeak.gz NHDF-Ad DnaseSeq Hotspots 2 broadPeak UW Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeUwDnase/wgEncodeUwDnaseNhdfadPkRep1.narrowPeak.gz NHDF-Ad DnaseSeq Peaks 1 narrowPeak UW Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeUwDnase/wgEncodeUwDnaseNhdfadPkRep2.narrowPeak.gz NHDF-Ad DnaseSeq Peaks 2 narrowPeak UW Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeUwDnase/wgEncodeUwDnaseNhdfadRawRep1.bigWig NHDF-Ad DnaseSeq RawSignal 1 bigWig UW Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeUwDnase/wgEncodeUwDnaseNhdfadRawRep2.bigWig NHDF-Ad DnaseSeq RawSignal 2 bigWig UW Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeUwDnase/wgEncodeUwDnaseNhdfneoAlnRep1.bam NHDF-neo DnaseSeq Alignments 1 bam UW Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeUwDnase/wgEncodeUwDnaseNhdfneoAlnRep2.bam NHDF-neo DnaseSeq Alignments 2 bam UW Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeUwDnase/wgEncodeUwDnaseNhdfneoHotspotsRep1.broadPeak.gz NHDF-neo DnaseSeq Hotspots 1 broadPeak UW Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeUwDnase/wgEncodeUwDnaseNhdfneoHotspotsRep2.broadPeak.gz NHDF-neo DnaseSeq Hotspots 2 broadPeak UW Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeUwDnase/wgEncodeUwDnaseNhdfneoPkRep1.narrowPeak.gz NHDF-neo DnaseSeq Peaks 1 narrowPeak UW Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeUwDnase/wgEncodeUwDnaseNhdfneoPkRep2.narrowPeak.gz NHDF-neo DnaseSeq Peaks 2 narrowPeak UW Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeUwDnase/wgEncodeUwDnaseNhdfneoRawRep1.bigWig NHDF-neo DnaseSeq RawSignal 1 bigWig UW Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeUwDnase/wgEncodeUwDnaseNhdfneoRawRep2.bigWig NHDF-neo DnaseSeq RawSignal 2 bigWig UW Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeUwDnase/wgEncodeUwDnaseNhekAlnRep1.bam NHEK DnaseSeq Alignments 1 bam UW Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeUwDnase/wgEncodeUwDnaseNhekAlnRep2.bam NHEK DnaseSeq Alignments 2 bam UW Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeUwDnase/wgEncodeUwDnaseNhekHotspotsRep1.broadPeak.gz NHEK DnaseSeq Hotspots 1 broadPeak UW Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeUwDnase/wgEncodeUwDnaseNhekHotspotsRep2.broadPeak.gz NHEK DnaseSeq Hotspots 2 broadPeak UW Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeUwDnase/wgEncodeUwDnaseNhekPkRep1.narrowPeak.gz NHEK DnaseSeq Peaks 1 narrowPeak UW Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeUwDnase/wgEncodeUwDnaseNhekPkRep2.narrowPeak.gz NHEK DnaseSeq Peaks 2 narrowPeak UW Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeUwDnase/wgEncodeUwDnaseNhekRawRep1.bigWig NHEK DnaseSeq RawSignal 1 bigWig UW Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeUwDnase/wgEncodeUwDnaseNhekRawRep2.bigWig NHEK DnaseSeq RawSignal 2 bigWig UW Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeUwDnase/wgEncodeUwDnaseNhlfAlnRep1.bam NHLF DnaseSeq Alignments 1 bam UW Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeUwDnase/wgEncodeUwDnaseNhlfAlnRep2.bam NHLF DnaseSeq Alignments 2 bam UW Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeUwDnase/wgEncodeUwDnaseNhlfHotspotsRep1.broadPeak.gz NHLF DnaseSeq Hotspots 1 broadPeak UW Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeUwDnase/wgEncodeUwDnaseNhlfHotspotsRep2.broadPeak.gz NHLF DnaseSeq Hotspots 2 broadPeak UW Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeUwDnase/wgEncodeUwDnaseNhlfPkRep1.narrowPeak.gz NHLF DnaseSeq Peaks 1 narrowPeak UW Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeUwDnase/wgEncodeUwDnaseNhlfPkRep2.narrowPeak.gz NHLF DnaseSeq Peaks 2 narrowPeak UW Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeUwDnase/wgEncodeUwDnaseNhlfRawRep1.bigWig NHLF DnaseSeq RawSignal 1 bigWig UW Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeUwDnase/wgEncodeUwDnaseNhlfRawRep2.bigWig NHLF DnaseSeq RawSignal 2 bigWig UW Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeUwDnase/wgEncodeUwDnaseNt2d1AlnRep1.bam NT2-D1 DnaseSeq Alignments 1 bam UW Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeUwDnase/wgEncodeUwDnaseNt2d1AlnRep2.bam NT2-D1 DnaseSeq Alignments 2 bam UW Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeUwDnase/wgEncodeUwDnaseNt2d1HotspotsRep1.broadPeak.gz NT2-D1 DnaseSeq Hotspots 1 broadPeak UW Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeUwDnase/wgEncodeUwDnaseNt2d1HotspotsRep2.broadPeak.gz NT2-D1 DnaseSeq Hotspots 2 broadPeak UW Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeUwDnase/wgEncodeUwDnaseNt2d1PkRep1.narrowPeak.gz NT2-D1 DnaseSeq Peaks 1 narrowPeak UW Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeUwDnase/wgEncodeUwDnaseNt2d1PkRep2.narrowPeak.gz NT2-D1 DnaseSeq Peaks 2 narrowPeak UW Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeUwDnase/wgEncodeUwDnaseNt2d1RawRep1.bigWig NT2-D1 DnaseSeq RawSignal 1 bigWig UW Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeUwDnase/wgEncodeUwDnaseNt2d1RawRep2.bigWig NT2-D1 DnaseSeq RawSignal 2 bigWig UW Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeUwDnase/wgEncodeUwDnasePanc1AlnRep1.bam PANC-1 DnaseSeq Alignments 1 bam UW Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeUwDnase/wgEncodeUwDnasePanc1AlnRep2.bam PANC-1 DnaseSeq Alignments 2 bam UW Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeUwDnase/wgEncodeUwDnasePanc1HotspotsRep1.broadPeak.gz PANC-1 DnaseSeq Hotspots 1 broadPeak UW Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeUwDnase/wgEncodeUwDnasePanc1HotspotsRep2.broadPeak.gz PANC-1 DnaseSeq Hotspots 2 broadPeak UW Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeUwDnase/wgEncodeUwDnasePanc1PkRep1.narrowPeak.gz PANC-1 DnaseSeq Peaks 1 narrowPeak UW Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeUwDnase/wgEncodeUwDnasePanc1PkRep2.narrowPeak.gz PANC-1 DnaseSeq Peaks 2 narrowPeak UW Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeUwDnase/wgEncodeUwDnasePanc1RawRep1.bigWig PANC-1 DnaseSeq RawSignal 1 bigWig UW Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeUwDnase/wgEncodeUwDnasePanc1RawRep2.bigWig PANC-1 DnaseSeq RawSignal 2 bigWig UW Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeUwDnase/wgEncodeUwDnasePrecAlnRep1.bam PrEC DnaseSeq Alignments 1 bam UW Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeUwDnase/wgEncodeUwDnasePrecAlnRep2.bam PrEC DnaseSeq Alignments 2 bam UW Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeUwDnase/wgEncodeUwDnasePrecHotspotsRep1.broadPeak.gz PrEC DnaseSeq Hotspots 1 broadPeak UW Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeUwDnase/wgEncodeUwDnasePrecHotspotsRep2.broadPeak.gz PrEC DnaseSeq Hotspots 2 broadPeak UW Data 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http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeUwDnase/wgEncodeUwDnaseTh1HotspotsRep1.broadPeak.gz Th1 DnaseSeq Hotspots 1 broadPeak UW Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeUwDnase/wgEncodeUwDnaseTh1HotspotsRep2.broadPeak.gz Th1 DnaseSeq Hotspots 2 broadPeak UW Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeUwDnase/wgEncodeUwDnaseTh1PkRep1.narrowPeak.gz Th1 DnaseSeq Peaks 1 narrowPeak UW Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeUwDnase/wgEncodeUwDnaseTh1PkRep2.narrowPeak.gz Th1 DnaseSeq Peaks 2 narrowPeak UW Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeUwDnase/wgEncodeUwDnaseTh1RawRep1.bigWig Th1 DnaseSeq RawSignal 1 bigWig UW Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeUwDnase/wgEncodeUwDnaseTh1RawRep2.bigWig Th1 DnaseSeq RawSignal 2 bigWig UW Data 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http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeUwRepliSeq/wgEncodeUwRepliSeqHepg2G2AlnRep1.bam HepG2 RepliSeq Alignments 1 bam UW Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeUwRepliSeq/wgEncodeUwRepliSeqHepg2G2PctSignalRep1.bigWig HepG2 RepliSeq PctSignal 1 bigWig UW Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeUwRepliSeq/wgEncodeUwRepliSeqHepg2PkRep1.bed.gz HepG2 RepliSeq Peaks 1 bed UW Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeUwRepliSeq/wgEncodeUwRepliSeqHepg2S1AlnRep1.bam HepG2 RepliSeq Alignments 1 bam UW Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeUwRepliSeq/wgEncodeUwRepliSeqHepg2S1PctSignalRep1.bigWig HepG2 RepliSeq PctSignal 1 bigWig UW Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeUwRepliSeq/wgEncodeUwRepliSeqHepg2S2AlnRep1.bam HepG2 RepliSeq Alignments 1 bam UW Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeUwRepliSeq/wgEncodeUwRepliSeqHepg2S2PctSignalRep1.bigWig HepG2 RepliSeq PctSignal 1 bigWig UW Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeUwRepliSeq/wgEncodeUwRepliSeqHepg2S3AlnRep1.bam HepG2 RepliSeq Alignments 1 bam UW Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeUwRepliSeq/wgEncodeUwRepliSeqHepg2S3PctSignalRep1.bigWig HepG2 RepliSeq PctSignal 1 bigWig UW Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeUwRepliSeq/wgEncodeUwRepliSeqHepg2S4AlnRep1.bam HepG2 RepliSeq Alignments 1 bam UW Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeUwRepliSeq/wgEncodeUwRepliSeqHepg2S4PctSignalRep1.bigWig HepG2 RepliSeq PctSignal 1 bigWig UW Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeUwRepliSeq/wgEncodeUwRepliSeqHepg2SumSignalRep1.bigWig HepG2 RepliSeq SumSignal 1 bigWig UW Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeUwRepliSeq/wgEncodeUwRepliSeqHepg2ValleysRep1.bed.gz HepG2 RepliSeq Valleys 1 bed UW Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeUwRepliSeq/wgEncodeUwRepliSeqHepg2WaveSignalRep1.bigWig HepG2 RepliSeq WaveSignal 1 bigWig UW Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeUwRepliSeq/wgEncodeUwRepliSeqHuvecG1bAlnRep1.bam HUVEC RepliSeq Alignments 1 bam UW Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeUwRepliSeq/wgEncodeUwRepliSeqHuvecG1bPctSignalRep1.bigWig HUVEC RepliSeq PctSignal 1 bigWig UW Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeUwRepliSeq/wgEncodeUwRepliSeqHuvecG2AlnRep1.bam HUVEC RepliSeq Alignments 1 bam UW Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeUwRepliSeq/wgEncodeUwRepliSeqHuvecG2PctSignalRep1.bigWig HUVEC RepliSeq PctSignal 1 bigWig UW Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeUwRepliSeq/wgEncodeUwRepliSeqHuvecPkRep1.bed.gz HUVEC RepliSeq Peaks 1 bed UW Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeUwRepliSeq/wgEncodeUwRepliSeqHuvecS1AlnRep1.bam HUVEC RepliSeq Alignments 1 bam UW Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeUwRepliSeq/wgEncodeUwRepliSeqHuvecS1PctSignalRep1.bigWig HUVEC RepliSeq PctSignal 1 bigWig UW Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeUwRepliSeq/wgEncodeUwRepliSeqHuvecS2AlnRep1.bam HUVEC RepliSeq Alignments 1 bam UW Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeUwRepliSeq/wgEncodeUwRepliSeqHuvecS2PctSignalRep1.bigWig HUVEC RepliSeq PctSignal 1 bigWig UW Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeUwRepliSeq/wgEncodeUwRepliSeqHuvecS3AlnRep1.bam HUVEC RepliSeq Alignments 1 bam UW Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeUwRepliSeq/wgEncodeUwRepliSeqHuvecS3PctSignalRep1.bigWig HUVEC RepliSeq PctSignal 1 bigWig UW Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeUwRepliSeq/wgEncodeUwRepliSeqHuvecS4AlnRep1.bam HUVEC RepliSeq Alignments 1 bam UW Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeUwRepliSeq/wgEncodeUwRepliSeqHuvecS4PctSignalRep1.bigWig HUVEC RepliSeq PctSignal 1 bigWig UW Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeUwRepliSeq/wgEncodeUwRepliSeqHuvecSumSignalRep1.bigWig HUVEC RepliSeq SumSignal 1 bigWig UW Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeUwRepliSeq/wgEncodeUwRepliSeqHuvecValleysRep1.bed.gz HUVEC RepliSeq Valleys 1 bed UW Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeUwRepliSeq/wgEncodeUwRepliSeqHuvecWaveSignalRep1.bigWig HUVEC RepliSeq WaveSignal 1 bigWig UW Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeUwRepliSeq/wgEncodeUwRepliSeqImr90G1bAlnRep1.bam IMR90 RepliSeq Alignments 1 bam UW Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeUwRepliSeq/wgEncodeUwRepliSeqImr90G1bPctSignalRep1.bigWig IMR90 RepliSeq PctSignal 1 bigWig UW Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeUwRepliSeq/wgEncodeUwRepliSeqImr90G2AlnRep1.bam IMR90 RepliSeq Alignments 1 bam UW Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeUwRepliSeq/wgEncodeUwRepliSeqImr90G2PctSignalRep1.bigWig IMR90 RepliSeq PctSignal 1 bigWig UW Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeUwRepliSeq/wgEncodeUwRepliSeqImr90PkRep1.bed.gz IMR90 RepliSeq Peaks 1 bed UW Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeUwRepliSeq/wgEncodeUwRepliSeqImr90S1AlnRep1.bam IMR90 RepliSeq Alignments 1 bam UW Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeUwRepliSeq/wgEncodeUwRepliSeqImr90S1PctSignalRep1.bigWig IMR90 RepliSeq PctSignal 1 bigWig UW Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeUwRepliSeq/wgEncodeUwRepliSeqImr90S2AlnRep1.bam IMR90 RepliSeq Alignments 1 bam UW Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeUwRepliSeq/wgEncodeUwRepliSeqImr90S2PctSignalRep1.bigWig IMR90 RepliSeq PctSignal 1 bigWig UW Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeUwRepliSeq/wgEncodeUwRepliSeqImr90S3AlnRep1.bam IMR90 RepliSeq Alignments 1 bam UW Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeUwRepliSeq/wgEncodeUwRepliSeqImr90S3PctSignalRep1.bigWig IMR90 RepliSeq PctSignal 1 bigWig UW Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeUwRepliSeq/wgEncodeUwRepliSeqImr90S4AlnRep1.bam IMR90 RepliSeq Alignments 1 bam UW Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeUwRepliSeq/wgEncodeUwRepliSeqImr90S4PctSignalRep1.bigWig IMR90 RepliSeq PctSignal 1 bigWig UW Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeUwRepliSeq/wgEncodeUwRepliSeqImr90SumSignalRep1.bigWig IMR90 RepliSeq SumSignal 1 bigWig UW Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeUwRepliSeq/wgEncodeUwRepliSeqImr90ValleysRep1.bed.gz IMR90 RepliSeq Valleys 1 bed UW Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeUwRepliSeq/wgEncodeUwRepliSeqImr90WaveSignalRep1.bigWig IMR90 RepliSeq WaveSignal 1 bigWig UW Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeUwRepliSeq/wgEncodeUwRepliSeqK562G1AlnRep1.bam K562 RepliSeq Alignments 1 bam UW Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeUwRepliSeq/wgEncodeUwRepliSeqK562G1PctSignalRep1.bigWig K562 RepliSeq PctSignal 1 bigWig UW Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeUwRepliSeq/wgEncodeUwRepliSeqK562G2AlnRep1.bam K562 RepliSeq Alignments 1 bam UW Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeUwRepliSeq/wgEncodeUwRepliSeqK562G2PctSignalRep1.bigWig K562 RepliSeq PctSignal 1 bigWig UW Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeUwRepliSeq/wgEncodeUwRepliSeqK562PkRep1.bed.gz K562 RepliSeq Peaks 1 bed UW Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeUwRepliSeq/wgEncodeUwRepliSeqK562S1AlnRep1.bam K562 RepliSeq Alignments 1 bam UW Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeUwRepliSeq/wgEncodeUwRepliSeqK562S1PctSignalRep1.bigWig K562 RepliSeq PctSignal 1 bigWig UW Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeUwRepliSeq/wgEncodeUwRepliSeqK562S2AlnRep1.bam K562 RepliSeq Alignments 1 bam UW Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeUwRepliSeq/wgEncodeUwRepliSeqK562S2PctSignalRep1.bigWig K562 RepliSeq PctSignal 1 bigWig UW Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeUwRepliSeq/wgEncodeUwRepliSeqK562S3AlnRep1.bam K562 RepliSeq Alignments 1 bam UW Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeUwRepliSeq/wgEncodeUwRepliSeqK562S3PctSignalRep1.bigWig K562 RepliSeq PctSignal 1 bigWig UW Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeUwRepliSeq/wgEncodeUwRepliSeqK562S4AlnRep1.bam K562 RepliSeq Alignments 1 bam UW Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeUwRepliSeq/wgEncodeUwRepliSeqK562S4PctSignalRep1.bigWig K562 RepliSeq PctSignal 1 bigWig UW Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeUwRepliSeq/wgEncodeUwRepliSeqK562SumSignalRep1.bigWig K562 RepliSeq SumSignal 1 bigWig UW Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeUwRepliSeq/wgEncodeUwRepliSeqK562ValleysRep1.bed.gz K562 RepliSeq Valleys 1 bed UW Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeUwRepliSeq/wgEncodeUwRepliSeqK562WaveSignalRep1.bigWig K562 RepliSeq WaveSignal 1 bigWig UW Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeUwRepliSeq/wgEncodeUwRepliSeqMcf7G1bAlnRep1.bam MCF-7 RepliSeq Alignments 1 bam UW Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeUwRepliSeq/wgEncodeUwRepliSeqMcf7G1bPctSignalRep1.bigWig MCF-7 RepliSeq PctSignal 1 bigWig UW Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeUwRepliSeq/wgEncodeUwRepliSeqMcf7G2AlnRep1.bam MCF-7 RepliSeq Alignments 1 bam UW Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeUwRepliSeq/wgEncodeUwRepliSeqMcf7G2PctSignalRep1.bigWig MCF-7 RepliSeq PctSignal 1 bigWig UW Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeUwRepliSeq/wgEncodeUwRepliSeqMcf7PkRep1.bed.gz MCF-7 RepliSeq Peaks 1 bed UW Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeUwRepliSeq/wgEncodeUwRepliSeqMcf7S1AlnRep1.bam MCF-7 RepliSeq Alignments 1 bam UW Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeUwRepliSeq/wgEncodeUwRepliSeqMcf7S1PctSignalRep1.bigWig MCF-7 RepliSeq PctSignal 1 bigWig UW Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeUwRepliSeq/wgEncodeUwRepliSeqMcf7S2AlnRep1.bam MCF-7 RepliSeq Alignments 1 bam UW Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeUwRepliSeq/wgEncodeUwRepliSeqMcf7S2PctSignalRep1.bigWig MCF-7 RepliSeq PctSignal 1 bigWig UW Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeUwRepliSeq/wgEncodeUwRepliSeqMcf7S3AlnRep1.bam MCF-7 RepliSeq Alignments 1 bam UW Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeUwRepliSeq/wgEncodeUwRepliSeqMcf7S3PctSignalRep1.bigWig MCF-7 RepliSeq PctSignal 1 bigWig UW Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeUwRepliSeq/wgEncodeUwRepliSeqMcf7S4AlnRep1.bam MCF-7 RepliSeq Alignments 1 bam UW Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeUwRepliSeq/wgEncodeUwRepliSeqMcf7S4PctSignalRep1.bigWig MCF-7 RepliSeq PctSignal 1 bigWig UW Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeUwRepliSeq/wgEncodeUwRepliSeqMcf7SumSignalRep1.bigWig MCF-7 RepliSeq SumSignal 1 bigWig UW Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeUwRepliSeq/wgEncodeUwRepliSeqMcf7ValleysRep1.bed.gz MCF-7 RepliSeq Valleys 1 bed UW Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeUwRepliSeq/wgEncodeUwRepliSeqMcf7WaveSignalRep1.bigWig MCF-7 RepliSeq WaveSignal 1 bigWig UW Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeUwRepliSeq/wgEncodeUwRepliSeqNhekG1bAlnRep1.bam NHEK RepliSeq Alignments 1 bam UW Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeUwRepliSeq/wgEncodeUwRepliSeqNhekG1bPctSignalRep1.bigWig NHEK RepliSeq PctSignal 1 bigWig UW Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeUwRepliSeq/wgEncodeUwRepliSeqNhekG2AlnRep1.bam NHEK RepliSeq Alignments 1 bam UW Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeUwRepliSeq/wgEncodeUwRepliSeqNhekG2PctSignalRep1.bigWig NHEK RepliSeq PctSignal 1 bigWig UW Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeUwRepliSeq/wgEncodeUwRepliSeqNhekPkRep1.bed.gz NHEK RepliSeq Peaks 1 bed UW Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeUwRepliSeq/wgEncodeUwRepliSeqNhekS1AlnRep1.bam NHEK RepliSeq Alignments 1 bam UW Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeUwRepliSeq/wgEncodeUwRepliSeqNhekS1PctSignalRep1.bigWig NHEK RepliSeq PctSignal 1 bigWig UW Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeUwRepliSeq/wgEncodeUwRepliSeqNhekS2AlnRep1.bam NHEK RepliSeq Alignments 1 bam UW Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeUwRepliSeq/wgEncodeUwRepliSeqNhekS2PctSignalRep1.bigWig NHEK RepliSeq PctSignal 1 bigWig UW Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeUwRepliSeq/wgEncodeUwRepliSeqNhekS3AlnRep1.bam NHEK RepliSeq Alignments 1 bam UW Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeUwRepliSeq/wgEncodeUwRepliSeqNhekS3PctSignalRep1.bigWig NHEK RepliSeq PctSignal 1 bigWig UW Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeUwRepliSeq/wgEncodeUwRepliSeqNhekS4AlnRep1.bam NHEK RepliSeq Alignments 1 bam UW Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeUwRepliSeq/wgEncodeUwRepliSeqNhekS4PctSignalRep1.bigWig NHEK RepliSeq PctSignal 1 bigWig UW Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeUwRepliSeq/wgEncodeUwRepliSeqNhekSumSignalRep1.bigWig NHEK RepliSeq SumSignal 1 bigWig UW Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeUwRepliSeq/wgEncodeUwRepliSeqNhekValleysRep1.bed.gz NHEK RepliSeq Valleys 1 bed UW Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeUwRepliSeq/wgEncodeUwRepliSeqNhekWaveSignalRep1.bigWig NHEK RepliSeq WaveSignal 1 bigWig UW Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeUwRepliSeq/wgEncodeUwRepliSeqSknshG1bAlnRep1.bam SK-N-SH RepliSeq Alignments 1 bam UW Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeUwRepliSeq/wgEncodeUwRepliSeqSknshG1bPctSignalRep1.bigWig SK-N-SH RepliSeq PctSignal 1 bigWig UW Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeUwRepliSeq/wgEncodeUwRepliSeqSknshG2AlnRep1.bam SK-N-SH RepliSeq Alignments 1 bam UW Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeUwRepliSeq/wgEncodeUwRepliSeqSknshG2PctSignalRep1.bigWig SK-N-SH RepliSeq PctSignal 1 bigWig UW Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeUwRepliSeq/wgEncodeUwRepliSeqSknshPkRep1.bed.gz SK-N-SH RepliSeq Peaks 1 bed UW Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeUwRepliSeq/wgEncodeUwRepliSeqSknshS1AlnRep1.bam SK-N-SH RepliSeq Alignments 1 bam UW Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeUwRepliSeq/wgEncodeUwRepliSeqSknshS1PctSignalRep1.bigWig SK-N-SH RepliSeq PctSignal 1 bigWig UW Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeUwRepliSeq/wgEncodeUwRepliSeqSknshS2AlnRep1.bam SK-N-SH RepliSeq Alignments 1 bam UW Data 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http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeUwRepliSeq/wgEncodeUwRepliSeqSknshValleysRep1.bed.gz SK-N-SH RepliSeq Valleys 1 bed UW Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeUwRepliSeq/wgEncodeUwRepliSeqSknshWaveSignalRep1.bigWig SK-N-SH RepliSeq WaveSignal 1 bigWig UW Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeUwTfbs/wgEncodeUwTfbsA549CtcfStdAlnRep1.bam A549 ChipSeq CTCF Alignments 1 bam UW Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeUwTfbs/wgEncodeUwTfbsA549CtcfStdAlnRep2.bam A549 ChipSeq CTCF Alignments 2 bam UW Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeUwTfbs/wgEncodeUwTfbsA549CtcfStdHotspotsRep1.broadPeak.gz A549 ChipSeq CTCF Hotspots 1 broadPeak UW Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeUwTfbs/wgEncodeUwTfbsA549CtcfStdHotspotsRep2.broadPeak.gz A549 ChipSeq CTCF Hotspots 2 broadPeak UW Data 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RawSignal 1 bigWig UW Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeUwTfbs/wgEncodeUwTfbsGm12864CtcfStdRawRep2.bigWig GM12864 ChipSeq CTCF RawSignal 2 bigWig UW Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeUwTfbs/wgEncodeUwTfbsGm12864CtcfStdRawRep3.bigWig GM12864 ChipSeq CTCF RawSignal 3 bigWig UW Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeUwTfbs/wgEncodeUwTfbsGm12864InputStdAlnRep1.bam GM12864 ChipSeq Input Alignments 1 bam UW Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeUwTfbs/wgEncodeUwTfbsGm12864InputStdRawRep1.bigWig GM12864 ChipSeq Input RawSignal 1 bigWig UW Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeUwTfbs/wgEncodeUwTfbsGm12865CtcfStdAlnRep1.bam GM12865 ChipSeq CTCF Alignments 1 bam UW Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeUwTfbs/wgEncodeUwTfbsGm12865CtcfStdAlnRep2.bam GM12865 ChipSeq CTCF Alignments 2 bam UW Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeUwTfbs/wgEncodeUwTfbsGm12865CtcfStdAlnRep3.bam GM12865 ChipSeq CTCF Alignments 3 bam UW Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeUwTfbs/wgEncodeUwTfbsGm12865CtcfStdHotspotsRep1.broadPeak.gz GM12865 ChipSeq CTCF Hotspots 1 broadPeak UW Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeUwTfbs/wgEncodeUwTfbsGm12865CtcfStdHotspotsRep2.broadPeak.gz GM12865 ChipSeq CTCF Hotspots 2 broadPeak UW Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeUwTfbs/wgEncodeUwTfbsGm12865CtcfStdHotspotsRep3.broadPeak.gz GM12865 ChipSeq CTCF Hotspots 3 broadPeak UW Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeUwTfbs/wgEncodeUwTfbsGm12865CtcfStdPkRep1.narrowPeak.gz GM12865 ChipSeq CTCF Peaks 1 narrowPeak UW Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeUwTfbs/wgEncodeUwTfbsGm12865CtcfStdPkRep2.narrowPeak.gz GM12865 ChipSeq CTCF Peaks 2 narrowPeak UW Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeUwTfbs/wgEncodeUwTfbsGm12865CtcfStdPkRep3.narrowPeak.gz GM12865 ChipSeq CTCF Peaks 3 narrowPeak UW Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeUwTfbs/wgEncodeUwTfbsGm12865CtcfStdRawRep1.bigWig GM12865 ChipSeq CTCF RawSignal 1 bigWig UW Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeUwTfbs/wgEncodeUwTfbsGm12865CtcfStdRawRep2.bigWig GM12865 ChipSeq CTCF RawSignal 2 bigWig UW Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeUwTfbs/wgEncodeUwTfbsGm12865CtcfStdRawRep3.bigWig GM12865 ChipSeq CTCF RawSignal 3 bigWig UW Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeUwTfbs/wgEncodeUwTfbsGm12865InputStdAlnRep1.bam GM12865 ChipSeq Input Alignments 1 bam UW Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeUwTfbs/wgEncodeUwTfbsGm12865InputStdRawRep1.bigWig GM12865 ChipSeq Input RawSignal 1 bigWig UW Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeUwTfbs/wgEncodeUwTfbsGm12866CtcfStdAlnRep1.bam GM12866 ChipSeq CTCF Alignments 1 bam UW Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeUwTfbs/wgEncodeUwTfbsGm12866CtcfStdAlnRep2.bam GM12866 ChipSeq CTCF Alignments 2 bam UW Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeUwTfbs/wgEncodeUwTfbsGm12866CtcfStdHotspotsRep1.broadPeak.gz GM12866 ChipSeq CTCF Hotspots 1 broadPeak UW Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeUwTfbs/wgEncodeUwTfbsGm12866CtcfStdHotspotsRep2.broadPeak.gz GM12866 ChipSeq CTCF Hotspots 2 broadPeak UW Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeUwTfbs/wgEncodeUwTfbsGm12866CtcfStdPkRep1.narrowPeak.gz GM12866 ChipSeq CTCF Peaks 1 narrowPeak UW Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeUwTfbs/wgEncodeUwTfbsGm12866CtcfStdPkRep2.narrowPeak.gz GM12866 ChipSeq CTCF Peaks 2 narrowPeak UW Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeUwTfbs/wgEncodeUwTfbsGm12866CtcfStdRawRep1.bigWig GM12866 ChipSeq CTCF RawSignal 1 bigWig UW Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeUwTfbs/wgEncodeUwTfbsGm12866CtcfStdRawRep2.bigWig GM12866 ChipSeq CTCF RawSignal 2 bigWig UW Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeUwTfbs/wgEncodeUwTfbsGm12867CtcfStdAlnRep1.bam GM12867 ChipSeq CTCF Alignments 1 bam UW Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeUwTfbs/wgEncodeUwTfbsGm12867CtcfStdAlnRep2.bam GM12867 ChipSeq CTCF Alignments 2 bam UW Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeUwTfbs/wgEncodeUwTfbsGm12867CtcfStdHotspotsRep1.broadPeak.gz GM12867 ChipSeq CTCF Hotspots 1 broadPeak UW Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeUwTfbs/wgEncodeUwTfbsGm12867CtcfStdHotspotsRep2.broadPeak.gz GM12867 ChipSeq CTCF Hotspots 2 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bigWig UW Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeUwTfbs/wgEncodeUwTfbsGm12869CtcfStdAlnRep1.bam GM12869 ChipSeq CTCF Alignments 1 bam UW Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeUwTfbs/wgEncodeUwTfbsGm12869CtcfStdAlnRep2.bam GM12869 ChipSeq CTCF Alignments 2 bam UW Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeUwTfbs/wgEncodeUwTfbsGm12869CtcfStdHotspotsRep1.broadPeak.gz GM12869 ChipSeq CTCF Hotspots 1 broadPeak UW Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeUwTfbs/wgEncodeUwTfbsGm12869CtcfStdHotspotsRep2.broadPeak.gz GM12869 ChipSeq CTCF Hotspots 2 broadPeak UW Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeUwTfbs/wgEncodeUwTfbsGm12869CtcfStdPkRep1.narrowPeak.gz GM12869 ChipSeq CTCF Peaks 1 narrowPeak UW Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeUwTfbs/wgEncodeUwTfbsGm12869CtcfStdPkRep2.narrowPeak.gz GM12869 ChipSeq CTCF Peaks 2 narrowPeak UW Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeUwTfbs/wgEncodeUwTfbsGm12869CtcfStdRawRep1.bigWig GM12869 ChipSeq CTCF RawSignal 1 bigWig UW Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeUwTfbs/wgEncodeUwTfbsGm12869CtcfStdRawRep2.bigWig GM12869 ChipSeq CTCF RawSignal 2 bigWig UW Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeUwTfbs/wgEncodeUwTfbsGm12870CtcfStdAlnRep1.bam GM12870 ChipSeq CTCF Alignments 1 bam UW Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeUwTfbs/wgEncodeUwTfbsGm12870CtcfStdAlnRep2.bam GM12870 ChipSeq CTCF Alignments 2 bam UW Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeUwTfbs/wgEncodeUwTfbsGm12870CtcfStdHotspotsRep1.broadPeak.gz GM12870 ChipSeq CTCF Hotspots 1 broadPeak UW Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeUwTfbs/wgEncodeUwTfbsGm12870CtcfStdHotspotsRep2.broadPeak.gz GM12870 ChipSeq CTCF Hotspots 2 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bigWig UW Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeUwTfbs/wgEncodeUwTfbsHct116InputStdAlnRep1.bam HCT-116 ChipSeq Input Alignments 1 bam UW Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeUwTfbs/wgEncodeUwTfbsHct116InputStdRawRep1.bigWig HCT-116 ChipSeq Input RawSignal 1 bigWig UW Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeUwTfbs/wgEncodeUwTfbsHeeCtcfStdAlnRep1.bam HEEpiC ChipSeq CTCF Alignments 1 bam UW Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeUwTfbs/wgEncodeUwTfbsHeeCtcfStdAlnRep2.bam HEEpiC ChipSeq CTCF Alignments 2 bam UW Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeUwTfbs/wgEncodeUwTfbsHeeCtcfStdHotspotsRep1.broadPeak.gz HEEpiC ChipSeq CTCF Hotspots 1 broadPeak UW Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeUwTfbs/wgEncodeUwTfbsHeeCtcfStdHotspotsRep2.broadPeak.gz HEEpiC ChipSeq CTCF Hotspots 2 broadPeak UW Data 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http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeUwTfbs/wgEncodeUwTfbsHek293CtcfStdAlnRep1.bam HEK293 ChipSeq CTCF Alignments 1 bam UW Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeUwTfbs/wgEncodeUwTfbsHek293CtcfStdAlnRep2.bam HEK293 ChipSeq CTCF Alignments 2 bam UW Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeUwTfbs/wgEncodeUwTfbsHek293CtcfStdHotspotsRep1.broadPeak.gz HEK293 ChipSeq CTCF Hotspots 1 broadPeak UW Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeUwTfbs/wgEncodeUwTfbsHek293CtcfStdHotspotsRep2.broadPeak.gz HEK293 ChipSeq CTCF Hotspots 2 broadPeak UW Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeUwTfbs/wgEncodeUwTfbsHek293CtcfStdPkRep1.narrowPeak.gz HEK293 ChipSeq CTCF Peaks 1 narrowPeak UW Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeUwTfbs/wgEncodeUwTfbsHek293CtcfStdPkRep2.narrowPeak.gz HEK293 ChipSeq CTCF Peaks 2 narrowPeak UW Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeUwTfbs/wgEncodeUwTfbsHek293CtcfStdRawRep1.bigWig HEK293 ChipSeq CTCF RawSignal 1 bigWig UW Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeUwTfbs/wgEncodeUwTfbsHek293CtcfStdRawRep2.bigWig HEK293 ChipSeq CTCF RawSignal 2 bigWig UW Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeUwTfbs/wgEncodeUwTfbsHek293InputStdAlnRep1.bam HEK293 ChipSeq Input Alignments 1 bam UW Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeUwTfbs/wgEncodeUwTfbsHek293InputStdRawRep1.bigWig HEK293 ChipSeq Input RawSignal 1 bigWig UW Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeUwTfbs/wgEncodeUwTfbsHelas3CtcfStdAlnRep1.bam HeLa-S3 ChipSeq CTCF Alignments 1 bam UW Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeUwTfbs/wgEncodeUwTfbsHelas3CtcfStdAlnRep2.bam HeLa-S3 ChipSeq CTCF Alignments 2 bam UW Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeUwTfbs/wgEncodeUwTfbsHelas3CtcfStdHotspotsRep1.broadPeak.gz HeLa-S3 ChipSeq CTCF Hotspots 1 broadPeak UW Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeUwTfbs/wgEncodeUwTfbsHelas3CtcfStdHotspotsRep2.broadPeak.gz HeLa-S3 ChipSeq CTCF Hotspots 2 broadPeak UW Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeUwTfbs/wgEncodeUwTfbsHelas3CtcfStdPkRep1.narrowPeak.gz HeLa-S3 ChipSeq CTCF Peaks 1 narrowPeak UW Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeUwTfbs/wgEncodeUwTfbsHelas3CtcfStdPkRep2.narrowPeak.gz HeLa-S3 ChipSeq CTCF Peaks 2 narrowPeak UW Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeUwTfbs/wgEncodeUwTfbsHelas3CtcfStdRawRep1.bigWig HeLa-S3 ChipSeq CTCF RawSignal 1 bigWig UW Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeUwTfbs/wgEncodeUwTfbsHelas3CtcfStdRawRep2.bigWig HeLa-S3 ChipSeq CTCF RawSignal 2 bigWig UW Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeUwTfbs/wgEncodeUwTfbsHelas3InputStdAlnRep1.bam HeLa-S3 ChipSeq Input Alignments 1 bam UW Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeUwTfbs/wgEncodeUwTfbsHelas3InputStdRawRep1.bigWig HeLa-S3 ChipSeq Input RawSignal 1 bigWig UW Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeUwTfbs/wgEncodeUwTfbsHepg2CtcfStdAlnRep1.bam HepG2 ChipSeq CTCF Alignments 1 bam UW Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeUwTfbs/wgEncodeUwTfbsHepg2CtcfStdAlnRep2.bam HepG2 ChipSeq CTCF Alignments 2 bam UW Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeUwTfbs/wgEncodeUwTfbsHepg2CtcfStdHotspotsRep1.broadPeak.gz HepG2 ChipSeq CTCF Hotspots 1 broadPeak UW Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeUwTfbs/wgEncodeUwTfbsHepg2CtcfStdHotspotsRep2.broadPeak.gz HepG2 ChipSeq CTCF Hotspots 2 broadPeak UW Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeUwTfbs/wgEncodeUwTfbsHepg2CtcfStdPkRep1.narrowPeak.gz HepG2 ChipSeq CTCF Peaks 1 narrowPeak UW Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeUwTfbs/wgEncodeUwTfbsHepg2CtcfStdPkRep2.narrowPeak.gz HepG2 ChipSeq CTCF Peaks 2 narrowPeak UW Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeUwTfbs/wgEncodeUwTfbsHepg2CtcfStdRawRep1.bigWig HepG2 ChipSeq CTCF RawSignal 1 bigWig UW Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeUwTfbs/wgEncodeUwTfbsHepg2CtcfStdRawRep2.bigWig HepG2 ChipSeq CTCF RawSignal 2 bigWig UW Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeUwTfbs/wgEncodeUwTfbsHepg2InputStdAlnRep1.bam HepG2 ChipSeq Input Alignments 1 bam UW Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeUwTfbs/wgEncodeUwTfbsHepg2InputStdRawRep1.bigWig HepG2 ChipSeq Input RawSignal 1 bigWig UW Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeUwTfbs/wgEncodeUwTfbsHffCtcfStdAlnRep1.bam HFF ChipSeq CTCF Alignments 1 bam UW Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeUwTfbs/wgEncodeUwTfbsHffCtcfStdHotspotsRep1.broadPeak.gz HFF ChipSeq CTCF Hotspots 1 broadPeak UW Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeUwTfbs/wgEncodeUwTfbsHffCtcfStdPkRep1.narrowPeak.gz HFF ChipSeq CTCF Peaks 1 narrowPeak UW Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeUwTfbs/wgEncodeUwTfbsHffCtcfStdRawRep1.bigWig HFF ChipSeq CTCF RawSignal 1 bigWig UW Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeUwTfbs/wgEncodeUwTfbsHffInputStdAlnRep1.bam HFF ChipSeq Input Alignments 1 bam UW Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeUwTfbs/wgEncodeUwTfbsHffInputStdRawRep1.bigWig HFF ChipSeq Input RawSignal 1 bigWig UW Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeUwTfbs/wgEncodeUwTfbsHffmycCtcfStdAlnRep1.bam HFF-Myc ChipSeq CTCF Alignments 1 bam UW Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeUwTfbs/wgEncodeUwTfbsHffmycCtcfStdAlnRep2.bam HFF-Myc ChipSeq CTCF Alignments 2 bam UW Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeUwTfbs/wgEncodeUwTfbsHffmycCtcfStdHotspotsRep1.broadPeak.gz HFF-Myc ChipSeq CTCF Hotspots 1 broadPeak UW Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeUwTfbs/wgEncodeUwTfbsHffmycCtcfStdHotspotsRep2.broadPeak.gz HFF-Myc ChipSeq CTCF Hotspots 2 broadPeak UW Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeUwTfbs/wgEncodeUwTfbsHffmycCtcfStdPkRep1.narrowPeak.gz HFF-Myc ChipSeq CTCF Peaks 1 narrowPeak UW Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeUwTfbs/wgEncodeUwTfbsHffmycCtcfStdPkRep2.narrowPeak.gz HFF-Myc ChipSeq CTCF Peaks 2 narrowPeak UW Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeUwTfbs/wgEncodeUwTfbsHffmycCtcfStdRawRep1.bigWig HFF-Myc ChipSeq CTCF RawSignal 1 bigWig UW Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeUwTfbs/wgEncodeUwTfbsHffmycCtcfStdRawRep2.bigWig HFF-Myc ChipSeq CTCF RawSignal 2 bigWig UW Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeUwTfbs/wgEncodeUwTfbsHffmycInputStdAlnRep1.bam HFF-Myc ChipSeq Input Alignments 1 bam UW Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeUwTfbs/wgEncodeUwTfbsHffmycInputStdRawRep1.bigWig HFF-Myc ChipSeq Input RawSignal 1 bigWig UW Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeUwTfbs/wgEncodeUwTfbsHl60CtcfStdAlnRep1.bam HL-60 ChipSeq CTCF Alignments 1 bam UW Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeUwTfbs/wgEncodeUwTfbsHl60CtcfStdHotspotsRep1.broadPeak.gz HL-60 ChipSeq CTCF Hotspots 1 broadPeak UW Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeUwTfbs/wgEncodeUwTfbsHl60CtcfStdPkRep1.narrowPeak.gz HL-60 ChipSeq CTCF Peaks 1 narrowPeak UW Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeUwTfbs/wgEncodeUwTfbsHl60CtcfStdRawRep1.bigWig HL-60 ChipSeq CTCF RawSignal 1 bigWig UW Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeUwTfbs/wgEncodeUwTfbsHl60InputStdAlnRep1.bam HL-60 ChipSeq Input Alignments 1 bam UW Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeUwTfbs/wgEncodeUwTfbsHl60InputStdRawRep1.bigWig HL-60 ChipSeq Input RawSignal 1 bigWig UW Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeUwTfbs/wgEncodeUwTfbsHmecCtcfStdAlnRep1.bam HMEC ChipSeq CTCF Alignments 1 bam UW Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeUwTfbs/wgEncodeUwTfbsHmecCtcfStdAlnRep2.bam HMEC ChipSeq CTCF Alignments 2 bam UW Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeUwTfbs/wgEncodeUwTfbsHmecCtcfStdHotspotsRep1.broadPeak.gz HMEC ChipSeq CTCF Hotspots 1 broadPeak UW Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeUwTfbs/wgEncodeUwTfbsHmecCtcfStdHotspotsRep2.broadPeak.gz HMEC ChipSeq CTCF Hotspots 2 broadPeak UW Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeUwTfbs/wgEncodeUwTfbsHmecCtcfStdPkRep1.narrowPeak.gz HMEC ChipSeq CTCF Peaks 1 narrowPeak UW Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeUwTfbs/wgEncodeUwTfbsHmecCtcfStdPkRep2.narrowPeak.gz HMEC ChipSeq CTCF Peaks 2 narrowPeak UW Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeUwTfbs/wgEncodeUwTfbsHmecCtcfStdRawRep1.bigWig HMEC ChipSeq CTCF RawSignal 1 bigWig UW Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeUwTfbs/wgEncodeUwTfbsHmecCtcfStdRawRep2.bigWig HMEC ChipSeq CTCF RawSignal 2 bigWig UW Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeUwTfbs/wgEncodeUwTfbsHmecInputStdAlnRep1.bam HMEC ChipSeq Input Alignments 1 bam UW Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeUwTfbs/wgEncodeUwTfbsHmecInputStdRawRep1.bigWig HMEC ChipSeq Input RawSignal 1 bigWig UW Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeUwTfbs/wgEncodeUwTfbsHmfCtcfStdAlnRep1.bam HMF ChipSeq CTCF Alignments 1 bam UW Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeUwTfbs/wgEncodeUwTfbsHmfCtcfStdAlnRep2.bam HMF ChipSeq CTCF Alignments 2 bam UW Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeUwTfbs/wgEncodeUwTfbsHmfCtcfStdHotspotsRep1.broadPeak.gz HMF ChipSeq CTCF Hotspots 1 broadPeak UW Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeUwTfbs/wgEncodeUwTfbsHmfCtcfStdHotspotsRep2.broadPeak.gz HMF ChipSeq CTCF Hotspots 2 broadPeak UW Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeUwTfbs/wgEncodeUwTfbsHmfCtcfStdPkRep1.narrowPeak.gz HMF ChipSeq CTCF Peaks 1 narrowPeak UW Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeUwTfbs/wgEncodeUwTfbsHmfCtcfStdPkRep2.narrowPeak.gz HMF ChipSeq CTCF Peaks 2 narrowPeak UW Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeUwTfbs/wgEncodeUwTfbsHmfCtcfStdRawRep1.bigWig HMF ChipSeq CTCF RawSignal 1 bigWig UW Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeUwTfbs/wgEncodeUwTfbsHmfCtcfStdRawRep2.bigWig HMF ChipSeq CTCF RawSignal 2 bigWig UW Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeUwTfbs/wgEncodeUwTfbsHmfInputStdAlnRep1.bam HMF ChipSeq Input Alignments 1 bam UW Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeUwTfbs/wgEncodeUwTfbsHmfInputStdRawRep1.bigWig HMF ChipSeq Input RawSignal 1 bigWig UW Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeUwTfbs/wgEncodeUwTfbsHpafCtcfStdAlnRep1.bam HPAF ChipSeq CTCF Alignments 1 bam UW Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeUwTfbs/wgEncodeUwTfbsHpafCtcfStdAlnRep2.bam HPAF ChipSeq CTCF Alignments 2 bam UW Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeUwTfbs/wgEncodeUwTfbsHpafCtcfStdHotspotsRep1.broadPeak.gz HPAF ChipSeq CTCF Hotspots 1 broadPeak UW Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeUwTfbs/wgEncodeUwTfbsHpafCtcfStdHotspotsRep2.broadPeak.gz HPAF ChipSeq CTCF Hotspots 2 broadPeak UW Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeUwTfbs/wgEncodeUwTfbsHpafCtcfStdPkRep1.narrowPeak.gz HPAF ChipSeq CTCF Peaks 1 narrowPeak UW Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeUwTfbs/wgEncodeUwTfbsHpafCtcfStdPkRep2.narrowPeak.gz HPAF ChipSeq CTCF Peaks 2 narrowPeak UW Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeUwTfbs/wgEncodeUwTfbsHpafCtcfStdRawRep1.bigWig HPAF ChipSeq CTCF RawSignal 1 bigWig UW Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeUwTfbs/wgEncodeUwTfbsHpafCtcfStdRawRep2.bigWig HPAF ChipSeq CTCF RawSignal 2 bigWig UW Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeUwTfbs/wgEncodeUwTfbsHpafInputStdAlnRep1.bam HPAF ChipSeq Input Alignments 1 bam UW Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeUwTfbs/wgEncodeUwTfbsHpafInputStdRawRep1.bigWig HPAF ChipSeq Input RawSignal 1 bigWig UW Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeUwTfbs/wgEncodeUwTfbsHpfCtcfStdAlnRep1.bam HPF ChipSeq CTCF Alignments 1 bam UW Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeUwTfbs/wgEncodeUwTfbsHpfCtcfStdAlnRep2.bam HPF ChipSeq CTCF Alignments 2 bam UW Data 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http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeUwTfbs/wgEncodeUwTfbsHpfInputStdAlnRep1.bam HPF ChipSeq Input Alignments 1 bam UW Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeUwTfbs/wgEncodeUwTfbsHpfInputStdRawRep1.bigWig HPF ChipSeq Input RawSignal 1 bigWig UW Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeUwTfbs/wgEncodeUwTfbsHreCtcfStdAlnRep1.bam HRE ChipSeq CTCF Alignments 1 bam UW Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeUwTfbs/wgEncodeUwTfbsHreCtcfStdAlnRep2.bam HRE ChipSeq CTCF Alignments 2 bam UW Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeUwTfbs/wgEncodeUwTfbsHreCtcfStdHotspotsRep1.broadPeak.gz HRE ChipSeq CTCF Hotspots 1 broadPeak UW Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeUwTfbs/wgEncodeUwTfbsHreCtcfStdHotspotsRep2.broadPeak.gz HRE ChipSeq CTCF Hotspots 2 broadPeak UW Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeUwTfbs/wgEncodeUwTfbsHreCtcfStdPkRep1.narrowPeak.gz HRE ChipSeq CTCF Peaks 1 narrowPeak UW Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeUwTfbs/wgEncodeUwTfbsHreCtcfStdPkRep2.narrowPeak.gz HRE ChipSeq CTCF Peaks 2 narrowPeak UW Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeUwTfbs/wgEncodeUwTfbsHreCtcfStdRawRep1.bigWig HRE ChipSeq CTCF RawSignal 1 bigWig UW Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeUwTfbs/wgEncodeUwTfbsHreCtcfStdRawRep2.bigWig HRE ChipSeq CTCF RawSignal 2 bigWig UW Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeUwTfbs/wgEncodeUwTfbsHreInputStdAlnRep1.bam HRE ChipSeq Input Alignments 1 bam UW Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeUwTfbs/wgEncodeUwTfbsHreInputStdRawRep1.bigWig HRE ChipSeq Input RawSignal 1 bigWig UW Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeUwTfbs/wgEncodeUwTfbsHrpeCtcfStdAlnRep1.bam HRPEpiC ChipSeq CTCF Alignments 1 bam UW Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeUwTfbs/wgEncodeUwTfbsHrpeCtcfStdAlnRep2.bam HRPEpiC ChipSeq CTCF Alignments 2 bam UW Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeUwTfbs/wgEncodeUwTfbsHrpeCtcfStdHotspotsRep1.broadPeak.gz HRPEpiC ChipSeq CTCF Hotspots 1 broadPeak UW Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeUwTfbs/wgEncodeUwTfbsHrpeCtcfStdHotspotsRep2.broadPeak.gz HRPEpiC ChipSeq CTCF Hotspots 2 broadPeak UW Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeUwTfbs/wgEncodeUwTfbsHrpeCtcfStdPkRep1.narrowPeak.gz HRPEpiC ChipSeq CTCF Peaks 1 narrowPeak UW Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeUwTfbs/wgEncodeUwTfbsHrpeCtcfStdPkRep2.narrowPeak.gz HRPEpiC ChipSeq CTCF Peaks 2 narrowPeak UW Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeUwTfbs/wgEncodeUwTfbsHrpeCtcfStdRawRep1.bigWig HRPEpiC ChipSeq CTCF RawSignal 1 bigWig UW Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeUwTfbs/wgEncodeUwTfbsHrpeCtcfStdRawRep2.bigWig HRPEpiC ChipSeq CTCF RawSignal 2 bigWig UW Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeUwTfbs/wgEncodeUwTfbsHrpeInputStdAlnRep1.bam HRPEpiC ChipSeq Input Alignments 1 bam UW Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeUwTfbs/wgEncodeUwTfbsHrpeInputStdRawRep1.bigWig HRPEpiC ChipSeq Input RawSignal 1 bigWig UW Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeUwTfbs/wgEncodeUwTfbsHuvecCtcfStdAlnRep1.bam HUVEC ChipSeq CTCF Alignments 1 bam UW Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeUwTfbs/wgEncodeUwTfbsHuvecCtcfStdAlnRep2.bam HUVEC ChipSeq CTCF Alignments 2 bam UW Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeUwTfbs/wgEncodeUwTfbsHuvecCtcfStdHotspotsRep1.broadPeak.gz HUVEC ChipSeq CTCF Hotspots 1 broadPeak UW Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeUwTfbs/wgEncodeUwTfbsHuvecCtcfStdHotspotsRep2.broadPeak.gz HUVEC ChipSeq CTCF Hotspots 2 broadPeak UW Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeUwTfbs/wgEncodeUwTfbsHuvecCtcfStdPkRep1.narrowPeak.gz HUVEC ChipSeq CTCF Peaks 1 narrowPeak UW Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeUwTfbs/wgEncodeUwTfbsHuvecCtcfStdPkRep2.narrowPeak.gz HUVEC ChipSeq CTCF Peaks 2 narrowPeak UW Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeUwTfbs/wgEncodeUwTfbsHuvecCtcfStdRawRep1.bigWig HUVEC ChipSeq CTCF RawSignal 1 bigWig UW Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeUwTfbs/wgEncodeUwTfbsHuvecCtcfStdRawRep2.bigWig HUVEC ChipSeq CTCF RawSignal 2 bigWig UW Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeUwTfbs/wgEncodeUwTfbsHuvecInputStdAlnRep1.bam HUVEC ChipSeq Input Alignments 1 bam UW Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeUwTfbs/wgEncodeUwTfbsHuvecInputStdRawRep1.bigWig HUVEC ChipSeq Input RawSignal 1 bigWig UW Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeUwTfbs/wgEncodeUwTfbsHvmfCtcfStdAlnRep1.bam HVMF ChipSeq CTCF Alignments 1 bam UW Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeUwTfbs/wgEncodeUwTfbsHvmfCtcfStdAlnRep2.bam HVMF ChipSeq CTCF Alignments 2 bam UW Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeUwTfbs/wgEncodeUwTfbsHvmfCtcfStdHotspotsRep1.broadPeak.gz HVMF ChipSeq CTCF Hotspots 1 broadPeak UW Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeUwTfbs/wgEncodeUwTfbsHvmfCtcfStdHotspotsRep2.broadPeak.gz HVMF ChipSeq CTCF Hotspots 2 broadPeak UW Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeUwTfbs/wgEncodeUwTfbsHvmfCtcfStdPkRep1.narrowPeak.gz HVMF ChipSeq CTCF Peaks 1 narrowPeak UW Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeUwTfbs/wgEncodeUwTfbsHvmfCtcfStdPkRep2.narrowPeak.gz HVMF ChipSeq CTCF Peaks 2 narrowPeak UW Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeUwTfbs/wgEncodeUwTfbsHvmfCtcfStdRawRep1.bigWig HVMF ChipSeq CTCF RawSignal 1 bigWig UW Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeUwTfbs/wgEncodeUwTfbsHvmfCtcfStdRawRep2.bigWig HVMF ChipSeq CTCF RawSignal 2 bigWig UW Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeUwTfbs/wgEncodeUwTfbsHvmfInputStdAlnRep1.bam HVMF ChipSeq Input Alignments 1 bam UW Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeUwTfbs/wgEncodeUwTfbsHvmfInputStdRawRep1.bigWig HVMF ChipSeq Input RawSignal 1 bigWig UW Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeUwTfbs/wgEncodeUwTfbsJurkatInputStdAlnRep1.bam Jurkat ChipSeq Input Alignments 1 bam UW Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeUwTfbs/wgEncodeUwTfbsJurkatInputStdRawRep1.bigWig Jurkat ChipSeq Input RawSignal 1 bigWig UW Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeUwTfbs/wgEncodeUwTfbsK562CtcfStdAlnRep1.bam K562 ChipSeq CTCF Alignments 1 bam UW Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeUwTfbs/wgEncodeUwTfbsK562CtcfStdAlnRep2.bam K562 ChipSeq CTCF Alignments 2 bam UW Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeUwTfbs/wgEncodeUwTfbsK562CtcfStdHotspotsRep1.broadPeak.gz K562 ChipSeq CTCF Hotspots 1 broadPeak UW Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeUwTfbs/wgEncodeUwTfbsK562CtcfStdHotspotsRep2.broadPeak.gz K562 ChipSeq CTCF Hotspots 2 broadPeak UW Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeUwTfbs/wgEncodeUwTfbsK562CtcfStdPkRep1.narrowPeak.gz K562 ChipSeq CTCF Peaks 1 narrowPeak UW Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeUwTfbs/wgEncodeUwTfbsK562CtcfStdPkRep2.narrowPeak.gz K562 ChipSeq CTCF Peaks 2 narrowPeak UW Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeUwTfbs/wgEncodeUwTfbsK562CtcfStdRawRep1.bigWig K562 ChipSeq CTCF RawSignal 1 bigWig UW Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeUwTfbs/wgEncodeUwTfbsK562CtcfStdRawRep2.bigWig K562 ChipSeq CTCF RawSignal 2 bigWig UW Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeUwTfbs/wgEncodeUwTfbsK562InputStdAlnRep1.bam K562 ChipSeq Input Alignments 1 bam UW Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeUwTfbs/wgEncodeUwTfbsK562InputStdRawRep1.bigWig K562 ChipSeq Input RawSignal 1 bigWig UW Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeUwTfbs/wgEncodeUwTfbsLncapInputStdAlnRep1.bam LNCaP ChipSeq Input Alignments 1 bam UW Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeUwTfbs/wgEncodeUwTfbsLncapInputStdRawRep1.bigWig LNCaP ChipSeq Input RawSignal 1 bigWig UW Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeUwTfbs/wgEncodeUwTfbsMcf7CtcfStdAlnRep1.bam MCF-7 ChipSeq CTCF Alignments 1 bam UW Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeUwTfbs/wgEncodeUwTfbsMcf7CtcfStdAlnRep2.bam MCF-7 ChipSeq CTCF Alignments 2 bam UW Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeUwTfbs/wgEncodeUwTfbsMcf7CtcfStdHotspotsRep1.broadPeak.gz MCF-7 ChipSeq CTCF Hotspots 1 broadPeak UW Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeUwTfbs/wgEncodeUwTfbsMcf7CtcfStdHotspotsRep2.broadPeak.gz MCF-7 ChipSeq CTCF Hotspots 2 broadPeak UW Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeUwTfbs/wgEncodeUwTfbsMcf7CtcfStdPkRep1.narrowPeak.gz MCF-7 ChipSeq CTCF Peaks 1 narrowPeak UW Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeUwTfbs/wgEncodeUwTfbsMcf7CtcfStdPkRep2.narrowPeak.gz MCF-7 ChipSeq CTCF Peaks 2 narrowPeak UW Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeUwTfbs/wgEncodeUwTfbsMcf7CtcfStdRawRep1.bigWig MCF-7 ChipSeq CTCF RawSignal 1 bigWig UW Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeUwTfbs/wgEncodeUwTfbsMcf7CtcfStdRawRep2.bigWig MCF-7 ChipSeq CTCF RawSignal 2 bigWig UW Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeUwTfbs/wgEncodeUwTfbsMcf7InputStdAlnRep1.bam MCF-7 ChipSeq Input Alignments 1 bam UW Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeUwTfbs/wgEncodeUwTfbsMcf7InputStdRawRep1.bigWig MCF-7 ChipSeq Input RawSignal 1 bigWig UW Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeUwTfbs/wgEncodeUwTfbsMonocd14ro1746InputStdAlnRep1.bam Monocytes-CD14+_RO01746 ChipSeq Input Alignments 1 bam UW Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeUwTfbs/wgEncodeUwTfbsMonocd14ro1746InputStdRawRep1.bigWig Monocytes-CD14+_RO01746 ChipSeq Input RawSignal 1 bigWig UW Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeUwTfbs/wgEncodeUwTfbsNb4CtcfStdAlnRep1.bam NB4 ChipSeq CTCF Alignments 1 bam UW Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeUwTfbs/wgEncodeUwTfbsNb4CtcfStdHotspotsRep1.broadPeak.gz NB4 ChipSeq CTCF Hotspots 1 broadPeak UW Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeUwTfbs/wgEncodeUwTfbsNb4CtcfStdPkRep1.narrowPeak.gz NB4 ChipSeq CTCF Peaks 1 narrowPeak UW Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeUwTfbs/wgEncodeUwTfbsNb4CtcfStdRawRep1.bigWig NB4 ChipSeq CTCF RawSignal 1 bigWig UW Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeUwTfbs/wgEncodeUwTfbsNb4InputStdAlnRep1.bam NB4 ChipSeq Input Alignments 1 bam UW Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeUwTfbs/wgEncodeUwTfbsNb4InputStdRawRep1.bigWig NB4 ChipSeq Input RawSignal 1 bigWig UW Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeUwTfbs/wgEncodeUwTfbsNhdfneoCtcfStdAlnRep1.bam NHDF-neo ChipSeq CTCF Alignments 1 bam UW Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeUwTfbs/wgEncodeUwTfbsNhdfneoCtcfStdAlnRep2.bam NHDF-neo ChipSeq CTCF Alignments 2 bam UW Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeUwTfbs/wgEncodeUwTfbsNhdfneoCtcfStdHotspotsRep1.broadPeak.gz NHDF-neo ChipSeq CTCF Hotspots 1 broadPeak UW Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeUwTfbs/wgEncodeUwTfbsNhdfneoCtcfStdHotspotsRep2.broadPeak.gz NHDF-neo ChipSeq CTCF Hotspots 2 broadPeak UW Data 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http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeUwTfbs/wgEncodeUwTfbsWi38InputStdAlnRep1.bam WI-38 ChipSeq Input Alignments 1 bam UW Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeUwTfbs/wgEncodeUwTfbsWi38InputStdRawRep1.bigWig WI-38 ChipSeq Input RawSignal 1 bigWig UW Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeAffyRnaChip/wgEncodeAffyRnaChipFiltTransfragsGm12878CellTotal.broadPeak.gz GM12878 RnaChip CellTotal FiltTransfrags broadPeak Affy Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeAffyRnaChip/wgEncodeAffyRnaChipFiltTransfragsGm12878CytosolLongnonpolya.broadPeak.gz GM12878 RnaChip Longnonpolya FiltTransfrags broadPeak Affy Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeAffyRnaChip/wgEncodeAffyRnaChipFiltTransfragsGm12878CytosolLongpolya.broadPeak.gz GM12878 RnaChip Longpolya FiltTransfrags broadPeak Affy Data 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RnaChip Longpolya FiltTransfrags broadPeak Affy Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeAffyRnaChip/wgEncodeAffyRnaChipFiltTransfragsHepg2NucleolusTotal.broadPeak.gz HepG2 RnaChip NucleolusTotal FiltTransfrags broadPeak Affy Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeAffyRnaChip/wgEncodeAffyRnaChipFiltTransfragsHepg2NucleusLongnonpolya.broadPeak.gz HepG2 RnaChip Longnonpolya FiltTransfrags broadPeak Affy Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeAffyRnaChip/wgEncodeAffyRnaChipFiltTransfragsHepg2NucleusLongpolya.broadPeak.gz HepG2 RnaChip Longpolya FiltTransfrags broadPeak Affy Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeAffyRnaChip/wgEncodeAffyRnaChipFiltTransfragsK562CellTotal.broadPeak.gz K562 RnaChip CellTotal FiltTransfrags broadPeak Affy Data 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FiltTransfrags broadPeak Affy Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeAffyRnaChip/wgEncodeAffyRnaChipFiltTransfragsK562NucleusLongnonpolya.broadPeak.gz K562 RnaChip Longnonpolya FiltTransfrags broadPeak Affy Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeAffyRnaChip/wgEncodeAffyRnaChipFiltTransfragsK562NucleusLongpolya.broadPeak.gz K562 RnaChip Longpolya FiltTransfrags broadPeak Affy Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeAffyRnaChip/wgEncodeAffyRnaChipFiltTransfragsK562PolysomeLongnonpolya.broadPeak.gz K562 RnaChip Longnonpolya FiltTransfrags broadPeak Affy Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeAffyRnaChip/wgEncodeAffyRnaChipFiltTransfragsKeratinocyteCytosolLongnonpolya.broadPeak.gz NHEK RnaChip Longnonpolya FiltTransfrags broadPeak Affy Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeAffyRnaChip/wgEncodeAffyRnaChipFiltTransfragsKeratinocyteCytosolLongpolya.broadPeak.gz NHEK RnaChip Longpolya FiltTransfrags broadPeak Affy Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeAffyRnaChip/wgEncodeAffyRnaChipFiltTransfragsKeratinocyteNucleusLongnonpolya.broadPeak.gz NHEK RnaChip Longnonpolya FiltTransfrags broadPeak Affy Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeAffyRnaChip/wgEncodeAffyRnaChipFiltTransfragsKeratinocyteNucleusLongpolya.broadPeak.gz NHEK RnaChip Longpolya FiltTransfrags broadPeak Affy Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeAffyRnaChip/wgEncodeAffyRnaChipFiltTransfragsProstateCellLongnonpolya.broadPeak.gz prostate RnaChip Longnonpolya FiltTransfrags broadPeak Affy Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeAffyRnaChip/wgEncodeAffyRnaChipFiltTransfragsProstateCellLongpolya.broadPeak.gz prostate RnaChip Longpolya FiltTransfrags broadPeak Affy Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeAffyRnaChip/wgEncodeAffyRnaChipTransfragsGm12878CellTotal.broadPeak.gz GM12878 RnaChip CellTotal Transfrags broadPeak Affy Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeAffyRnaChip/wgEncodeAffyRnaChipTransfragsGm12878CytosolLongnonpolya.broadPeak.gz GM12878 RnaChip Longnonpolya Transfrags broadPeak Affy Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeAffyRnaChip/wgEncodeAffyRnaChipTransfragsGm12878CytosolLongpolya.broadPeak.gz GM12878 RnaChip Longpolya Transfrags broadPeak Affy Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeAffyRnaChip/wgEncodeAffyRnaChipTransfragsGm12878NucleolusTotal.broadPeak.gz GM12878 RnaChip NucleolusTotal Transfrags broadPeak Affy Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeAffyRnaChip/wgEncodeAffyRnaChipTransfragsGm12878NucleusLongnonpolya.broadPeak.gz GM12878 RnaChip Longnonpolya Transfrags broadPeak Affy Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeAffyRnaChip/wgEncodeAffyRnaChipTransfragsGm12878NucleusLongpolya.broadPeak.gz GM12878 RnaChip Longpolya Transfrags broadPeak Affy Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeAffyRnaChip/wgEncodeAffyRnaChipTransfragsHepg2CytosolLongnonpolya.broadPeak.gz HepG2 RnaChip Longnonpolya Transfrags broadPeak Affy Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeAffyRnaChip/wgEncodeAffyRnaChipTransfragsHepg2CytosolLongpolya.broadPeak.gz HepG2 RnaChip Longpolya Transfrags broadPeak Affy Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeAffyRnaChip/wgEncodeAffyRnaChipTransfragsHepg2NucleolusTotal.broadPeak.gz HepG2 RnaChip NucleolusTotal Transfrags broadPeak Affy Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeAffyRnaChip/wgEncodeAffyRnaChipTransfragsHepg2NucleusLongnonpolya.broadPeak.gz HepG2 RnaChip Longnonpolya Transfrags broadPeak Affy Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeAffyRnaChip/wgEncodeAffyRnaChipTransfragsHepg2NucleusLongpolya.broadPeak.gz HepG2 RnaChip Longpolya Transfrags broadPeak Affy Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeAffyRnaChip/wgEncodeAffyRnaChipTransfragsK562CellTotal.broadPeak.gz K562 RnaChip CellTotal Transfrags broadPeak Affy Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeAffyRnaChip/wgEncodeAffyRnaChipTransfragsK562ChromatinTotal.broadPeak.gz K562 RnaChip ChromatinTotal Transfrags broadPeak Affy Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeAffyRnaChip/wgEncodeAffyRnaChipTransfragsK562CytosolLongnonpolya.broadPeak.gz K562 RnaChip Longnonpolya Transfrags broadPeak Affy Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeAffyRnaChip/wgEncodeAffyRnaChipTransfragsK562CytosolLongpolya.broadPeak.gz K562 RnaChip Longpolya Transfrags broadPeak Affy Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeAffyRnaChip/wgEncodeAffyRnaChipTransfragsK562NucleolusTotal.broadPeak.gz K562 RnaChip NucleolusTotal Transfrags broadPeak Affy Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeAffyRnaChip/wgEncodeAffyRnaChipTransfragsK562NucleoplasmTotal.broadPeak.gz K562 RnaChip NucleoplasmTotal Transfrags broadPeak Affy Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeAffyRnaChip/wgEncodeAffyRnaChipTransfragsK562NucleusLongnonpolya.broadPeak.gz K562 RnaChip Longnonpolya Transfrags broadPeak Affy Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeAffyRnaChip/wgEncodeAffyRnaChipTransfragsK562NucleusLongpolya.broadPeak.gz K562 RnaChip Longpolya Transfrags broadPeak Affy Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeAffyRnaChip/wgEncodeAffyRnaChipTransfragsK562PolysomeLongnonpolya.broadPeak.gz K562 RnaChip Longnonpolya Transfrags broadPeak Affy Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeAffyRnaChip/wgEncodeAffyRnaChipTransfragsKeratinocyteCytosolLongnonpolya.broadPeak.gz NHEK RnaChip Longnonpolya Transfrags broadPeak Affy Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeAffyRnaChip/wgEncodeAffyRnaChipTransfragsKeratinocyteCytosolLongpolya.broadPeak.gz NHEK RnaChip Longpolya Transfrags broadPeak Affy Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeAffyRnaChip/wgEncodeAffyRnaChipTransfragsKeratinocyteNucleusLongnonpolya.broadPeak.gz NHEK RnaChip Longnonpolya Transfrags broadPeak Affy Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeAffyRnaChip/wgEncodeAffyRnaChipTransfragsKeratinocyteNucleusLongpolya.broadPeak.gz NHEK RnaChip Longpolya Transfrags broadPeak Affy Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeAffyRnaChip/wgEncodeAffyRnaChipTransfragsProstateCellLongnonpolya.broadPeak.gz prostate RnaChip Longnonpolya Transfrags broadPeak Affy Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeAffyRnaChip/wgEncodeAffyRnaChipTransfragsProstateCellLongpolya.broadPeak.gz prostate RnaChip Longpolya Transfrags broadPeak Affy Data http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/openchrom/jan2011/fdrPeaks/wgEncodeDukeDnase8988T.fdr01peaks.hg19.bb 8988T DnaseSeq Peaks bigBed Duke analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/openchrom/jan2011/fdrPeaks/wgEncodeDukeDnaseAoSMC.fdr01peaks.hg19.bb AoSMC DnaseSeq Peaks bigBed Duke analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/openchrom/jan2011/fdrPeaks/wgEncodeDukeDnaseChorion.fdr01peaks.hg19.bb Chorion DnaseSeq Peaks bigBed Duke analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/openchrom/jan2011/fdrPeaks/wgEncodeDukeDnaseCLL.fdr01peaks.hg19.bb CLL DnaseSeq Peaks bigBed Duke analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/openchrom/jan2011/fdrPeaks/wgEncodeDukeDnaseFibrobl.fdr01peaks.hg19.bb Fibrobl DnaseSeq Peaks bigBed Duke analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/openchrom/jan2011/fdrPeaks/wgEncodeDukeDnaseFibroP.fdr01peaks.hg19.bb FibroP DnaseSeq Peaks bigBed Duke analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/openchrom/jan2011/fdrPeaks/wgEncodeDukeDnaseGliobla.fdr01peaks.hg19.bb Gliobla DnaseSeq Peaks bigBed Duke analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/openchrom/jan2011/fdrPeaks/wgEncodeDukeDnaseGM12891.fdr01peaks.hg19.bb GM12891 DnaseSeq Peaks bigBed Duke analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/openchrom/jan2011/fdrPeaks/wgEncodeDukeDnaseGM12892.fdr01peaks.hg19.bb GM12892 DnaseSeq Peaks bigBed Duke analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/openchrom/jan2011/fdrPeaks/wgEncodeDukeDnaseGM18507.fdr01peaks.hg19.bb GM18507 DnaseSeq Peaks bigBed Duke analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/openchrom/jan2011/fdrPeaks/wgEncodeDukeDnaseGM19238.fdr01peaks.hg19.bb GM19238 DnaseSeq Peaks bigBed Duke analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/openchrom/jan2011/fdrPeaks/wgEncodeDukeDnaseGM19239.fdr01peaks.hg19.bb GM19239 DnaseSeq Peaks bigBed Duke analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/openchrom/jan2011/fdrPeaks/wgEncodeDukeDnaseGM19240.fdr01peaks.hg19.bb GM19240 DnaseSeq Peaks bigBed Duke analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/openchrom/jan2011/fdrPeaks/wgEncodeDukeDnaseH9ES.fdr01peaks.hg19.bb H9ES DnaseSeq Peaks bigBed Duke analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/openchrom/jan2011/fdrPeaks/wgEncodeDukeDnaseHeLaS3IFNa4h.fdr01peaks.hg19.bb HeLa-S3 DnaseSeq Peaks bigBed Duke analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/openchrom/jan2011/fdrPeaks/wgEncodeDukeDnaseHepatocytes.fdr01peaks.hg19.bb Hepatocytes DnaseSeq Peaks bigBed Duke analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/openchrom/jan2011/fdrPeaks/wgEncodeDukeDnaseHPDE6E6E7.fdr01peaks.hg19.bb HPDE6-E6E7 DnaseSeq Peaks bigBed Duke analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/openchrom/jan2011/fdrPeaks/wgEncodeDukeDnaseHSMMemb.fdr01peaks.hg19.bb HSMM_emb DnaseSeq Peaks bigBed Duke analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/openchrom/jan2011/fdrPeaks/wgEncodeDukeDnaseHTR8svn.fdr01peaks.hg19.bb HTR8svn DnaseSeq Peaks bigBed Duke analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/openchrom/jan2011/fdrPeaks/wgEncodeDukeDnaseHuh7.5.fdr01peaks.hg19.bb Huh-7.5 DnaseSeq Peaks bigBed Duke analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/openchrom/jan2011/fdrPeaks/wgEncodeDukeDnaseHuh7.fdr01peaks.hg19.bb Huh-7 DnaseSeq Peaks bigBed Duke analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/openchrom/jan2011/fdrPeaks/wgEncodeDukeDnaseiPS.fdr01peaks.hg19.bb iPS DnaseSeq Peaks bigBed Duke analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/openchrom/jan2011/fdrPeaks/wgEncodeDukeDnaseIshikawaEstradiol.fdr01peaks.hg19.bb Ishikawa DnaseSeq Peaks bigBed Duke analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/openchrom/jan2011/fdrPeaks/wgEncodeDukeDnaseIshikawaTamoxifen.fdr01peaks.hg19.bb Ishikawa DnaseSeq Peaks bigBed Duke analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/openchrom/jan2011/fdrPeaks/wgEncodeDukeDnaseLNCaPAndrogen.fdr01peaks.hg19.bb LNCaP DnaseSeq Peaks bigBed Duke analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/openchrom/jan2011/fdrPeaks/wgEncodeDukeDnaseMCF7Hypoxia.fdr01peaks.hg19.bb MCF-7 DnaseSeq Peaks bigBed Duke analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/openchrom/jan2011/fdrPeaks/wgEncodeDukeDnaseMedullo.fdr01peaks.hg19.bb Medullo DnaseSeq Peaks bigBed Duke analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/openchrom/jan2011/fdrPeaks/wgEncodeDukeDnaseMelano.fdr01peaks.hg19.bb Melano DnaseSeq Peaks bigBed Duke analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/openchrom/jan2011/fdrPeaks/wgEncodeDukeDnaseMyometr.fdr01peaks.hg19.bb Myometr DnaseSeq Peaks bigBed Duke analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/openchrom/jan2011/fdrPeaks/wgEncodeDukeDnaseOsteobl.fdr01peaks.hg19.bb Osteobl DnaseSeq Peaks bigBed Duke analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/openchrom/jan2011/fdrPeaks/wgEncodeDukeDnasePanIsletD.fdr01peaks.hg19.bb PanIsletD DnaseSeq Peaks bigBed Duke analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/openchrom/jan2011/fdrPeaks/wgEncodeDukeDnasePanIslets.fdr01peaks.hg19.bb PanIslets DnaseSeq Peaks bigBed Duke analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/openchrom/jan2011/fdrPeaks/wgEncodeDukeDnasepHTE.fdr01peaks.hg19.bb pHTE DnaseSeq Peaks bigBed Duke analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/openchrom/jan2011/fdrPeaks/wgEncodeDukeDnaseProgFib.fdr01peaks.hg19.bb ProgFib DnaseSeq Peaks bigBed Duke analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/openchrom/jan2011/fdrPeaks/wgEncodeDukeDnaseRWPE1.fdr01peaks.hg19.bb RWPE1 DnaseSeq Peaks bigBed Duke analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/openchrom/jan2011/fdrPeaks/wgEncodeDukeDnaseStellate.fdr01peaks.hg19.bb Stellate DnaseSeq Peaks bigBed Duke analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/openchrom/jan2011/fdrPeaks/wgEncodeDukeDnaseT47D.fdr01peaks.hg19.bb T-47D DnaseSeq Peaks bigBed Duke analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/openchrom/jan2011/fdrPeaks/wgEncodeDukeDnaseTh0.fdr01peaks.hg19.bb Th0 DnaseSeq Peaks bigBed Duke analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/openchrom/jan2011/fdrPeaks/wgEncodeDukeDnaseUrothelia.fdr01peaks.hg19.bb Urothelia DnaseSeq Peaks bigBed Duke analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/openchrom/jan2011/fdrPeaks/wgEncodeDukeDnaseUrotheliaUT189.fdr01peaks.hg19.bb Urothelia DnaseSeq Peaks bigBed Duke analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/openchrom/jan2011/fdrPeaks/wgEncodeUwDnaseAG04449.fdr01peaks.hg19.bb AG04449 DnaseSeq Peaks bigBed UW analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/openchrom/jan2011/fdrPeaks/wgEncodeUwDnaseAG04450.fdr01peaks.hg19.bb AG04450 DnaseSeq Peaks bigBed UW analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/openchrom/jan2011/fdrPeaks/wgEncodeUwDnaseAG09309.fdr01peaks.hg19.bb AG09309 DnaseSeq Peaks bigBed UW analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/openchrom/jan2011/fdrPeaks/wgEncodeUwDnaseAG09319.fdr01peaks.hg19.bb AG09319 DnaseSeq Peaks bigBed UW analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/openchrom/jan2011/fdrPeaks/wgEncodeUwDnaseAG10803.fdr01peaks.hg19.bb AG10803 DnaseSeq Peaks bigBed UW analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/openchrom/jan2011/fdrPeaks/wgEncodeUwDnaseAoAF.fdr01peaks.hg19.bb AoAF DnaseSeq Peaks bigBed UW analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/openchrom/jan2011/fdrPeaks/wgEncodeUwDnaseBE2C.fdr01peaks.hg19.bb BE2_C DnaseSeq Peaks bigBed UW analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/openchrom/jan2011/fdrPeaks/wgEncodeUwDnaseBJ.fdr01peaks.hg19.bb BJ DnaseSeq Peaks bigBed UW analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/openchrom/jan2011/fdrPeaks/wgEncodeUwDnaseCaco2.fdr01peaks.hg19.bb Caco-2 DnaseSeq Peaks bigBed UW analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/openchrom/jan2011/fdrPeaks/wgEncodeUwDnaseCD20.fdr01peaks.hg19.bb CD20+ DnaseSeq Peaks bigBed UW analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/openchrom/jan2011/fdrPeaks/wgEncodeUwDnaseCD34Mobilized.fdr01peaks.hg19.bb CD34+_Mobilized DnaseSeq Peaks bigBed UW analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/openchrom/jan2011/fdrPeaks/wgEncodeUwDnaseCMK.fdr01peaks.hg19.bb CMK DnaseSeq Peaks bigBed UW analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/openchrom/jan2011/fdrPeaks/wgEncodeUwDnaseGM06990.fdr01peaks.hg19.bb GM06990 DnaseSeq Peaks bigBed UW analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/openchrom/jan2011/fdrPeaks/wgEncodeUwDnaseGM12864.fdr01peaks.hg19.bb GM12864 DnaseSeq Peaks bigBed UW analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/openchrom/jan2011/fdrPeaks/wgEncodeUwDnaseGM12865.fdr01peaks.hg19.bb GM12865 DnaseSeq Peaks bigBed UW analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/openchrom/jan2011/fdrPeaks/wgEncodeUwDnaseH7hESC.fdr01peaks.hg19.bb H7-hESC DnaseSeq Peaks bigBed UW analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/openchrom/jan2011/fdrPeaks/wgEncodeUwDnaseHAc.fdr01peaks.hg19.bb HAc DnaseSeq Peaks bigBed UW analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/openchrom/jan2011/fdrPeaks/wgEncodeUwDnaseHAEpiC.fdr01peaks.hg19.bb HAEpiC DnaseSeq Peaks bigBed UW analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/openchrom/jan2011/fdrPeaks/wgEncodeUwDnaseHAh.fdr01peaks.hg19.bb HA-h DnaseSeq Peaks bigBed UW analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/openchrom/jan2011/fdrPeaks/wgEncodeUwDnaseHAsp.fdr01peaks.hg19.bb HA-sp DnaseSeq Peaks bigBed UW analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/openchrom/jan2011/fdrPeaks/wgEncodeUwDnaseHBMEC.fdr01peaks.hg19.bb HBMEC DnaseSeq Peaks bigBed UW analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/openchrom/jan2011/fdrPeaks/wgEncodeUwDnaseHCFaa.fdr01peaks.hg19.bb HCFaa DnaseSeq Peaks bigBed UW analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/openchrom/jan2011/fdrPeaks/wgEncodeUwDnaseHCF.fdr01peaks.hg19.bb HCF DnaseSeq Peaks bigBed UW analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/openchrom/jan2011/fdrPeaks/wgEncodeUwDnaseHCM.fdr01peaks.hg19.bb HCM DnaseSeq Peaks bigBed UW analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/openchrom/jan2011/fdrPeaks/wgEncodeUwDnaseHConF.fdr01peaks.hg19.bb HConF DnaseSeq Peaks bigBed UW analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/openchrom/jan2011/fdrPeaks/wgEncodeUwDnaseHCPEpiC.fdr01peaks.hg19.bb HCPEpiC DnaseSeq Peaks bigBed UW analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/openchrom/jan2011/fdrPeaks/wgEncodeUwDnaseHCT116.fdr01peaks.hg19.bb HCT-116 DnaseSeq Peaks bigBed UW analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/openchrom/jan2011/fdrPeaks/wgEncodeUwDnaseHEEpiC.fdr01peaks.hg19.bb HEEpiC DnaseSeq Peaks bigBed UW analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/openchrom/jan2011/fdrPeaks/wgEncodeUwDnaseHFF.fdr01peaks.hg19.bb HFF DnaseSeq Peaks bigBed UW analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/openchrom/jan2011/fdrPeaks/wgEncodeUwDnaseHFFMyc.fdr01peaks.hg19.bb HFF-Myc DnaseSeq Peaks bigBed UW analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/openchrom/jan2011/fdrPeaks/wgEncodeUwDnaseHGF.fdr01peaks.hg19.bb HGF DnaseSeq Peaks bigBed UW analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/openchrom/jan2011/fdrPeaks/wgEncodeUwDnaseHIPEpiC.fdr01peaks.hg19.bb HIPEpiC DnaseSeq Peaks bigBed UW analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/openchrom/jan2011/fdrPeaks/wgEncodeUwDnaseHL60.fdr01peaks.hg19.bb HL-60 DnaseSeq Peaks bigBed UW analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/openchrom/jan2011/fdrPeaks/wgEncodeUwDnaseHMF.fdr01peaks.hg19.bb HMF DnaseSeq Peaks bigBed UW analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/openchrom/jan2011/fdrPeaks/wgEncodeUwDnaseHMVECdAd.fdr01peaks.hg19.bb HMVEC-dAd DnaseSeq Peaks bigBed UW analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/openchrom/jan2011/fdrPeaks/wgEncodeUwDnaseHMVECdBlAd.fdr01peaks.hg19.bb HMVEC-dBl-Ad DnaseSeq Peaks bigBed UW analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/openchrom/jan2011/fdrPeaks/wgEncodeUwDnaseHMVECdBlNeo.fdr01peaks.hg19.bb HMVEC-dBl-Neo DnaseSeq Peaks bigBed UW analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/openchrom/jan2011/fdrPeaks/wgEncodeUwDnaseHMVECdLyAd.fdr01peaks.hg19.bb HMVEC-dLy-Ad DnaseSeq Peaks bigBed UW analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/openchrom/jan2011/fdrPeaks/wgEncodeUwDnaseHMVECdLyNeo.fdr01peaks.hg19.bb HMVEC-dLy-Neo DnaseSeq Peaks bigBed UW analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/openchrom/jan2011/fdrPeaks/wgEncodeUwDnaseHMVECdNeo.fdr01peaks.hg19.bb HMVEC-dNeo DnaseSeq Peaks bigBed UW analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/openchrom/jan2011/fdrPeaks/wgEncodeUwDnaseHMVECLBl.fdr01peaks.hg19.bb HMVEC-LBl DnaseSeq Peaks bigBed UW analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/openchrom/jan2011/fdrPeaks/wgEncodeUwDnaseHMVECLLy.fdr01peaks.hg19.bb HMVEC-LLy DnaseSeq Peaks bigBed UW analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/openchrom/jan2011/fdrPeaks/wgEncodeUwDnaseHNPCEpiC.fdr01peaks.hg19.bb HNPCEpiC DnaseSeq Peaks bigBed UW analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/openchrom/jan2011/fdrPeaks/wgEncodeUwDnaseHPAEC.fdr01peaks.hg19.bb HPAEC DnaseSeq Peaks bigBed UW analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/openchrom/jan2011/fdrPeaks/wgEncodeUwDnaseHPAF.fdr01peaks.hg19.bb HPAF DnaseSeq Peaks bigBed UW analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/openchrom/jan2011/fdrPeaks/wgEncodeUwDnaseHPdLF.fdr01peaks.hg19.bb HPdLF DnaseSeq Peaks bigBed UW analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/openchrom/jan2011/fdrPeaks/wgEncodeUwDnaseHPF.fdr01peaks.hg19.bb HPF DnaseSeq Peaks bigBed UW analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/openchrom/jan2011/fdrPeaks/wgEncodeUwDnaseHRCEpiC.fdr01peaks.hg19.bb HRCEpiC DnaseSeq Peaks bigBed UW analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/openchrom/jan2011/fdrPeaks/wgEncodeUwDnaseHRE.fdr01peaks.hg19.bb HRE DnaseSeq Peaks bigBed UW analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/openchrom/jan2011/fdrPeaks/wgEncodeUwDnaseHRGEC.fdr01peaks.hg19.bb HRGEC DnaseSeq Peaks bigBed UW analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/openchrom/jan2011/fdrPeaks/wgEncodeUwDnaseHRPEpiC.fdr01peaks.hg19.bb HRPEpiC DnaseSeq Peaks bigBed UW analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/openchrom/jan2011/fdrPeaks/wgEncodeUwDnaseHVMF.fdr01peaks.hg19.bb HVMF DnaseSeq Peaks bigBed UW analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/openchrom/jan2011/fdrPeaks/wgEncodeUwDnaseJurkat.fdr01peaks.hg19.bb Jurkat DnaseSeq Peaks bigBed UW analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/openchrom/jan2011/fdrPeaks/wgEncodeUwDnaseMonocytesCD14RO01746.fdr01peaks.hg19.bb Monocytes-CD14+_RO01746 DnaseSeq Peaks bigBed UW analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/openchrom/jan2011/fdrPeaks/wgEncodeUwDnaseNB4.fdr01peaks.hg19.bb NB4 DnaseSeq Peaks bigBed UW analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/openchrom/jan2011/fdrPeaks/wgEncodeUwDnaseNHA.fdr01peaks.hg19.bb NH-A DnaseSeq Peaks bigBed UW analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/openchrom/jan2011/fdrPeaks/wgEncodeUwDnaseNHDFAd.fdr01peaks.hg19.bb NHDF-Ad DnaseSeq Peaks bigBed UW analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/openchrom/jan2011/fdrPeaks/wgEncodeUwDnaseNHDFneo.fdr01peaks.hg19.bb NHDF-neo DnaseSeq Peaks bigBed UW analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/openchrom/jan2011/fdrPeaks/wgEncodeUwDnaseNHLF.fdr01peaks.hg19.bb NHLF DnaseSeq Peaks bigBed UW analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/openchrom/jan2011/fdrPeaks/wgEncodeUwDnaseNT2D1.fdr01peaks.hg19.bb NT2-D1 DnaseSeq Peaks bigBed UW analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/openchrom/jan2011/fdrPeaks/wgEncodeUwDnasePANC1.fdr01peaks.hg19.bb PANC-1 DnaseSeq Peaks bigBed UW analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/openchrom/jan2011/fdrPeaks/wgEncodeUwDnasePrEC.fdr01peaks.hg19.bb PrEC DnaseSeq Peaks bigBed UW analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/openchrom/jan2011/fdrPeaks/wgEncodeUwDnaseRPTEC.fdr01peaks.hg19.bb RPTEC DnaseSeq Peaks bigBed UW analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/openchrom/jan2011/fdrPeaks/wgEncodeUwDnaseSAEC.fdr01peaks.hg19.bb SAEC DnaseSeq Peaks bigBed UW analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/openchrom/jan2011/fdrPeaks/wgEncodeUwDnaseSKMC.fdr01peaks.hg19.bb SKMC DnaseSeq Peaks bigBed UW analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/openchrom/jan2011/fdrPeaks/wgEncodeUwDnaseSKNMC.fdr01peaks.hg19.bb SK-N-MC DnaseSeq Peaks bigBed UW analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/openchrom/jan2011/fdrPeaks/wgEncodeUwDnaseSKNSHRA.fdr01peaks.hg19.bb SK-N-SH_RA DnaseSeq Peaks bigBed UW analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/openchrom/jan2011/fdrPeaks/wgEncodeUwDnaseTh2.fdr01peaks.hg19.bb Th2 DnaseSeq Peaks bigBed UW analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/openchrom/jan2011/fdrPeaks/wgEncodeUwDnaseWERIRb1.fdr01peaks.hg19.bb WERI-Rb-1 DnaseSeq Peaks bigBed UW analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/openchrom/jan2011/fdrPeaks/wgEncodeUwDnaseWI38.fdr01peaks.hg19.bb WI-38 DnaseSeq Peaks bigBed UW analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/openchrom/jan2011/fdrPeaks/wgEncodeUwDnaseWI38TamoxifenTamoxifen.fdr01peaks.hg19.bb WI-38 DnaseSeq Peaks bigBed UW analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/openchrom/jan2011/fdrPeaks/wgEncodeUWDukeDnaseA549.fdr01peaks.hg19.bb A549 DnaseSeq Peaks bigBed UW-Duke analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/openchrom/jan2011/fdrPeaks/wgEncodeUWDukeDnaseGM12878.fdr01peaks.hg19.bb GM12878 DnaseSeq Peaks bigBed UW-Duke analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/openchrom/jan2011/fdrPeaks/wgEncodeUWDukeDnaseH1hESC.fdr01peaks.hg19.bb H1-hESC DnaseSeq Peaks bigBed UW-Duke analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/openchrom/jan2011/fdrPeaks/wgEncodeUWDukeDnaseHeLaS3.fdr01peaks.hg19.bb HeLa-S3 DnaseSeq Peaks bigBed UW-Duke analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/openchrom/jan2011/fdrPeaks/wgEncodeUWDukeDnaseHepG2.fdr01peaks.hg19.bb HepG2 DnaseSeq Peaks bigBed UW-Duke analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/openchrom/jan2011/fdrPeaks/wgEncodeUWDukeDnaseHMEC.fdr01peaks.hg19.bb HMEC DnaseSeq Peaks bigBed UW-Duke analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/openchrom/jan2011/fdrPeaks/wgEncodeUWDukeDnaseHSMM.fdr01peaks.hg19.bb HSMM DnaseSeq Peaks bigBed UW-Duke analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/openchrom/jan2011/fdrPeaks/wgEncodeUWDukeDnaseHSMMtube.fdr01peaks.hg19.bb HSMMtube DnaseSeq Peaks bigBed UW-Duke analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/openchrom/jan2011/fdrPeaks/wgEncodeUWDukeDnaseHUVEC.fdr01peaks.hg19.bb HUVEC DnaseSeq Peaks bigBed UW-Duke analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/openchrom/jan2011/fdrPeaks/wgEncodeUWDukeDnaseK562.fdr01peaks.hg19.bb K562 DnaseSeq Peaks bigBed UW-Duke analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/openchrom/jan2011/fdrPeaks/wgEncodeUWDukeDnaseLNCaP.fdr01peaks.hg19.bb LNCaP DnaseSeq Peaks bigBed UW-Duke analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/openchrom/jan2011/fdrPeaks/wgEncodeUWDukeDnaseMCF7.fdr01peaks.hg19.bb MCF-7 DnaseSeq Peaks bigBed UW-Duke analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/openchrom/jan2011/fdrPeaks/wgEncodeUWDukeDnaseNHEK.fdr01peaks.hg19.bb NHEK DnaseSeq Peaks bigBed UW-Duke analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/openchrom/jan2011/fdrPeaks/wgEncodeUWDukeDnaseTh1.fdr01peaks.hg19.bb Th1 DnaseSeq Peaks bigBed UW-Duke analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/openchrom/jan2011/faire_fseq_peaks/wgEncodeOpenChromFaireA549Pk.bb A549 FaireSeq Peaks bigBed UNC(Lieb) analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/openchrom/jan2011/faire_fseq_peaks/wgEncodeOpenChromFaireAstrocyPk.bb Astrocy FaireSeq Peaks bigBed UNC analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/openchrom/jan2011/faire_fseq_peaks/wgEncodeOpenChromFaireGlioblaPk.bb Gliobla FaireSeq Peaks bigBed UNC analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/openchrom/jan2011/faire_fseq_peaks/wgEncodeOpenChromFaireGm12878Pk.bb GM12878 FaireSeq Peaks bigBed UNC analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/openchrom/jan2011/faire_fseq_peaks/wgEncodeOpenChromFaireGm12891Pk.bb GM12891 FaireSeq Peaks bigBed UNC analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/openchrom/jan2011/faire_fseq_peaks/wgEncodeOpenChromFaireGm12892Pk.bb GM12892 FaireSeq Peaks bigBed UNC analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/openchrom/jan2011/faire_fseq_peaks/wgEncodeOpenChromFaireGm18507Pk.bb GM18507 FaireSeq Peaks bigBed UNC analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/openchrom/jan2011/faire_fseq_peaks/wgEncodeOpenChromFaireGm19239Pk.bb GM19239 FaireSeq Peaks bigBed UNC analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/openchrom/jan2011/faire_fseq_peaks/wgEncodeOpenChromFaireH1hescPk.bb H1-hESC FaireSeq Peaks bigBed UNC analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/openchrom/jan2011/faire_fseq_peaks/wgEncodeOpenChromFaireHelas3Ifna4hPk.bb HeLa-S3 FaireSeq Peaks bigBed UNC analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/openchrom/jan2011/faire_fseq_peaks/wgEncodeOpenChromFaireHelas3Ifng4hPk.bb HeLa-S3 FaireSeq Peaks bigBed UNC analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/openchrom/jan2011/faire_fseq_peaks/wgEncodeOpenChromFaireHelas3Pk.bb HeLa-S3 FaireSeq Peaks bigBed UNC analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/openchrom/jan2011/faire_fseq_peaks/wgEncodeOpenChromFaireHepg2Pk.bb HepG2 FaireSeq Peaks bigBed UNC analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/openchrom/jan2011/faire_fseq_peaks/wgEncodeOpenChromFaireHtr8Pk.bb HTR8svn FaireSeq Peaks bigBed UNC analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/openchrom/jan2011/faire_fseq_peaks/wgEncodeOpenChromFaireHuvecPk.bb HUVEC FaireSeq Peaks bigBed UNC analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/openchrom/jan2011/faire_fseq_peaks/wgEncodeOpenChromFaireK562_Hypoxia_LacAcidPk.bb bb analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/openchrom/jan2011/faire_fseq_peaks/wgEncodeOpenChromFaireK562NabutPk.bb K562 FaireSeq Peaks bigBed UNC analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/openchrom/jan2011/faire_fseq_peaks/wgEncodeOpenChromFaireK562OhureaPk.bb K562 FaireSeq Peaks bigBed UNC analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/openchrom/jan2011/faire_fseq_peaks/wgEncodeOpenChromFaireK562Pk.bb K562 FaireSeq Peaks bigBed UNC analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/openchrom/jan2011/faire_fseq_peaks/wgEncodeOpenChromFaireMedulloPk.bb Medullo FaireSeq Peaks bigBed UNC analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/openchrom/jan2011/faire_fseq_peaks/wgEncodeOpenChromFaireNhbePk.bb NHBE FaireSeq RawData 1 fastq UNC analysis 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http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/histone_macs/optimal/hub/wgEncodeSydhHistoneK562H3k9acbUcdAln.bb K562 ChIP-seq H3K9acB Peaks bigBed UCD analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/histone_macs/optimal/hub/wgEncodeSydhHistoneNt2d1H3k27me3StdAln.bb NT2-D1 ChIP-seq H3K27me3 Peaks bigBed UCD analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/histone_macs/optimal/hub/wgEncodeSydhHistoneNt2d1H3k36me3bUcdAln.bb NT2-D1 ChIP-seq H3K36me3B Peaks bigBed UCD analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/histone_macs/optimal/hub/wgEncodeSydhHistoneNt2d1H3k4me1UcdAln.bb NT2-D1 ChIP-seq H3K4me1 Peaks bigBed UCD analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/histone_macs/optimal/hub/wgEncodeSydhHistoneNt2d1H3k4me3StdAln.bb NT2-D1 ChIP-seq H3K4me3 Peaks bigBed UCD analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/histone_macs/optimal/hub/wgEncodeSydhHistoneNt2d1H3k9acStdAln.bb NT2-D1 ChIP-seq H3K9ac Peaks bigBed UCD analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/histone_macs/optimal/hub/wgEncodeSydhHistoneNt2d1H3k9me3UcdAln.bb NT2-D1 ChIP-seq H3K9me3 Peaks bigBed UCD analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/histone_macs/optimal/hub/wgEncodeSydhHistoneU2osH3k9me3UcdAln.bb U2OS ChIP-seq H3K9me3 Peaks bigBed UCD(Farnham) analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/histone_macs/optimal/hub/wgEncodeUwHistoneAg04449H3k4me3StdAln.bb AG04449 ChipSeq H3K4me3 Peaks bigBed UW analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/histone_macs/optimal/hub/wgEncodeUwHistoneAg04450H3k4me3StdAln.bb AG04450 ChipSeq H3K4me3 Peaks bigBed UW analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/histone_macs/optimal/hub/wgEncodeUwHistoneAg09309H3k4me3StdAln.bb AG09309 ChipSeq H3K4me3 Peaks bigBed UW analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/histone_macs/optimal/hub/wgEncodeUwHistoneAg09319H3k4me3StdAln.bb AG09319 ChipSeq H3K4me3 Peaks bigBed UW analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/histone_macs/optimal/hub/wgEncodeUwHistoneAg10803H3k4me3StdAln.bb AG10803 ChipSeq H3K4me3 Peaks bigBed UW analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/histone_macs/optimal/hub/wgEncodeUwHistoneAoafH3k4me3StdAln.bb AoAF ChipSeq H3K4me3 Peaks bigBed UW analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/histone_macs/optimal/hub/wgEncodeUwHistoneBjH3k27me3StdAln.bb BJ ChipSeq H3K27me3 Peaks bigBed UW analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/histone_macs/optimal/hub/wgEncodeUwHistoneBjH3k36me3StdAln.bb BJ ChipSeq H3K36me3 Peaks bigBed UW analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/histone_macs/optimal/hub/wgEncodeUwHistoneBjH3k4me3StdAln.bb BJ ChipSeq H3K4me3 Peaks bigBed UW analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/histone_macs/optimal/hub/wgEncodeUwHistoneCaco2H3k27me3StdAln.bb Caco-2 ChipSeq H3K27me3 Peaks bigBed UW analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/histone_macs/optimal/hub/wgEncodeUwHistoneCaco2H3k36me3StdAln.bb Caco-2 ChipSeq H3K36me3 Peaks bigBed UW analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/histone_macs/optimal/hub/wgEncodeUwHistoneCaco2H3k4me3StdAln.bb Caco-2 ChipSeq H3K4me3 Peaks bigBed UW analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/histone_macs/optimal/hub/wgEncodeUwHistoneGm06990H3k27me3StdAln.bb GM06990 ChipSeq H3K27me3 Peaks bigBed UW analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/histone_macs/optimal/hub/wgEncodeUwHistoneGm06990H3k36me3StdAln.bb GM06990 ChipSeq H3K36me3 Peaks bigBed UW analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/histone_macs/optimal/hub/wgEncodeUwHistoneGm06990H3k4me3StdAln.bb GM06990 ChipSeq H3K4me3 Peaks bigBed UW analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/histone_macs/optimal/hub/wgEncodeUwHistoneGm12878H3k27me3StdAln.bb GM12878 ChipSeq H3K27me3 Peaks bigBed UW analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/histone_macs/optimal/hub/wgEncodeUwHistoneGm12878H3k36me3StdAln.bb GM12878 ChipSeq H3K36me3 Peaks bigBed UW analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/histone_macs/optimal/hub/wgEncodeUwHistoneGm12878H3k4me3StdAln.bb GM12878 ChipSeq H3K4me3 Peaks bigBed UW analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/histone_macs/optimal/hub/wgEncodeUwHistoneH7esH3k27me3StdAln.bb H7-hESC ChipSeq H3K27me3 Peaks bigBed UW analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/histone_macs/optimal/hub/wgEncodeUwHistoneH7esH3k36me3StdAln.bb H7-hESC ChipSeq H3K36me3 Peaks bigBed UW analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/histone_macs/optimal/hub/wgEncodeUwHistoneH7esH3k4me3StdAln.bb H7-hESC ChipSeq H3K4me3 Peaks bigBed UW analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/histone_macs/optimal/hub/wgEncodeUwHistoneHaspH3k4me3StdAln.bb HA-sp ChipSeq H3K4me3 Peaks bigBed UW analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/histone_macs/optimal/hub/wgEncodeUwHistoneHbmecH3k4me3StdAln.bb HBMEC ChipSeq H3K4me3 Peaks bigBed UW analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/histone_macs/optimal/hub/wgEncodeUwHistoneHcfH3k4me3StdAln.bb HCF ChipSeq H3K4me3 Peaks bigBed UW analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/histone_macs/optimal/hub/wgEncodeUwHistoneHcmH3k4me3StdAln.bb HCM ChipSeq H3K4me3 Peaks bigBed UW analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/histone_macs/optimal/hub/wgEncodeUwHistoneHcpeH3k4me3StdAln.bb HCPEpiC ChipSeq H3K4me3 Peaks bigBed UW analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/histone_macs/optimal/hub/wgEncodeUwHistoneHct116H3k4me3StdAln.bb HCT-116 ChipSeq H3K4me3 Peaks bigBed UW analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/histone_macs/optimal/hub/wgEncodeUwHistoneHeeH3k4me3StdAln.bb HEEpiC ChipSeq H3K4me3 Peaks bigBed UW analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/histone_macs/optimal/hub/wgEncodeUwHistoneHek293H3k4me3StdAln.bb HEK293 ChipSeq H3K4me3 Peaks bigBed UW analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/histone_macs/optimal/hub/wgEncodeUwHistoneHelas3H3k27me3StdAln.bb HeLa-S3 ChipSeq H3K27me3 Peaks bigBed UW analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/histone_macs/optimal/hub/wgEncodeUwHistoneHelas3H3k36me3StdAln.bb HeLa-S3 ChipSeq H3K36me3 Peaks bigBed UW analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/histone_macs/optimal/hub/wgEncodeUwHistoneHelas3H3k4me3StdAln.bb HeLa-S3 ChipSeq H3K4me3 Peaks bigBed UW analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/histone_macs/optimal/hub/wgEncodeUwHistoneHepg2H3k27me3StdAln.bb HepG2 ChipSeq H3K27me3 Peaks bigBed UW analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/histone_macs/optimal/hub/wgEncodeUwHistoneHepg2H3k36me3StdAln.bb HepG2 ChipSeq H3K36me3 Peaks bigBed UW analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/histone_macs/optimal/hub/wgEncodeUwHistoneHepg2H3k4me3StdAln.bb HepG2 ChipSeq H3K4me3 Peaks bigBed UW analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/histone_macs/optimal/hub/wgEncodeUwHistoneHl60H3k4me3StdAln.bb HL-60 ChipSeq H3K4me3 Peaks bigBed UW analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/histone_macs/optimal/hub/wgEncodeUwHistoneHmecH3k4me3StdAln.bb HMEC ChipSeq H3K4me3 Peaks bigBed UW analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/histone_macs/optimal/hub/wgEncodeUwHistoneHmfH3k4me3StdAln.bb HMF ChipSeq H3K4me3 Peaks bigBed UW analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/histone_macs/optimal/hub/wgEncodeUwHistoneHpafH3k4me3StdAln.bb HPAF ChipSeq H3K4me3 Peaks bigBed UW analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/histone_macs/optimal/hub/wgEncodeUwHistoneHpfH3k4me3StdAln.bb HPF ChipSeq H3K4me3 Peaks bigBed UW analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/histone_macs/optimal/hub/wgEncodeUwHistoneHreH3k27me3StdAln.bb HRE ChipSeq H3K27me3 Peaks bigBed UW analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/histone_macs/optimal/hub/wgEncodeUwHistoneHreH3k36me3StdAln.bb HRE ChipSeq H3K36me3 Peaks bigBed UW analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/histone_macs/optimal/hub/wgEncodeUwHistoneHreH3k4me3StdAln.bb HRE ChipSeq H3K4me3 Peaks bigBed UW analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/histone_macs/optimal/hub/wgEncodeUwHistoneHrpeH3k4me3StdAln.bb HRPEpiC ChipSeq H3K4me3 Peaks bigBed UW analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/histone_macs/optimal/hub/wgEncodeUwHistoneHuvecH3k27me3StdAln.bb HUVEC ChipSeq H3K27me3 Peaks bigBed UW analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/histone_macs/optimal/hub/wgEncodeUwHistoneHuvecH3k36me3StdAln.bb HUVEC ChipSeq H3K36me3 Peaks bigBed UW analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/histone_macs/optimal/hub/wgEncodeUwHistoneHuvecH3k4me3StdAln.bb HUVEC ChipSeq H3K4me3 Peaks bigBed UW analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/histone_macs/optimal/hub/wgEncodeUwHistoneHvmfH3k4me3StdAln.bb HVMF ChipSeq H3K4me3 Peaks bigBed UW analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/histone_macs/optimal/hub/wgEncodeUwHistoneJurkatH3k4me3StdAln.bb Jurkat ChipSeq H3K4me3 Peaks bigBed UW analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/histone_macs/optimal/hub/wgEncodeUwHistoneK562H3k27me3StdAln.bb K562 ChipSeq H3K27me3 Peaks bigBed UW analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/histone_macs/optimal/hub/wgEncodeUwHistoneK562H3k36me3StdAln.bb K562 ChipSeq H3K36me3 Peaks bigBed UW analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/histone_macs/optimal/hub/wgEncodeUwHistoneK562H3k4me3StdAln.bb K562 ChipSeq H3K4me3 Peaks bigBed UW analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/histone_macs/optimal/hub/wgEncodeUwHistoneNhdfneoH3k4me3StdAln.bb NHDF-neo ChipSeq H3K4me3 Peaks bigBed UW analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/histone_macs/optimal/hub/wgEncodeUwHistoneNhekH3k27me3StdAln.bb NHEK ChipSeq H3K27me3 Peaks bigBed UW analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/histone_macs/optimal/hub/wgEncodeUwHistoneNhekH3k36me3StdAln.bb NHEK ChipSeq H3K36me3 Peaks bigBed UW analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/histone_macs/optimal/hub/wgEncodeUwHistoneNhekH3k4me3StdAln.bb NHEK ChipSeq H3K4me3 Peaks bigBed UW analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/histone_macs/optimal/hub/wgEncodeUwHistoneSaecH3k27me3StdAln.bb SAEC ChipSeq H3K27me3 Peaks bigBed UW analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/histone_macs/optimal/hub/wgEncodeUwHistoneSaecH3k36me3StdAln.bb SAEC ChipSeq H3K36me3 Peaks bigBed UW analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/histone_macs/optimal/hub/wgEncodeUwHistoneSaecH3k4me3StdAln.bb SAEC ChipSeq H3K4me3 Peaks bigBed UW analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/histone_macs/optimal/hub/wgEncodeUwHistoneSknshraH3k27me3StdAln.bb SK-N-SH_RA ChipSeq H3K27me3 Peaks bigBed UW analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/histone_macs/optimal/hub/wgEncodeUwHistoneSknshraH3k36me3StdAln.bb SK-N-SH_RA ChipSeq H3K36me3 Peaks bigBed UW analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/histone_macs/optimal/hub/wgEncodeUwHistoneSknshraH3k4me3StdAln.bb SK-N-SH_RA ChipSeq H3K4me3 Peaks bigBed UW analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/spp/optimal/hub/spp.optimal.wgEncodeBroadHistoneGm12878CtcfStdAlnRep0_VS_wgEncodeBroadHistoneGm12878ControlStdAlnRep0.bb GM12878 ChipSeq CTCF Peaks bigBed Broad analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/spp/optimal/hub/spp.optimal.wgEncodeBroadHistoneH1hescCtcfStdAlnRep0_VS_wgEncodeBroadHistoneH1hescControlStdAlnRep0.bb H1-hESC ChipSeq CTCF Peaks bigBed Broad analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/spp/optimal/hub/spp.optimal.wgEncodeBroadHistoneHelas3CtcfStdAlnRep0_VS_wgEncodeBroadHistoneHelas3ControlStdAlnRep0.bb HeLa-S3 ChipSeq CTCF Peaks bigBed Broad analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/spp/optimal/hub/spp.optimal.wgEncodeBroadHistoneHelas3Pol2bStdAlnRep0_VS_wgEncodeBroadHistoneHelas3ControlStdAlnRep0.bb HeLa-S3 ChipSeq Pol2(b) Peaks bigBed Broad analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/spp/optimal/hub/spp.optimal.wgEncodeBroadHistoneHepg2CtcfStdAlnRep0_VS_wgEncodeBroadHistoneHepg2ControlStdAlnRep0.bb HepG2 ChipSeq CTCF Peaks bigBed Broad analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/spp/optimal/hub/spp.optimal.wgEncodeBroadHistoneHmecCtcfStdAlnRep0_VS_wgEncodeBroadHistoneHmecControlStdAlnRep0.bb HMEC ChipSeq CTCF Peaks bigBed Broad analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/spp/optimal/hub/spp.optimal.wgEncodeBroadHistoneHsmmCtcfStdAlnRep0_VS_wgEncodeBroadHistoneHsmmControlStdAlnRep0.bb HSMM ChipSeq CTCF Peaks bigBed Broad analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/spp/optimal/hub/spp.optimal.wgEncodeBroadHistoneHsmmtCtcfStdAlnRep0_VS_wgEncodeBroadHistoneHsmmtControlStdAlnRep0.bb HSMMtube ChipSeq CTCF Peaks bigBed Broad analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/spp/optimal/hub/spp.optimal.wgEncodeBroadHistoneHuvecCtcfStdAlnRep0_VS_wgEncodeBroadHistoneHuvecControlStdAlnRep0.bb HUVEC ChipSeq CTCF Peaks bigBed Broad analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/spp/optimal/hub/spp.optimal.wgEncodeBroadHistoneHuvecPol2bStdAlnRep0_VS_wgEncodeBroadHistoneHuvecControlStdAlnRep0.bb HUVEC ChipSeq Pol2(b) Peaks bigBed Broad analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/spp/optimal/hub/spp.optimal.wgEncodeBroadHistoneK562CtcfStdAlnRep0_VS_wgEncodeBroadHistoneK562ControlStdAlnRep1.bb K562 ChipSeq CTCF Peaks bigBed Broad analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/spp/optimal/hub/spp.optimal.wgEncodeBroadHistoneK562Pol2bStdAlnRep0_VS_wgEncodeBroadHistoneK562ControlStdAlnRep1.bb K562 ChipSeq Pol2(b) Peaks bigBed Broad analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/spp/optimal/hub/spp.optimal.wgEncodeBroadHistoneNhaCtcfStdAlnRep0_VS_wgEncodeBroadHistoneNhaControlStdAlnRep0.bb NH-A ChipSeq CTCF Peaks bigBed Broad analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/spp/optimal/hub/spp.optimal.wgEncodeBroadHistoneNhdfadCtcfStdAlnRep0_VS_wgEncodeBroadHistoneNhdfadControlStdAlnRep0.bb NHDF-Ad ChipSeq CTCF Peaks bigBed Broad analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/spp/optimal/hub/spp.optimal.wgEncodeBroadHistoneNhekCtcfStdAlnRep0_VS_wgEncodeBroadHistoneNhekControlStdAlnRep0.bb NHEK ChipSeq CTCF Peaks bigBed Broad analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/spp/optimal/hub/spp.optimal.wgEncodeBroadHistoneNhekPol2bStdAlnRep0_VS_wgEncodeBroadHistoneNhekControlStdAlnRep0.bb NHEK ChipSeq Pol2(b) Peaks bigBed Broad analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/spp/optimal/hub/spp.optimal.wgEncodeBroadHistoneNhlfCtcfStdAlnRep0_VS_wgEncodeBroadHistoneNhlfControlStdAlnRep0.bb NHLF ChipSeq CTCF Peaks bigBed Broad analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/spp/optimal/hub/spp.optimal.wgEncodeBroadHistoneOsteoblCtcfStdAlnRep0_VS_wgEncodeBroadHistoneOsteoblControlStdAlnRep0.bb Osteobl ChipSeq CTCF Peaks bigBed Broad analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/spp/optimal/hub/spp.optimal.wgEncodeHaibTfbsA549CtcfPcr1xDexaAlnRep0_VS_wgEncodeHaibTfbsA549ControlPcr1xDexaAlnRep0.bb A549 ChipSeq CTCF Peaks bigBed HudsonAlpha analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/spp/optimal/hub/spp.optimal.wgEncodeHaibTfbsA549CtcfPcr1xEtoh02AlnRep0_VS_wgEncodeHaibTfbsA549ControlPcr1xEtoh02AlnRep1.bb A549 ChipSeq CTCF Peaks bigBed HudsonAlpha analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/spp/optimal/hub/spp.optimal.wgEncodeHaibTfbsA549GrPcr1xDexbAlnRep0_VS_wgEncodeHaibTfbsA549GrPcr1xEtoh02AlnRep0.bb A549 ChipSeq GR Peaks bigBed HudsonAlpha analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/spp/optimal/hub/spp.optimal.wgEncodeHaibTfbsA549GrPcr1xDexcAlnRep0_VS_wgEncodeHaibTfbsA549GrPcr1xEtoh02AlnRep0.bb A549 ChipSeq GR Peaks bigBed HudsonAlpha analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/spp/optimal/hub/spp.optimal.wgEncodeHaibTfbsA549GrPcr1xDexdAlnRep0_VS_wgEncodeHaibTfbsA549GrPcr1xEtoh02AlnRep0.bb A549 ChipSeq GR Peaks bigBed HudsonAlpha analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/spp/optimal/hub/spp.optimal.wgEncodeHaibTfbsA549GrPcr2xDexaAlnRep0_VS_wgEncodeHaibTfbsA549GrPcr2xEtoh02AlnRep0.bb A549 ChipSeq GR Peaks bigBed HudsonAlpha analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/spp/optimal/hub/spp.optimal.wgEncodeHaibTfbsA549Pol2Pcr2xDexaAlnRep0_VS_wgEncodeHaibTfbsA549ControlPcr2xDexaAlnRep0.bb A549 ChipSeq Pol2 Peaks bigBed HudsonAlpha analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/spp/optimal/hub/spp.optimal.wgEncodeHaibTfbsA549Pol2Pcr2xEtoh02AlnRep0_VS_wgEncodeHaibTfbsA549ControlPcr2xEtoh02AlnRep2.bb A549 ChipSeq Pol2 Peaks bigBed HudsonAlpha analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/spp/optimal/hub/spp.optimal.wgEncodeHaibTfbsA549Usf1Pcr1xDexaAlnRep0_VS_wgEncodeHaibTfbsA549ControlPcr1xDexaAlnRep0.bb A549 ChipSeq USF-1 Peaks bigBed HudsonAlpha analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/spp/optimal/hub/spp.optimal.wgEncodeHaibTfbsA549Usf1Pcr1xEtoh02AlnRep0_VS_wgEncodeHaibTfbsA549ControlPcr1xEtoh02AlnRep1.bb A549 ChipSeq USF-1 Peaks bigBed HudsonAlpha analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/spp/optimal/hub/spp.optimal.wgEncodeHaibTfbsEcc1EralphaaV0416102Estradia1hAlnRep0_VS_wgEncodeHaibTfbsEcc1EralphaaV0416102Dmso2AlnRep0.bb ECC-1 ChipSeq ERalpha_a Peaks bigBed HudsonAlpha analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/spp/optimal/hub/spp.optimal.wgEncodeHaibTfbsEcc1EralphaaV0416102Gen1hAlnRep0_VS_wgEncodeHaibTfbsEcc1EralphaaV0416102Dmso2AlnRep0.bb ECC-1 ChipSeq ERalpha_a Peaks bigBed HudsonAlpha analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/spp/optimal/hub/spp.optimal.wgEncodeHaibTfbsEcc1Foxa1c20V0416102Dmso2AlnRep0_VS_wgEncodeHaibTfbsEcc1ControlV0416102Dmso2AlnRep0.bb ECC-1 ChipSeq FOXA1_(C-20) Peaks bigBed HudsonAlpha analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/spp/optimal/hub/spp.optimal.wgEncodeHaibTfbsEcc1GrV0416102DexaAlnRep0_VS_wgEncodeHaibTfbsEcc1GrV0416102Etoh02AlnRep0.bb ECC-1 ChipSeq GR Peaks bigBed HudsonAlpha analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/spp/optimal/hub/spp.optimal.wgEncodeHaibTfbsEcc1Pol2V0416102Dmso2AlnRep0_VS_wgEncodeHaibTfbsEcc1ControlV0416102Dmso2AlnRep0.bb ECC-1 ChipSeq Pol2 Peaks bigBed HudsonAlpha analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/spp/optimal/hub/spp.optimal.wgEncodeHaibTfbsGm12878Atf3Pcr1xAlnRep0_VS_wgEncodeHaibTfbsGm12878ControlPcr1xAlnRep0.bb GM12878 ChipSeq ATF3 Peaks bigBed HudsonAlpha analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/spp/optimal/hub/spp.optimal.wgEncodeHaibTfbsGm12878BatfPcr1xAlnRep0_VS_wgEncodeHaibTfbsGm12878ControlPcr1xAlnRep0.bb GM12878 ChipSeq BATF Peaks bigBed HudsonAlpha analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/spp/optimal/hub/spp.optimal.wgEncodeHaibTfbsGm12878Bcl11aPcr1xAlnRep0_VS_wgEncodeHaibTfbsGm12878ControlPcr1xAlnRep0.bb GM12878 ChipSeq BCL11A Peaks bigBed HudsonAlpha analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/spp/optimal/hub/spp.optimal.wgEncodeHaibTfbsGm12878Bcl3Pcr1xAlnRep0_VS_wgEncodeHaibTfbsGm12878ControlPcr1xAlnRep0.bb GM12878 ChipSeq BCL3 Peaks bigBed HudsonAlpha analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/spp/optimal/hub/spp.optimal.wgEncodeHaibTfbsGm12878Bclaf1m33V0416101AlnRep0_VS_wgEncodeHaibTfbsGm12878ControlPcr1xAlnRep0.bb GM12878 ChipSeq BCLAF1_(M33-P5B11) Peaks bigBed HudsonAlpha analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/spp/optimal/hub/spp.optimal.wgEncodeHaibTfbsGm12878Ebf1c8Pcr1xAlnRep0_VS_wgEncodeHaibTfbsGm12878ControlPcr1xAlnRep0.bb GM12878 ChipSeq EBF1_(C-8) Peaks bigBed HudsonAlpha analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/spp/optimal/hub/spp.optimal.wgEncodeHaibTfbsGm12878EbfPcr1xAlnRep0_VS_wgEncodeHaibTfbsGm12878ControlPcr1xAlnRep0.bb GM12878 ChipSeq EBF Peaks bigBed HudsonAlpha analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/spp/optimal/hub/spp.optimal.wgEncodeHaibTfbsGm12878Egr1Pcr2xAlnRep0_VS_wgEncodeHaibTfbsGm12878ControlPcr2xAlnRep0.bb GM12878 ChipSeq Egr-1 Peaks bigBed HudsonAlpha analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/spp/optimal/hub/spp.optimal.wgEncodeHaibTfbsGm12878Egr1V0416101AlnRep0_VS_wgEncodeHaibTfbsGm12878ControlPcr1xAlnRep0.bb GM12878 ChipSeq Egr-1 Peaks bigBed HudsonAlpha analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/spp/optimal/hub/spp.optimal.wgEncodeHaibTfbsGm12878Elf1sc631V0416101AlnRep0_VS_wgEncodeHaibTfbsGm12878ControlPcr1xAlnRep0.bb GM12878 ChipSeq ELF1_(SC-631) Peaks bigBed HudsonAlpha analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/spp/optimal/hub/spp.optimal.wgEncodeHaibTfbsGm12878Ets1Pcr1xAlnRep0_VS_wgEncodeHaibTfbsGm12878ControlPcr1xAlnRep0.bb GM12878 ChipSeq ETS1 Peaks bigBed HudsonAlpha analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/spp/optimal/hub/spp.optimal.wgEncodeHaibTfbsGm12878GabpPcr2xAlnRep0_VS_wgEncodeHaibTfbsGm12878ControlPcr2xAlnRep0.bb GM12878 ChipSeq GABP Peaks bigBed HudsonAlpha analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/spp/optimal/hub/spp.optimal.wgEncodeHaibTfbsGm12878Irf4m17Pcr1xAlnRep0_VS_wgEncodeHaibTfbsGm12878ControlPcr1xAlnRep0.bb GM12878 ChipSeq IRF4_(M-17) Peaks bigBed HudsonAlpha analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/spp/optimal/hub/spp.optimal.wgEncodeHaibTfbsGm12878Irf4Pcr1xAlnRep0_VS_wgEncodeHaibTfbsGm12878ControlPcr1xAlnRep0.bb GM12878 ChipSeq IRF4 Peaks bigBed HudsonAlpha analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/spp/optimal/hub/spp.optimal.wgEncodeHaibTfbsGm12878Mef2aPcr1xAlnRep0_VS_wgEncodeHaibTfbsGm12878ControlPcr1xAlnRep0.bb GM12878 ChipSeq MEF2A Peaks bigBed HudsonAlpha analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/spp/optimal/hub/spp.optimal.wgEncodeHaibTfbsGm12878Mef2csc13268Pcr1xAlnRep0_VS_wgEncodeHaibTfbsGm12878ControlPcr1xAlnRep0.bb GM12878 ChipSeq MEF2C_(SC-13268) Peaks bigBed HudsonAlpha analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/spp/optimal/hub/spp.optimal.wgEncodeHaibTfbsGm12878NrsfPcr2xAlnRep0_VS_wgEncodeHaibTfbsGm12878ControlPcr2xAlnRep0.bb GM12878 ChipSeq NRSF Peaks bigBed HudsonAlpha analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/spp/optimal/hub/spp.optimal.wgEncodeHaibTfbsGm12878Oct2Pcr1xAlnRep0_VS_wgEncodeHaibTfbsGm12878ControlPcr1xAlnRep0.bb GM12878 ChipSeq Oct-2 Peaks bigBed HudsonAlpha analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/spp/optimal/hub/spp.optimal.wgEncodeHaibTfbsGm12878P300Pcr1xAlnRep0_VS_wgEncodeHaibTfbsGm12878ControlPcr1xAlnRep0.bb GM12878 ChipSeq p300 Peaks bigBed HudsonAlpha analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/spp/optimal/hub/spp.optimal.wgEncodeHaibTfbsGm12878Pax5c20Pcr1xAlnRep0_VS_wgEncodeHaibTfbsGm12878ControlPcr1xAlnRep0.bb GM12878 ChipSeq PAX5-C20 Peaks bigBed HudsonAlpha analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/spp/optimal/hub/spp.optimal.wgEncodeHaibTfbsGm12878Pax5n19Pcr1xAlnRep0_VS_wgEncodeHaibTfbsGm12878ControlPcr1xAlnRep0.bb GM12878 ChipSeq PAX5-N19 Peaks bigBed HudsonAlpha analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/spp/optimal/hub/spp.optimal.wgEncodeHaibTfbsGm12878Pbx3Pcr1xAlnRep0_VS_wgEncodeHaibTfbsGm12878ControlPcr1xAlnRep0.bb GM12878 ChipSeq Pbx3 Peaks bigBed HudsonAlpha analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/spp/optimal/hub/spp.optimal.wgEncodeHaibTfbsGm12878Pol24h8Pcr1xAlnRep0_VS_wgEncodeHaibTfbsGm12878ControlPcr1xAlnRep0.bb GM12878 ChipSeq Pol2-4H8 Peaks bigBed HudsonAlpha analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/spp/optimal/hub/spp.optimal.wgEncodeHaibTfbsGm12878Pol2Pcr2xAlnRep0_VS_wgEncodeHaibTfbsGm12878ControlPcr2xAlnRep0.bb GM12878 ChipSeq Pol2 Peaks bigBed HudsonAlpha analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/spp/optimal/hub/spp.optimal.wgEncodeHaibTfbsGm12878Pou2f2Pcr1xAlnRep0_VS_wgEncodeHaibTfbsGm12878ControlPcr1xAlnRep0.bb GM12878 ChipSeq POU2F2 Peaks bigBed HudsonAlpha analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/spp/optimal/hub/spp.optimal.wgEncodeHaibTfbsGm12878Pu1Pcr1xAlnRep0_VS_wgEncodeHaibTfbsGm12878ControlPcr1xAlnRep0.bb GM12878 ChipSeq PU.1 Peaks bigBed HudsonAlpha analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/spp/optimal/hub/spp.optimal.wgEncodeHaibTfbsGm12878Rad21V0416101AlnRep0_VS_wgEncodeHaibTfbsGm12878ControlPcr1xAlnRep0.bb GM12878 ChipSeq Rad21 Peaks bigBed HudsonAlpha analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/spp/optimal/hub/spp.optimal.wgEncodeHaibTfbsGm12878RxraPcr1xAlnRep0_VS_wgEncodeHaibTfbsGm12878ControlPcr1xAlnRep0.bb GM12878 ChipSeq RXRA Peaks bigBed HudsonAlpha analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/spp/optimal/hub/spp.optimal.wgEncodeHaibTfbsGm12878Sin3ak20Pcr1xAlnRep0_VS_wgEncodeHaibTfbsGm12878ControlPcr1xAlnRep0.bb GM12878 ChipSeq Sin3Ak-20 Peaks bigBed HudsonAlpha analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/spp/optimal/hub/spp.optimal.wgEncodeHaibTfbsGm12878Six5Pcr1xAlnRep0_VS_wgEncodeHaibTfbsGm12878ControlPcr1xAlnRep0.bb GM12878 ChipSeq SIX5 Peaks bigBed HudsonAlpha analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/spp/optimal/hub/spp.optimal.wgEncodeHaibTfbsGm12878Sp1Pcr1xAlnRep0_VS_wgEncodeHaibTfbsGm12878ControlPcr1xAlnRep0.bb GM12878 ChipSeq SP1 Peaks bigBed HudsonAlpha analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/spp/optimal/hub/spp.optimal.wgEncodeHaibTfbsGm12878SrfPcr2xAlnRep0_VS_wgEncodeHaibTfbsGm12878ControlPcr2xAlnRep0.bb GM12878 ChipSeq SRF Peaks bigBed HudsonAlpha analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/spp/optimal/hub/spp.optimal.wgEncodeHaibTfbsGm12878SrfV0416101AlnRep0_VS_wgEncodeHaibTfbsGm12878ControlPcr1xAlnRep0.bb GM12878 ChipSeq SRF Peaks bigBed HudsonAlpha analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/spp/optimal/hub/spp.optimal.wgEncodeHaibTfbsGm12878Taf1Pcr1xAlnRep0_VS_wgEncodeHaibTfbsGm12878ControlPcr1xAlnRep0.bb GM12878 ChipSeq TAF1 Peaks bigBed HudsonAlpha analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/spp/optimal/hub/spp.optimal.wgEncodeHaibTfbsGm12878Tcf12Pcr1xAlnRep0_VS_wgEncodeHaibTfbsGm12878ControlPcr1xAlnRep0.bb GM12878 ChipSeq TCF12 Peaks bigBed HudsonAlpha analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/spp/optimal/hub/spp.optimal.wgEncodeHaibTfbsGm12878Usf1Pcr2xAlnRep0_VS_wgEncodeHaibTfbsGm12878ControlPcr2xAlnRep0.bb GM12878 ChipSeq USF-1 Peaks bigBed HudsonAlpha analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/spp/optimal/hub/spp.optimal.wgEncodeHaibTfbsGm12878Yy1V0416101AlnRep0_VS_wgEncodeHaibTfbsGm12878ControlV0416101AlnRep1.bb GM12878 ChipSeq YY1_(SC-281) Peaks bigBed HudsonAlpha analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/spp/optimal/hub/spp.optimal.wgEncodeHaibTfbsGm12878Zbtb33Pcr1xAlnRep0_VS_wgEncodeHaibTfbsGm12878ControlPcr1xAlnRep0.bb GM12878 ChipSeq ZBTB33 Peaks bigBed HudsonAlpha analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/spp/optimal/hub/spp.optimal.wgEncodeHaibTfbsGm12878Zeb1sc25388V0416102AlnRep0_VS_wgEncodeHaibTfbsGm12878ControlPcr1xAlnRep0.bb GM12878 ChipSeq ZEB1_(SC-25388) Peaks bigBed HudsonAlpha analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/spp/optimal/hub/spp.optimal.wgEncodeHaibTfbsGm12891Oct2Pcr1xAlnRep0_VS_wgEncodeHaibTfbsGm12891ControlPcr1xAlnRep0.bb GM12891 ChipSeq Oct-2 Peaks bigBed HudsonAlpha analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/spp/optimal/hub/spp.optimal.wgEncodeHaibTfbsGm12891Pax5c20Pcr1xAlnRep0_VS_wgEncodeHaibTfbsGm12891ControlPcr1xAlnRep0.bb GM12891 ChipSeq PAX5-C20 Peaks bigBed HudsonAlpha analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/spp/optimal/hub/spp.optimal.wgEncodeHaibTfbsGm12891Pol24h8Pcr1xAlnRep0_VS_wgEncodeHaibTfbsGm12891ControlPcr1xAlnRep0.bb GM12891 ChipSeq Pol2-4H8 Peaks bigBed HudsonAlpha analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/spp/optimal/hub/spp.optimal.wgEncodeHaibTfbsGm12891Pol2Pcr1xAlnRep0_VS_wgEncodeHaibTfbsGm12891ControlPcr1xAlnRep0.bb GM12891 ChipSeq Pol2 Peaks bigBed HudsonAlpha analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/spp/optimal/hub/spp.optimal.wgEncodeHaibTfbsGm12891Pou2f2Pcr1xAlnRep0_VS_wgEncodeHaibTfbsGm12891ControlPcr1xAlnRep0.bb GM12891 ChipSeq POU2F2 Peaks bigBed HudsonAlpha analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/spp/optimal/hub/spp.optimal.wgEncodeHaibTfbsGm12891Pu1Pcr1xAlnRep0_VS_wgEncodeHaibTfbsGm12891ControlPcr1xAlnRep0.bb GM12891 ChipSeq PU.1 Peaks bigBed HudsonAlpha analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/spp/optimal/hub/spp.optimal.wgEncodeHaibTfbsGm12891Taf1Pcr1xAlnRep0_VS_wgEncodeHaibTfbsGm12891ControlPcr1xAlnRep0.bb GM12891 ChipSeq TAF1 Peaks bigBed HudsonAlpha analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/spp/optimal/hub/spp.optimal.wgEncodeHaibTfbsGm12891Yy1c20V0416101AlnRep0_VS_wgEncodeHaibTfbsGm12891ControlPcr1xAlnRep0.bb GM12891 ChipSeq YY1_(C-20) Peaks bigBed HudsonAlpha analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/spp/optimal/hub/spp.optimal.wgEncodeHaibTfbsGm12892Pax5c20Pcr1xAlnRep0_VS_wgEncodeHaibTfbsGm12892ControlPcr1xAlnRep0.bb GM12892 ChipSeq PAX5-C20 Peaks bigBed HudsonAlpha analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/spp/optimal/hub/spp.optimal.wgEncodeHaibTfbsGm12892Pol24h8Pcr1xAlnRep0_VS_wgEncodeHaibTfbsGm12892ControlPcr1xAlnRep0.bb GM12892 ChipSeq Pol2-4H8 Peaks bigBed HudsonAlpha analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/spp/optimal/hub/spp.optimal.wgEncodeHaibTfbsGm12892Pol24h8V0416102AlnRep0_VS_wgEncodeHaibTfbsGm12892ControlPcr1xAlnRep0.bb GM12892 ChipSeq Pol2-4H8 Peaks bigBed HudsonAlpha analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/spp/optimal/hub/spp.optimal.wgEncodeHaibTfbsGm12892Pol2Pcr1xAlnRep0_VS_wgEncodeHaibTfbsGm12892ControlPcr1xAlnRep0.bb GM12892 ChipSeq Pol2 Peaks bigBed HudsonAlpha analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/spp/optimal/hub/spp.optimal.wgEncodeHaibTfbsGm12892Pol2V0416102AlnRep0_VS_wgEncodeHaibTfbsGm12892ControlPcr1xAlnRep0.bb GM12892 ChipSeq Pol2 Peaks bigBed HudsonAlpha analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/spp/optimal/hub/spp.optimal.wgEncodeHaibTfbsGm12892Taf1Pcr1xAlnRep0_VS_wgEncodeHaibTfbsGm12892ControlPcr1xAlnRep0.bb GM12892 ChipSeq TAF1 Peaks bigBed HudsonAlpha analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/spp/optimal/hub/spp.optimal.wgEncodeHaibTfbsGm12892Taf1V0416102AlnRep0_VS_wgEncodeHaibTfbsGm12892ControlPcr1xAlnRep0.bb GM12892 ChipSeq TAF1 Peaks bigBed HudsonAlpha analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/spp/optimal/hub/spp.optimal.wgEncodeHaibTfbsGm12892Yy1V0416101AlnRep0_VS_wgEncodeHaibTfbsGm12892ControlPcr1xAlnRep0.bb GM12892 ChipSeq YY1 Peaks bigBed HudsonAlpha analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/spp/optimal/hub/spp.optimal.wgEncodeHaibTfbsH1hescAtf3Pcr1xAlnRep0_VS_wgEncodeHaibTfbsH1hescControlPcr1xAlnRep0.bb H1-hESC ChipSeq ATF3 Peaks bigBed HudsonAlpha analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/spp/optimal/hub/spp.optimal.wgEncodeHaibTfbsH1hescBcl11aPcr1xAlnRep0_VS_wgEncodeHaibTfbsH1hescControlPcr1xAlnRep0.bb H1-hESC ChipSeq BCL11A Peaks bigBed HudsonAlpha analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/spp/optimal/hub/spp.optimal.wgEncodeHaibTfbsH1hescBcl3Pcr1xAlnRep0_VS_wgEncodeHaibTfbsH1hescControlPcr1xAlnRep0.bb H1-hESC ChipSeq BCL3 Peaks bigBed HudsonAlpha analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/spp/optimal/hub/spp.optimal.wgEncodeHaibTfbsH1hescCtcfsc5916V0416102AlnRep0_VS_wgEncodeHaibTfbsH1hescControlPcr1xAlnRep0.bb H1-hESC ChipSeq CTCF_(SC-5916) Peaks bigBed HudsonAlpha analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/spp/optimal/hub/spp.optimal.wgEncodeHaibTfbsH1hescEgr1V0416101AlnRep0_VS_wgEncodeHaibTfbsH1hescControlPcr1xAlnRep0.bb H1-hESC ChipSeq Egr-1 Peaks bigBed HudsonAlpha analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/spp/optimal/hub/spp.optimal.wgEncodeHaibTfbsH1hescEgr1V0416102AlnRep0_VS_wgEncodeHaibTfbsH1hescControlPcr1xAlnRep0.bb H1-hESC ChipSeq Egr-1 Peaks bigBed HudsonAlpha analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/spp/optimal/hub/spp.optimal.wgEncodeHaibTfbsH1hescGabpPcr1xAlnRep0_VS_wgEncodeHaibTfbsH1hescControlPcr1xAlnRep0.bb H1-hESC ChipSeq GABP Peaks bigBed HudsonAlpha analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/spp/optimal/hub/spp.optimal.wgEncodeHaibTfbsH1hescHdac2sc6296V0416102AlnRep0_VS_wgEncodeHaibTfbsH1hescControlPcr1xAlnRep0.bb H1-hESC ChipSeq HDAC2_(SC-6296) Peaks bigBed HudsonAlpha analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/spp/optimal/hub/spp.optimal.wgEncodeHaibTfbsH1hescJundV0416102AlnRep0_VS_wgEncodeHaibTfbsH1hescControlPcr1xAlnRep0.bb H1-hESC ChipSeq JunD Peaks bigBed HudsonAlpha analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/spp/optimal/hub/spp.optimal.wgEncodeHaibTfbsH1hescNanogsc33759V0416102AlnRep0_VS_wgEncodeHaibTfbsH1hescControlPcr1xAlnRep0.bb H1-hESC ChipSeq NANOG_(SC-33759) Peaks bigBed HudsonAlpha analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/spp/optimal/hub/spp.optimal.wgEncodeHaibTfbsH1hescNrsfPcr1xAlnRep0_VS_wgEncodeHaibTfbsH1hescControlPcr1xAlnRep0.bb H1-hESC ChipSeq NRSF Peaks bigBed HudsonAlpha analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/spp/optimal/hub/spp.optimal.wgEncodeHaibTfbsH1hescNrsfV0416102AlnRep0_VS_wgEncodeHaibTfbsH1hescControlPcr1xAlnRep0.bb H1-hESC ChipSeq NRSF Peaks bigBed HudsonAlpha analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/spp/optimal/hub/spp.optimal.wgEncodeHaibTfbsH1hescP300Pcr1xAlnRep0_VS_wgEncodeHaibTfbsH1hescControlPcr1xAlnRep0.bb H1-hESC ChipSeq p300 Peaks bigBed HudsonAlpha analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/spp/optimal/hub/spp.optimal.wgEncodeHaibTfbsH1hescPol24h8Pcr1xAlnRep0_VS_wgEncodeHaibTfbsH1hescControlPcr1xAlnRep0.bb H1-hESC ChipSeq Pol2-4H8 Peaks bigBed HudsonAlpha analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/spp/optimal/hub/spp.optimal.wgEncodeHaibTfbsH1hescPol24h8V0416102AlnRep0_VS_wgEncodeHaibTfbsH1hescControlPcr1xAlnRep0.bb H1-hESC ChipSeq Pol2-4H8 Peaks bigBed HudsonAlpha analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/spp/optimal/hub/spp.optimal.wgEncodeHaibTfbsH1hescPol2Pcr1xAlnRep0_VS_wgEncodeHaibTfbsH1hescControlPcr1xAlnRep0.bb H1-hESC ChipSeq Pol2 Peaks bigBed HudsonAlpha analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/spp/optimal/hub/spp.optimal.wgEncodeHaibTfbsH1hescPol2V0416102AlnRep0_VS_wgEncodeHaibTfbsH1hescControlPcr1xAlnRep0.bb H1-hESC ChipSeq Pol2 Peaks bigBed HudsonAlpha analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/spp/optimal/hub/spp.optimal.wgEncodeHaibTfbsH1hescPou5f1sc9081V0416102AlnRep0_VS_wgEncodeHaibTfbsH1hescControlPcr1xAlnRep0.bb H1-hESC ChipSeq POU5F1_(SC-9081) Peaks bigBed HudsonAlpha analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/spp/optimal/hub/spp.optimal.wgEncodeHaibTfbsH1hescRad21V0416102AlnRep0_VS_wgEncodeHaibTfbsH1hescControlPcr1xAlnRep0.bb H1-hESC ChipSeq Rad21 Peaks bigBed HudsonAlpha analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/spp/optimal/hub/spp.optimal.wgEncodeHaibTfbsH1hescRxraV0416102AlnRep0_VS_wgEncodeHaibTfbsH1hescControlPcr1xAlnRep0.bb H1-hESC ChipSeq RXRA Peaks bigBed HudsonAlpha analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/spp/optimal/hub/spp.optimal.wgEncodeHaibTfbsH1hescSin3ak20Pcr1xAlnRep0_VS_wgEncodeHaibTfbsH1hescControlPcr1xAlnRep0.bb H1-hESC ChipSeq Sin3Ak-20 Peaks bigBed HudsonAlpha analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/spp/optimal/hub/spp.optimal.wgEncodeHaibTfbsH1hescSix5Pcr1xAlnRep0_VS_wgEncodeHaibTfbsH1hescControlPcr1xAlnRep0.bb H1-hESC ChipSeq SIX5 Peaks bigBed HudsonAlpha analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/spp/optimal/hub/spp.optimal.wgEncodeHaibTfbsH1hescSp1Pcr1xAlnRep0_VS_wgEncodeHaibTfbsH1hescControlPcr1xAlnRep0.bb H1-hESC ChipSeq SP1 Peaks bigBed HudsonAlpha analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/spp/optimal/hub/spp.optimal.wgEncodeHaibTfbsH1hescSrfPcr1xAlnRep0_VS_wgEncodeHaibTfbsH1hescControlPcr1xAlnRep0.bb H1-hESC ChipSeq SRF Peaks bigBed HudsonAlpha analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/spp/optimal/hub/spp.optimal.wgEncodeHaibTfbsH1hescTaf1Pcr1xAlnRep0_VS_wgEncodeHaibTfbsH1hescControlPcr1xAlnRep0.bb H1-hESC ChipSeq TAF1 Peaks bigBed HudsonAlpha analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/spp/optimal/hub/spp.optimal.wgEncodeHaibTfbsH1hescTaf1V0416102AlnRep0_VS_wgEncodeHaibTfbsH1hescControlPcr1xAlnRep0.bb H1-hESC ChipSeq TAF1 Peaks bigBed HudsonAlpha analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/spp/optimal/hub/spp.optimal.wgEncodeHaibTfbsH1hescTaf7sq8V0416102AlnRep0_VS_wgEncodeHaibTfbsH1hescControlPcr1xAlnRep0.bb H1-hESC ChipSeq TAF7_(SQ-8) Peaks bigBed HudsonAlpha analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/spp/optimal/hub/spp.optimal.wgEncodeHaibTfbsH1hescTcf12Pcr1xAlnRep0_VS_wgEncodeHaibTfbsH1hescControlPcr1xAlnRep0.bb H1-hESC ChipSeq TCF12 Peaks bigBed HudsonAlpha analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/spp/optimal/hub/spp.optimal.wgEncodeHaibTfbsH1hescUsf1Pcr1xAlnRep0_VS_wgEncodeHaibTfbsH1hescControlPcr1xAlnRep0.bb H1-hESC ChipSeq USF-1 Peaks bigBed HudsonAlpha analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/spp/optimal/hub/spp.optimal.wgEncodeHaibTfbsH1hescYy1c20Pcr1xAlnRep0_VS_wgEncodeHaibTfbsH1hescControlPcr1xAlnRep0.bb H1-hESC ChipSeq YY1_(C-20) Peaks bigBed HudsonAlpha analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/spp/optimal/hub/spp.optimal.wgEncodeHaibTfbsHct116Pol24h8V0416101AlnRep0_VS_wgEncodeHaibTfbsHct116ControlV0416101AlnRep2.bb HCT-116 ChipSeq Pol2-4H8 Peaks bigBed HudsonAlpha analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/spp/optimal/hub/spp.optimal.wgEncodeHaibTfbsHelas3GabpPcr1xAlnRep0_VS_wgEncodeHaibTfbsHelas3ControlPcr1xAlnRep0.bb HeLa-S3 ChipSeq GABP Peaks bigBed HudsonAlpha analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/spp/optimal/hub/spp.optimal.wgEncodeHaibTfbsHelas3NrsfPcr1xAlnRep0_VS_wgEncodeHaibTfbsHelas3ControlPcr1xAlnRep0.bb HeLa-S3 ChipSeq NRSF Peaks bigBed HudsonAlpha analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/spp/optimal/hub/spp.optimal.wgEncodeHaibTfbsHelas3Pol2Pcr1xAlnRep0_VS_wgEncodeHaibTfbsHelas3ControlPcr1xAlnRep0.bb HeLa-S3 ChipSeq Pol2 Peaks bigBed HudsonAlpha analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/spp/optimal/hub/spp.optimal.wgEncodeHaibTfbsHelas3Taf1Pcr1xAlnRep0_VS_wgEncodeHaibTfbsHelas3ControlPcr1xAlnRep0.bb HeLa-S3 ChipSeq TAF1 Peaks bigBed HudsonAlpha analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/spp/optimal/hub/spp.optimal.wgEncodeHaibTfbsHepg2Atf3Pcr1xAlnRep0_VS_wgEncodeHaibTfbsHepg2ControlPcr1xAlnRep0.bb HepG2 ChipSeq ATF3 Peaks bigBed HudsonAlpha analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/spp/optimal/hub/spp.optimal.wgEncodeHaibTfbsHepg2Bhlhe40V0416101AlnRep0_VS_wgEncodeHaibTfbsHepg2ControlPcr1xAlnRep0.bb HepG2 ChipSeq BHLHE40 Peaks bigBed HudsonAlpha analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/spp/optimal/hub/spp.optimal.wgEncodeHaibTfbsHepg2CtcfV0416101AlnRep0_VS_wgEncodeHaibTfbsHepg2ControlV0416101AlnRep0.bb HepG2 ChipSeq CTCF Peaks bigBed HudsonAlpha analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/spp/optimal/hub/spp.optimal.wgEncodeHaibTfbsHepg2Elf1sc631V0416101AlnRep0_VS_wgEncodeHaibTfbsHepg2ControlV0416101AlnRep0.bb HepG2 ChipSeq ELF1_(SC-631) Peaks bigBed HudsonAlpha analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/spp/optimal/hub/spp.optimal.wgEncodeHaibTfbsHepg2Fosl2Pcr1xAlnRep0_VS_wgEncodeHaibTfbsHepg2ControlPcr1xAlnRep0.bb HepG2 ChipSeq FOSL2 Peaks bigBed HudsonAlpha analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/spp/optimal/hub/spp.optimal.wgEncodeHaibTfbsHepg2Foxa1c20Pcr1xAlnRep0_VS_wgEncodeHaibTfbsHepg2ControlPcr1xAlnRep0.bb HepG2 ChipSeq FOXA1_(C-20) Peaks bigBed HudsonAlpha analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/spp/optimal/hub/spp.optimal.wgEncodeHaibTfbsHepg2Foxa1sc101058Pcr1xAlnRep0_VS_wgEncodeHaibTfbsHepg2ControlPcr1xAlnRep0.bb HepG2 ChipSeq FOXA1_(SC-101058) Peaks bigBed HudsonAlpha analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/spp/optimal/hub/spp.optimal.wgEncodeHaibTfbsHepg2Foxa2sc6554V0416101AlnRep0_VS_wgEncodeHaibTfbsHepg2ControlV0416101AlnRep0.bb HepG2 ChipSeq FOXA2_(SC-6554) Peaks bigBed HudsonAlpha analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/spp/optimal/hub/spp.optimal.wgEncodeHaibTfbsHepg2GabpPcr2xAlnRep0_VS_wgEncodeHaibTfbsHepg2ControlPcr2xAlnRep0.bb HepG2 ChipSeq GABP Peaks bigBed HudsonAlpha analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/spp/optimal/hub/spp.optimal.wgEncodeHaibTfbsHepg2Hdac2sc6296V0416101AlnRep0_VS_wgEncodeHaibTfbsHepg2ControlV0416101AlnRep0.bb HepG2 ChipSeq HDAC2_(SC-6296) Peaks bigBed HudsonAlpha analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/spp/optimal/hub/spp.optimal.wgEncodeHaibTfbsHepg2Hey1V0416101AlnRep0_VS_wgEncodeHaibTfbsHepg2ControlPcr1xAlnRep0.bb HepG2 ChipSeq HEY1 Peaks bigBed HudsonAlpha analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/spp/optimal/hub/spp.optimal.wgEncodeHaibTfbsHepg2Hnf4ah171Pcr1xAlnRep0_VS_wgEncodeHaibTfbsHepg2ControlPcr1xAlnRep0.bb HepG2 ChipSeq HNF4A_(H-171) Peaks bigBed HudsonAlpha analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/spp/optimal/hub/spp.optimal.wgEncodeHaibTfbsHepg2Hnf4gsc6558V0416101AlnRep0_VS_wgEncodeHaibTfbsHepg2ControlV0416101AlnRep0.bb HepG2 ChipSeq HNF4G_(SC-6558) Peaks bigBed HudsonAlpha analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/spp/optimal/hub/spp.optimal.wgEncodeHaibTfbsHepg2JundPcr1xAlnRep0_VS_wgEncodeHaibTfbsHepg2ControlPcr1xAlnRep0.bb HepG2 ChipSeq JunD Peaks bigBed HudsonAlpha analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/spp/optimal/hub/spp.optimal.wgEncodeHaibTfbsHepg2NrsfPcr2xAlnRep0_VS_wgEncodeHaibTfbsHepg2ControlPcr2xAlnRep0.bb HepG2 ChipSeq NRSF Peaks bigBed HudsonAlpha analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/spp/optimal/hub/spp.optimal.wgEncodeHaibTfbsHepg2P300Pcr1xAlnRep0_VS_wgEncodeHaibTfbsHepg2ControlPcr1xAlnRep0.bb HepG2 ChipSeq p300 Peaks bigBed HudsonAlpha analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/spp/optimal/hub/spp.optimal.wgEncodeHaibTfbsHepg2P300V0416101AlnRep0_VS_wgEncodeHaibTfbsHepg2ControlV0416101AlnRep0.bb HepG2 ChipSeq p300 Peaks bigBed HudsonAlpha analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/spp/optimal/hub/spp.optimal.wgEncodeHaibTfbsHepg2Pol2Pcr2xAlnRep0_VS_wgEncodeHaibTfbsHepg2ControlPcr2xAlnRep0.bb HepG2 ChipSeq Pol2 Peaks bigBed HudsonAlpha analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/spp/optimal/hub/spp.optimal.wgEncodeHaibTfbsHepg2Rad21V0416101AlnRep0_VS_wgEncodeHaibTfbsHepg2ControlV0416101AlnRep0.bb HepG2 ChipSeq Rad21 Peaks bigBed HudsonAlpha analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/spp/optimal/hub/spp.optimal.wgEncodeHaibTfbsHepg2RxraPcr1xAlnRep0_VS_wgEncodeHaibTfbsHepg2ControlPcr1xAlnRep0.bb HepG2 ChipSeq RXRA Peaks bigBed HudsonAlpha analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/spp/optimal/hub/spp.optimal.wgEncodeHaibTfbsHepg2Sin3ak20Pcr1xAlnRep0_VS_wgEncodeHaibTfbsHepg2ControlPcr1xAlnRep0.bb HepG2 ChipSeq Sin3Ak-20 Peaks bigBed HudsonAlpha analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/spp/optimal/hub/spp.optimal.wgEncodeHaibTfbsHepg2Sp1Pcr1xAlnRep0_VS_wgEncodeHaibTfbsHepg2ControlPcr1xAlnRep0.bb HepG2 ChipSeq SP1 Peaks bigBed HudsonAlpha analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/spp/optimal/hub/spp.optimal.wgEncodeHaibTfbsHepg2SrfV0416101AlnRep0_VS_wgEncodeHaibTfbsHepg2ControlV0416101AlnRep0.bb HepG2 ChipSeq SRF Peaks bigBed HudsonAlpha analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/spp/optimal/hub/spp.optimal.wgEncodeHaibTfbsHepg2Taf1Pcr2xAlnRep0_VS_wgEncodeHaibTfbsHepg2ControlPcr2xAlnRep0.bb HepG2 ChipSeq TAF1 Peaks bigBed HudsonAlpha analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/spp/optimal/hub/spp.optimal.wgEncodeHaibTfbsHepg2Tcf12Pcr1xAlnRep0_VS_wgEncodeHaibTfbsHepg2ControlPcr1xAlnRep0.bb HepG2 ChipSeq TCF12 Peaks bigBed HudsonAlpha analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/spp/optimal/hub/spp.optimal.wgEncodeHaibTfbsHepg2Usf1Pcr1xAlnRep0_VS_wgEncodeHaibTfbsHepg2ControlPcr1xAlnRep0.bb HepG2 ChipSeq USF-1 Peaks bigBed HudsonAlpha analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/spp/optimal/hub/spp.optimal.wgEncodeHaibTfbsHepg2Zbtb33Pcr1xAlnRep0_VS_wgEncodeHaibTfbsHepg2ControlPcr1xAlnRep0.bb HepG2 ChipSeq ZBTB33 Peaks bigBed HudsonAlpha analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/spp/optimal/hub/spp.optimal.wgEncodeHaibTfbsHepg2Zbtb33V0416101AlnRep0_VS_wgEncodeHaibTfbsHepg2ControlV0416101AlnRep0.bb HepG2 ChipSeq ZBTB33 Peaks bigBed HudsonAlpha analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/spp/optimal/hub/spp.optimal.wgEncodeHaibTfbsHtb11NrsfPcr2xAlnRep0_VS_wgEncodeHaibTfbsHtb11ControlPcr2xAlnRep0.bb HTB-11 ChipSeq NRSF Peaks bigBed HudsonAlpha analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/spp/optimal/hub/spp.optimal.wgEncodeHaibTfbsK562Bcl3Pcr1xAlnRep0_VS_wgEncodeHaibTfbsK562ControlV0416101AlnRep0.bb K562 ChipSeq BCL3 Peaks bigBed HudsonAlpha analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/spp/optimal/hub/spp.optimal.wgEncodeHaibTfbsK562Bclaf1m33Pcr1xAlnRep0_VS_wgEncodeHaibTfbsK562ControlV0416101AlnRep0.bb K562 ChipSeq BCLAF1_(M33-P5B11) Peaks bigBed HudsonAlpha analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/spp/optimal/hub/spp.optimal.wgEncodeHaibTfbsK562Ctcflsc98982V0416101AlnRep0_VS_wgEncodeHaibTfbsK562ControlV0416101AlnRep0.bb K562 ChipSeq CTCFL_(SC-98982) Peaks bigBed HudsonAlpha analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/spp/optimal/hub/spp.optimal.wgEncodeHaibTfbsK562E2f6h50V0416102AlnRep0_VS_wgEncodeHaibTfbsK562ControlPcr1xAlnRep0.bb K562 ChipSeq E2F6_(H-50) Peaks bigBed HudsonAlpha analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/spp/optimal/hub/spp.optimal.wgEncodeHaibTfbsK562Egr1V0416101AlnRep0_VS_wgEncodeHaibTfbsK562ControlV0416101AlnRep0.bb K562 ChipSeq Egr-1 Peaks bigBed HudsonAlpha analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/spp/optimal/hub/spp.optimal.wgEncodeHaibTfbsK562Elf1sc631V0416102AlnRep0_VS_wgEncodeHaibTfbsK562ControlPcr1xAlnRep0.bb K562 ChipSeq ELF1_(SC-631) Peaks bigBed HudsonAlpha analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/spp/optimal/hub/spp.optimal.wgEncodeHaibTfbsK562Ets1V0416101AlnRep0_VS_wgEncodeHaibTfbsK562ControlV0416101AlnRep0.bb K562 ChipSeq ETS1 Peaks bigBed HudsonAlpha analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/spp/optimal/hub/spp.optimal.wgEncodeHaibTfbsK562Fosl1sc183V0416101AlnRep0_VS_wgEncodeHaibTfbsK562ControlV0416101AlnRep0.bb K562 ChipSeq FOSL1_(SC-183) Peaks bigBed HudsonAlpha analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/spp/optimal/hub/spp.optimal.wgEncodeHaibTfbsK562GabpV0416101AlnRep0_VS_wgEncodeHaibTfbsK562ControlV0416101AlnRep0.bb K562 ChipSeq GABP Peaks bigBed HudsonAlpha analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/spp/optimal/hub/spp.optimal.wgEncodeHaibTfbsK562Gata2cg2Pcr1xAlnRep0_VS_wgEncodeHaibTfbsK562ControlV0416101AlnRep0.bb K562 ChipSeq GATA2_(CG2-96) Peaks bigBed HudsonAlpha analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/spp/optimal/hub/spp.optimal.wgEncodeHaibTfbsK562Hdac2sc6296V0416102AlnRep0_VS_wgEncodeHaibTfbsK562ControlPcr1xAlnRep0.bb K562 ChipSeq HDAC2_(SC-6296) Peaks bigBed HudsonAlpha analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/spp/optimal/hub/spp.optimal.wgEncodeHaibTfbsK562Hey1Pcr1xAlnRep0_VS_wgEncodeHaibTfbsK562ControlPcr1xAlnRep0.bb K562 ChipSeq HEY1 Peaks bigBed HudsonAlpha analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/spp/optimal/hub/spp.optimal.wgEncodeHaibTfbsK562MaxV0416102AlnRep0_VS_wgEncodeHaibTfbsK562ControlPcr1xAlnRep0.bb K562 ChipSeq Max Peaks bigBed HudsonAlpha analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/spp/optimal/hub/spp.optimal.wgEncodeHaibTfbsK562NrsfV0416102AlnRep0_VS_wgEncodeHaibTfbsK562ControlV0416101AlnRep0.bb K562 ChipSeq NRSF Peaks bigBed HudsonAlpha analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/spp/optimal/hub/spp.optimal.wgEncodeHaibTfbsK562Pol24h8Pcr1xAlnRep0_VS_wgEncodeHaibTfbsK562ControlPcr1xAlnRep0.bb K562 ChipSeq Pol2-4H8 Peaks bigBed HudsonAlpha analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/spp/optimal/hub/spp.optimal.wgEncodeHaibTfbsK562Pol24h8V0416101AlnRep0_VS_wgEncodeHaibTfbsK562ControlV0416101AlnRep0.bb K562 ChipSeq Pol2-4H8 Peaks bigBed HudsonAlpha analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/spp/optimal/hub/spp.optimal.wgEncodeHaibTfbsK562Pol2V0416101AlnRep0_VS_wgEncodeHaibTfbsK562ControlV0416101AlnRep0.bb K562 ChipSeq Pol2 Peaks bigBed HudsonAlpha analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/spp/optimal/hub/spp.optimal.wgEncodeHaibTfbsK562Pu1Pcr1xAlnRep0_VS_wgEncodeHaibTfbsK562ControlPcr1xAlnRep0.bb K562 ChipSeq PU.1 Peaks bigBed HudsonAlpha analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/spp/optimal/hub/spp.optimal.wgEncodeHaibTfbsK562Rad21V0416102AlnRep0_VS_wgEncodeHaibTfbsK562ControlPcr1xAlnRep0.bb K562 ChipSeq Rad21 Peaks bigBed HudsonAlpha analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/spp/optimal/hub/spp.optimal.wgEncodeHaibTfbsK562Sin3ak20V0416101AlnRep0_VS_wgEncodeHaibTfbsK562ControlV0416101AlnRep0.bb K562 ChipSeq Sin3Ak-20 Peaks bigBed HudsonAlpha analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/spp/optimal/hub/spp.optimal.wgEncodeHaibTfbsK562Six5Pcr1xAlnRep0_VS_wgEncodeHaibTfbsK562ControlPcr1xAlnRep0.bb K562 ChipSeq SIX5 Peaks bigBed HudsonAlpha analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/spp/optimal/hub/spp.optimal.wgEncodeHaibTfbsK562Sp1Pcr1xAlnRep0_VS_wgEncodeHaibTfbsK562ControlV0416101AlnRep0.bb K562 ChipSeq SP1 Peaks bigBed HudsonAlpha analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/spp/optimal/hub/spp.optimal.wgEncodeHaibTfbsK562Sp2sc643V0416102AlnRep0_VS_wgEncodeHaibTfbsK562ControlPcr1xAlnRep0.bb K562 ChipSeq SP2_(SC-643) Peaks bigBed HudsonAlpha analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/spp/optimal/hub/spp.optimal.wgEncodeHaibTfbsK562SrfV0416101AlnRep0_VS_wgEncodeHaibTfbsK562ControlV0416101AlnRep0.bb K562 ChipSeq SRF Peaks bigBed HudsonAlpha analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/spp/optimal/hub/spp.optimal.wgEncodeHaibTfbsK562Taf1Pcr1xAlnRep0_VS_wgEncodeHaibTfbsK562ControlPcr1xAlnRep0.bb K562 ChipSeq TAF1 Peaks bigBed HudsonAlpha analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/spp/optimal/hub/spp.optimal.wgEncodeHaibTfbsK562Taf1V0416101AlnRep0_VS_wgEncodeHaibTfbsK562ControlV0416101AlnRep0.bb K562 ChipSeq TAF1 Peaks bigBed HudsonAlpha analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/spp/optimal/hub/spp.optimal.wgEncodeHaibTfbsK562Taf7sq8V0416101AlnRep0_VS_wgEncodeHaibTfbsK562ControlV0416101AlnRep0.bb K562 ChipSeq TAF7_(SQ-8) Peaks bigBed HudsonAlpha analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/spp/optimal/hub/spp.optimal.wgEncodeHaibTfbsK562Thap1sc98174V0416101AlnRep0_VS_wgEncodeHaibTfbsK562ControlV0416101AlnRep0.bb K562 ChipSeq THAP1_(SC-98174) Peaks bigBed HudsonAlpha analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/spp/optimal/hub/spp.optimal.wgEncodeHaibTfbsK562Usf1V0416101AlnRep0_VS_wgEncodeHaibTfbsK562ControlV0416101AlnRep0.bb K562 ChipSeq USF-1 Peaks bigBed HudsonAlpha analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/spp/optimal/hub/spp.optimal.wgEncodeHaibTfbsK562Yy1V0416101AlnRep0_VS_wgEncodeHaibTfbsK562ControlV0416101AlnRep0.bb K562 ChipSeq YY1 Peaks bigBed HudsonAlpha analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/spp/optimal/hub/spp.optimal.wgEncodeHaibTfbsK562Yy1V0416102AlnRep0_VS_wgEncodeHaibTfbsK562ControlPcr1xAlnRep0.bb K562 ChipSeq YY1 Peaks bigBed HudsonAlpha analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/spp/optimal/hub/spp.optimal.wgEncodeHaibTfbsK562Zbtb33Pcr1xAlnRep0_VS_wgEncodeHaibTfbsK562ControlV0416101AlnRep0.bb K562 ChipSeq ZBTB33 Peaks bigBed HudsonAlpha analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/spp/optimal/hub/spp.optimal.wgEncodeHaibTfbsK562Zbtb7asc34508V0416101AlnRep0_VS_wgEncodeHaibTfbsK562ControlV0416101AlnRep0.bb K562 ChipSeq ZBTB7A_(SC-34508) Peaks bigBed HudsonAlpha analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/spp/optimal/hub/spp.optimal.wgEncodeHaibTfbsPanc1NrsfPcr2xAlnRep0_VS_wgEncodeHaibTfbsPanc1ControlPcr2xAlnRep0.bb PANC-1 ChipSeq NRSF Peaks bigBed HudsonAlpha analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/spp/optimal/hub/spp.optimal.wgEncodeHaibTfbsPfsk1NrsfPcr2xAlnRep0_VS_wgEncodeHaibTfbsPfsk1ControlPcr2xAlnRep0.bb PFSK-1 ChipSeq NRSF Peaks bigBed HudsonAlpha analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/spp/optimal/hub/spp.optimal.wgEncodeHaibTfbsSknshraCtcfV0416102AlnRep0_VS_wgEncodeHaibTfbsSknshraControlV0416102AlnRep2.bb SK-N-SH_RA ChipSeq CTCF Peaks bigBed HudsonAlpha analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/spp/optimal/hub/spp.optimal.wgEncodeHaibTfbsSknshraP300V0416102AlnRep0_VS_wgEncodeHaibTfbsSknshraControlV0416102AlnRep2.bb SK-N-SH_RA ChipSeq p300 Peaks bigBed HudsonAlpha analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/spp/optimal/hub/spp.optimal.wgEncodeHaibTfbsSknshraRad21V0416102AlnRep0_VS_wgEncodeHaibTfbsSknshraControlV0416102AlnRep2.bb SK-N-SH_RA ChipSeq Rad21 Peaks bigBed HudsonAlpha analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/spp/optimal/hub/spp.optimal.wgEncodeHaibTfbsSknshraUsf1sc8983V0416102AlnRep0_VS_wgEncodeHaibTfbsSknshraControlV0416102AlnRep2.bb SK-N-SH_RA ChipSeq USF1_(SC-8983) Peaks bigBed HudsonAlpha analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/spp/optimal/hub/spp.optimal.wgEncodeHaibTfbsSknshraYy1c20V0416102AlnRep0_VS_wgEncodeHaibTfbsSknshraControlV0416102AlnRep2.bb SK-N-SH_RA ChipSeq YY1_(C-20) Peaks bigBed HudsonAlpha analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/spp/optimal/hub/spp.optimal.wgEncodeHaibTfbsT47dCtcfsc5916V0416102Dmso2AlnRep0_VS_wgEncodeHaibTfbsT47dControlV0416102Dmso2AlnRep2.bb T-47D ChipSeq CTCF_(SC-5916) Peaks bigBed HudsonAlpha analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/spp/optimal/hub/spp.optimal.wgEncodeHaibTfbsT47dEralphaaPcr2xGen1hAlnRep0_VS_wgEncodeHaibTfbsT47dEralphaaV0416102Dmso2AlnRep0.bb T-47D ChipSeq ERalpha_a Peaks bigBed HudsonAlpha analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/spp/optimal/hub/spp.optimal.wgEncodeHaibTfbsT47dEralphaaV0416102Estradia1hAlnRep0_VS_wgEncodeHaibTfbsT47dEralphaaV0416102Dmso2AlnRep0.bb T-47D ChipSeq ERalpha_a Peaks bigBed HudsonAlpha analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/spp/optimal/hub/spp.optimal.wgEncodeHaibTfbsT47dFoxa1c20V0416102Dmso2AlnRep0_VS_wgEncodeHaibTfbsT47dControlV0416102Dmso2AlnRep2.bb T-47D ChipSeq FOXA1_(C-20) Peaks bigBed HudsonAlpha analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/spp/optimal/hub/spp.optimal.wgEncodeHaibTfbsT47dGata3sc268V0416102Dmso2AlnRep0_VS_wgEncodeHaibTfbsT47dControlV0416102Dmso2AlnRep2.bb T-47D ChipSeq GATA3_(SC-268) Peaks bigBed HudsonAlpha analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/spp/optimal/hub/spp.optimal.wgEncodeHaibTfbsT47dP300V0416102Dmso2AlnRep0_VS_wgEncodeHaibTfbsT47dControlV0416102Dmso2AlnRep2.bb T-47D ChipSeq p300 Peaks bigBed HudsonAlpha analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/spp/optimal/hub/spp.optimal.wgEncodeHaibTfbsU87NrsfPcr2xAlnRep0_VS_wgEncodeHaibTfbsU87ControlPcr2xAlnRep0.bb U87 ChipSeq NRSF Peaks bigBed HudsonAlpha analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/spp/optimal/hub/spp.optimal.wgEncodeOpenChromChipFibroblCtcfAlnRep0_VS_wgEncodeOpenChromChipFibroblInputAln.bb Fibrobl ChipSeq CTCF Peaks bigBed UT-A analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/spp/optimal/hub/spp.optimal.wgEncodeOpenChromChipGlioblaCtcfAlnRep0_VS_wgEncodeOpenChromChipGlioblaInputAln.bb Gliobla ChipSeq CTCF Peaks bigBed UT-A analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/spp/optimal/hub/spp.optimal.wgEncodeOpenChromChipGlioblaPol2AlnRep0_VS_wgEncodeOpenChromChipGlioblaInputAln.bb Gliobla ChipSeq Pol2 Peaks bigBed UT-A analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/spp/optimal/hub/spp.optimal.wgEncodeOpenChromChipGm12878CmycAlnRep0_VS_wgEncodeOpenChromChipGm12878InputAln.bb GM12878 ChipSeq c-Myc Peaks bigBed UT-A analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/spp/optimal/hub/spp.optimal.wgEncodeOpenChromChipGm12878CtcfAlnRep0_VS_wgEncodeOpenChromChipGm12878InputAln.bb GM12878 ChipSeq CTCF Peaks bigBed UT-A analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/spp/optimal/hub/spp.optimal.wgEncodeOpenChromChipGm12878Pol2AlnRep0_VS_wgEncodeOpenChromChipGm12878InputAln.bb GM12878 ChipSeq Pol2 Peaks bigBed UT-A analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/spp/optimal/hub/spp.optimal.wgEncodeOpenChromChipHelas3CmycAlnRep0_VS_wgEncodeOpenChromChipHelas3InputAln.bb HeLa-S3 ChipSeq c-Myc Peaks bigBed UT-A analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/spp/optimal/hub/spp.optimal.wgEncodeOpenChromChipHelas3CtcfAlnRep0_VS_wgEncodeOpenChromChipHelas3InputAln.bb HeLa-S3 ChipSeq CTCF Peaks bigBed UT-A analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/spp/optimal/hub/spp.optimal.wgEncodeOpenChromChipHelas3Pol2AlnRep0_VS_wgEncodeOpenChromChipHelas3InputAln.bb HeLa-S3 ChipSeq Pol2 Peaks bigBed UT-A analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/spp/optimal/hub/spp.optimal.wgEncodeOpenChromChipHepg2CmycAlnRep0_VS_wgEncodeOpenChromChipHepg2InputAln.bb HepG2 ChipSeq c-Myc Peaks bigBed UT-A analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/spp/optimal/hub/spp.optimal.wgEncodeOpenChromChipHepg2CtcfAlnRep0_VS_wgEncodeOpenChromChipHepg2InputAln.bb HepG2 ChipSeq CTCF Peaks bigBed UT-A analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/spp/optimal/hub/spp.optimal.wgEncodeOpenChromChipHepg2Pol2AlnRep0_VS_wgEncodeOpenChromChipHepg2InputAln.bb HepG2 ChipSeq Pol2 Peaks bigBed UT-A analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/spp/optimal/hub/spp.optimal.wgEncodeOpenChromChipHuvecCmycAlnRep1_VS_wgEncodeOpenChromChipHuvecInputAln.bb HUVEC ChipSeq c-Myc Peaks bigBed UT-A analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/spp/optimal/hub/spp.optimal.wgEncodeOpenChromChipHuvecCtcfAlnRep0_VS_wgEncodeOpenChromChipHuvecInputAln.bb HUVEC ChipSeq CTCF Peaks bigBed UT-A analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/spp/optimal/hub/spp.optimal.wgEncodeOpenChromChipHuvecPol2AlnRep0_VS_wgEncodeOpenChromChipHuvecInputAln.bb HUVEC ChipSeq Pol2 Peaks bigBed UT-A analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/spp/optimal/hub/spp.optimal.wgEncodeOpenChromChipK562CmycAlnRep0_VS_wgEncodeOpenChromChipK562InputAln.bb K562 ChipSeq c-Myc Peaks bigBed UT-A analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/spp/optimal/hub/spp.optimal.wgEncodeOpenChromChipK562CtcfAlnRep0_VS_wgEncodeOpenChromChipK562InputAln.bb K562 ChipSeq CTCF Peaks bigBed UT-A analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/spp/optimal/hub/spp.optimal.wgEncodeOpenChromChipK562Pol2AlnRep0_VS_wgEncodeOpenChromChipK562InputAln.bb K562 ChipSeq Pol2 Peaks bigBed UT-A analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/spp/optimal/hub/spp.optimal.wgEncodeOpenChromChipMcf7CmycEstroAlnRep0_VS_wgEncodeOpenChromChipMcf7InputAln.bb MCF-7 ChipSeq c-Myc Peaks bigBed UT-A analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/spp/optimal/hub/spp.optimal.wgEncodeOpenChromChipMcf7CmycVehAlnRep0_VS_wgEncodeOpenChromChipMcf7InputAln.bb MCF-7 ChipSeq c-Myc Peaks bigBed UT-A analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/spp/optimal/hub/spp.optimal.wgEncodeOpenChromChipMcf7CtcfAlnRep0_VS_wgEncodeOpenChromChipMcf7InputAln.bb MCF-7 ChipSeq CTCF Peaks bigBed UT-A analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/spp/optimal/hub/spp.optimal.wgEncodeOpenChromChipMcf7CtcfEstroAlnRep0_VS_wgEncodeOpenChromChipMcf7InputAln.bb MCF-7 ChipSeq CTCF Peaks bigBed UT-A analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/spp/optimal/hub/spp.optimal.wgEncodeOpenChromChipMcf7CtcfVehAlnRep0_VS_wgEncodeOpenChromChipMcf7InputAln.bb MCF-7 ChipSeq CTCF Peaks bigBed UT-A analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/spp/optimal/hub/spp.optimal.wgEncodeOpenChromChipMcf7Pol2AlnRep0_VS_wgEncodeOpenChromChipMcf7InputAln.bb MCF-7 ChipSeq Pol2 Peaks bigBed UT-A analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/spp/optimal/hub/spp.optimal.wgEncodeOpenChromChipProgfibCtcfAlnRep0_VS_wgEncodeOpenChromChipProgfibInputAln.bb ProgFib ChipSeq CTCF Peaks bigBed UT-A analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/spp/optimal/hub/spp.optimal.wgEncodeOpenChromChipProgfibPol2AlnRep0_VS_wgEncodeOpenChromChipProgfibInputAln.bb ProgFib ChipSeq Pol2 Peaks bigBed UT-A analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/spp/optimal/hub/spp.optimal.wgEncodeSydhTfbsGm10847NfkbIggrabAlnRep0_VS_wgEncodeSydhTfbsGm10847InputIggrabAlnRep0.bb GM10847 ChipSeq NFKB Peaks bigBed Stanford analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/spp/optimal/hub/spp.optimal.wgEncodeSydhTfbsGm10847Pol2IggmusAlnRep1_VS_wgEncodeSydhTfbsGm10847InputIggmusAlnRep0.bb GM10847 ChipSeq Pol2 Peaks bigBed Stanford analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/spp/optimal/hub/spp.optimal.wgEncodeSydhTfbsGm12878Brca1cIggmusAlnRep0_VS_wgEncodeSydhTfbsGm12878InputIggmusAlnRep0.bb GM12878 ChipSeq BRCA1_(C-1863) Peaks bigBed Stanford analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/spp/optimal/hub/spp.optimal.wgEncodeSydhTfbsGm12878CfosStdAlnRep0_VS_wgEncodeSydhTfbsGm12878InputStdAlnRep1.bb GM12878 ChipSeq c-Fos Peaks bigBed Stanford analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/spp/optimal/hub/spp.optimal.wgEncodeSydhTfbsGm12878Chd21250IggmusAlnRep0_VS_wgEncodeSydhTfbsGm12878InputIggmusAlnRep0.bb GM12878 ChipSeq CHD2_(N-1250) Peaks bigBed Stanford analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/spp/optimal/hub/spp.optimal.wgEncodeSydhTfbsGm12878Ctcfc20StdAlnRep0_VS_wgEncodeSydhTfbsGm12878InputStdAlnRep1.bb GM12878 ChipSeq CTCF_(C-20) Peaks bigBed Stanford analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/spp/optimal/hub/spp.optimal.wgEncodeSydhTfbsGm12878EbfStdAlnRep0_VS_wgEncodeSydhTfbsGm12878InputStdAlnRep1.bb GM12878 ChipSeq EBF Peaks bigBed Stanford analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/spp/optimal/hub/spp.optimal.wgEncodeSydhTfbsGm12878Gcn5StdAlnRep0_VS_wgEncodeSydhTfbsGm12878InputStdAlnRep1.bb GM12878 ChipSeq GCN5 Peaks bigBed Harvard(Weissman) analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/spp/optimal/hub/spp.optimal.wgEncodeSydhTfbsGm12878Irf3StdAlnRep0_VS_wgEncodeSydhTfbsGm12878InputStdAlnRep1.bb GM12878 ChipSeq IRF3 Peaks bigBed Stanford analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/spp/optimal/hub/spp.optimal.wgEncodeSydhTfbsGm12878JundStdAlnRep0_VS_wgEncodeSydhTfbsGm12878InputStdAlnRep1.bb GM12878 ChipSeq JunD Peaks bigBed Stanford analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/spp/optimal/hub/spp.optimal.wgEncodeSydhTfbsGm12878MaxStdAlnRep0_VS_wgEncodeSydhTfbsGm12878InputStdAlnRep1.bb GM12878 ChipSeq Max Peaks bigBed Stanford analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/spp/optimal/hub/spp.optimal.wgEncodeSydhTfbsGm12878Nfe2hStdAlnRep0_VS_wgEncodeSydhTfbsGm12878InputStdAlnRep1.bb GM12878 ChipSeq NF-E2_(H-230) Peaks bigBed Stanford analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/spp/optimal/hub/spp.optimal.wgEncodeSydhTfbsGm12878NfkbIggrabAlnRep0_VS_wgEncodeSydhTfbsGm12878InputIggrabAlnRep0.bb GM12878 ChipSeq NFKB Peaks bigBed Stanford analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/spp/optimal/hub/spp.optimal.wgEncodeSydhTfbsGm12878NfkbTnfaStdAlnRep0_VS_wgEncodeSydhTfbsGm12878InputStdAlnRep1.bb GM12878 ChipSeq NFKB Peaks bigBed Stanford analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/spp/optimal/hub/spp.optimal.wgEncodeSydhTfbsGm12878Nrf1IggmusAlnRep0_VS_wgEncodeSydhTfbsGm12878InputIggmusAlnRep0.bb GM12878 ChipSeq Nrf1 Peaks bigBed Stanford analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/spp/optimal/hub/spp.optimal.wgEncodeSydhTfbsGm12878P300n15StdAlnRep0_VS_wgEncodeSydhTfbsGm12878InputStdAlnRep1.bb GM12878 ChipSeq p300_(N-15) Peaks bigBed Stanford analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/spp/optimal/hub/spp.optimal.wgEncodeSydhTfbsGm12878Pol2IggmusAlnRep0_VS_wgEncodeSydhTfbsGm12878InputIggmusAlnRep0.bb GM12878 ChipSeq Pol2 Peaks bigBed Stanford analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/spp/optimal/hub/spp.optimal.wgEncodeSydhTfbsGm12878Pol2StdAlnRep0_VS_wgEncodeSydhTfbsGm12878InputStdAlnRep1.bb GM12878 ChipSeq Pol2 Peaks bigBed Stanford analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/spp/optimal/hub/spp.optimal.wgEncodeSydhTfbsGm12878Pol3StdAlnRep0_VS_wgEncodeSydhTfbsGm12878InputStdAlnRep1.bb GM12878 ChipSeq Pol3 Peaks bigBed Stanford analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/spp/optimal/hub/spp.optimal.wgEncodeSydhTfbsGm12878Rad21IggrabAlnRep0_VS_wgEncodeSydhTfbsGm12878InputIggrabAlnRep0.bb GM12878 ChipSeq Rad21 Peaks bigBed Stanford analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/spp/optimal/hub/spp.optimal.wgEncodeSydhTfbsGm12878Rfx5n494IggmusAlnRep0_VS_wgEncodeSydhTfbsGm12878InputIggmusAlnRep0.bb GM12878 ChipSeq RFX5_(N-494) Peaks bigBed Stanford analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/spp/optimal/hub/spp.optimal.wgEncodeSydhTfbsGm12878Smc3ab9263IggmusAlnRep0_VS_wgEncodeSydhTfbsGm12878InputIggmusAlnRep0.bb GM12878 ChipSeq SMC3_(ab9263) Peaks bigBed Stanford analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/spp/optimal/hub/spp.optimal.wgEncodeSydhTfbsGm12878Spt20StdAlnRep0_VS_wgEncodeSydhTfbsGm12878InputStdAlnRep1.bb GM12878 ChipSeq SPT20 Peaks bigBed Harvard(Weissman) analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/spp/optimal/hub/spp.optimal.wgEncodeSydhTfbsGm12878Stat1StdAlnRep0_VS_wgEncodeSydhTfbsGm12878InputStdAlnRep1.bb GM12878 ChipSeq STAT1 Peaks bigBed Stanford analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/spp/optimal/hub/spp.optimal.wgEncodeSydhTfbsGm12878Stat3IggmusAlnRep0_VS_wgEncodeSydhTfbsGm12878InputIggmusAlnRep0.bb GM12878 ChipSeq STAT3 Peaks bigBed Stanford analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/spp/optimal/hub/spp.optimal.wgEncodeSydhTfbsGm12878TbpIggmusAlnRep0_VS_wgEncodeSydhTfbsGm12878InputIggmusAlnRep0.bb GM12878 ChipSeq TBP Peaks bigBed Stanford analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/spp/optimal/hub/spp.optimal.wgEncodeSydhTfbsGm12878Tr4StdAlnRep0_VS_wgEncodeSydhTfbsGm12878InputStdAlnRep1.bb GM12878 ChipSeq TR4 Peaks bigBed Stanford analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/spp/optimal/hub/spp.optimal.wgEncodeSydhTfbsGm12878Usf2IggmusAlnRep0_VS_wgEncodeSydhTfbsGm12878InputIggmusAlnRep0.bb GM12878 ChipSeq USF2 Peaks bigBed Stanford analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/spp/optimal/hub/spp.optimal.wgEncodeSydhTfbsGm12878WhipIggmusAlnRep0_VS_wgEncodeSydhTfbsGm12878InputIggmusAlnRep0.bb GM12878 ChipSeq WHIP Peaks bigBed Stanford analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/spp/optimal/hub/spp.optimal.wgEncodeSydhTfbsGm12878Yy1StdAlnRep0_VS_wgEncodeSydhTfbsGm12878InputStdAlnRep1.bb GM12878 ChipSeq YY1 Peaks bigBed Stanford analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/spp/optimal/hub/spp.optimal.wgEncodeSydhTfbsGm12878Znf143166181apStdAlnRep0_VS_wgEncodeSydhTfbsGm12878InputStdAlnRep1.bb GM12878 ChipSeq Znf143_(16618-1-AP) Peaks bigBed Stanford analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/spp/optimal/hub/spp.optimal.wgEncodeSydhTfbsGm12878Zzz3StdAlnRep0_VS_wgEncodeSydhTfbsGm12878InputStdAlnRep1.bb GM12878 ChipSeq ZZZ3 Peaks bigBed Stanford analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/spp/optimal/hub/spp.optimal.wgEncodeSydhTfbsGm12891NfkbIggrabAlnRep0_VS_wgEncodeSydhTfbsGm12891InputIggrabAlnRep0.bb GM12891 ChipSeq NFKB Peaks bigBed Stanford analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/spp/optimal/hub/spp.optimal.wgEncodeSydhTfbsGm12891Pol2IggmusAlnRep0_VS_wgEncodeSydhTfbsGm12891InputIggmusAlnRep0.bb GM12891 ChipSeq Pol2 Peaks bigBed Stanford analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/spp/optimal/hub/spp.optimal.wgEncodeSydhTfbsGm12892NfkbIggrabAlnRep0_VS_wgEncodeSydhTfbsGm12892InputIggrabAlnRep0.bb GM12892 ChipSeq NFKB Peaks bigBed Stanford analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/spp/optimal/hub/spp.optimal.wgEncodeSydhTfbsGm12892Pol2IggmusAlnRep0_VS_wgEncodeSydhTfbsGm12892InputIggmusAlnRep0.bb GM12892 ChipSeq Pol2 Peaks bigBed Stanford analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/spp/optimal/hub/spp.optimal.wgEncodeSydhTfbsGm15510NfkbIggrabAlnRep0_VS_wgEncodeSydhTfbsGm15510InputIggrabAlnRep0.bb GM15510 ChipSeq NFKB Peaks bigBed Stanford analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/spp/optimal/hub/spp.optimal.wgEncodeSydhTfbsGm15510Pol2IggmusAlnRep0_VS_wgEncodeSydhTfbsGm15510InputIggmusAlnRep0.bb GM15510 ChipSeq Pol2 Peaks bigBed Stanford analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/spp/optimal/hub/spp.optimal.wgEncodeSydhTfbsGm18505NfkbIggrabAlnRep0_VS_wgEncodeSydhTfbsGm18505InputIggrabAlnRep0.bb GM18505 ChipSeq NFKB Peaks bigBed Stanford analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/spp/optimal/hub/spp.optimal.wgEncodeSydhTfbsGm18505Pol2IggmusAlnRep0_VS_wgEncodeSydhTfbsGm18505InputIggmusAlnRep0.bb GM18505 ChipSeq Pol2 Peaks bigBed Stanford analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/spp/optimal/hub/spp.optimal.wgEncodeSydhTfbsGm18526NfkbIggrabAlnRep0_VS_wgEncodeSydhTfbsGm18526InputIggrabAlnRep0.bb GM18526 ChipSeq NFKB Peaks bigBed Stanford analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/spp/optimal/hub/spp.optimal.wgEncodeSydhTfbsGm18526Pol2IggmusAlnRep0_VS_wgEncodeSydhTfbsGm18526InputIggmusAlnRep0.bb GM18526 ChipSeq Pol2 Peaks bigBed Stanford analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/spp/optimal/hub/spp.optimal.wgEncodeSydhTfbsGm18951NfkbIggrabAlnRep0_VS_wgEncodeSydhTfbsGm18951InputIggrabAlnRep0.bb GM18951 ChipSeq NFKB Peaks bigBed Stanford analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/spp/optimal/hub/spp.optimal.wgEncodeSydhTfbsGm18951Pol2IggmusAlnRep0_VS_wgEncodeSydhTfbsGm18951InputIggmusAlnRep1.bb GM18951 ChipSeq Pol2 Peaks bigBed Stanford analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/spp/optimal/hub/spp.optimal.wgEncodeSydhTfbsGm19099NfkbIggrabAlnRep0_VS_wgEncodeSydhTfbsGm19099InputIggrabAlnRep0.bb GM19099 ChipSeq NFKB Peaks bigBed Stanford analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/spp/optimal/hub/spp.optimal.wgEncodeSydhTfbsGm19099Pol2IggmusAlnRep0_VS_wgEncodeSydhTfbsGm19099InputIggmusAlnRep0.bb GM19099 ChipSeq Pol2 Peaks bigBed Stanford analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/spp/optimal/hub/spp.optimal.wgEncodeSydhTfbsGm19193NfkbIggrabAlnRep0_VS_wgEncodeSydhTfbsGm19193InputIggrabAlnRep0.bb GM19193 ChipSeq NFKB Peaks bigBed Stanford analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/spp/optimal/hub/spp.optimal.wgEncodeSydhTfbsGm19193Pol2IggmusAlnRep0_VS_wgEncodeSydhTfbsGm19193InputIggmusAlnRep0.bb GM19193 ChipSeq Pol2 Peaks bigBed Stanford analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/spp/optimal/hub/spp.optimal.wgEncodeSydhTfbsH1hescCjunIggrabAlnRep0_VS_wgEncodeSydhTfbsH1hescInputIggrabAln.bb H1-hESC ChipSeq c-Jun Peaks bigBed Stanford analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/spp/optimal/hub/spp.optimal.wgEncodeSydhTfbsH1hescCtbp2UcdAlnRep0_VS_wgEncodeSydhTfbsH1hescInputUcdAln.bb H1-hESC ChipSeq CtBP2 Peaks bigBed UCD analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/spp/optimal/hub/spp.optimal.wgEncodeSydhTfbsH1hescMaxUcdAlnRep0_VS_wgEncodeSydhTfbsH1hescInputUcdAln.bb H1-hESC ChipSeq Max Peaks bigBed Stanford analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/spp/optimal/hub/spp.optimal.wgEncodeSydhTfbsH1hescNrf1IggrabAlnRep0_VS_wgEncodeSydhTfbsH1hescInputIggrabAln.bb H1-hESC ChipSeq Nrf1 Peaks bigBed Stanford analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/spp/optimal/hub/spp.optimal.wgEncodeSydhTfbsH1hescRad21IggrabAlnRep0_VS_wgEncodeSydhTfbsH1hescInputIggrabAln.bb H1-hESC ChipSeq Rad21 Peaks bigBed Stanford analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/spp/optimal/hub/spp.optimal.wgEncodeSydhTfbsH1hescRfx5n494IggrabAlnRep0_VS_wgEncodeSydhTfbsH1hescInputIggrabAln.bb H1-hESC ChipSeq RFX5_(N-494) Peaks bigBed Stanford analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/spp/optimal/hub/spp.optimal.wgEncodeSydhTfbsH1hescSuz12UcdAlnRep0_VS_wgEncodeSydhTfbsH1hescInputUcdAln.bb H1-hESC ChipSeq SUZ12 Peaks bigBed UCD analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/spp/optimal/hub/spp.optimal.wgEncodeSydhTfbsH1hescTbpStdAlnRep0_VS_wgEncodeSydhTfbsH1hescInputStdAln.bb H1-hESC ChipSeq TBP Peaks bigBed Stanford analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/spp/optimal/hub/spp.optimal.wgEncodeSydhTfbsH1hescUsf2IggrabAlnRep0_VS_wgEncodeSydhTfbsH1hescInputIggrabAln.bb H1-hESC ChipSeq USF2 Peaks bigBed Stanford analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/spp/optimal/hub/spp.optimal.wgEncodeSydhTfbsHct116Pol2UcdAlnRep0_VS_wgEncodeSydhTfbsHct116InputUcdAlnRep1.bb HCT-116 ChipSeq Pol2 Peaks bigBed Stanford analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/spp/optimal/hub/spp.optimal.wgEncodeSydhTfbsHct116Tcf4UcdAlnRep0_VS_wgEncodeSydhTfbsHct116InputUcdAlnRep1.bb HCT-116 ChipSeq TCF4 Peaks bigBed Stanford analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/spp/optimal/hub/spp.optimal.wgEncodeSydhTfbsHek293bElk4UcdAlnRep0_VS_wgEncodeSydhTfbsHek293InputUcdAln.bb HEK293(b) ChipSeq ELK4 Peaks bigBed UCD analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/spp/optimal/hub/spp.optimal.wgEncodeSydhTfbsHek293bKap1UcdAlnRep0_VS_wgEncodeSydhTfbsHek293InputUcdAln.bb HEK293(b) ChipSeq KAP1 Peaks bigBed UCD analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/spp/optimal/hub/spp.optimal.wgEncodeSydhTfbsHek293bPol2StdAlnRep0_VS_wgEncodeSydhTfbsHek293bInputStdAlnRep1.bb HEK293(b) ChipSeq Pol2 Peaks bigBed Stanford analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/spp/optimal/hub/spp.optimal.wgEncodeSydhTfbsHelas3Ap2alphaStdAlnRep0_VS_wgEncodeSydhTfbsHelas3InputStdAlnRep1.bb HeLa-S3 ChipSeq AP-2alpha Peaks bigBed Stanford analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/spp/optimal/hub/spp.optimal.wgEncodeSydhTfbsHelas3Ap2gammaStdAlnRep0_VS_wgEncodeSydhTfbsHelas3InputStdAlnRep1.bb HeLa-S3 ChipSeq AP-2gamma Peaks bigBed Stanford analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/spp/optimal/hub/spp.optimal.wgEncodeSydhTfbsHelas3Baf155IggmusAlnRep0_VS_wgEncodeSydhTfbsHelas3InputIggmusAlnRep0.bb HeLa-S3 ChipSeq BAF155 Peaks bigBed Stanford analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/spp/optimal/hub/spp.optimal.wgEncodeSydhTfbsHelas3Baf170IggmusAlnRep0_VS_wgEncodeSydhTfbsHelas3InputIggmusAlnRep0.bb HeLa-S3 ChipSeq BAF170 Peaks bigBed Stanford analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/spp/optimal/hub/spp.optimal.wgEncodeSydhTfbsHelas3Bdp1StdAlnRep0_VS_wgEncodeSydhTfbsHelas3InputStdAlnRep1.bb HeLa-S3 ChipSeq BDP1 Peaks bigBed Stanford analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/spp/optimal/hub/spp.optimal.wgEncodeSydhTfbsHelas3Brca1cIggrabAlnRep0_VS_wgEncodeSydhTfbsHelas3InputIggrabAlnRep1.bb HeLa-S3 ChipSeq BRCA1_(C-1863) Peaks bigBed Stanford analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/spp/optimal/hub/spp.optimal.wgEncodeSydhTfbsHelas3Brf1StdAlnRep0_VS_wgEncodeSydhTfbsHelas3InputStdAlnRep1.bb HeLa-S3 ChipSeq BRF1 Peaks bigBed Stanford analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/spp/optimal/hub/spp.optimal.wgEncodeSydhTfbsHelas3Brf2StdAlnRep0_VS_wgEncodeSydhTfbsHelas3InputStdAlnRep1.bb HeLa-S3 ChipSeq BRF2 Peaks bigBed Stanford analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/spp/optimal/hub/spp.optimal.wgEncodeSydhTfbsHelas3Brg1IggmusAlnRep0_VS_wgEncodeSydhTfbsHelas3InputIggmusAlnRep0.bb HeLa-S3 ChipSeq Brg1 Peaks bigBed Stanford analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/spp/optimal/hub/spp.optimal.wgEncodeSydhTfbsHelas3CebpbIggrabAlnRep0_VS_wgEncodeSydhTfbsHelas3InputIggrabAlnRep1.bb HeLa-S3 ChipSeq CEBPB Peaks bigBed Stanford analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/spp/optimal/hub/spp.optimal.wgEncodeSydhTfbsHelas3CfosStdAlnRep0_VS_wgEncodeSydhTfbsHelas3InputStdAlnRep1.bb HeLa-S3 ChipSeq c-Fos Peaks bigBed Stanford analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/spp/optimal/hub/spp.optimal.wgEncodeSydhTfbsHelas3CjunIggrabAlnRep0_VS_wgEncodeSydhTfbsHelas3InputIggrabAlnRep1.bb HeLa-S3 ChipSeq c-Jun Peaks bigBed Stanford analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/spp/optimal/hub/spp.optimal.wgEncodeSydhTfbsHelas3CmycStdAlnRep0_VS_wgEncodeSydhTfbsHelas3InputStdAlnRep1.bb HeLa-S3 ChipSeq c-Myc Peaks bigBed Stanford analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/spp/optimal/hub/spp.optimal.wgEncodeSydhTfbsHelas3E2f1StdAlnRep0_VS_wgEncodeSydhTfbsHelas3InputStdAlnRep1.bb HeLa-S3 ChipSeq E2F1 Peaks bigBed Stanford analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/spp/optimal/hub/spp.optimal.wgEncodeSydhTfbsHelas3E2f4StdAlnRep0_VS_wgEncodeSydhTfbsHelas3InputStdAlnRep1.bb HeLa-S3 ChipSeq E2F4 Peaks bigBed Stanford analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/spp/optimal/hub/spp.optimal.wgEncodeSydhTfbsHelas3E2f6StdAlnRep0_VS_wgEncodeSydhTfbsHelas3InputStdAlnRep1.bb HeLa-S3 ChipSeq E2F6 Peaks bigBed Stanford analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/spp/optimal/hub/spp.optimal.wgEncodeSydhTfbsHelas3Elk4UcdAlnRep0_VS_wgEncodeSydhTfbsHelas3InputUcdAln.bb HeLa-S3 ChipSeq ELK4 Peaks bigBed UCD analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/spp/optimal/hub/spp.optimal.wgEncodeSydhTfbsHelas3Gcn5StdAlnRep0_VS_wgEncodeSydhTfbsHelas3InputStdAlnRep1.bb HeLa-S3 ChipSeq GCN5 Peaks bigBed Stanford analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/spp/optimal/hub/spp.optimal.wgEncodeSydhTfbsHelas3Gtf2f1rapIggrabAlnRep0_VS_wgEncodeSydhTfbsHelas3InputIggrabAlnRep1.bb HeLa-S3 ChipSeq GTF2F1_(RAP-74) Peaks bigBed Stanford analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/spp/optimal/hub/spp.optimal.wgEncodeSydhTfbsHelas3Hae2f1StdAlnRep0_VS_wgEncodeSydhTfbsHelas3InputStdAlnRep1.bb HeLa-S3 ChipSeq HA-E2F1 Peaks bigBed Stanford analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/spp/optimal/hub/spp.optimal.wgEncodeSydhTfbsHelas3Ini1IggmusAlnRep0_VS_wgEncodeSydhTfbsHelas3InputIggmusAlnRep0.bb HeLa-S3 ChipSeq Ini1 Peaks bigBed Stanford analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/spp/optimal/hub/spp.optimal.wgEncodeSydhTfbsHelas3Irf3IggrabAlnRep0_VS_wgEncodeSydhTfbsHelas3InputIggrabAlnRep1.bb HeLa-S3 ChipSeq IRF3 Peaks bigBed Stanford analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/spp/optimal/hub/spp.optimal.wgEncodeSydhTfbsHelas3JundIggrabAlnRep0_VS_wgEncodeSydhTfbsHelas3InputIggrabAlnRep1.bb HeLa-S3 ChipSeq JunD Peaks bigBed Stanford analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/spp/optimal/hub/spp.optimal.wgEncodeSydhTfbsHelas3MaxStdAlnRep0_VS_wgEncodeSydhTfbsHelas3InputStdAlnRep1.bb HeLa-S3 ChipSeq Max Peaks bigBed Stanford analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/spp/optimal/hub/spp.optimal.wgEncodeSydhTfbsHelas3Mxi1bhlhIggrabAlnRep0_VS_wgEncodeSydhTfbsHelas3InputIggrabAlnRep1.bb HeLa-S3 ChipSeq Mxi1_(bHLH) Peaks bigBed Stanford analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/spp/optimal/hub/spp.optimal.wgEncodeSydhTfbsHelas3Nrf1IggmusAlnRep0_VS_wgEncodeSydhTfbsHelas3InputIggmusAlnRep0.bb HeLa-S3 ChipSeq Nrf1 Peaks bigBed Stanford analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/spp/optimal/hub/spp.optimal.wgEncodeSydhTfbsHelas3P300n15IggrabAlnRep0_VS_wgEncodeSydhTfbsHelas3InputIggrabAlnRep1.bb HeLa-S3 ChipSeq p300_(N-15) Peaks bigBed Stanford analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/spp/optimal/hub/spp.optimal.wgEncodeSydhTfbsHelas3Pol2s2IggrabAlnRep0_VS_wgEncodeSydhTfbsHelas3InputIggrabAlnRep1.bb HeLa-S3 ChipSeq Pol2(phosphoS2) Peaks bigBed Stanford analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/spp/optimal/hub/spp.optimal.wgEncodeSydhTfbsHelas3Pol2StdAlnRep0_VS_wgEncodeSydhTfbsHelas3InputStdAlnRep1.bb HeLa-S3 ChipSeq Pol2 Peaks bigBed Stanford analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/spp/optimal/hub/spp.optimal.wgEncodeSydhTfbsHelas3Prdm1vIggrabAlnRep0_VS_wgEncodeSydhTfbsHelas3InputIggrabAlnRep1.bb HeLa-S3 ChipSeq PRDM1_(Val90) Peaks bigBed Stanford analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/spp/optimal/hub/spp.optimal.wgEncodeSydhTfbsHelas3Rad21IggrabAlnRep0_VS_wgEncodeSydhTfbsHelas3InputIggrabAlnRep1.bb HeLa-S3 ChipSeq Rad21 Peaks bigBed Stanford analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/spp/optimal/hub/spp.optimal.wgEncodeSydhTfbsHelas3Rfx5n494IggrabAlnRep0_VS_wgEncodeSydhTfbsHelas3InputIggrabAlnRep1.bb HeLa-S3 ChipSeq RFX5_(N-494) Peaks bigBed Stanford analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/spp/optimal/hub/spp.optimal.wgEncodeSydhTfbsHelas3Rpc155StdAlnRep0_VS_wgEncodeSydhTfbsHelas3InputStdAlnRep1.bb HeLa-S3 ChipSeq RPC155 Peaks bigBed Stanford analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/spp/optimal/hub/spp.optimal.wgEncodeSydhTfbsHelas3Smc3ab9263IggrabAlnRep0_VS_wgEncodeSydhTfbsHelas3InputIggrabAlnRep1.bb HeLa-S3 ChipSeq SMC3_(ab9263) Peaks bigBed Stanford analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/spp/optimal/hub/spp.optimal.wgEncodeSydhTfbsHelas3Spt20StdAlnRep0_VS_wgEncodeSydhTfbsHelas3InputStdAlnRep1.bb HeLa-S3 ChipSeq SPT20 Peaks bigBed Stanford analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/spp/optimal/hub/spp.optimal.wgEncodeSydhTfbsHelas3Stat1Ifng30StdAlnRep0_VS_wgEncodeSydhTfbsHelas3InputIfng30StdAlnRep1.bb HeLa-S3 ChipSeq STAT1 Peaks bigBed Stanford analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/spp/optimal/hub/spp.optimal.wgEncodeSydhTfbsHelas3Stat3IggrabAlnRep0_VS_wgEncodeSydhTfbsHelas3InputIggrabAlnRep1.bb HeLa-S3 ChipSeq STAT3 Peaks bigBed Stanford analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/spp/optimal/hub/spp.optimal.wgEncodeSydhTfbsHelas3TbpIggrabAlnRep0_VS_wgEncodeSydhTfbsHelas3InputIggrabAlnRep1.bb HeLa-S3 ChipSeq TBP Peaks bigBed Stanford analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/spp/optimal/hub/spp.optimal.wgEncodeSydhTfbsHelas3Tf3c110StdAlnRep0_VS_wgEncodeSydhTfbsHelas3InputStdAlnRep1.bb HeLa-S3 ChipSeq TFIIIC-110 Peaks bigBed Stanford analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/spp/optimal/hub/spp.optimal.wgEncodeSydhTfbsHelas3Tr4StdAlnRep0_VS_wgEncodeSydhTfbsHelas3InputStdAlnRep1.bb HeLa-S3 ChipSeq TR4 Peaks bigBed Stanford analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/spp/optimal/hub/spp.optimal.wgEncodeSydhTfbsHelas3Usf2IggmusAlnRep0_VS_wgEncodeSydhTfbsHelas3InputIggmusAlnRep0.bb HeLa-S3 ChipSeq USF2 Peaks bigBed Stanford analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/spp/optimal/hub/spp.optimal.wgEncodeSydhTfbsHelas3Znf274UcdAlnRep0_VS_wgEncodeSydhTfbsHelas3InputUcdAln.bb HeLa-S3 ChipSeq ZNF274 Peaks bigBed UCD analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/spp/optimal/hub/spp.optimal.wgEncodeSydhTfbsHelas3Zzz3StdAlnRep0_VS_wgEncodeSydhTfbsHelas3InputStdAlnRep1.bb HeLa-S3 ChipSeq ZZZ3 Peaks bigBed Harvard(Weissman) analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/spp/optimal/hub/spp.optimal.wgEncodeSydhTfbsHepg2bTr4UcdAlnRep0_VS_wgEncodeSydhTfbsHepg2bInputUcdAlnRep1.bb HepG2b ChipSeq TR4 Peaks bigBed Stanford analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/spp/optimal/hub/spp.optimal.wgEncodeSydhTfbsHepg2bZnf274UcdAlnRep0_VS_wgEncodeSydhTfbsHepg2bInputUcdAlnRep1.bb HepG2b ChipSeq ZNF274 Peaks bigBed UCD analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/spp/optimal/hub/spp.optimal.wgEncodeSydhTfbsHepg2CebpbForsklnStdAlnRep0_VS_wgEncodeSydhTfbsHepg2InputForsklnStdAlnRep0.bb HepG2 ChipSeq CEBPB Peaks bigBed Stanford analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/spp/optimal/hub/spp.optimal.wgEncodeSydhTfbsHepg2CebpbIggrabAlnRep0_VS_wgEncodeSydhTfbsHepg2InputIggrabAln.bb HepG2 ChipSeq CEBPB Peaks bigBed Stanford analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/spp/optimal/hub/spp.optimal.wgEncodeSydhTfbsHepg2Chd21250IggrabAlnRep0_VS_wgEncodeSydhTfbsHepg2InputIggrabAln.bb HepG2 ChipSeq CHD2_(N-1250) Peaks bigBed Stanford analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/spp/optimal/hub/spp.optimal.wgEncodeSydhTfbsHepg2CjunIggrabAlnRep0_VS_wgEncodeSydhTfbsHepg2InputIggrabAln.bb HepG2 ChipSeq c-Jun Peaks bigBed Stanford analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/spp/optimal/hub/spp.optimal.wgEncodeSydhTfbsHepg2ErraForsklnStdAlnRep0_VS_wgEncodeSydhTfbsHepg2InputForsklnStdAlnRep0.bb HepG2 ChipSeq ERRA Peaks bigBed Stanford analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/spp/optimal/hub/spp.optimal.wgEncodeSydhTfbsHepg2Grp20ForsklnStdAlnRep0_VS_wgEncodeSydhTfbsHepg2InputForsklnStdAlnRep0.bb HepG2 ChipSeq GRp20 Peaks bigBed Stanford analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/spp/optimal/hub/spp.optimal.wgEncodeSydhTfbsHepg2Hnf4aForsklnStdAlnRep0_VS_wgEncodeSydhTfbsHepg2InputForsklnStdAlnRep0.bb HepG2 ChipSeq HNF4A Peaks bigBed Stanford analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/spp/optimal/hub/spp.optimal.wgEncodeSydhTfbsHepg2Hsf1ForsklnStdAlnRep0_VS_wgEncodeSydhTfbsHepg2InputForsklnStdAlnRep0.bb HepG2 ChipSeq HSF1 Peaks bigBed Stanford analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/spp/optimal/hub/spp.optimal.wgEncodeSydhTfbsHepg2Irf3IggrabAlnRep0_VS_wgEncodeSydhTfbsHepg2InputIggrabAln.bb HepG2 ChipSeq IRF3 Peaks bigBed Stanford analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/spp/optimal/hub/spp.optimal.wgEncodeSydhTfbsHepg2JundIggrabAlnRep0_VS_wgEncodeSydhTfbsHepg2InputIggrabAln.bb HepG2 ChipSeq JunD Peaks bigBed Stanford analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/spp/optimal/hub/spp.optimal.wgEncodeSydhTfbsHepg2Maffm8194IggrabAlnRep0_VS_wgEncodeSydhTfbsHepg2InputIggrabAln.bb HepG2 ChipSeq MafF_(M8194) Peaks bigBed Stanford analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/spp/optimal/hub/spp.optimal.wgEncodeSydhTfbsHepg2Mafkab50322IggrabAlnRep0_VS_wgEncodeSydhTfbsHepg2InputIggrabAln.bb HepG2 ChipSeq MafK_(ab50322) Peaks bigBed Stanford analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/spp/optimal/hub/spp.optimal.wgEncodeSydhTfbsHepg2Mafksc477IggrabAlnRep0_VS_wgEncodeSydhTfbsHepg2InputIggrabAln.bb HepG2 ChipSeq MafK_(SC-477) Peaks bigBed Stanford analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/spp/optimal/hub/spp.optimal.wgEncodeSydhTfbsHepg2Nrf1IggrabAlnRep0_VS_wgEncodeSydhTfbsHepg2InputIggrabAln.bb HepG2 ChipSeq Nrf1 Peaks bigBed Stanford analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/spp/optimal/hub/spp.optimal.wgEncodeSydhTfbsHepg2Pgc1aForsklnStdAlnRep0_VS_wgEncodeSydhTfbsHepg2InputForsklnStdAlnRep0.bb HepG2 ChipSeq PGC1A Peaks bigBed Stanford analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/spp/optimal/hub/spp.optimal.wgEncodeSydhTfbsHepg2Pol2ForsklnStdAlnRep0_VS_wgEncodeSydhTfbsHepg2InputForsklnStdAlnRep0.bb HepG2 ChipSeq Pol2 Peaks bigBed Stanford analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/spp/optimal/hub/spp.optimal.wgEncodeSydhTfbsHepg2Pol2IggrabAlnRep0_VS_wgEncodeSydhTfbsHepg2InputIggrabAln.bb HepG2 ChipSeq Pol2 Peaks bigBed Stanford analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/spp/optimal/hub/spp.optimal.wgEncodeSydhTfbsHepg2Pol2PravastStdAlnRep0_VS_wgEncodeSydhTfbsHepg2InputPravastStdAlnRep0.bb HepG2 ChipSeq Pol2 Peaks bigBed Stanford analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/spp/optimal/hub/spp.optimal.wgEncodeSydhTfbsHepg2Rad21IggrabAlnRep0_VS_wgEncodeSydhTfbsHepg2InputIggrabAln.bb HepG2 ChipSeq Rad21 Peaks bigBed Stanford analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/spp/optimal/hub/spp.optimal.wgEncodeSydhTfbsHepg2Rfx5n494IggrabAlnRep0_VS_wgEncodeSydhTfbsHepg2InputIggrabAln.bb HepG2 ChipSeq RFX5_(N-494) Peaks bigBed Stanford analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/spp/optimal/hub/spp.optimal.wgEncodeSydhTfbsHepg2Srebp1InslnStdAlnRep0_VS_wgEncodeSydhTfbsHepg2InputInslnStdAlnRep0.bb HepG2 ChipSeq SREBP1 Peaks bigBed Stanford analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/spp/optimal/hub/spp.optimal.wgEncodeSydhTfbsHepg2Srebp1PravastStdAlnRep0_VS_wgEncodeSydhTfbsHepg2InputPravastStdAlnRep0.bb HepG2 ChipSeq SREBP1 Peaks bigBed Stanford analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/spp/optimal/hub/spp.optimal.wgEncodeSydhTfbsHepg2Srebp2PravastStdAlnRep0_VS_wgEncodeSydhTfbsHepg2InputPravastStdAlnRep0.bb HepG2 ChipSeq SREBP2 Peaks bigBed Stanford analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/spp/optimal/hub/spp.optimal.wgEncodeSydhTfbsHepg2TbpIggrabAlnRep0_VS_wgEncodeSydhTfbsHepg2InputIggrabAln.bb HepG2 ChipSeq TBP Peaks bigBed Stanford analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/spp/optimal/hub/spp.optimal.wgEncodeSydhTfbsHepg2Tcf4UcdAlnRep0_VS_wgEncodeSydhTfbsHepg2bInputUcdAlnRep1.bb HepG2b ChipSeq TCF4 Peaks bigBed UCD analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/spp/optimal/hub/spp.optimal.wgEncodeSydhTfbsHepg2Usf2IggrabAlnRep0_VS_wgEncodeSydhTfbsHepg2InputIggrabAln.bb HepG2 ChipSeq USF2 Peaks bigBed Stanford analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/spp/optimal/hub/spp.optimal.wgEncodeSydhTfbsHuvecCfosUcdAlnRep0_VS_wgEncodeSydhTfbsHuvecInputUcdAlnRep1.bb HUVEC ChipSeq c-Fos Peaks bigBed UCD analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/spp/optimal/hub/spp.optimal.wgEncodeSydhTfbsHuvecCjunStdAlnRep0_VS_wgEncodeSydhTfbsHuvecInputStdAlnRep0.bb HUVEC ChipSeq c-Jun Peaks bigBed Stanford analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/spp/optimal/hub/spp.optimal.wgEncodeSydhTfbsHuvecGata2UcdAlnRep0_VS_wgEncodeSydhTfbsHuvecInputUcdAlnRep1.bb HUVEC ChipSeq GATA-2 Peaks bigBed UCD analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/spp/optimal/hub/spp.optimal.wgEncodeSydhTfbsHuvecMaxStdAlnRep0_VS_wgEncodeSydhTfbsHuvecInputStdAlnRep0.bb HUVEC ChipSeq Max Peaks bigBed Stanford analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/spp/optimal/hub/spp.optimal.wgEncodeSydhTfbsHuvecPol2StdAlnRep0_VS_wgEncodeSydhTfbsHuvecInputStdAlnRep0.bb HUVEC ChipSeq Pol2 Peaks bigBed Stanford analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/spp/optimal/hub/spp.optimal.wgEncodeSydhTfbsK562Atf3StdAlnRep0_VS_wgEncodeSydhTfbsK562InputStdAlnRep0.bb K562 ChipSeq ATF3 Peaks bigBed Stanford analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/spp/optimal/hub/spp.optimal.wgEncodeSydhTfbsK562Bdp1StdAlnRep0_VS_wgEncodeSydhTfbsK562InputStdAlnRep0.bb K562 ChipSeq BDP1 Peaks bigBed Stanford analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/spp/optimal/hub/spp.optimal.wgEncodeSydhTfbsK562bE2f4UcdAlnRep0_VS_wgEncodeSydhTfbsK562bInputUcdAlnRep1.bb K562b ChipSeq E2F4 Peaks bigBed Stanford analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/spp/optimal/hub/spp.optimal.wgEncodeSydhTfbsK562bE2f6UcdAlnRep0_VS_wgEncodeSydhTfbsK562bInputUcdAlnRep1.bb K562b ChipSeq E2F6 Peaks bigBed Stanford analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/spp/optimal/hub/spp.optimal.wgEncodeSydhTfbsK562bGata1UcdAlnRep0_VS_wgEncodeSydhTfbsK562bInputUcdAlnRep1.bb K562b ChipSeq GATA-1 Peaks bigBed Stanford analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/spp/optimal/hub/spp.optimal.wgEncodeSydhTfbsK562bGata2UcdAlnRep0_VS_wgEncodeSydhTfbsK562bInputUcdAlnRep1.bb K562b ChipSeq GATA-2 Peaks bigBed Stanford analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/spp/optimal/hub/spp.optimal.wgEncodeSydhTfbsK562bKap1UcdAlnRep0_VS_wgEncodeSydhTfbsK562bInputUcdAlnRep1.bb K562b ChipSeq KAP1 Peaks bigBed UCD analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/spp/optimal/hub/spp.optimal.wgEncodeSydhTfbsK562Brf1StdAlnRep0_VS_wgEncodeSydhTfbsK562InputStdAlnRep0.bb K562 ChipSeq BRF1 Peaks bigBed Stanford analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/spp/optimal/hub/spp.optimal.wgEncodeSydhTfbsK562Brf2StdAlnRep0_VS_wgEncodeSydhTfbsK562InputStdAlnRep0.bb K562 ChipSeq BRF2 Peaks bigBed Stanford analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/spp/optimal/hub/spp.optimal.wgEncodeSydhTfbsK562Brg1IggmusAlnRep0_VS_wgEncodeSydhTfbsK562InputIggmusAlnRep0.bb K562 ChipSeq Brg1 Peaks bigBed Stanford analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/spp/optimal/hub/spp.optimal.wgEncodeSydhTfbsK562bSetdb1MnasedUcdAlnRep0_VS_wgEncodeSydhTfbsK562bInputUcdAlnRep1.bb K562b ChipSeq SETDB1 Peaks bigBed Stanford analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/spp/optimal/hub/spp.optimal.wgEncodeSydhTfbsK562bSetdb1UcdAlnRep0_VS_wgEncodeSydhTfbsK562bInputUcdAlnRep1.bb K562b ChipSeq SETDB1 Peaks bigBed Stanford analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/spp/optimal/hub/spp.optimal.wgEncodeSydhTfbsK562bTr4UcdAlnRep0_VS_wgEncodeSydhTfbsK562bInputUcdAlnRep1.bb K562b ChipSeq TR4 Peaks bigBed Stanford analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/spp/optimal/hub/spp.optimal.wgEncodeSydhTfbsK562bYy1UcdAlnRep0_VS_wgEncodeSydhTfbsK562bInputUcdAlnRep1.bb K562b ChipSeq YY1 Peaks bigBed Stanford analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/spp/optimal/hub/spp.optimal.wgEncodeSydhTfbsK562bZnf263UcdAlnRep0_VS_wgEncodeSydhTfbsK562bInputUcdAlnRep1.bb K562b ChipSeq ZNF263 Peaks bigBed Stanford analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/spp/optimal/hub/spp.optimal.wgEncodeSydhTfbsK562bZnf274UcdAlnRep0_VS_wgEncodeSydhTfbsK562bInputUcdAlnRep1.bb K562b ChipSeq ZNF274 Peaks bigBed Stanford analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/spp/optimal/hub/spp.optimal.wgEncodeSydhTfbsK562Ccnt2StdAlnRep0_VS_wgEncodeSydhTfbsK562InputStdAlnRep0.bb K562 ChipSeq CCNT2 Peaks bigBed Harvard analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/spp/optimal/hub/spp.optimal.wgEncodeSydhTfbsK562CebpbIggrabAlnRep0_VS_wgEncodeSydhTfbsK562InputIggrabAln.bb K562 ChipSeq CEBPB Peaks bigBed Stanford analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/spp/optimal/hub/spp.optimal.wgEncodeSydhTfbsK562CfosStdAlnRep0_VS_wgEncodeSydhTfbsK562InputStdAlnRep0.bb K562 ChipSeq c-Fos Peaks bigBed Stanford analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/spp/optimal/hub/spp.optimal.wgEncodeSydhTfbsK562Chd21250IggrabAlnRep0_VS_wgEncodeSydhTfbsK562InputIggrabAln.bb K562 ChipSeq CHD2_(N-1250) Peaks bigBed Stanford analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/spp/optimal/hub/spp.optimal.wgEncodeSydhTfbsK562CjunIfna6hStdAlnRep0_VS_wgEncodeSydhTfbsK562InputIfna6hStdAlnRep1.bb K562 ChipSeq c-Jun Peaks bigBed Stanford analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/spp/optimal/hub/spp.optimal.wgEncodeSydhTfbsK562CjunIfng30StdAlnRep0_VS_wgEncodeSydhTfbsK562InputIfng30StdAlnRep1.bb K562 ChipSeq c-Jun Peaks bigBed Stanford analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/spp/optimal/hub/spp.optimal.wgEncodeSydhTfbsK562CjunIfng6hStdAlnRep0_VS_wgEncodeSydhTfbsK562InputIfng6hStdAlnRep1.bb K562 ChipSeq c-Jun Peaks bigBed Stanford analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/spp/optimal/hub/spp.optimal.wgEncodeSydhTfbsK562CjunStdAlnRep0_VS_wgEncodeSydhTfbsK562InputStdAlnRep0.bb K562 ChipSeq c-Jun Peaks bigBed Stanford analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/spp/optimal/hub/spp.optimal.wgEncodeSydhTfbsK562CmycIfna30StdAlnRep0_VS_wgEncodeSydhTfbsK562InputIfna30StdAlnRep1.bb K562 ChipSeq c-Myc Peaks bigBed Stanford analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/spp/optimal/hub/spp.optimal.wgEncodeSydhTfbsK562CmycIfna6hStdAlnRep0_VS_wgEncodeSydhTfbsK562InputIfna6hStdAlnRep1.bb K562 ChipSeq c-Myc Peaks bigBed Stanford analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/spp/optimal/hub/spp.optimal.wgEncodeSydhTfbsK562CmycIfng30StdAlnRep0_VS_wgEncodeSydhTfbsK562InputIfng30StdAlnRep1.bb K562 ChipSeq c-Myc Peaks bigBed Stanford analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/spp/optimal/hub/spp.optimal.wgEncodeSydhTfbsK562CmycIfng6hStdAlnRep0_VS_wgEncodeSydhTfbsK562InputIfng6hStdAlnRep1.bb K562 ChipSeq c-Myc Peaks bigBed Stanford analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/spp/optimal/hub/spp.optimal.wgEncodeSydhTfbsK562CmycStdAlnRep0_VS_wgEncodeSydhTfbsK562InputStdAlnRep0.bb K562 ChipSeq c-Myc Peaks bigBed Stanford analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/spp/optimal/hub/spp.optimal.wgEncodeSydhTfbsK562Gtf2bStdAlnRep0_VS_wgEncodeSydhTfbsK562InputStdAlnRep0.bb K562 ChipSeq GTF2B Peaks bigBed Harvard analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/spp/optimal/hub/spp.optimal.wgEncodeSydhTfbsK562Gtf2f1rapIggrabAlnRep0_VS_wgEncodeSydhTfbsK562InputIggrabAln.bb K562 ChipSeq GTF2F1_(RAP-74) Peaks bigBed Stanford analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/spp/optimal/hub/spp.optimal.wgEncodeSydhTfbsK562Hmgn3StdAlnRep0_VS_wgEncodeSydhTfbsK562InputStdAlnRep0.bb K562 ChipSeq HMGN3 Peaks bigBed Harvard analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/spp/optimal/hub/spp.optimal.wgEncodeSydhTfbsK562Ini1IggmusAlnRep0_VS_wgEncodeSydhTfbsK562InputIggmusAlnRep0.bb K562 ChipSeq Ini1 Peaks bigBed Stanford analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/spp/optimal/hub/spp.optimal.wgEncodeSydhTfbsK562Irf1Ifna30StdAlnRep0_VS_wgEncodeSydhTfbsK562InputIfna30StdAlnRep1.bb K562 ChipSeq IRF1 Peaks bigBed Stanford analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/spp/optimal/hub/spp.optimal.wgEncodeSydhTfbsK562Irf1Ifng6hStdAlnRep0_VS_wgEncodeSydhTfbsK562InputIfng6hStdAlnRep1.bb K562 ChipSeq IRF1 Peaks bigBed Stanford analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/spp/optimal/hub/spp.optimal.wgEncodeSydhTfbsK562JundStdAlnRep0_VS_wgEncodeSydhTfbsK562InputStdAlnRep0.bb K562 ChipSeq JunD Peaks bigBed Stanford analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/spp/optimal/hub/spp.optimal.wgEncodeSydhTfbsK562Mafkab50322IggrabAlnRep0_VS_wgEncodeSydhTfbsK562InputIggrabAln.bb K562 ChipSeq MafK_(ab50322) Peaks bigBed Stanford analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/spp/optimal/hub/spp.optimal.wgEncodeSydhTfbsK562MaxStdAlnRep0_VS_wgEncodeSydhTfbsK562InputStdAlnRep0.bb K562 ChipSeq Max Peaks bigBed Stanford analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/spp/optimal/hub/spp.optimal.wgEncodeSydhTfbsK562Mxi1bhlhIggrabAlnRep0_VS_wgEncodeSydhTfbsK562InputIggrabAln.bb K562 ChipSeq Mxi1_(bHLH) Peaks bigBed Stanford analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/spp/optimal/hub/spp.optimal.wgEncodeSydhTfbsK562NelfeStdAlnRep0_VS_wgEncodeSydhTfbsK562InputStdAlnRep0.bb K562 ChipSeq NELFe Peaks bigBed Stanford analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/spp/optimal/hub/spp.optimal.wgEncodeSydhTfbsK562Nfe2StdAlnRep0_VS_wgEncodeSydhTfbsK562InputStdAlnRep0.bb K562 ChipSeq NF-E2 Peaks bigBed Stanford analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/spp/optimal/hub/spp.optimal.wgEncodeSydhTfbsK562NfyaStdAlnRep0_VS_wgEncodeSydhTfbsK562InputStdAlnRep0.bb K562 ChipSeq NF-YA Peaks bigBed Stanford analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/spp/optimal/hub/spp.optimal.wgEncodeSydhTfbsK562NfybStdAlnRep0_VS_wgEncodeSydhTfbsK562InputStdAlnRep0.bb K562 ChipSeq NF-YB Peaks bigBed Stanford analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/spp/optimal/hub/spp.optimal.wgEncodeSydhTfbsK562Nrf1IggrabAlnRep0_VS_wgEncodeSydhTfbsK562InputIggrabAln.bb K562 ChipSeq Nrf1 Peaks bigBed Stanford analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/spp/optimal/hub/spp.optimal.wgEncodeSydhTfbsK562P300f4IggrabAlnRep0_VS_wgEncodeSydhTfbsK562InputIggrabAln.bb K562 ChipSeq p300_(F-4) Peaks bigBed Stanford analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/spp/optimal/hub/spp.optimal.wgEncodeSydhTfbsK562Pol2Ifna30StdAlnRep0_VS_wgEncodeSydhTfbsK562InputIfna30StdAlnRep1.bb K562 ChipSeq Pol2 Peaks bigBed Stanford analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/spp/optimal/hub/spp.optimal.wgEncodeSydhTfbsK562Pol2Ifna6hStdAlnRep0_VS_wgEncodeSydhTfbsK562InputIfna6hStdAlnRep1.bb K562 ChipSeq Pol2 Peaks bigBed Stanford analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/spp/optimal/hub/spp.optimal.wgEncodeSydhTfbsK562Pol2Ifng30StdAlnRep0_VS_wgEncodeSydhTfbsK562InputIfng30StdAlnRep1.bb K562 ChipSeq Pol2 Peaks bigBed Stanford analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/spp/optimal/hub/spp.optimal.wgEncodeSydhTfbsK562Pol2Ifng6hStdAlnRep0_VS_wgEncodeSydhTfbsK562InputIfng6hStdAlnRep1.bb K562 ChipSeq Pol2 Peaks bigBed Stanford analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/spp/optimal/hub/spp.optimal.wgEncodeSydhTfbsK562Pol2IggmusAlnRep0_VS_wgEncodeSydhTfbsK562InputIggmusAlnRep0.bb K562 ChipSeq Pol2 Peaks bigBed Stanford analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/spp/optimal/hub/spp.optimal.wgEncodeSydhTfbsK562Pol2s2StdAlnRep0_VS_wgEncodeSydhTfbsK562InputStdAlnRep0.bb K562 ChipSeq Pol2(phosphoS2) Peaks bigBed Stanford analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/spp/optimal/hub/spp.optimal.wgEncodeSydhTfbsK562Pol2StdAlnRep0_VS_wgEncodeSydhTfbsK562InputStdAlnRep0.bb K562 ChipSeq Pol2 Peaks bigBed Stanford analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/spp/optimal/hub/spp.optimal.wgEncodeSydhTfbsK562Pol3StdAlnRep0_VS_wgEncodeSydhTfbsK562InputStdAlnRep0.bb K562 ChipSeq Pol3 Peaks bigBed Stanford analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/spp/optimal/hub/spp.optimal.wgEncodeSydhTfbsK562Rad21StdAlnRep0_VS_wgEncodeSydhTfbsK562InputStdAlnRep0.bb K562 ChipSeq Rad21 Peaks bigBed Stanford analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/spp/optimal/hub/spp.optimal.wgEncodeSydhTfbsK562Rpc155StdAlnRep0_VS_wgEncodeSydhTfbsK562InputStdAlnRep0.bb K562 ChipSeq RPC155 Peaks bigBed Stanford analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/spp/optimal/hub/spp.optimal.wgEncodeSydhTfbsK562Sirt6StdAlnRep0_VS_wgEncodeSydhTfbsK562InputStdAlnRep0.bb K562 ChipSeq SIRT6 Peaks bigBed Stanford analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/spp/optimal/hub/spp.optimal.wgEncodeSydhTfbsK562Smc3ab9263IggrabAlnRep0_VS_wgEncodeSydhTfbsK562InputIggrabAln.bb K562 ChipSeq SMC3_(ab9263) Peaks bigBed Stanford analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/spp/optimal/hub/spp.optimal.wgEncodeSydhTfbsK562Stat1Ifna30StdAlnRep0_VS_wgEncodeSydhTfbsK562InputIfna30StdAlnRep1.bb K562 ChipSeq STAT1 Peaks bigBed Stanford analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/spp/optimal/hub/spp.optimal.wgEncodeSydhTfbsK562Stat1Ifna6hStdAlnRep0_VS_wgEncodeSydhTfbsK562InputIfna6hStdAlnRep1.bb K562 ChipSeq STAT1 Peaks bigBed Stanford analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/spp/optimal/hub/spp.optimal.wgEncodeSydhTfbsK562Stat1Ifng30StdAlnRep0_VS_wgEncodeSydhTfbsK562InputIfng30StdAlnRep1.bb K562 ChipSeq STAT1 Peaks bigBed Stanford analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/spp/optimal/hub/spp.optimal.wgEncodeSydhTfbsK562Stat1Ifng6hStdAlnRep0_VS_wgEncodeSydhTfbsK562InputIfng6hStdAlnRep1.bb K562 ChipSeq STAT1 Peaks bigBed Stanford analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/spp/optimal/hub/spp.optimal.wgEncodeSydhTfbsK562Stat2Ifna30StdAlnRep0_VS_wgEncodeSydhTfbsK562InputIfna30StdAlnRep1.bb K562 ChipSeq STAT2 Peaks bigBed Stanford analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/spp/optimal/hub/spp.optimal.wgEncodeSydhTfbsK562Stat2Ifna6hStdAlnRep0_VS_wgEncodeSydhTfbsK562InputIfna6hStdAlnRep1.bb K562 ChipSeq STAT2 Peaks bigBed Stanford analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/spp/optimal/hub/spp.optimal.wgEncodeSydhTfbsK562Tal1sc12984IggmusAlnRep0_VS_wgEncodeSydhTfbsK562InputIggmusAlnRep0.bb K562 ChipSeq TAL1_(SC-12984) Peaks bigBed Stanford analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/spp/optimal/hub/spp.optimal.wgEncodeSydhTfbsK562TbpIggmusAlnRep0_VS_wgEncodeSydhTfbsK562InputIggmusAlnRep0.bb K562 ChipSeq TBP Peaks bigBed Stanford analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/spp/optimal/hub/spp.optimal.wgEncodeSydhTfbsK562Tf3c110StdAlnRep0_VS_wgEncodeSydhTfbsK562InputStdAlnRep0.bb K562 ChipSeq TFIIIC-110 Peaks bigBed Stanford analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/spp/optimal/hub/spp.optimal.wgEncodeSydhTfbsK562Usf2StdAlnRep0_VS_wgEncodeSydhTfbsK562InputStdAlnRep0.bb K562 ChipSeq USF2 Peaks bigBed Stanford analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/spp/optimal/hub/spp.optimal.wgEncodeSydhTfbsK562Xrcc4StdAlnRep0_VS_wgEncodeSydhTfbsK562InputStdAlnRep0.bb K562 ChipSeq XRCC4 Peaks bigBed Stanford analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/spp/optimal/hub/spp.optimal.wgEncodeSydhTfbsMcf10aesPol2Etoh01StdAlnRep0_VS_wgEncodeSydhTfbsMcf10aesInputUcdAln.bb MCF10A-Er-Src ChipSeq Pol2 Peaks bigBed Stanford analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/spp/optimal/hub/spp.optimal.wgEncodeSydhTfbsMcf10aesPol2TamStdAlnRep0_VS_wgEncodeSydhTfbsMcf10aesInputUcdAln.bb MCF10A-Er-Src ChipSeq Pol2 Peaks bigBed Harvard(Weissman) analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/spp/optimal/hub/spp.optimal.wgEncodeSydhTfbsMcf10aesStat3Etoh01bStdAlnRep0_VS_wgEncodeSydhTfbsMcf10aesInputEtoh01bStdAln.bb MCF10A-Er-Src ChipSeq STAT3 Peaks bigBed Harvard(Weissman) analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/spp/optimal/hub/spp.optimal.wgEncodeSydhTfbsMcf10aesStat3Etoh01cStdAlnRep0_VS_wgEncodeSydhTfbsMcf10aesInputEtoh01cStdAln.bb MCF10A-Er-Src ChipSeq STAT3 Peaks bigBed Stanford analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/spp/optimal/hub/spp.optimal.wgEncodeSydhTfbsMcf10aesStat3Etoh01StdAlnRep0_VS_wgEncodeSydhTfbsMcf10aesInputUcdAln.bb MCF10A-Er-Src ChipSeq STAT3 Peaks bigBed Harvard(Weissman) analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/spp/optimal/hub/spp.optimal.wgEncodeSydhTfbsMcf10aesStat3TamStdAlnRep0_VS_wgEncodeSydhTfbsMcf10aesInputUcdAln.bb MCF10A-Er-Src ChipSeq STAT3 Peaks bigBed Harvard(Weissman) analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/spp/optimal/hub/spp.optimal.wgEncodeSydhTfbsMcf7Hae2f1UcdAlnRep0_VS_wgEncodeSydhTfbsMcf7InputUcdAlnRep0.bb MCF-7 ChipSeq HA-E2F1 Peaks bigBed Stanford analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/spp/optimal/hub/spp.optimal.wgEncodeSydhTfbsNb4CmycStdAlnRep0_VS_wgEncodeSydhTfbsNb4InputStdAlnRep1.bb NB4 ChipSeq c-Myc Peaks bigBed Stanford analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/spp/optimal/hub/spp.optimal.wgEncodeSydhTfbsNb4MaxStdAlnRep0_VS_wgEncodeSydhTfbsNb4InputStdAlnRep1.bb NB4 ChipSeq Max Peaks bigBed Stanford analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/spp/optimal/hub/spp.optimal.wgEncodeSydhTfbsNb4Pol2StdAlnRep0_VS_wgEncodeSydhTfbsNb4InputStdAlnRep1.bb NB4 ChipSeq Pol2 Peaks bigBed Stanford analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/spp/optimal/hub/spp.optimal.wgEncodeSydhTfbsNt2d1Suz12UcdAlnRep0_VS_wgEncodeSydhTfbsNt2d1InputUcdAlnRep1.bb NT2-D1 ChipSeq SUZ12 Peaks bigBed Stanford analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/spp/optimal/hub/spp.optimal.wgEncodeSydhTfbsNt2d1Yy1UcdAlnRep0_VS_wgEncodeSydhTfbsNt2d1InputUcdAlnRep1.bb NT2-D1 ChipSeq YY1 Peaks bigBed Stanford analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/spp/optimal/hub/spp.optimal.wgEncodeSydhTfbsNt2d1Znf274UcdAlnRep0_VS_wgEncodeSydhTfbsNt2d1InputUcdAlnRep1.bb NT2-D1 ChipSeq ZNF274 Peaks bigBed UCD analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/spp/optimal/hub/spp.optimal.wgEncodeSydhTfbsPbdeGata1UcdAlnRep0_VS_wgEncodeSydhTfbsPbdeInputUcdAln.bb PBDE ChipSeq GATA-1 Peaks bigBed UCD analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/spp/optimal/hub/spp.optimal.wgEncodeSydhTfbsPbdePol2UcdAlnRep0_VS_wgEncodeSydhTfbsPbdeInputUcdAln.bb PBDE ChipSeq Pol2 Peaks bigBed UCD analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/spp/optimal/hub/spp.optimal.wgEncodeSydhTfbsRajiPol2UcdAlnRep0_VS_wgEncodeSydhTfbsRajiInputUcdAln.bb Raji ChipSeq Pol2 Peaks bigBed UCD analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/spp/optimal/hub/spp.optimal.wgEncodeSydhTfbsShsy5yGata2UcdAlnRep0_VS_wgEncodeSydhTfbsShsy5yInputUcdAln.bb SH-SY5Y ChipSeq GATA-2 Peaks bigBed UCD analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/spp/optimal/hub/spp.optimal.wgEncodeSydhTfbsTrexhek293Znf263UcdAlnRep0_VS_wgEncodeSydhTfbsThek293InputUcdAln.bb T-REx-HEK293 ChipSeq ZNF263 Peaks bigBed UCD analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/spp/optimal/hub/spp.optimal.wgEncodeSydhTfbsU2osKap1UcdAlnRep0_VS_wgEncodeSydhTfbsU2osInputUcdAln.bb U2OS ChipSeq KAP1 Peaks bigBed Stanford analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/spp/optimal/hub/spp.optimal.wgEncodeSydhTfbsU2osSetdb1UcdAlnRep0_VS_wgEncodeSydhTfbsU2osInputUcdAln.bb U2OS ChipSeq SETDB1 Peaks bigBed UCD analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/spp/optimal/hub/spp.optimal.wgEncodeUchicagoTfbsK562EfosControlAlnRep0_VS_wgEncodeUchicagoTfbsK562InputControlAlnRep0.bb K562 ChipSeq eGFP-FOS Peaks bigBed UChicago analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/spp/optimal/hub/spp.optimal.wgEncodeUchicagoTfbsK562Egata2ControlAlnRep0_VS_wgEncodeUchicagoTfbsK562InputControlAlnRep0.bb K562 ChipSeq eGFP-GATA2 Peaks bigBed UChicago analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/spp/optimal/hub/spp.optimal.wgEncodeUchicagoTfbsK562Ehdac8ControlAlnRep0_VS_wgEncodeUchicagoTfbsK562InputControlAlnRep0.bb K562 ChipSeq eGFP-HDAC8 Peaks bigBed UChicago analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/spp/optimal/hub/spp.optimal.wgEncodeUchicagoTfbsK562EjunbControlAlnRep0_VS_wgEncodeUchicagoTfbsK562InputControlAlnRep0.bb K562 ChipSeq eGFP-JunB Peaks bigBed UChicago analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/spp/optimal/hub/spp.optimal.wgEncodeUchicagoTfbsK562EjundControlAlnRep0_VS_wgEncodeUchicagoTfbsK562InputControlAlnRep0.bb K562 ChipSeq eGFP-JunD Peaks bigBed UChicago analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/spp/optimal/hub/spp.optimal.wgEncodeUchicagoTfbsK562Enr4a1ControlAlnRep0_VS_wgEncodeUchicagoTfbsK562InputControlAlnRep0.bb K562 ChipSeq eGFP-NR4A1 Peaks bigBed UChicago analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/spp/optimal/hub/spp.optimal.wgEncodeUwTfbsAg04449CtcfStdAlnRep0_VS_wgEncodeUwTfbsAg04449InputStdAlnRep1.bb AG04449 ChipSeq CTCF Peaks bigBed UW analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/spp/optimal/hub/spp.optimal.wgEncodeUwTfbsAg04450CtcfStdAlnRep1_VS_wgEncodeUwTfbsAg04450InputStdAlnRep1.bb AG04450 ChipSeq CTCF Peaks bigBed UW analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/spp/optimal/hub/spp.optimal.wgEncodeUwTfbsAg09309CtcfStdAlnRep0_VS_wgEncodeUwTfbsAg09309InputStdAlnRep1.bb AG09309 ChipSeq CTCF Peaks bigBed UW analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/spp/optimal/hub/spp.optimal.wgEncodeUwTfbsAg09319CtcfStdAlnRep0_VS_wgEncodeUwTfbsAg09319InputStdAlnRep1.bb AG09319 ChipSeq CTCF Peaks bigBed UW analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/spp/optimal/hub/spp.optimal.wgEncodeUwTfbsAg10803CtcfStdAlnRep0_VS_wgEncodeUwTfbsAg10803InputStdAlnRep1.bb AG10803 ChipSeq CTCF Peaks bigBed UW analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/spp/optimal/hub/spp.optimal.wgEncodeUwTfbsAoafCtcfStdAlnRep0_VS_wgEncodeUwTfbsAoafInputStdAlnRep1.bb AoAF ChipSeq CTCF Peaks bigBed UW analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/spp/optimal/hub/spp.optimal.wgEncodeUwTfbsBjCtcfStdAlnRep0_VS_wgEncodeUwTfbsBjInputStdAlnRep1.bb BJ ChipSeq CTCF Peaks bigBed UW analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/spp/optimal/hub/spp.optimal.wgEncodeUwTfbsCaco2CtcfStdAlnRep0_VS_wgEncodeUwTfbsCaco2InputStdAlnRep1.bb Caco-2 ChipSeq CTCF Peaks bigBed UW analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/spp/optimal/hub/spp.optimal.wgEncodeUwTfbsGm06990CtcfStdAlnRep0_VS_wgEncodeUwTfbsGm06990InputStdAlnRep1.bb GM06990 ChipSeq CTCF Peaks bigBed UW analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/spp/optimal/hub/spp.optimal.wgEncodeUwTfbsGm12801CtcfStdAlnRep1_VS_wgEncodeUwTfbsGm12801InputStdAlnRep1.bb GM12801 ChipSeq CTCF Peaks bigBed UW analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/spp/optimal/hub/spp.optimal.wgEncodeUwTfbsGm12864CtcfStdAlnRep0_VS_wgEncodeUwTfbsGm12864InputStdAlnRep1.bb GM12864 ChipSeq CTCF Peaks bigBed UW analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/spp/optimal/hub/spp.optimal.wgEncodeUwTfbsGm12865CtcfStdAlnRep0_VS_wgEncodeUwTfbsGm12865InputStdAlnRep1.bb GM12865 ChipSeq CTCF Peaks bigBed UW analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/spp/optimal/hub/spp.optimal.wgEncodeUwTfbsGm12872CtcfStdAlnRep0_VS_wgEncodeUwTfbsGm12872InputStdAlnRep1.bb GM12872 ChipSeq CTCF Peaks bigBed UW analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/spp/optimal/hub/spp.optimal.wgEncodeUwTfbsGm12873CtcfStdAlnRep0_VS_wgEncodeUwTfbsGm12873InputStdAlnRep1.bb GM12873 ChipSeq CTCF Peaks bigBed UW analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/spp/optimal/hub/spp.optimal.wgEncodeUwTfbsGm12874CtcfStdAlnRep0_VS_wgEncodeUwTfbsGm12874InputStdAlnRep1.bb GM12874 ChipSeq CTCF Peaks bigBed UW analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/spp/optimal/hub/spp.optimal.wgEncodeUwTfbsGm12875CtcfStdAlnRep0_VS_wgEncodeUwTfbsGm12875InputStdAlnRep1.bb GM12875 ChipSeq CTCF Peaks bigBed UW analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/spp/optimal/hub/spp.optimal.wgEncodeUwTfbsGm12878CtcfStdAlnRep0_VS_wgEncodeUwTfbsGm12878InputStdAlnRep1.bb GM12878 ChipSeq CTCF Peaks bigBed UW analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/spp/optimal/hub/spp.optimal.wgEncodeUwTfbsHaspCtcfStdAlnRep1_VS_wgEncodeUwTfbsHaspInputStdAlnRep1.bb HA-sp ChipSeq CTCF Peaks bigBed UW analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/spp/optimal/hub/spp.optimal.wgEncodeUwTfbsHbmecCtcfStdAlnRep0_VS_wgEncodeUwTfbsHbmecInputStdAlnRep1.bb HBMEC ChipSeq CTCF Peaks bigBed UW analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/spp/optimal/hub/spp.optimal.wgEncodeUwTfbsHcfaaCtcfStdAlnRep1_VS_wgEncodeUwTfbsHcfaaInputStdAlnRep1.bb HCFaa ChipSeq CTCF Peaks bigBed UW analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/spp/optimal/hub/spp.optimal.wgEncodeUwTfbsHcpeCtcfStdAlnRep0_VS_wgEncodeUwTfbsHcpeInputStdAlnRep1.bb HCPEpiC ChipSeq CTCF Peaks bigBed UW analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/spp/optimal/hub/spp.optimal.wgEncodeUwTfbsHeeCtcfStdAlnRep0_VS_wgEncodeUwTfbsHeeInputStdAlnRep1.bb HEEpiC ChipSeq CTCF Peaks bigBed UW analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/spp/optimal/hub/spp.optimal.wgEncodeUwTfbsHek293CtcfStdAlnRep0_VS_wgEncodeUwTfbsHek293InputStdAlnRep1.bb HEK293 ChipSeq CTCF Peaks bigBed UW analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/spp/optimal/hub/spp.optimal.wgEncodeUwTfbsHelas3CtcfStdAlnRep0_VS_wgEncodeUwTfbsHelas3InputStdAlnRep1.bb HeLa-S3 ChipSeq CTCF Peaks bigBed UW analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/spp/optimal/hub/spp.optimal.wgEncodeUwTfbsHepg2CtcfStdAlnRep0_VS_wgEncodeUwTfbsHepg2InputStdAlnRep1.bb HepG2 ChipSeq CTCF Peaks bigBed UW analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/spp/optimal/hub/spp.optimal.wgEncodeUwTfbsHl60CtcfStdAlnRep1_VS_wgEncodeUwTfbsHl60InputStdAlnRep1.bb HL-60 ChipSeq CTCF Peaks bigBed UW analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/spp/optimal/hub/spp.optimal.wgEncodeUwTfbsHmecCtcfStdAlnRep1_VS_wgEncodeUwTfbsHmecInputStdAlnRep1.bb HMEC ChipSeq CTCF Peaks bigBed UW analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/spp/optimal/hub/spp.optimal.wgEncodeUwTfbsHmfCtcfStdAlnRep0_VS_wgEncodeUwTfbsHmfInputStdAlnRep1.bb HMF ChipSeq CTCF Peaks bigBed UW analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/spp/optimal/hub/spp.optimal.wgEncodeUwTfbsHpafCtcfStdAlnRep0_VS_wgEncodeUwTfbsHpafInputStdAlnRep1.bb HPAF ChipSeq CTCF Peaks bigBed UW analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/spp/optimal/hub/spp.optimal.wgEncodeUwTfbsHpfCtcfStdAlnRep0_VS_wgEncodeUwTfbsHpfInputStdAlnRep1.bb HPF ChipSeq CTCF Peaks bigBed UW analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/spp/optimal/hub/spp.optimal.wgEncodeUwTfbsHreCtcfStdAlnRep0_VS_wgEncodeUwTfbsHreInputStdAlnRep1.bb HRE ChipSeq CTCF Peaks bigBed UW analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/spp/optimal/hub/spp.optimal.wgEncodeUwTfbsHrpeCtcfStdAlnRep1_VS_wgEncodeUwTfbsHrpeInputStdAlnRep1.bb HRPEpiC ChipSeq CTCF Peaks bigBed UW analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/spp/optimal/hub/spp.optimal.wgEncodeUwTfbsHuvecCtcfStdAlnRep0_VS_wgEncodeUwTfbsHuvecInputStdAlnRep1.bb HUVEC ChipSeq CTCF Peaks bigBed UW analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/spp/optimal/hub/spp.optimal.wgEncodeUwTfbsK562CtcfStdAlnRep0_VS_wgEncodeUwTfbsK562InputStdAlnRep1.bb K562 ChipSeq CTCF Peaks bigBed UW analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/spp/optimal/hub/spp.optimal.wgEncodeUwTfbsNhekCtcfStdAlnRep0_VS_wgEncodeUwTfbsNhekInputStdAlnRep1.bb NHEK ChipSeq CTCF Peaks bigBed UW analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/spp/optimal/hub/spp.optimal.wgEncodeUwTfbsSaecCtcfStdAlnRep0_VS_wgEncodeUwTfbsSaecInputStdAlnRep1.bb SAEC ChipSeq CTCF Peaks bigBed UW analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/spp/optimal/hub/spp.optimal.wgEncodeUwTfbsSknshraCtcfStdAlnRep0_VS_wgEncodeUwTfbsSknshraInputStdAlnRep1.bb SK-N-SH_RA ChipSeq CTCF Peaks bigBed UW analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/spp/optimal/hub/spp.optimal.wgEncodeUwTfbsWerirb1CtcfStdAlnRep0_VS_wgEncodeUwTfbsWerirb1InputStdAlnRep1.bb WERI-Rb-1 ChipSeq CTCF Peaks bigBed UW analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/peakSeq/optimal/hub/peakSeq.optimal.wgEncodeBroadHistoneGm12878CtcfStdAlnRep0_vs_wgEncodeBroadHistoneGm12878ControlStdAlnRep0.bb GM12878 ChipSeq CTCF Peaks bigBed Broad analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/peakSeq/optimal/hub/peakSeq.optimal.wgEncodeBroadHistoneH1hescCtcfStdAlnRep0_vs_wgEncodeBroadHistoneH1hescControlStdAlnRep0.bb H1-hESC ChipSeq CTCF Peaks bigBed Broad analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/peakSeq/optimal/hub/peakSeq.optimal.wgEncodeBroadHistoneHelas3CtcfStdAlnRep0_vs_wgEncodeBroadHistoneHelas3ControlStdAlnRep0.bb HeLa-S3 ChipSeq CTCF Peaks bigBed Broad analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/peakSeq/optimal/hub/peakSeq.optimal.wgEncodeBroadHistoneHelas3Pol2bStdAlnRep0_vs_wgEncodeBroadHistoneHelas3ControlStdAlnRep0.bb HeLa-S3 ChipSeq Pol2(b) Peaks bigBed Broad analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/peakSeq/optimal/hub/peakSeq.optimal.wgEncodeBroadHistoneHepg2CtcfStdAlnRep0_vs_wgEncodeBroadHistoneHepg2ControlStdAlnRep0.bb HepG2 ChipSeq CTCF Peaks bigBed Broad analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/peakSeq/optimal/hub/peakSeq.optimal.wgEncodeBroadHistoneHmecCtcfStdAlnRep0_vs_wgEncodeBroadHistoneHmecControlStdAlnRep0.bb HMEC ChipSeq CTCF Peaks bigBed Broad analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/peakSeq/optimal/hub/peakSeq.optimal.wgEncodeBroadHistoneHsmmCtcfStdAlnRep0_vs_wgEncodeBroadHistoneHsmmControlStdAlnRep0.bb HSMM ChipSeq CTCF Peaks bigBed Broad analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/peakSeq/optimal/hub/peakSeq.optimal.wgEncodeBroadHistoneHsmmtCtcfStdAlnRep0_vs_wgEncodeBroadHistoneHsmmtControlStdAlnRep0.bb HSMMtube ChipSeq CTCF Peaks bigBed Broad analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/peakSeq/optimal/hub/peakSeq.optimal.wgEncodeBroadHistoneHuvecCtcfStdAlnRep0_vs_wgEncodeBroadHistoneHuvecControlStdAlnRep0.bb HUVEC ChipSeq CTCF Peaks bigBed Broad analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/peakSeq/optimal/hub/peakSeq.optimal.wgEncodeBroadHistoneHuvecPol2bStdAlnRep0_vs_wgEncodeBroadHistoneHuvecControlStdAlnRep0.bb HUVEC ChipSeq Pol2(b) Peaks bigBed Broad analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/peakSeq/optimal/hub/peakSeq.optimal.wgEncodeBroadHistoneK562CtcfStdAlnRep0_vs_wgEncodeBroadHistoneK562ControlStdAlnRep1.bb K562 ChipSeq CTCF Peaks bigBed Broad analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/peakSeq/optimal/hub/peakSeq.optimal.wgEncodeBroadHistoneK562Pol2bStdAlnRep0_vs_wgEncodeBroadHistoneK562ControlStdAlnRep1.bb K562 ChipSeq Pol2(b) Peaks bigBed Broad analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/peakSeq/optimal/hub/peakSeq.optimal.wgEncodeBroadHistoneNhaCtcfStdAlnRep0_vs_wgEncodeBroadHistoneNhaControlStdAlnRep0.bb NH-A ChipSeq CTCF Peaks bigBed Broad analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/peakSeq/optimal/hub/peakSeq.optimal.wgEncodeBroadHistoneNhdfadCtcfStdAlnRep0_vs_wgEncodeBroadHistoneNhdfadControlStdAlnRep0.bb NHDF-Ad ChipSeq CTCF Peaks bigBed Broad analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/peakSeq/optimal/hub/peakSeq.optimal.wgEncodeBroadHistoneNhekCtcfStdAlnRep0_vs_wgEncodeBroadHistoneNhekControlStdAlnRep0.bb NHEK ChipSeq CTCF Peaks bigBed Broad analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/peakSeq/optimal/hub/peakSeq.optimal.wgEncodeBroadHistoneNhekPol2bStdAlnRep0_vs_wgEncodeBroadHistoneNhekControlStdAlnRep0.bb NHEK ChipSeq Pol2(b) Peaks bigBed Broad analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/peakSeq/optimal/hub/peakSeq.optimal.wgEncodeBroadHistoneNhlfCtcfStdAlnRep0_vs_wgEncodeBroadHistoneNhlfControlStdAlnRep0.bb NHLF ChipSeq CTCF Peaks bigBed Broad analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/peakSeq/optimal/hub/peakSeq.optimal.wgEncodeBroadHistoneOsteoblCtcfStdAlnRep0_vs_wgEncodeBroadHistoneOsteoblControlStdAlnRep0.bb Osteobl ChipSeq CTCF Peaks bigBed Broad analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/peakSeq/optimal/hub/peakSeq.optimal.wgEncodeHaibTfbsA549CtcfPcr1xDexaAlnRep0_vs_wgEncodeHaibTfbsA549ControlPcr1xDexaAlnRep0.bb A549 ChipSeq CTCF Peaks bigBed HudsonAlpha analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/peakSeq/optimal/hub/peakSeq.optimal.wgEncodeHaibTfbsA549CtcfPcr1xEtoh02AlnRep0_vs_wgEncodeHaibTfbsA549ControlPcr1xEtoh02AlnRep1.bb A549 ChipSeq CTCF Peaks bigBed HudsonAlpha analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/peakSeq/optimal/hub/peakSeq.optimal.wgEncodeHaibTfbsA549GrPcr1xDexbAlnRep0_vs_wgEncodeHaibTfbsA549GrPcr1xEtoh02AlnRep0.bb A549 ChipSeq GR Peaks bigBed HudsonAlpha analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/peakSeq/optimal/hub/peakSeq.optimal.wgEncodeHaibTfbsA549GrPcr1xDexcAlnRep0_vs_wgEncodeHaibTfbsA549GrPcr1xEtoh02AlnRep0.bb A549 ChipSeq GR Peaks bigBed HudsonAlpha analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/peakSeq/optimal/hub/peakSeq.optimal.wgEncodeHaibTfbsA549GrPcr1xDexdAlnRep0_vs_wgEncodeHaibTfbsA549GrPcr1xEtoh02AlnRep0.bb A549 ChipSeq GR Peaks bigBed HudsonAlpha analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/peakSeq/optimal/hub/peakSeq.optimal.wgEncodeHaibTfbsA549GrPcr2xDexaAlnRep0_vs_wgEncodeHaibTfbsA549GrPcr2xEtoh02AlnRep0.bb A549 ChipSeq GR Peaks bigBed HudsonAlpha analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/peakSeq/optimal/hub/peakSeq.optimal.wgEncodeHaibTfbsA549Pol2Pcr2xDexaAlnRep0_vs_wgEncodeHaibTfbsA549ControlPcr2xDexaAlnRep0.bb A549 ChipSeq Pol2 Peaks bigBed HudsonAlpha analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/peakSeq/optimal/hub/peakSeq.optimal.wgEncodeHaibTfbsA549Pol2Pcr2xEtoh02AlnRep0_vs_wgEncodeHaibTfbsA549ControlPcr2xEtoh02AlnRep2.bb A549 ChipSeq Pol2 Peaks bigBed HudsonAlpha analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/peakSeq/optimal/hub/peakSeq.optimal.wgEncodeHaibTfbsA549Usf1Pcr1xDexaAlnRep0_vs_wgEncodeHaibTfbsA549ControlPcr1xDexaAlnRep0.bb A549 ChipSeq USF-1 Peaks bigBed HudsonAlpha analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/peakSeq/optimal/hub/peakSeq.optimal.wgEncodeHaibTfbsA549Usf1Pcr1xEtoh02AlnRep0_vs_wgEncodeHaibTfbsA549ControlPcr1xEtoh02AlnRep1.bb A549 ChipSeq USF-1 Peaks bigBed HudsonAlpha analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/peakSeq/optimal/hub/peakSeq.optimal.wgEncodeHaibTfbsEcc1EralphaaV0416102Estradia1hAlnRep0_vs_wgEncodeHaibTfbsEcc1EralphaaV0416102Dmso2AlnRep0.bb ECC-1 ChipSeq ERalpha_a Peaks bigBed HudsonAlpha analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/peakSeq/optimal/hub/peakSeq.optimal.wgEncodeHaibTfbsEcc1EralphaaV0416102Gen1hAlnRep0_vs_wgEncodeHaibTfbsEcc1EralphaaV0416102Dmso2AlnRep0.bb ECC-1 ChipSeq ERalpha_a Peaks bigBed HudsonAlpha analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/peakSeq/optimal/hub/peakSeq.optimal.wgEncodeHaibTfbsEcc1Foxa1c20V0416102Dmso2AlnRep0_vs_wgEncodeHaibTfbsEcc1ControlV0416102Dmso2AlnRep0.bb ECC-1 ChipSeq FOXA1_(C-20) Peaks bigBed HudsonAlpha analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/peakSeq/optimal/hub/peakSeq.optimal.wgEncodeHaibTfbsEcc1GrV0416102DexaAlnRep0_vs_wgEncodeHaibTfbsEcc1GrV0416102Etoh02AlnRep0.bb ECC-1 ChipSeq GR Peaks bigBed HudsonAlpha analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/peakSeq/optimal/hub/peakSeq.optimal.wgEncodeHaibTfbsEcc1Pol2V0416102Dmso2AlnRep0_vs_wgEncodeHaibTfbsEcc1ControlV0416102Dmso2AlnRep0.bb ECC-1 ChipSeq Pol2 Peaks bigBed HudsonAlpha analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/peakSeq/optimal/hub/peakSeq.optimal.wgEncodeHaibTfbsGm12878Atf3Pcr1xAlnRep0_vs_wgEncodeHaibTfbsGm12878ControlV0416101AlnRep0.bb GM12878 ChipSeq ATF3 Peaks bigBed HudsonAlpha analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/peakSeq/optimal/hub/peakSeq.optimal.wgEncodeHaibTfbsGm12878BatfPcr1xAlnRep0_vs_wgEncodeHaibTfbsGm12878ControlPcr1xAlnRep0.bb GM12878 ChipSeq BATF Peaks bigBed HudsonAlpha analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/peakSeq/optimal/hub/peakSeq.optimal.wgEncodeHaibTfbsGm12878Bcl11aPcr1xAlnRep0_vs_wgEncodeHaibTfbsGm12878ControlPcr1xAlnRep0.bb GM12878 ChipSeq BCL11A Peaks bigBed HudsonAlpha analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/peakSeq/optimal/hub/peakSeq.optimal.wgEncodeHaibTfbsGm12878Bcl3Pcr1xAlnRep0_vs_wgEncodeHaibTfbsGm12878ControlPcr1xAlnRep0.bb GM12878 ChipSeq BCL3 Peaks bigBed HudsonAlpha analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/peakSeq/optimal/hub/peakSeq.optimal.wgEncodeHaibTfbsGm12878Bclaf1m33V0416101AlnRep0_vs_wgEncodeHaibTfbsGm12878ControlV0416101AlnRep0.bb GM12878 ChipSeq BCLAF1_(M33-P5B11) Peaks bigBed HudsonAlpha analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/peakSeq/optimal/hub/peakSeq.optimal.wgEncodeHaibTfbsGm12878Ebf1c8Pcr1xAlnRep0_vs_wgEncodeHaibTfbsGm12878ControlPcr1xAlnRep0.bb GM12878 ChipSeq EBF1_(C-8) Peaks bigBed HudsonAlpha analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/peakSeq/optimal/hub/peakSeq.optimal.wgEncodeHaibTfbsGm12878EbfPcr1xAlnRep0_vs_wgEncodeHaibTfbsGm12878ControlPcr1xAlnRep0.bb GM12878 ChipSeq EBF Peaks bigBed HudsonAlpha analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/peakSeq/optimal/hub/peakSeq.optimal.wgEncodeHaibTfbsGm12878Egr1Pcr2xAlnRep0_vs_wgEncodeHaibTfbsGm12878ControlPcr2xAlnRep0.bb GM12878 ChipSeq Egr-1 Peaks bigBed HudsonAlpha analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/peakSeq/optimal/hub/peakSeq.optimal.wgEncodeHaibTfbsGm12878Egr1V0416101AlnRep0_vs_wgEncodeHaibTfbsGm12878ControlV0416101AlnRep0.bb GM12878 ChipSeq Egr-1 Peaks bigBed HudsonAlpha analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/peakSeq/optimal/hub/peakSeq.optimal.wgEncodeHaibTfbsGm12878Elf1sc631V0416101AlnRep0_vs_wgEncodeHaibTfbsGm12878ControlV0416101AlnRep0.bb GM12878 ChipSeq ELF1_(SC-631) Peaks bigBed HudsonAlpha analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/peakSeq/optimal/hub/peakSeq.optimal.wgEncodeHaibTfbsGm12878Ets1Pcr1xAlnRep0_vs_wgEncodeHaibTfbsGm12878ControlV0416101AlnRep0.bb GM12878 ChipSeq ETS1 Peaks bigBed HudsonAlpha analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/peakSeq/optimal/hub/peakSeq.optimal.wgEncodeHaibTfbsGm12878GabpPcr2xAlnRep0_vs_wgEncodeHaibTfbsGm12878ControlPcr2xAlnRep0.bb GM12878 ChipSeq GABP Peaks bigBed HudsonAlpha analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/peakSeq/optimal/hub/peakSeq.optimal.wgEncodeHaibTfbsGm12878Irf4m17Pcr1xAlnRep0_vs_wgEncodeHaibTfbsGm12878ControlPcr1xAlnRep0.bb GM12878 ChipSeq IRF4_(M-17) Peaks bigBed HudsonAlpha analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/peakSeq/optimal/hub/peakSeq.optimal.wgEncodeHaibTfbsGm12878Irf4Pcr1xAlnRep0_vs_wgEncodeHaibTfbsGm12878ControlPcr1xAlnRep0.bb GM12878 ChipSeq IRF4 Peaks bigBed HudsonAlpha analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/peakSeq/optimal/hub/peakSeq.optimal.wgEncodeHaibTfbsGm12878Mef2aPcr1xAlnRep0_vs_wgEncodeHaibTfbsGm12878ControlV0416101AlnRep0.bb GM12878 ChipSeq MEF2A Peaks bigBed HudsonAlpha analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/peakSeq/optimal/hub/peakSeq.optimal.wgEncodeHaibTfbsGm12878Mef2csc13268Pcr1xAlnRep0_vs_wgEncodeHaibTfbsGm12878ControlV0416101AlnRep0.bb GM12878 ChipSeq MEF2C_(SC-13268) Peaks bigBed HudsonAlpha analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/peakSeq/optimal/hub/peakSeq.optimal.wgEncodeHaibTfbsGm12878NrsfPcr2xAlnRep0_vs_wgEncodeHaibTfbsGm12878ControlPcr2xAlnRep0.bb GM12878 ChipSeq NRSF Peaks bigBed HudsonAlpha analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/peakSeq/optimal/hub/peakSeq.optimal.wgEncodeHaibTfbsGm12878Oct2Pcr1xAlnRep0_vs_wgEncodeHaibTfbsGm12878ControlPcr1xAlnRep0.bb GM12878 ChipSeq Oct-2 Peaks bigBed HudsonAlpha analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/peakSeq/optimal/hub/peakSeq.optimal.wgEncodeHaibTfbsGm12878P300Pcr1xAlnRep0_vs_wgEncodeHaibTfbsGm12878ControlPcr1xAlnRep0.bb GM12878 ChipSeq p300 Peaks bigBed HudsonAlpha analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/peakSeq/optimal/hub/peakSeq.optimal.wgEncodeHaibTfbsGm12878Pax5c20Pcr1xAlnRep0_vs_wgEncodeHaibTfbsGm12878ControlPcr1xAlnRep0.bb GM12878 ChipSeq PAX5-C20 Peaks bigBed HudsonAlpha analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/peakSeq/optimal/hub/peakSeq.optimal.wgEncodeHaibTfbsGm12878Pax5n19Pcr1xAlnRep0_vs_wgEncodeHaibTfbsGm12878ControlPcr1xAlnRep0.bb GM12878 ChipSeq PAX5-N19 Peaks bigBed HudsonAlpha analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/peakSeq/optimal/hub/peakSeq.optimal.wgEncodeHaibTfbsGm12878Pbx3Pcr1xAlnRep0_vs_wgEncodeHaibTfbsGm12878ControlPcr1xAlnRep0.bb GM12878 ChipSeq Pbx3 Peaks bigBed HudsonAlpha analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/peakSeq/optimal/hub/peakSeq.optimal.wgEncodeHaibTfbsGm12878Pol24h8Pcr1xAlnRep0_vs_wgEncodeHaibTfbsGm12878ControlPcr1xAlnRep0.bb GM12878 ChipSeq Pol2-4H8 Peaks bigBed HudsonAlpha analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/peakSeq/optimal/hub/peakSeq.optimal.wgEncodeHaibTfbsGm12878Pol2Pcr2xAlnRep0_vs_wgEncodeHaibTfbsGm12878ControlPcr2xAlnRep0.bb GM12878 ChipSeq Pol2 Peaks bigBed HudsonAlpha analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/peakSeq/optimal/hub/peakSeq.optimal.wgEncodeHaibTfbsGm12878Pou2f2Pcr1xAlnRep0_vs_wgEncodeHaibTfbsGm12878ControlPcr1xAlnRep0.bb GM12878 ChipSeq POU2F2 Peaks bigBed HudsonAlpha analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/peakSeq/optimal/hub/peakSeq.optimal.wgEncodeHaibTfbsGm12878Pu1Pcr1xAlnRep0_vs_wgEncodeHaibTfbsGm12878ControlPcr1xAlnRep0.bb GM12878 ChipSeq PU.1 Peaks bigBed HudsonAlpha analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/peakSeq/optimal/hub/peakSeq.optimal.wgEncodeHaibTfbsGm12878Rad21V0416101AlnRep0_vs_wgEncodeHaibTfbsGm12878ControlV0416101AlnRep0.bb GM12878 ChipSeq Rad21 Peaks bigBed HudsonAlpha analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/peakSeq/optimal/hub/peakSeq.optimal.wgEncodeHaibTfbsGm12878RxraPcr1xAlnRep0_vs_wgEncodeHaibTfbsGm12878ControlPcr1xAlnRep0.bb GM12878 ChipSeq RXRA Peaks bigBed HudsonAlpha analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/peakSeq/optimal/hub/peakSeq.optimal.wgEncodeHaibTfbsGm12878Sin3ak20Pcr2xAlnRep0_vs_wgEncodeHaibTfbsGm12878ControlPcr1xAlnRep0.bb GM12878 ChipSeq Sin3Ak-20 Peaks bigBed HudsonAlpha analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/peakSeq/optimal/hub/peakSeq.optimal.wgEncodeHaibTfbsGm12878Six5Pcr1xAlnRep0_vs_wgEncodeHaibTfbsGm12878ControlPcr1xAlnRep0.bb GM12878 ChipSeq SIX5 Peaks bigBed HudsonAlpha analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/peakSeq/optimal/hub/peakSeq.optimal.wgEncodeHaibTfbsGm12878Sp1Pcr1xAlnRep0_vs_wgEncodeHaibTfbsGm12878ControlPcr1xAlnRep0.bb GM12878 ChipSeq SP1 Peaks bigBed HudsonAlpha analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/peakSeq/optimal/hub/peakSeq.optimal.wgEncodeHaibTfbsGm12878SrfPcr2xAlnRep0_vs_wgEncodeHaibTfbsGm12878ControlPcr2xAlnRep0.bb GM12878 ChipSeq SRF Peaks bigBed HudsonAlpha analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/peakSeq/optimal/hub/peakSeq.optimal.wgEncodeHaibTfbsGm12878SrfV0416101AlnRep0_vs_wgEncodeHaibTfbsGm12878ControlV0416101AlnRep0.bb GM12878 ChipSeq SRF Peaks bigBed HudsonAlpha analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/peakSeq/optimal/hub/peakSeq.optimal.wgEncodeHaibTfbsGm12878Taf1Pcr1xAlnRep0_vs_wgEncodeHaibTfbsGm12878ControlPcr1xAlnRep0.bb GM12878 ChipSeq TAF1 Peaks bigBed HudsonAlpha analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/peakSeq/optimal/hub/peakSeq.optimal.wgEncodeHaibTfbsGm12878Tcf12Pcr1xAlnRep0_vs_wgEncodeHaibTfbsGm12878ControlPcr1xAlnRep0.bb GM12878 ChipSeq TCF12 Peaks bigBed HudsonAlpha analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/peakSeq/optimal/hub/peakSeq.optimal.wgEncodeHaibTfbsGm12878Usf1Pcr2xAlnRep0_vs_wgEncodeHaibTfbsGm12878ControlPcr2xAlnRep0.bb GM12878 ChipSeq USF-1 Peaks bigBed HudsonAlpha analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/peakSeq/optimal/hub/peakSeq.optimal.wgEncodeHaibTfbsGm12878Yy1V0416101AlnRep0_vs_wgEncodeHaibTfbsGm12878ControlV0416101AlnRep1.bb GM12878 ChipSeq YY1_(SC-281) Peaks bigBed HudsonAlpha analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/peakSeq/optimal/hub/peakSeq.optimal.wgEncodeHaibTfbsGm12878Zbtb33Pcr1xAlnRep0_vs_wgEncodeHaibTfbsGm12878ControlPcr1xAlnRep0.bb GM12878 ChipSeq ZBTB33 Peaks bigBed HudsonAlpha analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/peakSeq/optimal/hub/peakSeq.optimal.wgEncodeHaibTfbsGm12878Zeb1sc25388V0416102AlnRep0_vs_wgEncodeHaibTfbsGm12878ControlPcr1xAlnRep0.bb GM12878 ChipSeq ZEB1_(SC-25388) Peaks bigBed HudsonAlpha analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/peakSeq/optimal/hub/peakSeq.optimal.wgEncodeHaibTfbsGm12891Oct2Pcr1xAlnRep0_vs_wgEncodeHaibTfbsGm12891ControlPcr1xAlnRep0.bb GM12891 ChipSeq Oct-2 Peaks bigBed HudsonAlpha analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/peakSeq/optimal/hub/peakSeq.optimal.wgEncodeHaibTfbsGm12891Pax5c20Pcr1xAlnRep0_vs_wgEncodeHaibTfbsGm12891ControlPcr1xAlnRep0.bb GM12891 ChipSeq PAX5-C20 Peaks bigBed HudsonAlpha analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/peakSeq/optimal/hub/peakSeq.optimal.wgEncodeHaibTfbsGm12891Pol24h8Pcr1xAlnRep0_vs_wgEncodeHaibTfbsGm12891ControlPcr1xAlnRep0.bb GM12891 ChipSeq Pol2-4H8 Peaks bigBed HudsonAlpha analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/peakSeq/optimal/hub/peakSeq.optimal.wgEncodeHaibTfbsGm12891Pol2Pcr1xAlnRep0_vs_wgEncodeHaibTfbsGm12891ControlPcr1xAlnRep0.bb GM12891 ChipSeq Pol2 Peaks bigBed HudsonAlpha analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/peakSeq/optimal/hub/peakSeq.optimal.wgEncodeHaibTfbsGm12891Pou2f2Pcr1xAlnRep0_vs_wgEncodeHaibTfbsGm12891ControlPcr1xAlnRep0.bb GM12891 ChipSeq POU2F2 Peaks bigBed HudsonAlpha analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/peakSeq/optimal/hub/peakSeq.optimal.wgEncodeHaibTfbsGm12891Pu1Pcr1xAlnRep0_vs_wgEncodeHaibTfbsGm12891ControlPcr1xAlnRep0.bb GM12891 ChipSeq PU.1 Peaks bigBed HudsonAlpha analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/peakSeq/optimal/hub/peakSeq.optimal.wgEncodeHaibTfbsGm12891Taf1Pcr1xAlnRep0_vs_wgEncodeHaibTfbsGm12891ControlPcr1xAlnRep0.bb GM12891 ChipSeq TAF1 Peaks bigBed HudsonAlpha analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/peakSeq/optimal/hub/peakSeq.optimal.wgEncodeHaibTfbsGm12891Yy1c20V0416101AlnRep0_vs_wgEncodeHaibTfbsGm12891ControlPcr1xAlnRep0.bb GM12891 ChipSeq YY1_(C-20) Peaks bigBed HudsonAlpha analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/peakSeq/optimal/hub/peakSeq.optimal.wgEncodeHaibTfbsGm12892Pax5c20Pcr1xAlnRep0_vs_wgEncodeHaibTfbsGm12892ControlPcr1xAlnRep0.bb GM12892 ChipSeq PAX5-C20 Peaks bigBed HudsonAlpha analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/peakSeq/optimal/hub/peakSeq.optimal.wgEncodeHaibTfbsGm12892Pol24h8Pcr1xAlnRep0_vs_wgEncodeHaibTfbsGm12892ControlPcr1xAlnRep0.bb GM12892 ChipSeq Pol2-4H8 Peaks bigBed HudsonAlpha analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/peakSeq/optimal/hub/peakSeq.optimal.wgEncodeHaibTfbsGm12892Pol24h8V0416102AlnRep0_vs_wgEncodeHaibTfbsGm12892ControlPcr1xAlnRep0.bb GM12892 ChipSeq Pol2-4H8 Peaks bigBed HudsonAlpha analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/peakSeq/optimal/hub/peakSeq.optimal.wgEncodeHaibTfbsGm12892Pol2Pcr1xAlnRep0_vs_wgEncodeHaibTfbsGm12892ControlPcr1xAlnRep0.bb GM12892 ChipSeq Pol2 Peaks bigBed HudsonAlpha analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/peakSeq/optimal/hub/peakSeq.optimal.wgEncodeHaibTfbsGm12892Pol2V0416102AlnRep0_vs_wgEncodeHaibTfbsGm12892ControlPcr1xAlnRep0.bb GM12892 ChipSeq Pol2 Peaks bigBed HudsonAlpha analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/peakSeq/optimal/hub/peakSeq.optimal.wgEncodeHaibTfbsGm12892Taf1Pcr1xAlnRep0_vs_wgEncodeHaibTfbsGm12892ControlPcr1xAlnRep0.bb GM12892 ChipSeq TAF1 Peaks bigBed HudsonAlpha analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/peakSeq/optimal/hub/peakSeq.optimal.wgEncodeHaibTfbsGm12892Taf1V0416102AlnRep0_vs_wgEncodeHaibTfbsGm12892ControlPcr1xAlnRep0.bb GM12892 ChipSeq TAF1 Peaks bigBed HudsonAlpha analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/peakSeq/optimal/hub/peakSeq.optimal.wgEncodeHaibTfbsGm12892Yy1V0416101AlnRep0_vs_wgEncodeHaibTfbsGm12892ControlPcr1xAlnRep0.bb GM12892 ChipSeq YY1 Peaks bigBed HudsonAlpha analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/peakSeq/optimal/hub/peakSeq.optimal.wgEncodeHaibTfbsH1hescAtf3Pcr1xAlnRep0_vs_wgEncodeHaibTfbsH1hescControlPcr1xAlnRep0.bb H1-hESC ChipSeq ATF3 Peaks bigBed HudsonAlpha analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/peakSeq/optimal/hub/peakSeq.optimal.wgEncodeHaibTfbsH1hescBcl11aPcr1xAlnRep0_vs_wgEncodeHaibTfbsH1hescControlPcr1xAlnRep0.bb H1-hESC ChipSeq BCL11A Peaks bigBed HudsonAlpha analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/peakSeq/optimal/hub/peakSeq.optimal.wgEncodeHaibTfbsH1hescBcl3Pcr1xAlnRep0_vs_wgEncodeHaibTfbsH1hescControlPcr1xAlnRep0.bb H1-hESC ChipSeq BCL3 Peaks bigBed HudsonAlpha analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/peakSeq/optimal/hub/peakSeq.optimal.wgEncodeHaibTfbsH1hescCtcfsc5916V0416102AlnRep0_vs_wgEncodeHaibTfbsH1hescControlPcr1xAlnRep0.bb H1-hESC ChipSeq CTCF_(SC-5916) Peaks bigBed HudsonAlpha analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/peakSeq/optimal/hub/peakSeq.optimal.wgEncodeHaibTfbsH1hescEgr1V0416101AlnRep0_vs_wgEncodeHaibTfbsH1hescControlPcr1xAlnRep0.bb H1-hESC ChipSeq Egr-1 Peaks bigBed HudsonAlpha analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/peakSeq/optimal/hub/peakSeq.optimal.wgEncodeHaibTfbsH1hescEgr1V0416102AlnRep0_vs_wgEncodeHaibTfbsH1hescControlPcr1xAlnRep0.bb H1-hESC ChipSeq Egr-1 Peaks bigBed HudsonAlpha analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/peakSeq/optimal/hub/peakSeq.optimal.wgEncodeHaibTfbsH1hescGabpPcr1xAlnRep0_vs_wgEncodeHaibTfbsH1hescControlPcr1xAlnRep0.bb H1-hESC ChipSeq GABP Peaks bigBed HudsonAlpha analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/peakSeq/optimal/hub/peakSeq.optimal.wgEncodeHaibTfbsH1hescHdac2sc6296V0416102AlnRep0_vs_wgEncodeHaibTfbsH1hescControlPcr1xAlnRep0.bb H1-hESC ChipSeq HDAC2_(SC-6296) Peaks bigBed HudsonAlpha analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/peakSeq/optimal/hub/peakSeq.optimal.wgEncodeHaibTfbsH1hescJundV0416102AlnRep0_vs_wgEncodeHaibTfbsH1hescControlPcr1xAlnRep0.bb H1-hESC ChipSeq JunD Peaks bigBed HudsonAlpha analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/peakSeq/optimal/hub/peakSeq.optimal.wgEncodeHaibTfbsH1hescNanogsc33759V0416102AlnRep0_vs_wgEncodeHaibTfbsH1hescControlPcr1xAlnRep0.bb H1-hESC ChipSeq NANOG_(SC-33759) Peaks bigBed HudsonAlpha analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/peakSeq/optimal/hub/peakSeq.optimal.wgEncodeHaibTfbsH1hescNrsfPcr1xAlnRep0_vs_wgEncodeHaibTfbsH1hescControlPcr1xAlnRep0.bb H1-hESC ChipSeq NRSF Peaks bigBed HudsonAlpha analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/peakSeq/optimal/hub/peakSeq.optimal.wgEncodeHaibTfbsH1hescNrsfV0416102AlnRep0_vs_wgEncodeHaibTfbsH1hescControlPcr1xAlnRep0.bb H1-hESC ChipSeq NRSF Peaks bigBed HudsonAlpha analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/peakSeq/optimal/hub/peakSeq.optimal.wgEncodeHaibTfbsH1hescP300V0416102AlnRep0_vs_wgEncodeHaibTfbsH1hescControlPcr1xAlnRep0.bb H1-hESC ChipSeq p300 Peaks bigBed HudsonAlpha analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/peakSeq/optimal/hub/peakSeq.optimal.wgEncodeHaibTfbsH1hescPol24h8Pcr1xAlnRep0_vs_wgEncodeHaibTfbsH1hescControlPcr1xAlnRep0.bb H1-hESC ChipSeq Pol2-4H8 Peaks bigBed HudsonAlpha analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/peakSeq/optimal/hub/peakSeq.optimal.wgEncodeHaibTfbsH1hescPol24h8V0416102AlnRep0_vs_wgEncodeHaibTfbsH1hescControlPcr1xAlnRep0.bb H1-hESC ChipSeq Pol2-4H8 Peaks bigBed HudsonAlpha analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/peakSeq/optimal/hub/peakSeq.optimal.wgEncodeHaibTfbsH1hescPol2Pcr1xAlnRep0_vs_wgEncodeHaibTfbsH1hescControlPcr1xAlnRep0.bb H1-hESC ChipSeq Pol2 Peaks bigBed HudsonAlpha analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/peakSeq/optimal/hub/peakSeq.optimal.wgEncodeHaibTfbsH1hescPol2V0416102AlnRep0_vs_wgEncodeHaibTfbsH1hescControlPcr1xAlnRep0.bb H1-hESC ChipSeq Pol2 Peaks bigBed HudsonAlpha analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/peakSeq/optimal/hub/peakSeq.optimal.wgEncodeHaibTfbsH1hescPou5f1sc9081V0416102AlnRep0_vs_wgEncodeHaibTfbsH1hescControlPcr1xAlnRep0.bb H1-hESC ChipSeq POU5F1_(SC-9081) Peaks bigBed HudsonAlpha analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/peakSeq/optimal/hub/peakSeq.optimal.wgEncodeHaibTfbsH1hescRad21V0416102AlnRep0_vs_wgEncodeHaibTfbsH1hescControlPcr1xAlnRep0.bb H1-hESC ChipSeq Rad21 Peaks bigBed HudsonAlpha analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/peakSeq/optimal/hub/peakSeq.optimal.wgEncodeHaibTfbsH1hescRxraV0416102AlnRep0_vs_wgEncodeHaibTfbsH1hescControlPcr1xAlnRep0.bb H1-hESC ChipSeq RXRA Peaks bigBed HudsonAlpha analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/peakSeq/optimal/hub/peakSeq.optimal.wgEncodeHaibTfbsH1hescSin3ak20Pcr1xAlnRep0_vs_wgEncodeHaibTfbsH1hescControlPcr1xAlnRep0.bb H1-hESC ChipSeq Sin3Ak-20 Peaks bigBed HudsonAlpha analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/peakSeq/optimal/hub/peakSeq.optimal.wgEncodeHaibTfbsH1hescSix5Pcr1xAlnRep0_vs_wgEncodeHaibTfbsH1hescControlPcr1xAlnRep0.bb H1-hESC ChipSeq SIX5 Peaks bigBed HudsonAlpha analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/peakSeq/optimal/hub/peakSeq.optimal.wgEncodeHaibTfbsH1hescSp1Pcr1xAlnRep0_vs_wgEncodeHaibTfbsH1hescControlPcr1xAlnRep0.bb H1-hESC ChipSeq SP1 Peaks bigBed HudsonAlpha analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/peakSeq/optimal/hub/peakSeq.optimal.wgEncodeHaibTfbsH1hescSrfPcr1xAlnRep0_vs_wgEncodeHaibTfbsH1hescControlPcr1xAlnRep0.bb H1-hESC ChipSeq SRF Peaks bigBed HudsonAlpha analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/peakSeq/optimal/hub/peakSeq.optimal.wgEncodeHaibTfbsH1hescTaf1Pcr1xAlnRep0_vs_wgEncodeHaibTfbsH1hescControlPcr1xAlnRep0.bb H1-hESC ChipSeq TAF1 Peaks bigBed HudsonAlpha analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/peakSeq/optimal/hub/peakSeq.optimal.wgEncodeHaibTfbsH1hescTaf1V0416102AlnRep0_vs_wgEncodeHaibTfbsH1hescControlPcr1xAlnRep0.bb H1-hESC ChipSeq TAF1 Peaks bigBed HudsonAlpha analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/peakSeq/optimal/hub/peakSeq.optimal.wgEncodeHaibTfbsH1hescTaf7sq8V0416102AlnRep0_vs_wgEncodeHaibTfbsH1hescControlPcr1xAlnRep0.bb H1-hESC ChipSeq TAF7_(SQ-8) Peaks bigBed HudsonAlpha analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/peakSeq/optimal/hub/peakSeq.optimal.wgEncodeHaibTfbsH1hescTcf12Pcr1xAlnRep0_vs_wgEncodeHaibTfbsH1hescControlPcr1xAlnRep0.bb H1-hESC ChipSeq TCF12 Peaks bigBed HudsonAlpha analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/peakSeq/optimal/hub/peakSeq.optimal.wgEncodeHaibTfbsH1hescUsf1Pcr1xAlnRep0_vs_wgEncodeHaibTfbsH1hescControlPcr1xAlnRep0.bb H1-hESC ChipSeq USF-1 Peaks bigBed HudsonAlpha analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/peakSeq/optimal/hub/peakSeq.optimal.wgEncodeHaibTfbsH1hescYy1c20Pcr1xAlnRep0_vs_wgEncodeHaibTfbsH1hescControlPcr1xAlnRep0.bb H1-hESC ChipSeq YY1_(C-20) Peaks bigBed HudsonAlpha analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/peakSeq/optimal/hub/peakSeq.optimal.wgEncodeHaibTfbsHct116Pol24h8V0416101AlnRep0_vs_wgEncodeHaibTfbsHct116ControlV0416101AlnRep2.bb HCT-116 ChipSeq Pol2-4H8 Peaks bigBed HudsonAlpha analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/peakSeq/optimal/hub/peakSeq.optimal.wgEncodeHaibTfbsHelas3GabpPcr1xAlnRep0_vs_wgEncodeHaibTfbsHelas3ControlPcr1xAlnRep0.bb HeLa-S3 ChipSeq GABP Peaks bigBed HudsonAlpha analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/peakSeq/optimal/hub/peakSeq.optimal.wgEncodeHaibTfbsHelas3NrsfPcr1xAlnRep0_vs_wgEncodeHaibTfbsHelas3ControlPcr1xAlnRep0.bb HeLa-S3 ChipSeq NRSF Peaks bigBed HudsonAlpha analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/peakSeq/optimal/hub/peakSeq.optimal.wgEncodeHaibTfbsHelas3Pol2Pcr1xAlnRep0_vs_wgEncodeHaibTfbsHelas3ControlPcr1xAlnRep0.bb HeLa-S3 ChipSeq Pol2 Peaks bigBed HudsonAlpha analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/peakSeq/optimal/hub/peakSeq.optimal.wgEncodeHaibTfbsHelas3Taf1Pcr1xAlnRep0_vs_wgEncodeHaibTfbsHelas3ControlPcr1xAlnRep0.bb HeLa-S3 ChipSeq TAF1 Peaks bigBed HudsonAlpha analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/peakSeq/optimal/hub/peakSeq.optimal.wgEncodeHaibTfbsHepg2Atf3V0416101AlnRep0_vs_wgEncodeHaibTfbsHepg2ControlV0416101AlnRep0.bb HepG2 ChipSeq ATF3 Peaks bigBed HudsonAlpha analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/peakSeq/optimal/hub/peakSeq.optimal.wgEncodeHaibTfbsHepg2Bhlhe40V0416101AlnRep0_vs_wgEncodeHaibTfbsHepg2ControlPcr1xAlnRep0.bb HepG2 ChipSeq BHLHE40 Peaks bigBed HudsonAlpha analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/peakSeq/optimal/hub/peakSeq.optimal.wgEncodeHaibTfbsHepg2CtcfV0416101AlnRep0_vs_wgEncodeHaibTfbsHepg2ControlV0416101AlnRep0.bb HepG2 ChipSeq CTCF Peaks bigBed HudsonAlpha analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/peakSeq/optimal/hub/peakSeq.optimal.wgEncodeHaibTfbsHepg2Elf1sc631V0416101AlnRep0_vs_wgEncodeHaibTfbsHepg2ControlV0416101AlnRep0.bb HepG2 ChipSeq ELF1_(SC-631) Peaks bigBed HudsonAlpha analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/peakSeq/optimal/hub/peakSeq.optimal.wgEncodeHaibTfbsHepg2Fosl2Pcr1xAlnRep0_vs_wgEncodeHaibTfbsHepg2ControlPcr1xAlnRep0.bb HepG2 ChipSeq FOSL2 Peaks bigBed HudsonAlpha analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/peakSeq/optimal/hub/peakSeq.optimal.wgEncodeHaibTfbsHepg2Foxa1c20Pcr1xAlnRep0_vs_wgEncodeHaibTfbsHepg2ControlV0416101AlnRep0.bb HepG2 ChipSeq FOXA1_(C-20) Peaks bigBed HudsonAlpha analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/peakSeq/optimal/hub/peakSeq.optimal.wgEncodeHaibTfbsHepg2Foxa1sc101058Pcr1xAlnRep0_vs_wgEncodeHaibTfbsHepg2ControlV0416101AlnRep0.bb HepG2 ChipSeq FOXA1_(SC-101058) Peaks bigBed HudsonAlpha analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/peakSeq/optimal/hub/peakSeq.optimal.wgEncodeHaibTfbsHepg2Foxa2sc6554V0416101AlnRep0_vs_wgEncodeHaibTfbsHepg2ControlV0416101AlnRep0.bb HepG2 ChipSeq FOXA2_(SC-6554) Peaks bigBed HudsonAlpha analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/peakSeq/optimal/hub/peakSeq.optimal.wgEncodeHaibTfbsHepg2GabpPcr2xAlnRep0_vs_wgEncodeHaibTfbsHepg2ControlPcr2xAlnRep0.bb HepG2 ChipSeq GABP Peaks bigBed HudsonAlpha analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/peakSeq/optimal/hub/peakSeq.optimal.wgEncodeHaibTfbsHepg2Hdac2sc6296V0416101AlnRep0_vs_wgEncodeHaibTfbsHepg2ControlV0416101AlnRep0.bb HepG2 ChipSeq HDAC2_(SC-6296) Peaks bigBed HudsonAlpha analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/peakSeq/optimal/hub/peakSeq.optimal.wgEncodeHaibTfbsHepg2Hey1V0416101AlnRep0_vs_wgEncodeHaibTfbsHepg2ControlPcr1xAlnRep0.bb HepG2 ChipSeq HEY1 Peaks bigBed HudsonAlpha analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/peakSeq/optimal/hub/peakSeq.optimal.wgEncodeHaibTfbsHepg2Hnf4ah171Pcr1xAlnRep0_vs_wgEncodeHaibTfbsHepg2ControlV0416101AlnRep0.bb HepG2 ChipSeq HNF4A_(H-171) Peaks bigBed HudsonAlpha analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/peakSeq/optimal/hub/peakSeq.optimal.wgEncodeHaibTfbsHepg2Hnf4gsc6558V0416101AlnRep0_vs_wgEncodeHaibTfbsHepg2ControlV0416101AlnRep0.bb HepG2 ChipSeq HNF4G_(SC-6558) Peaks bigBed HudsonAlpha analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/peakSeq/optimal/hub/peakSeq.optimal.wgEncodeHaibTfbsHepg2JundPcr1xAlnRep0_vs_wgEncodeHaibTfbsHepg2ControlPcr1xAlnRep0.bb HepG2 ChipSeq JunD Peaks bigBed HudsonAlpha analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/peakSeq/optimal/hub/peakSeq.optimal.wgEncodeHaibTfbsHepg2NrsfPcr2xAlnRep0_vs_wgEncodeHaibTfbsHepg2ControlPcr2xAlnRep0.bb HepG2 ChipSeq NRSF Peaks bigBed HudsonAlpha analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/peakSeq/optimal/hub/peakSeq.optimal.wgEncodeHaibTfbsHepg2P300Pcr1xAlnRep0_vs_wgEncodeHaibTfbsHepg2ControlPcr1xAlnRep0.bb HepG2 ChipSeq p300 Peaks bigBed HudsonAlpha analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/peakSeq/optimal/hub/peakSeq.optimal.wgEncodeHaibTfbsHepg2P300V0416101AlnRep0_vs_wgEncodeHaibTfbsHepg2ControlV0416101AlnRep0.bb HepG2 ChipSeq p300 Peaks bigBed HudsonAlpha analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/peakSeq/optimal/hub/peakSeq.optimal.wgEncodeHaibTfbsHepg2Pol2Pcr2xAlnRep0_vs_wgEncodeHaibTfbsHepg2ControlPcr2xAlnRep0.bb HepG2 ChipSeq Pol2 Peaks bigBed HudsonAlpha analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/peakSeq/optimal/hub/peakSeq.optimal.wgEncodeHaibTfbsHepg2Rad21V0416101AlnRep0_vs_wgEncodeHaibTfbsHepg2ControlV0416101AlnRep0.bb HepG2 ChipSeq Rad21 Peaks bigBed HudsonAlpha analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/peakSeq/optimal/hub/peakSeq.optimal.wgEncodeHaibTfbsHepg2RxraPcr1xAlnRep0_vs_wgEncodeHaibTfbsHepg2ControlPcr1xAlnRep0.bb HepG2 ChipSeq RXRA Peaks bigBed HudsonAlpha analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/peakSeq/optimal/hub/peakSeq.optimal.wgEncodeHaibTfbsHepg2Sin3ak20Pcr1xAlnRep0_vs_wgEncodeHaibTfbsHepg2ControlPcr1xAlnRep0.bb HepG2 ChipSeq Sin3Ak-20 Peaks bigBed HudsonAlpha analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/peakSeq/optimal/hub/peakSeq.optimal.wgEncodeHaibTfbsHepg2Sp1Pcr1xAlnRep0_vs_wgEncodeHaibTfbsHepg2ControlPcr1xAlnRep0.bb HepG2 ChipSeq SP1 Peaks bigBed HudsonAlpha analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/peakSeq/optimal/hub/peakSeq.optimal.wgEncodeHaibTfbsHepg2SrfV0416101AlnRep0_vs_wgEncodeHaibTfbsHepg2ControlV0416101AlnRep0.bb HepG2 ChipSeq SRF Peaks bigBed HudsonAlpha analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/peakSeq/optimal/hub/peakSeq.optimal.wgEncodeHaibTfbsHepg2Taf1Pcr2xAlnRep0_vs_wgEncodeHaibTfbsHepg2ControlPcr2xAlnRep0.bb HepG2 ChipSeq TAF1 Peaks bigBed HudsonAlpha analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/peakSeq/optimal/hub/peakSeq.optimal.wgEncodeHaibTfbsHepg2Tcf12Pcr1xAlnRep0_vs_wgEncodeHaibTfbsHepg2ControlPcr1xAlnRep0.bb HepG2 ChipSeq TCF12 Peaks bigBed HudsonAlpha analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/peakSeq/optimal/hub/peakSeq.optimal.wgEncodeHaibTfbsHepg2Usf1Pcr1xAlnRep0_vs_wgEncodeHaibTfbsHepg2ControlPcr1xAlnRep0.bb HepG2 ChipSeq USF-1 Peaks bigBed HudsonAlpha analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/peakSeq/optimal/hub/peakSeq.optimal.wgEncodeHaibTfbsHepg2Zbtb33Pcr1xAlnRep0_vs_wgEncodeHaibTfbsHepg2ControlPcr1xAlnRep0.bb HepG2 ChipSeq ZBTB33 Peaks bigBed HudsonAlpha analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/peakSeq/optimal/hub/peakSeq.optimal.wgEncodeHaibTfbsHepg2Zbtb33V0416101AlnRep0_vs_wgEncodeHaibTfbsHepg2ControlV0416101AlnRep0.bb HepG2 ChipSeq ZBTB33 Peaks bigBed HudsonAlpha analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/peakSeq/optimal/hub/peakSeq.optimal.wgEncodeHaibTfbsHtb11NrsfPcr2xAlnRep0_vs_wgEncodeHaibTfbsHtb11ControlPcr2xAlnRep0.bb HTB-11 ChipSeq NRSF Peaks bigBed HudsonAlpha analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/peakSeq/optimal/hub/peakSeq.optimal.wgEncodeHaibTfbsK562Bcl3Pcr1xAlnRep0_vs_wgEncodeHaibTfbsK562ControlV0416101AlnRep0.bb K562 ChipSeq BCL3 Peaks bigBed HudsonAlpha analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/peakSeq/optimal/hub/peakSeq.optimal.wgEncodeHaibTfbsK562Bclaf1m33Pcr1xAlnRep0_vs_wgEncodeHaibTfbsK562ControlV0416101AlnRep0.bb K562 ChipSeq BCLAF1_(M33-P5B11) Peaks bigBed HudsonAlpha analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/peakSeq/optimal/hub/peakSeq.optimal.wgEncodeHaibTfbsK562Ctcflsc98982V0416101AlnRep0_vs_wgEncodeHaibTfbsK562ControlV0416101AlnRep0.bb K562 ChipSeq CTCFL_(SC-98982) Peaks bigBed HudsonAlpha analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/peakSeq/optimal/hub/peakSeq.optimal.wgEncodeHaibTfbsK562E2f6h50V0416102AlnRep0_vs_wgEncodeHaibTfbsK562ControlPcr1xAlnRep0.bb K562 ChipSeq E2F6_(H-50) Peaks bigBed HudsonAlpha analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/peakSeq/optimal/hub/peakSeq.optimal.wgEncodeHaibTfbsK562Egr1V0416101AlnRep0_vs_wgEncodeHaibTfbsK562ControlV0416101AlnRep0.bb K562 ChipSeq Egr-1 Peaks bigBed HudsonAlpha analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/peakSeq/optimal/hub/peakSeq.optimal.wgEncodeHaibTfbsK562Elf1sc631V0416102AlnRep0_vs_wgEncodeHaibTfbsK562ControlPcr1xAlnRep0.bb K562 ChipSeq ELF1_(SC-631) Peaks bigBed HudsonAlpha analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/peakSeq/optimal/hub/peakSeq.optimal.wgEncodeHaibTfbsK562Ets1V0416101AlnRep0_vs_wgEncodeHaibTfbsK562ControlV0416101AlnRep0.bb K562 ChipSeq ETS1 Peaks bigBed HudsonAlpha analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/peakSeq/optimal/hub/peakSeq.optimal.wgEncodeHaibTfbsK562Fosl1sc183V0416101AlnRep0_vs_wgEncodeHaibTfbsK562ControlV0416101AlnRep0.bb K562 ChipSeq FOSL1_(SC-183) Peaks bigBed HudsonAlpha analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/peakSeq/optimal/hub/peakSeq.optimal.wgEncodeHaibTfbsK562GabpV0416101AlnRep0_vs_wgEncodeHaibTfbsK562ControlV0416101AlnRep0.bb K562 ChipSeq GABP Peaks bigBed HudsonAlpha analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/peakSeq/optimal/hub/peakSeq.optimal.wgEncodeHaibTfbsK562Gata2cg2Pcr1xAlnRep0_vs_wgEncodeHaibTfbsK562ControlV0416101AlnRep0.bb K562 ChipSeq GATA2_(CG2-96) Peaks bigBed HudsonAlpha analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/peakSeq/optimal/hub/peakSeq.optimal.wgEncodeHaibTfbsK562Hdac2sc6296V0416102AlnRep0_vs_wgEncodeHaibTfbsK562ControlPcr1xAlnRep0.bb K562 ChipSeq HDAC2_(SC-6296) Peaks bigBed HudsonAlpha analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/peakSeq/optimal/hub/peakSeq.optimal.wgEncodeHaibTfbsK562Hey1Pcr1xAlnRep0_vs_wgEncodeHaibTfbsK562ControlPcr1xAlnRep0.bb K562 ChipSeq HEY1 Peaks bigBed HudsonAlpha analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/peakSeq/optimal/hub/peakSeq.optimal.wgEncodeHaibTfbsK562MaxV0416102AlnRep0_vs_wgEncodeHaibTfbsK562ControlPcr1xAlnRep0.bb K562 ChipSeq Max Peaks bigBed HudsonAlpha analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/peakSeq/optimal/hub/peakSeq.optimal.wgEncodeHaibTfbsK562NrsfV0416102AlnRep0_vs_wgEncodeHaibTfbsK562ControlV0416101AlnRep0.bb K562 ChipSeq NRSF Peaks bigBed HudsonAlpha analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/peakSeq/optimal/hub/peakSeq.optimal.wgEncodeHaibTfbsK562Pol24h8Pcr1xAlnRep0_vs_wgEncodeHaibTfbsK562ControlPcr1xAlnRep0.bb K562 ChipSeq Pol2-4H8 Peaks bigBed HudsonAlpha analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/peakSeq/optimal/hub/peakSeq.optimal.wgEncodeHaibTfbsK562Pol24h8V0416101AlnRep0_vs_wgEncodeHaibTfbsK562ControlV0416101AlnRep0.bb K562 ChipSeq Pol2-4H8 Peaks bigBed HudsonAlpha analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/peakSeq/optimal/hub/peakSeq.optimal.wgEncodeHaibTfbsK562Pol2V0416101AlnRep0_vs_wgEncodeHaibTfbsK562ControlV0416101AlnRep0.bb K562 ChipSeq Pol2 Peaks bigBed HudsonAlpha analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/peakSeq/optimal/hub/peakSeq.optimal.wgEncodeHaibTfbsK562Pu1Pcr1xAlnRep0_vs_wgEncodeHaibTfbsK562ControlPcr1xAlnRep0.bb K562 ChipSeq PU.1 Peaks bigBed HudsonAlpha analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/peakSeq/optimal/hub/peakSeq.optimal.wgEncodeHaibTfbsK562Rad21V0416102AlnRep0_vs_wgEncodeHaibTfbsK562ControlPcr1xAlnRep0.bb K562 ChipSeq Rad21 Peaks bigBed HudsonAlpha analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/peakSeq/optimal/hub/peakSeq.optimal.wgEncodeHaibTfbsK562Sin3ak20V0416101AlnRep0_vs_wgEncodeHaibTfbsK562ControlV0416101AlnRep0.bb K562 ChipSeq Sin3Ak-20 Peaks bigBed HudsonAlpha analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/peakSeq/optimal/hub/peakSeq.optimal.wgEncodeHaibTfbsK562Six5Pcr1xAlnRep0_vs_wgEncodeHaibTfbsK562ControlPcr1xAlnRep0.bb K562 ChipSeq SIX5 Peaks bigBed HudsonAlpha analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/peakSeq/optimal/hub/peakSeq.optimal.wgEncodeHaibTfbsK562Sp1Pcr1xAlnRep0_vs_wgEncodeHaibTfbsK562ControlV0416101AlnRep0.bb K562 ChipSeq SP1 Peaks bigBed HudsonAlpha analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/peakSeq/optimal/hub/peakSeq.optimal.wgEncodeHaibTfbsK562Sp2sc643V0416102AlnRep0_vs_wgEncodeHaibTfbsK562ControlPcr1xAlnRep0.bb K562 ChipSeq SP2_(SC-643) Peaks bigBed HudsonAlpha analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/peakSeq/optimal/hub/peakSeq.optimal.wgEncodeHaibTfbsK562SrfV0416101AlnRep0_vs_wgEncodeHaibTfbsK562ControlV0416101AlnRep0.bb K562 ChipSeq SRF Peaks bigBed HudsonAlpha analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/peakSeq/optimal/hub/peakSeq.optimal.wgEncodeHaibTfbsK562Taf1Pcr1xAlnRep0_vs_wgEncodeHaibTfbsK562ControlPcr1xAlnRep0.bb K562 ChipSeq TAF1 Peaks bigBed HudsonAlpha analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/peakSeq/optimal/hub/peakSeq.optimal.wgEncodeHaibTfbsK562Taf1V0416101AlnRep0_vs_wgEncodeHaibTfbsK562ControlV0416101AlnRep0.bb K562 ChipSeq TAF1 Peaks bigBed HudsonAlpha analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/peakSeq/optimal/hub/peakSeq.optimal.wgEncodeHaibTfbsK562Taf7sq8V0416101AlnRep0_vs_wgEncodeHaibTfbsK562ControlV0416101AlnRep0.bb K562 ChipSeq TAF7_(SQ-8) Peaks bigBed HudsonAlpha analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/peakSeq/optimal/hub/peakSeq.optimal.wgEncodeHaibTfbsK562Thap1sc98174V0416101AlnRep0_vs_wgEncodeHaibTfbsK562ControlV0416101AlnRep0.bb K562 ChipSeq THAP1_(SC-98174) Peaks bigBed HudsonAlpha analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/peakSeq/optimal/hub/peakSeq.optimal.wgEncodeHaibTfbsK562Usf1V0416101AlnRep0_vs_wgEncodeHaibTfbsK562ControlV0416101AlnRep0.bb K562 ChipSeq USF-1 Peaks bigBed HudsonAlpha analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/peakSeq/optimal/hub/peakSeq.optimal.wgEncodeHaibTfbsK562Yy1V0416101AlnRep0_vs_wgEncodeHaibTfbsK562ControlV0416101AlnRep0.bb K562 ChipSeq YY1 Peaks bigBed HudsonAlpha analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/peakSeq/optimal/hub/peakSeq.optimal.wgEncodeHaibTfbsK562Yy1V0416102AlnRep0_vs_wgEncodeHaibTfbsK562ControlPcr1xAlnRep0.bb K562 ChipSeq YY1 Peaks bigBed HudsonAlpha analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/peakSeq/optimal/hub/peakSeq.optimal.wgEncodeHaibTfbsK562Zbtb33Pcr1xAlnRep0_vs_wgEncodeHaibTfbsK562ControlV0416101AlnRep0.bb K562 ChipSeq ZBTB33 Peaks bigBed HudsonAlpha analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/peakSeq/optimal/hub/peakSeq.optimal.wgEncodeHaibTfbsK562Zbtb7asc34508V0416101AlnRep0_vs_wgEncodeHaibTfbsK562ControlV0416101AlnRep0.bb K562 ChipSeq ZBTB7A_(SC-34508) Peaks bigBed HudsonAlpha analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/peakSeq/optimal/hub/peakSeq.optimal.wgEncodeHaibTfbsPanc1NrsfPcr2xAlnRep0_vs_wgEncodeHaibTfbsPanc1ControlPcr2xAlnRep0.bb PANC-1 ChipSeq NRSF Peaks bigBed HudsonAlpha analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/peakSeq/optimal/hub/peakSeq.optimal.wgEncodeHaibTfbsPfsk1NrsfPcr2xAlnRep0_vs_wgEncodeHaibTfbsPfsk1ControlPcr2xAlnRep0.bb PFSK-1 ChipSeq NRSF Peaks bigBed HudsonAlpha analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/peakSeq/optimal/hub/peakSeq.optimal.wgEncodeHaibTfbsSknshraCtcfV0416102AlnRep0_vs_wgEncodeHaibTfbsSknshraControlV0416102AlnRep2.bb SK-N-SH_RA ChipSeq CTCF Peaks bigBed HudsonAlpha analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/peakSeq/optimal/hub/peakSeq.optimal.wgEncodeHaibTfbsSknshraP300V0416102AlnRep0_vs_wgEncodeHaibTfbsSknshraControlV0416102AlnRep2.bb SK-N-SH_RA ChipSeq p300 Peaks bigBed HudsonAlpha analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/peakSeq/optimal/hub/peakSeq.optimal.wgEncodeHaibTfbsSknshraRad21V0416102AlnRep0_vs_wgEncodeHaibTfbsSknshraControlV0416102AlnRep2.bb SK-N-SH_RA ChipSeq Rad21 Peaks bigBed HudsonAlpha analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/peakSeq/optimal/hub/peakSeq.optimal.wgEncodeHaibTfbsSknshraUsf1sc8983V0416102AlnRep0_vs_wgEncodeHaibTfbsSknshraControlV0416102AlnRep2.bb SK-N-SH_RA ChipSeq USF1_(SC-8983) Peaks bigBed HudsonAlpha analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/peakSeq/optimal/hub/peakSeq.optimal.wgEncodeHaibTfbsSknshraYy1c20V0416102AlnRep0_vs_wgEncodeHaibTfbsSknshraControlV0416102AlnRep2.bb SK-N-SH_RA ChipSeq YY1_(C-20) Peaks bigBed HudsonAlpha analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/peakSeq/optimal/hub/peakSeq.optimal.wgEncodeHaibTfbsT47dCtcfsc5916V0416102Dmso2AlnRep0_vs_wgEncodeHaibTfbsT47dControlV0416102Dmso2AlnRep2.bb T-47D ChipSeq CTCF_(SC-5916) Peaks bigBed HudsonAlpha analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/peakSeq/optimal/hub/peakSeq.optimal.wgEncodeHaibTfbsT47dEralphaaPcr2xGen1hAlnRep0_vs_wgEncodeHaibTfbsT47dEralphaaV0416102Dmso2AlnRep0.bb T-47D ChipSeq ERalpha_a Peaks bigBed HudsonAlpha analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/peakSeq/optimal/hub/peakSeq.optimal.wgEncodeHaibTfbsT47dEralphaaV0416102Estradia1hAlnRep0_vs_wgEncodeHaibTfbsT47dEralphaaV0416102Dmso2AlnRep0.bb T-47D ChipSeq ERalpha_a Peaks bigBed HudsonAlpha analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/peakSeq/optimal/hub/peakSeq.optimal.wgEncodeHaibTfbsT47dFoxa1c20V0416102Dmso2AlnRep0_vs_wgEncodeHaibTfbsT47dControlV0416102Dmso2AlnRep2.bb T-47D ChipSeq FOXA1_(C-20) Peaks bigBed HudsonAlpha analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/peakSeq/optimal/hub/peakSeq.optimal.wgEncodeHaibTfbsT47dGata3sc268V0416102Dmso2AlnRep0_vs_wgEncodeHaibTfbsT47dControlV0416102Dmso2AlnRep2.bb T-47D ChipSeq GATA3_(SC-268) Peaks bigBed HudsonAlpha analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/peakSeq/optimal/hub/peakSeq.optimal.wgEncodeHaibTfbsT47dP300V0416102Dmso2AlnRep0_vs_wgEncodeHaibTfbsT47dControlV0416102Dmso2AlnRep2.bb T-47D ChipSeq p300 Peaks bigBed HudsonAlpha analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/peakSeq/optimal/hub/peakSeq.optimal.wgEncodeHaibTfbsU87NrsfPcr2xAlnRep0_vs_wgEncodeHaibTfbsU87ControlPcr2xAlnRep0.bb U87 ChipSeq NRSF Peaks bigBed HudsonAlpha analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/peakSeq/optimal/hub/peakSeq.optimal.wgEncodeOpenChromChipFibroblCtcfAlnRep0_vs_wgEncodeOpenChromChipFibroblInputAlnRep1.bb Fibrobl ChipSeq CTCF Peaks bigBed UT-A analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/peakSeq/optimal/hub/peakSeq.optimal.wgEncodeOpenChromChipGlioblaCtcfAlnRep0_vs_wgEncodeOpenChromChipGlioblaInputAlnRep1.bb Gliobla ChipSeq CTCF Peaks bigBed UT-A analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/peakSeq/optimal/hub/peakSeq.optimal.wgEncodeOpenChromChipGlioblaPol2AlnRep0_vs_wgEncodeOpenChromChipGlioblaInputAlnRep1.bb Gliobla ChipSeq Pol2 Peaks bigBed UT-A analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/peakSeq/optimal/hub/peakSeq.optimal.wgEncodeOpenChromChipGm12878CmycAlnRep0_vs_wgEncodeOpenChromChipGm12878InputAlnRep1.bb GM12878 ChipSeq c-Myc Peaks bigBed UT-A analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/peakSeq/optimal/hub/peakSeq.optimal.wgEncodeOpenChromChipGm12878CtcfAlnRep0_vs_wgEncodeOpenChromChipGm12878InputAlnRep1.bb GM12878 ChipSeq CTCF Peaks bigBed UT-A analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/peakSeq/optimal/hub/peakSeq.optimal.wgEncodeOpenChromChipGm12878Pol2AlnRep0_vs_wgEncodeOpenChromChipGm12878InputAlnRep1.bb GM12878 ChipSeq Pol2 Peaks bigBed UT-A analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/peakSeq/optimal/hub/peakSeq.optimal.wgEncodeOpenChromChipHelas3CmycAlnRep0_vs_wgEncodeOpenChromChipHelas3InputAlnRep1.bb HeLa-S3 ChipSeq c-Myc Peaks bigBed UT-A analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/peakSeq/optimal/hub/peakSeq.optimal.wgEncodeOpenChromChipHelas3CtcfAlnRep0_vs_wgEncodeOpenChromChipHelas3InputAlnRep1.bb HeLa-S3 ChipSeq CTCF Peaks bigBed UT-A analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/peakSeq/optimal/hub/peakSeq.optimal.wgEncodeOpenChromChipHelas3Pol2AlnRep0_vs_wgEncodeOpenChromChipHelas3InputAlnRep1.bb HeLa-S3 ChipSeq Pol2 Peaks bigBed UT-A analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/peakSeq/optimal/hub/peakSeq.optimal.wgEncodeOpenChromChipHepg2CmycAlnRep0_vs_wgEncodeOpenChromChipHepg2InputAlnRep1.bb HepG2 ChipSeq c-Myc Peaks bigBed UT-A analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/peakSeq/optimal/hub/peakSeq.optimal.wgEncodeOpenChromChipHepg2CtcfAlnRep0_vs_wgEncodeOpenChromChipHepg2InputAlnRep1.bb HepG2 ChipSeq CTCF Peaks bigBed UT-A analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/peakSeq/optimal/hub/peakSeq.optimal.wgEncodeOpenChromChipHepg2Pol2AlnRep0_vs_wgEncodeOpenChromChipHepg2InputAlnRep1.bb HepG2 ChipSeq Pol2 Peaks bigBed UT-A analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/peakSeq/optimal/hub/peakSeq.optimal.wgEncodeOpenChromChipHuvecCmycAlnRep1_vs_wgEncodeOpenChromChipHuvecInputAlnRep1.bb HUVEC ChipSeq c-Myc Peaks bigBed UT-A analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/peakSeq/optimal/hub/peakSeq.optimal.wgEncodeOpenChromChipHuvecCtcfAlnRep0_vs_wgEncodeOpenChromChipHuvecInputAlnRep1.bb HUVEC ChipSeq CTCF Peaks bigBed UT-A analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/peakSeq/optimal/hub/peakSeq.optimal.wgEncodeOpenChromChipHuvecPol2AlnRep0_vs_wgEncodeOpenChromChipHuvecInputAlnRep1.bb HUVEC ChipSeq Pol2 Peaks bigBed UT-A analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/peakSeq/optimal/hub/peakSeq.optimal.wgEncodeOpenChromChipK562CmycAlnRep0_vs_wgEncodeOpenChromChipK562InputAlnRep1.bb K562 ChipSeq c-Myc Peaks bigBed UT-A analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/peakSeq/optimal/hub/peakSeq.optimal.wgEncodeOpenChromChipK562CtcfAlnRep0_vs_wgEncodeOpenChromChipK562InputAlnRep1.bb K562 ChipSeq CTCF Peaks bigBed UT-A analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/peakSeq/optimal/hub/peakSeq.optimal.wgEncodeOpenChromChipK562Pol2AlnRep0_vs_wgEncodeOpenChromChipK562InputAlnRep1.bb K562 ChipSeq Pol2 Peaks bigBed UT-A analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/peakSeq/optimal/hub/peakSeq.optimal.wgEncodeOpenChromChipMcf7CmycEstroAlnRep0_vs_wgEncodeOpenChromChipMcf7InputAlnRep1.bb MCF-7 ChipSeq c-Myc Peaks bigBed UT-A analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/peakSeq/optimal/hub/peakSeq.optimal.wgEncodeOpenChromChipMcf7CmycVehAlnRep0_vs_wgEncodeOpenChromChipMcf7InputAlnRep1.bb MCF-7 ChipSeq c-Myc Peaks bigBed UT-A analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/peakSeq/optimal/hub/peakSeq.optimal.wgEncodeOpenChromChipMcf7CtcfAlnRep0_vs_wgEncodeOpenChromChipMcf7InputAlnRep1.bb MCF-7 ChipSeq CTCF Peaks bigBed UT-A analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/peakSeq/optimal/hub/peakSeq.optimal.wgEncodeOpenChromChipMcf7CtcfEstroAlnRep0_vs_wgEncodeOpenChromChipMcf7InputAlnRep1.bb MCF-7 ChipSeq CTCF Peaks bigBed UT-A analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/peakSeq/optimal/hub/peakSeq.optimal.wgEncodeOpenChromChipMcf7CtcfVehAlnRep0_vs_wgEncodeOpenChromChipMcf7InputAlnRep1.bb MCF-7 ChipSeq CTCF Peaks bigBed UT-A analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/peakSeq/optimal/hub/peakSeq.optimal.wgEncodeOpenChromChipMcf7Pol2AlnRep0_vs_wgEncodeOpenChromChipMcf7InputAlnRep1.bb MCF-7 ChipSeq Pol2 Peaks bigBed UT-A analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/peakSeq/optimal/hub/peakSeq.optimal.wgEncodeOpenChromChipProgfibCtcfAlnRep0_vs_wgEncodeOpenChromChipProgfibInputAlnRep1.bb ProgFib ChipSeq CTCF Peaks bigBed UT-A analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/peakSeq/optimal/hub/peakSeq.optimal.wgEncodeOpenChromChipProgfibPol2AlnRep0_vs_wgEncodeOpenChromChipProgfibInputAlnRep1.bb ProgFib ChipSeq Pol2 Peaks bigBed UT-A analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/peakSeq/optimal/hub/peakSeq.optimal.wgEncodeSydhTfbsGm10847NfkbIggrabAlnRep0_vs_wgEncodeSydhTfbsGm10847InputIggrabAlnRep0.bb GM10847 ChipSeq NFKB Peaks bigBed Stanford analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/peakSeq/optimal/hub/peakSeq.optimal.wgEncodeSydhTfbsGm10847Pol2IggmusAlnRep1_vs_wgEncodeSydhTfbsGm10847InputIggmusAlnRep0.bb GM10847 ChipSeq Pol2 Peaks bigBed Stanford analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/peakSeq/optimal/hub/peakSeq.optimal.wgEncodeSydhTfbsGm12878Brca1cIggmusAlnRep0_vs_wgEncodeSydhTfbsGm12878InputIggmusAlnRep0.bb GM12878 ChipSeq BRCA1_(C-1863) Peaks bigBed Stanford analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/peakSeq/optimal/hub/peakSeq.optimal.wgEncodeSydhTfbsGm12878CfosStdAlnRep0_vs_wgEncodeSydhTfbsGm12878InputStdAlnRep1.bb GM12878 ChipSeq c-Fos Peaks bigBed Stanford analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/peakSeq/optimal/hub/peakSeq.optimal.wgEncodeSydhTfbsGm12878Chd21250IggmusAlnRep0_vs_wgEncodeSydhTfbsGm12878InputIggmusAlnRep0.bb GM12878 ChipSeq CHD2_(N-1250) Peaks bigBed Stanford analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/peakSeq/optimal/hub/peakSeq.optimal.wgEncodeSydhTfbsGm12878Ctcfc20StdAlnRep0_vs_wgEncodeSydhTfbsGm12878InputStdAlnRep1.bb GM12878 ChipSeq CTCF_(C-20) Peaks bigBed Stanford analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/peakSeq/optimal/hub/peakSeq.optimal.wgEncodeSydhTfbsGm12878EbfStdAlnRep0_vs_wgEncodeSydhTfbsGm12878InputStdAlnRep1.bb GM12878 ChipSeq EBF Peaks bigBed Stanford analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/peakSeq/optimal/hub/peakSeq.optimal.wgEncodeSydhTfbsGm12878Gcn5StdAlnRep0_vs_wgEncodeSydhTfbsGm12878InputStdAlnRep1.bb GM12878 ChipSeq GCN5 Peaks bigBed Harvard(Weissman) analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/peakSeq/optimal/hub/peakSeq.optimal.wgEncodeSydhTfbsGm12878Irf3StdAlnRep0_vs_wgEncodeSydhTfbsGm12878InputStdAlnRep1.bb GM12878 ChipSeq IRF3 Peaks bigBed Stanford analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/peakSeq/optimal/hub/peakSeq.optimal.wgEncodeSydhTfbsGm12878JundStdAlnRep0_vs_wgEncodeSydhTfbsGm12878InputStdAlnRep1.bb GM12878 ChipSeq JunD Peaks bigBed Stanford analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/peakSeq/optimal/hub/peakSeq.optimal.wgEncodeSydhTfbsGm12878MaxStdAlnRep0_vs_wgEncodeSydhTfbsGm12878InputStdAlnRep1.bb GM12878 ChipSeq Max Peaks bigBed Stanford analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/peakSeq/optimal/hub/peakSeq.optimal.wgEncodeSydhTfbsGm12878Nfe2hStdAlnRep0_vs_wgEncodeSydhTfbsGm12878InputStdAlnRep1.bb GM12878 ChipSeq NF-E2_(H-230) Peaks bigBed Stanford analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/peakSeq/optimal/hub/peakSeq.optimal.wgEncodeSydhTfbsGm12878NfkbIggrabAlnRep0_vs_wgEncodeSydhTfbsGm12878InputIggrabAlnRep0.bb GM12878 ChipSeq NFKB Peaks bigBed Stanford analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/peakSeq/optimal/hub/peakSeq.optimal.wgEncodeSydhTfbsGm12878NfkbTnfaStdAlnRep0_vs_wgEncodeSydhTfbsGm12878InputStdAlnRep1.bb GM12878 ChipSeq NFKB Peaks bigBed Stanford analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/peakSeq/optimal/hub/peakSeq.optimal.wgEncodeSydhTfbsGm12878Nrf1IggmusAlnRep0_vs_wgEncodeSydhTfbsGm12878InputIggmusAlnRep0.bb GM12878 ChipSeq Nrf1 Peaks bigBed Stanford analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/peakSeq/optimal/hub/peakSeq.optimal.wgEncodeSydhTfbsGm12878P300n15StdAlnRep0_vs_wgEncodeSydhTfbsGm12878InputStdAlnRep1.bb GM12878 ChipSeq p300_(N-15) Peaks bigBed Stanford analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/peakSeq/optimal/hub/peakSeq.optimal.wgEncodeSydhTfbsGm12878Pol2IggmusAlnRep0_vs_wgEncodeSydhTfbsGm12878InputIggmusAlnRep0.bb GM12878 ChipSeq Pol2 Peaks bigBed Stanford analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/peakSeq/optimal/hub/peakSeq.optimal.wgEncodeSydhTfbsGm12878Pol2StdAlnRep0_vs_wgEncodeSydhTfbsGm12878InputStdAlnRep1.bb GM12878 ChipSeq Pol2 Peaks bigBed Stanford analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/peakSeq/optimal/hub/peakSeq.optimal.wgEncodeSydhTfbsGm12878Pol3StdAlnRep0_vs_wgEncodeSydhTfbsGm12878InputStdAlnRep1.bb GM12878 ChipSeq Pol3 Peaks bigBed Stanford analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/peakSeq/optimal/hub/peakSeq.optimal.wgEncodeSydhTfbsGm12878Rad21IggrabAlnRep0_vs_wgEncodeSydhTfbsGm12878InputIggrabAlnRep0.bb GM12878 ChipSeq Rad21 Peaks bigBed Stanford analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/peakSeq/optimal/hub/peakSeq.optimal.wgEncodeSydhTfbsGm12878Rfx5n494IggmusAlnRep0_vs_wgEncodeSydhTfbsGm12878InputIggmusAlnRep0.bb GM12878 ChipSeq RFX5_(N-494) Peaks bigBed Stanford analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/peakSeq/optimal/hub/peakSeq.optimal.wgEncodeSydhTfbsGm12878Smc3ab9263IggmusAlnRep0_vs_wgEncodeSydhTfbsGm12878InputIggmusAlnRep0.bb GM12878 ChipSeq SMC3_(ab9263) Peaks bigBed Stanford analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/peakSeq/optimal/hub/peakSeq.optimal.wgEncodeSydhTfbsGm12878Spt20StdAlnRep0_vs_wgEncodeSydhTfbsGm12878InputStdAlnRep1.bb GM12878 ChipSeq SPT20 Peaks bigBed Harvard(Weissman) analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/peakSeq/optimal/hub/peakSeq.optimal.wgEncodeSydhTfbsGm12878Stat1StdAlnRep0_vs_wgEncodeSydhTfbsGm12878InputStdAlnRep1.bb GM12878 ChipSeq STAT1 Peaks bigBed Stanford analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/peakSeq/optimal/hub/peakSeq.optimal.wgEncodeSydhTfbsGm12878Stat3IggmusAlnRep0_vs_wgEncodeSydhTfbsGm12878InputIggmusAlnRep0.bb GM12878 ChipSeq STAT3 Peaks bigBed Stanford analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/peakSeq/optimal/hub/peakSeq.optimal.wgEncodeSydhTfbsGm12878TbpIggmusAlnRep0_vs_wgEncodeSydhTfbsGm12878InputIggmusAlnRep0.bb GM12878 ChipSeq TBP Peaks bigBed Stanford analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/peakSeq/optimal/hub/peakSeq.optimal.wgEncodeSydhTfbsGm12878Tr4StdAlnRep0_vs_wgEncodeSydhTfbsGm12878InputStdAlnRep1.bb GM12878 ChipSeq TR4 Peaks bigBed Stanford analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/peakSeq/optimal/hub/peakSeq.optimal.wgEncodeSydhTfbsGm12878Usf2IggmusAlnRep0_vs_wgEncodeSydhTfbsGm12878InputIggmusAlnRep0.bb GM12878 ChipSeq USF2 Peaks bigBed Stanford analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/peakSeq/optimal/hub/peakSeq.optimal.wgEncodeSydhTfbsGm12878WhipIggmusAlnRep0_vs_wgEncodeSydhTfbsGm12878InputIggmusAlnRep0.bb GM12878 ChipSeq WHIP Peaks bigBed Stanford analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/peakSeq/optimal/hub/peakSeq.optimal.wgEncodeSydhTfbsGm12878Yy1StdAlnRep0_vs_wgEncodeSydhTfbsGm12878InputStdAlnRep1.bb GM12878 ChipSeq YY1 Peaks bigBed Stanford analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/peakSeq/optimal/hub/peakSeq.optimal.wgEncodeSydhTfbsGm12878Znf143166181apStdAlnRep0_vs_wgEncodeSydhTfbsGm12878InputStdAlnRep1.bb GM12878 ChipSeq Znf143_(16618-1-AP) Peaks bigBed Stanford analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/peakSeq/optimal/hub/peakSeq.optimal.wgEncodeSydhTfbsGm12878Zzz3StdAlnRep0_vs_wgEncodeSydhTfbsGm12878InputStdAlnRep1.bb GM12878 ChipSeq ZZZ3 Peaks bigBed Stanford analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/peakSeq/optimal/hub/peakSeq.optimal.wgEncodeSydhTfbsGm12891NfkbIggrabAlnRep0_vs_wgEncodeSydhTfbsGm12891InputIggrabAlnRep0.bb GM12891 ChipSeq NFKB Peaks bigBed Stanford analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/peakSeq/optimal/hub/peakSeq.optimal.wgEncodeSydhTfbsGm12891Pol2IggmusAlnRep0_vs_wgEncodeSydhTfbsGm12891InputIggmusAlnRep0.bb GM12891 ChipSeq Pol2 Peaks bigBed Stanford analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/peakSeq/optimal/hub/peakSeq.optimal.wgEncodeSydhTfbsGm12892NfkbIggrabAlnRep0_vs_wgEncodeSydhTfbsGm12892InputIggrabAlnRep0.bb GM12892 ChipSeq NFKB Peaks bigBed Stanford analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/peakSeq/optimal/hub/peakSeq.optimal.wgEncodeSydhTfbsGm12892Pol2IggmusAlnRep0_vs_wgEncodeSydhTfbsGm12892InputIggmusAlnRep0.bb GM12892 ChipSeq Pol2 Peaks bigBed Stanford analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/peakSeq/optimal/hub/peakSeq.optimal.wgEncodeSydhTfbsGm15510NfkbIggrabAlnRep0_vs_wgEncodeSydhTfbsGm15510InputIggrabAlnRep0.bb GM15510 ChipSeq NFKB Peaks bigBed Stanford analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/peakSeq/optimal/hub/peakSeq.optimal.wgEncodeSydhTfbsGm15510Pol2IggmusAlnRep0_vs_wgEncodeSydhTfbsGm15510InputIggmusAlnRep0.bb GM15510 ChipSeq Pol2 Peaks bigBed Stanford analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/peakSeq/optimal/hub/peakSeq.optimal.wgEncodeSydhTfbsGm18505NfkbIggrabAlnRep0_vs_wgEncodeSydhTfbsGm18505InputIggrabAlnRep0.bb GM18505 ChipSeq NFKB Peaks bigBed Stanford analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/peakSeq/optimal/hub/peakSeq.optimal.wgEncodeSydhTfbsGm18505Pol2IggmusAlnRep0_vs_wgEncodeSydhTfbsGm18505InputIggmusAlnRep0.bb GM18505 ChipSeq Pol2 Peaks bigBed Stanford analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/peakSeq/optimal/hub/peakSeq.optimal.wgEncodeSydhTfbsGm18526NfkbIggrabAlnRep0_vs_wgEncodeSydhTfbsGm18526InputIggrabAlnRep0.bb GM18526 ChipSeq NFKB Peaks bigBed Stanford analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/peakSeq/optimal/hub/peakSeq.optimal.wgEncodeSydhTfbsGm18526Pol2IggmusAlnRep0_vs_wgEncodeSydhTfbsGm18526InputIggmusAlnRep0.bb GM18526 ChipSeq Pol2 Peaks bigBed Stanford analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/peakSeq/optimal/hub/peakSeq.optimal.wgEncodeSydhTfbsGm18951NfkbIggrabAlnRep0_vs_wgEncodeSydhTfbsGm18951InputIggrabAlnRep0.bb GM18951 ChipSeq NFKB Peaks bigBed Stanford analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/peakSeq/optimal/hub/peakSeq.optimal.wgEncodeSydhTfbsGm18951Pol2IggmusAlnRep0_vs_wgEncodeSydhTfbsGm18951InputIggmusAlnRep1.bb GM18951 ChipSeq Pol2 Peaks bigBed Stanford analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/peakSeq/optimal/hub/peakSeq.optimal.wgEncodeSydhTfbsGm19099NfkbIggrabAlnRep0_vs_wgEncodeSydhTfbsGm19099InputIggrabAlnRep0.bb GM19099 ChipSeq NFKB Peaks bigBed Stanford analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/peakSeq/optimal/hub/peakSeq.optimal.wgEncodeSydhTfbsGm19099Pol2IggmusAlnRep0_vs_wgEncodeSydhTfbsGm19099InputIggmusAlnRep0.bb GM19099 ChipSeq Pol2 Peaks bigBed Stanford analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/peakSeq/optimal/hub/peakSeq.optimal.wgEncodeSydhTfbsGm19193NfkbIggrabAlnRep0_vs_wgEncodeSydhTfbsGm19193InputIggrabAlnRep0.bb GM19193 ChipSeq NFKB Peaks bigBed Stanford analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/peakSeq/optimal/hub/peakSeq.optimal.wgEncodeSydhTfbsGm19193Pol2IggmusAlnRep0_vs_wgEncodeSydhTfbsGm19193InputIggmusAlnRep0.bb GM19193 ChipSeq Pol2 Peaks bigBed Stanford analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/peakSeq/optimal/hub/peakSeq.optimal.wgEncodeSydhTfbsH1hescCjunIggrabAlnRep0_vs_wgEncodeSydhTfbsH1hescInputIggrabAlnRep1.bb H1-hESC ChipSeq c-Jun Peaks bigBed Stanford analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/peakSeq/optimal/hub/peakSeq.optimal.wgEncodeSydhTfbsH1hescCtbp2UcdAlnRep0_vs_wgEncodeSydhTfbsH1hescInputUcdAlnRep1.bb H1-hESC ChipSeq CtBP2 Peaks bigBed UCD analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/peakSeq/optimal/hub/peakSeq.optimal.wgEncodeSydhTfbsH1hescMaxUcdAlnRep0_vs_wgEncodeSydhTfbsH1hescInputUcdAlnRep1.bb H1-hESC ChipSeq Max Peaks bigBed Stanford analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/peakSeq/optimal/hub/peakSeq.optimal.wgEncodeSydhTfbsH1hescNrf1IggrabAlnRep0_vs_wgEncodeSydhTfbsH1hescInputIggrabAlnRep1.bb H1-hESC ChipSeq Nrf1 Peaks bigBed Stanford analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/peakSeq/optimal/hub/peakSeq.optimal.wgEncodeSydhTfbsH1hescRad21IggrabAlnRep0_vs_wgEncodeSydhTfbsH1hescInputIggrabAlnRep1.bb H1-hESC ChipSeq Rad21 Peaks bigBed Stanford analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/peakSeq/optimal/hub/peakSeq.optimal.wgEncodeSydhTfbsH1hescRfx5n494IggrabAlnRep0_vs_wgEncodeSydhTfbsH1hescInputIggrabAlnRep1.bb H1-hESC ChipSeq RFX5_(N-494) Peaks bigBed Stanford analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/peakSeq/optimal/hub/peakSeq.optimal.wgEncodeSydhTfbsH1hescSuz12UcdAlnRep0_vs_wgEncodeSydhTfbsH1hescInputUcdAlnRep1.bb H1-hESC ChipSeq SUZ12 Peaks bigBed UCD analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/peakSeq/optimal/hub/peakSeq.optimal.wgEncodeSydhTfbsH1hescTbpStdAlnRep0_vs_wgEncodeSydhTfbsH1hescInputStdAlnRep1.bb H1-hESC ChipSeq TBP Peaks bigBed Stanford analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/peakSeq/optimal/hub/peakSeq.optimal.wgEncodeSydhTfbsH1hescUsf2IggrabAlnRep0_vs_wgEncodeSydhTfbsH1hescInputIggrabAlnRep1.bb H1-hESC ChipSeq USF2 Peaks bigBed Stanford analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/peakSeq/optimal/hub/peakSeq.optimal.wgEncodeSydhTfbsHct116Pol2UcdAlnRep0_vs_wgEncodeSydhTfbsHct116InputUcdAlnRep1.bb HCT-116 ChipSeq Pol2 Peaks bigBed Stanford analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/peakSeq/optimal/hub/peakSeq.optimal.wgEncodeSydhTfbsHct116Tcf4UcdAlnRep0_vs_wgEncodeSydhTfbsHct116InputUcdAlnRep1.bb HCT-116 ChipSeq TCF4 Peaks bigBed Stanford analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/peakSeq/optimal/hub/peakSeq.optimal.wgEncodeSydhTfbsHek293bElk4UcdAlnRep0_vs_wgEncodeSydhTfbsHek293InputUcdAlnRep1.bb HEK293(b) ChipSeq ELK4 Peaks bigBed UCD analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/peakSeq/optimal/hub/peakSeq.optimal.wgEncodeSydhTfbsHek293bKap1UcdAlnRep0_vs_wgEncodeSydhTfbsHek293InputUcdAlnRep1.bb HEK293(b) ChipSeq KAP1 Peaks bigBed UCD analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/peakSeq/optimal/hub/peakSeq.optimal.wgEncodeSydhTfbsHek293bPol2StdAlnRep0_vs_wgEncodeSydhTfbsHek293bInputStdAlnRep1.bb HEK293(b) ChipSeq Pol2 Peaks bigBed Stanford analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/peakSeq/optimal/hub/peakSeq.optimal.wgEncodeSydhTfbsHelas3Ap2alphaStdAlnRep0_vs_wgEncodeSydhTfbsHelas3InputStdAlnRep1.bb HeLa-S3 ChipSeq AP-2alpha Peaks bigBed Stanford analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/peakSeq/optimal/hub/peakSeq.optimal.wgEncodeSydhTfbsHelas3Ap2gammaStdAlnRep0_vs_wgEncodeSydhTfbsHelas3InputStdAlnRep1.bb HeLa-S3 ChipSeq AP-2gamma Peaks bigBed Stanford analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/peakSeq/optimal/hub/peakSeq.optimal.wgEncodeSydhTfbsHelas3Baf155IggmusAlnRep0_vs_wgEncodeSydhTfbsHelas3InputIggmusAlnRep0.bb HeLa-S3 ChipSeq BAF155 Peaks bigBed Stanford analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/peakSeq/optimal/hub/peakSeq.optimal.wgEncodeSydhTfbsHelas3Baf170IggmusAlnRep0_vs_wgEncodeSydhTfbsHelas3InputIggmusAlnRep0.bb HeLa-S3 ChipSeq BAF170 Peaks bigBed Stanford analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/peakSeq/optimal/hub/peakSeq.optimal.wgEncodeSydhTfbsHelas3Bdp1StdAlnRep0_vs_wgEncodeSydhTfbsHelas3InputStdAlnRep1.bb HeLa-S3 ChipSeq BDP1 Peaks bigBed Stanford analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/peakSeq/optimal/hub/peakSeq.optimal.wgEncodeSydhTfbsHelas3Brca1cIggrabAlnRep0_vs_wgEncodeSydhTfbsHelas3InputIggrabAlnRep1.bb HeLa-S3 ChipSeq BRCA1_(C-1863) Peaks bigBed Stanford analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/peakSeq/optimal/hub/peakSeq.optimal.wgEncodeSydhTfbsHelas3Brf1StdAlnRep0_vs_wgEncodeSydhTfbsHelas3InputStdAlnRep1.bb HeLa-S3 ChipSeq BRF1 Peaks bigBed Stanford analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/peakSeq/optimal/hub/peakSeq.optimal.wgEncodeSydhTfbsHelas3Brf2StdAlnRep0_vs_wgEncodeSydhTfbsHelas3InputStdAlnRep1.bb HeLa-S3 ChipSeq BRF2 Peaks bigBed Stanford analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/peakSeq/optimal/hub/peakSeq.optimal.wgEncodeSydhTfbsHelas3Brg1IggmusAlnRep0_vs_wgEncodeSydhTfbsHelas3InputIggmusAlnRep0.bb HeLa-S3 ChipSeq Brg1 Peaks bigBed Stanford analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/peakSeq/optimal/hub/peakSeq.optimal.wgEncodeSydhTfbsHelas3CebpbIggrabAlnRep0_vs_wgEncodeSydhTfbsHelas3InputIggrabAlnRep1.bb HeLa-S3 ChipSeq CEBPB Peaks bigBed Stanford analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/peakSeq/optimal/hub/peakSeq.optimal.wgEncodeSydhTfbsHelas3CfosStdAlnRep0_vs_wgEncodeSydhTfbsHelas3InputStdAlnRep1.bb HeLa-S3 ChipSeq c-Fos Peaks bigBed Stanford analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/peakSeq/optimal/hub/peakSeq.optimal.wgEncodeSydhTfbsHelas3CjunIggrabAlnRep0_vs_wgEncodeSydhTfbsHelas3InputIggrabAlnRep1.bb HeLa-S3 ChipSeq c-Jun Peaks bigBed Stanford analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/peakSeq/optimal/hub/peakSeq.optimal.wgEncodeSydhTfbsHelas3CmycStdAlnRep0_vs_wgEncodeSydhTfbsHelas3InputStdAlnRep1.bb HeLa-S3 ChipSeq c-Myc Peaks bigBed Stanford analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/peakSeq/optimal/hub/peakSeq.optimal.wgEncodeSydhTfbsHelas3E2f1StdAlnRep0_vs_wgEncodeSydhTfbsHelas3InputStdAlnRep1.bb HeLa-S3 ChipSeq E2F1 Peaks bigBed Stanford analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/peakSeq/optimal/hub/peakSeq.optimal.wgEncodeSydhTfbsHelas3E2f4StdAlnRep0_vs_wgEncodeSydhTfbsHelas3InputStdAlnRep1.bb HeLa-S3 ChipSeq E2F4 Peaks bigBed Stanford analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/peakSeq/optimal/hub/peakSeq.optimal.wgEncodeSydhTfbsHelas3E2f6StdAlnRep0_vs_wgEncodeSydhTfbsHelas3InputStdAlnRep1.bb HeLa-S3 ChipSeq E2F6 Peaks bigBed Stanford analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/peakSeq/optimal/hub/peakSeq.optimal.wgEncodeSydhTfbsHelas3Elk4UcdAlnRep0_vs_wgEncodeSydhTfbsHelas3InputUcdAlnRep1.bb HeLa-S3 ChipSeq ELK4 Peaks bigBed UCD analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/peakSeq/optimal/hub/peakSeq.optimal.wgEncodeSydhTfbsHelas3Gcn5StdAlnRep0_vs_wgEncodeSydhTfbsHelas3InputStdAlnRep1.bb HeLa-S3 ChipSeq GCN5 Peaks bigBed Stanford analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/peakSeq/optimal/hub/peakSeq.optimal.wgEncodeSydhTfbsHelas3Gtf2f1rapIggrabAlnRep0_vs_wgEncodeSydhTfbsHelas3InputIggrabAlnRep1.bb HeLa-S3 ChipSeq GTF2F1_(RAP-74) Peaks bigBed Stanford analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/peakSeq/optimal/hub/peakSeq.optimal.wgEncodeSydhTfbsHelas3Hae2f1StdAlnRep0_vs_wgEncodeSydhTfbsHelas3InputStdAlnRep1.bb HeLa-S3 ChipSeq HA-E2F1 Peaks bigBed Stanford analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/peakSeq/optimal/hub/peakSeq.optimal.wgEncodeSydhTfbsHelas3Ini1IggmusAlnRep0_vs_wgEncodeSydhTfbsHelas3InputIggmusAlnRep0.bb HeLa-S3 ChipSeq Ini1 Peaks bigBed Stanford analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/peakSeq/optimal/hub/peakSeq.optimal.wgEncodeSydhTfbsHelas3Irf3IggrabAlnRep0_vs_wgEncodeSydhTfbsHelas3InputIggrabAlnRep1.bb HeLa-S3 ChipSeq IRF3 Peaks bigBed Stanford analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/peakSeq/optimal/hub/peakSeq.optimal.wgEncodeSydhTfbsHelas3JundIggrabAlnRep0_vs_wgEncodeSydhTfbsHelas3InputIggrabAlnRep1.bb HeLa-S3 ChipSeq JunD Peaks bigBed Stanford analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/peakSeq/optimal/hub/peakSeq.optimal.wgEncodeSydhTfbsHelas3MaxStdAlnRep0_vs_wgEncodeSydhTfbsHelas3InputStdAlnRep1.bb HeLa-S3 ChipSeq Max Peaks bigBed Stanford analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/peakSeq/optimal/hub/peakSeq.optimal.wgEncodeSydhTfbsHelas3Mxi1bhlhIggrabAlnRep0_vs_wgEncodeSydhTfbsHelas3InputIggrabAlnRep1.bb HeLa-S3 ChipSeq Mxi1_(bHLH) Peaks bigBed Stanford analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/peakSeq/optimal/hub/peakSeq.optimal.wgEncodeSydhTfbsHelas3Nrf1IggmusAlnRep0_vs_wgEncodeSydhTfbsHelas3InputIggmusAlnRep0.bb HeLa-S3 ChipSeq Nrf1 Peaks bigBed Stanford analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/peakSeq/optimal/hub/peakSeq.optimal.wgEncodeSydhTfbsHelas3P300n15IggrabAlnRep0_vs_wgEncodeSydhTfbsHelas3InputIggrabAlnRep1.bb HeLa-S3 ChipSeq p300_(N-15) Peaks bigBed Stanford analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/peakSeq/optimal/hub/peakSeq.optimal.wgEncodeSydhTfbsHelas3Pol2s2IggrabAlnRep0_vs_wgEncodeSydhTfbsHelas3InputIggrabAlnRep1.bb HeLa-S3 ChipSeq Pol2(phosphoS2) Peaks bigBed Stanford analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/peakSeq/optimal/hub/peakSeq.optimal.wgEncodeSydhTfbsHelas3Pol2StdAlnRep0_vs_wgEncodeSydhTfbsHelas3InputStdAlnRep1.bb HeLa-S3 ChipSeq Pol2 Peaks bigBed Stanford analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/peakSeq/optimal/hub/peakSeq.optimal.wgEncodeSydhTfbsHelas3Prdm1vIggrabAlnRep0_vs_wgEncodeSydhTfbsHelas3InputIggrabAlnRep1.bb HeLa-S3 ChipSeq PRDM1_(Val90) Peaks bigBed Stanford analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/peakSeq/optimal/hub/peakSeq.optimal.wgEncodeSydhTfbsHelas3Rad21IggrabAlnRep0_vs_wgEncodeSydhTfbsHelas3InputIggrabAlnRep1.bb HeLa-S3 ChipSeq Rad21 Peaks bigBed Stanford analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/peakSeq/optimal/hub/peakSeq.optimal.wgEncodeSydhTfbsHelas3Rfx5n494IggrabAlnRep0_vs_wgEncodeSydhTfbsHelas3InputIggrabAlnRep1.bb HeLa-S3 ChipSeq RFX5_(N-494) Peaks bigBed Stanford analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/peakSeq/optimal/hub/peakSeq.optimal.wgEncodeSydhTfbsHelas3Rpc155StdAlnRep0_vs_wgEncodeSydhTfbsHelas3InputStdAlnRep1.bb HeLa-S3 ChipSeq RPC155 Peaks bigBed Stanford analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/peakSeq/optimal/hub/peakSeq.optimal.wgEncodeSydhTfbsHelas3Smc3ab9263IggrabAlnRep0_vs_wgEncodeSydhTfbsHelas3InputIggrabAlnRep1.bb HeLa-S3 ChipSeq SMC3_(ab9263) Peaks bigBed Stanford analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/peakSeq/optimal/hub/peakSeq.optimal.wgEncodeSydhTfbsHelas3Spt20StdAlnRep0_vs_wgEncodeSydhTfbsHelas3InputStdAlnRep1.bb HeLa-S3 ChipSeq SPT20 Peaks bigBed Stanford analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/peakSeq/optimal/hub/peakSeq.optimal.wgEncodeSydhTfbsHelas3Stat1Ifng30StdAlnRep0_vs_wgEncodeSydhTfbsHelas3InputIfng30StdAlnRep1.bb HeLa-S3 ChipSeq STAT1 Peaks bigBed Stanford analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/peakSeq/optimal/hub/peakSeq.optimal.wgEncodeSydhTfbsHelas3Stat3IggrabAlnRep0_vs_wgEncodeSydhTfbsHelas3InputIggrabAlnRep1.bb HeLa-S3 ChipSeq STAT3 Peaks bigBed Stanford analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/peakSeq/optimal/hub/peakSeq.optimal.wgEncodeSydhTfbsHelas3TbpIggrabAlnRep0_vs_wgEncodeSydhTfbsHelas3InputIggrabAlnRep1.bb HeLa-S3 ChipSeq TBP Peaks bigBed Stanford analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/peakSeq/optimal/hub/peakSeq.optimal.wgEncodeSydhTfbsHelas3Tf3c110StdAlnRep0_vs_wgEncodeSydhTfbsHelas3InputStdAlnRep1.bb HeLa-S3 ChipSeq TFIIIC-110 Peaks bigBed Stanford analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/peakSeq/optimal/hub/peakSeq.optimal.wgEncodeSydhTfbsHelas3Tr4StdAlnRep0_vs_wgEncodeSydhTfbsHelas3InputStdAlnRep1.bb HeLa-S3 ChipSeq TR4 Peaks bigBed Stanford analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/peakSeq/optimal/hub/peakSeq.optimal.wgEncodeSydhTfbsHelas3Usf2IggmusAlnRep0_vs_wgEncodeSydhTfbsHelas3InputIggmusAlnRep0.bb HeLa-S3 ChipSeq USF2 Peaks bigBed Stanford analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/peakSeq/optimal/hub/peakSeq.optimal.wgEncodeSydhTfbsHelas3Znf274UcdAlnRep0_vs_wgEncodeSydhTfbsHelas3InputUcdAlnRep1.bb HeLa-S3 ChipSeq ZNF274 Peaks bigBed UCD analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/peakSeq/optimal/hub/peakSeq.optimal.wgEncodeSydhTfbsHelas3Zzz3StdAlnRep0_vs_wgEncodeSydhTfbsHelas3InputStdAlnRep1.bb HeLa-S3 ChipSeq ZZZ3 Peaks bigBed Harvard(Weissman) analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/peakSeq/optimal/hub/peakSeq.optimal.wgEncodeSydhTfbsHepg2bTr4UcdAlnRep0_vs_wgEncodeSydhTfbsHepg2bInputUcdAlnRep1.bb HepG2b ChipSeq TR4 Peaks bigBed Stanford analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/peakSeq/optimal/hub/peakSeq.optimal.wgEncodeSydhTfbsHepg2bZnf274UcdAlnRep0_vs_wgEncodeSydhTfbsHepg2bInputUcdAlnRep1.bb HepG2b ChipSeq ZNF274 Peaks bigBed UCD analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/peakSeq/optimal/hub/peakSeq.optimal.wgEncodeSydhTfbsHepg2CebpbForsklnStdAlnRep0_vs_wgEncodeSydhTfbsHepg2InputForsklnStdAlnRep0.bb HepG2 ChipSeq CEBPB Peaks bigBed Stanford analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/peakSeq/optimal/hub/peakSeq.optimal.wgEncodeSydhTfbsHepg2CebpbIggrabAlnRep0_vs_wgEncodeSydhTfbsHepg2InputIggrabAlnRep1.bb HepG2 ChipSeq CEBPB Peaks bigBed Stanford analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/peakSeq/optimal/hub/peakSeq.optimal.wgEncodeSydhTfbsHepg2Chd21250IggrabAlnRep0_vs_wgEncodeSydhTfbsHepg2InputIggrabAlnRep1.bb HepG2 ChipSeq CHD2_(N-1250) Peaks bigBed Stanford analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/peakSeq/optimal/hub/peakSeq.optimal.wgEncodeSydhTfbsHepg2CjunIggrabAlnRep0_vs_wgEncodeSydhTfbsHepg2InputIggrabAlnRep1.bb HepG2 ChipSeq c-Jun Peaks bigBed Stanford analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/peakSeq/optimal/hub/peakSeq.optimal.wgEncodeSydhTfbsHepg2ErraForsklnStdAlnRep0_vs_wgEncodeSydhTfbsHepg2InputForsklnStdAlnRep0.bb HepG2 ChipSeq ERRA Peaks bigBed Stanford analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/peakSeq/optimal/hub/peakSeq.optimal.wgEncodeSydhTfbsHepg2Grp20ForsklnStdAlnRep0_vs_wgEncodeSydhTfbsHepg2InputForsklnStdAlnRep0.bb HepG2 ChipSeq GRp20 Peaks bigBed Stanford analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/peakSeq/optimal/hub/peakSeq.optimal.wgEncodeSydhTfbsHepg2Hnf4aForsklnStdAlnRep0_vs_wgEncodeSydhTfbsHepg2InputForsklnStdAlnRep0.bb HepG2 ChipSeq HNF4A Peaks bigBed Stanford analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/peakSeq/optimal/hub/peakSeq.optimal.wgEncodeSydhTfbsHepg2Hsf1ForsklnStdAlnRep0_vs_wgEncodeSydhTfbsHepg2InputForsklnStdAlnRep0.bb HepG2 ChipSeq HSF1 Peaks bigBed Stanford analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/peakSeq/optimal/hub/peakSeq.optimal.wgEncodeSydhTfbsHepg2Irf3IggrabAlnRep0_vs_wgEncodeSydhTfbsHepg2InputIggrabAlnRep1.bb HepG2 ChipSeq IRF3 Peaks bigBed Stanford analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/peakSeq/optimal/hub/peakSeq.optimal.wgEncodeSydhTfbsHepg2JundIggrabAlnRep0_vs_wgEncodeSydhTfbsHepg2InputIggrabAlnRep1.bb HepG2 ChipSeq JunD Peaks bigBed Stanford analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/peakSeq/optimal/hub/peakSeq.optimal.wgEncodeSydhTfbsHepg2Maffm8194IggrabAlnRep0_vs_wgEncodeSydhTfbsHepg2InputIggrabAlnRep1.bb HepG2 ChipSeq MafF_(M8194) Peaks bigBed Stanford analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/peakSeq/optimal/hub/peakSeq.optimal.wgEncodeSydhTfbsHepg2Mafkab50322IggrabAlnRep0_vs_wgEncodeSydhTfbsHepg2InputIggrabAlnRep1.bb HepG2 ChipSeq MafK_(ab50322) Peaks bigBed Stanford analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/peakSeq/optimal/hub/peakSeq.optimal.wgEncodeSydhTfbsHepg2Mafksc477IggrabAlnRep0_vs_wgEncodeSydhTfbsHepg2InputIggrabAlnRep1.bb HepG2 ChipSeq MafK_(SC-477) Peaks bigBed Stanford analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/peakSeq/optimal/hub/peakSeq.optimal.wgEncodeSydhTfbsHepg2Nrf1IggrabAlnRep0_vs_wgEncodeSydhTfbsHepg2InputIggrabAlnRep1.bb HepG2 ChipSeq Nrf1 Peaks bigBed Stanford analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/peakSeq/optimal/hub/peakSeq.optimal.wgEncodeSydhTfbsHepg2Pgc1aForsklnStdAlnRep0_vs_wgEncodeSydhTfbsHepg2InputForsklnStdAlnRep0.bb HepG2 ChipSeq PGC1A Peaks bigBed Stanford analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/peakSeq/optimal/hub/peakSeq.optimal.wgEncodeSydhTfbsHepg2Pol2ForsklnStdAlnRep0_vs_wgEncodeSydhTfbsHepg2InputForsklnStdAlnRep0.bb HepG2 ChipSeq Pol2 Peaks bigBed Stanford analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/peakSeq/optimal/hub/peakSeq.optimal.wgEncodeSydhTfbsHepg2Pol2IggrabAlnRep0_vs_wgEncodeSydhTfbsHepg2InputIggrabAlnRep1.bb HepG2 ChipSeq Pol2 Peaks bigBed Stanford analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/peakSeq/optimal/hub/peakSeq.optimal.wgEncodeSydhTfbsHepg2Pol2PravastStdAlnRep0_vs_wgEncodeSydhTfbsHepg2InputPravastStdAlnRep0.bb HepG2 ChipSeq Pol2 Peaks bigBed Stanford analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/peakSeq/optimal/hub/peakSeq.optimal.wgEncodeSydhTfbsHepg2Rad21IggrabAlnRep0_vs_wgEncodeSydhTfbsHepg2InputIggrabAlnRep1.bb HepG2 ChipSeq Rad21 Peaks bigBed Stanford analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/peakSeq/optimal/hub/peakSeq.optimal.wgEncodeSydhTfbsHepg2Rfx5n494IggrabAlnRep0_vs_wgEncodeSydhTfbsHepg2InputIggrabAlnRep1.bb HepG2 ChipSeq RFX5_(N-494) Peaks bigBed Stanford analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/peakSeq/optimal/hub/peakSeq.optimal.wgEncodeSydhTfbsHepg2Srebp1InslnStdAlnRep0_vs_wgEncodeSydhTfbsHepg2InputInslnStdAlnRep0.bb HepG2 ChipSeq SREBP1 Peaks bigBed Stanford analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/peakSeq/optimal/hub/peakSeq.optimal.wgEncodeSydhTfbsHepg2Srebp1PravastStdAlnRep0_vs_wgEncodeSydhTfbsHepg2InputPravastStdAlnRep0.bb HepG2 ChipSeq SREBP1 Peaks bigBed Stanford analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/peakSeq/optimal/hub/peakSeq.optimal.wgEncodeSydhTfbsHepg2Srebp2PravastStdAlnRep0_vs_wgEncodeSydhTfbsHepg2InputPravastStdAlnRep0.bb HepG2 ChipSeq SREBP2 Peaks bigBed Stanford analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/peakSeq/optimal/hub/peakSeq.optimal.wgEncodeSydhTfbsHepg2TbpIggrabAlnRep0_vs_wgEncodeSydhTfbsHepg2InputIggrabAlnRep1.bb HepG2 ChipSeq TBP Peaks bigBed Stanford analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/peakSeq/optimal/hub/peakSeq.optimal.wgEncodeSydhTfbsHepg2Tcf4UcdAlnRep0_vs_wgEncodeSydhTfbsHepg2bInputUcdAlnRep1.bb HepG2b ChipSeq TCF4 Peaks bigBed UCD analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/peakSeq/optimal/hub/peakSeq.optimal.wgEncodeSydhTfbsHepg2Usf2IggrabAlnRep0_vs_wgEncodeSydhTfbsHepg2InputIggrabAlnRep1.bb HepG2 ChipSeq USF2 Peaks bigBed Stanford analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/peakSeq/optimal/hub/peakSeq.optimal.wgEncodeSydhTfbsHuvecCfosUcdAlnRep0_vs_wgEncodeSydhTfbsHuvecInputUcdAlnRep1.bb HUVEC ChipSeq c-Fos Peaks bigBed UCD analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/peakSeq/optimal/hub/peakSeq.optimal.wgEncodeSydhTfbsHuvecCjunStdAlnRep0_vs_wgEncodeSydhTfbsHuvecInputStdAlnRep0.bb HUVEC ChipSeq c-Jun Peaks bigBed Stanford analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/peakSeq/optimal/hub/peakSeq.optimal.wgEncodeSydhTfbsHuvecGata2UcdAlnRep0_vs_wgEncodeSydhTfbsHuvecInputUcdAlnRep1.bb HUVEC ChipSeq GATA-2 Peaks bigBed UCD analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/peakSeq/optimal/hub/peakSeq.optimal.wgEncodeSydhTfbsHuvecMaxStdAlnRep0_vs_wgEncodeSydhTfbsHuvecInputStdAlnRep0.bb HUVEC ChipSeq Max Peaks bigBed Stanford analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/peakSeq/optimal/hub/peakSeq.optimal.wgEncodeSydhTfbsHuvecPol2StdAlnRep0_vs_wgEncodeSydhTfbsHuvecInputStdAlnRep0.bb HUVEC ChipSeq Pol2 Peaks bigBed Stanford analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/peakSeq/optimal/hub/peakSeq.optimal.wgEncodeSydhTfbsK562Atf3StdAlnRep0_vs_wgEncodeSydhTfbsK562InputStdAlnRep0.bb K562 ChipSeq ATF3 Peaks bigBed Stanford analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/peakSeq/optimal/hub/peakSeq.optimal.wgEncodeSydhTfbsK562Bdp1StdAlnRep0_vs_wgEncodeSydhTfbsK562InputStdAlnRep0.bb K562 ChipSeq BDP1 Peaks bigBed Stanford analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/peakSeq/optimal/hub/peakSeq.optimal.wgEncodeSydhTfbsK562bE2f4UcdAlnRep0_vs_wgEncodeSydhTfbsK562bInputUcdAlnRep1.bb K562b ChipSeq E2F4 Peaks bigBed Stanford analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/peakSeq/optimal/hub/peakSeq.optimal.wgEncodeSydhTfbsK562bE2f6UcdAlnRep0_vs_wgEncodeSydhTfbsK562bInputUcdAlnRep1.bb K562b ChipSeq E2F6 Peaks bigBed Stanford analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/peakSeq/optimal/hub/peakSeq.optimal.wgEncodeSydhTfbsK562bGata1UcdAlnRep0_vs_wgEncodeSydhTfbsK562bInputUcdAlnRep1.bb K562b ChipSeq GATA-1 Peaks bigBed Stanford analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/peakSeq/optimal/hub/peakSeq.optimal.wgEncodeSydhTfbsK562bGata2UcdAlnRep0_vs_wgEncodeSydhTfbsK562bInputUcdAlnRep1.bb K562b ChipSeq GATA-2 Peaks bigBed Stanford analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/peakSeq/optimal/hub/peakSeq.optimal.wgEncodeSydhTfbsK562bKap1UcdAlnRep0_vs_wgEncodeSydhTfbsK562bInputUcdAlnRep1.bb K562b ChipSeq KAP1 Peaks bigBed UCD analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/peakSeq/optimal/hub/peakSeq.optimal.wgEncodeSydhTfbsK562Brf1StdAlnRep0_vs_wgEncodeSydhTfbsK562InputStdAlnRep0.bb K562 ChipSeq BRF1 Peaks bigBed Stanford analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/peakSeq/optimal/hub/peakSeq.optimal.wgEncodeSydhTfbsK562Brf2StdAlnRep0_vs_wgEncodeSydhTfbsK562InputStdAlnRep0.bb K562 ChipSeq BRF2 Peaks bigBed Stanford analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/peakSeq/optimal/hub/peakSeq.optimal.wgEncodeSydhTfbsK562Brg1IggmusAlnRep0_vs_wgEncodeSydhTfbsK562InputIggmusAlnRep0.bb K562 ChipSeq Brg1 Peaks bigBed Stanford analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/peakSeq/optimal/hub/peakSeq.optimal.wgEncodeSydhTfbsK562bSetdb1MnasedUcdAlnRep0_vs_wgEncodeSydhTfbsK562bInputUcdAlnRep1.bb K562b ChipSeq SETDB1 Peaks bigBed Stanford analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/peakSeq/optimal/hub/peakSeq.optimal.wgEncodeSydhTfbsK562bSetdb1UcdAlnRep0_vs_wgEncodeSydhTfbsK562bInputUcdAlnRep1.bb K562b ChipSeq SETDB1 Peaks bigBed Stanford analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/peakSeq/optimal/hub/peakSeq.optimal.wgEncodeSydhTfbsK562bTr4UcdAlnRep0_vs_wgEncodeSydhTfbsK562bInputUcdAlnRep1.bb K562b ChipSeq TR4 Peaks bigBed Stanford analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/peakSeq/optimal/hub/peakSeq.optimal.wgEncodeSydhTfbsK562bYy1UcdAlnRep0_vs_wgEncodeSydhTfbsK562bInputUcdAlnRep1.bb K562b ChipSeq YY1 Peaks bigBed Stanford analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/peakSeq/optimal/hub/peakSeq.optimal.wgEncodeSydhTfbsK562bZnf263UcdAlnRep0_vs_wgEncodeSydhTfbsK562bInputUcdAlnRep1.bb K562b ChipSeq ZNF263 Peaks bigBed Stanford analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/peakSeq/optimal/hub/peakSeq.optimal.wgEncodeSydhTfbsK562bZnf274UcdAlnRep0_vs_wgEncodeSydhTfbsK562bInputUcdAlnRep1.bb K562b ChipSeq ZNF274 Peaks bigBed Stanford analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/peakSeq/optimal/hub/peakSeq.optimal.wgEncodeSydhTfbsK562Ccnt2StdAlnRep0_vs_wgEncodeSydhTfbsK562InputStdAlnRep0.bb K562 ChipSeq CCNT2 Peaks bigBed Harvard analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/peakSeq/optimal/hub/peakSeq.optimal.wgEncodeSydhTfbsK562CebpbIggrabAlnRep0_vs_wgEncodeSydhTfbsK562InputIggrabAlnRep1.bb K562 ChipSeq CEBPB Peaks bigBed Stanford analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/peakSeq/optimal/hub/peakSeq.optimal.wgEncodeSydhTfbsK562CfosStdAlnRep0_vs_wgEncodeSydhTfbsK562InputStdAlnRep0.bb K562 ChipSeq c-Fos Peaks bigBed Stanford analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/peakSeq/optimal/hub/peakSeq.optimal.wgEncodeSydhTfbsK562Chd21250IggrabAlnRep0_vs_wgEncodeSydhTfbsK562InputIggrabAlnRep1.bb K562 ChipSeq CHD2_(N-1250) Peaks bigBed Stanford analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/peakSeq/optimal/hub/peakSeq.optimal.wgEncodeSydhTfbsK562CjunIfna6hStdAlnRep0_vs_wgEncodeSydhTfbsK562InputIfna6hStdAlnRep1.bb K562 ChipSeq c-Jun Peaks bigBed Stanford analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/peakSeq/optimal/hub/peakSeq.optimal.wgEncodeSydhTfbsK562CjunIfng30StdAlnRep0_vs_wgEncodeSydhTfbsK562InputIfng30StdAlnRep1.bb K562 ChipSeq c-Jun Peaks bigBed Stanford analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/peakSeq/optimal/hub/peakSeq.optimal.wgEncodeSydhTfbsK562CjunIfng6hStdAlnRep0_vs_wgEncodeSydhTfbsK562InputIfng6hStdAlnRep1.bb K562 ChipSeq c-Jun Peaks bigBed Stanford analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/peakSeq/optimal/hub/peakSeq.optimal.wgEncodeSydhTfbsK562CjunStdAlnRep0_vs_wgEncodeSydhTfbsK562InputStdAlnRep0.bb K562 ChipSeq c-Jun Peaks bigBed Stanford analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/peakSeq/optimal/hub/peakSeq.optimal.wgEncodeSydhTfbsK562CmycIfna30StdAlnRep0_vs_wgEncodeSydhTfbsK562InputIfna30StdAlnRep1.bb K562 ChipSeq c-Myc Peaks bigBed Stanford analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/peakSeq/optimal/hub/peakSeq.optimal.wgEncodeSydhTfbsK562CmycIfna6hStdAlnRep0_vs_wgEncodeSydhTfbsK562InputIfna6hStdAlnRep1.bb K562 ChipSeq c-Myc Peaks bigBed Stanford analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/peakSeq/optimal/hub/peakSeq.optimal.wgEncodeSydhTfbsK562CmycIfng30StdAlnRep0_vs_wgEncodeSydhTfbsK562InputIfng30StdAlnRep1.bb K562 ChipSeq c-Myc Peaks bigBed Stanford analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/peakSeq/optimal/hub/peakSeq.optimal.wgEncodeSydhTfbsK562CmycIfng6hStdAlnRep0_vs_wgEncodeSydhTfbsK562InputIfng6hStdAlnRep1.bb K562 ChipSeq c-Myc Peaks bigBed Stanford analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/peakSeq/optimal/hub/peakSeq.optimal.wgEncodeSydhTfbsK562CmycStdAlnRep0_vs_wgEncodeSydhTfbsK562InputStdAlnRep0.bb K562 ChipSeq c-Myc Peaks bigBed Stanford analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/peakSeq/optimal/hub/peakSeq.optimal.wgEncodeSydhTfbsK562Gtf2bStdAlnRep0_vs_wgEncodeSydhTfbsK562InputStdAlnRep0.bb K562 ChipSeq GTF2B Peaks bigBed Harvard analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/peakSeq/optimal/hub/peakSeq.optimal.wgEncodeSydhTfbsK562Gtf2f1rapIggrabAlnRep0_vs_wgEncodeSydhTfbsK562InputIggrabAlnRep1.bb K562 ChipSeq GTF2F1_(RAP-74) Peaks bigBed Stanford analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/peakSeq/optimal/hub/peakSeq.optimal.wgEncodeSydhTfbsK562Hmgn3StdAlnRep0_vs_wgEncodeSydhTfbsK562InputStdAlnRep0.bb K562 ChipSeq HMGN3 Peaks bigBed Harvard analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/peakSeq/optimal/hub/peakSeq.optimal.wgEncodeSydhTfbsK562Ini1IggmusAlnRep0_vs_wgEncodeSydhTfbsK562InputIggmusAlnRep0.bb K562 ChipSeq Ini1 Peaks bigBed Stanford analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/peakSeq/optimal/hub/peakSeq.optimal.wgEncodeSydhTfbsK562Irf1Ifna30StdAlnRep0_vs_wgEncodeSydhTfbsK562InputIfna30StdAlnRep1.bb K562 ChipSeq IRF1 Peaks bigBed Stanford analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/peakSeq/optimal/hub/peakSeq.optimal.wgEncodeSydhTfbsK562Irf1Ifng6hStdAlnRep0_vs_wgEncodeSydhTfbsK562InputIfng6hStdAlnRep1.bb K562 ChipSeq IRF1 Peaks bigBed Stanford analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/peakSeq/optimal/hub/peakSeq.optimal.wgEncodeSydhTfbsK562JundStdAlnRep0_vs_wgEncodeSydhTfbsK562InputStdAlnRep0.bb K562 ChipSeq JunD Peaks bigBed Stanford analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/peakSeq/optimal/hub/peakSeq.optimal.wgEncodeSydhTfbsK562Mafkab50322IggrabAlnRep0_vs_wgEncodeSydhTfbsK562InputIggrabAlnRep1.bb K562 ChipSeq MafK_(ab50322) Peaks bigBed Stanford analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/peakSeq/optimal/hub/peakSeq.optimal.wgEncodeSydhTfbsK562MaxStdAlnRep0_vs_wgEncodeSydhTfbsK562InputStdAlnRep0.bb K562 ChipSeq Max Peaks bigBed Stanford analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/peakSeq/optimal/hub/peakSeq.optimal.wgEncodeSydhTfbsK562Mxi1bhlhIggrabAlnRep0_vs_wgEncodeSydhTfbsK562InputIggrabAlnRep1.bb K562 ChipSeq Mxi1_(bHLH) Peaks bigBed Stanford analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/peakSeq/optimal/hub/peakSeq.optimal.wgEncodeSydhTfbsK562NelfeStdAlnRep0_vs_wgEncodeSydhTfbsK562InputStdAlnRep0.bb K562 ChipSeq NELFe Peaks bigBed Stanford analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/peakSeq/optimal/hub/peakSeq.optimal.wgEncodeSydhTfbsK562Nfe2StdAlnRep0_vs_wgEncodeSydhTfbsK562InputStdAlnRep0.bb K562 ChipSeq NF-E2 Peaks bigBed Stanford analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/peakSeq/optimal/hub/peakSeq.optimal.wgEncodeSydhTfbsK562NfyaStdAlnRep0_vs_wgEncodeSydhTfbsK562InputStdAlnRep0.bb K562 ChipSeq NF-YA Peaks bigBed Stanford analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/peakSeq/optimal/hub/peakSeq.optimal.wgEncodeSydhTfbsK562NfybStdAlnRep0_vs_wgEncodeSydhTfbsK562InputStdAlnRep0.bb K562 ChipSeq NF-YB Peaks bigBed Stanford analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/peakSeq/optimal/hub/peakSeq.optimal.wgEncodeSydhTfbsK562Nrf1IggrabAlnRep0_vs_wgEncodeSydhTfbsK562InputIggrabAlnRep1.bb K562 ChipSeq Nrf1 Peaks bigBed Stanford analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/peakSeq/optimal/hub/peakSeq.optimal.wgEncodeSydhTfbsK562P300f4IggrabAlnRep0_vs_wgEncodeSydhTfbsK562InputIggrabAlnRep1.bb K562 ChipSeq p300_(F-4) Peaks bigBed Stanford analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/peakSeq/optimal/hub/peakSeq.optimal.wgEncodeSydhTfbsK562Pol2Ifna30StdAlnRep0_vs_wgEncodeSydhTfbsK562InputIfna30StdAlnRep1.bb K562 ChipSeq Pol2 Peaks bigBed Stanford analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/peakSeq/optimal/hub/peakSeq.optimal.wgEncodeSydhTfbsK562Pol2Ifna6hStdAlnRep0_vs_wgEncodeSydhTfbsK562InputIfna6hStdAlnRep1.bb K562 ChipSeq Pol2 Peaks bigBed Stanford analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/peakSeq/optimal/hub/peakSeq.optimal.wgEncodeSydhTfbsK562Pol2Ifng30StdAlnRep0_vs_wgEncodeSydhTfbsK562InputIfng30StdAlnRep1.bb K562 ChipSeq Pol2 Peaks bigBed Stanford analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/peakSeq/optimal/hub/peakSeq.optimal.wgEncodeSydhTfbsK562Pol2Ifng6hStdAlnRep0_vs_wgEncodeSydhTfbsK562InputIfng6hStdAlnRep1.bb K562 ChipSeq Pol2 Peaks bigBed Stanford analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/peakSeq/optimal/hub/peakSeq.optimal.wgEncodeSydhTfbsK562Pol2IggmusAlnRep0_vs_wgEncodeSydhTfbsK562InputIggmusAlnRep0.bb K562 ChipSeq Pol2 Peaks bigBed Stanford analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/peakSeq/optimal/hub/peakSeq.optimal.wgEncodeSydhTfbsK562Pol2s2StdAlnRep0_vs_wgEncodeSydhTfbsK562InputStdAlnRep0.bb K562 ChipSeq Pol2(phosphoS2) Peaks bigBed Stanford analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/peakSeq/optimal/hub/peakSeq.optimal.wgEncodeSydhTfbsK562Pol2StdAlnRep0_vs_wgEncodeSydhTfbsK562InputStdAlnRep0.bb K562 ChipSeq Pol2 Peaks bigBed Stanford analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/peakSeq/optimal/hub/peakSeq.optimal.wgEncodeSydhTfbsK562Pol3StdAlnRep0_vs_wgEncodeSydhTfbsK562InputStdAlnRep0.bb K562 ChipSeq Pol3 Peaks bigBed Stanford analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/peakSeq/optimal/hub/peakSeq.optimal.wgEncodeSydhTfbsK562Rad21StdAlnRep0_vs_wgEncodeSydhTfbsK562InputStdAlnRep0.bb K562 ChipSeq Rad21 Peaks bigBed Stanford analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/peakSeq/optimal/hub/peakSeq.optimal.wgEncodeSydhTfbsK562Rpc155StdAlnRep0_vs_wgEncodeSydhTfbsK562InputStdAlnRep0.bb K562 ChipSeq RPC155 Peaks bigBed Stanford analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/peakSeq/optimal/hub/peakSeq.optimal.wgEncodeSydhTfbsK562Sirt6StdAlnRep0_vs_wgEncodeSydhTfbsK562InputStdAlnRep0.bb K562 ChipSeq SIRT6 Peaks bigBed Stanford analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/peakSeq/optimal/hub/peakSeq.optimal.wgEncodeSydhTfbsK562Smc3ab9263IggrabAlnRep0_vs_wgEncodeSydhTfbsK562InputIggrabAlnRep1.bb K562 ChipSeq SMC3_(ab9263) Peaks bigBed Stanford analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/peakSeq/optimal/hub/peakSeq.optimal.wgEncodeSydhTfbsK562Stat1Ifna30StdAlnRep0_vs_wgEncodeSydhTfbsK562InputIfna30StdAlnRep1.bb K562 ChipSeq STAT1 Peaks bigBed Stanford analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/peakSeq/optimal/hub/peakSeq.optimal.wgEncodeSydhTfbsK562Stat1Ifna6hStdAlnRep0_vs_wgEncodeSydhTfbsK562InputIfna6hStdAlnRep1.bb K562 ChipSeq STAT1 Peaks bigBed Stanford analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/peakSeq/optimal/hub/peakSeq.optimal.wgEncodeSydhTfbsK562Stat1Ifng30StdAlnRep0_vs_wgEncodeSydhTfbsK562InputIfng30StdAlnRep1.bb K562 ChipSeq STAT1 Peaks bigBed Stanford analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/peakSeq/optimal/hub/peakSeq.optimal.wgEncodeSydhTfbsK562Stat1Ifng6hStdAlnRep0_vs_wgEncodeSydhTfbsK562InputIfng6hStdAlnRep1.bb K562 ChipSeq STAT1 Peaks bigBed Stanford analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/peakSeq/optimal/hub/peakSeq.optimal.wgEncodeSydhTfbsK562Stat2Ifna30StdAlnRep0_vs_wgEncodeSydhTfbsK562InputIfna30StdAlnRep1.bb K562 ChipSeq STAT2 Peaks bigBed Stanford analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/peakSeq/optimal/hub/peakSeq.optimal.wgEncodeSydhTfbsK562Stat2Ifna6hStdAlnRep0_vs_wgEncodeSydhTfbsK562InputIfna6hStdAlnRep1.bb K562 ChipSeq STAT2 Peaks bigBed Stanford analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/peakSeq/optimal/hub/peakSeq.optimal.wgEncodeSydhTfbsK562Tal1sc12984IggmusAlnRep0_vs_wgEncodeSydhTfbsK562InputIggmusAlnRep0.bb K562 ChipSeq TAL1_(SC-12984) Peaks bigBed Stanford analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/peakSeq/optimal/hub/peakSeq.optimal.wgEncodeSydhTfbsK562TbpIggmusAlnRep0_vs_wgEncodeSydhTfbsK562InputIggmusAlnRep0.bb K562 ChipSeq TBP Peaks bigBed Stanford analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/peakSeq/optimal/hub/peakSeq.optimal.wgEncodeSydhTfbsK562Tf3c110StdAlnRep0_vs_wgEncodeSydhTfbsK562InputStdAlnRep0.bb K562 ChipSeq TFIIIC-110 Peaks bigBed Stanford analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/peakSeq/optimal/hub/peakSeq.optimal.wgEncodeSydhTfbsK562Usf2StdAlnRep0_vs_wgEncodeSydhTfbsK562InputStdAlnRep0.bb K562 ChipSeq USF2 Peaks bigBed Stanford analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/peakSeq/optimal/hub/peakSeq.optimal.wgEncodeSydhTfbsK562Xrcc4StdAlnRep0_vs_wgEncodeSydhTfbsK562InputStdAlnRep0.bb K562 ChipSeq XRCC4 Peaks bigBed Stanford analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/peakSeq/optimal/hub/peakSeq.optimal.wgEncodeSydhTfbsMcf10aesPol2Etoh01StdAlnRep0_vs_wgEncodeSydhTfbsMcf10aesInputUcdAlnRep1.bb MCF10A-Er-Src ChipSeq Pol2 Peaks bigBed Stanford analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/peakSeq/optimal/hub/peakSeq.optimal.wgEncodeSydhTfbsMcf10aesPol2TamStdAlnRep0_vs_wgEncodeSydhTfbsMcf10aesInputUcdAlnRep1.bb MCF10A-Er-Src ChipSeq Pol2 Peaks bigBed Harvard(Weissman) analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/peakSeq/optimal/hub/peakSeq.optimal.wgEncodeSydhTfbsMcf10aesStat3Etoh01bStdAlnRep0_vs_wgEncodeSydhTfbsMcf10aesInputEtoh01bStdAlnRep1.bb MCF10A-Er-Src ChipSeq STAT3 Peaks bigBed Harvard(Weissman) analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/peakSeq/optimal/hub/peakSeq.optimal.wgEncodeSydhTfbsMcf10aesStat3Etoh01cStdAlnRep0_vs_wgEncodeSydhTfbsMcf10aesInputEtoh01cStdAlnRep1.bb MCF10A-Er-Src ChipSeq STAT3 Peaks bigBed Stanford analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/peakSeq/optimal/hub/peakSeq.optimal.wgEncodeSydhTfbsMcf10aesStat3Etoh01StdAlnRep0_vs_wgEncodeSydhTfbsMcf10aesInputUcdAlnRep1.bb MCF10A-Er-Src ChipSeq STAT3 Peaks bigBed Harvard(Weissman) analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/peakSeq/optimal/hub/peakSeq.optimal.wgEncodeSydhTfbsMcf10aesStat3TamStdAlnRep0_vs_wgEncodeSydhTfbsMcf10aesInputUcdAlnRep1.bb MCF10A-Er-Src ChipSeq STAT3 Peaks bigBed Harvard(Weissman) analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/peakSeq/optimal/hub/peakSeq.optimal.wgEncodeSydhTfbsMcf7Hae2f1UcdAlnRep0_vs_wgEncodeSydhTfbsMcf7InputUcdAlnRep0.bb MCF-7 ChipSeq HA-E2F1 Peaks bigBed Stanford analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/peakSeq/optimal/hub/peakSeq.optimal.wgEncodeSydhTfbsNb4CmycStdAlnRep0_vs_wgEncodeSydhTfbsNb4InputStdAlnRep1.bb NB4 ChipSeq c-Myc Peaks bigBed Stanford analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/peakSeq/optimal/hub/peakSeq.optimal.wgEncodeSydhTfbsNb4MaxStdAlnRep0_vs_wgEncodeSydhTfbsNb4InputStdAlnRep1.bb NB4 ChipSeq Max Peaks bigBed Stanford analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/peakSeq/optimal/hub/peakSeq.optimal.wgEncodeSydhTfbsNb4Pol2StdAlnRep0_vs_wgEncodeSydhTfbsNb4InputStdAlnRep1.bb NB4 ChipSeq Pol2 Peaks bigBed Stanford analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/peakSeq/optimal/hub/peakSeq.optimal.wgEncodeSydhTfbsNt2d1Suz12UcdAlnRep0_vs_wgEncodeSydhTfbsNt2d1InputUcdAlnRep1.bb NT2-D1 ChipSeq SUZ12 Peaks bigBed Stanford analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/peakSeq/optimal/hub/peakSeq.optimal.wgEncodeSydhTfbsNt2d1Yy1UcdAlnRep0_vs_wgEncodeSydhTfbsNt2d1InputUcdAlnRep1.bb NT2-D1 ChipSeq YY1 Peaks bigBed Stanford analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/peakSeq/optimal/hub/peakSeq.optimal.wgEncodeSydhTfbsNt2d1Znf274UcdAlnRep0_vs_wgEncodeSydhTfbsNt2d1InputUcdAlnRep1.bb NT2-D1 ChipSeq ZNF274 Peaks bigBed UCD analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/peakSeq/optimal/hub/peakSeq.optimal.wgEncodeSydhTfbsPbdeGata1UcdAlnRep0_vs_wgEncodeSydhTfbsPbdeInputUcdAlnRep1.bb PBDE ChipSeq GATA-1 Peaks bigBed UCD analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/peakSeq/optimal/hub/peakSeq.optimal.wgEncodeSydhTfbsPbdePol2UcdAlnRep0_vs_wgEncodeSydhTfbsPbdeInputUcdAlnRep1.bb PBDE ChipSeq Pol2 Peaks bigBed UCD analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/peakSeq/optimal/hub/peakSeq.optimal.wgEncodeSydhTfbsRajiPol2UcdAlnRep0_vs_wgEncodeSydhTfbsRajiInputUcdAlnRep1.bb Raji ChipSeq Pol2 Peaks bigBed UCD analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/peakSeq/optimal/hub/peakSeq.optimal.wgEncodeSydhTfbsShsy5yGata2UcdAlnRep0_vs_wgEncodeSydhTfbsShsy5yInputUcdAlnRep1.bb SH-SY5Y ChipSeq GATA-2 Peaks bigBed UCD analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/peakSeq/optimal/hub/peakSeq.optimal.wgEncodeSydhTfbsTrexhek293Znf263UcdAlnRep0_vs_wgEncodeSydhTfbsThek293InputUcdAlnRep1.bb T-REx-HEK293 ChipSeq ZNF263 Peaks bigBed UCD analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/peakSeq/optimal/hub/peakSeq.optimal.wgEncodeSydhTfbsU2osKap1UcdAlnRep0_vs_wgEncodeSydhTfbsU2osInputUcdAlnRep1.bb U2OS ChipSeq KAP1 Peaks bigBed Stanford analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/peakSeq/optimal/hub/peakSeq.optimal.wgEncodeSydhTfbsU2osSetdb1UcdAlnRep0_vs_wgEncodeSydhTfbsU2osInputUcdAlnRep1.bb U2OS ChipSeq SETDB1 Peaks bigBed UCD analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/peakSeq/optimal/hub/peakSeq.optimal.wgEncodeUchicagoTfbsK562EfosControlAlnRep0_vs_wgEncodeUchicagoTfbsK562InputControlAlnRep0.bb K562 ChipSeq eGFP-FOS Peaks bigBed UChicago analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/peakSeq/optimal/hub/peakSeq.optimal.wgEncodeUchicagoTfbsK562Egata2ControlAlnRep0_vs_wgEncodeUchicagoTfbsK562InputControlAlnRep0.bb K562 ChipSeq eGFP-GATA2 Peaks bigBed UChicago analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/peakSeq/optimal/hub/peakSeq.optimal.wgEncodeUchicagoTfbsK562Ehdac8ControlAlnRep0_vs_wgEncodeUchicagoTfbsK562InputControlAlnRep0.bb K562 ChipSeq eGFP-HDAC8 Peaks bigBed UChicago analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/peakSeq/optimal/hub/peakSeq.optimal.wgEncodeUchicagoTfbsK562EjunbControlAlnRep0_vs_wgEncodeUchicagoTfbsK562InputControlAlnRep0.bb K562 ChipSeq eGFP-JunB Peaks bigBed UChicago analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/peakSeq/optimal/hub/peakSeq.optimal.wgEncodeUchicagoTfbsK562EjundControlAlnRep0_vs_wgEncodeUchicagoTfbsK562InputControlAlnRep0.bb K562 ChipSeq eGFP-JunD Peaks bigBed UChicago analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/peakSeq/optimal/hub/peakSeq.optimal.wgEncodeUchicagoTfbsK562Enr4a1ControlAlnRep0_vs_wgEncodeUchicagoTfbsK562InputControlAlnRep0.bb K562 ChipSeq eGFP-NR4A1 Peaks bigBed UChicago analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/peakSeq/optimal/hub/peakSeq.optimal.wgEncodeUwTfbsAg04449CtcfStdAlnRep0_vs_wgEncodeUwTfbsAg04449InputStdAlnRep1.bb AG04449 ChipSeq CTCF Peaks bigBed UW analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/peakSeq/optimal/hub/peakSeq.optimal.wgEncodeUwTfbsAg04450CtcfStdAlnRep1_vs_wgEncodeUwTfbsAg04450InputStdAlnRep1.bb AG04450 ChipSeq CTCF Peaks bigBed UW analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/peakSeq/optimal/hub/peakSeq.optimal.wgEncodeUwTfbsAg09309CtcfStdAlnRep0_vs_wgEncodeUwTfbsAg09309InputStdAlnRep1.bb AG09309 ChipSeq CTCF Peaks bigBed UW analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/peakSeq/optimal/hub/peakSeq.optimal.wgEncodeUwTfbsAg09319CtcfStdAlnRep0_vs_wgEncodeUwTfbsAg09319InputStdAlnRep1.bb AG09319 ChipSeq CTCF Peaks bigBed UW analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/peakSeq/optimal/hub/peakSeq.optimal.wgEncodeUwTfbsAg10803CtcfStdAlnRep0_vs_wgEncodeUwTfbsAg10803InputStdAlnRep1.bb AG10803 ChipSeq CTCF Peaks bigBed UW analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/peakSeq/optimal/hub/peakSeq.optimal.wgEncodeUwTfbsAoafCtcfStdAlnRep0_vs_wgEncodeUwTfbsAoafInputStdAlnRep1.bb AoAF ChipSeq CTCF Peaks bigBed UW analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/peakSeq/optimal/hub/peakSeq.optimal.wgEncodeUwTfbsBjCtcfStdAlnRep0_vs_wgEncodeUwTfbsBjInputStdAlnRep1.bb BJ ChipSeq CTCF Peaks bigBed UW analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/peakSeq/optimal/hub/peakSeq.optimal.wgEncodeUwTfbsCaco2CtcfStdAlnRep0_vs_wgEncodeUwTfbsCaco2InputStdAlnRep1.bb Caco-2 ChipSeq CTCF Peaks bigBed UW analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/peakSeq/optimal/hub/peakSeq.optimal.wgEncodeUwTfbsGm06990CtcfStdAlnRep0_vs_wgEncodeUwTfbsGm06990InputStdAlnRep1.bb GM06990 ChipSeq CTCF Peaks bigBed UW analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/peakSeq/optimal/hub/peakSeq.optimal.wgEncodeUwTfbsGm12801CtcfStdAlnRep1_vs_wgEncodeUwTfbsGm12801InputStdAlnRep1.bb GM12801 ChipSeq CTCF Peaks bigBed UW analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/peakSeq/optimal/hub/peakSeq.optimal.wgEncodeUwTfbsGm12864CtcfStdAlnRep0_vs_wgEncodeUwTfbsGm12864InputStdAlnRep1.bb GM12864 ChipSeq CTCF Peaks bigBed UW analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/peakSeq/optimal/hub/peakSeq.optimal.wgEncodeUwTfbsGm12865CtcfStdAlnRep0_vs_wgEncodeUwTfbsGm12865InputStdAlnRep1.bb GM12865 ChipSeq CTCF Peaks bigBed UW analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/peakSeq/optimal/hub/peakSeq.optimal.wgEncodeUwTfbsGm12872CtcfStdAlnRep0_vs_wgEncodeUwTfbsGm12872InputStdAlnRep1.bb GM12872 ChipSeq CTCF Peaks bigBed UW analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/peakSeq/optimal/hub/peakSeq.optimal.wgEncodeUwTfbsGm12873CtcfStdAlnRep0_vs_wgEncodeUwTfbsGm12873InputStdAlnRep1.bb GM12873 ChipSeq CTCF Peaks bigBed UW analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/peakSeq/optimal/hub/peakSeq.optimal.wgEncodeUwTfbsGm12874CtcfStdAlnRep0_vs_wgEncodeUwTfbsGm12874InputStdAlnRep1.bb GM12874 ChipSeq CTCF Peaks bigBed UW analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/peakSeq/optimal/hub/peakSeq.optimal.wgEncodeUwTfbsGm12875CtcfStdAlnRep0_vs_wgEncodeUwTfbsGm12875InputStdAlnRep1.bb GM12875 ChipSeq CTCF Peaks bigBed UW analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/peakSeq/optimal/hub/peakSeq.optimal.wgEncodeUwTfbsGm12878CtcfStdAlnRep0_vs_wgEncodeUwTfbsGm12878InputStdAlnRep1.bb GM12878 ChipSeq CTCF Peaks bigBed UW analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/peakSeq/optimal/hub/peakSeq.optimal.wgEncodeUwTfbsHaspCtcfStdAlnRep1_vs_wgEncodeUwTfbsHaspInputStdAlnRep1.bb HA-sp ChipSeq CTCF Peaks bigBed UW analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/peakSeq/optimal/hub/peakSeq.optimal.wgEncodeUwTfbsHbmecCtcfStdAlnRep0_vs_wgEncodeUwTfbsHbmecInputStdAlnRep1.bb HBMEC ChipSeq CTCF Peaks bigBed UW analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/peakSeq/optimal/hub/peakSeq.optimal.wgEncodeUwTfbsHcfaaCtcfStdAlnRep1_vs_wgEncodeUwTfbsHcfaaInputStdAlnRep1.bb HCFaa ChipSeq CTCF Peaks bigBed UW analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/peakSeq/optimal/hub/peakSeq.optimal.wgEncodeUwTfbsHcpeCtcfStdAlnRep0_vs_wgEncodeUwTfbsHcpeInputStdAlnRep1.bb HCPEpiC ChipSeq CTCF Peaks bigBed UW analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/peakSeq/optimal/hub/peakSeq.optimal.wgEncodeUwTfbsHeeCtcfStdAlnRep0_vs_wgEncodeUwTfbsHeeInputStdAlnRep1.bb HEEpiC ChipSeq CTCF Peaks bigBed UW analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/peakSeq/optimal/hub/peakSeq.optimal.wgEncodeUwTfbsHek293CtcfStdAlnRep0_vs_wgEncodeUwTfbsHek293InputStdAlnRep1.bb HEK293 ChipSeq CTCF Peaks bigBed UW analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/peakSeq/optimal/hub/peakSeq.optimal.wgEncodeUwTfbsHelas3CtcfStdAlnRep0_vs_wgEncodeUwTfbsHelas3InputStdAlnRep1.bb HeLa-S3 ChipSeq CTCF Peaks bigBed UW analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/peakSeq/optimal/hub/peakSeq.optimal.wgEncodeUwTfbsHepg2CtcfStdAlnRep0_vs_wgEncodeUwTfbsHepg2InputStdAlnRep1.bb HepG2 ChipSeq CTCF Peaks bigBed UW analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/peakSeq/optimal/hub/peakSeq.optimal.wgEncodeUwTfbsHl60CtcfStdAlnRep1_vs_wgEncodeUwTfbsHl60InputStdAlnRep1.bb HL-60 ChipSeq CTCF Peaks bigBed UW analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/peakSeq/optimal/hub/peakSeq.optimal.wgEncodeUwTfbsHmecCtcfStdAlnRep1_vs_wgEncodeUwTfbsHmecInputStdAlnRep1.bb HMEC ChipSeq CTCF Peaks bigBed UW analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/peakSeq/optimal/hub/peakSeq.optimal.wgEncodeUwTfbsHmfCtcfStdAlnRep0_vs_wgEncodeUwTfbsHmfInputStdAlnRep1.bb HMF ChipSeq CTCF Peaks bigBed UW analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/peakSeq/optimal/hub/peakSeq.optimal.wgEncodeUwTfbsHpafCtcfStdAlnRep0_vs_wgEncodeUwTfbsHpafInputStdAlnRep1.bb HPAF ChipSeq CTCF Peaks bigBed UW analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/peakSeq/optimal/hub/peakSeq.optimal.wgEncodeUwTfbsHpfCtcfStdAlnRep0_vs_wgEncodeUwTfbsHpfInputStdAlnRep1.bb HPF ChipSeq CTCF Peaks bigBed UW analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/peakSeq/optimal/hub/peakSeq.optimal.wgEncodeUwTfbsHreCtcfStdAlnRep0_vs_wgEncodeUwTfbsHreInputStdAlnRep1.bb HRE ChipSeq CTCF Peaks bigBed UW analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/peakSeq/optimal/hub/peakSeq.optimal.wgEncodeUwTfbsHrpeCtcfStdAlnRep1_vs_wgEncodeUwTfbsHrpeInputStdAlnRep1.bb HRPEpiC ChipSeq CTCF Peaks bigBed UW analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/peakSeq/optimal/hub/peakSeq.optimal.wgEncodeUwTfbsHuvecCtcfStdAlnRep0_vs_wgEncodeUwTfbsHuvecInputStdAlnRep1.bb HUVEC ChipSeq CTCF Peaks bigBed UW analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/peakSeq/optimal/hub/peakSeq.optimal.wgEncodeUwTfbsK562CtcfStdAlnRep0_vs_wgEncodeUwTfbsK562InputStdAlnRep1.bb K562 ChipSeq CTCF Peaks bigBed UW analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/peakSeq/optimal/hub/peakSeq.optimal.wgEncodeUwTfbsNhekCtcfStdAlnRep0_vs_wgEncodeUwTfbsNhekInputStdAlnRep1.bb NHEK ChipSeq CTCF Peaks bigBed UW analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/peakSeq/optimal/hub/peakSeq.optimal.wgEncodeUwTfbsSaecCtcfStdAlnRep0_vs_wgEncodeUwTfbsSaecInputStdAlnRep1.bb SAEC ChipSeq CTCF Peaks bigBed UW analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/peakSeq/optimal/hub/peakSeq.optimal.wgEncodeUwTfbsSknshraCtcfStdAlnRep0_vs_wgEncodeUwTfbsSknshraInputStdAlnRep1.bb SK-N-SH_RA ChipSeq CTCF Peaks bigBed UW analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/peakSeq/optimal/hub/peakSeq.optimal.wgEncodeUwTfbsWerirb1CtcfStdAlnRep0_vs_wgEncodeUwTfbsWerirb1InputStdAlnRep1.bb WERI-Rb-1 ChipSeq CTCF Peaks bigBed UW analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/rna_elements/jan2011/LongRnaSeq/A549_WholeCell_Am_Long_CSHL_Contig.CSHL_LID9005-021WC-b1.LID9006-022WC-b2.idrFilt0.1.bb A549 RnaSeq Contigs pooled bigBed CSHL analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/rna_elements/jan2011/LongRnaSeq/A549_WholeCell_Ap_Long_CSHL_Contig.CSHL_LID8963-021WC-b1.LID8964-022WC-b2.idrFilt0.1.bb A549 RnaSeq Contigs pooled bigBed CSHL analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/rna_elements/jan2011/LongRnaSeq/AGO4450_WholeCell_Am_Long_CSHL_Contig.CSHL_LID9001-017WC-b1.LID9002-018WC-b2.idrFilt0.1.bb AG04450 RnaSeq Contigs pooled bigBed CSHL analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/rna_elements/jan2011/LongRnaSeq/AGO4450_WholeCell_Ap_Long_CSHL_Contig.CSHL_LID8965-017WC-b1.LID8966-018WC-b2.idrFilt0.1.bb AG04450 RnaSeq Contigs pooled bigBed CSHL analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/rna_elements/jan2011/LongRnaSeq/BJ_WholeCell_Am_Long_CSHL_Contig.CSHL_LID9007-037WC-b1.LID9008-038WC-b2.idrFilt0.1.bb BJ RnaSeq Contigs pooled bigBed CSHL analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/rna_elements/jan2011/LongRnaSeq/BJ_WholeCell_Ap_Long_CSHL_Contig.CSHL_LID8969-037WC-b1.LID8970-038WC-b2.idrFilt0.1.bb BJ RnaSeq Contigs pooled bigBed CSHL analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/rna_elements/jan2011/LongRnaSeq/GM12878_Cytoplasm_Am_Long_CSHL_Contig.CSHL_LID18547-003C-b1.LID18548-004C-b2.idrFilt0.1.bb GM12878 RnaSeq Contigs pooled bigBed CSHL analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/rna_elements/jan2011/LongRnaSeq/GM12878_Cytoplasm_Ap_Long_CSHL_Contig.CSHL_LID8467-003C-b1.LID8468-004C-b2.idrFilt0.1.bb GM12878 RnaSeq Contigs pooled bigBed CSHL analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/rna_elements/jan2011/LongRnaSeq/GM12878_Nucleus_Am_Long_CSHL_Contig.CSHL_LID9197-003N-b1.LID9198-004N-b2.idrFilt0.1.bb GM12878 RnaSeq Contigs pooled bigBed CSHL analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/rna_elements/jan2011/LongRnaSeq/GM12878_Nucleus_Ap_Long_CSHL_Contig.CSHL_LID8532-003N-b1.LID8533-004N-b2.idrFilt0.1.bb GM12878 RnaSeq Contigs pooled bigBed CSHL analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/rna_elements/jan2011/LongRnaSeq/GM12878_WholeCell_Am_Long_CSHL_Contig.CSHL_LID8661-003WC-b1.LID8662-004WC-b2.idrFilt0.1.bb GM12878 RnaSeq Contigs pooled bigBed CSHL analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/rna_elements/jan2011/LongRnaSeq/GM12878_WholeCell_Ap_Long_CSHL_Contig.CSHL_LID16629-003WC-b1.LID16630-004WC-b2.idrFilt0.1.bb GM12878 RnaSeq Contigs pooled bigBed CSHL analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/rna_elements/jan2011/LongRnaSeq/H1ES_WholeCell_Am_Long_CSHL_Contig.CSHL_LID8663-005WC-b1.LID8664-006WC-b2.idrFilt0.1.bb H1-hESC RnaSeq Contigs pooled bigBed CSHL analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/rna_elements/jan2011/LongRnaSeq/H1ES_WholeCell_Ap_Long_CSHL_Contig.CSHL_LID8461-005WC-b1.LID8462-006WC-b2.idrFilt0.1.bb H1-hESC RnaSeq Contigs pooled bigBed CSHL analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/rna_elements/jan2011/LongRnaSeq/HeLa_Cytoplasm_Ap_Long_CSHL_Contig.CSHL_LID8469-011C-b1.LID8470-012C-b2.idrFilt0.1.bb HeLa-S3 RnaSeq Contigs pooled bigBed CSHL analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/rna_elements/jan2011/LongRnaSeq/HeLa_Nucleus_Am_Long_CSHL_Contig.CSHL_LID9200-011N-b1.LID9201-012N-b2.idrFilt0.1.bb HeLa-S3 RnaSeq Contigs pooled bigBed CSHL analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/rna_elements/jan2011/LongRnaSeq/HeLa_Nucleus_Ap_Long_CSHL_Contig.CSHL_LID8559-011N-b1.LID8560-012N-b2.idrFilt0.1.bb HeLa-S3 RnaSeq Contigs pooled bigBed CSHL analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/rna_elements/jan2011/LongRnaSeq/HeLa_WholeCell_Am_Long_CSHL_Contig.CSHL_LID8790-011WC-b1.LID8791-012WC-b2.idrFilt0.1.bb HeLa-S3 RnaSeq Contigs pooled bigBed CSHL analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/rna_elements/jan2011/LongRnaSeq/HeLa_WholeCell_Ap_Long_CSHL_Contig.CSHL_LID16633-011WC-b1.LID16634-012WC-b2.idrFilt0.1.bb HeLa-S3 RnaSeq Contigs pooled bigBed CSHL analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/rna_elements/jan2011/LongRnaSeq/HepG2_Cytoplasm_Am_Long_CSHL_Contig.CSHL_LID18552-013C-b1.LID18553-014C-b2.idrFilt0.1.bb HepG2 RnaSeq Contigs pooled bigBed CSHL analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/rna_elements/jan2011/LongRnaSeq/HepG2_Cytoplasm_Ap_Long_CSHL_Contig.CSHL_LID8471-013C-b1.LID8472-014C-b2.idrFilt0.1.bb HepG2 RnaSeq Contigs pooled bigBed CSHL analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/rna_elements/jan2011/LongRnaSeq/HepG2_Nucleus_Am_Long_CSHL_Contig.CSHL_LID9202-013N-b1.LID9203-014N-b2.idrFilt0.1.bb HepG2 RnaSeq Contigs pooled bigBed CSHL analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/rna_elements/jan2011/LongRnaSeq/HepG2_Nucleus_Ap_Long_CSHL_Contig.CSHL_LID8534-013N-b1.LID8535-014N-b2.idrFilt0.1.bb HepG2 RnaSeq Contigs pooled bigBed CSHL analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/rna_elements/jan2011/LongRnaSeq/HepG2_WholeCell_Am_Long_CSHL_Contig.CSHL_LID8792-013WC-b1.LID8793-014WC-b2.idrFilt0.1.bb HepG2 RnaSeq Contigs pooled bigBed CSHL analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/rna_elements/jan2011/LongRnaSeq/HepG2_WholeCell_Ap_Long_CSHL_Contig.CSHL_LID16635-013WC-b1.LID16636-014WC-b2.idrFilt0.1.bb HepG2 RnaSeq Contigs pooled bigBed CSHL analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/rna_elements/jan2011/LongRnaSeq/HSMM_WholeCell_Am_Long_CSHL_Contig.CSHL_LID8826-023WC-b1.LID8827-024WC-b2.idrFilt0.1.bb HSMM RnaSeq Contigs pooled bigBed CSHL analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/rna_elements/jan2011/LongRnaSeq/HSMM_WholeCell_Ap_Long_CSHL_Contig.CSHL_LID8710-023WC-b1.LID8711-024WC-b2.idrFilt0.1.bb HSMM RnaSeq Contigs pooled bigBed CSHL analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/rna_elements/jan2011/LongRnaSeq/HUVEC_Cytoplasm_Ap_Long_CSHL_Contig.CSHL_LID8688-029C-b3.LID8689-030C-b4.idrFilt0.1.bb HUVEC RnaSeq Contigs pooled bigBed CSHL analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/rna_elements/jan2011/LongRnaSeq/HUVEC_Nucleus_Am_Long_CSHL_Contig.CSHL_LID9206-029N-b3.LID9207-030N-b4.idrFilt0.1.bb HUVEC RnaSeq Contigs pooled bigBed CSHL analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/rna_elements/jan2011/LongRnaSeq/HUVEC_Nucleus_Ap_Long_CSHL_Contig.CSHL_LID8690-029N-b3.LID8691-030N-b4.idrFilt0.1.bb HUVEC RnaSeq Contigs pooled bigBed CSHL analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/rna_elements/jan2011/LongRnaSeq/HUVEC_WholeCell_Am_Long_CSHL_Contig.CSHL_LID8788-009WC-b1.LID8789-010WC-b2.idrFilt0.1.bb HUVEC RnaSeq Contigs pooled bigBed CSHL analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/rna_elements/jan2011/LongRnaSeq/HUVEC_WholeCell_Ap_Long_CSHL_Contig.CSHL_LID8463-009WC-b1.LID8464-010WC-b2.idrFilt0.1.bb HUVEC RnaSeq Contigs pooled bigBed CSHL analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/rna_elements/jan2011/LongRnaSeq/K562_Chromatin_Total_Long_CSHL_Contig.CSHL_LID9185-025CH-b3.LID9186-026CH-b4.idrFilt0.1.bb K562 RnaSeq Contigs pooled bigBed CSHL analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/rna_elements/jan2011/LongRnaSeq/K562_Cytoplasm_Am_Long_CSHL_Contig.CSHL_LID18545-001C-b1.LID18546-002C-b2.idrFilt0.1.bb K562 RnaSeq Contigs pooled bigBed CSHL analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/rna_elements/jan2011/LongRnaSeq/K562_Cytoplasm_Ap_Long_CSHL_Contig.CSHL_LID8465-001C-b1.LID8466-002C-b2.idrFilt0.1.bb K562 RnaSeq Contigs pooled bigBed CSHL analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/rna_elements/jan2011/LongRnaSeq/K562_Nucleolus_Total_Long_CSHL_Contig.CSHL_LID9187-025NL-b3.LID9188-026NL-b4.idrFilt0.1.bb K562 RnaSeq Contigs pooled bigBed CSHL analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/rna_elements/jan2011/LongRnaSeq/K562_Nucleoplasm_Total_Long_CSHL_Contig.CSHL_LID9189-025NP-b3.LID9190-026NP-b4.idrFilt0.1.bb K562 RnaSeq Contigs pooled bigBed CSHL analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/rna_elements/jan2011/LongRnaSeq/K562_Nucleus_Am_Long_CSHL_Contig.CSHL_LID9195-001N-b1.LID9196-002N-b2.idrFilt0.1.bb K562 RnaSeq Contigs pooled bigBed CSHL analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/rna_elements/jan2011/LongRnaSeq/K562_Nucleus_Ap_Long_CSHL_Contig.CSHL_LID8556-001N-b1.LID8557-002N-b2.idrFilt0.1.bb K562 RnaSeq Contigs pooled bigBed CSHL analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/rna_elements/jan2011/LongRnaSeq/K562_WholeCell_Am_Long_CSHL_Contig.CSHL_LID8659-001WC-b1.LID8660-002WC-b2.idrFilt0.1.bb K562 RnaSeq Contigs pooled bigBed CSHL analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/rna_elements/jan2011/LongRnaSeq/K562_WholeCell_Ap_Long_CSHL_Contig.CSHL_LID16627-001WC-b1.LID16628-002WC-b2.idrFilt0.1.bb K562 RnaSeq Contigs pooled bigBed CSHL analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/rna_elements/jan2011/LongRnaSeq/MCF-7_WholeCell_Am_Long_CSHL_Contig.CSHL_LID8824-015WC-b1.LID8825-016WC-b2.idrFilt0.1.bb MCF-7 RnaSeq Contigs pooled bigBed CSHL analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/rna_elements/jan2011/LongRnaSeq/MCF-7_WholeCell_Ap_Long_CSHL_Contig.CSHL_LID8686-015WC-b1.LID8687-016WC-b2.idrFilt0.1.bb MCF-7 RnaSeq Contigs pooled bigBed CSHL analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/rna_elements/jan2011/LongRnaSeq/NHEK_Cytoplasm_Ap_Long_CSHL_Contig.CSHL_LID8795-027C-b3.LID8796-028C-b4.idrFilt0.1.bb NHEK RnaSeq Contigs pooled bigBed CSHL analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/rna_elements/jan2011/LongRnaSeq/NHEK_Nucleus_Am_Long_CSHL_Contig.CSHL_LID9204-027N-b3.LID9205-028N-b4.idrFilt0.1.bb NHEK RnaSeq Contigs pooled bigBed CSHL analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/rna_elements/jan2011/LongRnaSeq/NHEK_Nucleus_Ap_Long_CSHL_Contig.CSHL_LID8797-027N-b3.LID8798-028N-b4.idrFilt0.1.bb NHEK RnaSeq Contigs pooled bigBed CSHL analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/rna_elements/jan2011/LongRnaSeq/NHEK_WholeCell_Am_Long_CSHL_Contig.CSHL_LID8665-007WC-b1.LID8666-008WC-b2.idrFilt0.1.bb NHEK RnaSeq Contigs pooled bigBed CSHL analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/rna_elements/jan2011/LongRnaSeq/NHEK_WholeCell_Ap_Long_CSHL_Contig.CSHL_LID16631-007WC-b1.LID16632-008WC-b2.idrFilt0.1.bb NHEK RnaSeq Contigs pooled bigBed CSHL analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/rna_elements/jan2011/LongRnaSeq/NHLF_WholeCell_Am_Long_CSHL_Contig.CSHL_LID8828-033WC-b1.LID8829-034WC-b2.idrFilt0.1.bb NHLF RnaSeq Contigs pooled bigBed CSHL analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/rna_elements/jan2011/LongRnaSeq/NHLF_WholeCell_Ap_Long_CSHL_Contig.CSHL_LID8692-033WC-b1.LID8701-034WC-b2.idrFilt0.1.bb NHLF RnaSeq Contigs pooled bigBed CSHL analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/rna_elements/jan2011/LongRnaSeq/SK-N-SH_RA_WholeCell_Am_Long_CSHL_Contig.CSHL_LID9003-019WC-b1.LID9011-020WC-b2.idrFilt0.1.bb SK-N-SH_RA RnaSeq Contigs pooled bigBed CSHL analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/rna_elements/jan2011/LongRnaSeq/SK-N-SH_RA_WholeCell_Ap_Long_CSHL_Contig.CSHL_LID8967-019WC-b1.LID8968-020WC-b2.idrFilt0.1.bb SK-N-SH_RA RnaSeq Contigs pooled bigBed CSHL analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/rna_elements/jan2011/ShortRnaSeq/A549-Stam_WholeCell_Short_RNA_CSHL_Contig.CSHL_LID20749-021WC-r1.LID20750-022WC-r2.idrFilt0.1.bb A549 RnaSeq Contigs pooled bigBed CSHL analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/rna_elements/jan2011/ShortRnaSeq/AGO4450-Stam_WholeCell_Short_RNA_CSHL_Contig.CSHL_LID20745-017WC-r1.LID20746-018WC-r2.idrFilt0.1.bb AG04450 RnaSeq Contigs pooled bigBed CSHL analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/rna_elements/jan2011/ShortRnaSeq/BJ_WholeCell_Short_RNA_CSHL_Contig.CSHL_LID20909-037WC-r1.LID20910-038WC-r2.idrFilt0.1.bb BJ RnaSeq Contigs pooled bigBed CSHL analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/rna_elements/jan2011/ShortRnaSeq/GM12878_Cytosol_Short_RNA_CSHL_Contig.CSHL_LID20901-003C-r1.LID20904-004C-r2.idrFilt0.1.bb GM12878 RnaSeq Contigs pooled bigBed CSHL analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/rna_elements/jan2011/ShortRnaSeq/GM12878_Nucleus_Short_RNA_CSHL_Contig.CSHL_LID20900-003N-r1.LID20903-004N-r2.idrFilt0.1.bb GM12878 RnaSeq Contigs pooled bigBed CSHL analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/rna_elements/jan2011/ShortRnaSeq/GM12878_WholeCell_Short_RNA_CSHL_Contig.CSHL_LID20899-003WC-r1.LID20902-004WC-r2.idrFilt0.1.bb GM12878 RnaSeq Contigs pooled bigBed CSHL analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/rna_elements/jan2011/ShortRnaSeq/H1ES_WholeCell_Short_RNA_CSHL_Contig.CSHL_LID20905-005WC-r1.LID20906-006WC-r2.idrFilt0.1.bb H1-hESC RnaSeq Contigs pooled bigBed CSHL analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/rna_elements/jan2011/ShortRnaSeq/HelaS3_Cytosol_Short_RNA_CSHL_Contig.CSHL_LID21145-011C-r1.LID21148-012C-r2.idrFilt0.1.bb HeLa-S3 RnaSeq Contigs pooled bigBed CSHL analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/rna_elements/jan2011/ShortRnaSeq/HelaS3_Nucleus_Short_RNA_CSHL_Contig.CSHL_LID21144-011N-r1.LID21147-012N-r2.idrFilt0.1.bb HeLa-S3 RnaSeq Contigs pooled bigBed CSHL analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/rna_elements/jan2011/ShortRnaSeq/HelaS3_WholeCell_Short_RNA_CSHL_Contig.CSHL_LID21143-011WC-r1.LID21146-012WC-r2.idrFilt0.1.bb HeLa-S3 RnaSeq Contigs pooled bigBed CSHL analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/rna_elements/jan2011/ShortRnaSeq/HUVEC_Cytosol_Short_RNA_CSHL_Contig.CSHL_LID21057-029C-r1.LID21059-030C-r2.idrFilt0.1.bb HUVEC RnaSeq Contigs pooled bigBed CSHL analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/rna_elements/jan2011/ShortRnaSeq/HUVEC_Nucleus_Short_RNA_CSHL_Contig.CSHL_LID21056-029N-r1.LID21058-030N-r2.idrFilt0.1.bb HUVEC RnaSeq Contigs pooled bigBed CSHL analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/rna_elements/jan2011/ShortRnaSeq/HUVEC_WholeCell_Short_RNA_CSHL_Contig.CSHL_LID21054-009WC-r1.LID21055-010WC-r2.idrFilt0.1.bb HUVEC RnaSeq Contigs pooled bigBed CSHL analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/rna_elements/jan2011/ShortRnaSeq/K562_Chromatin_Short_RNA_CSHL_Contig.CSHL_LID8930-025CH-r1.LID18560-026CH-r2.idrFilt0.1.bb K562 RnaSeq Contigs pooled bigBed CSHL analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/rna_elements/jan2011/ShortRnaSeq/K562_Cytosol_Short_RNA_CSHL_Contig.CSHL_LID10572-001C-r1.LID10571-002C-r2.idrFilt0.1.bb K562 RnaSeq Contigs pooled bigBed CSHL analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/rna_elements/jan2011/ShortRnaSeq/K562_Nucleoli_Short_RNA_CSHL_Contig.CSHL_LID8928-025NL-r1.LID18558-026NL-r2.idrFilt0.1.bb K562 RnaSeq Contigs pooled bigBed CSHL analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/rna_elements/jan2011/ShortRnaSeq/K562_Nucleoplasm_Short_RNA_CSHL_Contig.CSHL_LID8929-025NP-r1.LID18559-026NP-r2.idrFilt0.1.bb K562 RnaSeq Contigs pooled bigBed CSHL analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/rna_elements/jan2011/ShortRnaSeq/K562_Nucleus_Short_RNA_CSHL_Contig.CSHL_LID10570-001N-r1.LID10569-002N-r2.idrFilt0.1.bb K562 RnaSeq Contigs pooled bigBed CSHL analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/rna_elements/jan2011/ShortRnaSeq/K562_WholeCell_Short_RNA_CSHL_Contig.CSHL_LID10567-001WC-r1.LID10568-002WC-r2.idrFilt0.1.bb K562 RnaSeq Contigs pooled bigBed CSHL analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/rna_elements/jan2011/ShortRnaSeq/NHEK_Cytosol_Short_RNA_CSHL_Contig.CSHL_LID21002-027C-r1.LID21004-028C-r2.idrFilt0.1.bb NHEK RnaSeq Contigs pooled bigBed CSHL analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/rna_elements/jan2011/ShortRnaSeq/NHEK_Nucleus_Short_RNA_CSHL_Contig.CSHL_LID21001-027N-r1.LID21003-028N-r2.idrFilt0.1.bb NHEK RnaSeq Contigs pooled bigBed CSHL analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/rna_elements/jan2011/ShortRnaSeq/NHEK_WholeCell_Short_RNA_CSHL_Contig.CSHL_LID20999-007WC-r1.LID21000-008WC-r2.idrFilt0.1.bb NHEK RnaSeq Contigs pooled bigBed CSHL analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/rna_elements/jan2011/ShortRnaSeq/SK-N-SH-Stan_WholeCell_Short_RNA_CSHL_Contig.CSHL_LID20747-019WC-r1.LID20748-020WC-r2.idrFilt0.1.bb SK-N-SH_RA RnaSeq Contigs pooled bigBed CSHL analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/segmentations/jan2011/hub/gm12878.ChromHMM.bb GM12878 genomeSegmentation Segmentation bigBed analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/segmentations/jan2011/hub/h1hesc.ChromHMM.bb H1 genomeSegmentation Segmentation bigBed analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/segmentations/jan2011/hub/helas3.ChromHMM.bb HeLa-S3 genomeSegmentation Segmentation bigBed analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/segmentations/jan2011/hub/hepg2.ChromHMM.bb HepG2 genomeSegmentation Segmentation bigBed analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/segmentations/jan2011/hub/huvec.ChromHMM.bb HUVEC genomeSegmentation Segmentation bigBed analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/segmentations/jan2011/hub/k562.ChromHMM.bb K562 genomeSegmentation Segmentation bigBed analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/segmentations/jan2011/hub/segway_gm12878_relabel.bb GM12878 genomeSegmentation Segmentation bigBed analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/segmentations/jan2011/hub/segway_h1hesc_relabel.bb H1-hESC genomeSegmentation Segmentation bigBed analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/segmentations/jan2011/hub/segway_helas3_relabel.bb HeLa-S3 genomeSegmentation Segmentation bigBed analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/segmentations/jan2011/hub/segway_hepg2_relabel.bb HepG2 genomeSegmentation Segmentation bigBed analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/segmentations/jan2011/hub/segway_huvec_relabel.bb HUVEC genomeSegmentation Segmentation bigBed analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/segmentations/jan2011/hub/segway_k562_relabel.bb K562 genomeSegmentation Segmentation bigBed analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/segmentations/jan2011/hub/gm12878.combined.bb GM12878 genomeSegmentation Segmentation bigBed analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/segmentations/jan2011/hub/h1hesc.combined.bb H1-hESC genomeSegmentation Segmentation bigBed analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/segmentations/jan2011/hub/helas3.combined.bb HeLa-S3 genomeSegmentation Segmentation bigBed analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/segmentations/jan2011/hub/hepg2.combined.bb HepG2 genomeSegmentation Segmentation bigBed analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/segmentations/jan2011/hub/huvec.combined.bb HUVEC genomeSegmentation Segmentation bigBed analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/segmentations/jan2011/hub/k562.combined.bb K562 genomeSegmentation Segmentation bigBed analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeBroadHistoneGm12878ControlStdAln_2Reps.norm5.rawsignal.bw GM12878 ChipSeq Control Signal bigWig Broad analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeBroadHistoneGm12878CtcfStdAln_2Reps.norm5.rawsignal.bw GM12878 ChipSeq CTCF Signal bigWig Broad analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeBroadHistoneGm12878H2azStdAln_2Reps.norm5.rawsignal.bw GM12878 ChipSeq H2A.Z Signal bigWig Broad analysis 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http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeBroadHistoneH1hescH3k4me2StdAln_2Reps.norm5.rawsignal.bw H1-hESC ChipSeq H3K4me2 Signal bigWig Broad analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeBroadHistoneH1hescH3k4me3StdAln_2Reps.norm5.rawsignal.bw H1-hESC ChipSeq H3K4me3 Signal bigWig Broad analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeBroadHistoneH1hescH3k9acStdAln_2Reps.norm5.rawsignal.bw H1-hESC ChipSeq H3K9ac Signal bigWig Broad analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeBroadHistoneH1hescH4k20me1StdAln_2Reps.norm5.rawsignal.bw H1-hESC ChipSeq H4K20me1 Signal bigWig Broad analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeBroadHistoneHelas3ControlStdAln_2Reps.norm5.rawsignal.bw HeLa-S3 ChipSeq Control Signal bigWig Broad analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeBroadHistoneHelas3CtcfStdAln_2Reps.norm5.rawsignal.bw HeLa-S3 ChipSeq CTCF Signal bigWig Broad analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeBroadHistoneHelas3H3k27acStdAln_2Reps.norm5.rawsignal.bw HeLa-S3 ChipSeq H3K27ac Signal bigWig Broad analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeBroadHistoneHelas3H3k27me3StdAln_2Reps.norm5.rawsignal.bw HeLa-S3 ChipSeq H3K27me3 Signal bigWig Broad analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeBroadHistoneHelas3H3k36me3StdAln_2Reps.norm5.rawsignal.bw HeLa-S3 ChipSeq H3K36me3 Signal bigWig Broad analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeBroadHistoneHelas3H3k4me1Std_1Reps.norm5.rawsignal.bw bw analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeBroadHistoneHelas3H3k4me2StdAln_2Reps.norm5.rawsignal.bw HeLa-S3 ChipSeq H3K4me2 Signal bigWig Broad analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeBroadHistoneHelas3H3k4me3StdAln_2Reps.norm5.rawsignal.bw HeLa-S3 ChipSeq H3K4me3 Signal bigWig Broad analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeBroadHistoneHelas3H3k79me2StdAln_2Reps.norm5.rawsignal.bw HeLa-S3 ChipSeq H3K79me2 Signal bigWig Broad analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeBroadHistoneHelas3H3k9acStdAln_2Reps.norm5.rawsignal.bw HeLa-S3 ChipSeq H3K9ac Signal bigWig Broad analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeBroadHistoneHelas3H4k20me1StdAln_2Reps.norm5.rawsignal.bw HeLa-S3 ChipSeq H4K20me1 Signal bigWig Broad analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeBroadHistoneHelas3Pol2bStdAln_2Reps.norm5.rawsignal.bw HeLa-S3 ChipSeq Pol2(b) Signal bigWig Broad analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeBroadHistoneHepg2ControlStdAln_2Reps.norm5.rawsignal.bw HepG2 ChipSeq Control Signal bigWig Broad analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeBroadHistoneHepg2CtcfStdAln_2Reps.norm5.rawsignal.bw HepG2 ChipSeq CTCF Signal bigWig Broad analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeBroadHistoneHepg2H2azStdAln_2Reps.norm5.rawsignal.bw HepG2 ChipSeq H2A.Z Signal bigWig Broad analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeBroadHistoneHepg2H3k27acStdAln_2Reps.norm5.rawsignal.bw HepG2 ChipSeq H3K27ac Signal bigWig Broad analysis 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http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeBroadHistoneHepg2H3k4me3StdAln_2Reps.norm5.rawsignal.bw HepG2 ChipSeq H3K4me3 Signal bigWig Broad analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeBroadHistoneHepg2H3k79me2StdAln_2Reps.norm5.rawsignal.bw HepG2 ChipSeq H3K79me2 Signal bigWig Broad analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeBroadHistoneHepg2H3k9acStdAln_2Reps.norm5.rawsignal.bw HepG2 ChipSeq H3K9ac Signal bigWig Broad analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeBroadHistoneHepg2H4k20me1StdAln_2Reps.norm5.rawsignal.bw HepG2 ChipSeq H4K20me1 Signal bigWig Broad analysis 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http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeBroadHistoneNhekH3k36me3StdAln_3Reps.norm5.rawsignal.bw NHEK ChipSeq H3K36me3 Signal bigWig Broad analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeBroadHistoneNhekH3k4me1StdAln_3Reps.norm5.rawsignal.bw NHEK ChipSeq H3K4me1 Signal bigWig Broad analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeBroadHistoneNhekH3k4me2StdAln_3Reps.norm5.rawsignal.bw NHEK ChipSeq H3K4me2 Signal bigWig Broad analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeBroadHistoneNhekH3k4me3StdAln_3Reps.norm5.rawsignal.bw NHEK ChipSeq H3K4me3 Signal bigWig Broad analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeBroadHistoneNhekH3k9acStdAln_3Reps.norm5.rawsignal.bw NHEK ChipSeq H3K9ac Signal bigWig Broad analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeBroadHistoneNhekH3k9me1StdAln_3Reps.norm5.rawsignal.bw NHEK ChipSeq H3K9me1 Signal bigWig Broad analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeBroadHistoneNhekH4k20me1StdAln_3Reps.norm5.rawsignal.bw NHEK ChipSeq H4K20me1 Signal bigWig Broad analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeBroadHistoneNhekPol2bStdAln_2Reps.norm5.rawsignal.bw NHEK ChipSeq Pol2(b) Signal bigWig Broad analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeBroadHistoneNhlfControlStdAln_2Reps.norm5.rawsignal.bw NHLF ChipSeq Control Signal bigWig Broad analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeBroadHistoneNhlfCtcfStdAln_2Reps.norm5.rawsignal.bw NHLF ChipSeq CTCF Signal bigWig Broad analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeBroadHistoneNhlfH3k27acStdAln_2Reps.norm5.rawsignal.bw NHLF ChipSeq H3K27ac Signal bigWig Broad analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeBroadHistoneNhlfH3k27me3StdAln_2Reps.norm5.rawsignal.bw NHLF ChipSeq H3K27me3 Signal bigWig Broad analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeBroadHistoneNhlfH3k36me3StdAln_2Reps.norm5.rawsignal.bw NHLF ChipSeq H3K36me3 Signal bigWig Broad analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeBroadHistoneNhlfH3k4me1StdAln_2Reps.norm5.rawsignal.bw NHLF ChipSeq H3K4me1 Signal bigWig Broad analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeBroadHistoneNhlfH3k4me2StdAln_2Reps.norm5.rawsignal.bw NHLF ChipSeq H3K4me2 Signal bigWig Broad analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeBroadHistoneNhlfH3k4me3StdAln_2Reps.norm5.rawsignal.bw NHLF ChipSeq H3K4me3 Signal bigWig Broad analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeBroadHistoneNhlfH3k9acStdAln_2Reps.norm5.rawsignal.bw NHLF ChipSeq H3K9ac Signal bigWig Broad analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeBroadHistoneNhlfH4k20me1StdAln_2Reps.norm5.rawsignal.bw NHLF ChipSeq H4K20me1 Signal bigWig Broad analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeBroadHistoneOsteoblControlStdAln_2Reps.norm5.rawsignal.bw Osteobl ChipSeq Control Signal bigWig Broad analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeBroadHistoneOsteoblCtcfStdAln_2Reps.norm5.rawsignal.bw Osteobl ChipSeq CTCF Signal bigWig Broad analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeBroadHistoneOsteoblH2azStdAln_2Reps.norm5.rawsignal.bw Osteobl ChipSeq H2A.Z Signal bigWig Broad analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeBroadHistoneOsteoblH3k27acStdAln_2Reps.norm5.rawsignal.bw Osteobl ChipSeq H3K27ac Signal bigWig Broad analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeBroadHistoneOsteoblH3k36me3StdAln_2Reps.norm5.rawsignal.bw Osteobl ChipSeq H3K36me3 Signal bigWig Broad analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeBroadHistoneOsteoblH3k4me1StdAln_2Reps.norm5.rawsignal.bw Osteobl ChipSeq H3K4me1 Signal bigWig Broad analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeBroadHistoneOsteoblH3k4me2StdAln_2Reps.norm5.rawsignal.bw Osteobl ChipSeq H3K4me2 Signal bigWig Broad analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeBroadHistoneOsteoblH3k9me3StdAln_2Reps.norm5.rawsignal.bw Osteobl ChipSeq H3K9me3 Signal bigWig Broad analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeHaibTfbsA549ControlPcr1xDexaAln_2Reps.norm5.rawsignal.bw A549 ChipSeq Control Signal bigWig HudsonAlpha analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeHaibTfbsA549ControlPcr1xEtoh02Aln_2Reps.norm5.rawsignal.bw A549 ChipSeq Control Signal bigWig HudsonAlpha analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeHaibTfbsA549ControlPcr2xDexaAln_2Reps.norm5.rawsignal.bw A549 ChipSeq Control Signal bigWig HudsonAlpha analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeHaibTfbsA549CtcfPcr1xDexaAln_2Reps.norm5.rawsignal.bw A549 ChipSeq CTCF Signal bigWig HudsonAlpha analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeHaibTfbsA549CtcfPcr1xEtoh02Aln_2Reps.norm5.rawsignal.bw A549 ChipSeq CTCF Signal bigWig HudsonAlpha analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeHaibTfbsA549GrPcr1xDexbAln_2Reps.norm5.rawsignal.bw A549 ChipSeq GR Signal bigWig HudsonAlpha analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeHaibTfbsA549GrPcr1xDexcAln_2Reps.norm5.rawsignal.bw A549 ChipSeq GR Signal bigWig HudsonAlpha analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeHaibTfbsA549GrPcr1xDexdAln_2Reps.norm5.rawsignal.bw A549 ChipSeq GR Signal bigWig HudsonAlpha analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeHaibTfbsA549GrPcr1xEtoh02Aln_2Reps.norm5.rawsignal.bw A549 ChipSeq GR Signal bigWig HudsonAlpha analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeHaibTfbsA549GrPcr2xDexaAln_2Reps.norm5.rawsignal.bw A549 ChipSeq GR Signal bigWig HudsonAlpha analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeHaibTfbsA549GrPcr2xEtoh02Aln_2Reps.norm5.rawsignal.bw A549 ChipSeq GR Signal bigWig HudsonAlpha analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeHaibTfbsA549Pol2Pcr2xDexaAln_2Reps.norm5.rawsignal.bw A549 ChipSeq Pol2 Signal bigWig HudsonAlpha analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeHaibTfbsA549Pol2Pcr2xEtoh02Aln_2Reps.norm5.rawsignal.bw A549 ChipSeq Pol2 Signal bigWig HudsonAlpha analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeHaibTfbsA549Usf1Pcr1xDexaAln_2Reps.norm5.rawsignal.bw A549 ChipSeq USF-1 Signal bigWig HudsonAlpha analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeHaibTfbsA549Usf1Pcr1xEtoh02Aln_2Reps.norm5.rawsignal.bw A549 ChipSeq USF-1 Signal bigWig HudsonAlpha analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeHaibTfbsEcc1ControlV0416102Dmso2Aln_2Reps.norm5.rawsignal.bw ECC-1 ChipSeq Control Signal bigWig HudsonAlpha analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeHaibTfbsEcc1EralphaaV0416102Dmso2Aln_2Reps.norm5.rawsignal.bw ECC-1 ChipSeq ERalpha_a Signal bigWig HudsonAlpha analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeHaibTfbsEcc1EralphaaV0416102Estradia1hAln_2Reps.norm5.rawsignal.bw ECC-1 ChipSeq ERalpha_a Signal bigWig HudsonAlpha analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeHaibTfbsEcc1EralphaaV0416102Gen1hAln_2Reps.norm5.rawsignal.bw ECC-1 ChipSeq ERalpha_a Signal bigWig HudsonAlpha analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeHaibTfbsEcc1Foxa1c20V0416102Dmso2Aln_2Reps.norm5.rawsignal.bw ECC-1 ChipSeq FOXA1_(C-20) Signal bigWig HudsonAlpha analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeHaibTfbsEcc1GrV0416102DexaAln_2Reps.norm5.rawsignal.bw ECC-1 ChipSeq GR Signal bigWig HudsonAlpha analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeHaibTfbsEcc1GrV0416102Etoh02Aln_2Reps.norm5.rawsignal.bw ECC-1 ChipSeq GR Signal bigWig HudsonAlpha analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeHaibTfbsEcc1Pol2V0416102Dmso2Aln_2Reps.norm5.rawsignal.bw ECC-1 ChipSeq Pol2 Signal bigWig HudsonAlpha analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeHaibTfbsGm12878Atf3Pcr1xAln_2Reps.norm5.rawsignal.bw GM12878 ChipSeq ATF3 Signal bigWig HudsonAlpha analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeHaibTfbsGm12878BatfPcr1xAln_2Reps.norm5.rawsignal.bw GM12878 ChipSeq BATF Signal bigWig HudsonAlpha analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeHaibTfbsGm12878Bcl11aPcr1xAln_2Reps.norm5.rawsignal.bw GM12878 ChipSeq BCL11A Signal bigWig HudsonAlpha analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeHaibTfbsGm12878Bcl3Pcr1xAln_2Reps.norm5.rawsignal.bw GM12878 ChipSeq BCL3 Signal bigWig HudsonAlpha analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeHaibTfbsGm12878Bclaf1m33V0416101Aln_2Reps.norm5.rawsignal.bw GM12878 ChipSeq BCLAF1_(M33-P5B11) Signal bigWig HudsonAlpha analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeHaibTfbsGm12878ControlPcr1xAln_6Reps.norm5.rawsignal.bw GM12878 ChipSeq Control Signal bigWig HudsonAlpha analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeHaibTfbsGm12878ControlPcr2xAln_3Reps.norm5.rawsignal.bw GM12878 ChipSeq Control Signal bigWig HudsonAlpha analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeHaibTfbsGm12878Ebf1c8Pcr1xAln_2Reps.norm5.rawsignal.bw GM12878 ChipSeq EBF1_(C-8) Signal bigWig HudsonAlpha analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeHaibTfbsGm12878EbfPcr1xAln_2Reps.norm5.rawsignal.bw GM12878 ChipSeq EBF Signal bigWig HudsonAlpha analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeHaibTfbsGm12878Egr1Pcr2xAln_2Reps.norm5.rawsignal.bw GM12878 ChipSeq Egr-1 Signal bigWig HudsonAlpha analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeHaibTfbsGm12878Egr1V0416101Aln_2Reps.norm5.rawsignal.bw GM12878 ChipSeq Egr-1 Signal bigWig HudsonAlpha analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeHaibTfbsGm12878Elf1sc631V0416101Aln_2Reps.norm5.rawsignal.bw GM12878 ChipSeq ELF1_(SC-631) Signal bigWig HudsonAlpha analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeHaibTfbsGm12878Ets1Pcr1xAln_2Reps.norm5.rawsignal.bw GM12878 ChipSeq ETS1 Signal bigWig HudsonAlpha analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeHaibTfbsGm12878GabpPcr2xAln_2Reps.norm5.rawsignal.bw GM12878 ChipSeq GABP Signal bigWig HudsonAlpha analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeHaibTfbsGm12878Irf4m17Pcr1xAln_2Reps.norm5.rawsignal.bw GM12878 ChipSeq IRF4_(M-17) Signal bigWig HudsonAlpha analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeHaibTfbsGm12878Irf4Pcr1xAln_2Reps.norm5.rawsignal.bw GM12878 ChipSeq IRF4 Signal bigWig HudsonAlpha analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeHaibTfbsGm12878Mef2aPcr1xAln_2Reps.norm5.rawsignal.bw GM12878 ChipSeq MEF2A Signal bigWig HudsonAlpha analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeHaibTfbsGm12878Mef2csc13268Pcr1xAln_2Reps.norm5.rawsignal.bw GM12878 ChipSeq MEF2C_(SC-13268) Signal bigWig HudsonAlpha analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeHaibTfbsGm12878NrsfPcr2xAln_2Reps.norm5.rawsignal.bw GM12878 ChipSeq NRSF Signal bigWig HudsonAlpha analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeHaibTfbsGm12878Oct2Pcr1xAln_2Reps.norm5.rawsignal.bw GM12878 ChipSeq Oct-2 Signal bigWig HudsonAlpha analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeHaibTfbsGm12878P300Pcr1xAln_2Reps.norm5.rawsignal.bw GM12878 ChipSeq p300 Signal bigWig HudsonAlpha analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeHaibTfbsGm12878Pax5c20Pcr1xAln_2Reps.norm5.rawsignal.bw GM12878 ChipSeq PAX5-C20 Signal bigWig HudsonAlpha analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeHaibTfbsGm12878Pax5n19Pcr1xAln_2Reps.norm5.rawsignal.bw GM12878 ChipSeq PAX5-N19 Signal bigWig HudsonAlpha analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeHaibTfbsGm12878Pbx3Pcr1xAln_2Reps.norm5.rawsignal.bw GM12878 ChipSeq Pbx3 Signal bigWig HudsonAlpha analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeHaibTfbsGm12878Pol24h8Pcr1xAln_2Reps.norm5.rawsignal.bw GM12878 ChipSeq Pol2-4H8 Signal bigWig HudsonAlpha analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeHaibTfbsGm12878Pol2Pcr2xAln_2Reps.norm5.rawsignal.bw GM12878 ChipSeq Pol2 Signal bigWig HudsonAlpha analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeHaibTfbsGm12878Pou2f2Pcr1xAln_2Reps.norm5.rawsignal.bw GM12878 ChipSeq POU2F2 Signal bigWig HudsonAlpha analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeHaibTfbsGm12878Pu1Pcr1xAln_2Reps.norm5.rawsignal.bw GM12878 ChipSeq PU.1 Signal bigWig HudsonAlpha analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeHaibTfbsGm12878Rad21V0416101Aln_2Reps.norm5.rawsignal.bw GM12878 ChipSeq Rad21 Signal bigWig HudsonAlpha analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeHaibTfbsGm12878RxraPcr1xAln_2Reps.norm5.rawsignal.bw GM12878 ChipSeq RXRA Signal bigWig HudsonAlpha analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeHaibTfbsGm12878Sin3ak20Pcr1xAln_3Reps.norm5.rawsignal.bw GM12878 ChipSeq Sin3Ak-20 Signal bigWig HudsonAlpha analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeHaibTfbsGm12878Six5Pcr1xAln_2Reps.norm5.rawsignal.bw GM12878 ChipSeq SIX5 Signal bigWig HudsonAlpha analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeHaibTfbsGm12878Sp1Pcr1xAln_2Reps.norm5.rawsignal.bw GM12878 ChipSeq SP1 Signal bigWig HudsonAlpha analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeHaibTfbsGm12878SrfPcr2xAln_2Reps.norm5.rawsignal.bw GM12878 ChipSeq SRF Signal bigWig HudsonAlpha analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeHaibTfbsGm12878SrfV0416101Aln_2Reps.norm5.rawsignal.bw GM12878 ChipSeq SRF Signal bigWig HudsonAlpha analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeHaibTfbsGm12878Taf1Pcr1xAln_2Reps.norm5.rawsignal.bw GM12878 ChipSeq TAF1 Signal bigWig HudsonAlpha analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeHaibTfbsGm12878Tcf12Pcr1xAln_2Reps.norm5.rawsignal.bw GM12878 ChipSeq TCF12 Signal bigWig HudsonAlpha analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeHaibTfbsGm12878Usf1Pcr2xAln_2Reps.norm5.rawsignal.bw GM12878 ChipSeq USF-1 Signal bigWig HudsonAlpha analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeHaibTfbsGm12878Yy1V0416101Aln_2Reps.norm5.rawsignal.bw GM12878 ChipSeq YY1_(SC-281) Signal 1 bigWig HudsonAlpha analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeHaibTfbsGm12878Zbtb33Pcr1xAln_2Reps.norm5.rawsignal.bw GM12878 ChipSeq ZBTB33 Signal bigWig HudsonAlpha analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeHaibTfbsGm12878Zeb1sc25388V0416102Aln_2Reps.norm5.rawsignal.bw GM12878 ChipSeq ZEB1_(SC-25388) Signal bigWig HudsonAlpha analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeHaibTfbsGm12891ControlPcr1xAln_2Reps.norm5.rawsignal.bw GM12891 ChipSeq Control Signal bigWig HudsonAlpha analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeHaibTfbsGm12891Oct2Pcr1xAln_2Reps.norm5.rawsignal.bw GM12891 ChipSeq Oct-2 Signal bigWig HudsonAlpha analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeHaibTfbsGm12891Pax5c20Pcr1xAln_2Reps.norm5.rawsignal.bw GM12891 ChipSeq PAX5-C20 Signal bigWig HudsonAlpha analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeHaibTfbsGm12891Pol24h8Pcr1xAln_2Reps.norm5.rawsignal.bw GM12891 ChipSeq Pol2-4H8 Signal bigWig HudsonAlpha analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeHaibTfbsGm12891Pol2Pcr1xAln_2Reps.norm5.rawsignal.bw GM12891 ChipSeq Pol2 Signal bigWig HudsonAlpha analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeHaibTfbsGm12891Pou2f2Pcr1xAln_2Reps.norm5.rawsignal.bw GM12891 ChipSeq POU2F2 Signal bigWig HudsonAlpha analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeHaibTfbsGm12891Pu1Pcr1xAln_2Reps.norm5.rawsignal.bw GM12891 ChipSeq PU.1 Signal bigWig HudsonAlpha analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeHaibTfbsGm12891Taf1Pcr1xAln_2Reps.norm5.rawsignal.bw GM12891 ChipSeq TAF1 Signal bigWig HudsonAlpha analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeHaibTfbsGm12891Yy1c20V0416101Aln_2Reps.norm5.rawsignal.bw GM12891 ChipSeq YY1_(C-20) Signal bigWig HudsonAlpha analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeHaibTfbsGm12892ControlPcr1xAln_4Reps.norm5.rawsignal.bw GM12892 ChipSeq Control Signal bigWig HudsonAlpha analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeHaibTfbsGm12892Pax5c20Pcr1xAln_2Reps.norm5.rawsignal.bw GM12892 ChipSeq PAX5-C20 Signal bigWig HudsonAlpha analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeHaibTfbsGm12892Pol24h8Pcr1xAln_2Reps.norm5.rawsignal.bw GM12892 ChipSeq Pol2-4H8 Signal bigWig HudsonAlpha analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeHaibTfbsGm12892Pol24h8V0416102Aln_2Reps.norm5.rawsignal.bw GM12892 ChipSeq Pol2-4H8 Signal bigWig HudsonAlpha analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeHaibTfbsGm12892Pol2Pcr1xAln_2Reps.norm5.rawsignal.bw GM12892 ChipSeq Pol2 Signal bigWig HudsonAlpha analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeHaibTfbsGm12892Pol2V0416102Aln_2Reps.norm5.rawsignal.bw GM12892 ChipSeq Pol2 Signal bigWig HudsonAlpha analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeHaibTfbsGm12892Taf1Pcr1xAln_2Reps.norm5.rawsignal.bw GM12892 ChipSeq TAF1 Signal bigWig HudsonAlpha analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeHaibTfbsGm12892Taf1V0416102Aln_2Reps.norm5.rawsignal.bw GM12892 ChipSeq TAF1 Signal bigWig HudsonAlpha analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeHaibTfbsGm12892Yy1V0416101Aln_2Reps.norm5.rawsignal.bw GM12892 ChipSeq YY1 Signal bigWig HudsonAlpha analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeHaibTfbsH1hescAtf3Pcr1xAln_2Reps.norm5.rawsignal.bw H1-hESC ChipSeq ATF3 Signal bigWig HudsonAlpha analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeHaibTfbsH1hescBcl11aPcr1xAln_3Reps.norm5.rawsignal.bw H1-hESC ChipSeq BCL11A Signal bigWig HudsonAlpha analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeHaibTfbsH1hescBcl3Pcr1xAln_2Reps.norm5.rawsignal.bw H1-hESC ChipSeq BCL3 Signal bigWig HudsonAlpha analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeHaibTfbsH1hescControlPcr1xAln_2Reps.norm5.rawsignal.bw H1-hESC ChipSeq Control Signal bigWig HudsonAlpha analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeHaibTfbsH1hescCtcfsc5916V0416102Aln_2Reps.norm5.rawsignal.bw H1-hESC ChipSeq CTCF_(SC-5916) Signal bigWig HudsonAlpha analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeHaibTfbsH1hescEgr1V0416101Aln_2Reps.norm5.rawsignal.bw H1-hESC ChipSeq Egr-1 Signal bigWig HudsonAlpha analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeHaibTfbsH1hescEgr1V0416102Aln_2Reps.norm5.rawsignal.bw H1-hESC ChipSeq Egr-1 Signal bigWig HudsonAlpha analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeHaibTfbsH1hescGabpPcr1xAln_2Reps.norm5.rawsignal.bw H1-hESC ChipSeq GABP Signal bigWig HudsonAlpha analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeHaibTfbsH1hescHdac2sc6296V0416102Aln_2Reps.norm5.rawsignal.bw H1-hESC ChipSeq HDAC2_(SC-6296) Signal bigWig HudsonAlpha analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeHaibTfbsH1hescJundV0416102Aln_2Reps.norm5.rawsignal.bw H1-hESC ChipSeq JunD Signal bigWig HudsonAlpha analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeHaibTfbsH1hescNanogsc33759V0416102Aln_2Reps.norm5.rawsignal.bw H1-hESC ChipSeq NANOG_(SC-33759) Signal bigWig HudsonAlpha analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeHaibTfbsH1hescNrsfPcr1xAln_2Reps.norm5.rawsignal.bw H1-hESC ChipSeq NRSF Signal bigWig HudsonAlpha analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeHaibTfbsH1hescNrsfV0416102Aln_2Reps.norm5.rawsignal.bw H1-hESC ChipSeq NRSF Signal bigWig HudsonAlpha analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeHaibTfbsH1hescP300Pcr1xAln_2Reps.norm5.rawsignal.bw H1-hESC ChipSeq p300 Signal bigWig HudsonAlpha analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeHaibTfbsH1hescPol24h8Pcr1xAln_2Reps.norm5.rawsignal.bw H1-hESC ChipSeq Pol2-4H8 Signal bigWig HudsonAlpha analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeHaibTfbsH1hescPol24h8V0416102Aln_2Reps.norm5.rawsignal.bw H1-hESC ChipSeq Pol2-4H8 Signal bigWig HudsonAlpha analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeHaibTfbsH1hescPol2Pcr1xAln_2Reps.norm5.rawsignal.bw H1-hESC ChipSeq Pol2 Signal bigWig HudsonAlpha analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeHaibTfbsH1hescPol2V0416102Aln_2Reps.norm5.rawsignal.bw H1-hESC ChipSeq Pol2 Signal bigWig HudsonAlpha analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeHaibTfbsH1hescPou5f1sc9081V0416102Aln_2Reps.norm5.rawsignal.bw H1-hESC ChipSeq POU5F1_(SC-9081) Signal bigWig HudsonAlpha analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeHaibTfbsH1hescRad21V0416102Aln_2Reps.norm5.rawsignal.bw H1-hESC ChipSeq Rad21 Signal bigWig HudsonAlpha analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeHaibTfbsH1hescRxraV0416102Aln_2Reps.norm5.rawsignal.bw H1-hESC ChipSeq RXRA Signal bigWig HudsonAlpha analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeHaibTfbsH1hescSin3ak20Pcr1xAln_2Reps.norm5.rawsignal.bw H1-hESC ChipSeq Sin3Ak-20 Signal bigWig HudsonAlpha analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeHaibTfbsH1hescSix5Pcr1xAln_2Reps.norm5.rawsignal.bw H1-hESC ChipSeq SIX5 Signal bigWig HudsonAlpha analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeHaibTfbsH1hescSp1Pcr1xAln_2Reps.norm5.rawsignal.bw H1-hESC ChipSeq SP1 Signal bigWig HudsonAlpha analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeHaibTfbsH1hescSrfPcr1xAln_2Reps.norm5.rawsignal.bw H1-hESC ChipSeq SRF Signal bigWig HudsonAlpha analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeHaibTfbsH1hescTaf1Pcr1xAln_2Reps.norm5.rawsignal.bw H1-hESC ChipSeq TAF1 Signal bigWig HudsonAlpha analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeHaibTfbsH1hescTaf1V0416102Aln_2Reps.norm5.rawsignal.bw H1-hESC ChipSeq TAF1 Signal bigWig HudsonAlpha analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeHaibTfbsH1hescTaf7sq8V0416102Aln_2Reps.norm5.rawsignal.bw H1-hESC ChipSeq TAF7_(SQ-8) Signal bigWig HudsonAlpha analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeHaibTfbsH1hescTcf12Pcr1xAln_2Reps.norm5.rawsignal.bw H1-hESC ChipSeq TCF12 Signal bigWig HudsonAlpha analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeHaibTfbsH1hescUsf1Pcr1xAln_2Reps.norm5.rawsignal.bw H1-hESC ChipSeq USF-1 Signal bigWig HudsonAlpha analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeHaibTfbsH1hescYy1c20Pcr1xAln_2Reps.norm5.rawsignal.bw H1-hESC ChipSeq YY1_(C-20) Signal bigWig HudsonAlpha analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeHaibTfbsHct116ControlV0416101Aln_1Reps.norm5.rawsignal.bw HCT-116 ChipSeq Control Signal bigWig HudsonAlpha analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeHaibTfbsHct116Pol24h8V0416101Aln_2Reps.norm5.rawsignal.bw HCT-116 ChipSeq Pol2-4H8 Signal bigWig HudsonAlpha analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeHaibTfbsHelas3ControlPcr1xAln_2Reps.norm5.rawsignal.bw HeLa-S3 ChipSeq Control Signal bigWig HudsonAlpha analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeHaibTfbsHelas3GabpPcr1xAln_2Reps.norm5.rawsignal.bw HeLa-S3 ChipSeq GABP Signal bigWig HudsonAlpha analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeHaibTfbsHelas3NrsfPcr1xAln_2Reps.norm5.rawsignal.bw HeLa-S3 ChipSeq NRSF Signal bigWig HudsonAlpha analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeHaibTfbsHelas3Pol2Pcr1xAln_2Reps.norm5.rawsignal.bw HeLa-S3 ChipSeq Pol2 Signal bigWig HudsonAlpha analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeHaibTfbsHelas3Taf1Pcr1xAln_2Reps.norm5.rawsignal.bw HeLa-S3 ChipSeq TAF1 Signal bigWig HudsonAlpha analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeHaibTfbsHepg2Atf3Pcr1xAln_2Reps.norm5.rawsignal.bw HepG2 ChipSeq ATF3 Signal bigWig HudsonAlpha analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeHaibTfbsHepg2Bhlhe40V0416101Aln_3Reps.norm5.rawsignal.bw HepG2 ChipSeq BHLHE40 Signal bigWig HudsonAlpha analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeHaibTfbsHepg2ControlPcr1xAln_6Reps.norm5.rawsignal.bw HepG2 ChipSeq Control Signal bigWig HudsonAlpha analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeHaibTfbsHepg2ControlPcr2xAln_2Reps.norm5.rawsignal.bw HepG2 ChipSeq Control Signal bigWig HudsonAlpha analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeHaibTfbsHepg2CtcfV0416101Aln_2Reps.norm5.rawsignal.bw HepG2 ChipSeq CTCF Signal bigWig HudsonAlpha analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeHaibTfbsHepg2Elf1sc631V0416101Aln_2Reps.norm5.rawsignal.bw HepG2 ChipSeq ELF1_(SC-631) Signal bigWig HudsonAlpha analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeHaibTfbsHepg2Fosl2Pcr1xAln_2Reps.norm5.rawsignal.bw HepG2 ChipSeq FOSL2 Signal bigWig HudsonAlpha analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeHaibTfbsHepg2Foxa1c20Pcr1xAln_2Reps.norm5.rawsignal.bw HepG2 ChipSeq FOXA1_(C-20) Signal bigWig HudsonAlpha analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeHaibTfbsHepg2Foxa1sc101058Pcr1xAln_2Reps.norm5.rawsignal.bw HepG2 ChipSeq FOXA1_(SC-101058) Signal bigWig HudsonAlpha analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeHaibTfbsHepg2Foxa2sc6554V0416101Aln_2Reps.norm5.rawsignal.bw HepG2 ChipSeq FOXA2_(SC-6554) Signal bigWig HudsonAlpha analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeHaibTfbsHepg2GabpPcr2xAln_2Reps.norm5.rawsignal.bw HepG2 ChipSeq GABP Signal bigWig HudsonAlpha analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeHaibTfbsHepg2Hdac2sc6296V0416101Aln_2Reps.norm5.rawsignal.bw HepG2 ChipSeq HDAC2_(SC-6296) Signal bigWig HudsonAlpha analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeHaibTfbsHepg2Hey1V0416101Aln_2Reps.norm5.rawsignal.bw HepG2 ChipSeq HEY1 Signal bigWig HudsonAlpha analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeHaibTfbsHepg2Hnf4ah171Pcr1xAln_2Reps.norm5.rawsignal.bw HepG2 ChipSeq HNF4A_(H-171) Signal bigWig HudsonAlpha analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeHaibTfbsHepg2Hnf4gsc6558V0416101Aln_2Reps.norm5.rawsignal.bw HepG2 ChipSeq HNF4G_(SC-6558) Signal bigWig HudsonAlpha analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeHaibTfbsHepg2JundPcr1xAln_2Reps.norm5.rawsignal.bw HepG2 ChipSeq JunD Signal bigWig HudsonAlpha analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeHaibTfbsHepg2NrsfPcr2xAln_2Reps.norm5.rawsignal.bw HepG2 ChipSeq NRSF Signal bigWig HudsonAlpha analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeHaibTfbsHepg2P300Pcr1xAln_2Reps.norm5.rawsignal.bw HepG2 ChipSeq p300 Signal bigWig HudsonAlpha analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeHaibTfbsHepg2P300V0416101Aln_2Reps.norm5.rawsignal.bw HepG2 ChipSeq p300 Signal bigWig HudsonAlpha analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeHaibTfbsHepg2Pol2Pcr2xAln_2Reps.norm5.rawsignal.bw HepG2 ChipSeq Pol2 Signal bigWig HudsonAlpha analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeHaibTfbsHepg2Rad21V0416101Aln_2Reps.norm5.rawsignal.bw HepG2 ChipSeq Rad21 Signal bigWig HudsonAlpha analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeHaibTfbsHepg2RxraPcr1xAln_2Reps.norm5.rawsignal.bw HepG2 ChipSeq RXRA Signal bigWig HudsonAlpha analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeHaibTfbsHepg2Sin3ak20Pcr1xAln_2Reps.norm5.rawsignal.bw HepG2 ChipSeq Sin3Ak-20 Signal bigWig HudsonAlpha analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeHaibTfbsHepg2Sp1Pcr1xAln_2Reps.norm5.rawsignal.bw HepG2 ChipSeq SP1 Signal bigWig HudsonAlpha analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeHaibTfbsHepg2SrfV0416101Aln_2Reps.norm5.rawsignal.bw HepG2 ChipSeq SRF Signal bigWig HudsonAlpha analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeHaibTfbsHepg2Taf1Pcr2xAln_2Reps.norm5.rawsignal.bw HepG2 ChipSeq TAF1 Signal bigWig HudsonAlpha analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeHaibTfbsHepg2Tcf12Pcr1xAln_2Reps.norm5.rawsignal.bw HepG2 ChipSeq TCF12 Signal bigWig HudsonAlpha analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeHaibTfbsHepg2Usf1Pcr1xAln_2Reps.norm5.rawsignal.bw HepG2 ChipSeq USF-1 Signal bigWig HudsonAlpha analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeHaibTfbsHepg2Zbtb33Pcr1xAln_2Reps.norm5.rawsignal.bw HepG2 ChipSeq ZBTB33 Signal bigWig HudsonAlpha analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeHaibTfbsHepg2Zbtb33V0416101Aln_2Reps.norm5.rawsignal.bw HepG2 ChipSeq ZBTB33 Signal bigWig HudsonAlpha analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeHaibTfbsHtb11ControlPcr2xAln_2Reps.norm5.rawsignal.bw HTB-11 ChipSeq Control Signal bigWig HudsonAlpha analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeHaibTfbsHtb11NrsfPcr2xAln_2Reps.norm5.rawsignal.bw HTB-11 ChipSeq NRSF Signal bigWig HudsonAlpha analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeHaibTfbsK562Bcl3Pcr1xAln_2Reps.norm5.rawsignal.bw K562 ChipSeq BCL3 Signal bigWig HudsonAlpha analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeHaibTfbsK562Bclaf1m33Pcr1xAln_2Reps.norm5.rawsignal.bw K562 ChipSeq BCLAF1_(M33-P5B11) Signal bigWig HudsonAlpha analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeHaibTfbsK562ControlPcr1xAln_6Reps.norm5.rawsignal.bw K562 ChipSeq Control Signal bigWig HudsonAlpha analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeHaibTfbsK562Ctcflsc98982V0416101Aln_2Reps.norm5.rawsignal.bw K562 ChipSeq CTCFL_(SC-98982) Signal bigWig HudsonAlpha analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeHaibTfbsK562E2f6h50V0416102Aln_2Reps.norm5.rawsignal.bw K562 ChipSeq E2F6_(H-50) Signal bigWig HudsonAlpha analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeHaibTfbsK562Egr1V0416101Aln_2Reps.norm5.rawsignal.bw K562 ChipSeq Egr-1 Signal bigWig HudsonAlpha analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeHaibTfbsK562Elf1sc631V0416102Aln_2Reps.norm5.rawsignal.bw K562 ChipSeq ELF1_(SC-631) Signal bigWig HudsonAlpha analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeHaibTfbsK562Ets1V0416101Aln_2Reps.norm5.rawsignal.bw K562 ChipSeq ETS1 Signal bigWig HudsonAlpha analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeHaibTfbsK562Fosl1sc183V0416101Aln_2Reps.norm5.rawsignal.bw K562 ChipSeq FOSL1_(SC-183) Signal bigWig HudsonAlpha analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeHaibTfbsK562GabpV0416101Aln_2Reps.norm5.rawsignal.bw K562 ChipSeq GABP Signal bigWig HudsonAlpha analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeHaibTfbsK562Gata2cg2Pcr1xAln_2Reps.norm5.rawsignal.bw K562 ChipSeq GATA2_(CG2-96) Signal bigWig HudsonAlpha analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeHaibTfbsK562Hdac2sc6296V0416102Aln_2Reps.norm5.rawsignal.bw K562 ChipSeq HDAC2_(SC-6296) Signal bigWig HudsonAlpha analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeHaibTfbsK562Hey1Pcr1xAln_2Reps.norm5.rawsignal.bw K562 ChipSeq HEY1 Signal bigWig HudsonAlpha analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeHaibTfbsK562MaxV0416102Aln_2Reps.norm5.rawsignal.bw K562 ChipSeq Max Signal bigWig HudsonAlpha analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeHaibTfbsK562NrsfV0416102Aln_2Reps.norm5.rawsignal.bw K562 ChipSeq NRSF Signal bigWig HudsonAlpha analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeHaibTfbsK562Pol24h8Pcr1xAln_2Reps.norm5.rawsignal.bw K562 ChipSeq Pol2-4H8 Signal bigWig HudsonAlpha analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeHaibTfbsK562Pol24h8V0416101Aln_2Reps.norm5.rawsignal.bw K562 ChipSeq Pol2-4H8 Signal bigWig HudsonAlpha analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeHaibTfbsK562Pol2V0416101Aln_2Reps.norm5.rawsignal.bw K562 ChipSeq Pol2 Signal bigWig HudsonAlpha analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeHaibTfbsK562Pu1Pcr1xAln_2Reps.norm5.rawsignal.bw K562 ChipSeq PU.1 Signal bigWig HudsonAlpha analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeHaibTfbsK562Rad21V0416102Aln_2Reps.norm5.rawsignal.bw K562 ChipSeq Rad21 Signal bigWig HudsonAlpha analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeHaibTfbsK562Sin3ak20V0416101Aln_2Reps.norm5.rawsignal.bw K562 ChipSeq Sin3Ak-20 Signal bigWig HudsonAlpha analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeHaibTfbsK562Six5Pcr1xAln_2Reps.norm5.rawsignal.bw K562 ChipSeq SIX5 Signal bigWig HudsonAlpha analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeHaibTfbsK562Sp1Pcr1xAln_2Reps.norm5.rawsignal.bw K562 ChipSeq SP1 Signal bigWig HudsonAlpha analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeHaibTfbsK562Sp2sc643V0416102Aln_2Reps.norm5.rawsignal.bw K562 ChipSeq SP2_(SC-643) Signal bigWig HudsonAlpha analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeHaibTfbsK562SrfV0416101Aln_2Reps.norm5.rawsignal.bw K562 ChipSeq SRF Signal bigWig HudsonAlpha analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeHaibTfbsK562Taf1Pcr1xAln_2Reps.norm5.rawsignal.bw K562 ChipSeq TAF1 Signal bigWig HudsonAlpha analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeHaibTfbsK562Taf1V0416101Aln_2Reps.norm5.rawsignal.bw K562 ChipSeq TAF1 Signal bigWig HudsonAlpha analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeHaibTfbsK562Taf7sq8V0416101Aln_2Reps.norm5.rawsignal.bw K562 ChipSeq TAF7_(SQ-8) Signal bigWig HudsonAlpha analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeHaibTfbsK562Thap1sc98174V0416101Aln_2Reps.norm5.rawsignal.bw K562 ChipSeq THAP1_(SC-98174) Signal bigWig HudsonAlpha analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeHaibTfbsK562Usf1V0416101Aln_2Reps.norm5.rawsignal.bw K562 ChipSeq USF-1 Signal bigWig HudsonAlpha analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeHaibTfbsK562Yy1V0416101Aln_2Reps.norm5.rawsignal.bw K562 ChipSeq YY1 Signal bigWig HudsonAlpha analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeHaibTfbsK562Yy1V0416102Aln_2Reps.norm5.rawsignal.bw K562 ChipSeq YY1 Signal bigWig HudsonAlpha analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeHaibTfbsK562Zbtb33Pcr1xAln_2Reps.norm5.rawsignal.bw K562 ChipSeq ZBTB33 Signal bigWig HudsonAlpha analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeHaibTfbsK562Zbtb7asc34508V0416101Aln_2Reps.norm5.rawsignal.bw K562 ChipSeq ZBTB7A_(SC-34508) Signal bigWig HudsonAlpha analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeHaibTfbsPanc1ControlPcr2xAln_2Reps.norm5.rawsignal.bw PANC-1 ChipSeq Control Signal bigWig HudsonAlpha analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeHaibTfbsPanc1NrsfPcr2xAln_2Reps.norm5.rawsignal.bw PANC-1 ChipSeq NRSF Signal bigWig HudsonAlpha analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeHaibTfbsPfsk1ControlPcr2xAln_2Reps.norm5.rawsignal.bw PFSK-1 ChipSeq Control Signal bigWig HudsonAlpha analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeHaibTfbsPfsk1NrsfPcr2xAln_2Reps.norm5.rawsignal.bw PFSK-1 ChipSeq NRSF Signal bigWig HudsonAlpha analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeHaibTfbsSknmcControlV0416101Aln_1Reps.norm5.rawsignal.bw SK-N-MC ChipSeq Control Signal bigWig HudsonAlpha analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeHaibTfbsSknshraControlV0416102Aln_1Reps.norm5.rawsignal.bw SK-N-SH_RA ChipSeq Control Signal bigWig HudsonAlpha analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeHaibTfbsSknshraCtcfV0416102Aln_2Reps.norm5.rawsignal.bw SK-N-SH_RA ChipSeq CTCF Signal bigWig HudsonAlpha analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeHaibTfbsSknshraP300V0416102Aln_2Reps.norm5.rawsignal.bw SK-N-SH_RA ChipSeq p300 Signal bigWig HudsonAlpha analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeHaibTfbsSknshraRad21V0416102Aln_2Reps.norm5.rawsignal.bw SK-N-SH_RA ChipSeq Rad21 Signal bigWig HudsonAlpha analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeHaibTfbsSknshraUsf1sc8983V0416102Aln_2Reps.norm5.rawsignal.bw SK-N-SH_RA ChipSeq USF1_(SC-8983) Signal bigWig HudsonAlpha analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeHaibTfbsSknshraYy1c20V0416102Aln_2Reps.norm5.rawsignal.bw SK-N-SH_RA ChipSeq YY1_(C-20) Signal bigWig HudsonAlpha analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeHaibTfbsT47dControlV0416102Dmso2Aln_1Reps.norm5.rawsignal.bw T-47D ChipSeq Control Signal bigWig HudsonAlpha analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeHaibTfbsT47dCtcfsc5916V0416102Dmso2Aln_2Reps.norm5.rawsignal.bw T-47D ChipSeq CTCF_(SC-5916) Signal bigWig HudsonAlpha analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeHaibTfbsT47dEralphaaPcr2xGen1hAln_2Reps.norm5.rawsignal.bw T-47D ChipSeq ERalpha_a Signal bigWig HudsonAlpha analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeHaibTfbsT47dEralphaaV0416102Dmso2Aln_2Reps.norm5.rawsignal.bw T-47D ChipSeq ERalpha_a Signal bigWig HudsonAlpha analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeHaibTfbsT47dEralphaaV0416102Estradia1hAln_2Reps.norm5.rawsignal.bw T-47D ChipSeq ERalpha_a Signal bigWig HudsonAlpha analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeHaibTfbsT47dFoxa1c20V0416102Dmso2Aln_2Reps.norm5.rawsignal.bw T-47D ChipSeq FOXA1_(C-20) Signal bigWig HudsonAlpha analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeHaibTfbsT47dGata3sc268V0416102Dmso2Aln_2Reps.norm5.rawsignal.bw T-47D ChipSeq GATA3_(SC-268) Signal bigWig HudsonAlpha analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeHaibTfbsT47dP300V0416102Dmso2Aln_2Reps.norm5.rawsignal.bw T-47D ChipSeq p300 Signal bigWig HudsonAlpha analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeHaibTfbsU87ControlPcr2xAln_2Reps.norm5.rawsignal.bw U87 ChipSeq Control Signal bigWig HudsonAlpha analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeHaibTfbsU87NrsfPcr2xAln_2Reps.norm5.rawsignal.bw U87 ChipSeq NRSF Signal bigWig HudsonAlpha analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeOpenChromChipFibroblCtcfAln_2Reps.norm5.rawsignal.bw Fibrobl ChipSeq CTCF Signal bigWig UT-A analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeOpenChromChipFibroblInputAln_1Reps.norm5.rawsignal.bw Fibrobl ChipSeq Input Signal bigWig UT-A analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeOpenChromChipGlioblaCtcfAln_2Reps.norm5.rawsignal.bw Gliobla ChipSeq CTCF Signal bigWig UT-A analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeOpenChromChipGlioblaInputAln_1Reps.norm5.rawsignal.bw Gliobla ChipSeq Input Signal bigWig UT-A analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeOpenChromChipGlioblaPol2Aln_2Reps.norm5.rawsignal.bw Gliobla ChipSeq Pol2 Signal bigWig UT-A analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeOpenChromChipGm12878CmycAln_2Reps.norm5.rawsignal.bw GM12878 ChipSeq c-Myc Signal bigWig UT-A analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeOpenChromChipGm12878CtcfAln_3Reps.norm5.rawsignal.bw GM12878 ChipSeq CTCF Signal bigWig UT-A analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeOpenChromChipGm12878InputAln_1Reps.norm5.rawsignal.bw GM12878 ChipSeq Input Signal bigWig UT-A analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeOpenChromChipGm12878Pol2Aln_2Reps.norm5.rawsignal.bw GM12878 ChipSeq Pol2 Signal bigWig UT-A analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeOpenChromChipGm12891CtcfAln_2Reps.norm5.rawsignal.bw GM12891 ChipSeq CTCF Signal bigWig UT-A analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeOpenChromChipGm12892CtcfAln_2Reps.norm5.rawsignal.bw GM12892 ChipSeq CTCF Signal bigWig UT-A analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeOpenChromChipGm19238CtcfAln_2Reps.norm5.rawsignal.bw GM19238 ChipSeq CTCF Signal bigWig UT-A analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeOpenChromChipGm19239CtcfAln_2Reps.norm5.rawsignal.bw GM19239 ChipSeq CTCF Signal bigWig UT-A analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeOpenChromChipGm19240CtcfAln_2Reps.norm5.rawsignal.bw GM19240 ChipSeq CTCF Signal bigWig UT-A analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeOpenChromChipH1hescCmycAln_1Reps.norm5.rawsignal.bw H1-hESC ChipSeq c-Myc Signal bigWig UT-A analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeOpenChromChipH1hescCtcfAln_1Reps.norm5.rawsignal.bw H1-hESC ChipSeq CTCF Signal bigWig UT-A analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeOpenChromChipH1hescPol2Aln_1Reps.norm5.rawsignal.bw H1-hESC ChipSeq Pol2 Signal bigWig UT-A analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeOpenChromChipHelas3CmycAln_2Reps.norm5.rawsignal.bw HeLa-S3 ChipSeq c-Myc Signal bigWig UT-A analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeOpenChromChipHelas3CtcfAln_2Reps.norm5.rawsignal.bw HeLa-S3 ChipSeq CTCF Signal bigWig UT-A analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeOpenChromChipHelas3InputAln_1Reps.norm5.rawsignal.bw HeLa-S3 ChipSeq Input Signal bigWig UT-A analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeOpenChromChipHelas3Pol2Aln_2Reps.norm5.rawsignal.bw HeLa-S3 ChipSeq Pol2 Signal bigWig UT-A analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeOpenChromChipHepg2CmycAln_3Reps.norm5.rawsignal.bw HepG2 ChipSeq c-Myc Signal bigWig UT-A analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeOpenChromChipHepg2CtcfAln_2Reps.norm5.rawsignal.bw HepG2 ChipSeq CTCF Signal bigWig UT-A analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeOpenChromChipHepg2InputAln_1Reps.norm5.rawsignal.bw HepG2 ChipSeq Input Signal bigWig UT-A analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeOpenChromChipHepg2Pol2Aln_3Reps.norm5.rawsignal.bw HepG2 ChipSeq Pol2 Signal bigWig UT-A analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeOpenChromChipHuvecCmycAln_1Reps.norm5.rawsignal.bw HUVEC ChipSeq c-Myc Signal bigWig UT-A analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeOpenChromChipHuvecCtcfAln_2Reps.norm5.rawsignal.bw HUVEC ChipSeq CTCF Signal bigWig UT-A analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeOpenChromChipHuvecInputAln_1Reps.norm5.rawsignal.bw HUVEC ChipSeq Input Signal bigWig UT-A analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeOpenChromChipHuvecPol2Aln_2Reps.norm5.rawsignal.bw HUVEC ChipSeq Pol2 Signal bigWig UT-A analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeOpenChromChipK562CmycAln_3Reps.norm5.rawsignal.bw K562 ChipSeq c-Myc Signal bigWig UT-A analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeOpenChromChipK562CtcfAln_3Reps.norm5.rawsignal.bw K562 ChipSeq CTCF Signal bigWig UT-A analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeOpenChromChipK562InputAln_1Reps.norm5.rawsignal.bw K562 ChipSeq Input Signal bigWig UT-A analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeOpenChromChipK562Pol2Aln_2Reps.norm5.rawsignal.bw K562 ChipSeq Pol2 Signal bigWig UT-A analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeOpenChromChipMcf7CmycEstroAln_2Reps.norm5.rawsignal.bw MCF-7 ChipSeq c-Myc Signal bigWig UT-A analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeOpenChromChipMcf7CmycVehAln_2Reps.norm5.rawsignal.bw MCF-7 ChipSeq c-Myc Signal bigWig UT-A analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeOpenChromChipMcf7CtcfAln_2Reps.norm5.rawsignal.bw MCF-7 ChipSeq CTCF Signal bigWig UT-A analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeOpenChromChipMcf7CtcfEstroAln_2Reps.norm5.rawsignal.bw MCF-7 ChipSeq CTCF Signal bigWig UT-A analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeOpenChromChipMcf7CtcfVehAln_2Reps.norm5.rawsignal.bw MCF-7 ChipSeq CTCF Signal bigWig UT-A analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeOpenChromChipMcf7InputAln_1Reps.norm5.rawsignal.bw MCF-7 ChipSeq Input Signal bigWig UT-A analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeOpenChromChipMcf7Pol2Aln_2Reps.norm5.rawsignal.bw MCF-7 ChipSeq Pol2 Signal bigWig UT-A analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeOpenChromChipMonocd14InputAln_1Reps.norm5.rawsignal.bw Monocytes-CD14+ ChipSeq Input Signal bigWig UT-A analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeOpenChromChipNhekCtcfAln_2Reps.norm5.rawsignal.bw NHEK ChipSeq CTCF Signal bigWig UT-A analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeOpenChromChipProgfibCtcfAln_2Reps.norm5.rawsignal.bw ProgFib ChipSeq CTCF Signal bigWig UT-A analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeOpenChromChipProgfibInputAln_1Reps.norm5.rawsignal.bw ProgFib ChipSeq Input Signal bigWig UT-A analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeOpenChromChipProgfibPol2Aln_2Reps.norm5.rawsignal.bw ProgFib ChipSeq Pol2 Signal bigWig UT-A analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeOpenChromDnase8988tAln_2Reps.norm5.rawsignal.bw 8988T DnaseSeq Signal bigWig Duke analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeOpenChromDnaseA549Aln_2Reps.norm5.rawsignal.bw A549 DnaseSeq Signal bigWig Duke analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeOpenChromDnaseAosmcSerumfreeAln_2Reps.norm5.rawsignal.bw AoSMC DnaseSeq Signal bigWig Duke analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeOpenChromDnaseChorionAln_2Reps.norm5.rawsignal.bw Chorion DnaseSeq Signal bigWig Duke analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeOpenChromDnaseCllAln_3Reps.norm5.rawsignal.bw CLL DnaseSeq Signal bigWig Duke analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeOpenChromDnaseFibroblAln_2Reps.norm5.rawsignal.bw Fibrobl DnaseSeq Signal bigWig Duke analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeOpenChromDnaseFibropAln_3Reps.norm5.rawsignal.bw FibroP DnaseSeq Signal bigWig Duke analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeOpenChromDnaseGlioblaAln_2Reps.norm5.rawsignal.bw Gliobla DnaseSeq Signal bigWig Duke analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeOpenChromDnaseGm12878Aln_5Reps.norm5.rawsignal.bw GM12878 DnaseSeq Signal bigWig Duke analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeOpenChromDnaseGm12891Aln_2Reps.norm5.rawsignal.bw GM12891 DnaseSeq Signal bigWig Duke analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeOpenChromDnaseGm12892Aln_2Reps.norm5.rawsignal.bw GM12892 DnaseSeq Signal bigWig Duke analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeOpenChromDnaseGm18507Aln_3Reps.norm5.rawsignal.bw GM18507 DnaseSeq Signal bigWig Duke analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeOpenChromDnaseGm19238Aln_2Reps.norm5.rawsignal.bw GM19238 DnaseSeq Signal bigWig Duke analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeOpenChromDnaseGm19239Aln_2Reps.norm5.rawsignal.bw GM19239 DnaseSeq Signal bigWig Duke analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeOpenChromDnaseGm19240Aln_2Reps.norm5.rawsignal.bw GM19240 DnaseSeq Signal bigWig Duke analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeOpenChromDnaseH1hescAln_2Reps.norm5.rawsignal.bw H1-hESC DnaseSeq Signal bigWig Duke analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeOpenChromDnaseH9esAln_2Reps.norm5.rawsignal.bw H9ES DnaseSeq Signal bigWig Duke analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeOpenChromDnaseHelas3Aln_3Reps.norm5.rawsignal.bw HeLa-S3 DnaseSeq Signal bigWig Duke analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeOpenChromDnaseHelas3Ifna4hAln_2Reps.norm5.rawsignal.bw HeLa-S3 DnaseSeq Signal bigWig Duke analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeOpenChromDnaseHepatocytesAln_2Reps.norm5.rawsignal.bw Hepatocytes DnaseSeq Signal bigWig Duke analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeOpenChromDnaseHepg2Aln_3Reps.norm5.rawsignal.bw HepG2 DnaseSeq Signal bigWig Duke analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeOpenChromDnaseHmecAln_2Reps.norm5.rawsignal.bw HMEC DnaseSeq Signal bigWig Duke analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeOpenChromDnaseHpde6e6e7Aln_2Reps.norm5.rawsignal.bw HPDE6-E6E7 DnaseSeq Signal bigWig Duke analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeOpenChromDnaseHsmmAln_3Reps.norm5.rawsignal.bw HSMM DnaseSeq Signal bigWig Duke analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeOpenChromDnaseHsmmtAln_3Reps.norm5.rawsignal.bw HSMMtube DnaseSeq Signal bigWig Duke analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeOpenChromDnaseHtr8Aln_2Reps.norm5.rawsignal.bw HTR8svn DnaseSeq Signal bigWig Duke analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeOpenChromDnaseHuh75Aln_2Reps.norm5.rawsignal.bw Huh-7.5 DnaseSeq Signal bigWig Duke analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeOpenChromDnaseHuh7Aln_2Reps.norm5.rawsignal.bw Huh-7 DnaseSeq Signal bigWig Duke analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeOpenChromDnaseHuvecAln_2Reps.norm5.rawsignal.bw HUVEC DnaseSeq Signal bigWig Duke analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeOpenChromDnaseIpsAln_3Reps.norm5.rawsignal.bw iPS DnaseSeq Signal bigWig Duke analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeOpenChromDnaseK562Aln_2Reps.norm5.rawsignal.bw K562 DnaseSeq Signal bigWig Duke analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeOpenChromDnaseLncapAln_3Reps.norm5.rawsignal.bw LNCaP DnaseSeq Signal bigWig Duke analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeOpenChromDnaseLncapAndroAln_2Reps.norm5.rawsignal.bw LNCaP DnaseSeq Signal bigWig Duke analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeOpenChromDnaseMcf7Aln_2Reps.norm5.rawsignal.bw MCF-7 DnaseSeq Signal bigWig Duke analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeOpenChromDnaseMedulloAln_2Reps.norm5.rawsignal.bw Medullo DnaseSeq Signal bigWig Duke analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeOpenChromDnaseMelanoAln_2Reps.norm5.rawsignal.bw Melano DnaseSeq Signal bigWig Duke analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeOpenChromDnaseMyometrAln_2Reps.norm5.rawsignal.bw Myometr DnaseSeq Signal bigWig Duke analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeOpenChromDnaseNhekAln_2Reps.norm5.rawsignal.bw NHEK DnaseSeq Signal bigWig Duke analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeOpenChromDnaseOsteoblAln_3Reps.norm5.rawsignal.bw Osteobl DnaseSeq Signal bigWig Duke analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeOpenChromDnasePanisdAln_3Reps.norm5.rawsignal.bw PanIsletD DnaseSeq Signal bigWig Duke analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeOpenChromDnasePanisletsAln_3Reps.norm5.rawsignal.bw PanIslets DnaseSeq Signal bigWig Duke analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeOpenChromDnasePhteAln_2Reps.norm5.rawsignal.bw pHTE DnaseSeq Signal bigWig Duke analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeOpenChromDnaseProgfibAln_2Reps.norm5.rawsignal.bw ProgFib DnaseSeq Signal bigWig Duke analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeOpenChromDnaseStellateAln_2Reps.norm5.rawsignal.bw Stellate DnaseSeq Signal bigWig Duke analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeOpenChromDnaseT47dAln_2Reps.norm5.rawsignal.bw T-47D DnaseSeq Signal bigWig Duke analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeOpenChromDnaseUrotsaAln_2Reps.norm5.rawsignal.bw Urothelia DnaseSeq Signal bigWig Duke analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeOpenChromDnaseUrotsaUt189Aln_2Reps.norm5.rawsignal.bw Urothelia DnaseSeq Signal bigWig Duke analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeOpenChromFaireA549Aln_2Reps.norm5.rawsignal.bw A549 FaireSeq Signal bigWig UNC(Lieb) analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeOpenChromFaireAstrocyAln_2Reps.norm5.rawsignal.bw Astrocy FaireSeq Signal bigWig UNC analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeOpenChromFaireGlioblaAln_3Reps.norm5.rawsignal.bw Gliobla FaireSeq Signal bigWig UNC analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeOpenChromFaireGm12878Aln_3Reps.norm5.rawsignal.bw GM12878 FaireSeq Signal bigWig UNC analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeOpenChromFaireGm12891Aln_2Reps.norm5.rawsignal.bw GM12891 FaireSeq Signal bigWig UNC analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeOpenChromFaireGm12892Aln_2Reps.norm5.rawsignal.bw GM12892 FaireSeq Signal bigWig UNC analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeOpenChromFaireGm18507Aln_2Reps.norm5.rawsignal.bw GM18507 FaireSeq Signal bigWig UNC analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeOpenChromFaireGm19239Aln_2Reps.norm5.rawsignal.bw GM19239 FaireSeq Signal bigWig UNC analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeOpenChromFaireH1hescAln_2Reps.norm5.rawsignal.bw H1-hESC FaireSeq Signal bigWig UNC analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeOpenChromFaireHelas3Aln_2Reps.norm5.rawsignal.bw HeLa-S3 FaireSeq Signal bigWig UNC analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeOpenChromFaireHelas3Ifna4hAln_2Reps.norm5.rawsignal.bw HeLa-S3 FaireSeq Signal bigWig UNC analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeOpenChromFaireHelas3Ifng4hAln_2Reps.norm5.rawsignal.bw HeLa-S3 FaireSeq Signal bigWig UNC analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeOpenChromFaireHepg2Aln_3Reps.norm5.rawsignal.bw HepG2 FaireSeq Signal bigWig UNC analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeOpenChromFaireHtr8Aln_2Reps.norm5.rawsignal.bw HTR8svn FaireSeq Signal bigWig UNC analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeOpenChromFaireHuvecAln_2Reps.norm5.rawsignal.bw HUVEC FaireSeq Signal bigWig UNC analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeOpenChromFaireK562Aln_2Reps.norm5.rawsignal.bw K562 FaireSeq Signal bigWig UNC analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeOpenChromFaireK562NabutAln_2Reps.norm5.rawsignal.bw K562 FaireSeq Signal bigWig UNC analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeOpenChromFaireK562OhureaAln_2Reps.norm5.rawsignal.bw K562 FaireSeq Signal bigWig UNC analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeOpenChromFaireMcf7HypoxlacAln_2Reps.norm5.rawsignal.bw MCF-7 FaireSeq Signal bigWig UNC analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeOpenChromFaireMedulloAln_2Reps.norm5.rawsignal.bw Medullo FaireSeq Signal bigWig UNC analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeOpenChromFaireNhbeAln_2Reps.norm5.rawsignal.bw NHBE FaireSeq Signal bigWig UNC analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeOpenChromFaireNhekAln_2Reps.norm5.rawsignal.bw NHEK FaireSeq Signal bigWig UNC analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeOpenChromFairePanisletsAln_1Reps.norm5.rawsignal.bw PanIslets FaireSeq Signal bigWig UNC analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeOpenChromFaireUrotsaAln_2Reps.norm5.rawsignal.bw Urothelia FaireSeq Signal bigWig UNC analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeOpenChromFaireUrotsaUt189Aln_2Reps.norm5.rawsignal.bw Urothelia FaireSeq Signal bigWig UNC analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeSydhGm12878NucleosomeRep0.bw30.norm5.rawsignal.bw bw analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeSydhHistoneK562H3k27me3UcdAln_2Reps.norm5.rawsignal.bw K562 ChIP-seq H3K27me3 Signal bigWig UCD analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeSydhHistoneK562H3k4me1UcdAln_2Reps.norm5.rawsignal.bw K562 ChIP-seq H3K4me1 Signal bigWig UCD analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeSydhHistoneK562H3k4me3UcdAln_2Reps.norm5.rawsignal.bw K562 ChIP-seq H3K4me3 Signal bigWig UCD analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeSydhHistoneK562H3k9acbUcdAln_2Reps.norm5.rawsignal.bw K562 ChIP-seq H3K9acB Signal bigWig UCD analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeSydhHistoneNt2d1H3k27me3StdAln_2Reps.norm5.rawsignal.bw NT2-D1 ChIP-seq H3K27me3 Signal bigWig UCD analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeSydhHistoneNt2d1H3k36me3bUcdAln_2Reps.norm5.rawsignal.bw NT2-D1 ChIP-seq H3K36me3B Signal bigWig UCD analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeSydhHistoneNt2d1H3k4me1UcdAln_2Reps.norm5.rawsignal.bw NT2-D1 ChIP-seq H3K4me1 Signal bigWig UCD analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeSydhHistoneNt2d1H3k4me3StdAln_2Reps.norm5.rawsignal.bw NT2-D1 ChIP-seq H3K4me3 Signal bigWig UCD analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeSydhHistoneNt2d1H3k9acStdAln_2Reps.norm5.rawsignal.bw NT2-D1 ChIP-seq H3K9ac Signal bigWig UCD analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeSydhHistoneNt2d1H3k9me3UcdAln_2Reps.norm5.rawsignal.bw NT2-D1 ChIP-seq H3K9me3 Signal bigWig UCD analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeSydhHistoneNt2d1InputStdAln_1Reps.norm5.rawsignal.bw NT2-D1 ChIP-seq Input Signal bigWig UCD analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeSydhHistoneU2osH3k9me3UcdAln_2Reps.norm5.rawsignal.bw U2OS ChIP-seq H3K9me3 Signal bigWig UCD(Farnham) analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeSydhK562NucleosomeRep0.bw30.norm5.rawsignal.bw bw analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeSydhTfbsGm10847InputIggmusAln_2Reps.norm5.rawsignal.bw GM10847 ChipSeq Input Signal bigWig Stanford analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeSydhTfbsGm10847InputIggrabAln_2Reps.norm5.rawsignal.bw GM10847 ChipSeq Input Signal bigWig Stanford analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeSydhTfbsGm10847NfkbIggrabAln_5Reps.norm5.rawsignal.bw GM10847 ChipSeq NFKB Signal bigWig Stanford analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeSydhTfbsGm10847Pol2IggmusAln_1Reps.norm5.rawsignal.bw GM10847 ChipSeq Pol2 Signal bigWig Stanford analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeSydhTfbsGm12878Brca1cIggmusAln_2Reps.norm5.rawsignal.bw GM12878 ChipSeq BRCA1_(C-1863) Signal bigWig Stanford analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeSydhTfbsGm12878CfosStdAln_3Reps.norm5.rawsignal.bw GM12878 ChipSeq c-Fos Signal bigWig Stanford analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeSydhTfbsGm12878Chd21250IggmusAln_2Reps.norm5.rawsignal.bw GM12878 ChipSeq CHD2_(N-1250) Signal bigWig Stanford analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeSydhTfbsGm12878Ctcfc20StdAln_2Reps.norm5.rawsignal.bw GM12878 ChipSeq CTCF_(C-20) Signal bigWig Stanford analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeSydhTfbsGm12878EbfStdAln_2Reps.norm5.rawsignal.bw GM12878 ChipSeq EBF Signal bigWig Stanford analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeSydhTfbsGm12878Gcn5StdAln_2Reps.norm5.rawsignal.bw GM12878 ChipSeq GCN5 Signal bigWig Harvard(Weissman) analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeSydhTfbsGm12878InputIggmusAln_2Reps.norm5.rawsignal.bw GM12878 ChipSeq Input Signal bigWig Stanford analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeSydhTfbsGm12878InputIggrabAln_2Reps.norm5.rawsignal.bw GM12878 ChipSeq Input Signal bigWig Stanford analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeSydhTfbsGm12878InputStdAln_1Reps.norm5.rawsignal.bw GM12878 ChipSeq Input Signal bigWig Stanford analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeSydhTfbsGm12878Irf3StdAln_2Reps.norm5.rawsignal.bw GM12878 ChipSeq IRF3 Signal bigWig Stanford analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeSydhTfbsGm12878JundStdAln_2Reps.norm5.rawsignal.bw GM12878 ChipSeq JunD Signal bigWig Stanford analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeSydhTfbsGm12878MaxStdAln_2Reps.norm5.rawsignal.bw GM12878 ChipSeq Max Signal bigWig Stanford analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeSydhTfbsGm12878Nfe2hStdAln_2Reps.norm5.rawsignal.bw GM12878 ChipSeq NF-E2_(H-230) Signal bigWig Stanford analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeSydhTfbsGm12878NfkbIggrabAln_4Reps.norm5.rawsignal.bw GM12878 ChipSeq NFKB Signal bigWig Stanford analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeSydhTfbsGm12878NfkbTnfaStdAln_4Reps.norm5.rawsignal.bw GM12878 ChipSeq NFKB Signal bigWig Stanford analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeSydhTfbsGm12878Nrf1IggmusAln_2Reps.norm5.rawsignal.bw GM12878 ChipSeq Nrf1 Signal bigWig Stanford analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeSydhTfbsGm12878P300n15StdAln_2Reps.norm5.rawsignal.bw GM12878 ChipSeq p300_(N-15) Signal bigWig Stanford analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeSydhTfbsGm12878Pol2IggmusAln_7Reps.norm5.rawsignal.bw GM12878 ChipSeq Pol2 Signal bigWig Stanford analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeSydhTfbsGm12878Pol2StdAln_2Reps.norm5.rawsignal.bw GM12878 ChipSeq Pol2 Signal bigWig Stanford analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeSydhTfbsGm12878Pol3StdAln_2Reps.norm5.rawsignal.bw GM12878 ChipSeq Pol3 Signal bigWig Stanford analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeSydhTfbsGm12878Rad21IggrabAln_2Reps.norm5.rawsignal.bw GM12878 ChipSeq Rad21 Signal bigWig Stanford analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeSydhTfbsGm12878Rfx5n494IggmusAln_2Reps.norm5.rawsignal.bw GM12878 ChipSeq RFX5_(N-494) Signal bigWig Stanford analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeSydhTfbsGm12878Smc3ab9263IggmusAln_2Reps.norm5.rawsignal.bw GM12878 ChipSeq SMC3_(ab9263) Signal bigWig Stanford analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeSydhTfbsGm12878Spt20StdAln_2Reps.norm5.rawsignal.bw GM12878 ChipSeq SPT20 Signal bigWig Harvard(Weissman) analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeSydhTfbsGm12878Stat1StdAln_2Reps.norm5.rawsignal.bw GM12878 ChipSeq STAT1 Signal bigWig Stanford analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeSydhTfbsGm12878Stat3IggmusAln_2Reps.norm5.rawsignal.bw GM12878 ChipSeq STAT3 Signal bigWig Stanford analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeSydhTfbsGm12878TbpIggmusAln_2Reps.norm5.rawsignal.bw GM12878 ChipSeq TBP Signal bigWig Stanford analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeSydhTfbsGm12878Tr4StdAln_2Reps.norm5.rawsignal.bw GM12878 ChipSeq TR4 Signal bigWig Stanford analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeSydhTfbsGm12878Usf2IggmusAln_2Reps.norm5.rawsignal.bw GM12878 ChipSeq USF2 Signal bigWig Stanford analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeSydhTfbsGm12878WhipIggmusAln_2Reps.norm5.rawsignal.bw GM12878 ChipSeq WHIP Signal bigWig Stanford analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeSydhTfbsGm12878Yy1StdAln_2Reps.norm5.rawsignal.bw GM12878 ChipSeq YY1 Signal bigWig Stanford analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeSydhTfbsGm12878Znf143166181apStdAln_2Reps.norm5.rawsignal.bw GM12878 ChipSeq Znf143_(16618-1-AP) Signal bigWig Stanford analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeSydhTfbsGm12878Zzz3StdAln_2Reps.norm5.rawsignal.bw GM12878 ChipSeq ZZZ3 Signal bigWig Stanford analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeSydhTfbsGm12891InputIggmusAln_2Reps.norm5.rawsignal.bw GM12891 ChipSeq Input Signal bigWig Stanford analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeSydhTfbsGm12891InputIggrabAln_2Reps.norm5.rawsignal.bw GM12891 ChipSeq Input Signal bigWig Stanford analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeSydhTfbsGm12891NfkbIggrabAln_3Reps.norm5.rawsignal.bw GM12891 ChipSeq NFKB Signal bigWig Stanford analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeSydhTfbsGm12891Pol2IggmusAln_6Reps.norm5.rawsignal.bw GM12891 ChipSeq Pol2 Signal bigWig Stanford analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeSydhTfbsGm12892InputIggmusAln_2Reps.norm5.rawsignal.bw GM12892 ChipSeq Input Signal bigWig Stanford analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeSydhTfbsGm12892InputIggrabAln_2Reps.norm5.rawsignal.bw GM12892 ChipSeq Input Signal bigWig Stanford analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeSydhTfbsGm12892NfkbIggrabAln_3Reps.norm5.rawsignal.bw GM12892 ChipSeq NFKB Signal bigWig Stanford analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeSydhTfbsGm12892Pol2IggmusAln_3Reps.norm5.rawsignal.bw GM12892 ChipSeq Pol2 Signal bigWig Stanford analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeSydhTfbsGm15510InputIggmusAln_2Reps.norm5.rawsignal.bw GM15510 ChipSeq Input Signal bigWig Stanford analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeSydhTfbsGm15510InputIggrabAln_2Reps.norm5.rawsignal.bw GM15510 ChipSeq Input Signal bigWig Stanford analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeSydhTfbsGm15510NfkbIggrabAln_5Reps.norm5.rawsignal.bw GM15510 ChipSeq NFKB Signal bigWig Stanford analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeSydhTfbsGm15510Pol2IggmusAln_3Reps.norm5.rawsignal.bw GM15510 ChipSeq Pol2 Signal bigWig Stanford analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeSydhTfbsGm18505InputIggmusAln_2Reps.norm5.rawsignal.bw GM18505 ChipSeq Input Signal bigWig Stanford analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeSydhTfbsGm18505InputIggrabAln_2Reps.norm5.rawsignal.bw GM18505 ChipSeq Input Signal bigWig Stanford analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeSydhTfbsGm18505NfkbIggrabAln_5Reps.norm5.rawsignal.bw GM18505 ChipSeq NFKB Signal bigWig Stanford analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeSydhTfbsGm18505Pol2IggmusAln_4Reps.norm5.rawsignal.bw GM18505 ChipSeq Pol2 Signal bigWig Stanford analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeSydhTfbsGm18526InputIggmusAln_3Reps.norm5.rawsignal.bw GM18526 ChipSeq Input Signal bigWig Stanford analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeSydhTfbsGm18526InputIggrabAln_2Reps.norm5.rawsignal.bw GM18526 ChipSeq Input Signal bigWig Stanford analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeSydhTfbsGm18526NfkbIggrabAln_3Reps.norm5.rawsignal.bw GM18526 ChipSeq NFKB Signal bigWig Stanford analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeSydhTfbsGm18526Pol2IggmusAln_3Reps.norm5.rawsignal.bw GM18526 ChipSeq Pol2 Signal bigWig Stanford analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeSydhTfbsGm18951InputIggmusAln_1Reps.norm5.rawsignal.bw GM18951 ChipSeq Input Signal bigWig Stanford analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeSydhTfbsGm18951InputIggrabAln_2Reps.norm5.rawsignal.bw GM18951 ChipSeq Input Signal bigWig Stanford analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeSydhTfbsGm18951NfkbIggrabAln_4Reps.norm5.rawsignal.bw GM18951 ChipSeq NFKB Signal bigWig Stanford analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeSydhTfbsGm18951Pol2IggmusAln_4Reps.norm5.rawsignal.bw GM18951 ChipSeq Pol2 Signal bigWig Stanford analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeSydhTfbsGm19099InputIggmusAln_2Reps.norm5.rawsignal.bw GM19099 ChipSeq Input Signal bigWig Stanford analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeSydhTfbsGm19099InputIggrabAln_2Reps.norm5.rawsignal.bw GM19099 ChipSeq Input Signal bigWig Stanford analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeSydhTfbsGm19099NfkbIggrabAln_3Reps.norm5.rawsignal.bw GM19099 ChipSeq NFKB Signal bigWig Stanford analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeSydhTfbsGm19099Pol2IggmusAln_3Reps.norm5.rawsignal.bw GM19099 ChipSeq Pol2 Signal bigWig Stanford analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeSydhTfbsGm19193InputIggmusAln_2Reps.norm5.rawsignal.bw GM19193 ChipSeq Input Signal bigWig Stanford analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeSydhTfbsGm19193InputIggrabAln_2Reps.norm5.rawsignal.bw GM19193 ChipSeq Input Signal bigWig Stanford analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeSydhTfbsGm19193NfkbIggrabAln_3Reps.norm5.rawsignal.bw GM19193 ChipSeq NFKB Signal bigWig Stanford analysis 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http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeSydhTfbsH1hescUsf2IggrabAln_2Reps.norm5.rawsignal.bw H1-hESC ChipSeq USF2 Signal bigWig Stanford analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeSydhTfbsHct116InputUcdAln_1Reps.norm5.rawsignal.bw HCT-116 ChipSeq Input Signal bigWig Stanford analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeSydhTfbsHct116Pol2UcdAln_2Reps.norm5.rawsignal.bw HCT-116 ChipSeq Pol2 Signal bigWig Stanford analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeSydhTfbsHct116Tcf4UcdAln_2Reps.norm5.rawsignal.bw HCT-116 ChipSeq TCF4 Signal bigWig Stanford analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeSydhTfbsHek293bElk4UcdAln_2Reps.norm5.rawsignal.bw HEK293(b) ChipSeq ELK4 Signal bigWig UCD analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeSydhTfbsHek293bInputStdAln_1Reps.norm5.rawsignal.bw HEK293(b) ChipSeq Input Signal bigWig Stanford analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeSydhTfbsHek293bKap1UcdAln_2Reps.norm5.rawsignal.bw HEK293(b) ChipSeq KAP1 Signal bigWig UCD analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeSydhTfbsHek293bPol2StdAln_3Reps.norm5.rawsignal.bw HEK293(b) ChipSeq Pol2 Signal bigWig Stanford analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeSydhTfbsHek293InputUcdAln_1Reps.norm5.rawsignal.bw HEK293(b) ChipSeq Input Signal bigWig UCD analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeSydhTfbsHelas3Ap2alphaStdAln_2Reps.norm5.rawsignal.bw HeLa-S3 ChipSeq AP-2alpha Signal bigWig Stanford analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeSydhTfbsHelas3Ap2gammaStdAln_2Reps.norm5.rawsignal.bw HeLa-S3 ChipSeq AP-2gamma Signal bigWig Stanford analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeSydhTfbsHelas3Baf155IggmusAln_3Reps.norm5.rawsignal.bw HeLa-S3 ChipSeq BAF155 Signal bigWig Stanford analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeSydhTfbsHelas3Baf170IggmusAln_3Reps.norm5.rawsignal.bw HeLa-S3 ChipSeq BAF170 Signal bigWig Stanford analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeSydhTfbsHelas3Bdp1StdAln_2Reps.norm5.rawsignal.bw HeLa-S3 ChipSeq BDP1 Signal bigWig Stanford analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeSydhTfbsHelas3Brca1cIggrabAln_2Reps.norm5.rawsignal.bw HeLa-S3 ChipSeq BRCA1_(C-1863) Signal bigWig Stanford analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeSydhTfbsHelas3Brf1StdAln_2Reps.norm5.rawsignal.bw HeLa-S3 ChipSeq BRF1 Signal bigWig Stanford analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeSydhTfbsHelas3Brf2StdAln_2Reps.norm5.rawsignal.bw HeLa-S3 ChipSeq BRF2 Signal bigWig Stanford analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeSydhTfbsHelas3Brg1IggmusAln_3Reps.norm5.rawsignal.bw HeLa-S3 ChipSeq Brg1 Signal bigWig Stanford analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeSydhTfbsHelas3CebpbIggrabAln_2Reps.norm5.rawsignal.bw HeLa-S3 ChipSeq CEBPB Signal bigWig Stanford analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeSydhTfbsHelas3CfosStdAln_2Reps.norm5.rawsignal.bw HeLa-S3 ChipSeq c-Fos Signal bigWig Stanford analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeSydhTfbsHelas3CjunIggrabAln_2Reps.norm5.rawsignal.bw HeLa-S3 ChipSeq c-Jun Signal bigWig Stanford analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeSydhTfbsHelas3CmycStdAln_2Reps.norm5.rawsignal.bw HeLa-S3 ChipSeq c-Myc Signal bigWig Stanford analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeSydhTfbsHelas3E2f1StdAln_2Reps.norm5.rawsignal.bw HeLa-S3 ChipSeq E2F1 Signal bigWig Stanford analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeSydhTfbsHelas3E2f4StdAln_2Reps.norm5.rawsignal.bw HeLa-S3 ChipSeq E2F4 Signal bigWig Stanford analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeSydhTfbsHelas3E2f6StdAln_2Reps.norm5.rawsignal.bw HeLa-S3 ChipSeq E2F6 Signal bigWig Stanford analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeSydhTfbsHelas3Elk4UcdAln_2Reps.norm5.rawsignal.bw HeLa-S3 ChipSeq ELK4 Signal bigWig UCD analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeSydhTfbsHelas3Gcn5StdAln_2Reps.norm5.rawsignal.bw HeLa-S3 ChipSeq GCN5 Signal bigWig Stanford analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeSydhTfbsHelas3Gtf2f1rapIggrabAln_2Reps.norm5.rawsignal.bw HeLa-S3 ChipSeq GTF2F1_(RAP-74) Signal bigWig Stanford analysis 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http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeSydhTfbsHelas3InputIggrabAln_1Reps.norm5.rawsignal.bw HeLa-S3 ChipSeq Input Signal bigWig Stanford analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeSydhTfbsHelas3InputLargefragmentAln_2Reps.norm5.rawsignal.bw HeLa-S3 ChipSeq Input Signal bigWig Stanford analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeSydhTfbsHelas3InputMnaseAln_2Reps.norm5.rawsignal.bw HeLa-S3 ChipSeq Input Signal bigWig Stanford analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeSydhTfbsHelas3InputNakeddnaAln_3Reps.norm5.rawsignal.bw HeLa-S3 ChipSeq Input Signal bigWig Stanford analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeSydhTfbsHelas3InputStdAln_1Reps.norm5.rawsignal.bw HeLa-S3 ChipSeq Input Signal bigWig Stanford analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeSydhTfbsHelas3InputUcdAln_1Reps.norm5.rawsignal.bw HeLa-S3 ChipSeq Input Signal bigWig Stanford analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeSydhTfbsHelas3Irf3IggrabAln_2Reps.norm5.rawsignal.bw HeLa-S3 ChipSeq IRF3 Signal bigWig Stanford analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeSydhTfbsHelas3JundIggrabAln_2Reps.norm5.rawsignal.bw HeLa-S3 ChipSeq JunD Signal bigWig Stanford analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeSydhTfbsHelas3MaxStdAln_2Reps.norm5.rawsignal.bw HeLa-S3 ChipSeq Max Signal bigWig Stanford analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeSydhTfbsHelas3Mxi1bhlhIggrabAln_2Reps.norm5.rawsignal.bw HeLa-S3 ChipSeq Mxi1_(bHLH) Signal bigWig Stanford analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeSydhTfbsHelas3Nrf1IggmusAln_2Reps.norm5.rawsignal.bw HeLa-S3 ChipSeq Nrf1 Signal bigWig Stanford analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeSydhTfbsHelas3P300n15IggrabAln_2Reps.norm5.rawsignal.bw HeLa-S3 ChipSeq p300_(N-15) Signal bigWig Stanford analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeSydhTfbsHelas3Pol2s2IggrabAln_2Reps.norm5.rawsignal.bw HeLa-S3 ChipSeq Pol2(phosphoS2) Signal bigWig Stanford analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeSydhTfbsHelas3Pol2StdAln_3Reps.norm5.rawsignal.bw HeLa-S3 ChipSeq Pol2 Signal bigWig Stanford analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeSydhTfbsHelas3Prdm1vIggrabAln_2Reps.norm5.rawsignal.bw HeLa-S3 ChipSeq PRDM1_(Val90) Signal bigWig Stanford analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeSydhTfbsHelas3Rad21IggrabAln_2Reps.norm5.rawsignal.bw HeLa-S3 ChipSeq Rad21 Signal bigWig Stanford analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeSydhTfbsHelas3Rfx5n494IggrabAln_2Reps.norm5.rawsignal.bw HeLa-S3 ChipSeq RFX5_(N-494) Signal bigWig Stanford analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeSydhTfbsHelas3Rpc155StdAln_2Reps.norm5.rawsignal.bw HeLa-S3 ChipSeq RPC155 Signal bigWig Stanford analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeSydhTfbsHelas3Smc3ab9263IggrabAln_2Reps.norm5.rawsignal.bw HeLa-S3 ChipSeq SMC3_(ab9263) Signal bigWig Stanford analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeSydhTfbsHelas3Spt20StdAln_2Reps.norm5.rawsignal.bw HeLa-S3 ChipSeq SPT20 Signal bigWig Stanford analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeSydhTfbsHelas3Stat1Ifng30StdAln_2Reps.norm5.rawsignal.bw HeLa-S3 ChipSeq STAT1 Signal bigWig Stanford analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeSydhTfbsHelas3Stat3IggrabAln_2Reps.norm5.rawsignal.bw HeLa-S3 ChipSeq STAT3 Signal bigWig Stanford analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeSydhTfbsHelas3TbpIggrabAln_2Reps.norm5.rawsignal.bw HeLa-S3 ChipSeq TBP Signal bigWig Stanford analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeSydhTfbsHelas3Tf3c110StdAln_2Reps.norm5.rawsignal.bw HeLa-S3 ChipSeq TFIIIC-110 Signal bigWig Stanford analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeSydhTfbsHelas3Tr4StdAln_2Reps.norm5.rawsignal.bw HeLa-S3 ChipSeq TR4 Signal bigWig Stanford analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeSydhTfbsHelas3Usf2IggmusAln_2Reps.norm5.rawsignal.bw HeLa-S3 ChipSeq USF2 Signal bigWig Stanford analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeSydhTfbsHelas3Znf274UcdAln_2Reps.norm5.rawsignal.bw HeLa-S3 ChipSeq ZNF274 Signal bigWig UCD analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeSydhTfbsHelas3Zzz3StdAln_2Reps.norm5.rawsignal.bw HeLa-S3 ChipSeq ZZZ3 Signal bigWig Harvard(Weissman) analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeSydhTfbsHepg2bInputUcdAln_1Reps.norm5.rawsignal.bw HepG2b ChipSeq Input Signal bigWig Stanford analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeSydhTfbsHepg2bTr4UcdAln_2Reps.norm5.rawsignal.bw HepG2b ChipSeq TR4 Signal bigWig Stanford analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeSydhTfbsHepg2bZnf274UcdAln_2Reps.norm5.rawsignal.bw HepG2b ChipSeq ZNF274 Signal bigWig UCD analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeSydhTfbsHepg2CebpbForsklnStdAln_2Reps.norm5.rawsignal.bw HepG2 ChipSeq CEBPB Signal bigWig Stanford analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeSydhTfbsHepg2CebpbIggrabAln_2Reps.norm5.rawsignal.bw HepG2 ChipSeq CEBPB Signal bigWig Stanford analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeSydhTfbsHepg2Chd21250IggrabAln_2Reps.norm5.rawsignal.bw HepG2 ChipSeq CHD2_(N-1250) Signal bigWig Stanford analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeSydhTfbsHepg2CjunIggrabAln_2Reps.norm5.rawsignal.bw HepG2 ChipSeq c-Jun Signal bigWig Stanford analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeSydhTfbsHepg2ErraForsklnStdAln_2Reps.norm5.rawsignal.bw HepG2 ChipSeq ERRA Signal bigWig Stanford analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeSydhTfbsHepg2Grp20ForsklnStdAln_2Reps.norm5.rawsignal.bw HepG2 ChipSeq GRp20 Signal bigWig Stanford analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeSydhTfbsHepg2Hnf4aForsklnStdAln_2Reps.norm5.rawsignal.bw HepG2 ChipSeq HNF4A Signal bigWig Stanford analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeSydhTfbsHepg2Hsf1ForsklnStdAln_2Reps.norm5.rawsignal.bw HepG2 ChipSeq HSF1 Signal bigWig Stanford analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeSydhTfbsHepg2InputForsklnStdAln_2Reps.norm5.rawsignal.bw HepG2 ChipSeq Input Signal bigWig Stanford analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeSydhTfbsHepg2InputIggrabAln_1Reps.norm5.rawsignal.bw HepG2 ChipSeq Input Signal bigWig Stanford analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeSydhTfbsHepg2InputInslnStdAln_2Reps.norm5.rawsignal.bw HepG2 ChipSeq Input Signal bigWig Stanford analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeSydhTfbsHepg2InputPravastStdAln_3Reps.norm5.rawsignal.bw HepG2 ChipSeq Input Signal bigWig Stanford analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeSydhTfbsHepg2Irf3IggrabAln_2Reps.norm5.rawsignal.bw HepG2 ChipSeq IRF3 Signal bigWig Stanford analysis 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http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeSydhTfbsK562Atf3StdAln_2Reps.norm5.rawsignal.bw K562 ChipSeq ATF3 Signal bigWig Stanford analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeSydhTfbsK562Bdp1StdAln_3Reps.norm5.rawsignal.bw K562 ChipSeq BDP1 Signal bigWig Stanford analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeSydhTfbsK562bE2f4UcdAln_2Reps.norm5.rawsignal.bw K562b ChipSeq E2F4 Signal bigWig Stanford analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeSydhTfbsK562bE2f6UcdAln_2Reps.norm5.rawsignal.bw K562b ChipSeq E2F6 Signal bigWig Stanford analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeSydhTfbsK562bGata1UcdAln_2Reps.norm5.rawsignal.bw K562b ChipSeq GATA-1 Signal bigWig Stanford analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeSydhTfbsK562bGata2UcdAln_2Reps.norm5.rawsignal.bw K562b ChipSeq GATA-2 Signal bigWig Stanford analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeSydhTfbsK562bInputUcdAln_1Reps.norm5.rawsignal.bw K562b ChipSeq Input Signal bigWig Stanford analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeSydhTfbsK562bKap1UcdAln_2Reps.norm5.rawsignal.bw K562b ChipSeq KAP1 Signal bigWig UCD analysis 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http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeSydhTfbsK562Chd21250IggrabAln_2Reps.norm5.rawsignal.bw K562 ChipSeq CHD2_(N-1250) Signal bigWig Stanford analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeSydhTfbsK562CjunIfna6hStdAln_2Reps.norm5.rawsignal.bw K562 ChipSeq c-Jun Signal bigWig Stanford analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeSydhTfbsK562CjunIfng30StdAln_2Reps.norm5.rawsignal.bw K562 ChipSeq c-Jun Signal bigWig Stanford analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeSydhTfbsK562CjunIfng6hStdAln_2Reps.norm5.rawsignal.bw K562 ChipSeq c-Jun Signal bigWig Stanford analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeSydhTfbsK562CjunStdAln_2Reps.norm5.rawsignal.bw K562 ChipSeq c-Jun Signal bigWig Stanford analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeSydhTfbsK562CmycIfna30StdAln_2Reps.norm5.rawsignal.bw K562 ChipSeq c-Myc Signal bigWig Stanford analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeSydhTfbsK562CmycIfna6hStdAln_2Reps.norm5.rawsignal.bw K562 ChipSeq c-Myc Signal bigWig Stanford analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeSydhTfbsK562CmycIfng30StdAln_2Reps.norm5.rawsignal.bw K562 ChipSeq c-Myc Signal bigWig Stanford analysis 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http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeSydhTfbsK562Hmgn3StdAln_2Reps.norm5.rawsignal.bw K562 ChipSeq HMGN3 Signal bigWig Harvard analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeSydhTfbsK562Ini1IggmusAln_2Reps.norm5.rawsignal.bw K562 ChipSeq Ini1 Signal bigWig Stanford analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeSydhTfbsK562InputIfna30StdAln_1Reps.norm5.rawsignal.bw K562 ChipSeq Input Signal bigWig Stanford analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeSydhTfbsK562InputIfna6hStdAln_1Reps.norm5.rawsignal.bw K562 ChipSeq Input Signal bigWig Stanford analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeSydhTfbsK562InputIfng30StdAln_1Reps.norm5.rawsignal.bw K562 ChipSeq Input Signal bigWig Stanford analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeSydhTfbsK562InputIfng6hStdAln_1Reps.norm5.rawsignal.bw K562 ChipSeq Input Signal bigWig Stanford analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeSydhTfbsK562InputIggmusAln_2Reps.norm5.rawsignal.bw K562 ChipSeq Input Signal bigWig Stanford analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeSydhTfbsK562InputIggrabAln_1Reps.norm5.rawsignal.bw K562 ChipSeq Input Signal bigWig Stanford analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeSydhTfbsK562InputStdAln_2Reps.norm5.rawsignal.bw K562 ChipSeq Input Signal bigWig Stanford analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeSydhTfbsK562Irf1Ifna30StdAln_2Reps.norm5.rawsignal.bw K562 ChipSeq IRF1 Signal bigWig Stanford analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeSydhTfbsK562Irf1Ifng6hStdAln_2Reps.norm5.rawsignal.bw K562 ChipSeq IRF1 Signal bigWig Stanford analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeSydhTfbsK562JundStdAln_2Reps.norm5.rawsignal.bw K562 ChipSeq JunD Signal bigWig Stanford analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeSydhTfbsK562Mafkab50322IggrabAln_2Reps.norm5.rawsignal.bw K562 ChipSeq MafK_(ab50322) Signal bigWig Stanford analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeSydhTfbsK562MaxStdAln_2Reps.norm5.rawsignal.bw K562 ChipSeq Max Signal bigWig Stanford analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeSydhTfbsK562Mxi1bhlhIggrabAln_2Reps.norm5.rawsignal.bw K562 ChipSeq Mxi1_(bHLH) Signal bigWig Stanford analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeSydhTfbsK562NelfeStdAln_2Reps.norm5.rawsignal.bw K562 ChipSeq NELFe Signal bigWig Stanford analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeSydhTfbsK562Nfe2StdAln_2Reps.norm5.rawsignal.bw K562 ChipSeq NF-E2 Signal bigWig Stanford analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeSydhTfbsK562NfyaStdAln_2Reps.norm5.rawsignal.bw K562 ChipSeq NF-YA Signal bigWig Stanford analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeSydhTfbsK562NfybStdAln_2Reps.norm5.rawsignal.bw K562 ChipSeq NF-YB Signal bigWig Stanford analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeSydhTfbsK562Nrf1IggrabAln_2Reps.norm5.rawsignal.bw K562 ChipSeq Nrf1 Signal bigWig Stanford analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeSydhTfbsK562P300f4IggrabAln_2Reps.norm5.rawsignal.bw K562 ChipSeq p300_(F-4) Signal bigWig Stanford analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeSydhTfbsK562Pol2Ifna30StdAln_2Reps.norm5.rawsignal.bw K562 ChipSeq Pol2 Signal bigWig Stanford analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeSydhTfbsK562Pol2Ifna6hStdAln_2Reps.norm5.rawsignal.bw K562 ChipSeq Pol2 Signal bigWig Stanford analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeSydhTfbsK562Pol2Ifng30StdAln_2Reps.norm5.rawsignal.bw K562 ChipSeq Pol2 Signal bigWig Stanford analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeSydhTfbsK562Pol2Ifng6hStdAln_2Reps.norm5.rawsignal.bw K562 ChipSeq Pol2 Signal bigWig Stanford analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeSydhTfbsK562Pol2IggmusAln_2Reps.norm5.rawsignal.bw K562 ChipSeq Pol2 Signal bigWig Stanford analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeSydhTfbsK562Pol2s2StdAln_2Reps.norm5.rawsignal.bw K562 ChipSeq Pol2(phosphoS2) Signal bigWig Stanford analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeSydhTfbsK562Pol2StdAln_2Reps.norm5.rawsignal.bw K562 ChipSeq Pol2 Signal bigWig Stanford analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeSydhTfbsK562Pol3StdAln_2Reps.norm5.rawsignal.bw K562 ChipSeq Pol3 Signal bigWig Stanford analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeSydhTfbsK562Rad21StdAln_2Reps.norm5.rawsignal.bw K562 ChipSeq Rad21 Signal bigWig Stanford analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeSydhTfbsK562Rpc155StdAln_2Reps.norm5.rawsignal.bw K562 ChipSeq RPC155 Signal bigWig Stanford analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeSydhTfbsK562Sirt6StdAln_2Reps.norm5.rawsignal.bw K562 ChipSeq SIRT6 Signal bigWig Stanford analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeSydhTfbsK562Smc3ab9263IggrabAln_2Reps.norm5.rawsignal.bw K562 ChipSeq SMC3_(ab9263) Signal bigWig Stanford analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeSydhTfbsK562Stat1Ifna30StdAln_2Reps.norm5.rawsignal.bw K562 ChipSeq STAT1 Signal bigWig Stanford analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeSydhTfbsK562Stat1Ifna6hStdAln_2Reps.norm5.rawsignal.bw K562 ChipSeq STAT1 Signal bigWig Stanford analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeSydhTfbsK562Stat1Ifng30StdAln_2Reps.norm5.rawsignal.bw K562 ChipSeq STAT1 Signal bigWig Stanford analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeSydhTfbsK562Stat1Ifng6hStdAln_2Reps.norm5.rawsignal.bw K562 ChipSeq STAT1 Signal bigWig Stanford analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeSydhTfbsK562Stat2Ifna30StdAln_2Reps.norm5.rawsignal.bw K562 ChipSeq STAT2 Signal bigWig Stanford analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeSydhTfbsK562Stat2Ifna6hStdAln_2Reps.norm5.rawsignal.bw K562 ChipSeq STAT2 Signal bigWig Stanford analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeSydhTfbsK562Tal1sc12984IggmusAln_2Reps.norm5.rawsignal.bw K562 ChipSeq TAL1_(SC-12984) Signal bigWig Stanford analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeSydhTfbsK562TbpIggmusAln_2Reps.norm5.rawsignal.bw K562 ChipSeq TBP Signal bigWig Stanford analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeSydhTfbsK562Tf3c110StdAln_3Reps.norm5.rawsignal.bw K562 ChipSeq TFIIIC-110 Signal bigWig Stanford analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeSydhTfbsK562Usf2StdAln_2Reps.norm5.rawsignal.bw K562 ChipSeq USF2 Signal bigWig Stanford analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeSydhTfbsK562Xrcc4StdAln_2Reps.norm5.rawsignal.bw K562 ChipSeq XRCC4 Signal bigWig Stanford analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeSydhTfbsMcf10aesInputEtoh01bStdAln_1Reps.norm5.rawsignal.bw MCF10A-Er-Src ChipSeq Input Signal bigWig Harvard(Weissman) analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeSydhTfbsMcf10aesInputEtoh01cStdAln_1Reps.norm5.rawsignal.bw MCF10A-Er-Src ChipSeq Input Signal bigWig Harvard(Weissman) analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeSydhTfbsMcf10aesInputUcdAln_1Reps.norm5.rawsignal.bw MCF10A-Er-Src ChipSeq Input Signal bigWig UCD(Farnham) analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeSydhTfbsMcf10aesPol2Etoh01StdAln_2Reps.norm5.rawsignal.bw MCF10A-Er-Src ChipSeq Pol2 Signal bigWig Stanford analysis 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http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeSydhTfbsMcf10aesStat3TamStdAln_2Reps.norm5.rawsignal.bw MCF10A-Er-Src ChipSeq STAT3 Signal bigWig Harvard(Weissman) analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeSydhTfbsMcf7Hae2f1UcdAln_2Reps.norm5.rawsignal.bw MCF-7 ChipSeq HA-E2F1 Signal bigWig Stanford analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeSydhTfbsMcf7InputUcdAln_2Reps.norm5.rawsignal.bw MCF-7 ChipSeq Input Signal bigWig Stanford analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeSydhTfbsNb4CmycStdAln_2Reps.norm5.rawsignal.bw NB4 ChipSeq c-Myc Signal bigWig Stanford analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeSydhTfbsNb4InputStdAln_1Reps.norm5.rawsignal.bw NB4 ChipSeq Input Signal bigWig Stanford analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeSydhTfbsNb4MaxStdAln_2Reps.norm5.rawsignal.bw NB4 ChipSeq Max Signal bigWig Stanford analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeSydhTfbsNb4Pol2StdAln_3Reps.norm5.rawsignal.bw NB4 ChipSeq Pol2 Signal bigWig Stanford analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeSydhTfbsNt2d1InputUcdAln_1Reps.norm5.rawsignal.bw NT2-D1 ChipSeq Input Signal bigWig Stanford analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeSydhTfbsNt2d1Suz12UcdAln_2Reps.norm5.rawsignal.bw NT2-D1 ChipSeq SUZ12 Signal bigWig Stanford analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeSydhTfbsNt2d1Yy1UcdAln_2Reps.norm5.rawsignal.bw NT2-D1 ChipSeq YY1 Signal bigWig Stanford analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeSydhTfbsNt2d1Znf274UcdAln_2Reps.norm5.rawsignal.bw NT2-D1 ChipSeq ZNF274 Signal bigWig UCD analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeSydhTfbsPbdeGata1UcdAln_2Reps.norm5.rawsignal.bw PBDE ChipSeq GATA-1 Signal bigWig UCD analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeSydhTfbsPbdeInputUcdAln_1Reps.norm5.rawsignal.bw PBDE ChipSeq Input Signal bigWig UCD analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeSydhTfbsPbdePol2UcdAln_2Reps.norm5.rawsignal.bw PBDE ChipSeq Pol2 Signal bigWig UCD analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeSydhTfbsRajiInputUcdAln_1Reps.norm5.rawsignal.bw Raji ChipSeq Input Signal bigWig Stanford analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeSydhTfbsRajiPol2UcdAln_2Reps.norm5.rawsignal.bw Raji ChipSeq Pol2 Signal bigWig UCD analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeSydhTfbsShsy5yGata2UcdAln_2Reps.norm5.rawsignal.bw SH-SY5Y ChipSeq GATA-2 Signal bigWig UCD analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeSydhTfbsShsy5yInputUcdAln_1Reps.norm5.rawsignal.bw SH-SY5Y ChipSeq Input Signal bigWig UCD(Farnham) analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeSydhTfbsThek293InputUcdAln_1Reps.norm5.rawsignal.bw T-REx-HEK293 ChipSeq Input Signal bigWig UCD(Farnham) analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeSydhTfbsTrexhek293Znf263UcdAln_2Reps.norm5.rawsignal.bw T-REx-HEK293 ChipSeq ZNF263 Signal bigWig UCD analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeSydhTfbsU2osInputUcdAln_1Reps.norm5.rawsignal.bw U2OS ChipSeq Input Signal bigWig Stanford analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeSydhTfbsU2osKap1UcdAln_2Reps.norm5.rawsignal.bw U2OS ChipSeq KAP1 Signal bigWig Stanford analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeSydhTfbsU2osSetdb1UcdAln_2Reps.norm5.rawsignal.bw U2OS ChipSeq SETDB1 Signal bigWig UCD analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeUchicagoTfbsK562EfosControlAln_3Reps.norm5.rawsignal.bw K562 ChipSeq eGFP-FOS Signal bigWig UChicago analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeUchicagoTfbsK562Egata2ControlAln_2Reps.norm5.rawsignal.bw K562 ChipSeq eGFP-GATA2 Signal bigWig UChicago analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeUchicagoTfbsK562Ehdac8ControlAln_2Reps.norm5.rawsignal.bw K562 ChipSeq eGFP-HDAC8 Signal bigWig UChicago analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeUchicagoTfbsK562EjunbControlAln_2Reps.norm5.rawsignal.bw K562 ChipSeq eGFP-JunB Signal bigWig UChicago analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeUchicagoTfbsK562EjundControlAln_3Reps.norm5.rawsignal.bw K562 ChipSeq eGFP-JunD Signal bigWig UChicago analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeUchicagoTfbsK562Enr4a1ControlAln_2Reps.norm5.rawsignal.bw K562 ChipSeq eGFP-NR4A1 Signal bigWig UChicago analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeUchicagoTfbsK562InputControlfosAln_3Reps.norm5.rawsignal.bw K562 ChipSeq Input Signal bigWig UChicago analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeUchicagoTfbsK562InputControlgata2Aln_2Reps.norm5.rawsignal.bw K562 ChipSeq Input Signal bigWig UChicago analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeUchicagoTfbsK562InputControlhdac8Aln_2Reps.norm5.rawsignal.bw K562 ChipSeq Input Signal bigWig UChicago analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeUchicagoTfbsK562InputControljunbAln_2Reps.norm5.rawsignal.bw K562 ChipSeq Input Signal bigWig UChicago analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeUchicagoTfbsK562InputControljundAln_3Reps.norm5.rawsignal.bw K562 ChipSeq Input Signal bigWig UChicago analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeUchicagoTfbsK562InputControlnr4a1Aln_2Reps.norm5.rawsignal.bw K562 ChipSeq Input Signal bigWig UChicago analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeUwDnaseA549Aln_2Reps.norm5.rawsignal.bw A549 DnaseSeq Signal bigWig UW analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeUwDnaseAg04449Aln_2Reps.norm5.rawsignal.bw AG04449 DnaseSeq Signal bigWig UW analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeUwDnaseAg04450Aln_2Reps.norm5.rawsignal.bw AG04450 DnaseSeq Signal bigWig UW analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeUwDnaseAg09309Aln_2Reps.norm5.rawsignal.bw AG09309 DnaseSeq Signal bigWig UW analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeUwDnaseAg09319Aln_2Reps.norm5.rawsignal.bw AG09319 DnaseSeq Signal bigWig UW analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeUwDnaseAg10803Aln_2Reps.norm5.rawsignal.bw AG10803 DnaseSeq Signal bigWig UW analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeUwDnaseAoafAln_2Reps.norm5.rawsignal.bw AoAF DnaseSeq Signal bigWig UW analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeUwDnaseBe2cAln_2Reps.norm5.rawsignal.bw BE2_C DnaseSeq Signal bigWig UW analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeUwDnaseBjAln_2Reps.norm5.rawsignal.bw BJ DnaseSeq Signal bigWig UW analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeUwDnaseCaco2Aln_2Reps.norm5.rawsignal.bw Caco-2 DnaseSeq Signal bigWig UW analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeUwDnaseCmkAln_1Reps.norm5.rawsignal.bw CMK DnaseSeq Signal bigWig UW analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeUwDnaseGm06990Aln_2Reps.norm5.rawsignal.bw GM06990 DnaseSeq Signal bigWig UW analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeUwDnaseGm12864Aln_1Reps.norm5.rawsignal.bw GM12864 DnaseSeq Signal bigWig UW analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeUwDnaseGm12865Aln_2Reps.norm5.rawsignal.bw GM12865 DnaseSeq Signal bigWig UW analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeUwDnaseGm12878Aln_2Reps.norm5.rawsignal.bw GM12878 DnaseSeq Signal bigWig UW analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeUwDnaseH1hescAln_1Reps.norm5.rawsignal.bw H1-hESC DnaseSeq Signal bigWig UW analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeUwDnaseH7esAln_2Reps.norm5.rawsignal.bw H7-hESC DnaseSeq Signal bigWig UW analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeUwDnaseHacAln_2Reps.norm5.rawsignal.bw HAc DnaseSeq Signal bigWig UW analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeUwDnaseHaeAln_2Reps.norm5.rawsignal.bw HAEpiC DnaseSeq Signal bigWig UW analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeUwDnaseHahAln_2Reps.norm5.rawsignal.bw HA-h DnaseSeq Signal bigWig UW analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeUwDnaseHaspAln_2Reps.norm5.rawsignal.bw HA-sp DnaseSeq Signal bigWig UW analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeUwDnaseHbmecAln_2Reps.norm5.rawsignal.bw HBMEC DnaseSeq Signal bigWig UW analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeUwDnaseHcfaaAln_2Reps.norm5.rawsignal.bw HCFaa DnaseSeq Signal bigWig UW analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeUwDnaseHcfAln_2Reps.norm5.rawsignal.bw HCF DnaseSeq Signal bigWig UW analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeUwDnaseHcmAln_2Reps.norm5.rawsignal.bw HCM DnaseSeq Signal bigWig UW analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeUwDnaseHconfAln_2Reps.norm5.rawsignal.bw HConF DnaseSeq Signal bigWig UW analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeUwDnaseHcpeAln_2Reps.norm5.rawsignal.bw HCPEpiC DnaseSeq Signal bigWig UW analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeUwDnaseHct116Aln_2Reps.norm5.rawsignal.bw HCT-116 DnaseSeq Signal bigWig UW analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeUwDnaseHeeAln_2Reps.norm5.rawsignal.bw HEEpiC DnaseSeq Signal bigWig UW analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeUwDnaseHelas3Aln_2Reps.norm5.rawsignal.bw HeLa-S3 DnaseSeq Signal bigWig UW analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeUwDnaseHepg2Aln_2Reps.norm5.rawsignal.bw HepG2 DnaseSeq Signal bigWig UW analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeUwDnaseHffAln_2Reps.norm5.rawsignal.bw HFF DnaseSeq Signal bigWig UW analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeUwDnaseHffmycAln_2Reps.norm5.rawsignal.bw HFF-Myc DnaseSeq Signal bigWig UW analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeUwDnaseHgfAln_2Reps.norm5.rawsignal.bw HGF DnaseSeq Signal bigWig UW analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeUwDnaseHipeAln_2Reps.norm5.rawsignal.bw HIPEpiC DnaseSeq Signal bigWig UW analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeUwDnaseHl60Aln_2Reps.norm5.rawsignal.bw HL-60 DnaseSeq Signal bigWig UW analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeUwDnaseHmecAln_2Reps.norm5.rawsignal.bw HMEC DnaseSeq Signal bigWig UW analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeUwDnaseHmfAln_2Reps.norm5.rawsignal.bw HMF DnaseSeq Signal bigWig UW analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeUwDnaseHmvecdbladAln_2Reps.norm5.rawsignal.bw HMVEC-dBl-Ad DnaseSeq Signal bigWig UW analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeUwDnaseHmvecdblneoAln_2Reps.norm5.rawsignal.bw HMVEC-dBl-Neo DnaseSeq Signal bigWig UW analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeUwDnaseHmvecdlyadAln_2Reps.norm5.rawsignal.bw HMVEC-dLy-Ad DnaseSeq Signal bigWig UW analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeUwDnaseHmvecdlyneoAln_2Reps.norm5.rawsignal.bw HMVEC-dLy-Neo DnaseSeq Signal bigWig UW analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeUwDnaseHmvecdneoAln_2Reps.norm5.rawsignal.bw HMVEC-dNeo DnaseSeq Signal bigWig UW analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeUwDnaseHmveclblAln_2Reps.norm5.rawsignal.bw HMVEC-LBl DnaseSeq Signal bigWig UW analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeUwDnaseHmvecllyAln_2Reps.norm5.rawsignal.bw HMVEC-LLy DnaseSeq Signal bigWig UW analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeUwDnaseHnpceAln_2Reps.norm5.rawsignal.bw HNPCEpiC DnaseSeq Signal bigWig UW analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeUwDnaseHpafAln_2Reps.norm5.rawsignal.bw HPAF DnaseSeq Signal bigWig UW analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeUwDnaseHpdlfAln_2Reps.norm5.rawsignal.bw HPdLF DnaseSeq Signal bigWig UW analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeUwDnaseHpfAln_2Reps.norm5.rawsignal.bw HPF DnaseSeq Signal bigWig UW analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeUwDnaseHrceAln_2Reps.norm5.rawsignal.bw HRCEpiC DnaseSeq Signal bigWig UW analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeUwDnaseHreAln_2Reps.norm5.rawsignal.bw HRE DnaseSeq Signal bigWig UW analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeUwDnaseHrgecAln_2Reps.norm5.rawsignal.bw HRGEC DnaseSeq Signal bigWig UW analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeUwDnaseHrpeAln_2Reps.norm5.rawsignal.bw HRPEpiC DnaseSeq Signal bigWig UW analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeUwDnaseHsmmAln_2Reps.norm5.rawsignal.bw HSMM DnaseSeq Signal bigWig UW analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeUwDnaseHsmmtAln_1Reps.norm5.rawsignal.bw HSMMtube DnaseSeq Signal bigWig UW analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeUwDnaseHuvecAln_2Reps.norm5.rawsignal.bw HUVEC DnaseSeq Signal bigWig UW analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeUwDnaseHvmfAln_2Reps.norm5.rawsignal.bw HVMF DnaseSeq Signal bigWig UW analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeUwDnaseJurkatAln_2Reps.norm5.rawsignal.bw Jurkat DnaseSeq Signal bigWig UW analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeUwDnaseK562Aln_2Reps.norm5.rawsignal.bw K562 DnaseSeq Signal bigWig UW analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeUwDnaseLncapAln_2Reps.norm5.rawsignal.bw LNCaP DnaseSeq Signal bigWig UW analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeUwDnaseMcf7Aln_2Reps.norm5.rawsignal.bw MCF-7 DnaseSeq Signal bigWig UW analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeUwDnaseMonocd14Aln_1Reps.norm5.rawsignal.bw Monocytes-CD14+ DnaseSeq Signal bigWig UW analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeUwDnaseNb4Aln_2Reps.norm5.rawsignal.bw NB4 DnaseSeq Signal bigWig UW analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeUwDnaseNhaAln_2Reps.norm5.rawsignal.bw NH-A DnaseSeq Signal bigWig UW analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeUwDnaseNhdfadAln_2Reps.norm5.rawsignal.bw NHDF-Ad DnaseSeq Signal bigWig UW analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeUwDnaseNhdfneoAln_2Reps.norm5.rawsignal.bw NHDF-neo DnaseSeq Signal bigWig UW analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeUwDnaseNhekAln_2Reps.norm5.rawsignal.bw NHEK DnaseSeq Signal bigWig UW analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeUwDnaseNhlfAln_2Reps.norm5.rawsignal.bw NHLF DnaseSeq Signal bigWig UW analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeUwDnasePanc1Aln_2Reps.norm5.rawsignal.bw PANC-1 DnaseSeq Signal bigWig UW analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeUwDnaseRptecAln_2Reps.norm5.rawsignal.bw RPTEC DnaseSeq Signal bigWig UW analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeUwDnaseSaecAln_2Reps.norm5.rawsignal.bw SAEC DnaseSeq Signal bigWig UW analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeUwDnaseSkmcAln_2Reps.norm5.rawsignal.bw SKMC DnaseSeq Signal bigWig UW analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeUwDnaseSknmcAln_2Reps.norm5.rawsignal.bw SK-N-MC DnaseSeq Signal bigWig UW analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeUwDnaseSknshraAln_2Reps.norm5.rawsignal.bw SK-N-SH_RA DnaseSeq Signal bigWig UW analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeUwDnaseTh1Aln_1Reps.norm5.rawsignal.bw Th1 DnaseSeq Signal bigWig UW analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeUwDnaseTh2Aln_1Reps.norm5.rawsignal.bw Th2 DnaseSeq Signal bigWig UW analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeUwDnaseWerirb1Aln_2Reps.norm5.rawsignal.bw WERI-Rb-1 DnaseSeq Signal bigWig UW analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeUwDnaseWi38Aln_2Reps.norm5.rawsignal.bw WI-38 DnaseSeq Signal bigWig UW analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeUwDnaseWi38OhtamAln_2Reps.norm5.rawsignal.bw WI-38 DnaseSeq Signal bigWig UW analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeUwHistoneAg04449H3k4me3StdAln_2Reps.norm5.rawsignal.bw AG04449 ChipSeq H3K4me3 Signal 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http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeUwHistoneAg09309InputStdAln_1Reps.norm5.rawsignal.bw AG09309 ChipSeq Input Signal bigWig UW analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeUwHistoneAg09319H3k4me3StdAln_2Reps.norm5.rawsignal.bw AG09319 ChipSeq H3K4me3 Signal bigWig UW analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeUwHistoneAg09319InputStdAln_1Reps.norm5.rawsignal.bw AG09319 ChipSeq Input Signal bigWig UW analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeUwHistoneAg10803H3k4me3StdAln_2Reps.norm5.rawsignal.bw AG10803 ChipSeq H3K4me3 Signal bigWig UW analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeUwHistoneAg10803InputStdAln_1Reps.norm5.rawsignal.bw AG10803 ChipSeq Input Signal bigWig UW analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeUwHistoneAoafH3k4me3StdAln_2Reps.norm5.rawsignal.bw AoAF ChipSeq H3K4me3 Signal bigWig UW analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeUwHistoneAoafInputStdAln_1Reps.norm5.rawsignal.bw AoAF ChipSeq Input Signal bigWig UW analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeUwHistoneBjH3k27me3StdAln_2Reps.norm5.rawsignal.bw BJ ChipSeq H3K27me3 Signal bigWig UW analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeUwHistoneBjH3k36me3StdAln_2Reps.norm5.rawsignal.bw BJ ChipSeq H3K36me3 Signal bigWig UW analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeUwHistoneBjH3k4me3StdAln_2Reps.norm5.rawsignal.bw BJ ChipSeq H3K4me3 Signal bigWig UW analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeUwHistoneBjInputStdAln_1Reps.norm5.rawsignal.bw BJ ChipSeq Input Signal bigWig UW analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeUwHistoneCaco2H3k27me3StdAln_2Reps.norm5.rawsignal.bw Caco-2 ChipSeq H3K27me3 Signal bigWig UW analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeUwHistoneCaco2H3k36me3StdAln_2Reps.norm5.rawsignal.bw Caco-2 ChipSeq H3K36me3 Signal bigWig UW analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeUwHistoneCaco2H3k4me3StdAln_2Reps.norm5.rawsignal.bw Caco-2 ChipSeq H3K4me3 Signal bigWig UW analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeUwHistoneCaco2InputStdAln_1Reps.norm5.rawsignal.bw Caco-2 ChipSeq Input Signal bigWig UW analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeUwHistoneGm06990H3k27me3StdAln_2Reps.norm5.rawsignal.bw GM06990 ChipSeq H3K27me3 Signal bigWig UW analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeUwHistoneGm06990H3k36me3StdAln_2Reps.norm5.rawsignal.bw GM06990 ChipSeq H3K36me3 Signal bigWig UW analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeUwHistoneGm06990H3k4me3StdAln_2Reps.norm5.rawsignal.bw GM06990 ChipSeq H3K4me3 Signal bigWig UW analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeUwHistoneGm06990InputStdAln_1Reps.norm5.rawsignal.bw GM06990 ChipSeq Input Signal bigWig UW analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeUwHistoneGm12878H3k27me3StdAln_2Reps.norm5.rawsignal.bw GM12878 ChipSeq H3K27me3 Signal bigWig UW analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeUwHistoneGm12878H3k36me3StdAln_2Reps.norm5.rawsignal.bw GM12878 ChipSeq H3K36me3 Signal bigWig UW analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeUwHistoneGm12878H3k4me3StdAln_2Reps.norm5.rawsignal.bw GM12878 ChipSeq H3K4me3 Signal bigWig UW analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeUwHistoneGm12878InputStdAln_1Reps.norm5.rawsignal.bw GM12878 ChipSeq Input Signal bigWig UW analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeUwHistoneH7esH3k27me3StdAln_2Reps.norm5.rawsignal.bw H7-hESC ChipSeq H3K27me3 Signal bigWig UW analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeUwHistoneH7esH3k36me3StdAln_2Reps.norm5.rawsignal.bw H7-hESC ChipSeq H3K36me3 Signal bigWig UW analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeUwHistoneH7esH3k4me3StdAln_2Reps.norm5.rawsignal.bw H7-hESC ChipSeq H3K4me3 Signal bigWig UW analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeUwHistoneH7esInputStdAln_1Reps.norm5.rawsignal.bw H7-hESC ChipSeq Input Signal bigWig UW analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeUwHistoneHaspH3k4me3StdAln_2Reps.norm5.rawsignal.bw HA-sp ChipSeq H3K4me3 Signal bigWig UW analysis 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http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeUwHistoneHcmInputStdAln_1Reps.norm5.rawsignal.bw HCM ChipSeq Input Signal bigWig UW analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeUwHistoneHcpeH3k4me3StdAln_2Reps.norm5.rawsignal.bw HCPEpiC ChipSeq H3K4me3 Signal bigWig UW analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeUwHistoneHcpeInputStdAln_1Reps.norm5.rawsignal.bw HCPEpiC ChipSeq Input Signal bigWig UW analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeUwHistoneHct116H3k4me3StdAln_2Reps.norm5.rawsignal.bw HCT-116 ChipSeq H3K4me3 Signal bigWig UW analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeUwHistoneHct116InputStdAln_1Reps.norm5.rawsignal.bw HCT-116 ChipSeq Input Signal bigWig UW analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeUwHistoneHeeH3k4me3StdAln_2Reps.norm5.rawsignal.bw HEEpiC ChipSeq H3K4me3 Signal bigWig UW analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeUwHistoneHeeInputStdAln_1Reps.norm5.rawsignal.bw HEEpiC ChipSeq Input Signal bigWig UW analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeUwHistoneHek293H3k4me3StdAln_2Reps.norm5.rawsignal.bw HEK293 ChipSeq H3K4me3 Signal bigWig UW analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeUwHistoneHek293InputStdAln_1Reps.norm5.rawsignal.bw HEK293 ChipSeq Input Signal bigWig UW analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeUwHistoneHelas3H3k27me3StdAln_2Reps.norm5.rawsignal.bw HeLa-S3 ChipSeq H3K27me3 Signal bigWig UW analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeUwHistoneHelas3H3k36me3StdAln_2Reps.norm5.rawsignal.bw HeLa-S3 ChipSeq H3K36me3 Signal bigWig UW analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeUwHistoneHelas3H3k4me3StdAln_2Reps.norm5.rawsignal.bw HeLa-S3 ChipSeq H3K4me3 Signal bigWig UW analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeUwHistoneHelas3InputStdAln_1Reps.norm5.rawsignal.bw HeLa-S3 ChipSeq Input Signal bigWig UW analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeUwHistoneHepg2H3k27me3StdAln_2Reps.norm5.rawsignal.bw HepG2 ChipSeq H3K27me3 Signal bigWig UW analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeUwHistoneHepg2H3k36me3StdAln_2Reps.norm5.rawsignal.bw HepG2 ChipSeq H3K36me3 Signal bigWig UW analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeUwHistoneHepg2H3k4me3StdAln_2Reps.norm5.rawsignal.bw HepG2 ChipSeq H3K4me3 Signal bigWig UW analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeUwHistoneHepg2InputStdAln_1Reps.norm5.rawsignal.bw HepG2 ChipSeq Input Signal bigWig UW analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeUwHistoneHl60H3k4me3StdAln_2Reps.norm5.rawsignal.bw HL-60 ChipSeq H3K4me3 Signal bigWig UW analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeUwHistoneHl60InputStdAln_1Reps.norm5.rawsignal.bw HL-60 ChipSeq Input Signal bigWig UW analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeUwHistoneHmecH3k27me3StdAln_1Reps.norm5.rawsignal.bw HMEC ChipSeq H3K27me3 Signal bigWig UW analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeUwHistoneHmecH3k4me3StdAln_2Reps.norm5.rawsignal.bw HMEC ChipSeq H3K4me3 Signal bigWig UW analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeUwHistoneHmecInputStdAln_1Reps.norm5.rawsignal.bw HMEC ChipSeq Input Signal bigWig UW analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeUwHistoneHmfH3k4me3StdAln_2Reps.norm5.rawsignal.bw HMF ChipSeq H3K4me3 Signal bigWig UW analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeUwHistoneHmfInputStdAln_1Reps.norm5.rawsignal.bw HMF ChipSeq Input Signal bigWig UW analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeUwHistoneHpafH3k4me3StdAln_2Reps.norm5.rawsignal.bw HPAF ChipSeq H3K4me3 Signal bigWig UW analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeUwHistoneHpafInputStdAln_1Reps.norm5.rawsignal.bw HPAF ChipSeq Input Signal bigWig UW analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeUwHistoneHpfH3k4me3StdAln_2Reps.norm5.rawsignal.bw HPF ChipSeq H3K4me3 Signal bigWig UW analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeUwHistoneHpfInputStdAln_1Reps.norm5.rawsignal.bw HPF ChipSeq Input Signal bigWig UW analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeUwHistoneHreH3k27me3StdAln_2Reps.norm5.rawsignal.bw HRE ChipSeq H3K27me3 Signal bigWig UW analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeUwHistoneHreH3k36me3StdAln_2Reps.norm5.rawsignal.bw HRE ChipSeq H3K36me3 Signal bigWig UW analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeUwHistoneHreH3k4me3StdAln_2Reps.norm5.rawsignal.bw HRE ChipSeq H3K4me3 Signal bigWig UW analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeUwHistoneHreInputStdAln_1Reps.norm5.rawsignal.bw HRE ChipSeq Input Signal bigWig UW analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeUwHistoneHrpeH3k4me3StdAln_2Reps.norm5.rawsignal.bw HRPEpiC ChipSeq H3K4me3 Signal bigWig UW analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeUwHistoneHrpeInputStdAln_1Reps.norm5.rawsignal.bw HRPEpiC ChipSeq Input Signal bigWig UW analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeUwHistoneHuvecH3k27me3StdAln_2Reps.norm5.rawsignal.bw HUVEC ChipSeq H3K27me3 Signal bigWig UW analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeUwHistoneHuvecH3k36me3StdAln_2Reps.norm5.rawsignal.bw HUVEC ChipSeq H3K36me3 Signal bigWig UW analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeUwHistoneHuvecH3k4me3StdAln_2Reps.norm5.rawsignal.bw HUVEC ChipSeq H3K4me3 Signal bigWig UW analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeUwHistoneHuvecInputStdAln_1Reps.norm5.rawsignal.bw HUVEC ChipSeq Input Signal bigWig UW analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeUwHistoneHvmfH3k4me3StdAln_2Reps.norm5.rawsignal.bw HVMF ChipSeq H3K4me3 Signal bigWig UW analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeUwHistoneHvmfInputStdAln_1Reps.norm5.rawsignal.bw HVMF ChipSeq Input Signal bigWig UW analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeUwHistoneJurkatH3k4me3StdAln_2Reps.norm5.rawsignal.bw Jurkat ChipSeq H3K4me3 Signal bigWig UW analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeUwHistoneJurkatInputStdAln_1Reps.norm5.rawsignal.bw Jurkat ChipSeq Input Signal bigWig UW analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeUwHistoneK562H3k27me3StdAln_2Reps.norm5.rawsignal.bw K562 ChipSeq H3K27me3 Signal bigWig UW analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeUwHistoneK562H3k36me3StdAln_2Reps.norm5.rawsignal.bw K562 ChipSeq H3K36me3 Signal bigWig UW analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeUwHistoneK562H3k4me3StdAln_2Reps.norm5.rawsignal.bw K562 ChipSeq H3K4me3 Signal bigWig UW analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeUwHistoneK562InputStdAln_1Reps.norm5.rawsignal.bw K562 ChipSeq Input Signal bigWig UW analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeUwHistoneMcf7H3k4me3StdAln_1Reps.norm5.rawsignal.bw MCF-7 ChipSeq H3K4me3 Signal bigWig UW analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeUwHistoneMcf7InputStdAln_1Reps.norm5.rawsignal.bw MCF-7 ChipSeq Input Signal bigWig UW analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeUwHistoneNb4H3k4me3StdAln_1Reps.norm5.rawsignal.bw NB4 ChipSeq H3K4me3 Signal bigWig UW analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeUwHistoneNb4InputStdAln_1Reps.norm5.rawsignal.bw NB4 ChipSeq Input Signal bigWig UW analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeUwHistoneNhdfneoH3k4me3StdAln_2Reps.norm5.rawsignal.bw NHDF-neo ChipSeq H3K4me3 Signal bigWig UW analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeUwHistoneNhdfneoInputStdAln_1Reps.norm5.rawsignal.bw NHDF-neo ChipSeq Input Signal bigWig UW analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeUwHistoneNhekH3k27me3StdAln_2Reps.norm5.rawsignal.bw NHEK ChipSeq H3K27me3 Signal bigWig UW analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeUwHistoneNhekH3k36me3StdAln_2Reps.norm5.rawsignal.bw NHEK ChipSeq H3K36me3 Signal bigWig UW analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeUwHistoneNhekH3k4me3StdAln_2Reps.norm5.rawsignal.bw NHEK ChipSeq H3K4me3 Signal bigWig UW analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeUwHistoneNhekInputStdAln_1Reps.norm5.rawsignal.bw NHEK ChipSeq Input Signal bigWig UW analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeUwHistoneSaecH3k27me3StdAln_2Reps.norm5.rawsignal.bw SAEC ChipSeq H3K27me3 Signal bigWig UW analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeUwHistoneSaecH3k36me3StdAln_2Reps.norm5.rawsignal.bw SAEC ChipSeq H3K36me3 Signal bigWig UW analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeUwHistoneSaecH3k4me3StdAln_2Reps.norm5.rawsignal.bw SAEC ChipSeq H3K4me3 Signal bigWig UW analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeUwHistoneSaecInputStdAln_1Reps.norm5.rawsignal.bw SAEC ChipSeq Input Signal bigWig UW analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeUwHistoneSknshraH3k27me3StdAln_2Reps.norm5.rawsignal.bw SK-N-SH_RA ChipSeq H3K27me3 Signal bigWig UW analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeUwHistoneSknshraH3k36me3StdAln_2Reps.norm5.rawsignal.bw SK-N-SH_RA ChipSeq H3K36me3 Signal bigWig UW analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeUwHistoneSknshraH3k4me3StdAln_2Reps.norm5.rawsignal.bw SK-N-SH_RA ChipSeq H3K4me3 Signal bigWig UW analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeUwHistoneSknshraInputStdAln_1Reps.norm5.rawsignal.bw SK-N-SH_RA ChipSeq Input Signal bigWig UW analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeUwTfbsAg04449CtcfStdAln_2Reps.norm5.rawsignal.bw AG04449 ChipSeq CTCF Signal bigWig UW analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeUwTfbsAg04449InputStdAln_1Reps.norm5.rawsignal.bw AG04449 ChipSeq Input Signal bigWig UW analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeUwTfbsAg04450CtcfStdAln_1Reps.norm5.rawsignal.bw AG04450 ChipSeq CTCF Signal bigWig UW analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeUwTfbsAg04450InputStdAln_1Reps.norm5.rawsignal.bw AG04450 ChipSeq Input Signal bigWig UW analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeUwTfbsAg09309CtcfStdAln_2Reps.norm5.rawsignal.bw AG09309 ChipSeq CTCF Signal bigWig UW analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeUwTfbsAg09309InputStdAln_1Reps.norm5.rawsignal.bw AG09309 ChipSeq Input Signal bigWig UW analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeUwTfbsAg09319CtcfStdAln_2Reps.norm5.rawsignal.bw AG09319 ChipSeq CTCF Signal bigWig UW analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeUwTfbsAg09319InputStdAln_1Reps.norm5.rawsignal.bw AG09319 ChipSeq Input Signal bigWig UW analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeUwTfbsAg10803CtcfStdAln_2Reps.norm5.rawsignal.bw AG10803 ChipSeq CTCF Signal bigWig UW analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeUwTfbsAg10803InputStdAln_1Reps.norm5.rawsignal.bw AG10803 ChipSeq Input Signal bigWig UW analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeUwTfbsAoafCtcfStdAln_2Reps.norm5.rawsignal.bw AoAF ChipSeq CTCF Signal bigWig UW analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeUwTfbsAoafInputStdAln_1Reps.norm5.rawsignal.bw AoAF ChipSeq Input Signal bigWig UW analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeUwTfbsBjCtcfStdAln_2Reps.norm5.rawsignal.bw BJ ChipSeq CTCF Signal bigWig UW analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeUwTfbsBjInputStdAln_1Reps.norm5.rawsignal.bw BJ ChipSeq Input Signal bigWig UW analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeUwTfbsCaco2CtcfStdAln_2Reps.norm5.rawsignal.bw Caco-2 ChipSeq CTCF Signal bigWig UW analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeUwTfbsCaco2InputStdAln_1Reps.norm5.rawsignal.bw Caco-2 ChipSeq Input Signal bigWig UW analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeUwTfbsGm06990CtcfStdAln_2Reps.norm5.rawsignal.bw GM06990 ChipSeq CTCF Signal bigWig UW analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeUwTfbsGm06990InputStdAln_1Reps.norm5.rawsignal.bw GM06990 ChipSeq Input Signal bigWig UW analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeUwTfbsGm12801CtcfStdAln_1Reps.norm5.rawsignal.bw GM12801 ChipSeq CTCF Signal bigWig UW analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeUwTfbsGm12801InputStdAln_1Reps.norm5.rawsignal.bw GM12801 ChipSeq Input Signal bigWig UW analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeUwTfbsGm12864CtcfStdAln_2Reps.norm5.rawsignal.bw GM12864 ChipSeq CTCF Signal bigWig UW analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeUwTfbsGm12864InputStdAln_1Reps.norm5.rawsignal.bw GM12864 ChipSeq Input Signal bigWig UW analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeUwTfbsGm12865CtcfStdAln_2Reps.norm5.rawsignal.bw GM12865 ChipSeq CTCF Signal bigWig UW analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeUwTfbsGm12865InputStdAln_1Reps.norm5.rawsignal.bw GM12865 ChipSeq Input Signal bigWig UW analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeUwTfbsGm12872CtcfStdAln_2Reps.norm5.rawsignal.bw GM12872 ChipSeq CTCF Signal bigWig UW analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeUwTfbsGm12872InputStdAln_1Reps.norm5.rawsignal.bw GM12872 ChipSeq Input Signal bigWig UW analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeUwTfbsGm12873CtcfStdAln_2Reps.norm5.rawsignal.bw GM12873 ChipSeq CTCF Signal bigWig UW analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeUwTfbsGm12873InputStdAln_1Reps.norm5.rawsignal.bw GM12873 ChipSeq Input Signal bigWig UW analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeUwTfbsGm12874CtcfStdAln_2Reps.norm5.rawsignal.bw GM12874 ChipSeq CTCF Signal bigWig UW analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeUwTfbsGm12874InputStdAln_1Reps.norm5.rawsignal.bw GM12874 ChipSeq Input Signal bigWig UW analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeUwTfbsGm12875CtcfStdAln_2Reps.norm5.rawsignal.bw GM12875 ChipSeq CTCF Signal bigWig UW analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeUwTfbsGm12875InputStdAln_1Reps.norm5.rawsignal.bw GM12875 ChipSeq Input Signal bigWig UW analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeUwTfbsGm12878CtcfStdAln_2Reps.norm5.rawsignal.bw GM12878 ChipSeq CTCF Signal bigWig UW analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeUwTfbsGm12878InputStdAln_1Reps.norm5.rawsignal.bw GM12878 ChipSeq Input Signal bigWig UW analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeUwTfbsHaspCtcfStdAln_1Reps.norm5.rawsignal.bw HA-sp ChipSeq CTCF Signal bigWig UW analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeUwTfbsHaspInputStdAln_1Reps.norm5.rawsignal.bw HA-sp ChipSeq Input Signal bigWig UW analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeUwTfbsHbmecCtcfStdAln_2Reps.norm5.rawsignal.bw HBMEC ChipSeq CTCF Signal bigWig UW analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeUwTfbsHbmecInputStdAln_1Reps.norm5.rawsignal.bw HBMEC ChipSeq Input Signal bigWig UW analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeUwTfbsHcfaaCtcfStdAln_1Reps.norm5.rawsignal.bw HCFaa ChipSeq CTCF Signal bigWig UW analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeUwTfbsHcfaaInputStdAln_1Reps.norm5.rawsignal.bw HCFaa ChipSeq Input Signal bigWig UW analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeUwTfbsHcfInputStdAln_1Reps.norm5.rawsignal.bw HCF ChipSeq Input Signal bigWig UW analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeUwTfbsHcmInputStdAln_1Reps.norm5.rawsignal.bw HCM ChipSeq Input Signal bigWig UW analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeUwTfbsHcpeCtcfStdAln_2Reps.norm5.rawsignal.bw HCPEpiC ChipSeq CTCF Signal bigWig UW analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeUwTfbsHcpeInputStdAln_1Reps.norm5.rawsignal.bw HCPEpiC ChipSeq Input Signal bigWig UW analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeUwTfbsHct116InputStdAln_1Reps.norm5.rawsignal.bw HCT-116 ChipSeq Input Signal bigWig UW analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeUwTfbsHeeCtcfStdAln_2Reps.norm5.rawsignal.bw HEEpiC ChipSeq CTCF Signal bigWig UW analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeUwTfbsHeeInputStdAln_1Reps.norm5.rawsignal.bw HEEpiC ChipSeq Input Signal bigWig UW analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeUwTfbsHek293CtcfStdAln_2Reps.norm5.rawsignal.bw HEK293 ChipSeq CTCF Signal bigWig UW analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeUwTfbsHek293InputStdAln_1Reps.norm5.rawsignal.bw HEK293 ChipSeq Input Signal bigWig UW analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeUwTfbsHelas3CtcfStdAln_2Reps.norm5.rawsignal.bw HeLa-S3 ChipSeq CTCF Signal bigWig UW analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeUwTfbsHelas3InputStdAln_1Reps.norm5.rawsignal.bw HeLa-S3 ChipSeq Input Signal bigWig UW analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeUwTfbsHepg2CtcfStdAln_2Reps.norm5.rawsignal.bw HepG2 ChipSeq CTCF Signal bigWig UW analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeUwTfbsHepg2InputStdAln_1Reps.norm5.rawsignal.bw HepG2 ChipSeq Input Signal bigWig UW analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeUwTfbsHl60CtcfStdAln_1Reps.norm5.rawsignal.bw HL-60 ChipSeq CTCF Signal bigWig UW analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeUwTfbsHl60InputStdAln_1Reps.norm5.rawsignal.bw HL-60 ChipSeq Input Signal bigWig UW analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeUwTfbsHmecCtcfStdAln_1Reps.norm5.rawsignal.bw HMEC ChipSeq CTCF Signal bigWig UW analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeUwTfbsHmecInputStdAln_1Reps.norm5.rawsignal.bw HMEC ChipSeq Input Signal bigWig UW analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeUwTfbsHmfCtcfStdAln_2Reps.norm5.rawsignal.bw HMF ChipSeq CTCF Signal bigWig UW analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeUwTfbsHmfInputStdAln_1Reps.norm5.rawsignal.bw HMF ChipSeq Input Signal bigWig UW analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeUwTfbsHpafCtcfStdAln_2Reps.norm5.rawsignal.bw HPAF ChipSeq CTCF Signal bigWig UW analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeUwTfbsHpafInputStdAln_1Reps.norm5.rawsignal.bw HPAF ChipSeq Input Signal bigWig UW analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeUwTfbsHpfCtcfStdAln_2Reps.norm5.rawsignal.bw HPF ChipSeq CTCF Signal bigWig UW analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeUwTfbsHpfInputStdAln_1Reps.norm5.rawsignal.bw HPF ChipSeq Input Signal bigWig UW analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeUwTfbsHreCtcfStdAln_2Reps.norm5.rawsignal.bw HRE ChipSeq CTCF Signal bigWig UW analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeUwTfbsHreInputStdAln_1Reps.norm5.rawsignal.bw HRE ChipSeq Input Signal bigWig UW analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeUwTfbsHrpeCtcfStdAln_1Reps.norm5.rawsignal.bw HRPEpiC ChipSeq CTCF Signal bigWig UW analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeUwTfbsHrpeInputStdAln_1Reps.norm5.rawsignal.bw HRPEpiC ChipSeq Input Signal bigWig UW analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeUwTfbsHuvecCtcfStdAln_2Reps.norm5.rawsignal.bw HUVEC ChipSeq CTCF Signal bigWig UW analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeUwTfbsHuvecInputStdAln_1Reps.norm5.rawsignal.bw HUVEC ChipSeq Input Signal bigWig UW analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeUwTfbsHvmfInputStdAln_1Reps.norm5.rawsignal.bw HVMF ChipSeq Input Signal bigWig UW analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeUwTfbsJurkatInputStdAln_1Reps.norm5.rawsignal.bw Jurkat ChipSeq Input Signal bigWig UW analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeUwTfbsK562CtcfStdAln_2Reps.norm5.rawsignal.bw K562 ChipSeq CTCF Signal bigWig UW analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeUwTfbsK562InputStdAln_1Reps.norm5.rawsignal.bw K562 ChipSeq Input Signal bigWig UW analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeUwTfbsMcf7InputStdAln_1Reps.norm5.rawsignal.bw MCF-7 ChipSeq Input Signal bigWig UW analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeUwTfbsNb4InputStdAln_1Reps.norm5.rawsignal.bw NB4 ChipSeq Input Signal bigWig UW analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeUwTfbsNhdfneoInputStdAln_1Reps.norm5.rawsignal.bw NHDF-neo ChipSeq Input Signal bigWig UW analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeUwTfbsNhekCtcfStdAln_2Reps.norm5.rawsignal.bw NHEK ChipSeq CTCF Signal bigWig UW analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeUwTfbsNhekInputStdAln_1Reps.norm5.rawsignal.bw NHEK ChipSeq Input Signal bigWig UW analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeUwTfbsSaecCtcfStdAln_2Reps.norm5.rawsignal.bw SAEC ChipSeq CTCF Signal bigWig UW analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeUwTfbsSaecInputStdAln_1Reps.norm5.rawsignal.bw SAEC ChipSeq Input Signal bigWig UW analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeUwTfbsSknshraCtcfStdAln_2Reps.norm5.rawsignal.bw SK-N-SH_RA ChipSeq CTCF Signal bigWig UW analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeUwTfbsSknshraInputStdAln_1Reps.norm5.rawsignal.bw SK-N-SH_RA ChipSeq Input Signal bigWig UW analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeUwTfbsWerirb1CtcfStdAln_2Reps.norm5.rawsignal.bw WERI-Rb-1 ChipSeq CTCF Signal bigWig UW analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeUwTfbsWerirb1InputStdAln_1Reps.norm5.rawsignal.bw WERI-Rb-1 ChipSeq Input Signal bigWig UW analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/rna_signal/jan2011/hub/wgEncodeCshlLongRnaSeqA549CellLongnonpolyaMinusRawSigRep1.bigWig A549 RnaSeq MinusSignal 1 bigWig CSHL analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/rna_signal/jan2011/hub/wgEncodeCshlLongRnaSeqA549CellLongnonpolyaMinusRawSigRep2.bigWig A549 RnaSeq MinusSignal 2 bigWig CSHL analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/rna_signal/jan2011/hub/wgEncodeCshlLongRnaSeqA549CellLongnonpolyaPlusRawSigRep1.bigWig A549 RnaSeq PlusSignal 1 bigWig CSHL analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/rna_signal/jan2011/hub/wgEncodeCshlLongRnaSeqA549CellLongnonpolyaPlusRawSigRep2.bigWig A549 RnaSeq PlusSignal 2 bigWig CSHL analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/rna_signal/jan2011/hub/wgEncodeCshlLongRnaSeqA549CellPapMinusRawSigRep1.bigWig A549 RnaSeq MinusSignal 1 bigWig CSHL analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/rna_signal/jan2011/hub/wgEncodeCshlLongRnaSeqA549CellPapMinusRawSigRep2.bigWig A549 RnaSeq MinusSignal 2 bigWig CSHL analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/rna_signal/jan2011/hub/wgEncodeCshlLongRnaSeqA549CellPapPlusRawSigRep1.bigWig A549 RnaSeq PlusSignal 1 bigWig CSHL analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/rna_signal/jan2011/hub/wgEncodeCshlLongRnaSeqA549CellPapPlusRawSigRep2.bigWig A549 RnaSeq PlusSignal 2 bigWig CSHL analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/rna_signal/jan2011/hub/wgEncodeCshlLongRnaSeqAg04450CellLongnonpolyaMinusRawSigRep1.bigWig AG04450 RnaSeq MinusSignal 1 bigWig CSHL analysis 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http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/rna_signal/jan2011/hub/wgEncodeCshlLongRnaSeqAg04450CellPapMinusRawSigRep2.bigWig AG04450 RnaSeq MinusSignal 2 bigWig CSHL analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/rna_signal/jan2011/hub/wgEncodeCshlLongRnaSeqAg04450CellPapPlusRawSigRep1.bigWig AG04450 RnaSeq PlusSignal 1 bigWig CSHL analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/rna_signal/jan2011/hub/wgEncodeCshlLongRnaSeqAg04450CellPapPlusRawSigRep2.bigWig AG04450 RnaSeq PlusSignal 2 bigWig CSHL analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/rna_signal/jan2011/hub/wgEncodeCshlLongRnaSeqBjCellLongnonpolyaMinusRawSigRep1.bigWig BJ RnaSeq MinusSignal 1 bigWig CSHL analysis 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http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/rna_signal/jan2011/hub/wgEncodeCshlShortRnaSeqHelas3CellShorttotalTapMinusRawRep2.bigWig HeLa-S3 RnaSeq MinusSignal 2 bigWig CSHL analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/rna_signal/jan2011/hub/wgEncodeCshlShortRnaSeqHelas3CellShorttotalTapPlusRawRep1.bigWig HeLa-S3 RnaSeq PlusSignal 1 bigWig CSHL analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/rna_signal/jan2011/hub/wgEncodeCshlShortRnaSeqHelas3CellShorttotalTapPlusRawRep2.bigWig HeLa-S3 RnaSeq PlusSignal 2 bigWig CSHL analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/rna_signal/jan2011/hub/wgEncodeCshlShortRnaSeqHelas3CytosolShorttotalTapMinusRawRep1.bigWig HeLa-S3 RnaSeq MinusSignal 1 bigWig CSHL analysis 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http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/rna_signal/jan2011/hub/wgEncodeCshlShortRnaSeqHelas3NucleusShorttotalTapMinusRawRep2.bigWig HeLa-S3 RnaSeq MinusSignal 2 bigWig CSHL analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/rna_signal/jan2011/hub/wgEncodeCshlShortRnaSeqHelas3NucleusShorttotalTapPlusRawRep1.bigWig HeLa-S3 RnaSeq PlusSignal 1 bigWig CSHL analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/rna_signal/jan2011/hub/wgEncodeCshlShortRnaSeqHelas3NucleusShorttotalTapPlusRawRep2.bigWig HeLa-S3 RnaSeq PlusSignal 2 bigWig CSHL analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/rna_signal/jan2011/hub/wgEncodeCshlShortRnaSeqHuvecNucleusShorttotalTapMinusRawRep3.bigWig HUVEC RnaSeq MinusSignal 3 bigWig CSHL analysis 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http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/rna_signal/jan2011/hub/wgEncodeCshlShortRnaSeqK562CellShortPlusRaw.bigWig K562 RnaSeq PlusSignal bigWig CSHL analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/rna_signal/jan2011/hub/wgEncodeCshlShortRnaSeqK562CellShorttotalTapMinusRawRep1.bigWig K562 RnaSeq MinusSignal 1 bigWig CSHL analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/rna_signal/jan2011/hub/wgEncodeCshlShortRnaSeqK562CellShorttotalTapMinusRawRep2.bigWig K562 RnaSeq MinusSignal 2 bigWig CSHL analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/rna_signal/jan2011/hub/wgEncodeCshlShortRnaSeqK562CellShorttotalTapPlusRawRep1.bigWig K562 RnaSeq PlusSignal 1 bigWig CSHL analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/rna_signal/jan2011/hub/wgEncodeCshlShortRnaSeqK562CellShorttotalTapPlusRawRep2.bigWig K562 RnaSeq PlusSignal 2 bigWig CSHL analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/rna_signal/jan2011/hub/wgEncodeCshlShortRnaSeqK562ChromatinShortMinusRaw.bigWig K562 RnaSeq MinusSignal bigWig CSHL analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/rna_signal/jan2011/hub/wgEncodeCshlShortRnaSeqK562ChromatinShortPlusRaw.bigWig K562 RnaSeq PlusSignal bigWig CSHL analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/rna_signal/jan2011/hub/wgEncodeCshlShortRnaSeqK562ChromatinShorttotalTapMinusRawRep3.bigWig K562 RnaSeq MinusSignal 3 bigWig CSHL analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/rna_signal/jan2011/hub/wgEncodeCshlShortRnaSeqK562ChromatinShorttotalTapMinusRawRep4.bigWig K562 RnaSeq MinusSignal 4 bigWig CSHL analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/rna_signal/jan2011/hub/wgEncodeCshlShortRnaSeqK562ChromatinShorttotalTapPlusRawRep3.bigWig K562 RnaSeq PlusSignal 3 bigWig CSHL analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/rna_signal/jan2011/hub/wgEncodeCshlShortRnaSeqK562ChromatinShorttotalTapPlusRawRep4.bigWig K562 RnaSeq PlusSignal 4 bigWig CSHL analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/rna_signal/jan2011/hub/wgEncodeCshlShortRnaSeqK562CytosolShortMinusRaw.bigWig K562 RnaSeq MinusSignal bigWig CSHL analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/rna_signal/jan2011/hub/wgEncodeCshlShortRnaSeqK562CytosolShortPlusRaw.bigWig K562 RnaSeq PlusSignal bigWig CSHL analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/rna_signal/jan2011/hub/wgEncodeCshlShortRnaSeqK562CytosolShorttotalTapMinusRawRep1.bigWig K562 RnaSeq MinusSignal 1 bigWig CSHL analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/rna_signal/jan2011/hub/wgEncodeCshlShortRnaSeqK562CytosolShorttotalTapMinusRawRep2.bigWig K562 RnaSeq MinusSignal 2 bigWig CSHL analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/rna_signal/jan2011/hub/wgEncodeCshlShortRnaSeqK562CytosolShorttotalTapPlusRawRep1.bigWig K562 RnaSeq PlusSignal 1 bigWig CSHL analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/rna_signal/jan2011/hub/wgEncodeCshlShortRnaSeqK562CytosolShorttotalTapPlusRawRep2.bigWig K562 RnaSeq PlusSignal 2 bigWig CSHL analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/rna_signal/jan2011/hub/wgEncodeCshlShortRnaSeqK562NucleolusShortMinusRaw.bigWig K562 RnaSeq MinusSignal bigWig CSHL analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/rna_signal/jan2011/hub/wgEncodeCshlShortRnaSeqK562NucleolusShortPlusRaw.bigWig K562 RnaSeq PlusSignal bigWig CSHL analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/rna_signal/jan2011/hub/wgEncodeCshlShortRnaSeqK562NucleolusShorttotalTapMinusRawRep3.bigWig K562 RnaSeq MinusSignal 3 bigWig CSHL analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/rna_signal/jan2011/hub/wgEncodeCshlShortRnaSeqK562NucleolusShorttotalTapMinusRawRep4.bigWig K562 RnaSeq MinusSignal 4 bigWig CSHL analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/rna_signal/jan2011/hub/wgEncodeCshlShortRnaSeqK562NucleolusShorttotalTapPlusRawRep3.bigWig K562 RnaSeq PlusSignal 3 bigWig CSHL analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/rna_signal/jan2011/hub/wgEncodeCshlShortRnaSeqK562NucleolusShorttotalTapPlusRawRep4.bigWig K562 RnaSeq PlusSignal 4 bigWig CSHL analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/rna_signal/jan2011/hub/wgEncodeCshlShortRnaSeqK562NucleoplasmShortMinusRaw.bigWig K562 RnaSeq MinusSignal bigWig CSHL analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/rna_signal/jan2011/hub/wgEncodeCshlShortRnaSeqK562NucleoplasmShortPlusRaw.bigWig K562 RnaSeq PlusSignal bigWig CSHL analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/rna_signal/jan2011/hub/wgEncodeCshlShortRnaSeqK562NucleoplasmShorttotalTapMinusRawRep3.bigWig K562 RnaSeq MinusSignal 3 bigWig CSHL analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/rna_signal/jan2011/hub/wgEncodeCshlShortRnaSeqK562NucleoplasmShorttotalTapMinusRawRep4.bigWig K562 RnaSeq MinusSignal 4 bigWig CSHL analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/rna_signal/jan2011/hub/wgEncodeCshlShortRnaSeqK562NucleoplasmShorttotalTapPlusRawRep3.bigWig K562 RnaSeq PlusSignal 3 bigWig CSHL analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/rna_signal/jan2011/hub/wgEncodeCshlShortRnaSeqK562NucleoplasmShorttotalTapPlusRawRep4.bigWig K562 RnaSeq PlusSignal 4 bigWig CSHL analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/rna_signal/jan2011/hub/wgEncodeCshlShortRnaSeqK562NucleusShortMinusRaw.bigWig K562 RnaSeq MinusSignal bigWig CSHL analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/rna_signal/jan2011/hub/wgEncodeCshlShortRnaSeqK562NucleusShortPlusRaw.bigWig K562 RnaSeq PlusSignal bigWig CSHL analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/rna_signal/jan2011/hub/wgEncodeCshlShortRnaSeqK562NucleusShorttotalTapMinusRawRep1.bigWig K562 RnaSeq MinusSignal 1 bigWig CSHL analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/rna_signal/jan2011/hub/wgEncodeCshlShortRnaSeqK562NucleusShorttotalTapMinusRawRep2.bigWig K562 RnaSeq MinusSignal 2 bigWig CSHL analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/rna_signal/jan2011/hub/wgEncodeCshlShortRnaSeqK562NucleusShorttotalTapPlusRawRep1.bigWig K562 RnaSeq PlusSignal 1 bigWig CSHL analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/rna_signal/jan2011/hub/wgEncodeCshlShortRnaSeqK562NucleusShorttotalTapPlusRawRep2.bigWig K562 RnaSeq PlusSignal 2 bigWig CSHL analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/rna_signal/jan2011/hub/wgEncodeCshlShortRnaSeqK562PolysomeShortMinusRaw.bigWig K562 RnaSeq MinusSignal bigWig CSHL analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/rna_signal/jan2011/hub/wgEncodeCshlShortRnaSeqK562PolysomeShortPlusRaw.bigWig K562 RnaSeq PlusSignal bigWig CSHL analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/rna_signal/jan2011/hub/wgEncodeCshlShortRnaSeqMcf7CellShorttotalTapMinusRawRep1.bigWig MCF-7 RnaSeq MinusSignal 1 bigWig CSHL analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/rna_signal/jan2011/hub/wgEncodeCshlShortRnaSeqMcf7CellShorttotalTapMinusRawRep2.bigWig MCF-7 RnaSeq MinusSignal 2 bigWig CSHL analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/rna_signal/jan2011/hub/wgEncodeCshlShortRnaSeqMcf7CellShorttotalTapPlusRawRep1.bigWig MCF-7 RnaSeq PlusSignal 1 bigWig CSHL analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/rna_signal/jan2011/hub/wgEncodeCshlShortRnaSeqMcf7CellShorttotalTapPlusRawRep2.bigWig MCF-7 RnaSeq PlusSignal 2 bigWig CSHL analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/rna_signal/jan2011/hub/wgEncodeCshlShortRnaSeqNhekCellShorttotalTapMinusRawRep1.bigWig NHEK RnaSeq MinusSignal 1 bigWig CSHL analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/rna_signal/jan2011/hub/wgEncodeCshlShortRnaSeqNhekCellShorttotalTapMinusRawRep2.bigWig NHEK RnaSeq MinusSignal 2 bigWig CSHL analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/rna_signal/jan2011/hub/wgEncodeCshlShortRnaSeqNhekCellShorttotalTapPlusRawRep1.bigWig NHEK RnaSeq PlusSignal 1 bigWig CSHL analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/rna_signal/jan2011/hub/wgEncodeCshlShortRnaSeqNhekCellShorttotalTapPlusRawRep2.bigWig NHEK RnaSeq PlusSignal 2 bigWig CSHL analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/rna_signal/jan2011/hub/wgEncodeCshlShortRnaSeqNhekCytosolShorttotalTapMinusRawRep3.bigWig NHEK RnaSeq MinusSignal 3 bigWig CSHL analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/rna_signal/jan2011/hub/wgEncodeCshlShortRnaSeqNhekCytosolShorttotalTapMinusRawRep4.bigWig NHEK RnaSeq MinusSignal 4 bigWig CSHL analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/rna_signal/jan2011/hub/wgEncodeCshlShortRnaSeqNhekCytosolShorttotalTapPlusRawRep3.bigWig NHEK RnaSeq PlusSignal 3 bigWig CSHL analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/rna_signal/jan2011/hub/wgEncodeCshlShortRnaSeqNhekCytosolShorttotalTapPlusRawRep4.bigWig NHEK RnaSeq PlusSignal 4 bigWig CSHL analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/rna_signal/jan2011/hub/wgEncodeCshlShortRnaSeqNhekNucleusShorttotalTapMinusRawRep3.bigWig NHEK RnaSeq MinusSignal 3 bigWig CSHL analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/rna_signal/jan2011/hub/wgEncodeCshlShortRnaSeqNhekNucleusShorttotalTapMinusRawRep4.bigWig NHEK RnaSeq MinusSignal 4 bigWig CSHL analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/rna_signal/jan2011/hub/wgEncodeCshlShortRnaSeqNhekNucleusShorttotalTapPlusRawRep3.bigWig NHEK RnaSeq PlusSignal 3 bigWig CSHL analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/rna_signal/jan2011/hub/wgEncodeCshlShortRnaSeqNhekNucleusShorttotalTapPlusRawRep4.bigWig NHEK RnaSeq PlusSignal 4 bigWig CSHL analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/rna_signal/jan2011/hub/wgEncodeCshlShortRnaSeqProstateCellTotalMinusRaw.bigWig prostate RnaSeq MinusSignal bigWig CSHL analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/rna_signal/jan2011/hub/wgEncodeCshlShortRnaSeqProstateCellTotalPlusRaw.bigWig prostate RnaSeq PlusSignal bigWig CSHL analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/rna_signal/jan2011/hub/wgEncodeCshlShortRnaSeqSknshraCellShorttotalTapMinusRawRep1.bigWig SK-N-SH_RA RnaSeq MinusSignal 1 bigWig CSHL analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/rna_signal/jan2011/hub/wgEncodeCshlShortRnaSeqSknshraCellShorttotalTapMinusRawRep2.bigWig SK-N-SH_RA RnaSeq MinusSignal 2 bigWig CSHL analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/rna_signal/jan2011/hub/wgEncodeCshlShortRnaSeqSknshraCellShorttotalTapPlusRawRep1.bigWig SK-N-SH_RA RnaSeq PlusSignal 1 bigWig CSHL analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/rna_signal/jan2011/hub/wgEncodeCshlShortRnaSeqSknshraCellShorttotalTapPlusRawRep2.bigWig SK-N-SH_RA RnaSeq PlusSignal 2 bigWig CSHL analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/openchrom/jan2011/fdrPeaks/wgEncodeDukeDnase8988T.fdr01peaks.hg19.bb 8988T DnaseSeq Peaks bigBed Duke analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/openchrom/jan2011/fdrPeaks/wgEncodeDukeDnaseAoSMC.fdr01peaks.hg19.bb AoSMC DnaseSeq Peaks bigBed Duke analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/openchrom/jan2011/fdrPeaks/wgEncodeDukeDnaseChorion.fdr01peaks.hg19.bb Chorion DnaseSeq Peaks bigBed Duke analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/openchrom/jan2011/fdrPeaks/wgEncodeDukeDnaseCLL.fdr01peaks.hg19.bb CLL DnaseSeq Peaks bigBed Duke analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/openchrom/jan2011/fdrPeaks/wgEncodeDukeDnaseFibrobl.fdr01peaks.hg19.bb Fibrobl DnaseSeq Peaks bigBed Duke analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/openchrom/jan2011/fdrPeaks/wgEncodeDukeDnaseFibroP.fdr01peaks.hg19.bb FibroP DnaseSeq Peaks bigBed Duke analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/openchrom/jan2011/fdrPeaks/wgEncodeDukeDnaseGliobla.fdr01peaks.hg19.bb Gliobla DnaseSeq Peaks bigBed Duke analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/openchrom/jan2011/fdrPeaks/wgEncodeDukeDnaseGM12891.fdr01peaks.hg19.bb GM12891 DnaseSeq Peaks bigBed Duke analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/openchrom/jan2011/fdrPeaks/wgEncodeDukeDnaseGM12892.fdr01peaks.hg19.bb GM12892 DnaseSeq Peaks bigBed Duke analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/openchrom/jan2011/fdrPeaks/wgEncodeDukeDnaseGM18507.fdr01peaks.hg19.bb GM18507 DnaseSeq Peaks bigBed Duke analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/openchrom/jan2011/fdrPeaks/wgEncodeDukeDnaseGM19238.fdr01peaks.hg19.bb GM19238 DnaseSeq Peaks bigBed Duke analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/openchrom/jan2011/fdrPeaks/wgEncodeDukeDnaseGM19239.fdr01peaks.hg19.bb GM19239 DnaseSeq Peaks bigBed Duke analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/openchrom/jan2011/fdrPeaks/wgEncodeDukeDnaseGM19240.fdr01peaks.hg19.bb GM19240 DnaseSeq Peaks bigBed Duke analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/openchrom/jan2011/fdrPeaks/wgEncodeDukeDnaseH9ES.fdr01peaks.hg19.bb H9ES DnaseSeq Peaks bigBed Duke analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/openchrom/jan2011/fdrPeaks/wgEncodeDukeDnaseHeLaS3IFNa4h.fdr01peaks.hg19.bb HeLa-S3 DnaseSeq Peaks bigBed Duke analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/openchrom/jan2011/fdrPeaks/wgEncodeDukeDnaseHepatocytes.fdr01peaks.hg19.bb Hepatocytes DnaseSeq Peaks bigBed Duke analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/openchrom/jan2011/fdrPeaks/wgEncodeDukeDnaseHPDE6E6E7.fdr01peaks.hg19.bb HPDE6-E6E7 DnaseSeq Peaks bigBed Duke analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/openchrom/jan2011/fdrPeaks/wgEncodeDukeDnaseHSMMemb.fdr01peaks.hg19.bb HSMM_emb DnaseSeq Peaks bigBed Duke analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/openchrom/jan2011/fdrPeaks/wgEncodeDukeDnaseHTR8svn.fdr01peaks.hg19.bb HTR8svn DnaseSeq Peaks bigBed Duke analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/openchrom/jan2011/fdrPeaks/wgEncodeDukeDnaseHuh7.5.fdr01peaks.hg19.bb Huh-7.5 DnaseSeq Peaks bigBed Duke analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/openchrom/jan2011/fdrPeaks/wgEncodeDukeDnaseHuh7.fdr01peaks.hg19.bb Huh-7 DnaseSeq Peaks bigBed Duke analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/openchrom/jan2011/fdrPeaks/wgEncodeDukeDnaseiPS.fdr01peaks.hg19.bb iPS DnaseSeq Peaks bigBed Duke analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/openchrom/jan2011/fdrPeaks/wgEncodeDukeDnaseIshikawaEstradiol.fdr01peaks.hg19.bb Ishikawa DnaseSeq Peaks bigBed Duke analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/openchrom/jan2011/fdrPeaks/wgEncodeDukeDnaseIshikawaTamoxifen.fdr01peaks.hg19.bb Ishikawa DnaseSeq Peaks bigBed Duke analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/openchrom/jan2011/fdrPeaks/wgEncodeDukeDnaseLNCaPAndrogen.fdr01peaks.hg19.bb LNCaP DnaseSeq Peaks bigBed Duke analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/openchrom/jan2011/fdrPeaks/wgEncodeDukeDnaseMCF7Hypoxia.fdr01peaks.hg19.bb MCF-7 DnaseSeq Peaks bigBed Duke analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/openchrom/jan2011/fdrPeaks/wgEncodeDukeDnaseMedullo.fdr01peaks.hg19.bb Medullo DnaseSeq Peaks bigBed Duke analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/openchrom/jan2011/fdrPeaks/wgEncodeDukeDnaseMelano.fdr01peaks.hg19.bb Melano DnaseSeq Peaks bigBed Duke analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/openchrom/jan2011/fdrPeaks/wgEncodeDukeDnaseMyometr.fdr01peaks.hg19.bb Myometr DnaseSeq Peaks bigBed Duke analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/openchrom/jan2011/fdrPeaks/wgEncodeDukeDnaseOsteobl.fdr01peaks.hg19.bb Osteobl DnaseSeq Peaks bigBed Duke analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/openchrom/jan2011/fdrPeaks/wgEncodeDukeDnasePanIsletD.fdr01peaks.hg19.bb PanIsletD DnaseSeq Peaks bigBed Duke analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/openchrom/jan2011/fdrPeaks/wgEncodeDukeDnasePanIslets.fdr01peaks.hg19.bb PanIslets DnaseSeq Peaks bigBed Duke analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/openchrom/jan2011/fdrPeaks/wgEncodeDukeDnasepHTE.fdr01peaks.hg19.bb pHTE DnaseSeq Peaks bigBed Duke analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/openchrom/jan2011/fdrPeaks/wgEncodeDukeDnaseProgFib.fdr01peaks.hg19.bb ProgFib DnaseSeq Peaks bigBed Duke analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/openchrom/jan2011/fdrPeaks/wgEncodeDukeDnaseRWPE1.fdr01peaks.hg19.bb RWPE1 DnaseSeq Peaks bigBed Duke analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/openchrom/jan2011/fdrPeaks/wgEncodeDukeDnaseStellate.fdr01peaks.hg19.bb Stellate DnaseSeq Peaks bigBed Duke analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/openchrom/jan2011/fdrPeaks/wgEncodeDukeDnaseT47D.fdr01peaks.hg19.bb T-47D DnaseSeq Peaks bigBed Duke analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/openchrom/jan2011/fdrPeaks/wgEncodeDukeDnaseTh0.fdr01peaks.hg19.bb Th0 DnaseSeq Peaks bigBed Duke analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/openchrom/jan2011/fdrPeaks/wgEncodeDukeDnaseUrothelia.fdr01peaks.hg19.bb Urothelia DnaseSeq Peaks bigBed Duke analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/openchrom/jan2011/fdrPeaks/wgEncodeDukeDnaseUrotheliaUT189.fdr01peaks.hg19.bb Urothelia DnaseSeq Peaks bigBed Duke analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/openchrom/jan2011/fdrPeaks/wgEncodeUwDnaseAG04449.fdr01peaks.hg19.bb AG04449 DnaseSeq Peaks bigBed UW analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/openchrom/jan2011/fdrPeaks/wgEncodeUwDnaseAG04450.fdr01peaks.hg19.bb AG04450 DnaseSeq Peaks bigBed UW analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/openchrom/jan2011/fdrPeaks/wgEncodeUwDnaseAG09309.fdr01peaks.hg19.bb AG09309 DnaseSeq Peaks bigBed UW analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/openchrom/jan2011/fdrPeaks/wgEncodeUwDnaseAG09319.fdr01peaks.hg19.bb AG09319 DnaseSeq Peaks bigBed UW analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/openchrom/jan2011/fdrPeaks/wgEncodeUwDnaseAG10803.fdr01peaks.hg19.bb AG10803 DnaseSeq Peaks bigBed UW analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/openchrom/jan2011/fdrPeaks/wgEncodeUwDnaseAoAF.fdr01peaks.hg19.bb AoAF DnaseSeq Peaks bigBed UW analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/openchrom/jan2011/fdrPeaks/wgEncodeUwDnaseBE2C.fdr01peaks.hg19.bb BE2_C DnaseSeq Peaks bigBed UW analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/openchrom/jan2011/fdrPeaks/wgEncodeUwDnaseBJ.fdr01peaks.hg19.bb BJ DnaseSeq Peaks bigBed UW analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/openchrom/jan2011/fdrPeaks/wgEncodeUwDnaseCaco2.fdr01peaks.hg19.bb Caco-2 DnaseSeq Peaks bigBed UW analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/openchrom/jan2011/fdrPeaks/wgEncodeUwDnaseCD20.fdr01peaks.hg19.bb CD20+ DnaseSeq Peaks bigBed UW analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/openchrom/jan2011/fdrPeaks/wgEncodeUwDnaseCD34Mobilized.fdr01peaks.hg19.bb CD34+_Mobilized DnaseSeq Peaks bigBed UW analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/openchrom/jan2011/fdrPeaks/wgEncodeUwDnaseCMK.fdr01peaks.hg19.bb CMK DnaseSeq Peaks bigBed UW analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/openchrom/jan2011/fdrPeaks/wgEncodeUwDnaseGM06990.fdr01peaks.hg19.bb GM06990 DnaseSeq Peaks bigBed UW analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/openchrom/jan2011/fdrPeaks/wgEncodeUwDnaseGM12864.fdr01peaks.hg19.bb GM12864 DnaseSeq Peaks bigBed UW analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/openchrom/jan2011/fdrPeaks/wgEncodeUwDnaseGM12865.fdr01peaks.hg19.bb GM12865 DnaseSeq Peaks bigBed UW analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/openchrom/jan2011/fdrPeaks/wgEncodeUwDnaseH7hESC.fdr01peaks.hg19.bb H7-hESC DnaseSeq Peaks bigBed UW analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/openchrom/jan2011/fdrPeaks/wgEncodeUwDnaseHAc.fdr01peaks.hg19.bb HAc DnaseSeq Peaks bigBed UW analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/openchrom/jan2011/fdrPeaks/wgEncodeUwDnaseHAEpiC.fdr01peaks.hg19.bb HAEpiC DnaseSeq Peaks bigBed UW analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/openchrom/jan2011/fdrPeaks/wgEncodeUwDnaseHAh.fdr01peaks.hg19.bb HA-h DnaseSeq Peaks bigBed UW analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/openchrom/jan2011/fdrPeaks/wgEncodeUwDnaseHAsp.fdr01peaks.hg19.bb HA-sp DnaseSeq Peaks bigBed UW analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/openchrom/jan2011/fdrPeaks/wgEncodeUwDnaseHBMEC.fdr01peaks.hg19.bb HBMEC DnaseSeq Peaks bigBed UW analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/openchrom/jan2011/fdrPeaks/wgEncodeUwDnaseHCFaa.fdr01peaks.hg19.bb HCFaa DnaseSeq Peaks bigBed UW analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/openchrom/jan2011/fdrPeaks/wgEncodeUwDnaseHCF.fdr01peaks.hg19.bb HCF DnaseSeq Peaks bigBed UW analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/openchrom/jan2011/fdrPeaks/wgEncodeUwDnaseHCM.fdr01peaks.hg19.bb HCM DnaseSeq Peaks bigBed UW analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/openchrom/jan2011/fdrPeaks/wgEncodeUwDnaseHConF.fdr01peaks.hg19.bb HConF DnaseSeq Peaks bigBed UW analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/openchrom/jan2011/fdrPeaks/wgEncodeUwDnaseHCPEpiC.fdr01peaks.hg19.bb HCPEpiC DnaseSeq Peaks bigBed UW analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/openchrom/jan2011/fdrPeaks/wgEncodeUwDnaseHCT116.fdr01peaks.hg19.bb HCT-116 DnaseSeq Peaks bigBed UW analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/openchrom/jan2011/fdrPeaks/wgEncodeUwDnaseHEEpiC.fdr01peaks.hg19.bb HEEpiC DnaseSeq Peaks bigBed UW analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/openchrom/jan2011/fdrPeaks/wgEncodeUwDnaseHFF.fdr01peaks.hg19.bb HFF DnaseSeq Peaks bigBed UW analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/openchrom/jan2011/fdrPeaks/wgEncodeUwDnaseHFFMyc.fdr01peaks.hg19.bb HFF-Myc DnaseSeq Peaks bigBed UW analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/openchrom/jan2011/fdrPeaks/wgEncodeUwDnaseHGF.fdr01peaks.hg19.bb HGF DnaseSeq Peaks bigBed UW analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/openchrom/jan2011/fdrPeaks/wgEncodeUwDnaseHIPEpiC.fdr01peaks.hg19.bb HIPEpiC DnaseSeq Peaks bigBed UW analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/openchrom/jan2011/fdrPeaks/wgEncodeUwDnaseHL60.fdr01peaks.hg19.bb HL-60 DnaseSeq Peaks bigBed UW analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/openchrom/jan2011/fdrPeaks/wgEncodeUwDnaseHMF.fdr01peaks.hg19.bb HMF DnaseSeq Peaks bigBed UW analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/openchrom/jan2011/fdrPeaks/wgEncodeUwDnaseHMVECdAd.fdr01peaks.hg19.bb HMVEC-dAd DnaseSeq Peaks bigBed UW analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/openchrom/jan2011/fdrPeaks/wgEncodeUwDnaseHMVECdBlAd.fdr01peaks.hg19.bb HMVEC-dBl-Ad DnaseSeq Peaks bigBed UW analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/openchrom/jan2011/fdrPeaks/wgEncodeUwDnaseHMVECdBlNeo.fdr01peaks.hg19.bb HMVEC-dBl-Neo DnaseSeq Peaks bigBed UW analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/openchrom/jan2011/fdrPeaks/wgEncodeUwDnaseHMVECdLyAd.fdr01peaks.hg19.bb HMVEC-dLy-Ad DnaseSeq Peaks bigBed UW analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/openchrom/jan2011/fdrPeaks/wgEncodeUwDnaseHMVECdLyNeo.fdr01peaks.hg19.bb HMVEC-dLy-Neo DnaseSeq Peaks bigBed UW analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/openchrom/jan2011/fdrPeaks/wgEncodeUwDnaseHMVECdNeo.fdr01peaks.hg19.bb HMVEC-dNeo DnaseSeq Peaks bigBed UW analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/openchrom/jan2011/fdrPeaks/wgEncodeUwDnaseHMVECLBl.fdr01peaks.hg19.bb HMVEC-LBl DnaseSeq Peaks bigBed UW analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/openchrom/jan2011/fdrPeaks/wgEncodeUwDnaseHMVECLLy.fdr01peaks.hg19.bb HMVEC-LLy DnaseSeq Peaks bigBed UW analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/openchrom/jan2011/fdrPeaks/wgEncodeUwDnaseHNPCEpiC.fdr01peaks.hg19.bb HNPCEpiC DnaseSeq Peaks bigBed UW analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/openchrom/jan2011/fdrPeaks/wgEncodeUwDnaseHPAEC.fdr01peaks.hg19.bb HPAEC DnaseSeq Peaks bigBed UW analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/openchrom/jan2011/fdrPeaks/wgEncodeUwDnaseHPAF.fdr01peaks.hg19.bb HPAF DnaseSeq Peaks bigBed UW analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/openchrom/jan2011/fdrPeaks/wgEncodeUwDnaseHPdLF.fdr01peaks.hg19.bb HPdLF DnaseSeq Peaks bigBed UW analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/openchrom/jan2011/fdrPeaks/wgEncodeUwDnaseHPF.fdr01peaks.hg19.bb HPF DnaseSeq Peaks bigBed UW analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/openchrom/jan2011/fdrPeaks/wgEncodeUwDnaseHRCEpiC.fdr01peaks.hg19.bb HRCEpiC DnaseSeq Peaks bigBed UW analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/openchrom/jan2011/fdrPeaks/wgEncodeUwDnaseHRE.fdr01peaks.hg19.bb HRE DnaseSeq Peaks bigBed UW analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/openchrom/jan2011/fdrPeaks/wgEncodeUwDnaseHRGEC.fdr01peaks.hg19.bb HRGEC DnaseSeq Peaks bigBed UW analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/openchrom/jan2011/fdrPeaks/wgEncodeUwDnaseHRPEpiC.fdr01peaks.hg19.bb HRPEpiC DnaseSeq Peaks bigBed UW analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/openchrom/jan2011/fdrPeaks/wgEncodeUwDnaseHVMF.fdr01peaks.hg19.bb HVMF DnaseSeq Peaks bigBed UW analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/openchrom/jan2011/fdrPeaks/wgEncodeUwDnaseJurkat.fdr01peaks.hg19.bb Jurkat DnaseSeq Peaks bigBed UW analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/openchrom/jan2011/fdrPeaks/wgEncodeUwDnaseMonocytesCD14RO01746.fdr01peaks.hg19.bb Monocytes-CD14+_RO01746 DnaseSeq Peaks bigBed UW analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/openchrom/jan2011/fdrPeaks/wgEncodeUwDnaseNB4.fdr01peaks.hg19.bb NB4 DnaseSeq Peaks bigBed UW analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/openchrom/jan2011/fdrPeaks/wgEncodeUwDnaseNHA.fdr01peaks.hg19.bb NH-A DnaseSeq Peaks bigBed UW analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/openchrom/jan2011/fdrPeaks/wgEncodeUwDnaseNHDFAd.fdr01peaks.hg19.bb NHDF-Ad DnaseSeq Peaks bigBed UW analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/openchrom/jan2011/fdrPeaks/wgEncodeUwDnaseNHDFneo.fdr01peaks.hg19.bb NHDF-neo DnaseSeq Peaks bigBed UW analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/openchrom/jan2011/fdrPeaks/wgEncodeUwDnaseNHLF.fdr01peaks.hg19.bb NHLF DnaseSeq Peaks bigBed UW analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/openchrom/jan2011/fdrPeaks/wgEncodeUwDnaseNT2D1.fdr01peaks.hg19.bb NT2-D1 DnaseSeq Peaks bigBed UW analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/openchrom/jan2011/fdrPeaks/wgEncodeUwDnasePANC1.fdr01peaks.hg19.bb PANC-1 DnaseSeq Peaks bigBed UW analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/openchrom/jan2011/fdrPeaks/wgEncodeUwDnasePrEC.fdr01peaks.hg19.bb PrEC DnaseSeq Peaks bigBed UW analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/openchrom/jan2011/fdrPeaks/wgEncodeUwDnaseRPTEC.fdr01peaks.hg19.bb RPTEC DnaseSeq Peaks bigBed UW analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/openchrom/jan2011/fdrPeaks/wgEncodeUwDnaseSAEC.fdr01peaks.hg19.bb SAEC DnaseSeq Peaks bigBed UW analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/openchrom/jan2011/fdrPeaks/wgEncodeUwDnaseSKMC.fdr01peaks.hg19.bb SKMC DnaseSeq Peaks bigBed UW analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/openchrom/jan2011/fdrPeaks/wgEncodeUwDnaseSKNMC.fdr01peaks.hg19.bb SK-N-MC DnaseSeq Peaks bigBed UW analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/openchrom/jan2011/fdrPeaks/wgEncodeUwDnaseSKNSHRA.fdr01peaks.hg19.bb SK-N-SH_RA DnaseSeq Peaks bigBed UW analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/openchrom/jan2011/fdrPeaks/wgEncodeUwDnaseTh2.fdr01peaks.hg19.bb Th2 DnaseSeq Peaks bigBed UW analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/openchrom/jan2011/fdrPeaks/wgEncodeUwDnaseWERIRb1.fdr01peaks.hg19.bb WERI-Rb-1 DnaseSeq Peaks bigBed UW analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/openchrom/jan2011/fdrPeaks/wgEncodeUwDnaseWI38.fdr01peaks.hg19.bb WI-38 DnaseSeq Peaks bigBed UW analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/openchrom/jan2011/fdrPeaks/wgEncodeUwDnaseWI38TamoxifenTamoxifen.fdr01peaks.hg19.bb WI-38 DnaseSeq Peaks bigBed UW analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/openchrom/jan2011/fdrPeaks/wgEncodeUWDukeDnaseA549.fdr01peaks.hg19.bb A549 DnaseSeq Peaks bigBed UW-Duke analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/openchrom/jan2011/fdrPeaks/wgEncodeUWDukeDnaseGM12878.fdr01peaks.hg19.bb GM12878 DnaseSeq Peaks bigBed UW-Duke analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/openchrom/jan2011/fdrPeaks/wgEncodeUWDukeDnaseH1hESC.fdr01peaks.hg19.bb H1-hESC DnaseSeq Peaks bigBed UW-Duke analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/openchrom/jan2011/fdrPeaks/wgEncodeUWDukeDnaseHeLaS3.fdr01peaks.hg19.bb HeLa-S3 DnaseSeq Peaks bigBed UW-Duke analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/openchrom/jan2011/fdrPeaks/wgEncodeUWDukeDnaseHepG2.fdr01peaks.hg19.bb HepG2 DnaseSeq Peaks bigBed UW-Duke analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/openchrom/jan2011/fdrPeaks/wgEncodeUWDukeDnaseHMEC.fdr01peaks.hg19.bb HMEC DnaseSeq Peaks bigBed UW-Duke analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/openchrom/jan2011/fdrPeaks/wgEncodeUWDukeDnaseHSMM.fdr01peaks.hg19.bb HSMM DnaseSeq Peaks bigBed UW-Duke analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/openchrom/jan2011/fdrPeaks/wgEncodeUWDukeDnaseHSMMtube.fdr01peaks.hg19.bb HSMMtube DnaseSeq Peaks bigBed UW-Duke analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/openchrom/jan2011/fdrPeaks/wgEncodeUWDukeDnaseHUVEC.fdr01peaks.hg19.bb HUVEC DnaseSeq Peaks bigBed UW-Duke analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/openchrom/jan2011/fdrPeaks/wgEncodeUWDukeDnaseK562.fdr01peaks.hg19.bb K562 DnaseSeq Peaks bigBed UW-Duke analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/openchrom/jan2011/fdrPeaks/wgEncodeUWDukeDnaseLNCaP.fdr01peaks.hg19.bb LNCaP DnaseSeq Peaks bigBed UW-Duke analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/openchrom/jan2011/fdrPeaks/wgEncodeUWDukeDnaseMCF7.fdr01peaks.hg19.bb MCF-7 DnaseSeq Peaks bigBed UW-Duke analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/openchrom/jan2011/fdrPeaks/wgEncodeUWDukeDnaseNHEK.fdr01peaks.hg19.bb NHEK DnaseSeq Peaks bigBed UW-Duke analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/openchrom/jan2011/fdrPeaks/wgEncodeUWDukeDnaseTh1.fdr01peaks.hg19.bb Th1 DnaseSeq Peaks bigBed UW-Duke analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/openchrom/jan2011/faire_fseq_peaks/wgEncodeOpenChromFaireA549Pk.bb A549 FaireSeq Peaks bigBed UNC(Lieb) analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/openchrom/jan2011/faire_fseq_peaks/wgEncodeOpenChromFaireAstrocyPk.bb Astrocy FaireSeq Peaks bigBed UNC analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/openchrom/jan2011/faire_fseq_peaks/wgEncodeOpenChromFaireGlioblaPk.bb Gliobla FaireSeq Peaks bigBed UNC analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/openchrom/jan2011/faire_fseq_peaks/wgEncodeOpenChromFaireGm12878Pk.bb GM12878 FaireSeq Peaks bigBed UNC analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/openchrom/jan2011/faire_fseq_peaks/wgEncodeOpenChromFaireGm12891Pk.bb GM12891 FaireSeq Peaks bigBed UNC analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/openchrom/jan2011/faire_fseq_peaks/wgEncodeOpenChromFaireGm12892Pk.bb GM12892 FaireSeq Peaks bigBed UNC analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/openchrom/jan2011/faire_fseq_peaks/wgEncodeOpenChromFaireGm18507Pk.bb GM18507 FaireSeq Peaks bigBed UNC analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/openchrom/jan2011/faire_fseq_peaks/wgEncodeOpenChromFaireGm19239Pk.bb GM19239 FaireSeq Peaks bigBed UNC analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/openchrom/jan2011/faire_fseq_peaks/wgEncodeOpenChromFaireH1hescPk.bb H1-hESC FaireSeq Peaks bigBed UNC analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/openchrom/jan2011/faire_fseq_peaks/wgEncodeOpenChromFaireHelas3Ifna4hPk.bb HeLa-S3 FaireSeq Peaks bigBed UNC analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/openchrom/jan2011/faire_fseq_peaks/wgEncodeOpenChromFaireHelas3Ifng4hPk.bb HeLa-S3 FaireSeq Peaks bigBed UNC analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/openchrom/jan2011/faire_fseq_peaks/wgEncodeOpenChromFaireHelas3Pk.bb HeLa-S3 FaireSeq Peaks bigBed UNC analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/openchrom/jan2011/faire_fseq_peaks/wgEncodeOpenChromFaireHepg2Pk.bb HepG2 FaireSeq Peaks bigBed UNC analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/openchrom/jan2011/faire_fseq_peaks/wgEncodeOpenChromFaireHtr8Pk.bb HTR8svn FaireSeq Peaks bigBed UNC analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/openchrom/jan2011/faire_fseq_peaks/wgEncodeOpenChromFaireHuvecPk.bb HUVEC FaireSeq Peaks bigBed UNC analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/openchrom/jan2011/faire_fseq_peaks/wgEncodeOpenChromFaireK562_Hypoxia_LacAcidPk.bb bb analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/openchrom/jan2011/faire_fseq_peaks/wgEncodeOpenChromFaireK562NabutPk.bb K562 FaireSeq Peaks bigBed UNC analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/openchrom/jan2011/faire_fseq_peaks/wgEncodeOpenChromFaireK562OhureaPk.bb K562 FaireSeq Peaks bigBed UNC analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/openchrom/jan2011/faire_fseq_peaks/wgEncodeOpenChromFaireK562Pk.bb K562 FaireSeq Peaks bigBed UNC analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/openchrom/jan2011/faire_fseq_peaks/wgEncodeOpenChromFaireMedulloPk.bb Medullo FaireSeq Peaks bigBed UNC analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/openchrom/jan2011/faire_fseq_peaks/wgEncodeOpenChromFaireNhbePk.bb NHBE FaireSeq RawData 1 fastq UNC analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/openchrom/jan2011/faire_fseq_peaks/wgEncodeOpenChromFaireNhekPk.bb NHEK FaireSeq Peaks bigBed UNC analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/openchrom/jan2011/faire_fseq_peaks/wgEncodeOpenChromFairePanisletsPk.bb PanIslets FaireSeq Peaks bigBed UNC analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/openchrom/jan2011/faire_fseq_peaks/FAIRE_Union_25cells_peaks.bb bb analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/openchrom/jan2011/faire_fseq_peaks/wgEncodeOpenChromFaireUrotsaPk.bb Urothelia FaireSeq Peaks bigBed UNC analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/openchrom/jan2011/faire_fseq_peaks/wgEncodeOpenChromFaireUrotsaUt189Pk.bb Urothelia FaireSeq Peaks bigBed UNC analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/histone_macs/optimal/hub/wgEncodeBroadHistoneGm12878H2azStdAln.bb GM12878 ChipSeq H2A.Z Peaks bigBed Broad analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/histone_macs/optimal/hub/wgEncodeBroadHistoneGm12878H3k27acStdAln.bb GM12878 ChipSeq H3K27ac Peaks bigBed Broad analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/histone_macs/optimal/hub/wgEncodeBroadHistoneGm12878H3k27me3StdAln.bb GM12878 ChipSeq H3K27me3 Peaks bigBed Broad analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/histone_macs/optimal/hub/wgEncodeBroadHistoneGm12878H3k36me3StdAln.bb GM12878 ChipSeq H3K36me3 Peaks bigBed Broad analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/histone_macs/optimal/hub/wgEncodeBroadHistoneGm12878H3k4me1StdAln.bb GM12878 ChipSeq H3K4me1 Peaks bigBed Broad analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/histone_macs/optimal/hub/wgEncodeBroadHistoneGm12878H3k4me2StdAln.bb GM12878 ChipSeq H3K4me2 Peaks bigBed Broad analysis 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http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/histone_macs/optimal/hub/wgEncodeBroadHistoneH1hescH4k20me1StdAln.bb H1-hESC ChipSeq H4K20me1 Peaks bigBed Broad analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/histone_macs/optimal/hub/wgEncodeBroadHistoneHelas3H3k27acStdAln.bb HeLa-S3 ChipSeq H3K27ac Peaks bigBed Broad analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/histone_macs/optimal/hub/wgEncodeBroadHistoneHelas3H3k27me3StdAln.bb HeLa-S3 ChipSeq H3K27me3 Peaks bigBed Broad analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/histone_macs/optimal/hub/wgEncodeBroadHistoneHelas3H3k36me3StdAln.bb HeLa-S3 ChipSeq H3K36me3 Peaks bigBed Broad analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/histone_macs/optimal/hub/wgEncodeBroadHistoneHelas3H3k4me2StdAln.bb HeLa-S3 ChipSeq H3K4me2 Peaks bigBed Broad analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/histone_macs/optimal/hub/wgEncodeBroadHistoneHelas3H3k4me3StdAln.bb HeLa-S3 ChipSeq H3K4me3 Peaks bigBed Broad analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/histone_macs/optimal/hub/wgEncodeBroadHistoneHelas3H3k79me2StdAln.bb HeLa-S3 ChipSeq H3K79me2 Peaks bigBed Broad analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/histone_macs/optimal/hub/wgEncodeBroadHistoneHelas3H3k9acStdAln.bb HeLa-S3 ChipSeq H3K9ac Peaks bigBed Broad analysis 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http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/histone_macs/optimal/hub/wgEncodeSydhHistoneNt2d1H3k9me3UcdAln.bb NT2-D1 ChIP-seq H3K9me3 Peaks bigBed UCD analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/histone_macs/optimal/hub/wgEncodeSydhHistoneU2osH3k9me3UcdAln.bb U2OS ChIP-seq H3K9me3 Peaks bigBed UCD(Farnham) analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/histone_macs/optimal/hub/wgEncodeUwHistoneAg04449H3k4me3StdAln.bb AG04449 ChipSeq H3K4me3 Peaks bigBed UW analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/histone_macs/optimal/hub/wgEncodeUwHistoneAg04450H3k4me3StdAln.bb AG04450 ChipSeq H3K4me3 Peaks bigBed UW analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/histone_macs/optimal/hub/wgEncodeUwHistoneAg09309H3k4me3StdAln.bb AG09309 ChipSeq H3K4me3 Peaks bigBed UW analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/histone_macs/optimal/hub/wgEncodeUwHistoneAg09319H3k4me3StdAln.bb AG09319 ChipSeq H3K4me3 Peaks bigBed UW analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/histone_macs/optimal/hub/wgEncodeUwHistoneAg10803H3k4me3StdAln.bb AG10803 ChipSeq H3K4me3 Peaks bigBed UW analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/histone_macs/optimal/hub/wgEncodeUwHistoneAoafH3k4me3StdAln.bb AoAF ChipSeq H3K4me3 Peaks bigBed UW analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/histone_macs/optimal/hub/wgEncodeUwHistoneBjH3k27me3StdAln.bb BJ ChipSeq H3K27me3 Peaks bigBed UW analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/histone_macs/optimal/hub/wgEncodeUwHistoneBjH3k36me3StdAln.bb BJ ChipSeq H3K36me3 Peaks bigBed UW analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/histone_macs/optimal/hub/wgEncodeUwHistoneBjH3k4me3StdAln.bb BJ ChipSeq H3K4me3 Peaks bigBed UW analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/histone_macs/optimal/hub/wgEncodeUwHistoneCaco2H3k27me3StdAln.bb Caco-2 ChipSeq H3K27me3 Peaks bigBed UW analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/histone_macs/optimal/hub/wgEncodeUwHistoneCaco2H3k36me3StdAln.bb Caco-2 ChipSeq H3K36me3 Peaks bigBed UW analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/histone_macs/optimal/hub/wgEncodeUwHistoneCaco2H3k4me3StdAln.bb Caco-2 ChipSeq H3K4me3 Peaks bigBed UW analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/histone_macs/optimal/hub/wgEncodeUwHistoneGm06990H3k27me3StdAln.bb GM06990 ChipSeq H3K27me3 Peaks bigBed UW analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/histone_macs/optimal/hub/wgEncodeUwHistoneGm06990H3k36me3StdAln.bb GM06990 ChipSeq H3K36me3 Peaks bigBed UW analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/histone_macs/optimal/hub/wgEncodeUwHistoneGm06990H3k4me3StdAln.bb GM06990 ChipSeq H3K4me3 Peaks bigBed UW analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/histone_macs/optimal/hub/wgEncodeUwHistoneGm12878H3k27me3StdAln.bb GM12878 ChipSeq H3K27me3 Peaks bigBed UW analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/histone_macs/optimal/hub/wgEncodeUwHistoneGm12878H3k36me3StdAln.bb GM12878 ChipSeq H3K36me3 Peaks bigBed UW analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/histone_macs/optimal/hub/wgEncodeUwHistoneGm12878H3k4me3StdAln.bb GM12878 ChipSeq H3K4me3 Peaks bigBed UW analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/histone_macs/optimal/hub/wgEncodeUwHistoneH7esH3k27me3StdAln.bb H7-hESC ChipSeq H3K27me3 Peaks bigBed UW analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/histone_macs/optimal/hub/wgEncodeUwHistoneH7esH3k36me3StdAln.bb H7-hESC ChipSeq H3K36me3 Peaks bigBed UW analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/histone_macs/optimal/hub/wgEncodeUwHistoneH7esH3k4me3StdAln.bb H7-hESC ChipSeq H3K4me3 Peaks bigBed UW analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/histone_macs/optimal/hub/wgEncodeUwHistoneHaspH3k4me3StdAln.bb HA-sp ChipSeq H3K4me3 Peaks bigBed UW analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/histone_macs/optimal/hub/wgEncodeUwHistoneHbmecH3k4me3StdAln.bb HBMEC ChipSeq H3K4me3 Peaks bigBed UW analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/histone_macs/optimal/hub/wgEncodeUwHistoneHcfH3k4me3StdAln.bb HCF ChipSeq H3K4me3 Peaks bigBed UW analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/histone_macs/optimal/hub/wgEncodeUwHistoneHcmH3k4me3StdAln.bb HCM ChipSeq H3K4me3 Peaks bigBed UW analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/histone_macs/optimal/hub/wgEncodeUwHistoneHcpeH3k4me3StdAln.bb HCPEpiC ChipSeq H3K4me3 Peaks bigBed UW analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/histone_macs/optimal/hub/wgEncodeUwHistoneHct116H3k4me3StdAln.bb HCT-116 ChipSeq H3K4me3 Peaks bigBed UW analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/histone_macs/optimal/hub/wgEncodeUwHistoneHeeH3k4me3StdAln.bb HEEpiC ChipSeq H3K4me3 Peaks bigBed UW analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/histone_macs/optimal/hub/wgEncodeUwHistoneHek293H3k4me3StdAln.bb HEK293 ChipSeq H3K4me3 Peaks bigBed UW analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/histone_macs/optimal/hub/wgEncodeUwHistoneHelas3H3k27me3StdAln.bb HeLa-S3 ChipSeq H3K27me3 Peaks bigBed UW analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/histone_macs/optimal/hub/wgEncodeUwHistoneHelas3H3k36me3StdAln.bb HeLa-S3 ChipSeq H3K36me3 Peaks bigBed UW analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/histone_macs/optimal/hub/wgEncodeUwHistoneHelas3H3k4me3StdAln.bb HeLa-S3 ChipSeq H3K4me3 Peaks bigBed UW analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/histone_macs/optimal/hub/wgEncodeUwHistoneHepg2H3k27me3StdAln.bb HepG2 ChipSeq H3K27me3 Peaks bigBed UW analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/histone_macs/optimal/hub/wgEncodeUwHistoneHepg2H3k36me3StdAln.bb HepG2 ChipSeq H3K36me3 Peaks bigBed UW analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/histone_macs/optimal/hub/wgEncodeUwHistoneHepg2H3k4me3StdAln.bb HepG2 ChipSeq H3K4me3 Peaks bigBed UW analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/histone_macs/optimal/hub/wgEncodeUwHistoneHl60H3k4me3StdAln.bb HL-60 ChipSeq H3K4me3 Peaks bigBed UW analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/histone_macs/optimal/hub/wgEncodeUwHistoneHmecH3k4me3StdAln.bb HMEC ChipSeq H3K4me3 Peaks bigBed UW analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/histone_macs/optimal/hub/wgEncodeUwHistoneHmfH3k4me3StdAln.bb HMF ChipSeq H3K4me3 Peaks bigBed UW analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/histone_macs/optimal/hub/wgEncodeUwHistoneHpafH3k4me3StdAln.bb HPAF ChipSeq H3K4me3 Peaks bigBed UW analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/histone_macs/optimal/hub/wgEncodeUwHistoneHpfH3k4me3StdAln.bb HPF ChipSeq H3K4me3 Peaks bigBed UW analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/histone_macs/optimal/hub/wgEncodeUwHistoneHreH3k27me3StdAln.bb HRE ChipSeq H3K27me3 Peaks bigBed UW analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/histone_macs/optimal/hub/wgEncodeUwHistoneHreH3k36me3StdAln.bb HRE ChipSeq H3K36me3 Peaks bigBed UW analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/histone_macs/optimal/hub/wgEncodeUwHistoneHreH3k4me3StdAln.bb HRE ChipSeq H3K4me3 Peaks bigBed UW analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/histone_macs/optimal/hub/wgEncodeUwHistoneHrpeH3k4me3StdAln.bb HRPEpiC ChipSeq H3K4me3 Peaks bigBed UW analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/histone_macs/optimal/hub/wgEncodeUwHistoneHuvecH3k27me3StdAln.bb HUVEC ChipSeq H3K27me3 Peaks bigBed UW analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/histone_macs/optimal/hub/wgEncodeUwHistoneHuvecH3k36me3StdAln.bb HUVEC ChipSeq H3K36me3 Peaks bigBed UW analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/histone_macs/optimal/hub/wgEncodeUwHistoneHuvecH3k4me3StdAln.bb HUVEC ChipSeq H3K4me3 Peaks bigBed UW analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/histone_macs/optimal/hub/wgEncodeUwHistoneHvmfH3k4me3StdAln.bb HVMF ChipSeq H3K4me3 Peaks bigBed UW analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/histone_macs/optimal/hub/wgEncodeUwHistoneJurkatH3k4me3StdAln.bb Jurkat ChipSeq H3K4me3 Peaks bigBed UW analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/histone_macs/optimal/hub/wgEncodeUwHistoneK562H3k27me3StdAln.bb K562 ChipSeq H3K27me3 Peaks bigBed UW analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/histone_macs/optimal/hub/wgEncodeUwHistoneK562H3k36me3StdAln.bb K562 ChipSeq H3K36me3 Peaks bigBed UW analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/histone_macs/optimal/hub/wgEncodeUwHistoneK562H3k4me3StdAln.bb K562 ChipSeq H3K4me3 Peaks bigBed UW analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/histone_macs/optimal/hub/wgEncodeUwHistoneNhdfneoH3k4me3StdAln.bb NHDF-neo ChipSeq H3K4me3 Peaks bigBed UW analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/histone_macs/optimal/hub/wgEncodeUwHistoneNhekH3k27me3StdAln.bb NHEK ChipSeq H3K27me3 Peaks bigBed UW analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/histone_macs/optimal/hub/wgEncodeUwHistoneNhekH3k36me3StdAln.bb NHEK ChipSeq H3K36me3 Peaks bigBed UW analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/histone_macs/optimal/hub/wgEncodeUwHistoneNhekH3k4me3StdAln.bb NHEK ChipSeq H3K4me3 Peaks bigBed UW analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/histone_macs/optimal/hub/wgEncodeUwHistoneSaecH3k27me3StdAln.bb SAEC ChipSeq H3K27me3 Peaks bigBed UW analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/histone_macs/optimal/hub/wgEncodeUwHistoneSaecH3k36me3StdAln.bb SAEC ChipSeq H3K36me3 Peaks bigBed UW analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/histone_macs/optimal/hub/wgEncodeUwHistoneSaecH3k4me3StdAln.bb SAEC ChipSeq H3K4me3 Peaks bigBed UW analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/histone_macs/optimal/hub/wgEncodeUwHistoneSknshraH3k27me3StdAln.bb SK-N-SH_RA ChipSeq H3K27me3 Peaks bigBed UW analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/histone_macs/optimal/hub/wgEncodeUwHistoneSknshraH3k36me3StdAln.bb SK-N-SH_RA ChipSeq H3K36me3 Peaks bigBed UW analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/histone_macs/optimal/hub/wgEncodeUwHistoneSknshraH3k4me3StdAln.bb SK-N-SH_RA ChipSeq H3K4me3 Peaks bigBed UW analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/spp/optimal/hub/spp.optimal.wgEncodeBroadHistoneGm12878CtcfStdAlnRep0_VS_wgEncodeBroadHistoneGm12878ControlStdAlnRep0.bb GM12878 ChipSeq CTCF Peaks bigBed Broad analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/spp/optimal/hub/spp.optimal.wgEncodeBroadHistoneH1hescCtcfStdAlnRep0_VS_wgEncodeBroadHistoneH1hescControlStdAlnRep0.bb H1-hESC ChipSeq CTCF Peaks bigBed Broad analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/spp/optimal/hub/spp.optimal.wgEncodeBroadHistoneHelas3CtcfStdAlnRep0_VS_wgEncodeBroadHistoneHelas3ControlStdAlnRep0.bb HeLa-S3 ChipSeq CTCF Peaks bigBed Broad analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/spp/optimal/hub/spp.optimal.wgEncodeBroadHistoneHelas3Pol2bStdAlnRep0_VS_wgEncodeBroadHistoneHelas3ControlStdAlnRep0.bb HeLa-S3 ChipSeq Pol2(b) Peaks bigBed Broad analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/spp/optimal/hub/spp.optimal.wgEncodeBroadHistoneHepg2CtcfStdAlnRep0_VS_wgEncodeBroadHistoneHepg2ControlStdAlnRep0.bb HepG2 ChipSeq CTCF Peaks bigBed Broad analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/spp/optimal/hub/spp.optimal.wgEncodeBroadHistoneHmecCtcfStdAlnRep0_VS_wgEncodeBroadHistoneHmecControlStdAlnRep0.bb HMEC ChipSeq CTCF Peaks bigBed Broad analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/spp/optimal/hub/spp.optimal.wgEncodeBroadHistoneHsmmCtcfStdAlnRep0_VS_wgEncodeBroadHistoneHsmmControlStdAlnRep0.bb HSMM ChipSeq CTCF Peaks bigBed Broad analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/spp/optimal/hub/spp.optimal.wgEncodeBroadHistoneHsmmtCtcfStdAlnRep0_VS_wgEncodeBroadHistoneHsmmtControlStdAlnRep0.bb HSMMtube ChipSeq CTCF Peaks bigBed Broad analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/spp/optimal/hub/spp.optimal.wgEncodeBroadHistoneHuvecCtcfStdAlnRep0_VS_wgEncodeBroadHistoneHuvecControlStdAlnRep0.bb HUVEC ChipSeq CTCF Peaks bigBed Broad analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/spp/optimal/hub/spp.optimal.wgEncodeBroadHistoneHuvecPol2bStdAlnRep0_VS_wgEncodeBroadHistoneHuvecControlStdAlnRep0.bb HUVEC ChipSeq Pol2(b) Peaks bigBed Broad analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/spp/optimal/hub/spp.optimal.wgEncodeBroadHistoneK562CtcfStdAlnRep0_VS_wgEncodeBroadHistoneK562ControlStdAlnRep1.bb K562 ChipSeq CTCF Peaks bigBed Broad analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/spp/optimal/hub/spp.optimal.wgEncodeBroadHistoneK562Pol2bStdAlnRep0_VS_wgEncodeBroadHistoneK562ControlStdAlnRep1.bb K562 ChipSeq Pol2(b) Peaks bigBed Broad analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/spp/optimal/hub/spp.optimal.wgEncodeBroadHistoneNhaCtcfStdAlnRep0_VS_wgEncodeBroadHistoneNhaControlStdAlnRep0.bb NH-A ChipSeq CTCF Peaks bigBed Broad analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/spp/optimal/hub/spp.optimal.wgEncodeBroadHistoneNhdfadCtcfStdAlnRep0_VS_wgEncodeBroadHistoneNhdfadControlStdAlnRep0.bb NHDF-Ad ChipSeq CTCF Peaks bigBed Broad analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/spp/optimal/hub/spp.optimal.wgEncodeBroadHistoneNhekCtcfStdAlnRep0_VS_wgEncodeBroadHistoneNhekControlStdAlnRep0.bb NHEK ChipSeq CTCF Peaks bigBed Broad analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/spp/optimal/hub/spp.optimal.wgEncodeBroadHistoneNhekPol2bStdAlnRep0_VS_wgEncodeBroadHistoneNhekControlStdAlnRep0.bb NHEK ChipSeq Pol2(b) Peaks bigBed Broad analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/spp/optimal/hub/spp.optimal.wgEncodeBroadHistoneNhlfCtcfStdAlnRep0_VS_wgEncodeBroadHistoneNhlfControlStdAlnRep0.bb NHLF ChipSeq CTCF Peaks bigBed Broad analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/spp/optimal/hub/spp.optimal.wgEncodeBroadHistoneOsteoblCtcfStdAlnRep0_VS_wgEncodeBroadHistoneOsteoblControlStdAlnRep0.bb Osteobl ChipSeq CTCF Peaks bigBed Broad analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/spp/optimal/hub/spp.optimal.wgEncodeHaibTfbsA549CtcfPcr1xDexaAlnRep0_VS_wgEncodeHaibTfbsA549ControlPcr1xDexaAlnRep0.bb A549 ChipSeq CTCF Peaks bigBed HudsonAlpha analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/spp/optimal/hub/spp.optimal.wgEncodeHaibTfbsA549CtcfPcr1xEtoh02AlnRep0_VS_wgEncodeHaibTfbsA549ControlPcr1xEtoh02AlnRep1.bb A549 ChipSeq CTCF Peaks bigBed HudsonAlpha analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/spp/optimal/hub/spp.optimal.wgEncodeHaibTfbsA549GrPcr1xDexbAlnRep0_VS_wgEncodeHaibTfbsA549GrPcr1xEtoh02AlnRep0.bb A549 ChipSeq GR Peaks bigBed HudsonAlpha analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/spp/optimal/hub/spp.optimal.wgEncodeHaibTfbsA549GrPcr1xDexcAlnRep0_VS_wgEncodeHaibTfbsA549GrPcr1xEtoh02AlnRep0.bb A549 ChipSeq GR Peaks bigBed HudsonAlpha analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/spp/optimal/hub/spp.optimal.wgEncodeHaibTfbsA549GrPcr1xDexdAlnRep0_VS_wgEncodeHaibTfbsA549GrPcr1xEtoh02AlnRep0.bb A549 ChipSeq GR Peaks bigBed HudsonAlpha analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/spp/optimal/hub/spp.optimal.wgEncodeHaibTfbsA549GrPcr2xDexaAlnRep0_VS_wgEncodeHaibTfbsA549GrPcr2xEtoh02AlnRep0.bb A549 ChipSeq GR Peaks bigBed HudsonAlpha analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/spp/optimal/hub/spp.optimal.wgEncodeHaibTfbsA549Pol2Pcr2xDexaAlnRep0_VS_wgEncodeHaibTfbsA549ControlPcr2xDexaAlnRep0.bb A549 ChipSeq Pol2 Peaks bigBed HudsonAlpha analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/spp/optimal/hub/spp.optimal.wgEncodeHaibTfbsA549Pol2Pcr2xEtoh02AlnRep0_VS_wgEncodeHaibTfbsA549ControlPcr2xEtoh02AlnRep2.bb A549 ChipSeq Pol2 Peaks bigBed HudsonAlpha analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/spp/optimal/hub/spp.optimal.wgEncodeHaibTfbsA549Usf1Pcr1xDexaAlnRep0_VS_wgEncodeHaibTfbsA549ControlPcr1xDexaAlnRep0.bb A549 ChipSeq USF-1 Peaks bigBed HudsonAlpha analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/spp/optimal/hub/spp.optimal.wgEncodeHaibTfbsA549Usf1Pcr1xEtoh02AlnRep0_VS_wgEncodeHaibTfbsA549ControlPcr1xEtoh02AlnRep1.bb A549 ChipSeq USF-1 Peaks bigBed HudsonAlpha analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/spp/optimal/hub/spp.optimal.wgEncodeHaibTfbsEcc1EralphaaV0416102Estradia1hAlnRep0_VS_wgEncodeHaibTfbsEcc1EralphaaV0416102Dmso2AlnRep0.bb ECC-1 ChipSeq ERalpha_a Peaks bigBed HudsonAlpha analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/spp/optimal/hub/spp.optimal.wgEncodeHaibTfbsEcc1EralphaaV0416102Gen1hAlnRep0_VS_wgEncodeHaibTfbsEcc1EralphaaV0416102Dmso2AlnRep0.bb ECC-1 ChipSeq ERalpha_a Peaks bigBed HudsonAlpha analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/spp/optimal/hub/spp.optimal.wgEncodeHaibTfbsEcc1Foxa1c20V0416102Dmso2AlnRep0_VS_wgEncodeHaibTfbsEcc1ControlV0416102Dmso2AlnRep0.bb ECC-1 ChipSeq FOXA1_(C-20) Peaks bigBed HudsonAlpha analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/spp/optimal/hub/spp.optimal.wgEncodeHaibTfbsEcc1GrV0416102DexaAlnRep0_VS_wgEncodeHaibTfbsEcc1GrV0416102Etoh02AlnRep0.bb ECC-1 ChipSeq GR Peaks bigBed HudsonAlpha analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/spp/optimal/hub/spp.optimal.wgEncodeHaibTfbsEcc1Pol2V0416102Dmso2AlnRep0_VS_wgEncodeHaibTfbsEcc1ControlV0416102Dmso2AlnRep0.bb ECC-1 ChipSeq Pol2 Peaks bigBed HudsonAlpha analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/spp/optimal/hub/spp.optimal.wgEncodeHaibTfbsGm12878Atf3Pcr1xAlnRep0_VS_wgEncodeHaibTfbsGm12878ControlPcr1xAlnRep0.bb GM12878 ChipSeq ATF3 Peaks bigBed HudsonAlpha analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/spp/optimal/hub/spp.optimal.wgEncodeHaibTfbsGm12878BatfPcr1xAlnRep0_VS_wgEncodeHaibTfbsGm12878ControlPcr1xAlnRep0.bb GM12878 ChipSeq BATF Peaks bigBed HudsonAlpha analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/spp/optimal/hub/spp.optimal.wgEncodeHaibTfbsGm12878Bcl11aPcr1xAlnRep0_VS_wgEncodeHaibTfbsGm12878ControlPcr1xAlnRep0.bb GM12878 ChipSeq BCL11A Peaks bigBed HudsonAlpha analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/spp/optimal/hub/spp.optimal.wgEncodeHaibTfbsGm12878Bcl3Pcr1xAlnRep0_VS_wgEncodeHaibTfbsGm12878ControlPcr1xAlnRep0.bb GM12878 ChipSeq BCL3 Peaks bigBed HudsonAlpha analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/spp/optimal/hub/spp.optimal.wgEncodeHaibTfbsGm12878Bclaf1m33V0416101AlnRep0_VS_wgEncodeHaibTfbsGm12878ControlPcr1xAlnRep0.bb GM12878 ChipSeq BCLAF1_(M33-P5B11) Peaks bigBed HudsonAlpha analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/spp/optimal/hub/spp.optimal.wgEncodeHaibTfbsGm12878Ebf1c8Pcr1xAlnRep0_VS_wgEncodeHaibTfbsGm12878ControlPcr1xAlnRep0.bb GM12878 ChipSeq EBF1_(C-8) Peaks bigBed HudsonAlpha analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/spp/optimal/hub/spp.optimal.wgEncodeHaibTfbsGm12878EbfPcr1xAlnRep0_VS_wgEncodeHaibTfbsGm12878ControlPcr1xAlnRep0.bb GM12878 ChipSeq EBF Peaks bigBed HudsonAlpha analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/spp/optimal/hub/spp.optimal.wgEncodeHaibTfbsGm12878Egr1Pcr2xAlnRep0_VS_wgEncodeHaibTfbsGm12878ControlPcr2xAlnRep0.bb GM12878 ChipSeq Egr-1 Peaks bigBed HudsonAlpha analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/spp/optimal/hub/spp.optimal.wgEncodeHaibTfbsGm12878Egr1V0416101AlnRep0_VS_wgEncodeHaibTfbsGm12878ControlPcr1xAlnRep0.bb GM12878 ChipSeq Egr-1 Peaks bigBed HudsonAlpha analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/spp/optimal/hub/spp.optimal.wgEncodeHaibTfbsGm12878Elf1sc631V0416101AlnRep0_VS_wgEncodeHaibTfbsGm12878ControlPcr1xAlnRep0.bb GM12878 ChipSeq ELF1_(SC-631) Peaks bigBed HudsonAlpha analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/spp/optimal/hub/spp.optimal.wgEncodeHaibTfbsGm12878Ets1Pcr1xAlnRep0_VS_wgEncodeHaibTfbsGm12878ControlPcr1xAlnRep0.bb GM12878 ChipSeq ETS1 Peaks bigBed HudsonAlpha analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/spp/optimal/hub/spp.optimal.wgEncodeHaibTfbsGm12878GabpPcr2xAlnRep0_VS_wgEncodeHaibTfbsGm12878ControlPcr2xAlnRep0.bb GM12878 ChipSeq GABP Peaks bigBed HudsonAlpha analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/spp/optimal/hub/spp.optimal.wgEncodeHaibTfbsGm12878Irf4m17Pcr1xAlnRep0_VS_wgEncodeHaibTfbsGm12878ControlPcr1xAlnRep0.bb GM12878 ChipSeq IRF4_(M-17) Peaks bigBed HudsonAlpha analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/spp/optimal/hub/spp.optimal.wgEncodeHaibTfbsGm12878Irf4Pcr1xAlnRep0_VS_wgEncodeHaibTfbsGm12878ControlPcr1xAlnRep0.bb GM12878 ChipSeq IRF4 Peaks bigBed HudsonAlpha analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/spp/optimal/hub/spp.optimal.wgEncodeHaibTfbsGm12878Mef2aPcr1xAlnRep0_VS_wgEncodeHaibTfbsGm12878ControlPcr1xAlnRep0.bb GM12878 ChipSeq MEF2A Peaks bigBed HudsonAlpha analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/spp/optimal/hub/spp.optimal.wgEncodeHaibTfbsGm12878Mef2csc13268Pcr1xAlnRep0_VS_wgEncodeHaibTfbsGm12878ControlPcr1xAlnRep0.bb GM12878 ChipSeq MEF2C_(SC-13268) Peaks bigBed HudsonAlpha analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/spp/optimal/hub/spp.optimal.wgEncodeHaibTfbsGm12878NrsfPcr2xAlnRep0_VS_wgEncodeHaibTfbsGm12878ControlPcr2xAlnRep0.bb GM12878 ChipSeq NRSF Peaks bigBed HudsonAlpha analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/spp/optimal/hub/spp.optimal.wgEncodeHaibTfbsGm12878Oct2Pcr1xAlnRep0_VS_wgEncodeHaibTfbsGm12878ControlPcr1xAlnRep0.bb GM12878 ChipSeq Oct-2 Peaks bigBed HudsonAlpha analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/spp/optimal/hub/spp.optimal.wgEncodeHaibTfbsGm12878P300Pcr1xAlnRep0_VS_wgEncodeHaibTfbsGm12878ControlPcr1xAlnRep0.bb GM12878 ChipSeq p300 Peaks bigBed HudsonAlpha analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/spp/optimal/hub/spp.optimal.wgEncodeHaibTfbsGm12878Pax5c20Pcr1xAlnRep0_VS_wgEncodeHaibTfbsGm12878ControlPcr1xAlnRep0.bb GM12878 ChipSeq PAX5-C20 Peaks bigBed HudsonAlpha analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/spp/optimal/hub/spp.optimal.wgEncodeHaibTfbsGm12878Pax5n19Pcr1xAlnRep0_VS_wgEncodeHaibTfbsGm12878ControlPcr1xAlnRep0.bb GM12878 ChipSeq PAX5-N19 Peaks bigBed HudsonAlpha analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/spp/optimal/hub/spp.optimal.wgEncodeHaibTfbsGm12878Pbx3Pcr1xAlnRep0_VS_wgEncodeHaibTfbsGm12878ControlPcr1xAlnRep0.bb GM12878 ChipSeq Pbx3 Peaks bigBed HudsonAlpha analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/spp/optimal/hub/spp.optimal.wgEncodeHaibTfbsGm12878Pol24h8Pcr1xAlnRep0_VS_wgEncodeHaibTfbsGm12878ControlPcr1xAlnRep0.bb GM12878 ChipSeq Pol2-4H8 Peaks bigBed HudsonAlpha analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/spp/optimal/hub/spp.optimal.wgEncodeHaibTfbsGm12878Pol2Pcr2xAlnRep0_VS_wgEncodeHaibTfbsGm12878ControlPcr2xAlnRep0.bb GM12878 ChipSeq Pol2 Peaks bigBed HudsonAlpha analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/spp/optimal/hub/spp.optimal.wgEncodeHaibTfbsGm12878Pou2f2Pcr1xAlnRep0_VS_wgEncodeHaibTfbsGm12878ControlPcr1xAlnRep0.bb GM12878 ChipSeq POU2F2 Peaks bigBed HudsonAlpha analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/spp/optimal/hub/spp.optimal.wgEncodeHaibTfbsGm12878Pu1Pcr1xAlnRep0_VS_wgEncodeHaibTfbsGm12878ControlPcr1xAlnRep0.bb GM12878 ChipSeq PU.1 Peaks bigBed HudsonAlpha analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/spp/optimal/hub/spp.optimal.wgEncodeHaibTfbsGm12878Rad21V0416101AlnRep0_VS_wgEncodeHaibTfbsGm12878ControlPcr1xAlnRep0.bb GM12878 ChipSeq Rad21 Peaks bigBed HudsonAlpha analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/spp/optimal/hub/spp.optimal.wgEncodeHaibTfbsGm12878RxraPcr1xAlnRep0_VS_wgEncodeHaibTfbsGm12878ControlPcr1xAlnRep0.bb GM12878 ChipSeq RXRA Peaks bigBed HudsonAlpha analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/spp/optimal/hub/spp.optimal.wgEncodeHaibTfbsGm12878Sin3ak20Pcr1xAlnRep0_VS_wgEncodeHaibTfbsGm12878ControlPcr1xAlnRep0.bb GM12878 ChipSeq Sin3Ak-20 Peaks bigBed HudsonAlpha analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/spp/optimal/hub/spp.optimal.wgEncodeHaibTfbsGm12878Six5Pcr1xAlnRep0_VS_wgEncodeHaibTfbsGm12878ControlPcr1xAlnRep0.bb GM12878 ChipSeq SIX5 Peaks bigBed HudsonAlpha analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/spp/optimal/hub/spp.optimal.wgEncodeHaibTfbsGm12878Sp1Pcr1xAlnRep0_VS_wgEncodeHaibTfbsGm12878ControlPcr1xAlnRep0.bb GM12878 ChipSeq SP1 Peaks bigBed HudsonAlpha analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/spp/optimal/hub/spp.optimal.wgEncodeHaibTfbsGm12878SrfPcr2xAlnRep0_VS_wgEncodeHaibTfbsGm12878ControlPcr2xAlnRep0.bb GM12878 ChipSeq SRF Peaks bigBed HudsonAlpha analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/spp/optimal/hub/spp.optimal.wgEncodeHaibTfbsGm12878SrfV0416101AlnRep0_VS_wgEncodeHaibTfbsGm12878ControlPcr1xAlnRep0.bb GM12878 ChipSeq SRF Peaks bigBed HudsonAlpha analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/spp/optimal/hub/spp.optimal.wgEncodeHaibTfbsGm12878Taf1Pcr1xAlnRep0_VS_wgEncodeHaibTfbsGm12878ControlPcr1xAlnRep0.bb GM12878 ChipSeq TAF1 Peaks bigBed HudsonAlpha analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/spp/optimal/hub/spp.optimal.wgEncodeHaibTfbsGm12878Tcf12Pcr1xAlnRep0_VS_wgEncodeHaibTfbsGm12878ControlPcr1xAlnRep0.bb GM12878 ChipSeq TCF12 Peaks bigBed HudsonAlpha analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/spp/optimal/hub/spp.optimal.wgEncodeHaibTfbsGm12878Usf1Pcr2xAlnRep0_VS_wgEncodeHaibTfbsGm12878ControlPcr2xAlnRep0.bb GM12878 ChipSeq USF-1 Peaks bigBed HudsonAlpha analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/spp/optimal/hub/spp.optimal.wgEncodeHaibTfbsGm12878Yy1V0416101AlnRep0_VS_wgEncodeHaibTfbsGm12878ControlV0416101AlnRep1.bb GM12878 ChipSeq YY1_(SC-281) Peaks bigBed HudsonAlpha analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/spp/optimal/hub/spp.optimal.wgEncodeHaibTfbsGm12878Zbtb33Pcr1xAlnRep0_VS_wgEncodeHaibTfbsGm12878ControlPcr1xAlnRep0.bb GM12878 ChipSeq ZBTB33 Peaks bigBed HudsonAlpha analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/spp/optimal/hub/spp.optimal.wgEncodeHaibTfbsGm12878Zeb1sc25388V0416102AlnRep0_VS_wgEncodeHaibTfbsGm12878ControlPcr1xAlnRep0.bb GM12878 ChipSeq ZEB1_(SC-25388) Peaks bigBed HudsonAlpha analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/spp/optimal/hub/spp.optimal.wgEncodeHaibTfbsGm12891Oct2Pcr1xAlnRep0_VS_wgEncodeHaibTfbsGm12891ControlPcr1xAlnRep0.bb GM12891 ChipSeq Oct-2 Peaks bigBed HudsonAlpha analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/spp/optimal/hub/spp.optimal.wgEncodeHaibTfbsGm12891Pax5c20Pcr1xAlnRep0_VS_wgEncodeHaibTfbsGm12891ControlPcr1xAlnRep0.bb GM12891 ChipSeq PAX5-C20 Peaks bigBed HudsonAlpha analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/spp/optimal/hub/spp.optimal.wgEncodeHaibTfbsGm12891Pol24h8Pcr1xAlnRep0_VS_wgEncodeHaibTfbsGm12891ControlPcr1xAlnRep0.bb GM12891 ChipSeq Pol2-4H8 Peaks bigBed HudsonAlpha analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/spp/optimal/hub/spp.optimal.wgEncodeHaibTfbsGm12891Pol2Pcr1xAlnRep0_VS_wgEncodeHaibTfbsGm12891ControlPcr1xAlnRep0.bb GM12891 ChipSeq Pol2 Peaks bigBed HudsonAlpha analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/spp/optimal/hub/spp.optimal.wgEncodeHaibTfbsGm12891Pou2f2Pcr1xAlnRep0_VS_wgEncodeHaibTfbsGm12891ControlPcr1xAlnRep0.bb GM12891 ChipSeq POU2F2 Peaks bigBed HudsonAlpha analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/spp/optimal/hub/spp.optimal.wgEncodeHaibTfbsGm12891Pu1Pcr1xAlnRep0_VS_wgEncodeHaibTfbsGm12891ControlPcr1xAlnRep0.bb GM12891 ChipSeq PU.1 Peaks bigBed HudsonAlpha analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/spp/optimal/hub/spp.optimal.wgEncodeHaibTfbsGm12891Taf1Pcr1xAlnRep0_VS_wgEncodeHaibTfbsGm12891ControlPcr1xAlnRep0.bb GM12891 ChipSeq TAF1 Peaks bigBed HudsonAlpha analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/spp/optimal/hub/spp.optimal.wgEncodeHaibTfbsGm12891Yy1c20V0416101AlnRep0_VS_wgEncodeHaibTfbsGm12891ControlPcr1xAlnRep0.bb GM12891 ChipSeq YY1_(C-20) Peaks bigBed HudsonAlpha analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/spp/optimal/hub/spp.optimal.wgEncodeHaibTfbsGm12892Pax5c20Pcr1xAlnRep0_VS_wgEncodeHaibTfbsGm12892ControlPcr1xAlnRep0.bb GM12892 ChipSeq PAX5-C20 Peaks bigBed HudsonAlpha analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/spp/optimal/hub/spp.optimal.wgEncodeHaibTfbsGm12892Pol24h8Pcr1xAlnRep0_VS_wgEncodeHaibTfbsGm12892ControlPcr1xAlnRep0.bb GM12892 ChipSeq Pol2-4H8 Peaks bigBed HudsonAlpha analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/spp/optimal/hub/spp.optimal.wgEncodeHaibTfbsGm12892Pol24h8V0416102AlnRep0_VS_wgEncodeHaibTfbsGm12892ControlPcr1xAlnRep0.bb GM12892 ChipSeq Pol2-4H8 Peaks bigBed HudsonAlpha analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/spp/optimal/hub/spp.optimal.wgEncodeHaibTfbsGm12892Pol2Pcr1xAlnRep0_VS_wgEncodeHaibTfbsGm12892ControlPcr1xAlnRep0.bb GM12892 ChipSeq Pol2 Peaks bigBed HudsonAlpha analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/spp/optimal/hub/spp.optimal.wgEncodeHaibTfbsGm12892Pol2V0416102AlnRep0_VS_wgEncodeHaibTfbsGm12892ControlPcr1xAlnRep0.bb GM12892 ChipSeq Pol2 Peaks bigBed HudsonAlpha analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/spp/optimal/hub/spp.optimal.wgEncodeHaibTfbsGm12892Taf1Pcr1xAlnRep0_VS_wgEncodeHaibTfbsGm12892ControlPcr1xAlnRep0.bb GM12892 ChipSeq TAF1 Peaks bigBed HudsonAlpha analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/spp/optimal/hub/spp.optimal.wgEncodeHaibTfbsGm12892Taf1V0416102AlnRep0_VS_wgEncodeHaibTfbsGm12892ControlPcr1xAlnRep0.bb GM12892 ChipSeq TAF1 Peaks bigBed HudsonAlpha analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/spp/optimal/hub/spp.optimal.wgEncodeHaibTfbsGm12892Yy1V0416101AlnRep0_VS_wgEncodeHaibTfbsGm12892ControlPcr1xAlnRep0.bb GM12892 ChipSeq YY1 Peaks bigBed HudsonAlpha analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/spp/optimal/hub/spp.optimal.wgEncodeHaibTfbsH1hescAtf3Pcr1xAlnRep0_VS_wgEncodeHaibTfbsH1hescControlPcr1xAlnRep0.bb H1-hESC ChipSeq ATF3 Peaks bigBed HudsonAlpha analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/spp/optimal/hub/spp.optimal.wgEncodeHaibTfbsH1hescBcl11aPcr1xAlnRep0_VS_wgEncodeHaibTfbsH1hescControlPcr1xAlnRep0.bb H1-hESC ChipSeq BCL11A Peaks bigBed HudsonAlpha analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/spp/optimal/hub/spp.optimal.wgEncodeHaibTfbsH1hescBcl3Pcr1xAlnRep0_VS_wgEncodeHaibTfbsH1hescControlPcr1xAlnRep0.bb H1-hESC ChipSeq BCL3 Peaks bigBed HudsonAlpha analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/spp/optimal/hub/spp.optimal.wgEncodeHaibTfbsH1hescCtcfsc5916V0416102AlnRep0_VS_wgEncodeHaibTfbsH1hescControlPcr1xAlnRep0.bb H1-hESC ChipSeq CTCF_(SC-5916) Peaks bigBed HudsonAlpha analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/spp/optimal/hub/spp.optimal.wgEncodeHaibTfbsH1hescEgr1V0416101AlnRep0_VS_wgEncodeHaibTfbsH1hescControlPcr1xAlnRep0.bb H1-hESC ChipSeq Egr-1 Peaks bigBed HudsonAlpha analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/spp/optimal/hub/spp.optimal.wgEncodeHaibTfbsH1hescEgr1V0416102AlnRep0_VS_wgEncodeHaibTfbsH1hescControlPcr1xAlnRep0.bb H1-hESC ChipSeq Egr-1 Peaks bigBed HudsonAlpha analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/spp/optimal/hub/spp.optimal.wgEncodeHaibTfbsH1hescGabpPcr1xAlnRep0_VS_wgEncodeHaibTfbsH1hescControlPcr1xAlnRep0.bb H1-hESC ChipSeq GABP Peaks bigBed HudsonAlpha analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/spp/optimal/hub/spp.optimal.wgEncodeHaibTfbsH1hescHdac2sc6296V0416102AlnRep0_VS_wgEncodeHaibTfbsH1hescControlPcr1xAlnRep0.bb H1-hESC ChipSeq HDAC2_(SC-6296) Peaks bigBed HudsonAlpha analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/spp/optimal/hub/spp.optimal.wgEncodeHaibTfbsH1hescJundV0416102AlnRep0_VS_wgEncodeHaibTfbsH1hescControlPcr1xAlnRep0.bb H1-hESC ChipSeq JunD Peaks bigBed HudsonAlpha analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/spp/optimal/hub/spp.optimal.wgEncodeHaibTfbsH1hescNanogsc33759V0416102AlnRep0_VS_wgEncodeHaibTfbsH1hescControlPcr1xAlnRep0.bb H1-hESC ChipSeq NANOG_(SC-33759) Peaks bigBed HudsonAlpha analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/spp/optimal/hub/spp.optimal.wgEncodeHaibTfbsH1hescNrsfPcr1xAlnRep0_VS_wgEncodeHaibTfbsH1hescControlPcr1xAlnRep0.bb H1-hESC ChipSeq NRSF Peaks bigBed HudsonAlpha analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/spp/optimal/hub/spp.optimal.wgEncodeHaibTfbsH1hescNrsfV0416102AlnRep0_VS_wgEncodeHaibTfbsH1hescControlPcr1xAlnRep0.bb H1-hESC ChipSeq NRSF Peaks bigBed HudsonAlpha analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/spp/optimal/hub/spp.optimal.wgEncodeHaibTfbsH1hescP300Pcr1xAlnRep0_VS_wgEncodeHaibTfbsH1hescControlPcr1xAlnRep0.bb H1-hESC ChipSeq p300 Peaks bigBed HudsonAlpha analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/spp/optimal/hub/spp.optimal.wgEncodeHaibTfbsH1hescPol24h8Pcr1xAlnRep0_VS_wgEncodeHaibTfbsH1hescControlPcr1xAlnRep0.bb H1-hESC ChipSeq Pol2-4H8 Peaks bigBed HudsonAlpha analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/spp/optimal/hub/spp.optimal.wgEncodeHaibTfbsH1hescPol24h8V0416102AlnRep0_VS_wgEncodeHaibTfbsH1hescControlPcr1xAlnRep0.bb H1-hESC ChipSeq Pol2-4H8 Peaks bigBed HudsonAlpha analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/spp/optimal/hub/spp.optimal.wgEncodeHaibTfbsH1hescPol2Pcr1xAlnRep0_VS_wgEncodeHaibTfbsH1hescControlPcr1xAlnRep0.bb H1-hESC ChipSeq Pol2 Peaks bigBed HudsonAlpha analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/spp/optimal/hub/spp.optimal.wgEncodeHaibTfbsH1hescPol2V0416102AlnRep0_VS_wgEncodeHaibTfbsH1hescControlPcr1xAlnRep0.bb H1-hESC ChipSeq Pol2 Peaks bigBed HudsonAlpha analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/spp/optimal/hub/spp.optimal.wgEncodeHaibTfbsH1hescPou5f1sc9081V0416102AlnRep0_VS_wgEncodeHaibTfbsH1hescControlPcr1xAlnRep0.bb H1-hESC ChipSeq POU5F1_(SC-9081) Peaks bigBed HudsonAlpha analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/spp/optimal/hub/spp.optimal.wgEncodeHaibTfbsH1hescRad21V0416102AlnRep0_VS_wgEncodeHaibTfbsH1hescControlPcr1xAlnRep0.bb H1-hESC ChipSeq Rad21 Peaks bigBed HudsonAlpha analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/spp/optimal/hub/spp.optimal.wgEncodeHaibTfbsH1hescRxraV0416102AlnRep0_VS_wgEncodeHaibTfbsH1hescControlPcr1xAlnRep0.bb H1-hESC ChipSeq RXRA Peaks bigBed HudsonAlpha analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/spp/optimal/hub/spp.optimal.wgEncodeHaibTfbsH1hescSin3ak20Pcr1xAlnRep0_VS_wgEncodeHaibTfbsH1hescControlPcr1xAlnRep0.bb H1-hESC ChipSeq Sin3Ak-20 Peaks bigBed HudsonAlpha analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/spp/optimal/hub/spp.optimal.wgEncodeHaibTfbsH1hescSix5Pcr1xAlnRep0_VS_wgEncodeHaibTfbsH1hescControlPcr1xAlnRep0.bb H1-hESC ChipSeq SIX5 Peaks bigBed HudsonAlpha analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/spp/optimal/hub/spp.optimal.wgEncodeHaibTfbsH1hescSp1Pcr1xAlnRep0_VS_wgEncodeHaibTfbsH1hescControlPcr1xAlnRep0.bb H1-hESC ChipSeq SP1 Peaks bigBed HudsonAlpha analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/spp/optimal/hub/spp.optimal.wgEncodeHaibTfbsH1hescSrfPcr1xAlnRep0_VS_wgEncodeHaibTfbsH1hescControlPcr1xAlnRep0.bb H1-hESC ChipSeq SRF Peaks bigBed HudsonAlpha analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/spp/optimal/hub/spp.optimal.wgEncodeHaibTfbsH1hescTaf1Pcr1xAlnRep0_VS_wgEncodeHaibTfbsH1hescControlPcr1xAlnRep0.bb H1-hESC ChipSeq TAF1 Peaks bigBed HudsonAlpha analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/spp/optimal/hub/spp.optimal.wgEncodeHaibTfbsH1hescTaf1V0416102AlnRep0_VS_wgEncodeHaibTfbsH1hescControlPcr1xAlnRep0.bb H1-hESC ChipSeq TAF1 Peaks bigBed HudsonAlpha analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/spp/optimal/hub/spp.optimal.wgEncodeHaibTfbsH1hescTaf7sq8V0416102AlnRep0_VS_wgEncodeHaibTfbsH1hescControlPcr1xAlnRep0.bb H1-hESC ChipSeq TAF7_(SQ-8) Peaks bigBed HudsonAlpha analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/spp/optimal/hub/spp.optimal.wgEncodeHaibTfbsH1hescTcf12Pcr1xAlnRep0_VS_wgEncodeHaibTfbsH1hescControlPcr1xAlnRep0.bb H1-hESC ChipSeq TCF12 Peaks bigBed HudsonAlpha analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/spp/optimal/hub/spp.optimal.wgEncodeHaibTfbsH1hescUsf1Pcr1xAlnRep0_VS_wgEncodeHaibTfbsH1hescControlPcr1xAlnRep0.bb H1-hESC ChipSeq USF-1 Peaks bigBed HudsonAlpha analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/spp/optimal/hub/spp.optimal.wgEncodeHaibTfbsH1hescYy1c20Pcr1xAlnRep0_VS_wgEncodeHaibTfbsH1hescControlPcr1xAlnRep0.bb H1-hESC ChipSeq YY1_(C-20) Peaks bigBed HudsonAlpha analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/spp/optimal/hub/spp.optimal.wgEncodeHaibTfbsHct116Pol24h8V0416101AlnRep0_VS_wgEncodeHaibTfbsHct116ControlV0416101AlnRep2.bb HCT-116 ChipSeq Pol2-4H8 Peaks bigBed HudsonAlpha analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/spp/optimal/hub/spp.optimal.wgEncodeHaibTfbsHelas3GabpPcr1xAlnRep0_VS_wgEncodeHaibTfbsHelas3ControlPcr1xAlnRep0.bb HeLa-S3 ChipSeq GABP Peaks bigBed HudsonAlpha analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/spp/optimal/hub/spp.optimal.wgEncodeHaibTfbsHelas3NrsfPcr1xAlnRep0_VS_wgEncodeHaibTfbsHelas3ControlPcr1xAlnRep0.bb HeLa-S3 ChipSeq NRSF Peaks bigBed HudsonAlpha analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/spp/optimal/hub/spp.optimal.wgEncodeHaibTfbsHelas3Pol2Pcr1xAlnRep0_VS_wgEncodeHaibTfbsHelas3ControlPcr1xAlnRep0.bb HeLa-S3 ChipSeq Pol2 Peaks bigBed HudsonAlpha analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/spp/optimal/hub/spp.optimal.wgEncodeHaibTfbsHelas3Taf1Pcr1xAlnRep0_VS_wgEncodeHaibTfbsHelas3ControlPcr1xAlnRep0.bb HeLa-S3 ChipSeq TAF1 Peaks bigBed HudsonAlpha analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/spp/optimal/hub/spp.optimal.wgEncodeHaibTfbsHepg2Atf3Pcr1xAlnRep0_VS_wgEncodeHaibTfbsHepg2ControlPcr1xAlnRep0.bb HepG2 ChipSeq ATF3 Peaks bigBed HudsonAlpha analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/spp/optimal/hub/spp.optimal.wgEncodeHaibTfbsHepg2Bhlhe40V0416101AlnRep0_VS_wgEncodeHaibTfbsHepg2ControlPcr1xAlnRep0.bb HepG2 ChipSeq BHLHE40 Peaks bigBed HudsonAlpha analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/spp/optimal/hub/spp.optimal.wgEncodeHaibTfbsHepg2CtcfV0416101AlnRep0_VS_wgEncodeHaibTfbsHepg2ControlV0416101AlnRep0.bb HepG2 ChipSeq CTCF Peaks bigBed HudsonAlpha analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/spp/optimal/hub/spp.optimal.wgEncodeHaibTfbsHepg2Elf1sc631V0416101AlnRep0_VS_wgEncodeHaibTfbsHepg2ControlV0416101AlnRep0.bb HepG2 ChipSeq ELF1_(SC-631) Peaks bigBed HudsonAlpha analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/spp/optimal/hub/spp.optimal.wgEncodeHaibTfbsHepg2Fosl2Pcr1xAlnRep0_VS_wgEncodeHaibTfbsHepg2ControlPcr1xAlnRep0.bb HepG2 ChipSeq FOSL2 Peaks bigBed HudsonAlpha analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/spp/optimal/hub/spp.optimal.wgEncodeHaibTfbsHepg2Foxa1c20Pcr1xAlnRep0_VS_wgEncodeHaibTfbsHepg2ControlPcr1xAlnRep0.bb HepG2 ChipSeq FOXA1_(C-20) Peaks bigBed HudsonAlpha analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/spp/optimal/hub/spp.optimal.wgEncodeHaibTfbsHepg2Foxa1sc101058Pcr1xAlnRep0_VS_wgEncodeHaibTfbsHepg2ControlPcr1xAlnRep0.bb HepG2 ChipSeq FOXA1_(SC-101058) Peaks bigBed HudsonAlpha analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/spp/optimal/hub/spp.optimal.wgEncodeHaibTfbsHepg2Foxa2sc6554V0416101AlnRep0_VS_wgEncodeHaibTfbsHepg2ControlV0416101AlnRep0.bb HepG2 ChipSeq FOXA2_(SC-6554) Peaks bigBed HudsonAlpha analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/spp/optimal/hub/spp.optimal.wgEncodeHaibTfbsHepg2GabpPcr2xAlnRep0_VS_wgEncodeHaibTfbsHepg2ControlPcr2xAlnRep0.bb HepG2 ChipSeq GABP Peaks bigBed HudsonAlpha analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/spp/optimal/hub/spp.optimal.wgEncodeHaibTfbsHepg2Hdac2sc6296V0416101AlnRep0_VS_wgEncodeHaibTfbsHepg2ControlV0416101AlnRep0.bb HepG2 ChipSeq HDAC2_(SC-6296) Peaks bigBed HudsonAlpha analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/spp/optimal/hub/spp.optimal.wgEncodeHaibTfbsHepg2Hey1V0416101AlnRep0_VS_wgEncodeHaibTfbsHepg2ControlPcr1xAlnRep0.bb HepG2 ChipSeq HEY1 Peaks bigBed HudsonAlpha analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/spp/optimal/hub/spp.optimal.wgEncodeHaibTfbsHepg2Hnf4ah171Pcr1xAlnRep0_VS_wgEncodeHaibTfbsHepg2ControlPcr1xAlnRep0.bb HepG2 ChipSeq HNF4A_(H-171) Peaks bigBed HudsonAlpha analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/spp/optimal/hub/spp.optimal.wgEncodeHaibTfbsHepg2Hnf4gsc6558V0416101AlnRep0_VS_wgEncodeHaibTfbsHepg2ControlV0416101AlnRep0.bb HepG2 ChipSeq HNF4G_(SC-6558) Peaks bigBed HudsonAlpha analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/spp/optimal/hub/spp.optimal.wgEncodeHaibTfbsHepg2JundPcr1xAlnRep0_VS_wgEncodeHaibTfbsHepg2ControlPcr1xAlnRep0.bb HepG2 ChipSeq JunD Peaks bigBed HudsonAlpha analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/spp/optimal/hub/spp.optimal.wgEncodeHaibTfbsHepg2NrsfPcr2xAlnRep0_VS_wgEncodeHaibTfbsHepg2ControlPcr2xAlnRep0.bb HepG2 ChipSeq NRSF Peaks bigBed HudsonAlpha analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/spp/optimal/hub/spp.optimal.wgEncodeHaibTfbsHepg2P300Pcr1xAlnRep0_VS_wgEncodeHaibTfbsHepg2ControlPcr1xAlnRep0.bb HepG2 ChipSeq p300 Peaks bigBed HudsonAlpha analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/spp/optimal/hub/spp.optimal.wgEncodeHaibTfbsHepg2P300V0416101AlnRep0_VS_wgEncodeHaibTfbsHepg2ControlV0416101AlnRep0.bb HepG2 ChipSeq p300 Peaks bigBed HudsonAlpha analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/spp/optimal/hub/spp.optimal.wgEncodeHaibTfbsHepg2Pol2Pcr2xAlnRep0_VS_wgEncodeHaibTfbsHepg2ControlPcr2xAlnRep0.bb HepG2 ChipSeq Pol2 Peaks bigBed HudsonAlpha analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/spp/optimal/hub/spp.optimal.wgEncodeHaibTfbsHepg2Rad21V0416101AlnRep0_VS_wgEncodeHaibTfbsHepg2ControlV0416101AlnRep0.bb HepG2 ChipSeq Rad21 Peaks bigBed HudsonAlpha analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/spp/optimal/hub/spp.optimal.wgEncodeHaibTfbsHepg2RxraPcr1xAlnRep0_VS_wgEncodeHaibTfbsHepg2ControlPcr1xAlnRep0.bb HepG2 ChipSeq RXRA Peaks bigBed HudsonAlpha analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/spp/optimal/hub/spp.optimal.wgEncodeHaibTfbsHepg2Sin3ak20Pcr1xAlnRep0_VS_wgEncodeHaibTfbsHepg2ControlPcr1xAlnRep0.bb HepG2 ChipSeq Sin3Ak-20 Peaks bigBed HudsonAlpha analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/spp/optimal/hub/spp.optimal.wgEncodeHaibTfbsHepg2Sp1Pcr1xAlnRep0_VS_wgEncodeHaibTfbsHepg2ControlPcr1xAlnRep0.bb HepG2 ChipSeq SP1 Peaks bigBed HudsonAlpha analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/spp/optimal/hub/spp.optimal.wgEncodeHaibTfbsHepg2SrfV0416101AlnRep0_VS_wgEncodeHaibTfbsHepg2ControlV0416101AlnRep0.bb HepG2 ChipSeq SRF Peaks bigBed HudsonAlpha analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/spp/optimal/hub/spp.optimal.wgEncodeHaibTfbsHepg2Taf1Pcr2xAlnRep0_VS_wgEncodeHaibTfbsHepg2ControlPcr2xAlnRep0.bb HepG2 ChipSeq TAF1 Peaks bigBed HudsonAlpha analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/spp/optimal/hub/spp.optimal.wgEncodeHaibTfbsHepg2Tcf12Pcr1xAlnRep0_VS_wgEncodeHaibTfbsHepg2ControlPcr1xAlnRep0.bb HepG2 ChipSeq TCF12 Peaks bigBed HudsonAlpha analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/spp/optimal/hub/spp.optimal.wgEncodeHaibTfbsHepg2Usf1Pcr1xAlnRep0_VS_wgEncodeHaibTfbsHepg2ControlPcr1xAlnRep0.bb HepG2 ChipSeq USF-1 Peaks bigBed HudsonAlpha analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/spp/optimal/hub/spp.optimal.wgEncodeHaibTfbsHepg2Zbtb33Pcr1xAlnRep0_VS_wgEncodeHaibTfbsHepg2ControlPcr1xAlnRep0.bb HepG2 ChipSeq ZBTB33 Peaks bigBed HudsonAlpha analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/spp/optimal/hub/spp.optimal.wgEncodeHaibTfbsHepg2Zbtb33V0416101AlnRep0_VS_wgEncodeHaibTfbsHepg2ControlV0416101AlnRep0.bb HepG2 ChipSeq ZBTB33 Peaks bigBed HudsonAlpha analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/spp/optimal/hub/spp.optimal.wgEncodeHaibTfbsHtb11NrsfPcr2xAlnRep0_VS_wgEncodeHaibTfbsHtb11ControlPcr2xAlnRep0.bb HTB-11 ChipSeq NRSF Peaks bigBed HudsonAlpha analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/spp/optimal/hub/spp.optimal.wgEncodeHaibTfbsK562Bcl3Pcr1xAlnRep0_VS_wgEncodeHaibTfbsK562ControlV0416101AlnRep0.bb K562 ChipSeq BCL3 Peaks bigBed HudsonAlpha analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/spp/optimal/hub/spp.optimal.wgEncodeHaibTfbsK562Bclaf1m33Pcr1xAlnRep0_VS_wgEncodeHaibTfbsK562ControlV0416101AlnRep0.bb K562 ChipSeq BCLAF1_(M33-P5B11) Peaks bigBed HudsonAlpha analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/spp/optimal/hub/spp.optimal.wgEncodeHaibTfbsK562Ctcflsc98982V0416101AlnRep0_VS_wgEncodeHaibTfbsK562ControlV0416101AlnRep0.bb K562 ChipSeq CTCFL_(SC-98982) Peaks bigBed HudsonAlpha analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/spp/optimal/hub/spp.optimal.wgEncodeHaibTfbsK562E2f6h50V0416102AlnRep0_VS_wgEncodeHaibTfbsK562ControlPcr1xAlnRep0.bb K562 ChipSeq E2F6_(H-50) Peaks bigBed HudsonAlpha analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/spp/optimal/hub/spp.optimal.wgEncodeHaibTfbsK562Egr1V0416101AlnRep0_VS_wgEncodeHaibTfbsK562ControlV0416101AlnRep0.bb K562 ChipSeq Egr-1 Peaks bigBed HudsonAlpha analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/spp/optimal/hub/spp.optimal.wgEncodeHaibTfbsK562Elf1sc631V0416102AlnRep0_VS_wgEncodeHaibTfbsK562ControlPcr1xAlnRep0.bb K562 ChipSeq ELF1_(SC-631) Peaks bigBed HudsonAlpha analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/spp/optimal/hub/spp.optimal.wgEncodeHaibTfbsK562Ets1V0416101AlnRep0_VS_wgEncodeHaibTfbsK562ControlV0416101AlnRep0.bb K562 ChipSeq ETS1 Peaks bigBed HudsonAlpha analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/spp/optimal/hub/spp.optimal.wgEncodeHaibTfbsK562Fosl1sc183V0416101AlnRep0_VS_wgEncodeHaibTfbsK562ControlV0416101AlnRep0.bb K562 ChipSeq FOSL1_(SC-183) Peaks bigBed HudsonAlpha analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/spp/optimal/hub/spp.optimal.wgEncodeHaibTfbsK562GabpV0416101AlnRep0_VS_wgEncodeHaibTfbsK562ControlV0416101AlnRep0.bb K562 ChipSeq GABP Peaks bigBed HudsonAlpha analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/spp/optimal/hub/spp.optimal.wgEncodeHaibTfbsK562Gata2cg2Pcr1xAlnRep0_VS_wgEncodeHaibTfbsK562ControlV0416101AlnRep0.bb K562 ChipSeq GATA2_(CG2-96) Peaks bigBed HudsonAlpha analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/spp/optimal/hub/spp.optimal.wgEncodeHaibTfbsK562Hdac2sc6296V0416102AlnRep0_VS_wgEncodeHaibTfbsK562ControlPcr1xAlnRep0.bb K562 ChipSeq HDAC2_(SC-6296) Peaks bigBed HudsonAlpha analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/spp/optimal/hub/spp.optimal.wgEncodeHaibTfbsK562Hey1Pcr1xAlnRep0_VS_wgEncodeHaibTfbsK562ControlPcr1xAlnRep0.bb K562 ChipSeq HEY1 Peaks bigBed HudsonAlpha analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/spp/optimal/hub/spp.optimal.wgEncodeHaibTfbsK562MaxV0416102AlnRep0_VS_wgEncodeHaibTfbsK562ControlPcr1xAlnRep0.bb K562 ChipSeq Max Peaks bigBed HudsonAlpha analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/spp/optimal/hub/spp.optimal.wgEncodeHaibTfbsK562NrsfV0416102AlnRep0_VS_wgEncodeHaibTfbsK562ControlV0416101AlnRep0.bb K562 ChipSeq NRSF Peaks bigBed HudsonAlpha analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/spp/optimal/hub/spp.optimal.wgEncodeHaibTfbsK562Pol24h8Pcr1xAlnRep0_VS_wgEncodeHaibTfbsK562ControlPcr1xAlnRep0.bb K562 ChipSeq Pol2-4H8 Peaks bigBed HudsonAlpha analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/spp/optimal/hub/spp.optimal.wgEncodeHaibTfbsK562Pol24h8V0416101AlnRep0_VS_wgEncodeHaibTfbsK562ControlV0416101AlnRep0.bb K562 ChipSeq Pol2-4H8 Peaks bigBed HudsonAlpha analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/spp/optimal/hub/spp.optimal.wgEncodeHaibTfbsK562Pol2V0416101AlnRep0_VS_wgEncodeHaibTfbsK562ControlV0416101AlnRep0.bb K562 ChipSeq Pol2 Peaks bigBed HudsonAlpha analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/spp/optimal/hub/spp.optimal.wgEncodeHaibTfbsK562Pu1Pcr1xAlnRep0_VS_wgEncodeHaibTfbsK562ControlPcr1xAlnRep0.bb K562 ChipSeq PU.1 Peaks bigBed HudsonAlpha analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/spp/optimal/hub/spp.optimal.wgEncodeHaibTfbsK562Rad21V0416102AlnRep0_VS_wgEncodeHaibTfbsK562ControlPcr1xAlnRep0.bb K562 ChipSeq Rad21 Peaks bigBed HudsonAlpha analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/spp/optimal/hub/spp.optimal.wgEncodeHaibTfbsK562Sin3ak20V0416101AlnRep0_VS_wgEncodeHaibTfbsK562ControlV0416101AlnRep0.bb K562 ChipSeq Sin3Ak-20 Peaks bigBed HudsonAlpha analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/spp/optimal/hub/spp.optimal.wgEncodeHaibTfbsK562Six5Pcr1xAlnRep0_VS_wgEncodeHaibTfbsK562ControlPcr1xAlnRep0.bb K562 ChipSeq SIX5 Peaks bigBed HudsonAlpha analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/spp/optimal/hub/spp.optimal.wgEncodeHaibTfbsK562Sp1Pcr1xAlnRep0_VS_wgEncodeHaibTfbsK562ControlV0416101AlnRep0.bb K562 ChipSeq SP1 Peaks bigBed HudsonAlpha analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/spp/optimal/hub/spp.optimal.wgEncodeHaibTfbsK562Sp2sc643V0416102AlnRep0_VS_wgEncodeHaibTfbsK562ControlPcr1xAlnRep0.bb K562 ChipSeq SP2_(SC-643) Peaks bigBed HudsonAlpha analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/spp/optimal/hub/spp.optimal.wgEncodeHaibTfbsK562SrfV0416101AlnRep0_VS_wgEncodeHaibTfbsK562ControlV0416101AlnRep0.bb K562 ChipSeq SRF Peaks bigBed HudsonAlpha analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/spp/optimal/hub/spp.optimal.wgEncodeHaibTfbsK562Taf1Pcr1xAlnRep0_VS_wgEncodeHaibTfbsK562ControlPcr1xAlnRep0.bb K562 ChipSeq TAF1 Peaks bigBed HudsonAlpha analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/spp/optimal/hub/spp.optimal.wgEncodeHaibTfbsK562Taf1V0416101AlnRep0_VS_wgEncodeHaibTfbsK562ControlV0416101AlnRep0.bb K562 ChipSeq TAF1 Peaks bigBed HudsonAlpha analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/spp/optimal/hub/spp.optimal.wgEncodeHaibTfbsK562Taf7sq8V0416101AlnRep0_VS_wgEncodeHaibTfbsK562ControlV0416101AlnRep0.bb K562 ChipSeq TAF7_(SQ-8) Peaks bigBed HudsonAlpha analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/spp/optimal/hub/spp.optimal.wgEncodeHaibTfbsK562Thap1sc98174V0416101AlnRep0_VS_wgEncodeHaibTfbsK562ControlV0416101AlnRep0.bb K562 ChipSeq THAP1_(SC-98174) Peaks bigBed HudsonAlpha analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/spp/optimal/hub/spp.optimal.wgEncodeHaibTfbsK562Usf1V0416101AlnRep0_VS_wgEncodeHaibTfbsK562ControlV0416101AlnRep0.bb K562 ChipSeq USF-1 Peaks bigBed HudsonAlpha analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/spp/optimal/hub/spp.optimal.wgEncodeHaibTfbsK562Yy1V0416101AlnRep0_VS_wgEncodeHaibTfbsK562ControlV0416101AlnRep0.bb K562 ChipSeq YY1 Peaks bigBed HudsonAlpha analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/spp/optimal/hub/spp.optimal.wgEncodeHaibTfbsK562Yy1V0416102AlnRep0_VS_wgEncodeHaibTfbsK562ControlPcr1xAlnRep0.bb K562 ChipSeq YY1 Peaks bigBed HudsonAlpha analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/spp/optimal/hub/spp.optimal.wgEncodeHaibTfbsK562Zbtb33Pcr1xAlnRep0_VS_wgEncodeHaibTfbsK562ControlV0416101AlnRep0.bb K562 ChipSeq ZBTB33 Peaks bigBed HudsonAlpha analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/spp/optimal/hub/spp.optimal.wgEncodeHaibTfbsK562Zbtb7asc34508V0416101AlnRep0_VS_wgEncodeHaibTfbsK562ControlV0416101AlnRep0.bb K562 ChipSeq ZBTB7A_(SC-34508) Peaks bigBed HudsonAlpha analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/spp/optimal/hub/spp.optimal.wgEncodeHaibTfbsPanc1NrsfPcr2xAlnRep0_VS_wgEncodeHaibTfbsPanc1ControlPcr2xAlnRep0.bb PANC-1 ChipSeq NRSF Peaks bigBed HudsonAlpha analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/spp/optimal/hub/spp.optimal.wgEncodeHaibTfbsPfsk1NrsfPcr2xAlnRep0_VS_wgEncodeHaibTfbsPfsk1ControlPcr2xAlnRep0.bb PFSK-1 ChipSeq NRSF Peaks bigBed HudsonAlpha analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/spp/optimal/hub/spp.optimal.wgEncodeHaibTfbsSknshraCtcfV0416102AlnRep0_VS_wgEncodeHaibTfbsSknshraControlV0416102AlnRep2.bb SK-N-SH_RA ChipSeq CTCF Peaks bigBed HudsonAlpha analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/spp/optimal/hub/spp.optimal.wgEncodeHaibTfbsSknshraP300V0416102AlnRep0_VS_wgEncodeHaibTfbsSknshraControlV0416102AlnRep2.bb SK-N-SH_RA ChipSeq p300 Peaks bigBed HudsonAlpha analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/spp/optimal/hub/spp.optimal.wgEncodeHaibTfbsSknshraRad21V0416102AlnRep0_VS_wgEncodeHaibTfbsSknshraControlV0416102AlnRep2.bb SK-N-SH_RA ChipSeq Rad21 Peaks bigBed HudsonAlpha analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/spp/optimal/hub/spp.optimal.wgEncodeHaibTfbsSknshraUsf1sc8983V0416102AlnRep0_VS_wgEncodeHaibTfbsSknshraControlV0416102AlnRep2.bb SK-N-SH_RA ChipSeq USF1_(SC-8983) Peaks bigBed HudsonAlpha analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/spp/optimal/hub/spp.optimal.wgEncodeHaibTfbsSknshraYy1c20V0416102AlnRep0_VS_wgEncodeHaibTfbsSknshraControlV0416102AlnRep2.bb SK-N-SH_RA ChipSeq YY1_(C-20) Peaks bigBed HudsonAlpha analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/spp/optimal/hub/spp.optimal.wgEncodeHaibTfbsT47dCtcfsc5916V0416102Dmso2AlnRep0_VS_wgEncodeHaibTfbsT47dControlV0416102Dmso2AlnRep2.bb T-47D ChipSeq CTCF_(SC-5916) Peaks bigBed HudsonAlpha analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/spp/optimal/hub/spp.optimal.wgEncodeHaibTfbsT47dEralphaaPcr2xGen1hAlnRep0_VS_wgEncodeHaibTfbsT47dEralphaaV0416102Dmso2AlnRep0.bb T-47D ChipSeq ERalpha_a Peaks bigBed HudsonAlpha analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/spp/optimal/hub/spp.optimal.wgEncodeHaibTfbsT47dEralphaaV0416102Estradia1hAlnRep0_VS_wgEncodeHaibTfbsT47dEralphaaV0416102Dmso2AlnRep0.bb T-47D ChipSeq ERalpha_a Peaks bigBed HudsonAlpha analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/spp/optimal/hub/spp.optimal.wgEncodeHaibTfbsT47dFoxa1c20V0416102Dmso2AlnRep0_VS_wgEncodeHaibTfbsT47dControlV0416102Dmso2AlnRep2.bb T-47D ChipSeq FOXA1_(C-20) Peaks bigBed HudsonAlpha analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/spp/optimal/hub/spp.optimal.wgEncodeHaibTfbsT47dGata3sc268V0416102Dmso2AlnRep0_VS_wgEncodeHaibTfbsT47dControlV0416102Dmso2AlnRep2.bb T-47D ChipSeq GATA3_(SC-268) Peaks bigBed HudsonAlpha analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/spp/optimal/hub/spp.optimal.wgEncodeHaibTfbsT47dP300V0416102Dmso2AlnRep0_VS_wgEncodeHaibTfbsT47dControlV0416102Dmso2AlnRep2.bb T-47D ChipSeq p300 Peaks bigBed HudsonAlpha analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/spp/optimal/hub/spp.optimal.wgEncodeHaibTfbsU87NrsfPcr2xAlnRep0_VS_wgEncodeHaibTfbsU87ControlPcr2xAlnRep0.bb U87 ChipSeq NRSF Peaks bigBed HudsonAlpha analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/spp/optimal/hub/spp.optimal.wgEncodeOpenChromChipFibroblCtcfAlnRep0_VS_wgEncodeOpenChromChipFibroblInputAln.bb Fibrobl ChipSeq CTCF Peaks bigBed UT-A analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/spp/optimal/hub/spp.optimal.wgEncodeOpenChromChipGlioblaCtcfAlnRep0_VS_wgEncodeOpenChromChipGlioblaInputAln.bb Gliobla ChipSeq CTCF Peaks bigBed UT-A analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/spp/optimal/hub/spp.optimal.wgEncodeOpenChromChipGlioblaPol2AlnRep0_VS_wgEncodeOpenChromChipGlioblaInputAln.bb Gliobla ChipSeq Pol2 Peaks bigBed UT-A analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/spp/optimal/hub/spp.optimal.wgEncodeOpenChromChipGm12878CmycAlnRep0_VS_wgEncodeOpenChromChipGm12878InputAln.bb GM12878 ChipSeq c-Myc Peaks bigBed UT-A analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/spp/optimal/hub/spp.optimal.wgEncodeOpenChromChipGm12878CtcfAlnRep0_VS_wgEncodeOpenChromChipGm12878InputAln.bb GM12878 ChipSeq CTCF Peaks bigBed UT-A analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/spp/optimal/hub/spp.optimal.wgEncodeOpenChromChipGm12878Pol2AlnRep0_VS_wgEncodeOpenChromChipGm12878InputAln.bb GM12878 ChipSeq Pol2 Peaks bigBed UT-A analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/spp/optimal/hub/spp.optimal.wgEncodeOpenChromChipHelas3CmycAlnRep0_VS_wgEncodeOpenChromChipHelas3InputAln.bb HeLa-S3 ChipSeq c-Myc Peaks bigBed UT-A analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/spp/optimal/hub/spp.optimal.wgEncodeOpenChromChipHelas3CtcfAlnRep0_VS_wgEncodeOpenChromChipHelas3InputAln.bb HeLa-S3 ChipSeq CTCF Peaks bigBed UT-A analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/spp/optimal/hub/spp.optimal.wgEncodeOpenChromChipHelas3Pol2AlnRep0_VS_wgEncodeOpenChromChipHelas3InputAln.bb HeLa-S3 ChipSeq Pol2 Peaks bigBed UT-A analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/spp/optimal/hub/spp.optimal.wgEncodeOpenChromChipHepg2CmycAlnRep0_VS_wgEncodeOpenChromChipHepg2InputAln.bb HepG2 ChipSeq c-Myc Peaks bigBed UT-A analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/spp/optimal/hub/spp.optimal.wgEncodeOpenChromChipHepg2CtcfAlnRep0_VS_wgEncodeOpenChromChipHepg2InputAln.bb HepG2 ChipSeq CTCF Peaks bigBed UT-A analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/spp/optimal/hub/spp.optimal.wgEncodeOpenChromChipHepg2Pol2AlnRep0_VS_wgEncodeOpenChromChipHepg2InputAln.bb HepG2 ChipSeq Pol2 Peaks bigBed UT-A analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/spp/optimal/hub/spp.optimal.wgEncodeOpenChromChipHuvecCmycAlnRep1_VS_wgEncodeOpenChromChipHuvecInputAln.bb HUVEC ChipSeq c-Myc Peaks bigBed UT-A analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/spp/optimal/hub/spp.optimal.wgEncodeOpenChromChipHuvecCtcfAlnRep0_VS_wgEncodeOpenChromChipHuvecInputAln.bb HUVEC ChipSeq CTCF Peaks bigBed UT-A analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/spp/optimal/hub/spp.optimal.wgEncodeOpenChromChipHuvecPol2AlnRep0_VS_wgEncodeOpenChromChipHuvecInputAln.bb HUVEC ChipSeq Pol2 Peaks bigBed UT-A analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/spp/optimal/hub/spp.optimal.wgEncodeOpenChromChipK562CmycAlnRep0_VS_wgEncodeOpenChromChipK562InputAln.bb K562 ChipSeq c-Myc Peaks bigBed UT-A analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/spp/optimal/hub/spp.optimal.wgEncodeOpenChromChipK562CtcfAlnRep0_VS_wgEncodeOpenChromChipK562InputAln.bb K562 ChipSeq CTCF Peaks bigBed UT-A analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/spp/optimal/hub/spp.optimal.wgEncodeOpenChromChipK562Pol2AlnRep0_VS_wgEncodeOpenChromChipK562InputAln.bb K562 ChipSeq Pol2 Peaks bigBed UT-A analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/spp/optimal/hub/spp.optimal.wgEncodeOpenChromChipMcf7CmycEstroAlnRep0_VS_wgEncodeOpenChromChipMcf7InputAln.bb MCF-7 ChipSeq c-Myc Peaks bigBed UT-A analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/spp/optimal/hub/spp.optimal.wgEncodeOpenChromChipMcf7CmycVehAlnRep0_VS_wgEncodeOpenChromChipMcf7InputAln.bb MCF-7 ChipSeq c-Myc Peaks bigBed UT-A analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/spp/optimal/hub/spp.optimal.wgEncodeOpenChromChipMcf7CtcfAlnRep0_VS_wgEncodeOpenChromChipMcf7InputAln.bb MCF-7 ChipSeq CTCF Peaks bigBed UT-A analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/spp/optimal/hub/spp.optimal.wgEncodeOpenChromChipMcf7CtcfEstroAlnRep0_VS_wgEncodeOpenChromChipMcf7InputAln.bb MCF-7 ChipSeq CTCF Peaks bigBed UT-A analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/spp/optimal/hub/spp.optimal.wgEncodeOpenChromChipMcf7CtcfVehAlnRep0_VS_wgEncodeOpenChromChipMcf7InputAln.bb MCF-7 ChipSeq CTCF Peaks bigBed UT-A analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/spp/optimal/hub/spp.optimal.wgEncodeOpenChromChipMcf7Pol2AlnRep0_VS_wgEncodeOpenChromChipMcf7InputAln.bb MCF-7 ChipSeq Pol2 Peaks bigBed UT-A analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/spp/optimal/hub/spp.optimal.wgEncodeOpenChromChipProgfibCtcfAlnRep0_VS_wgEncodeOpenChromChipProgfibInputAln.bb ProgFib ChipSeq CTCF Peaks bigBed UT-A analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/spp/optimal/hub/spp.optimal.wgEncodeOpenChromChipProgfibPol2AlnRep0_VS_wgEncodeOpenChromChipProgfibInputAln.bb ProgFib ChipSeq Pol2 Peaks bigBed UT-A analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/spp/optimal/hub/spp.optimal.wgEncodeSydhTfbsGm10847NfkbIggrabAlnRep0_VS_wgEncodeSydhTfbsGm10847InputIggrabAlnRep0.bb GM10847 ChipSeq NFKB Peaks bigBed Stanford analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/spp/optimal/hub/spp.optimal.wgEncodeSydhTfbsGm10847Pol2IggmusAlnRep1_VS_wgEncodeSydhTfbsGm10847InputIggmusAlnRep0.bb GM10847 ChipSeq Pol2 Peaks bigBed Stanford analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/spp/optimal/hub/spp.optimal.wgEncodeSydhTfbsGm12878Brca1cIggmusAlnRep0_VS_wgEncodeSydhTfbsGm12878InputIggmusAlnRep0.bb GM12878 ChipSeq BRCA1_(C-1863) Peaks bigBed Stanford analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/spp/optimal/hub/spp.optimal.wgEncodeSydhTfbsGm12878CfosStdAlnRep0_VS_wgEncodeSydhTfbsGm12878InputStdAlnRep1.bb GM12878 ChipSeq c-Fos Peaks bigBed Stanford analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/spp/optimal/hub/spp.optimal.wgEncodeSydhTfbsGm12878Chd21250IggmusAlnRep0_VS_wgEncodeSydhTfbsGm12878InputIggmusAlnRep0.bb GM12878 ChipSeq CHD2_(N-1250) Peaks bigBed Stanford analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/spp/optimal/hub/spp.optimal.wgEncodeSydhTfbsGm12878Ctcfc20StdAlnRep0_VS_wgEncodeSydhTfbsGm12878InputStdAlnRep1.bb GM12878 ChipSeq CTCF_(C-20) Peaks bigBed Stanford analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/spp/optimal/hub/spp.optimal.wgEncodeSydhTfbsGm12878EbfStdAlnRep0_VS_wgEncodeSydhTfbsGm12878InputStdAlnRep1.bb GM12878 ChipSeq EBF Peaks bigBed Stanford analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/spp/optimal/hub/spp.optimal.wgEncodeSydhTfbsGm12878Gcn5StdAlnRep0_VS_wgEncodeSydhTfbsGm12878InputStdAlnRep1.bb GM12878 ChipSeq GCN5 Peaks bigBed Harvard(Weissman) analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/spp/optimal/hub/spp.optimal.wgEncodeSydhTfbsGm12878Irf3StdAlnRep0_VS_wgEncodeSydhTfbsGm12878InputStdAlnRep1.bb GM12878 ChipSeq IRF3 Peaks bigBed Stanford analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/spp/optimal/hub/spp.optimal.wgEncodeSydhTfbsGm12878JundStdAlnRep0_VS_wgEncodeSydhTfbsGm12878InputStdAlnRep1.bb GM12878 ChipSeq JunD Peaks bigBed Stanford analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/spp/optimal/hub/spp.optimal.wgEncodeSydhTfbsGm12878MaxStdAlnRep0_VS_wgEncodeSydhTfbsGm12878InputStdAlnRep1.bb GM12878 ChipSeq Max Peaks bigBed Stanford analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/spp/optimal/hub/spp.optimal.wgEncodeSydhTfbsGm12878Nfe2hStdAlnRep0_VS_wgEncodeSydhTfbsGm12878InputStdAlnRep1.bb GM12878 ChipSeq NF-E2_(H-230) Peaks bigBed Stanford analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/spp/optimal/hub/spp.optimal.wgEncodeSydhTfbsGm12878NfkbIggrabAlnRep0_VS_wgEncodeSydhTfbsGm12878InputIggrabAlnRep0.bb GM12878 ChipSeq NFKB Peaks bigBed Stanford analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/spp/optimal/hub/spp.optimal.wgEncodeSydhTfbsGm12878NfkbTnfaStdAlnRep0_VS_wgEncodeSydhTfbsGm12878InputStdAlnRep1.bb GM12878 ChipSeq NFKB Peaks bigBed Stanford analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/spp/optimal/hub/spp.optimal.wgEncodeSydhTfbsGm12878Nrf1IggmusAlnRep0_VS_wgEncodeSydhTfbsGm12878InputIggmusAlnRep0.bb GM12878 ChipSeq Nrf1 Peaks bigBed Stanford analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/spp/optimal/hub/spp.optimal.wgEncodeSydhTfbsGm12878P300n15StdAlnRep0_VS_wgEncodeSydhTfbsGm12878InputStdAlnRep1.bb GM12878 ChipSeq p300_(N-15) Peaks bigBed Stanford analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/spp/optimal/hub/spp.optimal.wgEncodeSydhTfbsGm12878Pol2IggmusAlnRep0_VS_wgEncodeSydhTfbsGm12878InputIggmusAlnRep0.bb GM12878 ChipSeq Pol2 Peaks bigBed Stanford analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/spp/optimal/hub/spp.optimal.wgEncodeSydhTfbsGm12878Pol2StdAlnRep0_VS_wgEncodeSydhTfbsGm12878InputStdAlnRep1.bb GM12878 ChipSeq Pol2 Peaks bigBed Stanford analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/spp/optimal/hub/spp.optimal.wgEncodeSydhTfbsGm12878Pol3StdAlnRep0_VS_wgEncodeSydhTfbsGm12878InputStdAlnRep1.bb GM12878 ChipSeq Pol3 Peaks bigBed Stanford analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/spp/optimal/hub/spp.optimal.wgEncodeSydhTfbsGm12878Rad21IggrabAlnRep0_VS_wgEncodeSydhTfbsGm12878InputIggrabAlnRep0.bb GM12878 ChipSeq Rad21 Peaks bigBed Stanford analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/spp/optimal/hub/spp.optimal.wgEncodeSydhTfbsGm12878Rfx5n494IggmusAlnRep0_VS_wgEncodeSydhTfbsGm12878InputIggmusAlnRep0.bb GM12878 ChipSeq RFX5_(N-494) Peaks bigBed Stanford analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/spp/optimal/hub/spp.optimal.wgEncodeSydhTfbsGm12878Smc3ab9263IggmusAlnRep0_VS_wgEncodeSydhTfbsGm12878InputIggmusAlnRep0.bb GM12878 ChipSeq SMC3_(ab9263) Peaks bigBed Stanford analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/spp/optimal/hub/spp.optimal.wgEncodeSydhTfbsGm12878Spt20StdAlnRep0_VS_wgEncodeSydhTfbsGm12878InputStdAlnRep1.bb GM12878 ChipSeq SPT20 Peaks bigBed Harvard(Weissman) analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/spp/optimal/hub/spp.optimal.wgEncodeSydhTfbsGm12878Stat1StdAlnRep0_VS_wgEncodeSydhTfbsGm12878InputStdAlnRep1.bb GM12878 ChipSeq STAT1 Peaks bigBed Stanford analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/spp/optimal/hub/spp.optimal.wgEncodeSydhTfbsGm12878Stat3IggmusAlnRep0_VS_wgEncodeSydhTfbsGm12878InputIggmusAlnRep0.bb GM12878 ChipSeq STAT3 Peaks bigBed Stanford analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/spp/optimal/hub/spp.optimal.wgEncodeSydhTfbsGm12878TbpIggmusAlnRep0_VS_wgEncodeSydhTfbsGm12878InputIggmusAlnRep0.bb GM12878 ChipSeq TBP Peaks bigBed Stanford analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/spp/optimal/hub/spp.optimal.wgEncodeSydhTfbsGm12878Tr4StdAlnRep0_VS_wgEncodeSydhTfbsGm12878InputStdAlnRep1.bb GM12878 ChipSeq TR4 Peaks bigBed Stanford analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/spp/optimal/hub/spp.optimal.wgEncodeSydhTfbsGm12878Usf2IggmusAlnRep0_VS_wgEncodeSydhTfbsGm12878InputIggmusAlnRep0.bb GM12878 ChipSeq USF2 Peaks bigBed Stanford analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/spp/optimal/hub/spp.optimal.wgEncodeSydhTfbsGm12878WhipIggmusAlnRep0_VS_wgEncodeSydhTfbsGm12878InputIggmusAlnRep0.bb GM12878 ChipSeq WHIP Peaks bigBed Stanford analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/spp/optimal/hub/spp.optimal.wgEncodeSydhTfbsGm12878Yy1StdAlnRep0_VS_wgEncodeSydhTfbsGm12878InputStdAlnRep1.bb GM12878 ChipSeq YY1 Peaks bigBed Stanford analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/spp/optimal/hub/spp.optimal.wgEncodeSydhTfbsGm12878Znf143166181apStdAlnRep0_VS_wgEncodeSydhTfbsGm12878InputStdAlnRep1.bb GM12878 ChipSeq Znf143_(16618-1-AP) Peaks bigBed Stanford analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/spp/optimal/hub/spp.optimal.wgEncodeSydhTfbsGm12878Zzz3StdAlnRep0_VS_wgEncodeSydhTfbsGm12878InputStdAlnRep1.bb GM12878 ChipSeq ZZZ3 Peaks bigBed Stanford analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/spp/optimal/hub/spp.optimal.wgEncodeSydhTfbsGm12891NfkbIggrabAlnRep0_VS_wgEncodeSydhTfbsGm12891InputIggrabAlnRep0.bb GM12891 ChipSeq NFKB Peaks bigBed Stanford analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/spp/optimal/hub/spp.optimal.wgEncodeSydhTfbsGm12891Pol2IggmusAlnRep0_VS_wgEncodeSydhTfbsGm12891InputIggmusAlnRep0.bb GM12891 ChipSeq Pol2 Peaks bigBed Stanford analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/spp/optimal/hub/spp.optimal.wgEncodeSydhTfbsGm12892NfkbIggrabAlnRep0_VS_wgEncodeSydhTfbsGm12892InputIggrabAlnRep0.bb GM12892 ChipSeq NFKB Peaks bigBed Stanford analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/spp/optimal/hub/spp.optimal.wgEncodeSydhTfbsGm12892Pol2IggmusAlnRep0_VS_wgEncodeSydhTfbsGm12892InputIggmusAlnRep0.bb GM12892 ChipSeq Pol2 Peaks bigBed Stanford analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/spp/optimal/hub/spp.optimal.wgEncodeSydhTfbsGm15510NfkbIggrabAlnRep0_VS_wgEncodeSydhTfbsGm15510InputIggrabAlnRep0.bb GM15510 ChipSeq NFKB Peaks bigBed Stanford analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/spp/optimal/hub/spp.optimal.wgEncodeSydhTfbsGm15510Pol2IggmusAlnRep0_VS_wgEncodeSydhTfbsGm15510InputIggmusAlnRep0.bb GM15510 ChipSeq Pol2 Peaks bigBed Stanford analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/spp/optimal/hub/spp.optimal.wgEncodeSydhTfbsGm18505NfkbIggrabAlnRep0_VS_wgEncodeSydhTfbsGm18505InputIggrabAlnRep0.bb GM18505 ChipSeq NFKB Peaks bigBed Stanford analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/spp/optimal/hub/spp.optimal.wgEncodeSydhTfbsGm18505Pol2IggmusAlnRep0_VS_wgEncodeSydhTfbsGm18505InputIggmusAlnRep0.bb GM18505 ChipSeq Pol2 Peaks bigBed Stanford analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/spp/optimal/hub/spp.optimal.wgEncodeSydhTfbsGm18526NfkbIggrabAlnRep0_VS_wgEncodeSydhTfbsGm18526InputIggrabAlnRep0.bb GM18526 ChipSeq NFKB Peaks bigBed Stanford analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/spp/optimal/hub/spp.optimal.wgEncodeSydhTfbsGm18526Pol2IggmusAlnRep0_VS_wgEncodeSydhTfbsGm18526InputIggmusAlnRep0.bb GM18526 ChipSeq Pol2 Peaks bigBed Stanford analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/spp/optimal/hub/spp.optimal.wgEncodeSydhTfbsGm18951NfkbIggrabAlnRep0_VS_wgEncodeSydhTfbsGm18951InputIggrabAlnRep0.bb GM18951 ChipSeq NFKB Peaks bigBed Stanford analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/spp/optimal/hub/spp.optimal.wgEncodeSydhTfbsGm18951Pol2IggmusAlnRep0_VS_wgEncodeSydhTfbsGm18951InputIggmusAlnRep1.bb GM18951 ChipSeq Pol2 Peaks bigBed Stanford analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/spp/optimal/hub/spp.optimal.wgEncodeSydhTfbsGm19099NfkbIggrabAlnRep0_VS_wgEncodeSydhTfbsGm19099InputIggrabAlnRep0.bb GM19099 ChipSeq NFKB Peaks bigBed Stanford analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/spp/optimal/hub/spp.optimal.wgEncodeSydhTfbsGm19099Pol2IggmusAlnRep0_VS_wgEncodeSydhTfbsGm19099InputIggmusAlnRep0.bb GM19099 ChipSeq Pol2 Peaks bigBed Stanford analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/spp/optimal/hub/spp.optimal.wgEncodeSydhTfbsGm19193NfkbIggrabAlnRep0_VS_wgEncodeSydhTfbsGm19193InputIggrabAlnRep0.bb GM19193 ChipSeq NFKB Peaks bigBed Stanford analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/spp/optimal/hub/spp.optimal.wgEncodeSydhTfbsGm19193Pol2IggmusAlnRep0_VS_wgEncodeSydhTfbsGm19193InputIggmusAlnRep0.bb GM19193 ChipSeq Pol2 Peaks bigBed Stanford analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/spp/optimal/hub/spp.optimal.wgEncodeSydhTfbsH1hescCjunIggrabAlnRep0_VS_wgEncodeSydhTfbsH1hescInputIggrabAln.bb H1-hESC ChipSeq c-Jun Peaks bigBed Stanford analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/spp/optimal/hub/spp.optimal.wgEncodeSydhTfbsH1hescCtbp2UcdAlnRep0_VS_wgEncodeSydhTfbsH1hescInputUcdAln.bb H1-hESC ChipSeq CtBP2 Peaks bigBed UCD analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/spp/optimal/hub/spp.optimal.wgEncodeSydhTfbsH1hescMaxUcdAlnRep0_VS_wgEncodeSydhTfbsH1hescInputUcdAln.bb H1-hESC ChipSeq Max Peaks bigBed Stanford analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/spp/optimal/hub/spp.optimal.wgEncodeSydhTfbsH1hescNrf1IggrabAlnRep0_VS_wgEncodeSydhTfbsH1hescInputIggrabAln.bb H1-hESC ChipSeq Nrf1 Peaks bigBed Stanford analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/spp/optimal/hub/spp.optimal.wgEncodeSydhTfbsH1hescRad21IggrabAlnRep0_VS_wgEncodeSydhTfbsH1hescInputIggrabAln.bb H1-hESC ChipSeq Rad21 Peaks bigBed Stanford analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/spp/optimal/hub/spp.optimal.wgEncodeSydhTfbsH1hescRfx5n494IggrabAlnRep0_VS_wgEncodeSydhTfbsH1hescInputIggrabAln.bb H1-hESC ChipSeq RFX5_(N-494) Peaks bigBed Stanford analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/spp/optimal/hub/spp.optimal.wgEncodeSydhTfbsH1hescSuz12UcdAlnRep0_VS_wgEncodeSydhTfbsH1hescInputUcdAln.bb H1-hESC ChipSeq SUZ12 Peaks bigBed UCD analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/spp/optimal/hub/spp.optimal.wgEncodeSydhTfbsH1hescTbpStdAlnRep0_VS_wgEncodeSydhTfbsH1hescInputStdAln.bb H1-hESC ChipSeq TBP Peaks bigBed Stanford analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/spp/optimal/hub/spp.optimal.wgEncodeSydhTfbsH1hescUsf2IggrabAlnRep0_VS_wgEncodeSydhTfbsH1hescInputIggrabAln.bb H1-hESC ChipSeq USF2 Peaks bigBed Stanford analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/spp/optimal/hub/spp.optimal.wgEncodeSydhTfbsHct116Pol2UcdAlnRep0_VS_wgEncodeSydhTfbsHct116InputUcdAlnRep1.bb HCT-116 ChipSeq Pol2 Peaks bigBed Stanford analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/spp/optimal/hub/spp.optimal.wgEncodeSydhTfbsHct116Tcf4UcdAlnRep0_VS_wgEncodeSydhTfbsHct116InputUcdAlnRep1.bb HCT-116 ChipSeq TCF4 Peaks bigBed Stanford analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/spp/optimal/hub/spp.optimal.wgEncodeSydhTfbsHek293bElk4UcdAlnRep0_VS_wgEncodeSydhTfbsHek293InputUcdAln.bb HEK293(b) ChipSeq ELK4 Peaks bigBed UCD analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/spp/optimal/hub/spp.optimal.wgEncodeSydhTfbsHek293bKap1UcdAlnRep0_VS_wgEncodeSydhTfbsHek293InputUcdAln.bb HEK293(b) ChipSeq KAP1 Peaks bigBed UCD analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/spp/optimal/hub/spp.optimal.wgEncodeSydhTfbsHek293bPol2StdAlnRep0_VS_wgEncodeSydhTfbsHek293bInputStdAlnRep1.bb HEK293(b) ChipSeq Pol2 Peaks bigBed Stanford analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/spp/optimal/hub/spp.optimal.wgEncodeSydhTfbsHelas3Ap2alphaStdAlnRep0_VS_wgEncodeSydhTfbsHelas3InputStdAlnRep1.bb HeLa-S3 ChipSeq AP-2alpha Peaks bigBed Stanford analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/spp/optimal/hub/spp.optimal.wgEncodeSydhTfbsHelas3Ap2gammaStdAlnRep0_VS_wgEncodeSydhTfbsHelas3InputStdAlnRep1.bb HeLa-S3 ChipSeq AP-2gamma Peaks bigBed Stanford analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/spp/optimal/hub/spp.optimal.wgEncodeSydhTfbsHelas3Baf155IggmusAlnRep0_VS_wgEncodeSydhTfbsHelas3InputIggmusAlnRep0.bb HeLa-S3 ChipSeq BAF155 Peaks bigBed Stanford analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/spp/optimal/hub/spp.optimal.wgEncodeSydhTfbsHelas3Baf170IggmusAlnRep0_VS_wgEncodeSydhTfbsHelas3InputIggmusAlnRep0.bb HeLa-S3 ChipSeq BAF170 Peaks bigBed Stanford analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/spp/optimal/hub/spp.optimal.wgEncodeSydhTfbsHelas3Bdp1StdAlnRep0_VS_wgEncodeSydhTfbsHelas3InputStdAlnRep1.bb HeLa-S3 ChipSeq BDP1 Peaks bigBed Stanford analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/spp/optimal/hub/spp.optimal.wgEncodeSydhTfbsHelas3Brca1cIggrabAlnRep0_VS_wgEncodeSydhTfbsHelas3InputIggrabAlnRep1.bb HeLa-S3 ChipSeq BRCA1_(C-1863) Peaks bigBed Stanford analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/spp/optimal/hub/spp.optimal.wgEncodeSydhTfbsHelas3Brf1StdAlnRep0_VS_wgEncodeSydhTfbsHelas3InputStdAlnRep1.bb HeLa-S3 ChipSeq BRF1 Peaks bigBed Stanford analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/spp/optimal/hub/spp.optimal.wgEncodeSydhTfbsHelas3Brf2StdAlnRep0_VS_wgEncodeSydhTfbsHelas3InputStdAlnRep1.bb HeLa-S3 ChipSeq BRF2 Peaks bigBed Stanford analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/spp/optimal/hub/spp.optimal.wgEncodeSydhTfbsHelas3Brg1IggmusAlnRep0_VS_wgEncodeSydhTfbsHelas3InputIggmusAlnRep0.bb HeLa-S3 ChipSeq Brg1 Peaks bigBed Stanford analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/spp/optimal/hub/spp.optimal.wgEncodeSydhTfbsHelas3CebpbIggrabAlnRep0_VS_wgEncodeSydhTfbsHelas3InputIggrabAlnRep1.bb HeLa-S3 ChipSeq CEBPB Peaks bigBed Stanford analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/spp/optimal/hub/spp.optimal.wgEncodeSydhTfbsHelas3CfosStdAlnRep0_VS_wgEncodeSydhTfbsHelas3InputStdAlnRep1.bb HeLa-S3 ChipSeq c-Fos Peaks bigBed Stanford analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/spp/optimal/hub/spp.optimal.wgEncodeSydhTfbsHelas3CjunIggrabAlnRep0_VS_wgEncodeSydhTfbsHelas3InputIggrabAlnRep1.bb HeLa-S3 ChipSeq c-Jun Peaks bigBed Stanford analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/spp/optimal/hub/spp.optimal.wgEncodeSydhTfbsHelas3CmycStdAlnRep0_VS_wgEncodeSydhTfbsHelas3InputStdAlnRep1.bb HeLa-S3 ChipSeq c-Myc Peaks bigBed Stanford analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/spp/optimal/hub/spp.optimal.wgEncodeSydhTfbsHelas3E2f1StdAlnRep0_VS_wgEncodeSydhTfbsHelas3InputStdAlnRep1.bb HeLa-S3 ChipSeq E2F1 Peaks bigBed Stanford analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/spp/optimal/hub/spp.optimal.wgEncodeSydhTfbsHelas3E2f4StdAlnRep0_VS_wgEncodeSydhTfbsHelas3InputStdAlnRep1.bb HeLa-S3 ChipSeq E2F4 Peaks bigBed Stanford analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/spp/optimal/hub/spp.optimal.wgEncodeSydhTfbsHelas3E2f6StdAlnRep0_VS_wgEncodeSydhTfbsHelas3InputStdAlnRep1.bb HeLa-S3 ChipSeq E2F6 Peaks bigBed Stanford analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/spp/optimal/hub/spp.optimal.wgEncodeSydhTfbsHelas3Elk4UcdAlnRep0_VS_wgEncodeSydhTfbsHelas3InputUcdAln.bb HeLa-S3 ChipSeq ELK4 Peaks bigBed UCD analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/spp/optimal/hub/spp.optimal.wgEncodeSydhTfbsHelas3Gcn5StdAlnRep0_VS_wgEncodeSydhTfbsHelas3InputStdAlnRep1.bb HeLa-S3 ChipSeq GCN5 Peaks bigBed Stanford analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/spp/optimal/hub/spp.optimal.wgEncodeSydhTfbsHelas3Gtf2f1rapIggrabAlnRep0_VS_wgEncodeSydhTfbsHelas3InputIggrabAlnRep1.bb HeLa-S3 ChipSeq GTF2F1_(RAP-74) Peaks bigBed Stanford analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/spp/optimal/hub/spp.optimal.wgEncodeSydhTfbsHelas3Hae2f1StdAlnRep0_VS_wgEncodeSydhTfbsHelas3InputStdAlnRep1.bb HeLa-S3 ChipSeq HA-E2F1 Peaks bigBed Stanford analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/spp/optimal/hub/spp.optimal.wgEncodeSydhTfbsHelas3Ini1IggmusAlnRep0_VS_wgEncodeSydhTfbsHelas3InputIggmusAlnRep0.bb HeLa-S3 ChipSeq Ini1 Peaks bigBed Stanford analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/spp/optimal/hub/spp.optimal.wgEncodeSydhTfbsHelas3Irf3IggrabAlnRep0_VS_wgEncodeSydhTfbsHelas3InputIggrabAlnRep1.bb HeLa-S3 ChipSeq IRF3 Peaks bigBed Stanford analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/spp/optimal/hub/spp.optimal.wgEncodeSydhTfbsHelas3JundIggrabAlnRep0_VS_wgEncodeSydhTfbsHelas3InputIggrabAlnRep1.bb HeLa-S3 ChipSeq JunD Peaks bigBed Stanford analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/spp/optimal/hub/spp.optimal.wgEncodeSydhTfbsHelas3MaxStdAlnRep0_VS_wgEncodeSydhTfbsHelas3InputStdAlnRep1.bb HeLa-S3 ChipSeq Max Peaks bigBed Stanford analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/spp/optimal/hub/spp.optimal.wgEncodeSydhTfbsHelas3Mxi1bhlhIggrabAlnRep0_VS_wgEncodeSydhTfbsHelas3InputIggrabAlnRep1.bb HeLa-S3 ChipSeq Mxi1_(bHLH) Peaks bigBed Stanford analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/spp/optimal/hub/spp.optimal.wgEncodeSydhTfbsHelas3Nrf1IggmusAlnRep0_VS_wgEncodeSydhTfbsHelas3InputIggmusAlnRep0.bb HeLa-S3 ChipSeq Nrf1 Peaks bigBed Stanford analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/spp/optimal/hub/spp.optimal.wgEncodeSydhTfbsHelas3P300n15IggrabAlnRep0_VS_wgEncodeSydhTfbsHelas3InputIggrabAlnRep1.bb HeLa-S3 ChipSeq p300_(N-15) Peaks bigBed Stanford analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/spp/optimal/hub/spp.optimal.wgEncodeSydhTfbsHelas3Pol2s2IggrabAlnRep0_VS_wgEncodeSydhTfbsHelas3InputIggrabAlnRep1.bb HeLa-S3 ChipSeq Pol2(phosphoS2) Peaks bigBed Stanford analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/spp/optimal/hub/spp.optimal.wgEncodeSydhTfbsHelas3Pol2StdAlnRep0_VS_wgEncodeSydhTfbsHelas3InputStdAlnRep1.bb HeLa-S3 ChipSeq Pol2 Peaks bigBed Stanford analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/spp/optimal/hub/spp.optimal.wgEncodeSydhTfbsHelas3Prdm1vIggrabAlnRep0_VS_wgEncodeSydhTfbsHelas3InputIggrabAlnRep1.bb HeLa-S3 ChipSeq PRDM1_(Val90) Peaks bigBed Stanford analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/spp/optimal/hub/spp.optimal.wgEncodeSydhTfbsHelas3Rad21IggrabAlnRep0_VS_wgEncodeSydhTfbsHelas3InputIggrabAlnRep1.bb HeLa-S3 ChipSeq Rad21 Peaks bigBed Stanford analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/spp/optimal/hub/spp.optimal.wgEncodeSydhTfbsHelas3Rfx5n494IggrabAlnRep0_VS_wgEncodeSydhTfbsHelas3InputIggrabAlnRep1.bb HeLa-S3 ChipSeq RFX5_(N-494) Peaks bigBed Stanford analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/spp/optimal/hub/spp.optimal.wgEncodeSydhTfbsHelas3Rpc155StdAlnRep0_VS_wgEncodeSydhTfbsHelas3InputStdAlnRep1.bb HeLa-S3 ChipSeq RPC155 Peaks bigBed Stanford analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/spp/optimal/hub/spp.optimal.wgEncodeSydhTfbsHelas3Smc3ab9263IggrabAlnRep0_VS_wgEncodeSydhTfbsHelas3InputIggrabAlnRep1.bb HeLa-S3 ChipSeq SMC3_(ab9263) Peaks bigBed Stanford analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/spp/optimal/hub/spp.optimal.wgEncodeSydhTfbsHelas3Spt20StdAlnRep0_VS_wgEncodeSydhTfbsHelas3InputStdAlnRep1.bb HeLa-S3 ChipSeq SPT20 Peaks bigBed Stanford analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/spp/optimal/hub/spp.optimal.wgEncodeSydhTfbsHelas3Stat1Ifng30StdAlnRep0_VS_wgEncodeSydhTfbsHelas3InputIfng30StdAlnRep1.bb HeLa-S3 ChipSeq STAT1 Peaks bigBed Stanford analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/spp/optimal/hub/spp.optimal.wgEncodeSydhTfbsHelas3Stat3IggrabAlnRep0_VS_wgEncodeSydhTfbsHelas3InputIggrabAlnRep1.bb HeLa-S3 ChipSeq STAT3 Peaks bigBed Stanford analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/spp/optimal/hub/spp.optimal.wgEncodeSydhTfbsHelas3TbpIggrabAlnRep0_VS_wgEncodeSydhTfbsHelas3InputIggrabAlnRep1.bb HeLa-S3 ChipSeq TBP Peaks bigBed Stanford analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/spp/optimal/hub/spp.optimal.wgEncodeSydhTfbsHelas3Tf3c110StdAlnRep0_VS_wgEncodeSydhTfbsHelas3InputStdAlnRep1.bb HeLa-S3 ChipSeq TFIIIC-110 Peaks bigBed Stanford analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/spp/optimal/hub/spp.optimal.wgEncodeSydhTfbsHelas3Tr4StdAlnRep0_VS_wgEncodeSydhTfbsHelas3InputStdAlnRep1.bb HeLa-S3 ChipSeq TR4 Peaks bigBed Stanford analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/spp/optimal/hub/spp.optimal.wgEncodeSydhTfbsHelas3Usf2IggmusAlnRep0_VS_wgEncodeSydhTfbsHelas3InputIggmusAlnRep0.bb HeLa-S3 ChipSeq USF2 Peaks bigBed Stanford analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/spp/optimal/hub/spp.optimal.wgEncodeSydhTfbsHelas3Znf274UcdAlnRep0_VS_wgEncodeSydhTfbsHelas3InputUcdAln.bb HeLa-S3 ChipSeq ZNF274 Peaks bigBed UCD analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/spp/optimal/hub/spp.optimal.wgEncodeSydhTfbsHelas3Zzz3StdAlnRep0_VS_wgEncodeSydhTfbsHelas3InputStdAlnRep1.bb HeLa-S3 ChipSeq ZZZ3 Peaks bigBed Harvard(Weissman) analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/spp/optimal/hub/spp.optimal.wgEncodeSydhTfbsHepg2bTr4UcdAlnRep0_VS_wgEncodeSydhTfbsHepg2bInputUcdAlnRep1.bb HepG2b ChipSeq TR4 Peaks bigBed Stanford analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/spp/optimal/hub/spp.optimal.wgEncodeSydhTfbsHepg2bZnf274UcdAlnRep0_VS_wgEncodeSydhTfbsHepg2bInputUcdAlnRep1.bb HepG2b ChipSeq ZNF274 Peaks bigBed UCD analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/spp/optimal/hub/spp.optimal.wgEncodeSydhTfbsHepg2CebpbForsklnStdAlnRep0_VS_wgEncodeSydhTfbsHepg2InputForsklnStdAlnRep0.bb HepG2 ChipSeq CEBPB Peaks bigBed Stanford analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/spp/optimal/hub/spp.optimal.wgEncodeSydhTfbsHepg2CebpbIggrabAlnRep0_VS_wgEncodeSydhTfbsHepg2InputIggrabAln.bb HepG2 ChipSeq CEBPB Peaks bigBed Stanford analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/spp/optimal/hub/spp.optimal.wgEncodeSydhTfbsHepg2Chd21250IggrabAlnRep0_VS_wgEncodeSydhTfbsHepg2InputIggrabAln.bb HepG2 ChipSeq CHD2_(N-1250) Peaks bigBed Stanford analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/spp/optimal/hub/spp.optimal.wgEncodeSydhTfbsHepg2CjunIggrabAlnRep0_VS_wgEncodeSydhTfbsHepg2InputIggrabAln.bb HepG2 ChipSeq c-Jun Peaks bigBed Stanford analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/spp/optimal/hub/spp.optimal.wgEncodeSydhTfbsHepg2ErraForsklnStdAlnRep0_VS_wgEncodeSydhTfbsHepg2InputForsklnStdAlnRep0.bb HepG2 ChipSeq ERRA Peaks bigBed Stanford analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/spp/optimal/hub/spp.optimal.wgEncodeSydhTfbsHepg2Grp20ForsklnStdAlnRep0_VS_wgEncodeSydhTfbsHepg2InputForsklnStdAlnRep0.bb HepG2 ChipSeq GRp20 Peaks bigBed Stanford analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/spp/optimal/hub/spp.optimal.wgEncodeSydhTfbsHepg2Hnf4aForsklnStdAlnRep0_VS_wgEncodeSydhTfbsHepg2InputForsklnStdAlnRep0.bb HepG2 ChipSeq HNF4A Peaks bigBed Stanford analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/spp/optimal/hub/spp.optimal.wgEncodeSydhTfbsHepg2Hsf1ForsklnStdAlnRep0_VS_wgEncodeSydhTfbsHepg2InputForsklnStdAlnRep0.bb HepG2 ChipSeq HSF1 Peaks bigBed Stanford analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/spp/optimal/hub/spp.optimal.wgEncodeSydhTfbsHepg2Irf3IggrabAlnRep0_VS_wgEncodeSydhTfbsHepg2InputIggrabAln.bb HepG2 ChipSeq IRF3 Peaks bigBed Stanford analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/spp/optimal/hub/spp.optimal.wgEncodeSydhTfbsHepg2JundIggrabAlnRep0_VS_wgEncodeSydhTfbsHepg2InputIggrabAln.bb HepG2 ChipSeq JunD Peaks bigBed Stanford analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/spp/optimal/hub/spp.optimal.wgEncodeSydhTfbsHepg2Maffm8194IggrabAlnRep0_VS_wgEncodeSydhTfbsHepg2InputIggrabAln.bb HepG2 ChipSeq MafF_(M8194) Peaks bigBed Stanford analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/spp/optimal/hub/spp.optimal.wgEncodeSydhTfbsHepg2Mafkab50322IggrabAlnRep0_VS_wgEncodeSydhTfbsHepg2InputIggrabAln.bb HepG2 ChipSeq MafK_(ab50322) Peaks bigBed Stanford analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/spp/optimal/hub/spp.optimal.wgEncodeSydhTfbsHepg2Mafksc477IggrabAlnRep0_VS_wgEncodeSydhTfbsHepg2InputIggrabAln.bb HepG2 ChipSeq MafK_(SC-477) Peaks bigBed Stanford analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/spp/optimal/hub/spp.optimal.wgEncodeSydhTfbsHepg2Nrf1IggrabAlnRep0_VS_wgEncodeSydhTfbsHepg2InputIggrabAln.bb HepG2 ChipSeq Nrf1 Peaks bigBed Stanford analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/spp/optimal/hub/spp.optimal.wgEncodeSydhTfbsHepg2Pgc1aForsklnStdAlnRep0_VS_wgEncodeSydhTfbsHepg2InputForsklnStdAlnRep0.bb HepG2 ChipSeq PGC1A Peaks bigBed Stanford analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/spp/optimal/hub/spp.optimal.wgEncodeSydhTfbsHepg2Pol2ForsklnStdAlnRep0_VS_wgEncodeSydhTfbsHepg2InputForsklnStdAlnRep0.bb HepG2 ChipSeq Pol2 Peaks bigBed Stanford analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/spp/optimal/hub/spp.optimal.wgEncodeSydhTfbsHepg2Pol2IggrabAlnRep0_VS_wgEncodeSydhTfbsHepg2InputIggrabAln.bb HepG2 ChipSeq Pol2 Peaks bigBed Stanford analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/spp/optimal/hub/spp.optimal.wgEncodeSydhTfbsHepg2Pol2PravastStdAlnRep0_VS_wgEncodeSydhTfbsHepg2InputPravastStdAlnRep0.bb HepG2 ChipSeq Pol2 Peaks bigBed Stanford analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/spp/optimal/hub/spp.optimal.wgEncodeSydhTfbsHepg2Rad21IggrabAlnRep0_VS_wgEncodeSydhTfbsHepg2InputIggrabAln.bb HepG2 ChipSeq Rad21 Peaks bigBed Stanford analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/spp/optimal/hub/spp.optimal.wgEncodeSydhTfbsHepg2Rfx5n494IggrabAlnRep0_VS_wgEncodeSydhTfbsHepg2InputIggrabAln.bb HepG2 ChipSeq RFX5_(N-494) Peaks bigBed Stanford analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/spp/optimal/hub/spp.optimal.wgEncodeSydhTfbsHepg2Srebp1InslnStdAlnRep0_VS_wgEncodeSydhTfbsHepg2InputInslnStdAlnRep0.bb HepG2 ChipSeq SREBP1 Peaks bigBed Stanford analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/spp/optimal/hub/spp.optimal.wgEncodeSydhTfbsHepg2Srebp1PravastStdAlnRep0_VS_wgEncodeSydhTfbsHepg2InputPravastStdAlnRep0.bb HepG2 ChipSeq SREBP1 Peaks bigBed Stanford analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/spp/optimal/hub/spp.optimal.wgEncodeSydhTfbsHepg2Srebp2PravastStdAlnRep0_VS_wgEncodeSydhTfbsHepg2InputPravastStdAlnRep0.bb HepG2 ChipSeq SREBP2 Peaks bigBed Stanford analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/spp/optimal/hub/spp.optimal.wgEncodeSydhTfbsHepg2TbpIggrabAlnRep0_VS_wgEncodeSydhTfbsHepg2InputIggrabAln.bb HepG2 ChipSeq TBP Peaks bigBed Stanford analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/spp/optimal/hub/spp.optimal.wgEncodeSydhTfbsHepg2Tcf4UcdAlnRep0_VS_wgEncodeSydhTfbsHepg2bInputUcdAlnRep1.bb HepG2b ChipSeq TCF4 Peaks bigBed UCD analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/spp/optimal/hub/spp.optimal.wgEncodeSydhTfbsHepg2Usf2IggrabAlnRep0_VS_wgEncodeSydhTfbsHepg2InputIggrabAln.bb HepG2 ChipSeq USF2 Peaks bigBed Stanford analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/spp/optimal/hub/spp.optimal.wgEncodeSydhTfbsHuvecCfosUcdAlnRep0_VS_wgEncodeSydhTfbsHuvecInputUcdAlnRep1.bb HUVEC ChipSeq c-Fos Peaks bigBed UCD analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/spp/optimal/hub/spp.optimal.wgEncodeSydhTfbsHuvecCjunStdAlnRep0_VS_wgEncodeSydhTfbsHuvecInputStdAlnRep0.bb HUVEC ChipSeq c-Jun Peaks bigBed Stanford analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/spp/optimal/hub/spp.optimal.wgEncodeSydhTfbsHuvecGata2UcdAlnRep0_VS_wgEncodeSydhTfbsHuvecInputUcdAlnRep1.bb HUVEC ChipSeq GATA-2 Peaks bigBed UCD analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/spp/optimal/hub/spp.optimal.wgEncodeSydhTfbsHuvecMaxStdAlnRep0_VS_wgEncodeSydhTfbsHuvecInputStdAlnRep0.bb HUVEC ChipSeq Max Peaks bigBed Stanford analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/spp/optimal/hub/spp.optimal.wgEncodeSydhTfbsHuvecPol2StdAlnRep0_VS_wgEncodeSydhTfbsHuvecInputStdAlnRep0.bb HUVEC ChipSeq Pol2 Peaks bigBed Stanford analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/spp/optimal/hub/spp.optimal.wgEncodeSydhTfbsK562Atf3StdAlnRep0_VS_wgEncodeSydhTfbsK562InputStdAlnRep0.bb K562 ChipSeq ATF3 Peaks bigBed Stanford analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/spp/optimal/hub/spp.optimal.wgEncodeSydhTfbsK562Bdp1StdAlnRep0_VS_wgEncodeSydhTfbsK562InputStdAlnRep0.bb K562 ChipSeq BDP1 Peaks bigBed Stanford analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/spp/optimal/hub/spp.optimal.wgEncodeSydhTfbsK562bE2f4UcdAlnRep0_VS_wgEncodeSydhTfbsK562bInputUcdAlnRep1.bb K562b ChipSeq E2F4 Peaks bigBed Stanford analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/spp/optimal/hub/spp.optimal.wgEncodeSydhTfbsK562bE2f6UcdAlnRep0_VS_wgEncodeSydhTfbsK562bInputUcdAlnRep1.bb K562b ChipSeq E2F6 Peaks bigBed Stanford analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/spp/optimal/hub/spp.optimal.wgEncodeSydhTfbsK562bGata1UcdAlnRep0_VS_wgEncodeSydhTfbsK562bInputUcdAlnRep1.bb K562b ChipSeq GATA-1 Peaks bigBed Stanford analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/spp/optimal/hub/spp.optimal.wgEncodeSydhTfbsK562bGata2UcdAlnRep0_VS_wgEncodeSydhTfbsK562bInputUcdAlnRep1.bb K562b ChipSeq GATA-2 Peaks bigBed Stanford analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/spp/optimal/hub/spp.optimal.wgEncodeSydhTfbsK562bKap1UcdAlnRep0_VS_wgEncodeSydhTfbsK562bInputUcdAlnRep1.bb K562b ChipSeq KAP1 Peaks bigBed UCD analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/spp/optimal/hub/spp.optimal.wgEncodeSydhTfbsK562Brf1StdAlnRep0_VS_wgEncodeSydhTfbsK562InputStdAlnRep0.bb K562 ChipSeq BRF1 Peaks bigBed Stanford analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/spp/optimal/hub/spp.optimal.wgEncodeSydhTfbsK562Brf2StdAlnRep0_VS_wgEncodeSydhTfbsK562InputStdAlnRep0.bb K562 ChipSeq BRF2 Peaks bigBed Stanford analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/spp/optimal/hub/spp.optimal.wgEncodeSydhTfbsK562Brg1IggmusAlnRep0_VS_wgEncodeSydhTfbsK562InputIggmusAlnRep0.bb K562 ChipSeq Brg1 Peaks bigBed Stanford analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/spp/optimal/hub/spp.optimal.wgEncodeSydhTfbsK562bSetdb1MnasedUcdAlnRep0_VS_wgEncodeSydhTfbsK562bInputUcdAlnRep1.bb K562b ChipSeq SETDB1 Peaks bigBed Stanford analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/spp/optimal/hub/spp.optimal.wgEncodeSydhTfbsK562bSetdb1UcdAlnRep0_VS_wgEncodeSydhTfbsK562bInputUcdAlnRep1.bb K562b ChipSeq SETDB1 Peaks bigBed Stanford analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/spp/optimal/hub/spp.optimal.wgEncodeSydhTfbsK562bTr4UcdAlnRep0_VS_wgEncodeSydhTfbsK562bInputUcdAlnRep1.bb K562b ChipSeq TR4 Peaks bigBed Stanford analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/spp/optimal/hub/spp.optimal.wgEncodeSydhTfbsK562bYy1UcdAlnRep0_VS_wgEncodeSydhTfbsK562bInputUcdAlnRep1.bb K562b ChipSeq YY1 Peaks bigBed Stanford analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/spp/optimal/hub/spp.optimal.wgEncodeSydhTfbsK562bZnf263UcdAlnRep0_VS_wgEncodeSydhTfbsK562bInputUcdAlnRep1.bb K562b ChipSeq ZNF263 Peaks bigBed Stanford analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/spp/optimal/hub/spp.optimal.wgEncodeSydhTfbsK562bZnf274UcdAlnRep0_VS_wgEncodeSydhTfbsK562bInputUcdAlnRep1.bb K562b ChipSeq ZNF274 Peaks bigBed Stanford analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/spp/optimal/hub/spp.optimal.wgEncodeSydhTfbsK562Ccnt2StdAlnRep0_VS_wgEncodeSydhTfbsK562InputStdAlnRep0.bb K562 ChipSeq CCNT2 Peaks bigBed Harvard analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/spp/optimal/hub/spp.optimal.wgEncodeSydhTfbsK562CebpbIggrabAlnRep0_VS_wgEncodeSydhTfbsK562InputIggrabAln.bb K562 ChipSeq CEBPB Peaks bigBed Stanford analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/spp/optimal/hub/spp.optimal.wgEncodeSydhTfbsK562CfosStdAlnRep0_VS_wgEncodeSydhTfbsK562InputStdAlnRep0.bb K562 ChipSeq c-Fos Peaks bigBed Stanford analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/spp/optimal/hub/spp.optimal.wgEncodeSydhTfbsK562Chd21250IggrabAlnRep0_VS_wgEncodeSydhTfbsK562InputIggrabAln.bb K562 ChipSeq CHD2_(N-1250) Peaks bigBed Stanford analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/spp/optimal/hub/spp.optimal.wgEncodeSydhTfbsK562CjunIfna6hStdAlnRep0_VS_wgEncodeSydhTfbsK562InputIfna6hStdAlnRep1.bb K562 ChipSeq c-Jun Peaks bigBed Stanford analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/spp/optimal/hub/spp.optimal.wgEncodeSydhTfbsK562CjunIfng30StdAlnRep0_VS_wgEncodeSydhTfbsK562InputIfng30StdAlnRep1.bb K562 ChipSeq c-Jun Peaks bigBed Stanford analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/spp/optimal/hub/spp.optimal.wgEncodeSydhTfbsK562CjunIfng6hStdAlnRep0_VS_wgEncodeSydhTfbsK562InputIfng6hStdAlnRep1.bb K562 ChipSeq c-Jun Peaks bigBed Stanford analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/spp/optimal/hub/spp.optimal.wgEncodeSydhTfbsK562CjunStdAlnRep0_VS_wgEncodeSydhTfbsK562InputStdAlnRep0.bb K562 ChipSeq c-Jun Peaks bigBed Stanford analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/spp/optimal/hub/spp.optimal.wgEncodeSydhTfbsK562CmycIfna30StdAlnRep0_VS_wgEncodeSydhTfbsK562InputIfna30StdAlnRep1.bb K562 ChipSeq c-Myc Peaks bigBed Stanford analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/spp/optimal/hub/spp.optimal.wgEncodeSydhTfbsK562CmycIfna6hStdAlnRep0_VS_wgEncodeSydhTfbsK562InputIfna6hStdAlnRep1.bb K562 ChipSeq c-Myc Peaks bigBed Stanford analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/spp/optimal/hub/spp.optimal.wgEncodeSydhTfbsK562CmycIfng30StdAlnRep0_VS_wgEncodeSydhTfbsK562InputIfng30StdAlnRep1.bb K562 ChipSeq c-Myc Peaks bigBed Stanford analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/spp/optimal/hub/spp.optimal.wgEncodeSydhTfbsK562CmycIfng6hStdAlnRep0_VS_wgEncodeSydhTfbsK562InputIfng6hStdAlnRep1.bb K562 ChipSeq c-Myc Peaks bigBed Stanford analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/spp/optimal/hub/spp.optimal.wgEncodeSydhTfbsK562CmycStdAlnRep0_VS_wgEncodeSydhTfbsK562InputStdAlnRep0.bb K562 ChipSeq c-Myc Peaks bigBed Stanford analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/spp/optimal/hub/spp.optimal.wgEncodeSydhTfbsK562Gtf2bStdAlnRep0_VS_wgEncodeSydhTfbsK562InputStdAlnRep0.bb K562 ChipSeq GTF2B Peaks bigBed Harvard analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/spp/optimal/hub/spp.optimal.wgEncodeSydhTfbsK562Gtf2f1rapIggrabAlnRep0_VS_wgEncodeSydhTfbsK562InputIggrabAln.bb K562 ChipSeq GTF2F1_(RAP-74) Peaks bigBed Stanford analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/spp/optimal/hub/spp.optimal.wgEncodeSydhTfbsK562Hmgn3StdAlnRep0_VS_wgEncodeSydhTfbsK562InputStdAlnRep0.bb K562 ChipSeq HMGN3 Peaks bigBed Harvard analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/spp/optimal/hub/spp.optimal.wgEncodeSydhTfbsK562Ini1IggmusAlnRep0_VS_wgEncodeSydhTfbsK562InputIggmusAlnRep0.bb K562 ChipSeq Ini1 Peaks bigBed Stanford analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/spp/optimal/hub/spp.optimal.wgEncodeSydhTfbsK562Irf1Ifna30StdAlnRep0_VS_wgEncodeSydhTfbsK562InputIfna30StdAlnRep1.bb K562 ChipSeq IRF1 Peaks bigBed Stanford analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/spp/optimal/hub/spp.optimal.wgEncodeSydhTfbsK562Irf1Ifng6hStdAlnRep0_VS_wgEncodeSydhTfbsK562InputIfng6hStdAlnRep1.bb K562 ChipSeq IRF1 Peaks bigBed Stanford analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/spp/optimal/hub/spp.optimal.wgEncodeSydhTfbsK562JundStdAlnRep0_VS_wgEncodeSydhTfbsK562InputStdAlnRep0.bb K562 ChipSeq JunD Peaks bigBed Stanford analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/spp/optimal/hub/spp.optimal.wgEncodeSydhTfbsK562Mafkab50322IggrabAlnRep0_VS_wgEncodeSydhTfbsK562InputIggrabAln.bb K562 ChipSeq MafK_(ab50322) Peaks bigBed Stanford analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/spp/optimal/hub/spp.optimal.wgEncodeSydhTfbsK562MaxStdAlnRep0_VS_wgEncodeSydhTfbsK562InputStdAlnRep0.bb K562 ChipSeq Max Peaks bigBed Stanford analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/spp/optimal/hub/spp.optimal.wgEncodeSydhTfbsK562Mxi1bhlhIggrabAlnRep0_VS_wgEncodeSydhTfbsK562InputIggrabAln.bb K562 ChipSeq Mxi1_(bHLH) Peaks bigBed Stanford analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/spp/optimal/hub/spp.optimal.wgEncodeSydhTfbsK562NelfeStdAlnRep0_VS_wgEncodeSydhTfbsK562InputStdAlnRep0.bb K562 ChipSeq NELFe Peaks bigBed Stanford analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/spp/optimal/hub/spp.optimal.wgEncodeSydhTfbsK562Nfe2StdAlnRep0_VS_wgEncodeSydhTfbsK562InputStdAlnRep0.bb K562 ChipSeq NF-E2 Peaks bigBed Stanford analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/spp/optimal/hub/spp.optimal.wgEncodeSydhTfbsK562NfyaStdAlnRep0_VS_wgEncodeSydhTfbsK562InputStdAlnRep0.bb K562 ChipSeq NF-YA Peaks bigBed Stanford analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/spp/optimal/hub/spp.optimal.wgEncodeSydhTfbsK562NfybStdAlnRep0_VS_wgEncodeSydhTfbsK562InputStdAlnRep0.bb K562 ChipSeq NF-YB Peaks bigBed Stanford analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/spp/optimal/hub/spp.optimal.wgEncodeSydhTfbsK562Nrf1IggrabAlnRep0_VS_wgEncodeSydhTfbsK562InputIggrabAln.bb K562 ChipSeq Nrf1 Peaks bigBed Stanford analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/spp/optimal/hub/spp.optimal.wgEncodeSydhTfbsK562P300f4IggrabAlnRep0_VS_wgEncodeSydhTfbsK562InputIggrabAln.bb K562 ChipSeq p300_(F-4) Peaks bigBed Stanford analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/spp/optimal/hub/spp.optimal.wgEncodeSydhTfbsK562Pol2Ifna30StdAlnRep0_VS_wgEncodeSydhTfbsK562InputIfna30StdAlnRep1.bb K562 ChipSeq Pol2 Peaks bigBed Stanford analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/spp/optimal/hub/spp.optimal.wgEncodeSydhTfbsK562Pol2Ifna6hStdAlnRep0_VS_wgEncodeSydhTfbsK562InputIfna6hStdAlnRep1.bb K562 ChipSeq Pol2 Peaks bigBed Stanford analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/spp/optimal/hub/spp.optimal.wgEncodeSydhTfbsK562Pol2Ifng30StdAlnRep0_VS_wgEncodeSydhTfbsK562InputIfng30StdAlnRep1.bb K562 ChipSeq Pol2 Peaks bigBed Stanford analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/spp/optimal/hub/spp.optimal.wgEncodeSydhTfbsK562Pol2Ifng6hStdAlnRep0_VS_wgEncodeSydhTfbsK562InputIfng6hStdAlnRep1.bb K562 ChipSeq Pol2 Peaks bigBed Stanford analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/spp/optimal/hub/spp.optimal.wgEncodeSydhTfbsK562Pol2IggmusAlnRep0_VS_wgEncodeSydhTfbsK562InputIggmusAlnRep0.bb K562 ChipSeq Pol2 Peaks bigBed Stanford analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/spp/optimal/hub/spp.optimal.wgEncodeSydhTfbsK562Pol2s2StdAlnRep0_VS_wgEncodeSydhTfbsK562InputStdAlnRep0.bb K562 ChipSeq Pol2(phosphoS2) Peaks bigBed Stanford analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/spp/optimal/hub/spp.optimal.wgEncodeSydhTfbsK562Pol2StdAlnRep0_VS_wgEncodeSydhTfbsK562InputStdAlnRep0.bb K562 ChipSeq Pol2 Peaks bigBed Stanford analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/spp/optimal/hub/spp.optimal.wgEncodeSydhTfbsK562Pol3StdAlnRep0_VS_wgEncodeSydhTfbsK562InputStdAlnRep0.bb K562 ChipSeq Pol3 Peaks bigBed Stanford analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/spp/optimal/hub/spp.optimal.wgEncodeSydhTfbsK562Rad21StdAlnRep0_VS_wgEncodeSydhTfbsK562InputStdAlnRep0.bb K562 ChipSeq Rad21 Peaks bigBed Stanford analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/spp/optimal/hub/spp.optimal.wgEncodeSydhTfbsK562Rpc155StdAlnRep0_VS_wgEncodeSydhTfbsK562InputStdAlnRep0.bb K562 ChipSeq RPC155 Peaks bigBed Stanford analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/spp/optimal/hub/spp.optimal.wgEncodeSydhTfbsK562Sirt6StdAlnRep0_VS_wgEncodeSydhTfbsK562InputStdAlnRep0.bb K562 ChipSeq SIRT6 Peaks bigBed Stanford analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/spp/optimal/hub/spp.optimal.wgEncodeSydhTfbsK562Smc3ab9263IggrabAlnRep0_VS_wgEncodeSydhTfbsK562InputIggrabAln.bb K562 ChipSeq SMC3_(ab9263) Peaks bigBed Stanford analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/spp/optimal/hub/spp.optimal.wgEncodeSydhTfbsK562Stat1Ifna30StdAlnRep0_VS_wgEncodeSydhTfbsK562InputIfna30StdAlnRep1.bb K562 ChipSeq STAT1 Peaks bigBed Stanford analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/spp/optimal/hub/spp.optimal.wgEncodeSydhTfbsK562Stat1Ifna6hStdAlnRep0_VS_wgEncodeSydhTfbsK562InputIfna6hStdAlnRep1.bb K562 ChipSeq STAT1 Peaks bigBed Stanford analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/spp/optimal/hub/spp.optimal.wgEncodeSydhTfbsK562Stat1Ifng30StdAlnRep0_VS_wgEncodeSydhTfbsK562InputIfng30StdAlnRep1.bb K562 ChipSeq STAT1 Peaks bigBed Stanford analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/spp/optimal/hub/spp.optimal.wgEncodeSydhTfbsK562Stat1Ifng6hStdAlnRep0_VS_wgEncodeSydhTfbsK562InputIfng6hStdAlnRep1.bb K562 ChipSeq STAT1 Peaks bigBed Stanford analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/spp/optimal/hub/spp.optimal.wgEncodeSydhTfbsK562Stat2Ifna30StdAlnRep0_VS_wgEncodeSydhTfbsK562InputIfna30StdAlnRep1.bb K562 ChipSeq STAT2 Peaks bigBed Stanford analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/spp/optimal/hub/spp.optimal.wgEncodeSydhTfbsK562Stat2Ifna6hStdAlnRep0_VS_wgEncodeSydhTfbsK562InputIfna6hStdAlnRep1.bb K562 ChipSeq STAT2 Peaks bigBed Stanford analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/spp/optimal/hub/spp.optimal.wgEncodeSydhTfbsK562Tal1sc12984IggmusAlnRep0_VS_wgEncodeSydhTfbsK562InputIggmusAlnRep0.bb K562 ChipSeq TAL1_(SC-12984) Peaks bigBed Stanford analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/spp/optimal/hub/spp.optimal.wgEncodeSydhTfbsK562TbpIggmusAlnRep0_VS_wgEncodeSydhTfbsK562InputIggmusAlnRep0.bb K562 ChipSeq TBP Peaks bigBed Stanford analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/spp/optimal/hub/spp.optimal.wgEncodeSydhTfbsK562Tf3c110StdAlnRep0_VS_wgEncodeSydhTfbsK562InputStdAlnRep0.bb K562 ChipSeq TFIIIC-110 Peaks bigBed Stanford analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/spp/optimal/hub/spp.optimal.wgEncodeSydhTfbsK562Usf2StdAlnRep0_VS_wgEncodeSydhTfbsK562InputStdAlnRep0.bb K562 ChipSeq USF2 Peaks bigBed Stanford analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/spp/optimal/hub/spp.optimal.wgEncodeSydhTfbsK562Xrcc4StdAlnRep0_VS_wgEncodeSydhTfbsK562InputStdAlnRep0.bb K562 ChipSeq XRCC4 Peaks bigBed Stanford analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/spp/optimal/hub/spp.optimal.wgEncodeSydhTfbsMcf10aesPol2Etoh01StdAlnRep0_VS_wgEncodeSydhTfbsMcf10aesInputUcdAln.bb MCF10A-Er-Src ChipSeq Pol2 Peaks bigBed Stanford analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/spp/optimal/hub/spp.optimal.wgEncodeSydhTfbsMcf10aesPol2TamStdAlnRep0_VS_wgEncodeSydhTfbsMcf10aesInputUcdAln.bb MCF10A-Er-Src ChipSeq Pol2 Peaks bigBed Harvard(Weissman) analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/spp/optimal/hub/spp.optimal.wgEncodeSydhTfbsMcf10aesStat3Etoh01bStdAlnRep0_VS_wgEncodeSydhTfbsMcf10aesInputEtoh01bStdAln.bb MCF10A-Er-Src ChipSeq STAT3 Peaks bigBed Harvard(Weissman) analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/spp/optimal/hub/spp.optimal.wgEncodeSydhTfbsMcf10aesStat3Etoh01cStdAlnRep0_VS_wgEncodeSydhTfbsMcf10aesInputEtoh01cStdAln.bb MCF10A-Er-Src ChipSeq STAT3 Peaks bigBed Stanford analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/spp/optimal/hub/spp.optimal.wgEncodeSydhTfbsMcf10aesStat3Etoh01StdAlnRep0_VS_wgEncodeSydhTfbsMcf10aesInputUcdAln.bb MCF10A-Er-Src ChipSeq STAT3 Peaks bigBed Harvard(Weissman) analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/spp/optimal/hub/spp.optimal.wgEncodeSydhTfbsMcf10aesStat3TamStdAlnRep0_VS_wgEncodeSydhTfbsMcf10aesInputUcdAln.bb MCF10A-Er-Src ChipSeq STAT3 Peaks bigBed Harvard(Weissman) analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/spp/optimal/hub/spp.optimal.wgEncodeSydhTfbsMcf7Hae2f1UcdAlnRep0_VS_wgEncodeSydhTfbsMcf7InputUcdAlnRep0.bb MCF-7 ChipSeq HA-E2F1 Peaks bigBed Stanford analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/spp/optimal/hub/spp.optimal.wgEncodeSydhTfbsNb4CmycStdAlnRep0_VS_wgEncodeSydhTfbsNb4InputStdAlnRep1.bb NB4 ChipSeq c-Myc Peaks bigBed Stanford analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/spp/optimal/hub/spp.optimal.wgEncodeSydhTfbsNb4MaxStdAlnRep0_VS_wgEncodeSydhTfbsNb4InputStdAlnRep1.bb NB4 ChipSeq Max Peaks bigBed Stanford analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/spp/optimal/hub/spp.optimal.wgEncodeSydhTfbsNb4Pol2StdAlnRep0_VS_wgEncodeSydhTfbsNb4InputStdAlnRep1.bb NB4 ChipSeq Pol2 Peaks bigBed Stanford analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/spp/optimal/hub/spp.optimal.wgEncodeSydhTfbsNt2d1Suz12UcdAlnRep0_VS_wgEncodeSydhTfbsNt2d1InputUcdAlnRep1.bb NT2-D1 ChipSeq SUZ12 Peaks bigBed Stanford analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/spp/optimal/hub/spp.optimal.wgEncodeSydhTfbsNt2d1Yy1UcdAlnRep0_VS_wgEncodeSydhTfbsNt2d1InputUcdAlnRep1.bb NT2-D1 ChipSeq YY1 Peaks bigBed Stanford analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/spp/optimal/hub/spp.optimal.wgEncodeSydhTfbsNt2d1Znf274UcdAlnRep0_VS_wgEncodeSydhTfbsNt2d1InputUcdAlnRep1.bb NT2-D1 ChipSeq ZNF274 Peaks bigBed UCD analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/spp/optimal/hub/spp.optimal.wgEncodeSydhTfbsPbdeGata1UcdAlnRep0_VS_wgEncodeSydhTfbsPbdeInputUcdAln.bb PBDE ChipSeq GATA-1 Peaks bigBed UCD analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/spp/optimal/hub/spp.optimal.wgEncodeSydhTfbsPbdePol2UcdAlnRep0_VS_wgEncodeSydhTfbsPbdeInputUcdAln.bb PBDE ChipSeq Pol2 Peaks bigBed UCD analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/spp/optimal/hub/spp.optimal.wgEncodeSydhTfbsRajiPol2UcdAlnRep0_VS_wgEncodeSydhTfbsRajiInputUcdAln.bb Raji ChipSeq Pol2 Peaks bigBed UCD analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/spp/optimal/hub/spp.optimal.wgEncodeSydhTfbsShsy5yGata2UcdAlnRep0_VS_wgEncodeSydhTfbsShsy5yInputUcdAln.bb SH-SY5Y ChipSeq GATA-2 Peaks bigBed UCD analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/spp/optimal/hub/spp.optimal.wgEncodeSydhTfbsTrexhek293Znf263UcdAlnRep0_VS_wgEncodeSydhTfbsThek293InputUcdAln.bb T-REx-HEK293 ChipSeq ZNF263 Peaks bigBed UCD analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/spp/optimal/hub/spp.optimal.wgEncodeSydhTfbsU2osKap1UcdAlnRep0_VS_wgEncodeSydhTfbsU2osInputUcdAln.bb U2OS ChipSeq KAP1 Peaks bigBed Stanford analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/spp/optimal/hub/spp.optimal.wgEncodeSydhTfbsU2osSetdb1UcdAlnRep0_VS_wgEncodeSydhTfbsU2osInputUcdAln.bb U2OS ChipSeq SETDB1 Peaks bigBed UCD analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/spp/optimal/hub/spp.optimal.wgEncodeUchicagoTfbsK562EfosControlAlnRep0_VS_wgEncodeUchicagoTfbsK562InputControlAlnRep0.bb K562 ChipSeq eGFP-FOS Peaks bigBed UChicago analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/spp/optimal/hub/spp.optimal.wgEncodeUchicagoTfbsK562Egata2ControlAlnRep0_VS_wgEncodeUchicagoTfbsK562InputControlAlnRep0.bb K562 ChipSeq eGFP-GATA2 Peaks bigBed UChicago analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/spp/optimal/hub/spp.optimal.wgEncodeUchicagoTfbsK562Ehdac8ControlAlnRep0_VS_wgEncodeUchicagoTfbsK562InputControlAlnRep0.bb K562 ChipSeq eGFP-HDAC8 Peaks bigBed UChicago analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/spp/optimal/hub/spp.optimal.wgEncodeUchicagoTfbsK562EjunbControlAlnRep0_VS_wgEncodeUchicagoTfbsK562InputControlAlnRep0.bb K562 ChipSeq eGFP-JunB Peaks bigBed UChicago analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/spp/optimal/hub/spp.optimal.wgEncodeUchicagoTfbsK562EjundControlAlnRep0_VS_wgEncodeUchicagoTfbsK562InputControlAlnRep0.bb K562 ChipSeq eGFP-JunD Peaks bigBed UChicago analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/spp/optimal/hub/spp.optimal.wgEncodeUchicagoTfbsK562Enr4a1ControlAlnRep0_VS_wgEncodeUchicagoTfbsK562InputControlAlnRep0.bb K562 ChipSeq eGFP-NR4A1 Peaks bigBed UChicago analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/spp/optimal/hub/spp.optimal.wgEncodeUwTfbsAg04449CtcfStdAlnRep0_VS_wgEncodeUwTfbsAg04449InputStdAlnRep1.bb AG04449 ChipSeq CTCF Peaks bigBed UW analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/spp/optimal/hub/spp.optimal.wgEncodeUwTfbsAg04450CtcfStdAlnRep1_VS_wgEncodeUwTfbsAg04450InputStdAlnRep1.bb AG04450 ChipSeq CTCF Peaks bigBed UW analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/spp/optimal/hub/spp.optimal.wgEncodeUwTfbsAg09309CtcfStdAlnRep0_VS_wgEncodeUwTfbsAg09309InputStdAlnRep1.bb AG09309 ChipSeq CTCF Peaks bigBed UW analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/spp/optimal/hub/spp.optimal.wgEncodeUwTfbsAg09319CtcfStdAlnRep0_VS_wgEncodeUwTfbsAg09319InputStdAlnRep1.bb AG09319 ChipSeq CTCF Peaks bigBed UW analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/spp/optimal/hub/spp.optimal.wgEncodeUwTfbsAg10803CtcfStdAlnRep0_VS_wgEncodeUwTfbsAg10803InputStdAlnRep1.bb AG10803 ChipSeq CTCF Peaks bigBed UW analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/spp/optimal/hub/spp.optimal.wgEncodeUwTfbsAoafCtcfStdAlnRep0_VS_wgEncodeUwTfbsAoafInputStdAlnRep1.bb AoAF ChipSeq CTCF Peaks bigBed UW analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/spp/optimal/hub/spp.optimal.wgEncodeUwTfbsBjCtcfStdAlnRep0_VS_wgEncodeUwTfbsBjInputStdAlnRep1.bb BJ ChipSeq CTCF Peaks bigBed UW analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/spp/optimal/hub/spp.optimal.wgEncodeUwTfbsCaco2CtcfStdAlnRep0_VS_wgEncodeUwTfbsCaco2InputStdAlnRep1.bb Caco-2 ChipSeq CTCF Peaks bigBed UW analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/spp/optimal/hub/spp.optimal.wgEncodeUwTfbsGm06990CtcfStdAlnRep0_VS_wgEncodeUwTfbsGm06990InputStdAlnRep1.bb GM06990 ChipSeq CTCF Peaks bigBed UW analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/spp/optimal/hub/spp.optimal.wgEncodeUwTfbsGm12801CtcfStdAlnRep1_VS_wgEncodeUwTfbsGm12801InputStdAlnRep1.bb GM12801 ChipSeq CTCF Peaks bigBed UW analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/spp/optimal/hub/spp.optimal.wgEncodeUwTfbsGm12864CtcfStdAlnRep0_VS_wgEncodeUwTfbsGm12864InputStdAlnRep1.bb GM12864 ChipSeq CTCF Peaks bigBed UW analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/spp/optimal/hub/spp.optimal.wgEncodeUwTfbsGm12865CtcfStdAlnRep0_VS_wgEncodeUwTfbsGm12865InputStdAlnRep1.bb GM12865 ChipSeq CTCF Peaks bigBed UW analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/spp/optimal/hub/spp.optimal.wgEncodeUwTfbsGm12872CtcfStdAlnRep0_VS_wgEncodeUwTfbsGm12872InputStdAlnRep1.bb GM12872 ChipSeq CTCF Peaks bigBed UW analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/spp/optimal/hub/spp.optimal.wgEncodeUwTfbsGm12873CtcfStdAlnRep0_VS_wgEncodeUwTfbsGm12873InputStdAlnRep1.bb GM12873 ChipSeq CTCF Peaks bigBed UW analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/spp/optimal/hub/spp.optimal.wgEncodeUwTfbsGm12874CtcfStdAlnRep0_VS_wgEncodeUwTfbsGm12874InputStdAlnRep1.bb GM12874 ChipSeq CTCF Peaks bigBed UW analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/spp/optimal/hub/spp.optimal.wgEncodeUwTfbsGm12875CtcfStdAlnRep0_VS_wgEncodeUwTfbsGm12875InputStdAlnRep1.bb GM12875 ChipSeq CTCF Peaks bigBed UW analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/spp/optimal/hub/spp.optimal.wgEncodeUwTfbsGm12878CtcfStdAlnRep0_VS_wgEncodeUwTfbsGm12878InputStdAlnRep1.bb GM12878 ChipSeq CTCF Peaks bigBed UW analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/spp/optimal/hub/spp.optimal.wgEncodeUwTfbsHaspCtcfStdAlnRep1_VS_wgEncodeUwTfbsHaspInputStdAlnRep1.bb HA-sp ChipSeq CTCF Peaks bigBed UW analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/spp/optimal/hub/spp.optimal.wgEncodeUwTfbsHbmecCtcfStdAlnRep0_VS_wgEncodeUwTfbsHbmecInputStdAlnRep1.bb HBMEC ChipSeq CTCF Peaks bigBed UW analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/spp/optimal/hub/spp.optimal.wgEncodeUwTfbsHcfaaCtcfStdAlnRep1_VS_wgEncodeUwTfbsHcfaaInputStdAlnRep1.bb HCFaa ChipSeq CTCF Peaks bigBed UW analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/spp/optimal/hub/spp.optimal.wgEncodeUwTfbsHcpeCtcfStdAlnRep0_VS_wgEncodeUwTfbsHcpeInputStdAlnRep1.bb HCPEpiC ChipSeq CTCF Peaks bigBed UW analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/spp/optimal/hub/spp.optimal.wgEncodeUwTfbsHeeCtcfStdAlnRep0_VS_wgEncodeUwTfbsHeeInputStdAlnRep1.bb HEEpiC ChipSeq CTCF Peaks bigBed UW analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/spp/optimal/hub/spp.optimal.wgEncodeUwTfbsHek293CtcfStdAlnRep0_VS_wgEncodeUwTfbsHek293InputStdAlnRep1.bb HEK293 ChipSeq CTCF Peaks bigBed UW analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/spp/optimal/hub/spp.optimal.wgEncodeUwTfbsHelas3CtcfStdAlnRep0_VS_wgEncodeUwTfbsHelas3InputStdAlnRep1.bb HeLa-S3 ChipSeq CTCF Peaks bigBed UW analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/spp/optimal/hub/spp.optimal.wgEncodeUwTfbsHepg2CtcfStdAlnRep0_VS_wgEncodeUwTfbsHepg2InputStdAlnRep1.bb HepG2 ChipSeq CTCF Peaks bigBed UW analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/spp/optimal/hub/spp.optimal.wgEncodeUwTfbsHl60CtcfStdAlnRep1_VS_wgEncodeUwTfbsHl60InputStdAlnRep1.bb HL-60 ChipSeq CTCF Peaks bigBed UW analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/spp/optimal/hub/spp.optimal.wgEncodeUwTfbsHmecCtcfStdAlnRep1_VS_wgEncodeUwTfbsHmecInputStdAlnRep1.bb HMEC ChipSeq CTCF Peaks bigBed UW analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/spp/optimal/hub/spp.optimal.wgEncodeUwTfbsHmfCtcfStdAlnRep0_VS_wgEncodeUwTfbsHmfInputStdAlnRep1.bb HMF ChipSeq CTCF Peaks bigBed UW analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/spp/optimal/hub/spp.optimal.wgEncodeUwTfbsHpafCtcfStdAlnRep0_VS_wgEncodeUwTfbsHpafInputStdAlnRep1.bb HPAF ChipSeq CTCF Peaks bigBed UW analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/spp/optimal/hub/spp.optimal.wgEncodeUwTfbsHpfCtcfStdAlnRep0_VS_wgEncodeUwTfbsHpfInputStdAlnRep1.bb HPF ChipSeq CTCF Peaks bigBed UW analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/spp/optimal/hub/spp.optimal.wgEncodeUwTfbsHreCtcfStdAlnRep0_VS_wgEncodeUwTfbsHreInputStdAlnRep1.bb HRE ChipSeq CTCF Peaks bigBed UW analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/spp/optimal/hub/spp.optimal.wgEncodeUwTfbsHrpeCtcfStdAlnRep1_VS_wgEncodeUwTfbsHrpeInputStdAlnRep1.bb HRPEpiC ChipSeq CTCF Peaks bigBed UW analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/spp/optimal/hub/spp.optimal.wgEncodeUwTfbsHuvecCtcfStdAlnRep0_VS_wgEncodeUwTfbsHuvecInputStdAlnRep1.bb HUVEC ChipSeq CTCF Peaks bigBed UW analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/spp/optimal/hub/spp.optimal.wgEncodeUwTfbsK562CtcfStdAlnRep0_VS_wgEncodeUwTfbsK562InputStdAlnRep1.bb K562 ChipSeq CTCF Peaks bigBed UW analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/spp/optimal/hub/spp.optimal.wgEncodeUwTfbsNhekCtcfStdAlnRep0_VS_wgEncodeUwTfbsNhekInputStdAlnRep1.bb NHEK ChipSeq CTCF Peaks bigBed UW analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/spp/optimal/hub/spp.optimal.wgEncodeUwTfbsSaecCtcfStdAlnRep0_VS_wgEncodeUwTfbsSaecInputStdAlnRep1.bb SAEC ChipSeq CTCF Peaks bigBed UW analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/spp/optimal/hub/spp.optimal.wgEncodeUwTfbsSknshraCtcfStdAlnRep0_VS_wgEncodeUwTfbsSknshraInputStdAlnRep1.bb SK-N-SH_RA ChipSeq CTCF Peaks bigBed UW analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/spp/optimal/hub/spp.optimal.wgEncodeUwTfbsWerirb1CtcfStdAlnRep0_VS_wgEncodeUwTfbsWerirb1InputStdAlnRep1.bb WERI-Rb-1 ChipSeq CTCF Peaks bigBed UW analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/peakSeq/optimal/hub/peakSeq.optimal.wgEncodeBroadHistoneGm12878CtcfStdAlnRep0_vs_wgEncodeBroadHistoneGm12878ControlStdAlnRep0.bb GM12878 ChipSeq CTCF Peaks bigBed Broad analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/peakSeq/optimal/hub/peakSeq.optimal.wgEncodeBroadHistoneH1hescCtcfStdAlnRep0_vs_wgEncodeBroadHistoneH1hescControlStdAlnRep0.bb H1-hESC ChipSeq CTCF Peaks bigBed Broad analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/peakSeq/optimal/hub/peakSeq.optimal.wgEncodeBroadHistoneHelas3CtcfStdAlnRep0_vs_wgEncodeBroadHistoneHelas3ControlStdAlnRep0.bb HeLa-S3 ChipSeq CTCF Peaks bigBed Broad analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/peakSeq/optimal/hub/peakSeq.optimal.wgEncodeBroadHistoneHelas3Pol2bStdAlnRep0_vs_wgEncodeBroadHistoneHelas3ControlStdAlnRep0.bb HeLa-S3 ChipSeq Pol2(b) Peaks bigBed Broad analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/peakSeq/optimal/hub/peakSeq.optimal.wgEncodeBroadHistoneHepg2CtcfStdAlnRep0_vs_wgEncodeBroadHistoneHepg2ControlStdAlnRep0.bb HepG2 ChipSeq CTCF Peaks bigBed Broad analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/peakSeq/optimal/hub/peakSeq.optimal.wgEncodeBroadHistoneHmecCtcfStdAlnRep0_vs_wgEncodeBroadHistoneHmecControlStdAlnRep0.bb HMEC ChipSeq CTCF Peaks bigBed Broad analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/peakSeq/optimal/hub/peakSeq.optimal.wgEncodeBroadHistoneHsmmCtcfStdAlnRep0_vs_wgEncodeBroadHistoneHsmmControlStdAlnRep0.bb HSMM ChipSeq CTCF Peaks bigBed Broad analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/peakSeq/optimal/hub/peakSeq.optimal.wgEncodeBroadHistoneHsmmtCtcfStdAlnRep0_vs_wgEncodeBroadHistoneHsmmtControlStdAlnRep0.bb HSMMtube ChipSeq CTCF Peaks bigBed Broad analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/peakSeq/optimal/hub/peakSeq.optimal.wgEncodeBroadHistoneHuvecCtcfStdAlnRep0_vs_wgEncodeBroadHistoneHuvecControlStdAlnRep0.bb HUVEC ChipSeq CTCF Peaks bigBed Broad analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/peakSeq/optimal/hub/peakSeq.optimal.wgEncodeBroadHistoneHuvecPol2bStdAlnRep0_vs_wgEncodeBroadHistoneHuvecControlStdAlnRep0.bb HUVEC ChipSeq Pol2(b) Peaks bigBed Broad analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/peakSeq/optimal/hub/peakSeq.optimal.wgEncodeBroadHistoneK562CtcfStdAlnRep0_vs_wgEncodeBroadHistoneK562ControlStdAlnRep1.bb K562 ChipSeq CTCF Peaks bigBed Broad analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/peakSeq/optimal/hub/peakSeq.optimal.wgEncodeBroadHistoneK562Pol2bStdAlnRep0_vs_wgEncodeBroadHistoneK562ControlStdAlnRep1.bb K562 ChipSeq Pol2(b) Peaks bigBed Broad analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/peakSeq/optimal/hub/peakSeq.optimal.wgEncodeBroadHistoneNhaCtcfStdAlnRep0_vs_wgEncodeBroadHistoneNhaControlStdAlnRep0.bb NH-A ChipSeq CTCF Peaks bigBed Broad analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/peakSeq/optimal/hub/peakSeq.optimal.wgEncodeBroadHistoneNhdfadCtcfStdAlnRep0_vs_wgEncodeBroadHistoneNhdfadControlStdAlnRep0.bb NHDF-Ad ChipSeq CTCF Peaks bigBed Broad analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/peakSeq/optimal/hub/peakSeq.optimal.wgEncodeBroadHistoneNhekCtcfStdAlnRep0_vs_wgEncodeBroadHistoneNhekControlStdAlnRep0.bb NHEK ChipSeq CTCF Peaks bigBed Broad analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/peakSeq/optimal/hub/peakSeq.optimal.wgEncodeBroadHistoneNhekPol2bStdAlnRep0_vs_wgEncodeBroadHistoneNhekControlStdAlnRep0.bb NHEK ChipSeq Pol2(b) Peaks bigBed Broad analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/peakSeq/optimal/hub/peakSeq.optimal.wgEncodeBroadHistoneNhlfCtcfStdAlnRep0_vs_wgEncodeBroadHistoneNhlfControlStdAlnRep0.bb NHLF ChipSeq CTCF Peaks bigBed Broad analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/peakSeq/optimal/hub/peakSeq.optimal.wgEncodeBroadHistoneOsteoblCtcfStdAlnRep0_vs_wgEncodeBroadHistoneOsteoblControlStdAlnRep0.bb Osteobl ChipSeq CTCF Peaks bigBed Broad analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/peakSeq/optimal/hub/peakSeq.optimal.wgEncodeHaibTfbsA549CtcfPcr1xDexaAlnRep0_vs_wgEncodeHaibTfbsA549ControlPcr1xDexaAlnRep0.bb A549 ChipSeq CTCF Peaks bigBed HudsonAlpha analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/peakSeq/optimal/hub/peakSeq.optimal.wgEncodeHaibTfbsA549CtcfPcr1xEtoh02AlnRep0_vs_wgEncodeHaibTfbsA549ControlPcr1xEtoh02AlnRep1.bb A549 ChipSeq CTCF Peaks bigBed HudsonAlpha analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/peakSeq/optimal/hub/peakSeq.optimal.wgEncodeHaibTfbsA549GrPcr1xDexbAlnRep0_vs_wgEncodeHaibTfbsA549GrPcr1xEtoh02AlnRep0.bb A549 ChipSeq GR Peaks bigBed HudsonAlpha analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/peakSeq/optimal/hub/peakSeq.optimal.wgEncodeHaibTfbsA549GrPcr1xDexcAlnRep0_vs_wgEncodeHaibTfbsA549GrPcr1xEtoh02AlnRep0.bb A549 ChipSeq GR Peaks bigBed HudsonAlpha analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/peakSeq/optimal/hub/peakSeq.optimal.wgEncodeHaibTfbsA549GrPcr1xDexdAlnRep0_vs_wgEncodeHaibTfbsA549GrPcr1xEtoh02AlnRep0.bb A549 ChipSeq GR Peaks bigBed HudsonAlpha analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/peakSeq/optimal/hub/peakSeq.optimal.wgEncodeHaibTfbsA549GrPcr2xDexaAlnRep0_vs_wgEncodeHaibTfbsA549GrPcr2xEtoh02AlnRep0.bb A549 ChipSeq GR Peaks bigBed HudsonAlpha analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/peakSeq/optimal/hub/peakSeq.optimal.wgEncodeHaibTfbsA549Pol2Pcr2xDexaAlnRep0_vs_wgEncodeHaibTfbsA549ControlPcr2xDexaAlnRep0.bb A549 ChipSeq Pol2 Peaks bigBed HudsonAlpha analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/peakSeq/optimal/hub/peakSeq.optimal.wgEncodeHaibTfbsA549Pol2Pcr2xEtoh02AlnRep0_vs_wgEncodeHaibTfbsA549ControlPcr2xEtoh02AlnRep2.bb A549 ChipSeq Pol2 Peaks bigBed HudsonAlpha analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/peakSeq/optimal/hub/peakSeq.optimal.wgEncodeHaibTfbsA549Usf1Pcr1xDexaAlnRep0_vs_wgEncodeHaibTfbsA549ControlPcr1xDexaAlnRep0.bb A549 ChipSeq USF-1 Peaks bigBed HudsonAlpha analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/peakSeq/optimal/hub/peakSeq.optimal.wgEncodeHaibTfbsA549Usf1Pcr1xEtoh02AlnRep0_vs_wgEncodeHaibTfbsA549ControlPcr1xEtoh02AlnRep1.bb A549 ChipSeq USF-1 Peaks bigBed HudsonAlpha analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/peakSeq/optimal/hub/peakSeq.optimal.wgEncodeHaibTfbsEcc1EralphaaV0416102Estradia1hAlnRep0_vs_wgEncodeHaibTfbsEcc1EralphaaV0416102Dmso2AlnRep0.bb ECC-1 ChipSeq ERalpha_a Peaks bigBed HudsonAlpha analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/peakSeq/optimal/hub/peakSeq.optimal.wgEncodeHaibTfbsEcc1EralphaaV0416102Gen1hAlnRep0_vs_wgEncodeHaibTfbsEcc1EralphaaV0416102Dmso2AlnRep0.bb ECC-1 ChipSeq ERalpha_a Peaks bigBed HudsonAlpha analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/peakSeq/optimal/hub/peakSeq.optimal.wgEncodeHaibTfbsEcc1Foxa1c20V0416102Dmso2AlnRep0_vs_wgEncodeHaibTfbsEcc1ControlV0416102Dmso2AlnRep0.bb ECC-1 ChipSeq FOXA1_(C-20) Peaks bigBed HudsonAlpha analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/peakSeq/optimal/hub/peakSeq.optimal.wgEncodeHaibTfbsEcc1GrV0416102DexaAlnRep0_vs_wgEncodeHaibTfbsEcc1GrV0416102Etoh02AlnRep0.bb ECC-1 ChipSeq GR Peaks bigBed HudsonAlpha analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/peakSeq/optimal/hub/peakSeq.optimal.wgEncodeHaibTfbsEcc1Pol2V0416102Dmso2AlnRep0_vs_wgEncodeHaibTfbsEcc1ControlV0416102Dmso2AlnRep0.bb ECC-1 ChipSeq Pol2 Peaks bigBed HudsonAlpha analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/peakSeq/optimal/hub/peakSeq.optimal.wgEncodeHaibTfbsGm12878Atf3Pcr1xAlnRep0_vs_wgEncodeHaibTfbsGm12878ControlV0416101AlnRep0.bb GM12878 ChipSeq ATF3 Peaks bigBed HudsonAlpha analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/peakSeq/optimal/hub/peakSeq.optimal.wgEncodeHaibTfbsGm12878BatfPcr1xAlnRep0_vs_wgEncodeHaibTfbsGm12878ControlPcr1xAlnRep0.bb GM12878 ChipSeq BATF Peaks bigBed HudsonAlpha analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/peakSeq/optimal/hub/peakSeq.optimal.wgEncodeHaibTfbsGm12878Bcl11aPcr1xAlnRep0_vs_wgEncodeHaibTfbsGm12878ControlPcr1xAlnRep0.bb GM12878 ChipSeq BCL11A Peaks bigBed HudsonAlpha analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/peakSeq/optimal/hub/peakSeq.optimal.wgEncodeHaibTfbsGm12878Bcl3Pcr1xAlnRep0_vs_wgEncodeHaibTfbsGm12878ControlPcr1xAlnRep0.bb GM12878 ChipSeq BCL3 Peaks bigBed HudsonAlpha analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/peakSeq/optimal/hub/peakSeq.optimal.wgEncodeHaibTfbsGm12878Bclaf1m33V0416101AlnRep0_vs_wgEncodeHaibTfbsGm12878ControlV0416101AlnRep0.bb GM12878 ChipSeq BCLAF1_(M33-P5B11) Peaks bigBed HudsonAlpha analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/peakSeq/optimal/hub/peakSeq.optimal.wgEncodeHaibTfbsGm12878Ebf1c8Pcr1xAlnRep0_vs_wgEncodeHaibTfbsGm12878ControlPcr1xAlnRep0.bb GM12878 ChipSeq EBF1_(C-8) Peaks bigBed HudsonAlpha analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/peakSeq/optimal/hub/peakSeq.optimal.wgEncodeHaibTfbsGm12878EbfPcr1xAlnRep0_vs_wgEncodeHaibTfbsGm12878ControlPcr1xAlnRep0.bb GM12878 ChipSeq EBF Peaks bigBed HudsonAlpha analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/peakSeq/optimal/hub/peakSeq.optimal.wgEncodeHaibTfbsGm12878Egr1Pcr2xAlnRep0_vs_wgEncodeHaibTfbsGm12878ControlPcr2xAlnRep0.bb GM12878 ChipSeq Egr-1 Peaks bigBed HudsonAlpha analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/peakSeq/optimal/hub/peakSeq.optimal.wgEncodeHaibTfbsGm12878Egr1V0416101AlnRep0_vs_wgEncodeHaibTfbsGm12878ControlV0416101AlnRep0.bb GM12878 ChipSeq Egr-1 Peaks bigBed HudsonAlpha analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/peakSeq/optimal/hub/peakSeq.optimal.wgEncodeHaibTfbsGm12878Elf1sc631V0416101AlnRep0_vs_wgEncodeHaibTfbsGm12878ControlV0416101AlnRep0.bb GM12878 ChipSeq ELF1_(SC-631) Peaks bigBed HudsonAlpha analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/peakSeq/optimal/hub/peakSeq.optimal.wgEncodeHaibTfbsGm12878Ets1Pcr1xAlnRep0_vs_wgEncodeHaibTfbsGm12878ControlV0416101AlnRep0.bb GM12878 ChipSeq ETS1 Peaks bigBed HudsonAlpha analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/peakSeq/optimal/hub/peakSeq.optimal.wgEncodeHaibTfbsGm12878GabpPcr2xAlnRep0_vs_wgEncodeHaibTfbsGm12878ControlPcr2xAlnRep0.bb GM12878 ChipSeq GABP Peaks bigBed HudsonAlpha analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/peakSeq/optimal/hub/peakSeq.optimal.wgEncodeHaibTfbsGm12878Irf4m17Pcr1xAlnRep0_vs_wgEncodeHaibTfbsGm12878ControlPcr1xAlnRep0.bb GM12878 ChipSeq IRF4_(M-17) Peaks bigBed HudsonAlpha analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/peakSeq/optimal/hub/peakSeq.optimal.wgEncodeHaibTfbsGm12878Irf4Pcr1xAlnRep0_vs_wgEncodeHaibTfbsGm12878ControlPcr1xAlnRep0.bb GM12878 ChipSeq IRF4 Peaks bigBed HudsonAlpha analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/peakSeq/optimal/hub/peakSeq.optimal.wgEncodeHaibTfbsGm12878Mef2aPcr1xAlnRep0_vs_wgEncodeHaibTfbsGm12878ControlV0416101AlnRep0.bb GM12878 ChipSeq MEF2A Peaks bigBed HudsonAlpha analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/peakSeq/optimal/hub/peakSeq.optimal.wgEncodeHaibTfbsGm12878Mef2csc13268Pcr1xAlnRep0_vs_wgEncodeHaibTfbsGm12878ControlV0416101AlnRep0.bb GM12878 ChipSeq MEF2C_(SC-13268) Peaks bigBed HudsonAlpha analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/peakSeq/optimal/hub/peakSeq.optimal.wgEncodeHaibTfbsGm12878NrsfPcr2xAlnRep0_vs_wgEncodeHaibTfbsGm12878ControlPcr2xAlnRep0.bb GM12878 ChipSeq NRSF Peaks bigBed HudsonAlpha analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/peakSeq/optimal/hub/peakSeq.optimal.wgEncodeHaibTfbsGm12878Oct2Pcr1xAlnRep0_vs_wgEncodeHaibTfbsGm12878ControlPcr1xAlnRep0.bb GM12878 ChipSeq Oct-2 Peaks bigBed HudsonAlpha analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/peakSeq/optimal/hub/peakSeq.optimal.wgEncodeHaibTfbsGm12878P300Pcr1xAlnRep0_vs_wgEncodeHaibTfbsGm12878ControlPcr1xAlnRep0.bb GM12878 ChipSeq p300 Peaks bigBed HudsonAlpha analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/peakSeq/optimal/hub/peakSeq.optimal.wgEncodeHaibTfbsGm12878Pax5c20Pcr1xAlnRep0_vs_wgEncodeHaibTfbsGm12878ControlPcr1xAlnRep0.bb GM12878 ChipSeq PAX5-C20 Peaks bigBed HudsonAlpha analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/peakSeq/optimal/hub/peakSeq.optimal.wgEncodeHaibTfbsGm12878Pax5n19Pcr1xAlnRep0_vs_wgEncodeHaibTfbsGm12878ControlPcr1xAlnRep0.bb GM12878 ChipSeq PAX5-N19 Peaks bigBed HudsonAlpha analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/peakSeq/optimal/hub/peakSeq.optimal.wgEncodeHaibTfbsGm12878Pbx3Pcr1xAlnRep0_vs_wgEncodeHaibTfbsGm12878ControlPcr1xAlnRep0.bb GM12878 ChipSeq Pbx3 Peaks bigBed HudsonAlpha analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/peakSeq/optimal/hub/peakSeq.optimal.wgEncodeHaibTfbsGm12878Pol24h8Pcr1xAlnRep0_vs_wgEncodeHaibTfbsGm12878ControlPcr1xAlnRep0.bb GM12878 ChipSeq Pol2-4H8 Peaks bigBed HudsonAlpha analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/peakSeq/optimal/hub/peakSeq.optimal.wgEncodeHaibTfbsGm12878Pol2Pcr2xAlnRep0_vs_wgEncodeHaibTfbsGm12878ControlPcr2xAlnRep0.bb GM12878 ChipSeq Pol2 Peaks bigBed HudsonAlpha analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/peakSeq/optimal/hub/peakSeq.optimal.wgEncodeHaibTfbsGm12878Pou2f2Pcr1xAlnRep0_vs_wgEncodeHaibTfbsGm12878ControlPcr1xAlnRep0.bb GM12878 ChipSeq POU2F2 Peaks bigBed HudsonAlpha analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/peakSeq/optimal/hub/peakSeq.optimal.wgEncodeHaibTfbsGm12878Pu1Pcr1xAlnRep0_vs_wgEncodeHaibTfbsGm12878ControlPcr1xAlnRep0.bb GM12878 ChipSeq PU.1 Peaks bigBed HudsonAlpha analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/peakSeq/optimal/hub/peakSeq.optimal.wgEncodeHaibTfbsGm12878Rad21V0416101AlnRep0_vs_wgEncodeHaibTfbsGm12878ControlV0416101AlnRep0.bb GM12878 ChipSeq Rad21 Peaks bigBed HudsonAlpha analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/peakSeq/optimal/hub/peakSeq.optimal.wgEncodeHaibTfbsGm12878RxraPcr1xAlnRep0_vs_wgEncodeHaibTfbsGm12878ControlPcr1xAlnRep0.bb GM12878 ChipSeq RXRA Peaks bigBed HudsonAlpha analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/peakSeq/optimal/hub/peakSeq.optimal.wgEncodeHaibTfbsGm12878Sin3ak20Pcr2xAlnRep0_vs_wgEncodeHaibTfbsGm12878ControlPcr1xAlnRep0.bb GM12878 ChipSeq Sin3Ak-20 Peaks bigBed HudsonAlpha analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/peakSeq/optimal/hub/peakSeq.optimal.wgEncodeHaibTfbsGm12878Six5Pcr1xAlnRep0_vs_wgEncodeHaibTfbsGm12878ControlPcr1xAlnRep0.bb GM12878 ChipSeq SIX5 Peaks bigBed HudsonAlpha analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/peakSeq/optimal/hub/peakSeq.optimal.wgEncodeHaibTfbsGm12878Sp1Pcr1xAlnRep0_vs_wgEncodeHaibTfbsGm12878ControlPcr1xAlnRep0.bb GM12878 ChipSeq SP1 Peaks bigBed HudsonAlpha analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/peakSeq/optimal/hub/peakSeq.optimal.wgEncodeHaibTfbsGm12878SrfPcr2xAlnRep0_vs_wgEncodeHaibTfbsGm12878ControlPcr2xAlnRep0.bb GM12878 ChipSeq SRF Peaks bigBed HudsonAlpha analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/peakSeq/optimal/hub/peakSeq.optimal.wgEncodeHaibTfbsGm12878SrfV0416101AlnRep0_vs_wgEncodeHaibTfbsGm12878ControlV0416101AlnRep0.bb GM12878 ChipSeq SRF Peaks bigBed HudsonAlpha analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/peakSeq/optimal/hub/peakSeq.optimal.wgEncodeHaibTfbsGm12878Taf1Pcr1xAlnRep0_vs_wgEncodeHaibTfbsGm12878ControlPcr1xAlnRep0.bb GM12878 ChipSeq TAF1 Peaks bigBed HudsonAlpha analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/peakSeq/optimal/hub/peakSeq.optimal.wgEncodeHaibTfbsGm12878Tcf12Pcr1xAlnRep0_vs_wgEncodeHaibTfbsGm12878ControlPcr1xAlnRep0.bb GM12878 ChipSeq TCF12 Peaks bigBed HudsonAlpha analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/peakSeq/optimal/hub/peakSeq.optimal.wgEncodeHaibTfbsGm12878Usf1Pcr2xAlnRep0_vs_wgEncodeHaibTfbsGm12878ControlPcr2xAlnRep0.bb GM12878 ChipSeq USF-1 Peaks bigBed HudsonAlpha analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/peakSeq/optimal/hub/peakSeq.optimal.wgEncodeHaibTfbsGm12878Yy1V0416101AlnRep0_vs_wgEncodeHaibTfbsGm12878ControlV0416101AlnRep1.bb GM12878 ChipSeq YY1_(SC-281) Peaks bigBed HudsonAlpha analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/peakSeq/optimal/hub/peakSeq.optimal.wgEncodeHaibTfbsGm12878Zbtb33Pcr1xAlnRep0_vs_wgEncodeHaibTfbsGm12878ControlPcr1xAlnRep0.bb GM12878 ChipSeq ZBTB33 Peaks bigBed HudsonAlpha analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/peakSeq/optimal/hub/peakSeq.optimal.wgEncodeHaibTfbsGm12878Zeb1sc25388V0416102AlnRep0_vs_wgEncodeHaibTfbsGm12878ControlPcr1xAlnRep0.bb GM12878 ChipSeq ZEB1_(SC-25388) Peaks bigBed HudsonAlpha analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/peakSeq/optimal/hub/peakSeq.optimal.wgEncodeHaibTfbsGm12891Oct2Pcr1xAlnRep0_vs_wgEncodeHaibTfbsGm12891ControlPcr1xAlnRep0.bb GM12891 ChipSeq Oct-2 Peaks bigBed HudsonAlpha analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/peakSeq/optimal/hub/peakSeq.optimal.wgEncodeHaibTfbsGm12891Pax5c20Pcr1xAlnRep0_vs_wgEncodeHaibTfbsGm12891ControlPcr1xAlnRep0.bb GM12891 ChipSeq PAX5-C20 Peaks bigBed HudsonAlpha analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/peakSeq/optimal/hub/peakSeq.optimal.wgEncodeHaibTfbsGm12891Pol24h8Pcr1xAlnRep0_vs_wgEncodeHaibTfbsGm12891ControlPcr1xAlnRep0.bb GM12891 ChipSeq Pol2-4H8 Peaks bigBed HudsonAlpha analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/peakSeq/optimal/hub/peakSeq.optimal.wgEncodeHaibTfbsGm12891Pol2Pcr1xAlnRep0_vs_wgEncodeHaibTfbsGm12891ControlPcr1xAlnRep0.bb GM12891 ChipSeq Pol2 Peaks bigBed HudsonAlpha analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/peakSeq/optimal/hub/peakSeq.optimal.wgEncodeHaibTfbsGm12891Pou2f2Pcr1xAlnRep0_vs_wgEncodeHaibTfbsGm12891ControlPcr1xAlnRep0.bb GM12891 ChipSeq POU2F2 Peaks bigBed HudsonAlpha analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/peakSeq/optimal/hub/peakSeq.optimal.wgEncodeHaibTfbsGm12891Pu1Pcr1xAlnRep0_vs_wgEncodeHaibTfbsGm12891ControlPcr1xAlnRep0.bb GM12891 ChipSeq PU.1 Peaks bigBed HudsonAlpha analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/peakSeq/optimal/hub/peakSeq.optimal.wgEncodeHaibTfbsGm12891Taf1Pcr1xAlnRep0_vs_wgEncodeHaibTfbsGm12891ControlPcr1xAlnRep0.bb GM12891 ChipSeq TAF1 Peaks bigBed HudsonAlpha analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/peakSeq/optimal/hub/peakSeq.optimal.wgEncodeHaibTfbsGm12891Yy1c20V0416101AlnRep0_vs_wgEncodeHaibTfbsGm12891ControlPcr1xAlnRep0.bb GM12891 ChipSeq YY1_(C-20) Peaks bigBed HudsonAlpha analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/peakSeq/optimal/hub/peakSeq.optimal.wgEncodeHaibTfbsGm12892Pax5c20Pcr1xAlnRep0_vs_wgEncodeHaibTfbsGm12892ControlPcr1xAlnRep0.bb GM12892 ChipSeq PAX5-C20 Peaks bigBed HudsonAlpha analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/peakSeq/optimal/hub/peakSeq.optimal.wgEncodeHaibTfbsGm12892Pol24h8Pcr1xAlnRep0_vs_wgEncodeHaibTfbsGm12892ControlPcr1xAlnRep0.bb GM12892 ChipSeq Pol2-4H8 Peaks bigBed HudsonAlpha analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/peakSeq/optimal/hub/peakSeq.optimal.wgEncodeHaibTfbsGm12892Pol24h8V0416102AlnRep0_vs_wgEncodeHaibTfbsGm12892ControlPcr1xAlnRep0.bb GM12892 ChipSeq Pol2-4H8 Peaks bigBed HudsonAlpha analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/peakSeq/optimal/hub/peakSeq.optimal.wgEncodeHaibTfbsGm12892Pol2Pcr1xAlnRep0_vs_wgEncodeHaibTfbsGm12892ControlPcr1xAlnRep0.bb GM12892 ChipSeq Pol2 Peaks bigBed HudsonAlpha analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/peakSeq/optimal/hub/peakSeq.optimal.wgEncodeHaibTfbsGm12892Pol2V0416102AlnRep0_vs_wgEncodeHaibTfbsGm12892ControlPcr1xAlnRep0.bb GM12892 ChipSeq Pol2 Peaks bigBed HudsonAlpha analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/peakSeq/optimal/hub/peakSeq.optimal.wgEncodeHaibTfbsGm12892Taf1Pcr1xAlnRep0_vs_wgEncodeHaibTfbsGm12892ControlPcr1xAlnRep0.bb GM12892 ChipSeq TAF1 Peaks bigBed HudsonAlpha analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/peakSeq/optimal/hub/peakSeq.optimal.wgEncodeHaibTfbsGm12892Taf1V0416102AlnRep0_vs_wgEncodeHaibTfbsGm12892ControlPcr1xAlnRep0.bb GM12892 ChipSeq TAF1 Peaks bigBed HudsonAlpha analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/peakSeq/optimal/hub/peakSeq.optimal.wgEncodeHaibTfbsGm12892Yy1V0416101AlnRep0_vs_wgEncodeHaibTfbsGm12892ControlPcr1xAlnRep0.bb GM12892 ChipSeq YY1 Peaks bigBed HudsonAlpha analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/peakSeq/optimal/hub/peakSeq.optimal.wgEncodeHaibTfbsH1hescAtf3Pcr1xAlnRep0_vs_wgEncodeHaibTfbsH1hescControlPcr1xAlnRep0.bb H1-hESC ChipSeq ATF3 Peaks bigBed HudsonAlpha analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/peakSeq/optimal/hub/peakSeq.optimal.wgEncodeHaibTfbsH1hescBcl11aPcr1xAlnRep0_vs_wgEncodeHaibTfbsH1hescControlPcr1xAlnRep0.bb H1-hESC ChipSeq BCL11A Peaks bigBed HudsonAlpha analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/peakSeq/optimal/hub/peakSeq.optimal.wgEncodeHaibTfbsH1hescBcl3Pcr1xAlnRep0_vs_wgEncodeHaibTfbsH1hescControlPcr1xAlnRep0.bb H1-hESC ChipSeq BCL3 Peaks bigBed HudsonAlpha analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/peakSeq/optimal/hub/peakSeq.optimal.wgEncodeHaibTfbsH1hescCtcfsc5916V0416102AlnRep0_vs_wgEncodeHaibTfbsH1hescControlPcr1xAlnRep0.bb H1-hESC ChipSeq CTCF_(SC-5916) Peaks bigBed HudsonAlpha analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/peakSeq/optimal/hub/peakSeq.optimal.wgEncodeHaibTfbsH1hescEgr1V0416101AlnRep0_vs_wgEncodeHaibTfbsH1hescControlPcr1xAlnRep0.bb H1-hESC ChipSeq Egr-1 Peaks bigBed HudsonAlpha analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/peakSeq/optimal/hub/peakSeq.optimal.wgEncodeHaibTfbsH1hescEgr1V0416102AlnRep0_vs_wgEncodeHaibTfbsH1hescControlPcr1xAlnRep0.bb H1-hESC ChipSeq Egr-1 Peaks bigBed HudsonAlpha analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/peakSeq/optimal/hub/peakSeq.optimal.wgEncodeHaibTfbsH1hescGabpPcr1xAlnRep0_vs_wgEncodeHaibTfbsH1hescControlPcr1xAlnRep0.bb H1-hESC ChipSeq GABP Peaks bigBed HudsonAlpha analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/peakSeq/optimal/hub/peakSeq.optimal.wgEncodeHaibTfbsH1hescHdac2sc6296V0416102AlnRep0_vs_wgEncodeHaibTfbsH1hescControlPcr1xAlnRep0.bb H1-hESC ChipSeq HDAC2_(SC-6296) Peaks bigBed HudsonAlpha analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/peakSeq/optimal/hub/peakSeq.optimal.wgEncodeHaibTfbsH1hescJundV0416102AlnRep0_vs_wgEncodeHaibTfbsH1hescControlPcr1xAlnRep0.bb H1-hESC ChipSeq JunD Peaks bigBed HudsonAlpha analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/peakSeq/optimal/hub/peakSeq.optimal.wgEncodeHaibTfbsH1hescNanogsc33759V0416102AlnRep0_vs_wgEncodeHaibTfbsH1hescControlPcr1xAlnRep0.bb H1-hESC ChipSeq NANOG_(SC-33759) Peaks bigBed HudsonAlpha analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/peakSeq/optimal/hub/peakSeq.optimal.wgEncodeHaibTfbsH1hescNrsfPcr1xAlnRep0_vs_wgEncodeHaibTfbsH1hescControlPcr1xAlnRep0.bb H1-hESC ChipSeq NRSF Peaks bigBed HudsonAlpha analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/peakSeq/optimal/hub/peakSeq.optimal.wgEncodeHaibTfbsH1hescNrsfV0416102AlnRep0_vs_wgEncodeHaibTfbsH1hescControlPcr1xAlnRep0.bb H1-hESC ChipSeq NRSF Peaks bigBed HudsonAlpha analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/peakSeq/optimal/hub/peakSeq.optimal.wgEncodeHaibTfbsH1hescP300V0416102AlnRep0_vs_wgEncodeHaibTfbsH1hescControlPcr1xAlnRep0.bb H1-hESC ChipSeq p300 Peaks bigBed HudsonAlpha analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/peakSeq/optimal/hub/peakSeq.optimal.wgEncodeHaibTfbsH1hescPol24h8Pcr1xAlnRep0_vs_wgEncodeHaibTfbsH1hescControlPcr1xAlnRep0.bb H1-hESC ChipSeq Pol2-4H8 Peaks bigBed HudsonAlpha analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/peakSeq/optimal/hub/peakSeq.optimal.wgEncodeHaibTfbsH1hescPol24h8V0416102AlnRep0_vs_wgEncodeHaibTfbsH1hescControlPcr1xAlnRep0.bb H1-hESC ChipSeq Pol2-4H8 Peaks bigBed HudsonAlpha analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/peakSeq/optimal/hub/peakSeq.optimal.wgEncodeHaibTfbsH1hescPol2Pcr1xAlnRep0_vs_wgEncodeHaibTfbsH1hescControlPcr1xAlnRep0.bb H1-hESC ChipSeq Pol2 Peaks bigBed HudsonAlpha analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/peakSeq/optimal/hub/peakSeq.optimal.wgEncodeHaibTfbsH1hescPol2V0416102AlnRep0_vs_wgEncodeHaibTfbsH1hescControlPcr1xAlnRep0.bb H1-hESC ChipSeq Pol2 Peaks bigBed HudsonAlpha analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/peakSeq/optimal/hub/peakSeq.optimal.wgEncodeHaibTfbsH1hescPou5f1sc9081V0416102AlnRep0_vs_wgEncodeHaibTfbsH1hescControlPcr1xAlnRep0.bb H1-hESC ChipSeq POU5F1_(SC-9081) Peaks bigBed HudsonAlpha analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/peakSeq/optimal/hub/peakSeq.optimal.wgEncodeHaibTfbsH1hescRad21V0416102AlnRep0_vs_wgEncodeHaibTfbsH1hescControlPcr1xAlnRep0.bb H1-hESC ChipSeq Rad21 Peaks bigBed HudsonAlpha analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/peakSeq/optimal/hub/peakSeq.optimal.wgEncodeHaibTfbsH1hescRxraV0416102AlnRep0_vs_wgEncodeHaibTfbsH1hescControlPcr1xAlnRep0.bb H1-hESC ChipSeq RXRA Peaks bigBed HudsonAlpha analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/peakSeq/optimal/hub/peakSeq.optimal.wgEncodeHaibTfbsH1hescSin3ak20Pcr1xAlnRep0_vs_wgEncodeHaibTfbsH1hescControlPcr1xAlnRep0.bb H1-hESC ChipSeq Sin3Ak-20 Peaks bigBed HudsonAlpha analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/peakSeq/optimal/hub/peakSeq.optimal.wgEncodeHaibTfbsH1hescSix5Pcr1xAlnRep0_vs_wgEncodeHaibTfbsH1hescControlPcr1xAlnRep0.bb H1-hESC ChipSeq SIX5 Peaks bigBed HudsonAlpha analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/peakSeq/optimal/hub/peakSeq.optimal.wgEncodeHaibTfbsH1hescSp1Pcr1xAlnRep0_vs_wgEncodeHaibTfbsH1hescControlPcr1xAlnRep0.bb H1-hESC ChipSeq SP1 Peaks bigBed HudsonAlpha analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/peakSeq/optimal/hub/peakSeq.optimal.wgEncodeHaibTfbsH1hescSrfPcr1xAlnRep0_vs_wgEncodeHaibTfbsH1hescControlPcr1xAlnRep0.bb H1-hESC ChipSeq SRF Peaks bigBed HudsonAlpha analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/peakSeq/optimal/hub/peakSeq.optimal.wgEncodeHaibTfbsH1hescTaf1Pcr1xAlnRep0_vs_wgEncodeHaibTfbsH1hescControlPcr1xAlnRep0.bb H1-hESC ChipSeq TAF1 Peaks bigBed HudsonAlpha analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/peakSeq/optimal/hub/peakSeq.optimal.wgEncodeHaibTfbsH1hescTaf1V0416102AlnRep0_vs_wgEncodeHaibTfbsH1hescControlPcr1xAlnRep0.bb H1-hESC ChipSeq TAF1 Peaks bigBed HudsonAlpha analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/peakSeq/optimal/hub/peakSeq.optimal.wgEncodeHaibTfbsH1hescTaf7sq8V0416102AlnRep0_vs_wgEncodeHaibTfbsH1hescControlPcr1xAlnRep0.bb H1-hESC ChipSeq TAF7_(SQ-8) Peaks bigBed HudsonAlpha analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/peakSeq/optimal/hub/peakSeq.optimal.wgEncodeHaibTfbsH1hescTcf12Pcr1xAlnRep0_vs_wgEncodeHaibTfbsH1hescControlPcr1xAlnRep0.bb H1-hESC ChipSeq TCF12 Peaks bigBed HudsonAlpha analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/peakSeq/optimal/hub/peakSeq.optimal.wgEncodeHaibTfbsH1hescUsf1Pcr1xAlnRep0_vs_wgEncodeHaibTfbsH1hescControlPcr1xAlnRep0.bb H1-hESC ChipSeq USF-1 Peaks bigBed HudsonAlpha analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/peakSeq/optimal/hub/peakSeq.optimal.wgEncodeHaibTfbsH1hescYy1c20Pcr1xAlnRep0_vs_wgEncodeHaibTfbsH1hescControlPcr1xAlnRep0.bb H1-hESC ChipSeq YY1_(C-20) Peaks bigBed HudsonAlpha analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/peakSeq/optimal/hub/peakSeq.optimal.wgEncodeHaibTfbsHct116Pol24h8V0416101AlnRep0_vs_wgEncodeHaibTfbsHct116ControlV0416101AlnRep2.bb HCT-116 ChipSeq Pol2-4H8 Peaks bigBed HudsonAlpha analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/peakSeq/optimal/hub/peakSeq.optimal.wgEncodeHaibTfbsHelas3GabpPcr1xAlnRep0_vs_wgEncodeHaibTfbsHelas3ControlPcr1xAlnRep0.bb HeLa-S3 ChipSeq GABP Peaks bigBed HudsonAlpha analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/peakSeq/optimal/hub/peakSeq.optimal.wgEncodeHaibTfbsHelas3NrsfPcr1xAlnRep0_vs_wgEncodeHaibTfbsHelas3ControlPcr1xAlnRep0.bb HeLa-S3 ChipSeq NRSF Peaks bigBed HudsonAlpha analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/peakSeq/optimal/hub/peakSeq.optimal.wgEncodeHaibTfbsHelas3Pol2Pcr1xAlnRep0_vs_wgEncodeHaibTfbsHelas3ControlPcr1xAlnRep0.bb HeLa-S3 ChipSeq Pol2 Peaks bigBed HudsonAlpha analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/peakSeq/optimal/hub/peakSeq.optimal.wgEncodeHaibTfbsHelas3Taf1Pcr1xAlnRep0_vs_wgEncodeHaibTfbsHelas3ControlPcr1xAlnRep0.bb HeLa-S3 ChipSeq TAF1 Peaks bigBed HudsonAlpha analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/peakSeq/optimal/hub/peakSeq.optimal.wgEncodeHaibTfbsHepg2Atf3V0416101AlnRep0_vs_wgEncodeHaibTfbsHepg2ControlV0416101AlnRep0.bb HepG2 ChipSeq ATF3 Peaks bigBed HudsonAlpha analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/peakSeq/optimal/hub/peakSeq.optimal.wgEncodeHaibTfbsHepg2Bhlhe40V0416101AlnRep0_vs_wgEncodeHaibTfbsHepg2ControlPcr1xAlnRep0.bb HepG2 ChipSeq BHLHE40 Peaks bigBed HudsonAlpha analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/peakSeq/optimal/hub/peakSeq.optimal.wgEncodeHaibTfbsHepg2CtcfV0416101AlnRep0_vs_wgEncodeHaibTfbsHepg2ControlV0416101AlnRep0.bb HepG2 ChipSeq CTCF Peaks bigBed HudsonAlpha analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/peakSeq/optimal/hub/peakSeq.optimal.wgEncodeHaibTfbsHepg2Elf1sc631V0416101AlnRep0_vs_wgEncodeHaibTfbsHepg2ControlV0416101AlnRep0.bb HepG2 ChipSeq ELF1_(SC-631) Peaks bigBed HudsonAlpha analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/peakSeq/optimal/hub/peakSeq.optimal.wgEncodeHaibTfbsHepg2Fosl2Pcr1xAlnRep0_vs_wgEncodeHaibTfbsHepg2ControlPcr1xAlnRep0.bb HepG2 ChipSeq FOSL2 Peaks bigBed HudsonAlpha analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/peakSeq/optimal/hub/peakSeq.optimal.wgEncodeHaibTfbsHepg2Foxa1c20Pcr1xAlnRep0_vs_wgEncodeHaibTfbsHepg2ControlV0416101AlnRep0.bb HepG2 ChipSeq FOXA1_(C-20) Peaks bigBed HudsonAlpha analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/peakSeq/optimal/hub/peakSeq.optimal.wgEncodeHaibTfbsHepg2Foxa1sc101058Pcr1xAlnRep0_vs_wgEncodeHaibTfbsHepg2ControlV0416101AlnRep0.bb HepG2 ChipSeq FOXA1_(SC-101058) Peaks bigBed HudsonAlpha analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/peakSeq/optimal/hub/peakSeq.optimal.wgEncodeHaibTfbsHepg2Foxa2sc6554V0416101AlnRep0_vs_wgEncodeHaibTfbsHepg2ControlV0416101AlnRep0.bb HepG2 ChipSeq FOXA2_(SC-6554) Peaks bigBed HudsonAlpha analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/peakSeq/optimal/hub/peakSeq.optimal.wgEncodeHaibTfbsHepg2GabpPcr2xAlnRep0_vs_wgEncodeHaibTfbsHepg2ControlPcr2xAlnRep0.bb HepG2 ChipSeq GABP Peaks bigBed HudsonAlpha analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/peakSeq/optimal/hub/peakSeq.optimal.wgEncodeHaibTfbsHepg2Hdac2sc6296V0416101AlnRep0_vs_wgEncodeHaibTfbsHepg2ControlV0416101AlnRep0.bb HepG2 ChipSeq HDAC2_(SC-6296) Peaks bigBed HudsonAlpha analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/peakSeq/optimal/hub/peakSeq.optimal.wgEncodeHaibTfbsHepg2Hey1V0416101AlnRep0_vs_wgEncodeHaibTfbsHepg2ControlPcr1xAlnRep0.bb HepG2 ChipSeq HEY1 Peaks bigBed HudsonAlpha analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/peakSeq/optimal/hub/peakSeq.optimal.wgEncodeHaibTfbsHepg2Hnf4ah171Pcr1xAlnRep0_vs_wgEncodeHaibTfbsHepg2ControlV0416101AlnRep0.bb HepG2 ChipSeq HNF4A_(H-171) Peaks bigBed HudsonAlpha analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/peakSeq/optimal/hub/peakSeq.optimal.wgEncodeHaibTfbsHepg2Hnf4gsc6558V0416101AlnRep0_vs_wgEncodeHaibTfbsHepg2ControlV0416101AlnRep0.bb HepG2 ChipSeq HNF4G_(SC-6558) Peaks bigBed HudsonAlpha analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/peakSeq/optimal/hub/peakSeq.optimal.wgEncodeHaibTfbsHepg2JundPcr1xAlnRep0_vs_wgEncodeHaibTfbsHepg2ControlPcr1xAlnRep0.bb HepG2 ChipSeq JunD Peaks bigBed HudsonAlpha analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/peakSeq/optimal/hub/peakSeq.optimal.wgEncodeHaibTfbsHepg2NrsfPcr2xAlnRep0_vs_wgEncodeHaibTfbsHepg2ControlPcr2xAlnRep0.bb HepG2 ChipSeq NRSF Peaks bigBed HudsonAlpha analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/peakSeq/optimal/hub/peakSeq.optimal.wgEncodeHaibTfbsHepg2P300Pcr1xAlnRep0_vs_wgEncodeHaibTfbsHepg2ControlPcr1xAlnRep0.bb HepG2 ChipSeq p300 Peaks bigBed HudsonAlpha analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/peakSeq/optimal/hub/peakSeq.optimal.wgEncodeHaibTfbsHepg2P300V0416101AlnRep0_vs_wgEncodeHaibTfbsHepg2ControlV0416101AlnRep0.bb HepG2 ChipSeq p300 Peaks bigBed HudsonAlpha analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/peakSeq/optimal/hub/peakSeq.optimal.wgEncodeHaibTfbsHepg2Pol2Pcr2xAlnRep0_vs_wgEncodeHaibTfbsHepg2ControlPcr2xAlnRep0.bb HepG2 ChipSeq Pol2 Peaks bigBed HudsonAlpha analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/peakSeq/optimal/hub/peakSeq.optimal.wgEncodeHaibTfbsHepg2Rad21V0416101AlnRep0_vs_wgEncodeHaibTfbsHepg2ControlV0416101AlnRep0.bb HepG2 ChipSeq Rad21 Peaks bigBed HudsonAlpha analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/peakSeq/optimal/hub/peakSeq.optimal.wgEncodeHaibTfbsHepg2RxraPcr1xAlnRep0_vs_wgEncodeHaibTfbsHepg2ControlPcr1xAlnRep0.bb HepG2 ChipSeq RXRA Peaks bigBed HudsonAlpha analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/peakSeq/optimal/hub/peakSeq.optimal.wgEncodeHaibTfbsHepg2Sin3ak20Pcr1xAlnRep0_vs_wgEncodeHaibTfbsHepg2ControlPcr1xAlnRep0.bb HepG2 ChipSeq Sin3Ak-20 Peaks bigBed HudsonAlpha analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/peakSeq/optimal/hub/peakSeq.optimal.wgEncodeHaibTfbsHepg2Sp1Pcr1xAlnRep0_vs_wgEncodeHaibTfbsHepg2ControlPcr1xAlnRep0.bb HepG2 ChipSeq SP1 Peaks bigBed HudsonAlpha analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/peakSeq/optimal/hub/peakSeq.optimal.wgEncodeHaibTfbsHepg2SrfV0416101AlnRep0_vs_wgEncodeHaibTfbsHepg2ControlV0416101AlnRep0.bb HepG2 ChipSeq SRF Peaks bigBed HudsonAlpha analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/peakSeq/optimal/hub/peakSeq.optimal.wgEncodeHaibTfbsHepg2Taf1Pcr2xAlnRep0_vs_wgEncodeHaibTfbsHepg2ControlPcr2xAlnRep0.bb HepG2 ChipSeq TAF1 Peaks bigBed HudsonAlpha analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/peakSeq/optimal/hub/peakSeq.optimal.wgEncodeHaibTfbsHepg2Tcf12Pcr1xAlnRep0_vs_wgEncodeHaibTfbsHepg2ControlPcr1xAlnRep0.bb HepG2 ChipSeq TCF12 Peaks bigBed HudsonAlpha analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/peakSeq/optimal/hub/peakSeq.optimal.wgEncodeHaibTfbsHepg2Usf1Pcr1xAlnRep0_vs_wgEncodeHaibTfbsHepg2ControlPcr1xAlnRep0.bb HepG2 ChipSeq USF-1 Peaks bigBed HudsonAlpha analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/peakSeq/optimal/hub/peakSeq.optimal.wgEncodeHaibTfbsHepg2Zbtb33Pcr1xAlnRep0_vs_wgEncodeHaibTfbsHepg2ControlPcr1xAlnRep0.bb HepG2 ChipSeq ZBTB33 Peaks bigBed HudsonAlpha analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/peakSeq/optimal/hub/peakSeq.optimal.wgEncodeHaibTfbsHepg2Zbtb33V0416101AlnRep0_vs_wgEncodeHaibTfbsHepg2ControlV0416101AlnRep0.bb HepG2 ChipSeq ZBTB33 Peaks bigBed HudsonAlpha analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/peakSeq/optimal/hub/peakSeq.optimal.wgEncodeHaibTfbsHtb11NrsfPcr2xAlnRep0_vs_wgEncodeHaibTfbsHtb11ControlPcr2xAlnRep0.bb HTB-11 ChipSeq NRSF Peaks bigBed HudsonAlpha analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/peakSeq/optimal/hub/peakSeq.optimal.wgEncodeHaibTfbsK562Bcl3Pcr1xAlnRep0_vs_wgEncodeHaibTfbsK562ControlV0416101AlnRep0.bb K562 ChipSeq BCL3 Peaks bigBed HudsonAlpha analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/peakSeq/optimal/hub/peakSeq.optimal.wgEncodeHaibTfbsK562Bclaf1m33Pcr1xAlnRep0_vs_wgEncodeHaibTfbsK562ControlV0416101AlnRep0.bb K562 ChipSeq BCLAF1_(M33-P5B11) Peaks bigBed HudsonAlpha analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/peakSeq/optimal/hub/peakSeq.optimal.wgEncodeHaibTfbsK562Ctcflsc98982V0416101AlnRep0_vs_wgEncodeHaibTfbsK562ControlV0416101AlnRep0.bb K562 ChipSeq CTCFL_(SC-98982) Peaks bigBed HudsonAlpha analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/peakSeq/optimal/hub/peakSeq.optimal.wgEncodeHaibTfbsK562E2f6h50V0416102AlnRep0_vs_wgEncodeHaibTfbsK562ControlPcr1xAlnRep0.bb K562 ChipSeq E2F6_(H-50) Peaks bigBed HudsonAlpha analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/peakSeq/optimal/hub/peakSeq.optimal.wgEncodeHaibTfbsK562Egr1V0416101AlnRep0_vs_wgEncodeHaibTfbsK562ControlV0416101AlnRep0.bb K562 ChipSeq Egr-1 Peaks bigBed HudsonAlpha analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/peakSeq/optimal/hub/peakSeq.optimal.wgEncodeHaibTfbsK562Elf1sc631V0416102AlnRep0_vs_wgEncodeHaibTfbsK562ControlPcr1xAlnRep0.bb K562 ChipSeq ELF1_(SC-631) Peaks bigBed HudsonAlpha analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/peakSeq/optimal/hub/peakSeq.optimal.wgEncodeHaibTfbsK562Ets1V0416101AlnRep0_vs_wgEncodeHaibTfbsK562ControlV0416101AlnRep0.bb K562 ChipSeq ETS1 Peaks bigBed HudsonAlpha analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/peakSeq/optimal/hub/peakSeq.optimal.wgEncodeHaibTfbsK562Fosl1sc183V0416101AlnRep0_vs_wgEncodeHaibTfbsK562ControlV0416101AlnRep0.bb K562 ChipSeq FOSL1_(SC-183) Peaks bigBed HudsonAlpha analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/peakSeq/optimal/hub/peakSeq.optimal.wgEncodeHaibTfbsK562GabpV0416101AlnRep0_vs_wgEncodeHaibTfbsK562ControlV0416101AlnRep0.bb K562 ChipSeq GABP Peaks bigBed HudsonAlpha analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/peakSeq/optimal/hub/peakSeq.optimal.wgEncodeHaibTfbsK562Gata2cg2Pcr1xAlnRep0_vs_wgEncodeHaibTfbsK562ControlV0416101AlnRep0.bb K562 ChipSeq GATA2_(CG2-96) Peaks bigBed HudsonAlpha analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/peakSeq/optimal/hub/peakSeq.optimal.wgEncodeHaibTfbsK562Hdac2sc6296V0416102AlnRep0_vs_wgEncodeHaibTfbsK562ControlPcr1xAlnRep0.bb K562 ChipSeq HDAC2_(SC-6296) Peaks bigBed HudsonAlpha analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/peakSeq/optimal/hub/peakSeq.optimal.wgEncodeHaibTfbsK562Hey1Pcr1xAlnRep0_vs_wgEncodeHaibTfbsK562ControlPcr1xAlnRep0.bb K562 ChipSeq HEY1 Peaks bigBed HudsonAlpha analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/peakSeq/optimal/hub/peakSeq.optimal.wgEncodeHaibTfbsK562MaxV0416102AlnRep0_vs_wgEncodeHaibTfbsK562ControlPcr1xAlnRep0.bb K562 ChipSeq Max Peaks bigBed HudsonAlpha analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/peakSeq/optimal/hub/peakSeq.optimal.wgEncodeHaibTfbsK562NrsfV0416102AlnRep0_vs_wgEncodeHaibTfbsK562ControlV0416101AlnRep0.bb K562 ChipSeq NRSF Peaks bigBed HudsonAlpha analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/peakSeq/optimal/hub/peakSeq.optimal.wgEncodeHaibTfbsK562Pol24h8Pcr1xAlnRep0_vs_wgEncodeHaibTfbsK562ControlPcr1xAlnRep0.bb K562 ChipSeq Pol2-4H8 Peaks bigBed HudsonAlpha analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/peakSeq/optimal/hub/peakSeq.optimal.wgEncodeHaibTfbsK562Pol24h8V0416101AlnRep0_vs_wgEncodeHaibTfbsK562ControlV0416101AlnRep0.bb K562 ChipSeq Pol2-4H8 Peaks bigBed HudsonAlpha analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/peakSeq/optimal/hub/peakSeq.optimal.wgEncodeHaibTfbsK562Pol2V0416101AlnRep0_vs_wgEncodeHaibTfbsK562ControlV0416101AlnRep0.bb K562 ChipSeq Pol2 Peaks bigBed HudsonAlpha analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/peakSeq/optimal/hub/peakSeq.optimal.wgEncodeHaibTfbsK562Pu1Pcr1xAlnRep0_vs_wgEncodeHaibTfbsK562ControlPcr1xAlnRep0.bb K562 ChipSeq PU.1 Peaks bigBed HudsonAlpha analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/peakSeq/optimal/hub/peakSeq.optimal.wgEncodeHaibTfbsK562Rad21V0416102AlnRep0_vs_wgEncodeHaibTfbsK562ControlPcr1xAlnRep0.bb K562 ChipSeq Rad21 Peaks bigBed HudsonAlpha analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/peakSeq/optimal/hub/peakSeq.optimal.wgEncodeHaibTfbsK562Sin3ak20V0416101AlnRep0_vs_wgEncodeHaibTfbsK562ControlV0416101AlnRep0.bb K562 ChipSeq Sin3Ak-20 Peaks bigBed HudsonAlpha analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/peakSeq/optimal/hub/peakSeq.optimal.wgEncodeHaibTfbsK562Six5Pcr1xAlnRep0_vs_wgEncodeHaibTfbsK562ControlPcr1xAlnRep0.bb K562 ChipSeq SIX5 Peaks bigBed HudsonAlpha analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/peakSeq/optimal/hub/peakSeq.optimal.wgEncodeHaibTfbsK562Sp1Pcr1xAlnRep0_vs_wgEncodeHaibTfbsK562ControlV0416101AlnRep0.bb K562 ChipSeq SP1 Peaks bigBed HudsonAlpha analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/peakSeq/optimal/hub/peakSeq.optimal.wgEncodeHaibTfbsK562Sp2sc643V0416102AlnRep0_vs_wgEncodeHaibTfbsK562ControlPcr1xAlnRep0.bb K562 ChipSeq SP2_(SC-643) Peaks bigBed HudsonAlpha analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/peakSeq/optimal/hub/peakSeq.optimal.wgEncodeHaibTfbsK562SrfV0416101AlnRep0_vs_wgEncodeHaibTfbsK562ControlV0416101AlnRep0.bb K562 ChipSeq SRF Peaks bigBed HudsonAlpha analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/peakSeq/optimal/hub/peakSeq.optimal.wgEncodeHaibTfbsK562Taf1Pcr1xAlnRep0_vs_wgEncodeHaibTfbsK562ControlPcr1xAlnRep0.bb K562 ChipSeq TAF1 Peaks bigBed HudsonAlpha analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/peakSeq/optimal/hub/peakSeq.optimal.wgEncodeHaibTfbsK562Taf1V0416101AlnRep0_vs_wgEncodeHaibTfbsK562ControlV0416101AlnRep0.bb K562 ChipSeq TAF1 Peaks bigBed HudsonAlpha analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/peakSeq/optimal/hub/peakSeq.optimal.wgEncodeHaibTfbsK562Taf7sq8V0416101AlnRep0_vs_wgEncodeHaibTfbsK562ControlV0416101AlnRep0.bb K562 ChipSeq TAF7_(SQ-8) Peaks bigBed HudsonAlpha analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/peakSeq/optimal/hub/peakSeq.optimal.wgEncodeHaibTfbsK562Thap1sc98174V0416101AlnRep0_vs_wgEncodeHaibTfbsK562ControlV0416101AlnRep0.bb K562 ChipSeq THAP1_(SC-98174) Peaks bigBed HudsonAlpha analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/peakSeq/optimal/hub/peakSeq.optimal.wgEncodeHaibTfbsK562Usf1V0416101AlnRep0_vs_wgEncodeHaibTfbsK562ControlV0416101AlnRep0.bb K562 ChipSeq USF-1 Peaks bigBed HudsonAlpha analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/peakSeq/optimal/hub/peakSeq.optimal.wgEncodeHaibTfbsK562Yy1V0416101AlnRep0_vs_wgEncodeHaibTfbsK562ControlV0416101AlnRep0.bb K562 ChipSeq YY1 Peaks bigBed HudsonAlpha analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/peakSeq/optimal/hub/peakSeq.optimal.wgEncodeHaibTfbsK562Yy1V0416102AlnRep0_vs_wgEncodeHaibTfbsK562ControlPcr1xAlnRep0.bb K562 ChipSeq YY1 Peaks bigBed HudsonAlpha analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/peakSeq/optimal/hub/peakSeq.optimal.wgEncodeHaibTfbsK562Zbtb33Pcr1xAlnRep0_vs_wgEncodeHaibTfbsK562ControlV0416101AlnRep0.bb K562 ChipSeq ZBTB33 Peaks bigBed HudsonAlpha analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/peakSeq/optimal/hub/peakSeq.optimal.wgEncodeHaibTfbsK562Zbtb7asc34508V0416101AlnRep0_vs_wgEncodeHaibTfbsK562ControlV0416101AlnRep0.bb K562 ChipSeq ZBTB7A_(SC-34508) Peaks bigBed HudsonAlpha analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/peakSeq/optimal/hub/peakSeq.optimal.wgEncodeHaibTfbsPanc1NrsfPcr2xAlnRep0_vs_wgEncodeHaibTfbsPanc1ControlPcr2xAlnRep0.bb PANC-1 ChipSeq NRSF Peaks bigBed HudsonAlpha analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/peakSeq/optimal/hub/peakSeq.optimal.wgEncodeHaibTfbsPfsk1NrsfPcr2xAlnRep0_vs_wgEncodeHaibTfbsPfsk1ControlPcr2xAlnRep0.bb PFSK-1 ChipSeq NRSF Peaks bigBed HudsonAlpha analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/peakSeq/optimal/hub/peakSeq.optimal.wgEncodeHaibTfbsSknshraCtcfV0416102AlnRep0_vs_wgEncodeHaibTfbsSknshraControlV0416102AlnRep2.bb SK-N-SH_RA ChipSeq CTCF Peaks bigBed HudsonAlpha analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/peakSeq/optimal/hub/peakSeq.optimal.wgEncodeHaibTfbsSknshraP300V0416102AlnRep0_vs_wgEncodeHaibTfbsSknshraControlV0416102AlnRep2.bb SK-N-SH_RA ChipSeq p300 Peaks bigBed HudsonAlpha analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/peakSeq/optimal/hub/peakSeq.optimal.wgEncodeHaibTfbsSknshraRad21V0416102AlnRep0_vs_wgEncodeHaibTfbsSknshraControlV0416102AlnRep2.bb SK-N-SH_RA ChipSeq Rad21 Peaks bigBed HudsonAlpha analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/peakSeq/optimal/hub/peakSeq.optimal.wgEncodeHaibTfbsSknshraUsf1sc8983V0416102AlnRep0_vs_wgEncodeHaibTfbsSknshraControlV0416102AlnRep2.bb SK-N-SH_RA ChipSeq USF1_(SC-8983) Peaks bigBed HudsonAlpha analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/peakSeq/optimal/hub/peakSeq.optimal.wgEncodeHaibTfbsSknshraYy1c20V0416102AlnRep0_vs_wgEncodeHaibTfbsSknshraControlV0416102AlnRep2.bb SK-N-SH_RA ChipSeq YY1_(C-20) Peaks bigBed HudsonAlpha analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/peakSeq/optimal/hub/peakSeq.optimal.wgEncodeHaibTfbsT47dCtcfsc5916V0416102Dmso2AlnRep0_vs_wgEncodeHaibTfbsT47dControlV0416102Dmso2AlnRep2.bb T-47D ChipSeq CTCF_(SC-5916) Peaks bigBed HudsonAlpha analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/peakSeq/optimal/hub/peakSeq.optimal.wgEncodeHaibTfbsT47dEralphaaPcr2xGen1hAlnRep0_vs_wgEncodeHaibTfbsT47dEralphaaV0416102Dmso2AlnRep0.bb T-47D ChipSeq ERalpha_a Peaks bigBed HudsonAlpha analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/peakSeq/optimal/hub/peakSeq.optimal.wgEncodeHaibTfbsT47dEralphaaV0416102Estradia1hAlnRep0_vs_wgEncodeHaibTfbsT47dEralphaaV0416102Dmso2AlnRep0.bb T-47D ChipSeq ERalpha_a Peaks bigBed HudsonAlpha analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/peakSeq/optimal/hub/peakSeq.optimal.wgEncodeHaibTfbsT47dFoxa1c20V0416102Dmso2AlnRep0_vs_wgEncodeHaibTfbsT47dControlV0416102Dmso2AlnRep2.bb T-47D ChipSeq FOXA1_(C-20) Peaks bigBed HudsonAlpha analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/peakSeq/optimal/hub/peakSeq.optimal.wgEncodeHaibTfbsT47dGata3sc268V0416102Dmso2AlnRep0_vs_wgEncodeHaibTfbsT47dControlV0416102Dmso2AlnRep2.bb T-47D ChipSeq GATA3_(SC-268) Peaks bigBed HudsonAlpha analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/peakSeq/optimal/hub/peakSeq.optimal.wgEncodeHaibTfbsT47dP300V0416102Dmso2AlnRep0_vs_wgEncodeHaibTfbsT47dControlV0416102Dmso2AlnRep2.bb T-47D ChipSeq p300 Peaks bigBed HudsonAlpha analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/peakSeq/optimal/hub/peakSeq.optimal.wgEncodeHaibTfbsU87NrsfPcr2xAlnRep0_vs_wgEncodeHaibTfbsU87ControlPcr2xAlnRep0.bb U87 ChipSeq NRSF Peaks bigBed HudsonAlpha analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/peakSeq/optimal/hub/peakSeq.optimal.wgEncodeOpenChromChipFibroblCtcfAlnRep0_vs_wgEncodeOpenChromChipFibroblInputAlnRep1.bb Fibrobl ChipSeq CTCF Peaks bigBed UT-A analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/peakSeq/optimal/hub/peakSeq.optimal.wgEncodeOpenChromChipGlioblaCtcfAlnRep0_vs_wgEncodeOpenChromChipGlioblaInputAlnRep1.bb Gliobla ChipSeq CTCF Peaks bigBed UT-A analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/peakSeq/optimal/hub/peakSeq.optimal.wgEncodeOpenChromChipGlioblaPol2AlnRep0_vs_wgEncodeOpenChromChipGlioblaInputAlnRep1.bb Gliobla ChipSeq Pol2 Peaks bigBed UT-A analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/peakSeq/optimal/hub/peakSeq.optimal.wgEncodeOpenChromChipGm12878CmycAlnRep0_vs_wgEncodeOpenChromChipGm12878InputAlnRep1.bb GM12878 ChipSeq c-Myc Peaks bigBed UT-A analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/peakSeq/optimal/hub/peakSeq.optimal.wgEncodeOpenChromChipGm12878CtcfAlnRep0_vs_wgEncodeOpenChromChipGm12878InputAlnRep1.bb GM12878 ChipSeq CTCF Peaks bigBed UT-A analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/peakSeq/optimal/hub/peakSeq.optimal.wgEncodeOpenChromChipGm12878Pol2AlnRep0_vs_wgEncodeOpenChromChipGm12878InputAlnRep1.bb GM12878 ChipSeq Pol2 Peaks bigBed UT-A analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/peakSeq/optimal/hub/peakSeq.optimal.wgEncodeOpenChromChipHelas3CmycAlnRep0_vs_wgEncodeOpenChromChipHelas3InputAlnRep1.bb HeLa-S3 ChipSeq c-Myc Peaks bigBed UT-A analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/peakSeq/optimal/hub/peakSeq.optimal.wgEncodeOpenChromChipHelas3CtcfAlnRep0_vs_wgEncodeOpenChromChipHelas3InputAlnRep1.bb HeLa-S3 ChipSeq CTCF Peaks bigBed UT-A analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/peakSeq/optimal/hub/peakSeq.optimal.wgEncodeOpenChromChipHelas3Pol2AlnRep0_vs_wgEncodeOpenChromChipHelas3InputAlnRep1.bb HeLa-S3 ChipSeq Pol2 Peaks bigBed UT-A analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/peakSeq/optimal/hub/peakSeq.optimal.wgEncodeOpenChromChipHepg2CmycAlnRep0_vs_wgEncodeOpenChromChipHepg2InputAlnRep1.bb HepG2 ChipSeq c-Myc Peaks bigBed UT-A analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/peakSeq/optimal/hub/peakSeq.optimal.wgEncodeOpenChromChipHepg2CtcfAlnRep0_vs_wgEncodeOpenChromChipHepg2InputAlnRep1.bb HepG2 ChipSeq CTCF Peaks bigBed UT-A analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/peakSeq/optimal/hub/peakSeq.optimal.wgEncodeOpenChromChipHepg2Pol2AlnRep0_vs_wgEncodeOpenChromChipHepg2InputAlnRep1.bb HepG2 ChipSeq Pol2 Peaks bigBed UT-A analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/peakSeq/optimal/hub/peakSeq.optimal.wgEncodeOpenChromChipHuvecCmycAlnRep1_vs_wgEncodeOpenChromChipHuvecInputAlnRep1.bb HUVEC ChipSeq c-Myc Peaks bigBed UT-A analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/peakSeq/optimal/hub/peakSeq.optimal.wgEncodeOpenChromChipHuvecCtcfAlnRep0_vs_wgEncodeOpenChromChipHuvecInputAlnRep1.bb HUVEC ChipSeq CTCF Peaks bigBed UT-A analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/peakSeq/optimal/hub/peakSeq.optimal.wgEncodeOpenChromChipHuvecPol2AlnRep0_vs_wgEncodeOpenChromChipHuvecInputAlnRep1.bb HUVEC ChipSeq Pol2 Peaks bigBed UT-A analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/peakSeq/optimal/hub/peakSeq.optimal.wgEncodeOpenChromChipK562CmycAlnRep0_vs_wgEncodeOpenChromChipK562InputAlnRep1.bb K562 ChipSeq c-Myc Peaks bigBed UT-A analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/peakSeq/optimal/hub/peakSeq.optimal.wgEncodeOpenChromChipK562CtcfAlnRep0_vs_wgEncodeOpenChromChipK562InputAlnRep1.bb K562 ChipSeq CTCF Peaks bigBed UT-A analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/peakSeq/optimal/hub/peakSeq.optimal.wgEncodeOpenChromChipK562Pol2AlnRep0_vs_wgEncodeOpenChromChipK562InputAlnRep1.bb K562 ChipSeq Pol2 Peaks bigBed UT-A analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/peakSeq/optimal/hub/peakSeq.optimal.wgEncodeOpenChromChipMcf7CmycEstroAlnRep0_vs_wgEncodeOpenChromChipMcf7InputAlnRep1.bb MCF-7 ChipSeq c-Myc Peaks bigBed UT-A analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/peakSeq/optimal/hub/peakSeq.optimal.wgEncodeOpenChromChipMcf7CmycVehAlnRep0_vs_wgEncodeOpenChromChipMcf7InputAlnRep1.bb MCF-7 ChipSeq c-Myc Peaks bigBed UT-A analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/peakSeq/optimal/hub/peakSeq.optimal.wgEncodeOpenChromChipMcf7CtcfAlnRep0_vs_wgEncodeOpenChromChipMcf7InputAlnRep1.bb MCF-7 ChipSeq CTCF Peaks bigBed UT-A analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/peakSeq/optimal/hub/peakSeq.optimal.wgEncodeOpenChromChipMcf7CtcfEstroAlnRep0_vs_wgEncodeOpenChromChipMcf7InputAlnRep1.bb MCF-7 ChipSeq CTCF Peaks bigBed UT-A analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/peakSeq/optimal/hub/peakSeq.optimal.wgEncodeOpenChromChipMcf7CtcfVehAlnRep0_vs_wgEncodeOpenChromChipMcf7InputAlnRep1.bb MCF-7 ChipSeq CTCF Peaks bigBed UT-A analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/peakSeq/optimal/hub/peakSeq.optimal.wgEncodeOpenChromChipMcf7Pol2AlnRep0_vs_wgEncodeOpenChromChipMcf7InputAlnRep1.bb MCF-7 ChipSeq Pol2 Peaks bigBed UT-A analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/peakSeq/optimal/hub/peakSeq.optimal.wgEncodeOpenChromChipProgfibCtcfAlnRep0_vs_wgEncodeOpenChromChipProgfibInputAlnRep1.bb ProgFib ChipSeq CTCF Peaks bigBed UT-A analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/peakSeq/optimal/hub/peakSeq.optimal.wgEncodeOpenChromChipProgfibPol2AlnRep0_vs_wgEncodeOpenChromChipProgfibInputAlnRep1.bb ProgFib ChipSeq Pol2 Peaks bigBed UT-A analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/peakSeq/optimal/hub/peakSeq.optimal.wgEncodeSydhTfbsGm10847NfkbIggrabAlnRep0_vs_wgEncodeSydhTfbsGm10847InputIggrabAlnRep0.bb GM10847 ChipSeq NFKB Peaks bigBed Stanford analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/peakSeq/optimal/hub/peakSeq.optimal.wgEncodeSydhTfbsGm10847Pol2IggmusAlnRep1_vs_wgEncodeSydhTfbsGm10847InputIggmusAlnRep0.bb GM10847 ChipSeq Pol2 Peaks bigBed Stanford analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/peakSeq/optimal/hub/peakSeq.optimal.wgEncodeSydhTfbsGm12878Brca1cIggmusAlnRep0_vs_wgEncodeSydhTfbsGm12878InputIggmusAlnRep0.bb GM12878 ChipSeq BRCA1_(C-1863) Peaks bigBed Stanford analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/peakSeq/optimal/hub/peakSeq.optimal.wgEncodeSydhTfbsGm12878CfosStdAlnRep0_vs_wgEncodeSydhTfbsGm12878InputStdAlnRep1.bb GM12878 ChipSeq c-Fos Peaks bigBed Stanford analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/peakSeq/optimal/hub/peakSeq.optimal.wgEncodeSydhTfbsGm12878Chd21250IggmusAlnRep0_vs_wgEncodeSydhTfbsGm12878InputIggmusAlnRep0.bb GM12878 ChipSeq CHD2_(N-1250) Peaks bigBed Stanford analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/peakSeq/optimal/hub/peakSeq.optimal.wgEncodeSydhTfbsGm12878Ctcfc20StdAlnRep0_vs_wgEncodeSydhTfbsGm12878InputStdAlnRep1.bb GM12878 ChipSeq CTCF_(C-20) Peaks bigBed Stanford analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/peakSeq/optimal/hub/peakSeq.optimal.wgEncodeSydhTfbsGm12878EbfStdAlnRep0_vs_wgEncodeSydhTfbsGm12878InputStdAlnRep1.bb GM12878 ChipSeq EBF Peaks bigBed Stanford analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/peakSeq/optimal/hub/peakSeq.optimal.wgEncodeSydhTfbsGm12878Gcn5StdAlnRep0_vs_wgEncodeSydhTfbsGm12878InputStdAlnRep1.bb GM12878 ChipSeq GCN5 Peaks bigBed Harvard(Weissman) analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/peakSeq/optimal/hub/peakSeq.optimal.wgEncodeSydhTfbsGm12878Irf3StdAlnRep0_vs_wgEncodeSydhTfbsGm12878InputStdAlnRep1.bb GM12878 ChipSeq IRF3 Peaks bigBed Stanford analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/peakSeq/optimal/hub/peakSeq.optimal.wgEncodeSydhTfbsGm12878JundStdAlnRep0_vs_wgEncodeSydhTfbsGm12878InputStdAlnRep1.bb GM12878 ChipSeq JunD Peaks bigBed Stanford analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/peakSeq/optimal/hub/peakSeq.optimal.wgEncodeSydhTfbsGm12878MaxStdAlnRep0_vs_wgEncodeSydhTfbsGm12878InputStdAlnRep1.bb GM12878 ChipSeq Max Peaks bigBed Stanford analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/peakSeq/optimal/hub/peakSeq.optimal.wgEncodeSydhTfbsGm12878Nfe2hStdAlnRep0_vs_wgEncodeSydhTfbsGm12878InputStdAlnRep1.bb GM12878 ChipSeq NF-E2_(H-230) Peaks bigBed Stanford analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/peakSeq/optimal/hub/peakSeq.optimal.wgEncodeSydhTfbsGm12878NfkbIggrabAlnRep0_vs_wgEncodeSydhTfbsGm12878InputIggrabAlnRep0.bb GM12878 ChipSeq NFKB Peaks bigBed Stanford analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/peakSeq/optimal/hub/peakSeq.optimal.wgEncodeSydhTfbsGm12878NfkbTnfaStdAlnRep0_vs_wgEncodeSydhTfbsGm12878InputStdAlnRep1.bb GM12878 ChipSeq NFKB Peaks bigBed Stanford analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/peakSeq/optimal/hub/peakSeq.optimal.wgEncodeSydhTfbsGm12878Nrf1IggmusAlnRep0_vs_wgEncodeSydhTfbsGm12878InputIggmusAlnRep0.bb GM12878 ChipSeq Nrf1 Peaks bigBed Stanford analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/peakSeq/optimal/hub/peakSeq.optimal.wgEncodeSydhTfbsGm12878P300n15StdAlnRep0_vs_wgEncodeSydhTfbsGm12878InputStdAlnRep1.bb GM12878 ChipSeq p300_(N-15) Peaks bigBed Stanford analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/peakSeq/optimal/hub/peakSeq.optimal.wgEncodeSydhTfbsGm12878Pol2IggmusAlnRep0_vs_wgEncodeSydhTfbsGm12878InputIggmusAlnRep0.bb GM12878 ChipSeq Pol2 Peaks bigBed Stanford analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/peakSeq/optimal/hub/peakSeq.optimal.wgEncodeSydhTfbsGm12878Pol2StdAlnRep0_vs_wgEncodeSydhTfbsGm12878InputStdAlnRep1.bb GM12878 ChipSeq Pol2 Peaks bigBed Stanford analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/peakSeq/optimal/hub/peakSeq.optimal.wgEncodeSydhTfbsGm12878Pol3StdAlnRep0_vs_wgEncodeSydhTfbsGm12878InputStdAlnRep1.bb GM12878 ChipSeq Pol3 Peaks bigBed Stanford analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/peakSeq/optimal/hub/peakSeq.optimal.wgEncodeSydhTfbsGm12878Rad21IggrabAlnRep0_vs_wgEncodeSydhTfbsGm12878InputIggrabAlnRep0.bb GM12878 ChipSeq Rad21 Peaks bigBed Stanford analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/peakSeq/optimal/hub/peakSeq.optimal.wgEncodeSydhTfbsGm12878Rfx5n494IggmusAlnRep0_vs_wgEncodeSydhTfbsGm12878InputIggmusAlnRep0.bb GM12878 ChipSeq RFX5_(N-494) Peaks bigBed Stanford analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/peakSeq/optimal/hub/peakSeq.optimal.wgEncodeSydhTfbsGm12878Smc3ab9263IggmusAlnRep0_vs_wgEncodeSydhTfbsGm12878InputIggmusAlnRep0.bb GM12878 ChipSeq SMC3_(ab9263) Peaks bigBed Stanford analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/peakSeq/optimal/hub/peakSeq.optimal.wgEncodeSydhTfbsGm12878Spt20StdAlnRep0_vs_wgEncodeSydhTfbsGm12878InputStdAlnRep1.bb GM12878 ChipSeq SPT20 Peaks bigBed Harvard(Weissman) analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/peakSeq/optimal/hub/peakSeq.optimal.wgEncodeSydhTfbsGm12878Stat1StdAlnRep0_vs_wgEncodeSydhTfbsGm12878InputStdAlnRep1.bb GM12878 ChipSeq STAT1 Peaks bigBed Stanford analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/peakSeq/optimal/hub/peakSeq.optimal.wgEncodeSydhTfbsGm12878Stat3IggmusAlnRep0_vs_wgEncodeSydhTfbsGm12878InputIggmusAlnRep0.bb GM12878 ChipSeq STAT3 Peaks bigBed Stanford analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/peakSeq/optimal/hub/peakSeq.optimal.wgEncodeSydhTfbsGm12878TbpIggmusAlnRep0_vs_wgEncodeSydhTfbsGm12878InputIggmusAlnRep0.bb GM12878 ChipSeq TBP Peaks bigBed Stanford analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/peakSeq/optimal/hub/peakSeq.optimal.wgEncodeSydhTfbsGm12878Tr4StdAlnRep0_vs_wgEncodeSydhTfbsGm12878InputStdAlnRep1.bb GM12878 ChipSeq TR4 Peaks bigBed Stanford analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/peakSeq/optimal/hub/peakSeq.optimal.wgEncodeSydhTfbsGm12878Usf2IggmusAlnRep0_vs_wgEncodeSydhTfbsGm12878InputIggmusAlnRep0.bb GM12878 ChipSeq USF2 Peaks bigBed Stanford analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/peakSeq/optimal/hub/peakSeq.optimal.wgEncodeSydhTfbsGm12878WhipIggmusAlnRep0_vs_wgEncodeSydhTfbsGm12878InputIggmusAlnRep0.bb GM12878 ChipSeq WHIP Peaks bigBed Stanford analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/peakSeq/optimal/hub/peakSeq.optimal.wgEncodeSydhTfbsGm12878Yy1StdAlnRep0_vs_wgEncodeSydhTfbsGm12878InputStdAlnRep1.bb GM12878 ChipSeq YY1 Peaks bigBed Stanford analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/peakSeq/optimal/hub/peakSeq.optimal.wgEncodeSydhTfbsGm12878Znf143166181apStdAlnRep0_vs_wgEncodeSydhTfbsGm12878InputStdAlnRep1.bb GM12878 ChipSeq Znf143_(16618-1-AP) Peaks bigBed Stanford analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/peakSeq/optimal/hub/peakSeq.optimal.wgEncodeSydhTfbsGm12878Zzz3StdAlnRep0_vs_wgEncodeSydhTfbsGm12878InputStdAlnRep1.bb GM12878 ChipSeq ZZZ3 Peaks bigBed Stanford analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/peakSeq/optimal/hub/peakSeq.optimal.wgEncodeSydhTfbsGm12891NfkbIggrabAlnRep0_vs_wgEncodeSydhTfbsGm12891InputIggrabAlnRep0.bb GM12891 ChipSeq NFKB Peaks bigBed Stanford analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/peakSeq/optimal/hub/peakSeq.optimal.wgEncodeSydhTfbsGm12891Pol2IggmusAlnRep0_vs_wgEncodeSydhTfbsGm12891InputIggmusAlnRep0.bb GM12891 ChipSeq Pol2 Peaks bigBed Stanford analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/peakSeq/optimal/hub/peakSeq.optimal.wgEncodeSydhTfbsGm12892NfkbIggrabAlnRep0_vs_wgEncodeSydhTfbsGm12892InputIggrabAlnRep0.bb GM12892 ChipSeq NFKB Peaks bigBed Stanford analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/peakSeq/optimal/hub/peakSeq.optimal.wgEncodeSydhTfbsGm12892Pol2IggmusAlnRep0_vs_wgEncodeSydhTfbsGm12892InputIggmusAlnRep0.bb GM12892 ChipSeq Pol2 Peaks bigBed Stanford analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/peakSeq/optimal/hub/peakSeq.optimal.wgEncodeSydhTfbsGm15510NfkbIggrabAlnRep0_vs_wgEncodeSydhTfbsGm15510InputIggrabAlnRep0.bb GM15510 ChipSeq NFKB Peaks bigBed Stanford analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/peakSeq/optimal/hub/peakSeq.optimal.wgEncodeSydhTfbsGm15510Pol2IggmusAlnRep0_vs_wgEncodeSydhTfbsGm15510InputIggmusAlnRep0.bb GM15510 ChipSeq Pol2 Peaks bigBed Stanford analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/peakSeq/optimal/hub/peakSeq.optimal.wgEncodeSydhTfbsGm18505NfkbIggrabAlnRep0_vs_wgEncodeSydhTfbsGm18505InputIggrabAlnRep0.bb GM18505 ChipSeq NFKB Peaks bigBed Stanford analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/peakSeq/optimal/hub/peakSeq.optimal.wgEncodeSydhTfbsGm18505Pol2IggmusAlnRep0_vs_wgEncodeSydhTfbsGm18505InputIggmusAlnRep0.bb GM18505 ChipSeq Pol2 Peaks bigBed Stanford analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/peakSeq/optimal/hub/peakSeq.optimal.wgEncodeSydhTfbsGm18526NfkbIggrabAlnRep0_vs_wgEncodeSydhTfbsGm18526InputIggrabAlnRep0.bb GM18526 ChipSeq NFKB Peaks bigBed Stanford analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/peakSeq/optimal/hub/peakSeq.optimal.wgEncodeSydhTfbsGm18526Pol2IggmusAlnRep0_vs_wgEncodeSydhTfbsGm18526InputIggmusAlnRep0.bb GM18526 ChipSeq Pol2 Peaks bigBed Stanford analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/peakSeq/optimal/hub/peakSeq.optimal.wgEncodeSydhTfbsGm18951NfkbIggrabAlnRep0_vs_wgEncodeSydhTfbsGm18951InputIggrabAlnRep0.bb GM18951 ChipSeq NFKB Peaks bigBed Stanford analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/peakSeq/optimal/hub/peakSeq.optimal.wgEncodeSydhTfbsGm18951Pol2IggmusAlnRep0_vs_wgEncodeSydhTfbsGm18951InputIggmusAlnRep1.bb GM18951 ChipSeq Pol2 Peaks bigBed Stanford analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/peakSeq/optimal/hub/peakSeq.optimal.wgEncodeSydhTfbsGm19099NfkbIggrabAlnRep0_vs_wgEncodeSydhTfbsGm19099InputIggrabAlnRep0.bb GM19099 ChipSeq NFKB Peaks bigBed Stanford analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/peakSeq/optimal/hub/peakSeq.optimal.wgEncodeSydhTfbsGm19099Pol2IggmusAlnRep0_vs_wgEncodeSydhTfbsGm19099InputIggmusAlnRep0.bb GM19099 ChipSeq Pol2 Peaks bigBed Stanford analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/peakSeq/optimal/hub/peakSeq.optimal.wgEncodeSydhTfbsGm19193NfkbIggrabAlnRep0_vs_wgEncodeSydhTfbsGm19193InputIggrabAlnRep0.bb GM19193 ChipSeq NFKB Peaks bigBed Stanford analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/peakSeq/optimal/hub/peakSeq.optimal.wgEncodeSydhTfbsGm19193Pol2IggmusAlnRep0_vs_wgEncodeSydhTfbsGm19193InputIggmusAlnRep0.bb GM19193 ChipSeq Pol2 Peaks bigBed Stanford analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/peakSeq/optimal/hub/peakSeq.optimal.wgEncodeSydhTfbsH1hescCjunIggrabAlnRep0_vs_wgEncodeSydhTfbsH1hescInputIggrabAlnRep1.bb H1-hESC ChipSeq c-Jun Peaks bigBed Stanford analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/peakSeq/optimal/hub/peakSeq.optimal.wgEncodeSydhTfbsH1hescCtbp2UcdAlnRep0_vs_wgEncodeSydhTfbsH1hescInputUcdAlnRep1.bb H1-hESC ChipSeq CtBP2 Peaks bigBed UCD analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/peakSeq/optimal/hub/peakSeq.optimal.wgEncodeSydhTfbsH1hescMaxUcdAlnRep0_vs_wgEncodeSydhTfbsH1hescInputUcdAlnRep1.bb H1-hESC ChipSeq Max Peaks bigBed Stanford analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/peakSeq/optimal/hub/peakSeq.optimal.wgEncodeSydhTfbsH1hescNrf1IggrabAlnRep0_vs_wgEncodeSydhTfbsH1hescInputIggrabAlnRep1.bb H1-hESC ChipSeq Nrf1 Peaks bigBed Stanford analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/peakSeq/optimal/hub/peakSeq.optimal.wgEncodeSydhTfbsH1hescRad21IggrabAlnRep0_vs_wgEncodeSydhTfbsH1hescInputIggrabAlnRep1.bb H1-hESC ChipSeq Rad21 Peaks bigBed Stanford analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/peakSeq/optimal/hub/peakSeq.optimal.wgEncodeSydhTfbsH1hescRfx5n494IggrabAlnRep0_vs_wgEncodeSydhTfbsH1hescInputIggrabAlnRep1.bb H1-hESC ChipSeq RFX5_(N-494) Peaks bigBed Stanford analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/peakSeq/optimal/hub/peakSeq.optimal.wgEncodeSydhTfbsH1hescSuz12UcdAlnRep0_vs_wgEncodeSydhTfbsH1hescInputUcdAlnRep1.bb H1-hESC ChipSeq SUZ12 Peaks bigBed UCD analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/peakSeq/optimal/hub/peakSeq.optimal.wgEncodeSydhTfbsH1hescTbpStdAlnRep0_vs_wgEncodeSydhTfbsH1hescInputStdAlnRep1.bb H1-hESC ChipSeq TBP Peaks bigBed Stanford analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/peakSeq/optimal/hub/peakSeq.optimal.wgEncodeSydhTfbsH1hescUsf2IggrabAlnRep0_vs_wgEncodeSydhTfbsH1hescInputIggrabAlnRep1.bb H1-hESC ChipSeq USF2 Peaks bigBed Stanford analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/peakSeq/optimal/hub/peakSeq.optimal.wgEncodeSydhTfbsHct116Pol2UcdAlnRep0_vs_wgEncodeSydhTfbsHct116InputUcdAlnRep1.bb HCT-116 ChipSeq Pol2 Peaks bigBed Stanford analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/peakSeq/optimal/hub/peakSeq.optimal.wgEncodeSydhTfbsHct116Tcf4UcdAlnRep0_vs_wgEncodeSydhTfbsHct116InputUcdAlnRep1.bb HCT-116 ChipSeq TCF4 Peaks bigBed Stanford analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/peakSeq/optimal/hub/peakSeq.optimal.wgEncodeSydhTfbsHek293bElk4UcdAlnRep0_vs_wgEncodeSydhTfbsHek293InputUcdAlnRep1.bb HEK293(b) ChipSeq ELK4 Peaks bigBed UCD analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/peakSeq/optimal/hub/peakSeq.optimal.wgEncodeSydhTfbsHek293bKap1UcdAlnRep0_vs_wgEncodeSydhTfbsHek293InputUcdAlnRep1.bb HEK293(b) ChipSeq KAP1 Peaks bigBed UCD analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/peakSeq/optimal/hub/peakSeq.optimal.wgEncodeSydhTfbsHek293bPol2StdAlnRep0_vs_wgEncodeSydhTfbsHek293bInputStdAlnRep1.bb HEK293(b) ChipSeq Pol2 Peaks bigBed Stanford analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/peakSeq/optimal/hub/peakSeq.optimal.wgEncodeSydhTfbsHelas3Ap2alphaStdAlnRep0_vs_wgEncodeSydhTfbsHelas3InputStdAlnRep1.bb HeLa-S3 ChipSeq AP-2alpha Peaks bigBed Stanford analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/peakSeq/optimal/hub/peakSeq.optimal.wgEncodeSydhTfbsHelas3Ap2gammaStdAlnRep0_vs_wgEncodeSydhTfbsHelas3InputStdAlnRep1.bb HeLa-S3 ChipSeq AP-2gamma Peaks bigBed Stanford analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/peakSeq/optimal/hub/peakSeq.optimal.wgEncodeSydhTfbsHelas3Baf155IggmusAlnRep0_vs_wgEncodeSydhTfbsHelas3InputIggmusAlnRep0.bb HeLa-S3 ChipSeq BAF155 Peaks bigBed Stanford analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/peakSeq/optimal/hub/peakSeq.optimal.wgEncodeSydhTfbsHelas3Baf170IggmusAlnRep0_vs_wgEncodeSydhTfbsHelas3InputIggmusAlnRep0.bb HeLa-S3 ChipSeq BAF170 Peaks bigBed Stanford analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/peakSeq/optimal/hub/peakSeq.optimal.wgEncodeSydhTfbsHelas3Bdp1StdAlnRep0_vs_wgEncodeSydhTfbsHelas3InputStdAlnRep1.bb HeLa-S3 ChipSeq BDP1 Peaks bigBed Stanford analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/peakSeq/optimal/hub/peakSeq.optimal.wgEncodeSydhTfbsHelas3Brca1cIggrabAlnRep0_vs_wgEncodeSydhTfbsHelas3InputIggrabAlnRep1.bb HeLa-S3 ChipSeq BRCA1_(C-1863) Peaks bigBed Stanford analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/peakSeq/optimal/hub/peakSeq.optimal.wgEncodeSydhTfbsHelas3Brf1StdAlnRep0_vs_wgEncodeSydhTfbsHelas3InputStdAlnRep1.bb HeLa-S3 ChipSeq BRF1 Peaks bigBed Stanford analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/peakSeq/optimal/hub/peakSeq.optimal.wgEncodeSydhTfbsHelas3Brf2StdAlnRep0_vs_wgEncodeSydhTfbsHelas3InputStdAlnRep1.bb HeLa-S3 ChipSeq BRF2 Peaks bigBed Stanford analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/peakSeq/optimal/hub/peakSeq.optimal.wgEncodeSydhTfbsHelas3Brg1IggmusAlnRep0_vs_wgEncodeSydhTfbsHelas3InputIggmusAlnRep0.bb HeLa-S3 ChipSeq Brg1 Peaks bigBed Stanford analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/peakSeq/optimal/hub/peakSeq.optimal.wgEncodeSydhTfbsHelas3CebpbIggrabAlnRep0_vs_wgEncodeSydhTfbsHelas3InputIggrabAlnRep1.bb HeLa-S3 ChipSeq CEBPB Peaks bigBed Stanford analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/peakSeq/optimal/hub/peakSeq.optimal.wgEncodeSydhTfbsHelas3CfosStdAlnRep0_vs_wgEncodeSydhTfbsHelas3InputStdAlnRep1.bb HeLa-S3 ChipSeq c-Fos Peaks bigBed Stanford analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/peakSeq/optimal/hub/peakSeq.optimal.wgEncodeSydhTfbsHelas3CjunIggrabAlnRep0_vs_wgEncodeSydhTfbsHelas3InputIggrabAlnRep1.bb HeLa-S3 ChipSeq c-Jun Peaks bigBed Stanford analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/peakSeq/optimal/hub/peakSeq.optimal.wgEncodeSydhTfbsHelas3CmycStdAlnRep0_vs_wgEncodeSydhTfbsHelas3InputStdAlnRep1.bb HeLa-S3 ChipSeq c-Myc Peaks bigBed Stanford analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/peakSeq/optimal/hub/peakSeq.optimal.wgEncodeSydhTfbsHelas3E2f1StdAlnRep0_vs_wgEncodeSydhTfbsHelas3InputStdAlnRep1.bb HeLa-S3 ChipSeq E2F1 Peaks bigBed Stanford analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/peakSeq/optimal/hub/peakSeq.optimal.wgEncodeSydhTfbsHelas3E2f4StdAlnRep0_vs_wgEncodeSydhTfbsHelas3InputStdAlnRep1.bb HeLa-S3 ChipSeq E2F4 Peaks bigBed Stanford analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/peakSeq/optimal/hub/peakSeq.optimal.wgEncodeSydhTfbsHelas3E2f6StdAlnRep0_vs_wgEncodeSydhTfbsHelas3InputStdAlnRep1.bb HeLa-S3 ChipSeq E2F6 Peaks bigBed Stanford analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/peakSeq/optimal/hub/peakSeq.optimal.wgEncodeSydhTfbsHelas3Elk4UcdAlnRep0_vs_wgEncodeSydhTfbsHelas3InputUcdAlnRep1.bb HeLa-S3 ChipSeq ELK4 Peaks bigBed UCD analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/peakSeq/optimal/hub/peakSeq.optimal.wgEncodeSydhTfbsHelas3Gcn5StdAlnRep0_vs_wgEncodeSydhTfbsHelas3InputStdAlnRep1.bb HeLa-S3 ChipSeq GCN5 Peaks bigBed Stanford analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/peakSeq/optimal/hub/peakSeq.optimal.wgEncodeSydhTfbsHelas3Gtf2f1rapIggrabAlnRep0_vs_wgEncodeSydhTfbsHelas3InputIggrabAlnRep1.bb HeLa-S3 ChipSeq GTF2F1_(RAP-74) Peaks bigBed Stanford analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/peakSeq/optimal/hub/peakSeq.optimal.wgEncodeSydhTfbsHelas3Hae2f1StdAlnRep0_vs_wgEncodeSydhTfbsHelas3InputStdAlnRep1.bb HeLa-S3 ChipSeq HA-E2F1 Peaks bigBed Stanford analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/peakSeq/optimal/hub/peakSeq.optimal.wgEncodeSydhTfbsHelas3Ini1IggmusAlnRep0_vs_wgEncodeSydhTfbsHelas3InputIggmusAlnRep0.bb HeLa-S3 ChipSeq Ini1 Peaks bigBed Stanford analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/peakSeq/optimal/hub/peakSeq.optimal.wgEncodeSydhTfbsHelas3Irf3IggrabAlnRep0_vs_wgEncodeSydhTfbsHelas3InputIggrabAlnRep1.bb HeLa-S3 ChipSeq IRF3 Peaks bigBed Stanford analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/peakSeq/optimal/hub/peakSeq.optimal.wgEncodeSydhTfbsHelas3JundIggrabAlnRep0_vs_wgEncodeSydhTfbsHelas3InputIggrabAlnRep1.bb HeLa-S3 ChipSeq JunD Peaks bigBed Stanford analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/peakSeq/optimal/hub/peakSeq.optimal.wgEncodeSydhTfbsHelas3MaxStdAlnRep0_vs_wgEncodeSydhTfbsHelas3InputStdAlnRep1.bb HeLa-S3 ChipSeq Max Peaks bigBed Stanford analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/peakSeq/optimal/hub/peakSeq.optimal.wgEncodeSydhTfbsHelas3Mxi1bhlhIggrabAlnRep0_vs_wgEncodeSydhTfbsHelas3InputIggrabAlnRep1.bb HeLa-S3 ChipSeq Mxi1_(bHLH) Peaks bigBed Stanford analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/peakSeq/optimal/hub/peakSeq.optimal.wgEncodeSydhTfbsHelas3Nrf1IggmusAlnRep0_vs_wgEncodeSydhTfbsHelas3InputIggmusAlnRep0.bb HeLa-S3 ChipSeq Nrf1 Peaks bigBed Stanford analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/peakSeq/optimal/hub/peakSeq.optimal.wgEncodeSydhTfbsHelas3P300n15IggrabAlnRep0_vs_wgEncodeSydhTfbsHelas3InputIggrabAlnRep1.bb HeLa-S3 ChipSeq p300_(N-15) Peaks bigBed Stanford analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/peakSeq/optimal/hub/peakSeq.optimal.wgEncodeSydhTfbsHelas3Pol2s2IggrabAlnRep0_vs_wgEncodeSydhTfbsHelas3InputIggrabAlnRep1.bb HeLa-S3 ChipSeq Pol2(phosphoS2) Peaks bigBed Stanford analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/peakSeq/optimal/hub/peakSeq.optimal.wgEncodeSydhTfbsHelas3Pol2StdAlnRep0_vs_wgEncodeSydhTfbsHelas3InputStdAlnRep1.bb HeLa-S3 ChipSeq Pol2 Peaks bigBed Stanford analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/peakSeq/optimal/hub/peakSeq.optimal.wgEncodeSydhTfbsHelas3Prdm1vIggrabAlnRep0_vs_wgEncodeSydhTfbsHelas3InputIggrabAlnRep1.bb HeLa-S3 ChipSeq PRDM1_(Val90) Peaks bigBed Stanford analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/peakSeq/optimal/hub/peakSeq.optimal.wgEncodeSydhTfbsHelas3Rad21IggrabAlnRep0_vs_wgEncodeSydhTfbsHelas3InputIggrabAlnRep1.bb HeLa-S3 ChipSeq Rad21 Peaks bigBed Stanford analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/peakSeq/optimal/hub/peakSeq.optimal.wgEncodeSydhTfbsHelas3Rfx5n494IggrabAlnRep0_vs_wgEncodeSydhTfbsHelas3InputIggrabAlnRep1.bb HeLa-S3 ChipSeq RFX5_(N-494) Peaks bigBed Stanford analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/peakSeq/optimal/hub/peakSeq.optimal.wgEncodeSydhTfbsHelas3Rpc155StdAlnRep0_vs_wgEncodeSydhTfbsHelas3InputStdAlnRep1.bb HeLa-S3 ChipSeq RPC155 Peaks bigBed Stanford analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/peakSeq/optimal/hub/peakSeq.optimal.wgEncodeSydhTfbsHelas3Smc3ab9263IggrabAlnRep0_vs_wgEncodeSydhTfbsHelas3InputIggrabAlnRep1.bb HeLa-S3 ChipSeq SMC3_(ab9263) Peaks bigBed Stanford analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/peakSeq/optimal/hub/peakSeq.optimal.wgEncodeSydhTfbsHelas3Spt20StdAlnRep0_vs_wgEncodeSydhTfbsHelas3InputStdAlnRep1.bb HeLa-S3 ChipSeq SPT20 Peaks bigBed Stanford analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/peakSeq/optimal/hub/peakSeq.optimal.wgEncodeSydhTfbsHelas3Stat1Ifng30StdAlnRep0_vs_wgEncodeSydhTfbsHelas3InputIfng30StdAlnRep1.bb HeLa-S3 ChipSeq STAT1 Peaks bigBed Stanford analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/peakSeq/optimal/hub/peakSeq.optimal.wgEncodeSydhTfbsHelas3Stat3IggrabAlnRep0_vs_wgEncodeSydhTfbsHelas3InputIggrabAlnRep1.bb HeLa-S3 ChipSeq STAT3 Peaks bigBed Stanford analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/peakSeq/optimal/hub/peakSeq.optimal.wgEncodeSydhTfbsHelas3TbpIggrabAlnRep0_vs_wgEncodeSydhTfbsHelas3InputIggrabAlnRep1.bb HeLa-S3 ChipSeq TBP Peaks bigBed Stanford analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/peakSeq/optimal/hub/peakSeq.optimal.wgEncodeSydhTfbsHelas3Tf3c110StdAlnRep0_vs_wgEncodeSydhTfbsHelas3InputStdAlnRep1.bb HeLa-S3 ChipSeq TFIIIC-110 Peaks bigBed Stanford analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/peakSeq/optimal/hub/peakSeq.optimal.wgEncodeSydhTfbsHelas3Tr4StdAlnRep0_vs_wgEncodeSydhTfbsHelas3InputStdAlnRep1.bb HeLa-S3 ChipSeq TR4 Peaks bigBed Stanford analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/peakSeq/optimal/hub/peakSeq.optimal.wgEncodeSydhTfbsHelas3Usf2IggmusAlnRep0_vs_wgEncodeSydhTfbsHelas3InputIggmusAlnRep0.bb HeLa-S3 ChipSeq USF2 Peaks bigBed Stanford analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/peakSeq/optimal/hub/peakSeq.optimal.wgEncodeSydhTfbsHelas3Znf274UcdAlnRep0_vs_wgEncodeSydhTfbsHelas3InputUcdAlnRep1.bb HeLa-S3 ChipSeq ZNF274 Peaks bigBed UCD analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/peakSeq/optimal/hub/peakSeq.optimal.wgEncodeSydhTfbsHelas3Zzz3StdAlnRep0_vs_wgEncodeSydhTfbsHelas3InputStdAlnRep1.bb HeLa-S3 ChipSeq ZZZ3 Peaks bigBed Harvard(Weissman) analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/peakSeq/optimal/hub/peakSeq.optimal.wgEncodeSydhTfbsHepg2bTr4UcdAlnRep0_vs_wgEncodeSydhTfbsHepg2bInputUcdAlnRep1.bb HepG2b ChipSeq TR4 Peaks bigBed Stanford analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/peakSeq/optimal/hub/peakSeq.optimal.wgEncodeSydhTfbsHepg2bZnf274UcdAlnRep0_vs_wgEncodeSydhTfbsHepg2bInputUcdAlnRep1.bb HepG2b ChipSeq ZNF274 Peaks bigBed UCD analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/peakSeq/optimal/hub/peakSeq.optimal.wgEncodeSydhTfbsHepg2CebpbForsklnStdAlnRep0_vs_wgEncodeSydhTfbsHepg2InputForsklnStdAlnRep0.bb HepG2 ChipSeq CEBPB Peaks bigBed Stanford analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/peakSeq/optimal/hub/peakSeq.optimal.wgEncodeSydhTfbsHepg2CebpbIggrabAlnRep0_vs_wgEncodeSydhTfbsHepg2InputIggrabAlnRep1.bb HepG2 ChipSeq CEBPB Peaks bigBed Stanford analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/peakSeq/optimal/hub/peakSeq.optimal.wgEncodeSydhTfbsHepg2Chd21250IggrabAlnRep0_vs_wgEncodeSydhTfbsHepg2InputIggrabAlnRep1.bb HepG2 ChipSeq CHD2_(N-1250) Peaks bigBed Stanford analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/peakSeq/optimal/hub/peakSeq.optimal.wgEncodeSydhTfbsHepg2CjunIggrabAlnRep0_vs_wgEncodeSydhTfbsHepg2InputIggrabAlnRep1.bb HepG2 ChipSeq c-Jun Peaks bigBed Stanford analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/peakSeq/optimal/hub/peakSeq.optimal.wgEncodeSydhTfbsHepg2ErraForsklnStdAlnRep0_vs_wgEncodeSydhTfbsHepg2InputForsklnStdAlnRep0.bb HepG2 ChipSeq ERRA Peaks bigBed Stanford analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/peakSeq/optimal/hub/peakSeq.optimal.wgEncodeSydhTfbsHepg2Grp20ForsklnStdAlnRep0_vs_wgEncodeSydhTfbsHepg2InputForsklnStdAlnRep0.bb HepG2 ChipSeq GRp20 Peaks bigBed Stanford analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/peakSeq/optimal/hub/peakSeq.optimal.wgEncodeSydhTfbsHepg2Hnf4aForsklnStdAlnRep0_vs_wgEncodeSydhTfbsHepg2InputForsklnStdAlnRep0.bb HepG2 ChipSeq HNF4A Peaks bigBed Stanford analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/peakSeq/optimal/hub/peakSeq.optimal.wgEncodeSydhTfbsHepg2Hsf1ForsklnStdAlnRep0_vs_wgEncodeSydhTfbsHepg2InputForsklnStdAlnRep0.bb HepG2 ChipSeq HSF1 Peaks bigBed Stanford analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/peakSeq/optimal/hub/peakSeq.optimal.wgEncodeSydhTfbsHepg2Irf3IggrabAlnRep0_vs_wgEncodeSydhTfbsHepg2InputIggrabAlnRep1.bb HepG2 ChipSeq IRF3 Peaks bigBed Stanford analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/peakSeq/optimal/hub/peakSeq.optimal.wgEncodeSydhTfbsHepg2JundIggrabAlnRep0_vs_wgEncodeSydhTfbsHepg2InputIggrabAlnRep1.bb HepG2 ChipSeq JunD Peaks bigBed Stanford analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/peakSeq/optimal/hub/peakSeq.optimal.wgEncodeSydhTfbsHepg2Maffm8194IggrabAlnRep0_vs_wgEncodeSydhTfbsHepg2InputIggrabAlnRep1.bb HepG2 ChipSeq MafF_(M8194) Peaks bigBed Stanford analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/peakSeq/optimal/hub/peakSeq.optimal.wgEncodeSydhTfbsHepg2Mafkab50322IggrabAlnRep0_vs_wgEncodeSydhTfbsHepg2InputIggrabAlnRep1.bb HepG2 ChipSeq MafK_(ab50322) Peaks bigBed Stanford analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/peakSeq/optimal/hub/peakSeq.optimal.wgEncodeSydhTfbsHepg2Mafksc477IggrabAlnRep0_vs_wgEncodeSydhTfbsHepg2InputIggrabAlnRep1.bb HepG2 ChipSeq MafK_(SC-477) Peaks bigBed Stanford analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/peakSeq/optimal/hub/peakSeq.optimal.wgEncodeSydhTfbsHepg2Nrf1IggrabAlnRep0_vs_wgEncodeSydhTfbsHepg2InputIggrabAlnRep1.bb HepG2 ChipSeq Nrf1 Peaks bigBed Stanford analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/peakSeq/optimal/hub/peakSeq.optimal.wgEncodeSydhTfbsHepg2Pgc1aForsklnStdAlnRep0_vs_wgEncodeSydhTfbsHepg2InputForsklnStdAlnRep0.bb HepG2 ChipSeq PGC1A Peaks bigBed Stanford analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/peakSeq/optimal/hub/peakSeq.optimal.wgEncodeSydhTfbsHepg2Pol2ForsklnStdAlnRep0_vs_wgEncodeSydhTfbsHepg2InputForsklnStdAlnRep0.bb HepG2 ChipSeq Pol2 Peaks bigBed Stanford analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/peakSeq/optimal/hub/peakSeq.optimal.wgEncodeSydhTfbsHepg2Pol2IggrabAlnRep0_vs_wgEncodeSydhTfbsHepg2InputIggrabAlnRep1.bb HepG2 ChipSeq Pol2 Peaks bigBed Stanford analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/peakSeq/optimal/hub/peakSeq.optimal.wgEncodeSydhTfbsHepg2Pol2PravastStdAlnRep0_vs_wgEncodeSydhTfbsHepg2InputPravastStdAlnRep0.bb HepG2 ChipSeq Pol2 Peaks bigBed Stanford analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/peakSeq/optimal/hub/peakSeq.optimal.wgEncodeSydhTfbsHepg2Rad21IggrabAlnRep0_vs_wgEncodeSydhTfbsHepg2InputIggrabAlnRep1.bb HepG2 ChipSeq Rad21 Peaks bigBed Stanford analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/peakSeq/optimal/hub/peakSeq.optimal.wgEncodeSydhTfbsHepg2Rfx5n494IggrabAlnRep0_vs_wgEncodeSydhTfbsHepg2InputIggrabAlnRep1.bb HepG2 ChipSeq RFX5_(N-494) Peaks bigBed Stanford analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/peakSeq/optimal/hub/peakSeq.optimal.wgEncodeSydhTfbsHepg2Srebp1InslnStdAlnRep0_vs_wgEncodeSydhTfbsHepg2InputInslnStdAlnRep0.bb HepG2 ChipSeq SREBP1 Peaks bigBed Stanford analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/peakSeq/optimal/hub/peakSeq.optimal.wgEncodeSydhTfbsHepg2Srebp1PravastStdAlnRep0_vs_wgEncodeSydhTfbsHepg2InputPravastStdAlnRep0.bb HepG2 ChipSeq SREBP1 Peaks bigBed Stanford analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/peakSeq/optimal/hub/peakSeq.optimal.wgEncodeSydhTfbsHepg2Srebp2PravastStdAlnRep0_vs_wgEncodeSydhTfbsHepg2InputPravastStdAlnRep0.bb HepG2 ChipSeq SREBP2 Peaks bigBed Stanford analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/peakSeq/optimal/hub/peakSeq.optimal.wgEncodeSydhTfbsHepg2TbpIggrabAlnRep0_vs_wgEncodeSydhTfbsHepg2InputIggrabAlnRep1.bb HepG2 ChipSeq TBP Peaks bigBed Stanford analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/peakSeq/optimal/hub/peakSeq.optimal.wgEncodeSydhTfbsHepg2Tcf4UcdAlnRep0_vs_wgEncodeSydhTfbsHepg2bInputUcdAlnRep1.bb HepG2b ChipSeq TCF4 Peaks bigBed UCD analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/peakSeq/optimal/hub/peakSeq.optimal.wgEncodeSydhTfbsHepg2Usf2IggrabAlnRep0_vs_wgEncodeSydhTfbsHepg2InputIggrabAlnRep1.bb HepG2 ChipSeq USF2 Peaks bigBed Stanford analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/peakSeq/optimal/hub/peakSeq.optimal.wgEncodeSydhTfbsHuvecCfosUcdAlnRep0_vs_wgEncodeSydhTfbsHuvecInputUcdAlnRep1.bb HUVEC ChipSeq c-Fos Peaks bigBed UCD analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/peakSeq/optimal/hub/peakSeq.optimal.wgEncodeSydhTfbsHuvecCjunStdAlnRep0_vs_wgEncodeSydhTfbsHuvecInputStdAlnRep0.bb HUVEC ChipSeq c-Jun Peaks bigBed Stanford analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/peakSeq/optimal/hub/peakSeq.optimal.wgEncodeSydhTfbsHuvecGata2UcdAlnRep0_vs_wgEncodeSydhTfbsHuvecInputUcdAlnRep1.bb HUVEC ChipSeq GATA-2 Peaks bigBed UCD analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/peakSeq/optimal/hub/peakSeq.optimal.wgEncodeSydhTfbsHuvecMaxStdAlnRep0_vs_wgEncodeSydhTfbsHuvecInputStdAlnRep0.bb HUVEC ChipSeq Max Peaks bigBed Stanford analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/peakSeq/optimal/hub/peakSeq.optimal.wgEncodeSydhTfbsHuvecPol2StdAlnRep0_vs_wgEncodeSydhTfbsHuvecInputStdAlnRep0.bb HUVEC ChipSeq Pol2 Peaks bigBed Stanford analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/peakSeq/optimal/hub/peakSeq.optimal.wgEncodeSydhTfbsK562Atf3StdAlnRep0_vs_wgEncodeSydhTfbsK562InputStdAlnRep0.bb K562 ChipSeq ATF3 Peaks bigBed Stanford analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/peakSeq/optimal/hub/peakSeq.optimal.wgEncodeSydhTfbsK562Bdp1StdAlnRep0_vs_wgEncodeSydhTfbsK562InputStdAlnRep0.bb K562 ChipSeq BDP1 Peaks bigBed Stanford analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/peakSeq/optimal/hub/peakSeq.optimal.wgEncodeSydhTfbsK562bE2f4UcdAlnRep0_vs_wgEncodeSydhTfbsK562bInputUcdAlnRep1.bb K562b ChipSeq E2F4 Peaks bigBed Stanford analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/peakSeq/optimal/hub/peakSeq.optimal.wgEncodeSydhTfbsK562bE2f6UcdAlnRep0_vs_wgEncodeSydhTfbsK562bInputUcdAlnRep1.bb K562b ChipSeq E2F6 Peaks bigBed Stanford analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/peakSeq/optimal/hub/peakSeq.optimal.wgEncodeSydhTfbsK562bGata1UcdAlnRep0_vs_wgEncodeSydhTfbsK562bInputUcdAlnRep1.bb K562b ChipSeq GATA-1 Peaks bigBed Stanford analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/peakSeq/optimal/hub/peakSeq.optimal.wgEncodeSydhTfbsK562bGata2UcdAlnRep0_vs_wgEncodeSydhTfbsK562bInputUcdAlnRep1.bb K562b ChipSeq GATA-2 Peaks bigBed Stanford analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/peakSeq/optimal/hub/peakSeq.optimal.wgEncodeSydhTfbsK562bKap1UcdAlnRep0_vs_wgEncodeSydhTfbsK562bInputUcdAlnRep1.bb K562b ChipSeq KAP1 Peaks bigBed UCD analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/peakSeq/optimal/hub/peakSeq.optimal.wgEncodeSydhTfbsK562Brf1StdAlnRep0_vs_wgEncodeSydhTfbsK562InputStdAlnRep0.bb K562 ChipSeq BRF1 Peaks bigBed Stanford analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/peakSeq/optimal/hub/peakSeq.optimal.wgEncodeSydhTfbsK562Brf2StdAlnRep0_vs_wgEncodeSydhTfbsK562InputStdAlnRep0.bb K562 ChipSeq BRF2 Peaks bigBed Stanford analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/peakSeq/optimal/hub/peakSeq.optimal.wgEncodeSydhTfbsK562Brg1IggmusAlnRep0_vs_wgEncodeSydhTfbsK562InputIggmusAlnRep0.bb K562 ChipSeq Brg1 Peaks bigBed Stanford analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/peakSeq/optimal/hub/peakSeq.optimal.wgEncodeSydhTfbsK562bSetdb1MnasedUcdAlnRep0_vs_wgEncodeSydhTfbsK562bInputUcdAlnRep1.bb K562b ChipSeq SETDB1 Peaks bigBed Stanford analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/peakSeq/optimal/hub/peakSeq.optimal.wgEncodeSydhTfbsK562bSetdb1UcdAlnRep0_vs_wgEncodeSydhTfbsK562bInputUcdAlnRep1.bb K562b ChipSeq SETDB1 Peaks bigBed Stanford analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/peakSeq/optimal/hub/peakSeq.optimal.wgEncodeSydhTfbsK562bTr4UcdAlnRep0_vs_wgEncodeSydhTfbsK562bInputUcdAlnRep1.bb K562b ChipSeq TR4 Peaks bigBed Stanford analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/peakSeq/optimal/hub/peakSeq.optimal.wgEncodeSydhTfbsK562bYy1UcdAlnRep0_vs_wgEncodeSydhTfbsK562bInputUcdAlnRep1.bb K562b ChipSeq YY1 Peaks bigBed Stanford analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/peakSeq/optimal/hub/peakSeq.optimal.wgEncodeSydhTfbsK562bZnf263UcdAlnRep0_vs_wgEncodeSydhTfbsK562bInputUcdAlnRep1.bb K562b ChipSeq ZNF263 Peaks bigBed Stanford analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/peakSeq/optimal/hub/peakSeq.optimal.wgEncodeSydhTfbsK562bZnf274UcdAlnRep0_vs_wgEncodeSydhTfbsK562bInputUcdAlnRep1.bb K562b ChipSeq ZNF274 Peaks bigBed Stanford analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/peakSeq/optimal/hub/peakSeq.optimal.wgEncodeSydhTfbsK562Ccnt2StdAlnRep0_vs_wgEncodeSydhTfbsK562InputStdAlnRep0.bb K562 ChipSeq CCNT2 Peaks bigBed Harvard analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/peakSeq/optimal/hub/peakSeq.optimal.wgEncodeSydhTfbsK562CebpbIggrabAlnRep0_vs_wgEncodeSydhTfbsK562InputIggrabAlnRep1.bb K562 ChipSeq CEBPB Peaks bigBed Stanford analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/peakSeq/optimal/hub/peakSeq.optimal.wgEncodeSydhTfbsK562CfosStdAlnRep0_vs_wgEncodeSydhTfbsK562InputStdAlnRep0.bb K562 ChipSeq c-Fos Peaks bigBed Stanford analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/peakSeq/optimal/hub/peakSeq.optimal.wgEncodeSydhTfbsK562Chd21250IggrabAlnRep0_vs_wgEncodeSydhTfbsK562InputIggrabAlnRep1.bb K562 ChipSeq CHD2_(N-1250) Peaks bigBed Stanford analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/peakSeq/optimal/hub/peakSeq.optimal.wgEncodeSydhTfbsK562CjunIfna6hStdAlnRep0_vs_wgEncodeSydhTfbsK562InputIfna6hStdAlnRep1.bb K562 ChipSeq c-Jun Peaks bigBed Stanford analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/peakSeq/optimal/hub/peakSeq.optimal.wgEncodeSydhTfbsK562CjunIfng30StdAlnRep0_vs_wgEncodeSydhTfbsK562InputIfng30StdAlnRep1.bb K562 ChipSeq c-Jun Peaks bigBed Stanford analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/peakSeq/optimal/hub/peakSeq.optimal.wgEncodeSydhTfbsK562CjunIfng6hStdAlnRep0_vs_wgEncodeSydhTfbsK562InputIfng6hStdAlnRep1.bb K562 ChipSeq c-Jun Peaks bigBed Stanford analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/peakSeq/optimal/hub/peakSeq.optimal.wgEncodeSydhTfbsK562CjunStdAlnRep0_vs_wgEncodeSydhTfbsK562InputStdAlnRep0.bb K562 ChipSeq c-Jun Peaks bigBed Stanford analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/peakSeq/optimal/hub/peakSeq.optimal.wgEncodeSydhTfbsK562CmycIfna30StdAlnRep0_vs_wgEncodeSydhTfbsK562InputIfna30StdAlnRep1.bb K562 ChipSeq c-Myc Peaks bigBed Stanford analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/peakSeq/optimal/hub/peakSeq.optimal.wgEncodeSydhTfbsK562CmycIfna6hStdAlnRep0_vs_wgEncodeSydhTfbsK562InputIfna6hStdAlnRep1.bb K562 ChipSeq c-Myc Peaks bigBed Stanford analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/peakSeq/optimal/hub/peakSeq.optimal.wgEncodeSydhTfbsK562CmycIfng30StdAlnRep0_vs_wgEncodeSydhTfbsK562InputIfng30StdAlnRep1.bb K562 ChipSeq c-Myc Peaks bigBed Stanford analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/peakSeq/optimal/hub/peakSeq.optimal.wgEncodeSydhTfbsK562CmycIfng6hStdAlnRep0_vs_wgEncodeSydhTfbsK562InputIfng6hStdAlnRep1.bb K562 ChipSeq c-Myc Peaks bigBed Stanford analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/peakSeq/optimal/hub/peakSeq.optimal.wgEncodeSydhTfbsK562CmycStdAlnRep0_vs_wgEncodeSydhTfbsK562InputStdAlnRep0.bb K562 ChipSeq c-Myc Peaks bigBed Stanford analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/peakSeq/optimal/hub/peakSeq.optimal.wgEncodeSydhTfbsK562Gtf2bStdAlnRep0_vs_wgEncodeSydhTfbsK562InputStdAlnRep0.bb K562 ChipSeq GTF2B Peaks bigBed Harvard analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/peakSeq/optimal/hub/peakSeq.optimal.wgEncodeSydhTfbsK562Gtf2f1rapIggrabAlnRep0_vs_wgEncodeSydhTfbsK562InputIggrabAlnRep1.bb K562 ChipSeq GTF2F1_(RAP-74) Peaks bigBed Stanford analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/peakSeq/optimal/hub/peakSeq.optimal.wgEncodeSydhTfbsK562Hmgn3StdAlnRep0_vs_wgEncodeSydhTfbsK562InputStdAlnRep0.bb K562 ChipSeq HMGN3 Peaks bigBed Harvard analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/peakSeq/optimal/hub/peakSeq.optimal.wgEncodeSydhTfbsK562Ini1IggmusAlnRep0_vs_wgEncodeSydhTfbsK562InputIggmusAlnRep0.bb K562 ChipSeq Ini1 Peaks bigBed Stanford analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/peakSeq/optimal/hub/peakSeq.optimal.wgEncodeSydhTfbsK562Irf1Ifna30StdAlnRep0_vs_wgEncodeSydhTfbsK562InputIfna30StdAlnRep1.bb K562 ChipSeq IRF1 Peaks bigBed Stanford analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/peakSeq/optimal/hub/peakSeq.optimal.wgEncodeSydhTfbsK562Irf1Ifng6hStdAlnRep0_vs_wgEncodeSydhTfbsK562InputIfng6hStdAlnRep1.bb K562 ChipSeq IRF1 Peaks bigBed Stanford analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/peakSeq/optimal/hub/peakSeq.optimal.wgEncodeSydhTfbsK562JundStdAlnRep0_vs_wgEncodeSydhTfbsK562InputStdAlnRep0.bb K562 ChipSeq JunD Peaks bigBed Stanford analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/peakSeq/optimal/hub/peakSeq.optimal.wgEncodeSydhTfbsK562Mafkab50322IggrabAlnRep0_vs_wgEncodeSydhTfbsK562InputIggrabAlnRep1.bb K562 ChipSeq MafK_(ab50322) Peaks bigBed Stanford analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/peakSeq/optimal/hub/peakSeq.optimal.wgEncodeSydhTfbsK562MaxStdAlnRep0_vs_wgEncodeSydhTfbsK562InputStdAlnRep0.bb K562 ChipSeq Max Peaks bigBed Stanford analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/peakSeq/optimal/hub/peakSeq.optimal.wgEncodeSydhTfbsK562Mxi1bhlhIggrabAlnRep0_vs_wgEncodeSydhTfbsK562InputIggrabAlnRep1.bb K562 ChipSeq Mxi1_(bHLH) Peaks bigBed Stanford analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/peakSeq/optimal/hub/peakSeq.optimal.wgEncodeSydhTfbsK562NelfeStdAlnRep0_vs_wgEncodeSydhTfbsK562InputStdAlnRep0.bb K562 ChipSeq NELFe Peaks bigBed Stanford analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/peakSeq/optimal/hub/peakSeq.optimal.wgEncodeSydhTfbsK562Nfe2StdAlnRep0_vs_wgEncodeSydhTfbsK562InputStdAlnRep0.bb K562 ChipSeq NF-E2 Peaks bigBed Stanford analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/peakSeq/optimal/hub/peakSeq.optimal.wgEncodeSydhTfbsK562NfyaStdAlnRep0_vs_wgEncodeSydhTfbsK562InputStdAlnRep0.bb K562 ChipSeq NF-YA Peaks bigBed Stanford analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/peakSeq/optimal/hub/peakSeq.optimal.wgEncodeSydhTfbsK562NfybStdAlnRep0_vs_wgEncodeSydhTfbsK562InputStdAlnRep0.bb K562 ChipSeq NF-YB Peaks bigBed Stanford analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/peakSeq/optimal/hub/peakSeq.optimal.wgEncodeSydhTfbsK562Nrf1IggrabAlnRep0_vs_wgEncodeSydhTfbsK562InputIggrabAlnRep1.bb K562 ChipSeq Nrf1 Peaks bigBed Stanford analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/peakSeq/optimal/hub/peakSeq.optimal.wgEncodeSydhTfbsK562P300f4IggrabAlnRep0_vs_wgEncodeSydhTfbsK562InputIggrabAlnRep1.bb K562 ChipSeq p300_(F-4) Peaks bigBed Stanford analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/peakSeq/optimal/hub/peakSeq.optimal.wgEncodeSydhTfbsK562Pol2Ifna30StdAlnRep0_vs_wgEncodeSydhTfbsK562InputIfna30StdAlnRep1.bb K562 ChipSeq Pol2 Peaks bigBed Stanford analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/peakSeq/optimal/hub/peakSeq.optimal.wgEncodeSydhTfbsK562Pol2Ifna6hStdAlnRep0_vs_wgEncodeSydhTfbsK562InputIfna6hStdAlnRep1.bb K562 ChipSeq Pol2 Peaks bigBed Stanford analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/peakSeq/optimal/hub/peakSeq.optimal.wgEncodeSydhTfbsK562Pol2Ifng30StdAlnRep0_vs_wgEncodeSydhTfbsK562InputIfng30StdAlnRep1.bb K562 ChipSeq Pol2 Peaks bigBed Stanford analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/peakSeq/optimal/hub/peakSeq.optimal.wgEncodeSydhTfbsK562Pol2Ifng6hStdAlnRep0_vs_wgEncodeSydhTfbsK562InputIfng6hStdAlnRep1.bb K562 ChipSeq Pol2 Peaks bigBed Stanford analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/peakSeq/optimal/hub/peakSeq.optimal.wgEncodeSydhTfbsK562Pol2IggmusAlnRep0_vs_wgEncodeSydhTfbsK562InputIggmusAlnRep0.bb K562 ChipSeq Pol2 Peaks bigBed Stanford analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/peakSeq/optimal/hub/peakSeq.optimal.wgEncodeSydhTfbsK562Pol2s2StdAlnRep0_vs_wgEncodeSydhTfbsK562InputStdAlnRep0.bb K562 ChipSeq Pol2(phosphoS2) Peaks bigBed Stanford analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/peakSeq/optimal/hub/peakSeq.optimal.wgEncodeSydhTfbsK562Pol2StdAlnRep0_vs_wgEncodeSydhTfbsK562InputStdAlnRep0.bb K562 ChipSeq Pol2 Peaks bigBed Stanford analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/peakSeq/optimal/hub/peakSeq.optimal.wgEncodeSydhTfbsK562Pol3StdAlnRep0_vs_wgEncodeSydhTfbsK562InputStdAlnRep0.bb K562 ChipSeq Pol3 Peaks bigBed Stanford analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/peakSeq/optimal/hub/peakSeq.optimal.wgEncodeSydhTfbsK562Rad21StdAlnRep0_vs_wgEncodeSydhTfbsK562InputStdAlnRep0.bb K562 ChipSeq Rad21 Peaks bigBed Stanford analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/peakSeq/optimal/hub/peakSeq.optimal.wgEncodeSydhTfbsK562Rpc155StdAlnRep0_vs_wgEncodeSydhTfbsK562InputStdAlnRep0.bb K562 ChipSeq RPC155 Peaks bigBed Stanford analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/peakSeq/optimal/hub/peakSeq.optimal.wgEncodeSydhTfbsK562Sirt6StdAlnRep0_vs_wgEncodeSydhTfbsK562InputStdAlnRep0.bb K562 ChipSeq SIRT6 Peaks bigBed Stanford analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/peakSeq/optimal/hub/peakSeq.optimal.wgEncodeSydhTfbsK562Smc3ab9263IggrabAlnRep0_vs_wgEncodeSydhTfbsK562InputIggrabAlnRep1.bb K562 ChipSeq SMC3_(ab9263) Peaks bigBed Stanford analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/peakSeq/optimal/hub/peakSeq.optimal.wgEncodeSydhTfbsK562Stat1Ifna30StdAlnRep0_vs_wgEncodeSydhTfbsK562InputIfna30StdAlnRep1.bb K562 ChipSeq STAT1 Peaks bigBed Stanford analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/peakSeq/optimal/hub/peakSeq.optimal.wgEncodeSydhTfbsK562Stat1Ifna6hStdAlnRep0_vs_wgEncodeSydhTfbsK562InputIfna6hStdAlnRep1.bb K562 ChipSeq STAT1 Peaks bigBed Stanford analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/peakSeq/optimal/hub/peakSeq.optimal.wgEncodeSydhTfbsK562Stat1Ifng30StdAlnRep0_vs_wgEncodeSydhTfbsK562InputIfng30StdAlnRep1.bb K562 ChipSeq STAT1 Peaks bigBed Stanford analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/peakSeq/optimal/hub/peakSeq.optimal.wgEncodeSydhTfbsK562Stat1Ifng6hStdAlnRep0_vs_wgEncodeSydhTfbsK562InputIfng6hStdAlnRep1.bb K562 ChipSeq STAT1 Peaks bigBed Stanford analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/peakSeq/optimal/hub/peakSeq.optimal.wgEncodeSydhTfbsK562Stat2Ifna30StdAlnRep0_vs_wgEncodeSydhTfbsK562InputIfna30StdAlnRep1.bb K562 ChipSeq STAT2 Peaks bigBed Stanford analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/peakSeq/optimal/hub/peakSeq.optimal.wgEncodeSydhTfbsK562Stat2Ifna6hStdAlnRep0_vs_wgEncodeSydhTfbsK562InputIfna6hStdAlnRep1.bb K562 ChipSeq STAT2 Peaks bigBed Stanford analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/peakSeq/optimal/hub/peakSeq.optimal.wgEncodeSydhTfbsK562Tal1sc12984IggmusAlnRep0_vs_wgEncodeSydhTfbsK562InputIggmusAlnRep0.bb K562 ChipSeq TAL1_(SC-12984) Peaks bigBed Stanford analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/peakSeq/optimal/hub/peakSeq.optimal.wgEncodeSydhTfbsK562TbpIggmusAlnRep0_vs_wgEncodeSydhTfbsK562InputIggmusAlnRep0.bb K562 ChipSeq TBP Peaks bigBed Stanford analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/peakSeq/optimal/hub/peakSeq.optimal.wgEncodeSydhTfbsK562Tf3c110StdAlnRep0_vs_wgEncodeSydhTfbsK562InputStdAlnRep0.bb K562 ChipSeq TFIIIC-110 Peaks bigBed Stanford analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/peakSeq/optimal/hub/peakSeq.optimal.wgEncodeSydhTfbsK562Usf2StdAlnRep0_vs_wgEncodeSydhTfbsK562InputStdAlnRep0.bb K562 ChipSeq USF2 Peaks bigBed Stanford analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/peakSeq/optimal/hub/peakSeq.optimal.wgEncodeSydhTfbsK562Xrcc4StdAlnRep0_vs_wgEncodeSydhTfbsK562InputStdAlnRep0.bb K562 ChipSeq XRCC4 Peaks bigBed Stanford analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/peakSeq/optimal/hub/peakSeq.optimal.wgEncodeSydhTfbsMcf10aesPol2Etoh01StdAlnRep0_vs_wgEncodeSydhTfbsMcf10aesInputUcdAlnRep1.bb MCF10A-Er-Src ChipSeq Pol2 Peaks bigBed Stanford analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/peakSeq/optimal/hub/peakSeq.optimal.wgEncodeSydhTfbsMcf10aesPol2TamStdAlnRep0_vs_wgEncodeSydhTfbsMcf10aesInputUcdAlnRep1.bb MCF10A-Er-Src ChipSeq Pol2 Peaks bigBed Harvard(Weissman) analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/peakSeq/optimal/hub/peakSeq.optimal.wgEncodeSydhTfbsMcf10aesStat3Etoh01bStdAlnRep0_vs_wgEncodeSydhTfbsMcf10aesInputEtoh01bStdAlnRep1.bb MCF10A-Er-Src ChipSeq STAT3 Peaks bigBed Harvard(Weissman) analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/peakSeq/optimal/hub/peakSeq.optimal.wgEncodeSydhTfbsMcf10aesStat3Etoh01cStdAlnRep0_vs_wgEncodeSydhTfbsMcf10aesInputEtoh01cStdAlnRep1.bb MCF10A-Er-Src ChipSeq STAT3 Peaks bigBed Stanford analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/peakSeq/optimal/hub/peakSeq.optimal.wgEncodeSydhTfbsMcf10aesStat3Etoh01StdAlnRep0_vs_wgEncodeSydhTfbsMcf10aesInputUcdAlnRep1.bb MCF10A-Er-Src ChipSeq STAT3 Peaks bigBed Harvard(Weissman) analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/peakSeq/optimal/hub/peakSeq.optimal.wgEncodeSydhTfbsMcf10aesStat3TamStdAlnRep0_vs_wgEncodeSydhTfbsMcf10aesInputUcdAlnRep1.bb MCF10A-Er-Src ChipSeq STAT3 Peaks bigBed Harvard(Weissman) analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/peakSeq/optimal/hub/peakSeq.optimal.wgEncodeSydhTfbsMcf7Hae2f1UcdAlnRep0_vs_wgEncodeSydhTfbsMcf7InputUcdAlnRep0.bb MCF-7 ChipSeq HA-E2F1 Peaks bigBed Stanford analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/peakSeq/optimal/hub/peakSeq.optimal.wgEncodeSydhTfbsNb4CmycStdAlnRep0_vs_wgEncodeSydhTfbsNb4InputStdAlnRep1.bb NB4 ChipSeq c-Myc Peaks bigBed Stanford analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/peakSeq/optimal/hub/peakSeq.optimal.wgEncodeSydhTfbsNb4MaxStdAlnRep0_vs_wgEncodeSydhTfbsNb4InputStdAlnRep1.bb NB4 ChipSeq Max Peaks bigBed Stanford analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/peakSeq/optimal/hub/peakSeq.optimal.wgEncodeSydhTfbsNb4Pol2StdAlnRep0_vs_wgEncodeSydhTfbsNb4InputStdAlnRep1.bb NB4 ChipSeq Pol2 Peaks bigBed Stanford analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/peakSeq/optimal/hub/peakSeq.optimal.wgEncodeSydhTfbsNt2d1Suz12UcdAlnRep0_vs_wgEncodeSydhTfbsNt2d1InputUcdAlnRep1.bb NT2-D1 ChipSeq SUZ12 Peaks bigBed Stanford analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/peakSeq/optimal/hub/peakSeq.optimal.wgEncodeSydhTfbsNt2d1Yy1UcdAlnRep0_vs_wgEncodeSydhTfbsNt2d1InputUcdAlnRep1.bb NT2-D1 ChipSeq YY1 Peaks bigBed Stanford analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/peakSeq/optimal/hub/peakSeq.optimal.wgEncodeSydhTfbsNt2d1Znf274UcdAlnRep0_vs_wgEncodeSydhTfbsNt2d1InputUcdAlnRep1.bb NT2-D1 ChipSeq ZNF274 Peaks bigBed UCD analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/peakSeq/optimal/hub/peakSeq.optimal.wgEncodeSydhTfbsPbdeGata1UcdAlnRep0_vs_wgEncodeSydhTfbsPbdeInputUcdAlnRep1.bb PBDE ChipSeq GATA-1 Peaks bigBed UCD analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/peakSeq/optimal/hub/peakSeq.optimal.wgEncodeSydhTfbsPbdePol2UcdAlnRep0_vs_wgEncodeSydhTfbsPbdeInputUcdAlnRep1.bb PBDE ChipSeq Pol2 Peaks bigBed UCD analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/peakSeq/optimal/hub/peakSeq.optimal.wgEncodeSydhTfbsRajiPol2UcdAlnRep0_vs_wgEncodeSydhTfbsRajiInputUcdAlnRep1.bb Raji ChipSeq Pol2 Peaks bigBed UCD analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/peakSeq/optimal/hub/peakSeq.optimal.wgEncodeSydhTfbsShsy5yGata2UcdAlnRep0_vs_wgEncodeSydhTfbsShsy5yInputUcdAlnRep1.bb SH-SY5Y ChipSeq GATA-2 Peaks bigBed UCD analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/peakSeq/optimal/hub/peakSeq.optimal.wgEncodeSydhTfbsTrexhek293Znf263UcdAlnRep0_vs_wgEncodeSydhTfbsThek293InputUcdAlnRep1.bb T-REx-HEK293 ChipSeq ZNF263 Peaks bigBed UCD analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/peakSeq/optimal/hub/peakSeq.optimal.wgEncodeSydhTfbsU2osKap1UcdAlnRep0_vs_wgEncodeSydhTfbsU2osInputUcdAlnRep1.bb U2OS ChipSeq KAP1 Peaks bigBed Stanford analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/peakSeq/optimal/hub/peakSeq.optimal.wgEncodeSydhTfbsU2osSetdb1UcdAlnRep0_vs_wgEncodeSydhTfbsU2osInputUcdAlnRep1.bb U2OS ChipSeq SETDB1 Peaks bigBed UCD analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/peakSeq/optimal/hub/peakSeq.optimal.wgEncodeUchicagoTfbsK562EfosControlAlnRep0_vs_wgEncodeUchicagoTfbsK562InputControlAlnRep0.bb K562 ChipSeq eGFP-FOS Peaks bigBed UChicago analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/peakSeq/optimal/hub/peakSeq.optimal.wgEncodeUchicagoTfbsK562Egata2ControlAlnRep0_vs_wgEncodeUchicagoTfbsK562InputControlAlnRep0.bb K562 ChipSeq eGFP-GATA2 Peaks bigBed UChicago analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/peakSeq/optimal/hub/peakSeq.optimal.wgEncodeUchicagoTfbsK562Ehdac8ControlAlnRep0_vs_wgEncodeUchicagoTfbsK562InputControlAlnRep0.bb K562 ChipSeq eGFP-HDAC8 Peaks bigBed UChicago analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/peakSeq/optimal/hub/peakSeq.optimal.wgEncodeUchicagoTfbsK562EjunbControlAlnRep0_vs_wgEncodeUchicagoTfbsK562InputControlAlnRep0.bb K562 ChipSeq eGFP-JunB Peaks bigBed UChicago analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/peakSeq/optimal/hub/peakSeq.optimal.wgEncodeUchicagoTfbsK562EjundControlAlnRep0_vs_wgEncodeUchicagoTfbsK562InputControlAlnRep0.bb K562 ChipSeq eGFP-JunD Peaks bigBed UChicago analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/peakSeq/optimal/hub/peakSeq.optimal.wgEncodeUchicagoTfbsK562Enr4a1ControlAlnRep0_vs_wgEncodeUchicagoTfbsK562InputControlAlnRep0.bb K562 ChipSeq eGFP-NR4A1 Peaks bigBed UChicago analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/peakSeq/optimal/hub/peakSeq.optimal.wgEncodeUwTfbsAg04449CtcfStdAlnRep0_vs_wgEncodeUwTfbsAg04449InputStdAlnRep1.bb AG04449 ChipSeq CTCF Peaks bigBed UW analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/peakSeq/optimal/hub/peakSeq.optimal.wgEncodeUwTfbsAg04450CtcfStdAlnRep1_vs_wgEncodeUwTfbsAg04450InputStdAlnRep1.bb AG04450 ChipSeq CTCF Peaks bigBed UW analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/peakSeq/optimal/hub/peakSeq.optimal.wgEncodeUwTfbsAg09309CtcfStdAlnRep0_vs_wgEncodeUwTfbsAg09309InputStdAlnRep1.bb AG09309 ChipSeq CTCF Peaks bigBed UW analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/peakSeq/optimal/hub/peakSeq.optimal.wgEncodeUwTfbsAg09319CtcfStdAlnRep0_vs_wgEncodeUwTfbsAg09319InputStdAlnRep1.bb AG09319 ChipSeq CTCF Peaks bigBed UW analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/peakSeq/optimal/hub/peakSeq.optimal.wgEncodeUwTfbsAg10803CtcfStdAlnRep0_vs_wgEncodeUwTfbsAg10803InputStdAlnRep1.bb AG10803 ChipSeq CTCF Peaks bigBed UW analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/peakSeq/optimal/hub/peakSeq.optimal.wgEncodeUwTfbsAoafCtcfStdAlnRep0_vs_wgEncodeUwTfbsAoafInputStdAlnRep1.bb AoAF ChipSeq CTCF Peaks bigBed UW analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/peakSeq/optimal/hub/peakSeq.optimal.wgEncodeUwTfbsBjCtcfStdAlnRep0_vs_wgEncodeUwTfbsBjInputStdAlnRep1.bb BJ ChipSeq CTCF Peaks bigBed UW analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/peakSeq/optimal/hub/peakSeq.optimal.wgEncodeUwTfbsCaco2CtcfStdAlnRep0_vs_wgEncodeUwTfbsCaco2InputStdAlnRep1.bb Caco-2 ChipSeq CTCF Peaks bigBed UW analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/peakSeq/optimal/hub/peakSeq.optimal.wgEncodeUwTfbsGm06990CtcfStdAlnRep0_vs_wgEncodeUwTfbsGm06990InputStdAlnRep1.bb GM06990 ChipSeq CTCF Peaks bigBed UW analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/peakSeq/optimal/hub/peakSeq.optimal.wgEncodeUwTfbsGm12801CtcfStdAlnRep1_vs_wgEncodeUwTfbsGm12801InputStdAlnRep1.bb GM12801 ChipSeq CTCF Peaks bigBed UW analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/peakSeq/optimal/hub/peakSeq.optimal.wgEncodeUwTfbsGm12864CtcfStdAlnRep0_vs_wgEncodeUwTfbsGm12864InputStdAlnRep1.bb GM12864 ChipSeq CTCF Peaks bigBed UW analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/peakSeq/optimal/hub/peakSeq.optimal.wgEncodeUwTfbsGm12865CtcfStdAlnRep0_vs_wgEncodeUwTfbsGm12865InputStdAlnRep1.bb GM12865 ChipSeq CTCF Peaks bigBed UW analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/peakSeq/optimal/hub/peakSeq.optimal.wgEncodeUwTfbsGm12872CtcfStdAlnRep0_vs_wgEncodeUwTfbsGm12872InputStdAlnRep1.bb GM12872 ChipSeq CTCF Peaks bigBed UW analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/peakSeq/optimal/hub/peakSeq.optimal.wgEncodeUwTfbsGm12873CtcfStdAlnRep0_vs_wgEncodeUwTfbsGm12873InputStdAlnRep1.bb GM12873 ChipSeq CTCF Peaks bigBed UW analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/peakSeq/optimal/hub/peakSeq.optimal.wgEncodeUwTfbsGm12874CtcfStdAlnRep0_vs_wgEncodeUwTfbsGm12874InputStdAlnRep1.bb GM12874 ChipSeq CTCF Peaks bigBed UW analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/peakSeq/optimal/hub/peakSeq.optimal.wgEncodeUwTfbsGm12875CtcfStdAlnRep0_vs_wgEncodeUwTfbsGm12875InputStdAlnRep1.bb GM12875 ChipSeq CTCF Peaks bigBed UW analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/peakSeq/optimal/hub/peakSeq.optimal.wgEncodeUwTfbsGm12878CtcfStdAlnRep0_vs_wgEncodeUwTfbsGm12878InputStdAlnRep1.bb GM12878 ChipSeq CTCF Peaks bigBed UW analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/peakSeq/optimal/hub/peakSeq.optimal.wgEncodeUwTfbsHaspCtcfStdAlnRep1_vs_wgEncodeUwTfbsHaspInputStdAlnRep1.bb HA-sp ChipSeq CTCF Peaks bigBed UW analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/peakSeq/optimal/hub/peakSeq.optimal.wgEncodeUwTfbsHbmecCtcfStdAlnRep0_vs_wgEncodeUwTfbsHbmecInputStdAlnRep1.bb HBMEC ChipSeq CTCF Peaks bigBed UW analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/peakSeq/optimal/hub/peakSeq.optimal.wgEncodeUwTfbsHcfaaCtcfStdAlnRep1_vs_wgEncodeUwTfbsHcfaaInputStdAlnRep1.bb HCFaa ChipSeq CTCF Peaks bigBed UW analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/peakSeq/optimal/hub/peakSeq.optimal.wgEncodeUwTfbsHcpeCtcfStdAlnRep0_vs_wgEncodeUwTfbsHcpeInputStdAlnRep1.bb HCPEpiC ChipSeq CTCF Peaks bigBed UW analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/peakSeq/optimal/hub/peakSeq.optimal.wgEncodeUwTfbsHeeCtcfStdAlnRep0_vs_wgEncodeUwTfbsHeeInputStdAlnRep1.bb HEEpiC ChipSeq CTCF Peaks bigBed UW analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/peakSeq/optimal/hub/peakSeq.optimal.wgEncodeUwTfbsHek293CtcfStdAlnRep0_vs_wgEncodeUwTfbsHek293InputStdAlnRep1.bb HEK293 ChipSeq CTCF Peaks bigBed UW analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/peakSeq/optimal/hub/peakSeq.optimal.wgEncodeUwTfbsHelas3CtcfStdAlnRep0_vs_wgEncodeUwTfbsHelas3InputStdAlnRep1.bb HeLa-S3 ChipSeq CTCF Peaks bigBed UW analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/peakSeq/optimal/hub/peakSeq.optimal.wgEncodeUwTfbsHepg2CtcfStdAlnRep0_vs_wgEncodeUwTfbsHepg2InputStdAlnRep1.bb HepG2 ChipSeq CTCF Peaks bigBed UW analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/peakSeq/optimal/hub/peakSeq.optimal.wgEncodeUwTfbsHl60CtcfStdAlnRep1_vs_wgEncodeUwTfbsHl60InputStdAlnRep1.bb HL-60 ChipSeq CTCF Peaks bigBed UW analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/peakSeq/optimal/hub/peakSeq.optimal.wgEncodeUwTfbsHmecCtcfStdAlnRep1_vs_wgEncodeUwTfbsHmecInputStdAlnRep1.bb HMEC ChipSeq CTCF Peaks bigBed UW analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/peakSeq/optimal/hub/peakSeq.optimal.wgEncodeUwTfbsHmfCtcfStdAlnRep0_vs_wgEncodeUwTfbsHmfInputStdAlnRep1.bb HMF ChipSeq CTCF Peaks bigBed UW analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/peakSeq/optimal/hub/peakSeq.optimal.wgEncodeUwTfbsHpafCtcfStdAlnRep0_vs_wgEncodeUwTfbsHpafInputStdAlnRep1.bb HPAF ChipSeq CTCF Peaks bigBed UW analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/peakSeq/optimal/hub/peakSeq.optimal.wgEncodeUwTfbsHpfCtcfStdAlnRep0_vs_wgEncodeUwTfbsHpfInputStdAlnRep1.bb HPF ChipSeq CTCF Peaks bigBed UW analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/peakSeq/optimal/hub/peakSeq.optimal.wgEncodeUwTfbsHreCtcfStdAlnRep0_vs_wgEncodeUwTfbsHreInputStdAlnRep1.bb HRE ChipSeq CTCF Peaks bigBed UW analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/peakSeq/optimal/hub/peakSeq.optimal.wgEncodeUwTfbsHrpeCtcfStdAlnRep1_vs_wgEncodeUwTfbsHrpeInputStdAlnRep1.bb HRPEpiC ChipSeq CTCF Peaks bigBed UW analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/peakSeq/optimal/hub/peakSeq.optimal.wgEncodeUwTfbsHuvecCtcfStdAlnRep0_vs_wgEncodeUwTfbsHuvecInputStdAlnRep1.bb HUVEC ChipSeq CTCF Peaks bigBed UW analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/peakSeq/optimal/hub/peakSeq.optimal.wgEncodeUwTfbsK562CtcfStdAlnRep0_vs_wgEncodeUwTfbsK562InputStdAlnRep1.bb K562 ChipSeq CTCF Peaks bigBed UW analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/peakSeq/optimal/hub/peakSeq.optimal.wgEncodeUwTfbsNhekCtcfStdAlnRep0_vs_wgEncodeUwTfbsNhekInputStdAlnRep1.bb NHEK ChipSeq CTCF Peaks bigBed UW analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/peakSeq/optimal/hub/peakSeq.optimal.wgEncodeUwTfbsSaecCtcfStdAlnRep0_vs_wgEncodeUwTfbsSaecInputStdAlnRep1.bb SAEC ChipSeq CTCF Peaks bigBed UW analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/peakSeq/optimal/hub/peakSeq.optimal.wgEncodeUwTfbsSknshraCtcfStdAlnRep0_vs_wgEncodeUwTfbsSknshraInputStdAlnRep1.bb SK-N-SH_RA ChipSeq CTCF Peaks bigBed UW analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/peakSeq/optimal/hub/peakSeq.optimal.wgEncodeUwTfbsWerirb1CtcfStdAlnRep0_vs_wgEncodeUwTfbsWerirb1InputStdAlnRep1.bb WERI-Rb-1 ChipSeq CTCF Peaks bigBed UW analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/rna_elements/jan2011/LongRnaSeq/A549_WholeCell_Am_Long_CSHL_Contig.CSHL_LID9005-021WC-b1.LID9006-022WC-b2.idrFilt0.1.bb A549 RnaSeq Contigs pooled bigBed CSHL analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/rna_elements/jan2011/LongRnaSeq/A549_WholeCell_Ap_Long_CSHL_Contig.CSHL_LID8963-021WC-b1.LID8964-022WC-b2.idrFilt0.1.bb A549 RnaSeq Contigs pooled bigBed CSHL analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/rna_elements/jan2011/LongRnaSeq/AGO4450_WholeCell_Am_Long_CSHL_Contig.CSHL_LID9001-017WC-b1.LID9002-018WC-b2.idrFilt0.1.bb AG04450 RnaSeq Contigs pooled bigBed CSHL analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/rna_elements/jan2011/LongRnaSeq/AGO4450_WholeCell_Ap_Long_CSHL_Contig.CSHL_LID8965-017WC-b1.LID8966-018WC-b2.idrFilt0.1.bb AG04450 RnaSeq Contigs pooled bigBed CSHL analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/rna_elements/jan2011/LongRnaSeq/BJ_WholeCell_Am_Long_CSHL_Contig.CSHL_LID9007-037WC-b1.LID9008-038WC-b2.idrFilt0.1.bb BJ RnaSeq Contigs pooled bigBed CSHL analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/rna_elements/jan2011/LongRnaSeq/BJ_WholeCell_Ap_Long_CSHL_Contig.CSHL_LID8969-037WC-b1.LID8970-038WC-b2.idrFilt0.1.bb BJ RnaSeq Contigs pooled bigBed CSHL analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/rna_elements/jan2011/LongRnaSeq/GM12878_Cytoplasm_Am_Long_CSHL_Contig.CSHL_LID18547-003C-b1.LID18548-004C-b2.idrFilt0.1.bb GM12878 RnaSeq Contigs pooled bigBed CSHL analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/rna_elements/jan2011/LongRnaSeq/GM12878_Cytoplasm_Ap_Long_CSHL_Contig.CSHL_LID8467-003C-b1.LID8468-004C-b2.idrFilt0.1.bb GM12878 RnaSeq Contigs pooled bigBed CSHL analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/rna_elements/jan2011/LongRnaSeq/GM12878_Nucleus_Am_Long_CSHL_Contig.CSHL_LID9197-003N-b1.LID9198-004N-b2.idrFilt0.1.bb GM12878 RnaSeq Contigs pooled bigBed CSHL analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/rna_elements/jan2011/LongRnaSeq/GM12878_Nucleus_Ap_Long_CSHL_Contig.CSHL_LID8532-003N-b1.LID8533-004N-b2.idrFilt0.1.bb GM12878 RnaSeq Contigs pooled bigBed CSHL analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/rna_elements/jan2011/LongRnaSeq/GM12878_WholeCell_Am_Long_CSHL_Contig.CSHL_LID8661-003WC-b1.LID8662-004WC-b2.idrFilt0.1.bb GM12878 RnaSeq Contigs pooled bigBed CSHL analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/rna_elements/jan2011/LongRnaSeq/GM12878_WholeCell_Ap_Long_CSHL_Contig.CSHL_LID16629-003WC-b1.LID16630-004WC-b2.idrFilt0.1.bb GM12878 RnaSeq Contigs pooled bigBed CSHL analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/rna_elements/jan2011/LongRnaSeq/H1ES_WholeCell_Am_Long_CSHL_Contig.CSHL_LID8663-005WC-b1.LID8664-006WC-b2.idrFilt0.1.bb H1-hESC RnaSeq Contigs pooled bigBed CSHL analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/rna_elements/jan2011/LongRnaSeq/H1ES_WholeCell_Ap_Long_CSHL_Contig.CSHL_LID8461-005WC-b1.LID8462-006WC-b2.idrFilt0.1.bb H1-hESC RnaSeq Contigs pooled bigBed CSHL analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/rna_elements/jan2011/LongRnaSeq/HeLa_Cytoplasm_Ap_Long_CSHL_Contig.CSHL_LID8469-011C-b1.LID8470-012C-b2.idrFilt0.1.bb HeLa-S3 RnaSeq Contigs pooled bigBed CSHL analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/rna_elements/jan2011/LongRnaSeq/HeLa_Nucleus_Am_Long_CSHL_Contig.CSHL_LID9200-011N-b1.LID9201-012N-b2.idrFilt0.1.bb HeLa-S3 RnaSeq Contigs pooled bigBed CSHL analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/rna_elements/jan2011/LongRnaSeq/HeLa_Nucleus_Ap_Long_CSHL_Contig.CSHL_LID8559-011N-b1.LID8560-012N-b2.idrFilt0.1.bb HeLa-S3 RnaSeq Contigs pooled bigBed CSHL analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/rna_elements/jan2011/LongRnaSeq/HeLa_WholeCell_Am_Long_CSHL_Contig.CSHL_LID8790-011WC-b1.LID8791-012WC-b2.idrFilt0.1.bb HeLa-S3 RnaSeq Contigs pooled bigBed CSHL analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/rna_elements/jan2011/LongRnaSeq/HeLa_WholeCell_Ap_Long_CSHL_Contig.CSHL_LID16633-011WC-b1.LID16634-012WC-b2.idrFilt0.1.bb HeLa-S3 RnaSeq Contigs pooled bigBed CSHL analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/rna_elements/jan2011/LongRnaSeq/HepG2_Cytoplasm_Am_Long_CSHL_Contig.CSHL_LID18552-013C-b1.LID18553-014C-b2.idrFilt0.1.bb HepG2 RnaSeq Contigs pooled bigBed CSHL analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/rna_elements/jan2011/LongRnaSeq/HepG2_Cytoplasm_Ap_Long_CSHL_Contig.CSHL_LID8471-013C-b1.LID8472-014C-b2.idrFilt0.1.bb HepG2 RnaSeq Contigs pooled bigBed CSHL analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/rna_elements/jan2011/LongRnaSeq/HepG2_Nucleus_Am_Long_CSHL_Contig.CSHL_LID9202-013N-b1.LID9203-014N-b2.idrFilt0.1.bb HepG2 RnaSeq Contigs pooled bigBed CSHL analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/rna_elements/jan2011/LongRnaSeq/HepG2_Nucleus_Ap_Long_CSHL_Contig.CSHL_LID8534-013N-b1.LID8535-014N-b2.idrFilt0.1.bb HepG2 RnaSeq Contigs pooled bigBed CSHL analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/rna_elements/jan2011/LongRnaSeq/HepG2_WholeCell_Am_Long_CSHL_Contig.CSHL_LID8792-013WC-b1.LID8793-014WC-b2.idrFilt0.1.bb HepG2 RnaSeq Contigs pooled bigBed CSHL analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/rna_elements/jan2011/LongRnaSeq/HepG2_WholeCell_Ap_Long_CSHL_Contig.CSHL_LID16635-013WC-b1.LID16636-014WC-b2.idrFilt0.1.bb HepG2 RnaSeq Contigs pooled bigBed CSHL analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/rna_elements/jan2011/LongRnaSeq/HSMM_WholeCell_Am_Long_CSHL_Contig.CSHL_LID8826-023WC-b1.LID8827-024WC-b2.idrFilt0.1.bb HSMM RnaSeq Contigs pooled bigBed CSHL analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/rna_elements/jan2011/LongRnaSeq/HSMM_WholeCell_Ap_Long_CSHL_Contig.CSHL_LID8710-023WC-b1.LID8711-024WC-b2.idrFilt0.1.bb HSMM RnaSeq Contigs pooled bigBed CSHL analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/rna_elements/jan2011/LongRnaSeq/HUVEC_Cytoplasm_Ap_Long_CSHL_Contig.CSHL_LID8688-029C-b3.LID8689-030C-b4.idrFilt0.1.bb HUVEC RnaSeq Contigs pooled bigBed CSHL analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/rna_elements/jan2011/LongRnaSeq/HUVEC_Nucleus_Am_Long_CSHL_Contig.CSHL_LID9206-029N-b3.LID9207-030N-b4.idrFilt0.1.bb HUVEC RnaSeq Contigs pooled bigBed CSHL analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/rna_elements/jan2011/LongRnaSeq/HUVEC_Nucleus_Ap_Long_CSHL_Contig.CSHL_LID8690-029N-b3.LID8691-030N-b4.idrFilt0.1.bb HUVEC RnaSeq Contigs pooled bigBed CSHL analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/rna_elements/jan2011/LongRnaSeq/HUVEC_WholeCell_Am_Long_CSHL_Contig.CSHL_LID8788-009WC-b1.LID8789-010WC-b2.idrFilt0.1.bb HUVEC RnaSeq Contigs pooled bigBed CSHL analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/rna_elements/jan2011/LongRnaSeq/HUVEC_WholeCell_Ap_Long_CSHL_Contig.CSHL_LID8463-009WC-b1.LID8464-010WC-b2.idrFilt0.1.bb HUVEC RnaSeq Contigs pooled bigBed CSHL analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/rna_elements/jan2011/LongRnaSeq/K562_Chromatin_Total_Long_CSHL_Contig.CSHL_LID9185-025CH-b3.LID9186-026CH-b4.idrFilt0.1.bb K562 RnaSeq Contigs pooled bigBed CSHL analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/rna_elements/jan2011/LongRnaSeq/K562_Cytoplasm_Am_Long_CSHL_Contig.CSHL_LID18545-001C-b1.LID18546-002C-b2.idrFilt0.1.bb K562 RnaSeq Contigs pooled bigBed CSHL analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/rna_elements/jan2011/LongRnaSeq/K562_Cytoplasm_Ap_Long_CSHL_Contig.CSHL_LID8465-001C-b1.LID8466-002C-b2.idrFilt0.1.bb K562 RnaSeq Contigs pooled bigBed CSHL analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/rna_elements/jan2011/LongRnaSeq/K562_Nucleolus_Total_Long_CSHL_Contig.CSHL_LID9187-025NL-b3.LID9188-026NL-b4.idrFilt0.1.bb K562 RnaSeq Contigs pooled bigBed CSHL analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/rna_elements/jan2011/LongRnaSeq/K562_Nucleoplasm_Total_Long_CSHL_Contig.CSHL_LID9189-025NP-b3.LID9190-026NP-b4.idrFilt0.1.bb K562 RnaSeq Contigs pooled bigBed CSHL analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/rna_elements/jan2011/LongRnaSeq/K562_Nucleus_Am_Long_CSHL_Contig.CSHL_LID9195-001N-b1.LID9196-002N-b2.idrFilt0.1.bb K562 RnaSeq Contigs pooled bigBed CSHL analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/rna_elements/jan2011/LongRnaSeq/K562_Nucleus_Ap_Long_CSHL_Contig.CSHL_LID8556-001N-b1.LID8557-002N-b2.idrFilt0.1.bb K562 RnaSeq Contigs pooled bigBed CSHL analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/rna_elements/jan2011/LongRnaSeq/K562_WholeCell_Am_Long_CSHL_Contig.CSHL_LID8659-001WC-b1.LID8660-002WC-b2.idrFilt0.1.bb K562 RnaSeq Contigs pooled bigBed CSHL analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/rna_elements/jan2011/LongRnaSeq/K562_WholeCell_Ap_Long_CSHL_Contig.CSHL_LID16627-001WC-b1.LID16628-002WC-b2.idrFilt0.1.bb K562 RnaSeq Contigs pooled bigBed CSHL analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/rna_elements/jan2011/LongRnaSeq/MCF-7_WholeCell_Am_Long_CSHL_Contig.CSHL_LID8824-015WC-b1.LID8825-016WC-b2.idrFilt0.1.bb MCF-7 RnaSeq Contigs pooled bigBed CSHL analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/rna_elements/jan2011/LongRnaSeq/MCF-7_WholeCell_Ap_Long_CSHL_Contig.CSHL_LID8686-015WC-b1.LID8687-016WC-b2.idrFilt0.1.bb MCF-7 RnaSeq Contigs pooled bigBed CSHL analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/rna_elements/jan2011/LongRnaSeq/NHEK_Cytoplasm_Ap_Long_CSHL_Contig.CSHL_LID8795-027C-b3.LID8796-028C-b4.idrFilt0.1.bb NHEK RnaSeq Contigs pooled bigBed CSHL analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/rna_elements/jan2011/LongRnaSeq/NHEK_Nucleus_Am_Long_CSHL_Contig.CSHL_LID9204-027N-b3.LID9205-028N-b4.idrFilt0.1.bb NHEK RnaSeq Contigs pooled bigBed CSHL analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/rna_elements/jan2011/LongRnaSeq/NHEK_Nucleus_Ap_Long_CSHL_Contig.CSHL_LID8797-027N-b3.LID8798-028N-b4.idrFilt0.1.bb NHEK RnaSeq Contigs pooled bigBed CSHL analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/rna_elements/jan2011/LongRnaSeq/NHEK_WholeCell_Am_Long_CSHL_Contig.CSHL_LID8665-007WC-b1.LID8666-008WC-b2.idrFilt0.1.bb NHEK RnaSeq Contigs pooled bigBed CSHL analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/rna_elements/jan2011/LongRnaSeq/NHEK_WholeCell_Ap_Long_CSHL_Contig.CSHL_LID16631-007WC-b1.LID16632-008WC-b2.idrFilt0.1.bb NHEK RnaSeq Contigs pooled bigBed CSHL analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/rna_elements/jan2011/LongRnaSeq/NHLF_WholeCell_Am_Long_CSHL_Contig.CSHL_LID8828-033WC-b1.LID8829-034WC-b2.idrFilt0.1.bb NHLF RnaSeq Contigs pooled bigBed CSHL analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/rna_elements/jan2011/LongRnaSeq/NHLF_WholeCell_Ap_Long_CSHL_Contig.CSHL_LID8692-033WC-b1.LID8701-034WC-b2.idrFilt0.1.bb NHLF RnaSeq Contigs pooled bigBed CSHL analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/rna_elements/jan2011/LongRnaSeq/SK-N-SH_RA_WholeCell_Am_Long_CSHL_Contig.CSHL_LID9003-019WC-b1.LID9011-020WC-b2.idrFilt0.1.bb SK-N-SH_RA RnaSeq Contigs pooled bigBed CSHL analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/rna_elements/jan2011/LongRnaSeq/SK-N-SH_RA_WholeCell_Ap_Long_CSHL_Contig.CSHL_LID8967-019WC-b1.LID8968-020WC-b2.idrFilt0.1.bb SK-N-SH_RA RnaSeq Contigs pooled bigBed CSHL analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/rna_elements/jan2011/ShortRnaSeq/A549-Stam_WholeCell_Short_RNA_CSHL_Contig.CSHL_LID20749-021WC-r1.LID20750-022WC-r2.idrFilt0.1.bb A549 RnaSeq Contigs pooled bigBed CSHL analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/rna_elements/jan2011/ShortRnaSeq/AGO4450-Stam_WholeCell_Short_RNA_CSHL_Contig.CSHL_LID20745-017WC-r1.LID20746-018WC-r2.idrFilt0.1.bb AG04450 RnaSeq Contigs pooled bigBed CSHL analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/rna_elements/jan2011/ShortRnaSeq/BJ_WholeCell_Short_RNA_CSHL_Contig.CSHL_LID20909-037WC-r1.LID20910-038WC-r2.idrFilt0.1.bb BJ RnaSeq Contigs pooled bigBed CSHL analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/rna_elements/jan2011/ShortRnaSeq/GM12878_Cytosol_Short_RNA_CSHL_Contig.CSHL_LID20901-003C-r1.LID20904-004C-r2.idrFilt0.1.bb GM12878 RnaSeq Contigs pooled bigBed CSHL analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/rna_elements/jan2011/ShortRnaSeq/GM12878_Nucleus_Short_RNA_CSHL_Contig.CSHL_LID20900-003N-r1.LID20903-004N-r2.idrFilt0.1.bb GM12878 RnaSeq Contigs pooled bigBed CSHL analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/rna_elements/jan2011/ShortRnaSeq/GM12878_WholeCell_Short_RNA_CSHL_Contig.CSHL_LID20899-003WC-r1.LID20902-004WC-r2.idrFilt0.1.bb GM12878 RnaSeq Contigs pooled bigBed CSHL analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/rna_elements/jan2011/ShortRnaSeq/H1ES_WholeCell_Short_RNA_CSHL_Contig.CSHL_LID20905-005WC-r1.LID20906-006WC-r2.idrFilt0.1.bb H1-hESC RnaSeq Contigs pooled bigBed CSHL analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/rna_elements/jan2011/ShortRnaSeq/HelaS3_Cytosol_Short_RNA_CSHL_Contig.CSHL_LID21145-011C-r1.LID21148-012C-r2.idrFilt0.1.bb HeLa-S3 RnaSeq Contigs pooled bigBed CSHL analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/rna_elements/jan2011/ShortRnaSeq/HelaS3_Nucleus_Short_RNA_CSHL_Contig.CSHL_LID21144-011N-r1.LID21147-012N-r2.idrFilt0.1.bb HeLa-S3 RnaSeq Contigs pooled bigBed CSHL analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/rna_elements/jan2011/ShortRnaSeq/HelaS3_WholeCell_Short_RNA_CSHL_Contig.CSHL_LID21143-011WC-r1.LID21146-012WC-r2.idrFilt0.1.bb HeLa-S3 RnaSeq Contigs pooled bigBed CSHL analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/rna_elements/jan2011/ShortRnaSeq/HUVEC_Cytosol_Short_RNA_CSHL_Contig.CSHL_LID21057-029C-r1.LID21059-030C-r2.idrFilt0.1.bb HUVEC RnaSeq Contigs pooled bigBed CSHL analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/rna_elements/jan2011/ShortRnaSeq/HUVEC_Nucleus_Short_RNA_CSHL_Contig.CSHL_LID21056-029N-r1.LID21058-030N-r2.idrFilt0.1.bb HUVEC RnaSeq Contigs pooled bigBed CSHL analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/rna_elements/jan2011/ShortRnaSeq/HUVEC_WholeCell_Short_RNA_CSHL_Contig.CSHL_LID21054-009WC-r1.LID21055-010WC-r2.idrFilt0.1.bb HUVEC RnaSeq Contigs pooled bigBed CSHL analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/rna_elements/jan2011/ShortRnaSeq/K562_Chromatin_Short_RNA_CSHL_Contig.CSHL_LID8930-025CH-r1.LID18560-026CH-r2.idrFilt0.1.bb K562 RnaSeq Contigs pooled bigBed CSHL analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/rna_elements/jan2011/ShortRnaSeq/K562_Cytosol_Short_RNA_CSHL_Contig.CSHL_LID10572-001C-r1.LID10571-002C-r2.idrFilt0.1.bb K562 RnaSeq Contigs pooled bigBed CSHL analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/rna_elements/jan2011/ShortRnaSeq/K562_Nucleoli_Short_RNA_CSHL_Contig.CSHL_LID8928-025NL-r1.LID18558-026NL-r2.idrFilt0.1.bb K562 RnaSeq Contigs pooled bigBed CSHL analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/rna_elements/jan2011/ShortRnaSeq/K562_Nucleoplasm_Short_RNA_CSHL_Contig.CSHL_LID8929-025NP-r1.LID18559-026NP-r2.idrFilt0.1.bb K562 RnaSeq Contigs pooled bigBed CSHL analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/rna_elements/jan2011/ShortRnaSeq/K562_Nucleus_Short_RNA_CSHL_Contig.CSHL_LID10570-001N-r1.LID10569-002N-r2.idrFilt0.1.bb K562 RnaSeq Contigs pooled bigBed CSHL analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/rna_elements/jan2011/ShortRnaSeq/K562_WholeCell_Short_RNA_CSHL_Contig.CSHL_LID10567-001WC-r1.LID10568-002WC-r2.idrFilt0.1.bb K562 RnaSeq Contigs pooled bigBed CSHL analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/rna_elements/jan2011/ShortRnaSeq/NHEK_Cytosol_Short_RNA_CSHL_Contig.CSHL_LID21002-027C-r1.LID21004-028C-r2.idrFilt0.1.bb NHEK RnaSeq Contigs pooled bigBed CSHL analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/rna_elements/jan2011/ShortRnaSeq/NHEK_Nucleus_Short_RNA_CSHL_Contig.CSHL_LID21001-027N-r1.LID21003-028N-r2.idrFilt0.1.bb NHEK RnaSeq Contigs pooled bigBed CSHL analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/rna_elements/jan2011/ShortRnaSeq/NHEK_WholeCell_Short_RNA_CSHL_Contig.CSHL_LID20999-007WC-r1.LID21000-008WC-r2.idrFilt0.1.bb NHEK RnaSeq Contigs pooled bigBed CSHL analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/rna_elements/jan2011/ShortRnaSeq/SK-N-SH-Stan_WholeCell_Short_RNA_CSHL_Contig.CSHL_LID20747-019WC-r1.LID20748-020WC-r2.idrFilt0.1.bb SK-N-SH_RA RnaSeq Contigs pooled bigBed CSHL analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/segmentations/jan2011/hub/gm12878.ChromHMM.bb GM12878 genomeSegmentation Segmentation bigBed analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/segmentations/jan2011/hub/h1hesc.ChromHMM.bb H1 genomeSegmentation Segmentation bigBed analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/segmentations/jan2011/hub/helas3.ChromHMM.bb HeLa-S3 genomeSegmentation Segmentation bigBed analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/segmentations/jan2011/hub/hepg2.ChromHMM.bb HepG2 genomeSegmentation Segmentation bigBed analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/segmentations/jan2011/hub/huvec.ChromHMM.bb HUVEC genomeSegmentation Segmentation bigBed analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/segmentations/jan2011/hub/k562.ChromHMM.bb K562 genomeSegmentation Segmentation bigBed analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/segmentations/jan2011/hub/segway_gm12878_relabel.bb GM12878 genomeSegmentation Segmentation bigBed analysis 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http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeBroadHistoneHuvecH3k4me2StdAln_2Reps.norm5.rawsignal.bw HUVEC ChipSeq H3K4me2 Signal bigWig Broad analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeBroadHistoneHuvecH3k4me3StdAln_3Reps.norm5.rawsignal.bw HUVEC ChipSeq H3K4me3 Signal bigWig Broad analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeBroadHistoneHuvecH3k9acStdAln_3Reps.norm5.rawsignal.bw HUVEC ChipSeq H3K9ac Signal bigWig Broad analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeBroadHistoneHuvecH3k9me1StdAln_3Reps.norm5.rawsignal.bw HUVEC ChipSeq H3K9me1 Signal bigWig Broad analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeBroadHistoneHuvecH4k20me1StdAln_3Reps.norm5.rawsignal.bw HUVEC ChipSeq H4K20me1 Signal bigWig Broad analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeBroadHistoneHuvecPol2bStdAln_3Reps.norm5.rawsignal.bw HUVEC ChipSeq Pol2(b) Signal bigWig Broad analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeBroadHistoneK562ControlStdAln_1Reps.norm5.rawsignal.bw K562 ChipSeq Control Signal bigWig Broad analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeBroadHistoneK562CtcfStdAln_2Reps.norm5.rawsignal.bw K562 ChipSeq CTCF Signal bigWig Broad analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeBroadHistoneK562H2azStdAln_2Reps.norm5.rawsignal.bw K562 ChipSeq H2A.Z Signal bigWig Broad analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeBroadHistoneK562H3k27acStdAln_2Reps.norm5.rawsignal.bw K562 ChipSeq H3K27ac Signal bigWig Broad analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeBroadHistoneK562H3k27me3StdAln_2Reps.norm5.rawsignal.bw K562 ChipSeq H3K27me3 Signal bigWig Broad analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeBroadHistoneK562H3k36me3StdAln_2Reps.norm5.rawsignal.bw K562 ChipSeq H3K36me3 Signal bigWig Broad analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeBroadHistoneK562H3k4me1StdAln_2Reps.norm5.rawsignal.bw K562 ChipSeq H3K4me1 Signal bigWig Broad analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeBroadHistoneK562H3k4me2StdAln_2Reps.norm5.rawsignal.bw K562 ChipSeq H3K4me2 Signal bigWig Broad analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeBroadHistoneK562H3k4me3StdAln_2Reps.norm5.rawsignal.bw K562 ChipSeq H3K4me3 Signal bigWig Broad analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeBroadHistoneK562H3k79me2StdAln_2Reps.norm5.rawsignal.bw K562 ChipSeq H3K79me2 Signal bigWig Broad analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeBroadHistoneK562H3k9acStdAln_2Reps.norm5.rawsignal.bw K562 ChipSeq H3K9ac Signal bigWig Broad analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeBroadHistoneK562H3k9me1StdAln_1Reps.norm5.rawsignal.bw K562 ChipSeq H3K9me1 Signal bigWig Broad analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeBroadHistoneK562H3k9me3StdAln_2Reps.norm5.rawsignal.bw K562 ChipSeq H3K9me3 Signal bigWig Broad analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeBroadHistoneK562H4k20me1StdAln_2Reps.norm5.rawsignal.bw K562 ChipSeq H4K20me1 Signal bigWig Broad analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeBroadHistoneK562Pol2bStdAln_2Reps.norm5.rawsignal.bw K562 ChipSeq Pol2(b) Signal bigWig Broad analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeBroadHistoneNhaControlStdAln_2Reps.norm5.rawsignal.bw NH-A ChipSeq Control Signal bigWig Broad analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeBroadHistoneNhaCtcfStdAln_2Reps.norm5.rawsignal.bw NH-A ChipSeq CTCF Signal bigWig Broad analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeBroadHistoneNhaH3k27acStdAln_2Reps.norm5.rawsignal.bw NH-A ChipSeq H3K27ac Signal bigWig Broad analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeBroadHistoneNhaH3k27me3StdAln_2Reps.norm5.rawsignal.bw NH-A ChipSeq H3K27me3 Signal bigWig Broad analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeBroadHistoneNhaH3k36me3StdAln_2Reps.norm5.rawsignal.bw NH-A ChipSeq H3K36me3 Signal bigWig Broad analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeBroadHistoneNhaH3k4me1StdAln_2Reps.norm5.rawsignal.bw NH-A ChipSeq H3K4me1 Signal bigWig Broad analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeBroadHistoneNhaH3k4me3StdAln_2Reps.norm5.rawsignal.bw NH-A ChipSeq H3K4me3 Signal bigWig Broad analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeBroadHistoneNhdfadControlStdAln_2Reps.norm5.rawsignal.bw NHDF-Ad ChipSeq Control Signal bigWig Broad analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeBroadHistoneNhdfadCtcfStdAln_2Reps.norm5.rawsignal.bw NHDF-Ad ChipSeq CTCF Signal bigWig Broad analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeBroadHistoneNhdfadH3k27acStdAln_2Reps.norm5.rawsignal.bw NHDF-Ad ChipSeq H3K27ac Signal bigWig Broad analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeBroadHistoneNhdfadH3k27me3StdAln_2Reps.norm5.rawsignal.bw NHDF-Ad ChipSeq H3K27me3 Signal bigWig Broad analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeBroadHistoneNhdfadH3k36me3StdAln_2Reps.norm5.rawsignal.bw NHDF-Ad ChipSeq H3K36me3 Signal bigWig Broad analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeBroadHistoneNhdfadH3k4me2StdAln_2Reps.norm5.rawsignal.bw NHDF-Ad ChipSeq H3K4me2 Signal bigWig Broad analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeBroadHistoneNhdfadH3k4me3StdAln_2Reps.norm5.rawsignal.bw NHDF-Ad ChipSeq H3K4me3 Signal bigWig Broad analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeBroadHistoneNhdfadH3k9acStdAln_2Reps.norm5.rawsignal.bw NHDF-Ad ChipSeq H3K9ac Signal bigWig Broad analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeBroadHistoneNhekControlStdAln_2Reps.norm5.rawsignal.bw NHEK ChipSeq Control Signal bigWig Broad analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeBroadHistoneNhekCtcfStdAln_3Reps.norm5.rawsignal.bw NHEK ChipSeq CTCF Signal bigWig Broad analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeBroadHistoneNhekH3k27acStdAln_3Reps.norm5.rawsignal.bw NHEK ChipSeq H3K27ac Signal bigWig Broad analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeBroadHistoneNhekH3k27me3StdAln_3Reps.norm5.rawsignal.bw NHEK ChipSeq H3K27me3 Signal bigWig Broad analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeBroadHistoneNhekH3k36me3StdAln_3Reps.norm5.rawsignal.bw NHEK ChipSeq H3K36me3 Signal bigWig Broad analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeBroadHistoneNhekH3k4me1StdAln_3Reps.norm5.rawsignal.bw NHEK ChipSeq H3K4me1 Signal bigWig Broad analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeBroadHistoneNhekH3k4me2StdAln_3Reps.norm5.rawsignal.bw NHEK ChipSeq H3K4me2 Signal bigWig Broad analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeBroadHistoneNhekH3k4me3StdAln_3Reps.norm5.rawsignal.bw NHEK ChipSeq H3K4me3 Signal bigWig Broad analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeBroadHistoneNhekH3k9acStdAln_3Reps.norm5.rawsignal.bw NHEK ChipSeq H3K9ac Signal bigWig Broad analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeBroadHistoneNhekH3k9me1StdAln_3Reps.norm5.rawsignal.bw NHEK ChipSeq H3K9me1 Signal bigWig Broad analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeBroadHistoneNhekH4k20me1StdAln_3Reps.norm5.rawsignal.bw NHEK ChipSeq H4K20me1 Signal bigWig Broad analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeBroadHistoneNhekPol2bStdAln_2Reps.norm5.rawsignal.bw NHEK ChipSeq Pol2(b) Signal bigWig Broad analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeBroadHistoneNhlfControlStdAln_2Reps.norm5.rawsignal.bw NHLF ChipSeq Control Signal bigWig Broad analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeBroadHistoneNhlfCtcfStdAln_2Reps.norm5.rawsignal.bw NHLF ChipSeq CTCF Signal bigWig Broad analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeBroadHistoneNhlfH3k27acStdAln_2Reps.norm5.rawsignal.bw NHLF ChipSeq H3K27ac Signal bigWig Broad analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeBroadHistoneNhlfH3k27me3StdAln_2Reps.norm5.rawsignal.bw NHLF ChipSeq H3K27me3 Signal bigWig Broad analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeBroadHistoneNhlfH3k36me3StdAln_2Reps.norm5.rawsignal.bw NHLF ChipSeq H3K36me3 Signal bigWig Broad analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeBroadHistoneNhlfH3k4me1StdAln_2Reps.norm5.rawsignal.bw NHLF ChipSeq H3K4me1 Signal bigWig Broad analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeBroadHistoneNhlfH3k4me2StdAln_2Reps.norm5.rawsignal.bw NHLF ChipSeq H3K4me2 Signal bigWig Broad analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeBroadHistoneNhlfH3k4me3StdAln_2Reps.norm5.rawsignal.bw NHLF ChipSeq H3K4me3 Signal bigWig Broad analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeBroadHistoneNhlfH3k9acStdAln_2Reps.norm5.rawsignal.bw NHLF ChipSeq H3K9ac Signal bigWig Broad analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeBroadHistoneNhlfH4k20me1StdAln_2Reps.norm5.rawsignal.bw NHLF ChipSeq H4K20me1 Signal bigWig Broad analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeBroadHistoneOsteoblControlStdAln_2Reps.norm5.rawsignal.bw Osteobl ChipSeq Control Signal bigWig Broad analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeBroadHistoneOsteoblCtcfStdAln_2Reps.norm5.rawsignal.bw Osteobl ChipSeq CTCF Signal bigWig Broad analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeBroadHistoneOsteoblH2azStdAln_2Reps.norm5.rawsignal.bw Osteobl ChipSeq H2A.Z Signal bigWig Broad analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeBroadHistoneOsteoblH3k27acStdAln_2Reps.norm5.rawsignal.bw Osteobl ChipSeq H3K27ac Signal bigWig Broad analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeBroadHistoneOsteoblH3k36me3StdAln_2Reps.norm5.rawsignal.bw Osteobl ChipSeq H3K36me3 Signal bigWig Broad analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeBroadHistoneOsteoblH3k4me1StdAln_2Reps.norm5.rawsignal.bw Osteobl ChipSeq H3K4me1 Signal bigWig Broad analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeBroadHistoneOsteoblH3k4me2StdAln_2Reps.norm5.rawsignal.bw Osteobl ChipSeq H3K4me2 Signal bigWig Broad analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeBroadHistoneOsteoblH3k9me3StdAln_2Reps.norm5.rawsignal.bw Osteobl ChipSeq H3K9me3 Signal bigWig Broad analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeHaibTfbsA549ControlPcr1xDexaAln_2Reps.norm5.rawsignal.bw A549 ChipSeq Control Signal bigWig HudsonAlpha analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeHaibTfbsA549ControlPcr1xEtoh02Aln_2Reps.norm5.rawsignal.bw A549 ChipSeq Control Signal bigWig HudsonAlpha analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeHaibTfbsA549ControlPcr2xDexaAln_2Reps.norm5.rawsignal.bw A549 ChipSeq Control Signal bigWig HudsonAlpha analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeHaibTfbsA549CtcfPcr1xDexaAln_2Reps.norm5.rawsignal.bw A549 ChipSeq CTCF Signal bigWig HudsonAlpha analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeHaibTfbsA549CtcfPcr1xEtoh02Aln_2Reps.norm5.rawsignal.bw A549 ChipSeq CTCF Signal bigWig HudsonAlpha analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeHaibTfbsA549GrPcr1xDexbAln_2Reps.norm5.rawsignal.bw A549 ChipSeq GR Signal bigWig HudsonAlpha analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeHaibTfbsA549GrPcr1xDexcAln_2Reps.norm5.rawsignal.bw A549 ChipSeq GR Signal bigWig HudsonAlpha analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeHaibTfbsA549GrPcr1xDexdAln_2Reps.norm5.rawsignal.bw A549 ChipSeq GR Signal bigWig HudsonAlpha analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeHaibTfbsA549GrPcr1xEtoh02Aln_2Reps.norm5.rawsignal.bw A549 ChipSeq GR Signal bigWig HudsonAlpha analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeHaibTfbsA549GrPcr2xDexaAln_2Reps.norm5.rawsignal.bw A549 ChipSeq GR Signal bigWig HudsonAlpha analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeHaibTfbsA549GrPcr2xEtoh02Aln_2Reps.norm5.rawsignal.bw A549 ChipSeq GR Signal bigWig HudsonAlpha analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeHaibTfbsA549Pol2Pcr2xDexaAln_2Reps.norm5.rawsignal.bw A549 ChipSeq Pol2 Signal bigWig HudsonAlpha analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeHaibTfbsA549Pol2Pcr2xEtoh02Aln_2Reps.norm5.rawsignal.bw A549 ChipSeq Pol2 Signal bigWig HudsonAlpha analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeHaibTfbsA549Usf1Pcr1xDexaAln_2Reps.norm5.rawsignal.bw A549 ChipSeq USF-1 Signal bigWig HudsonAlpha analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeHaibTfbsA549Usf1Pcr1xEtoh02Aln_2Reps.norm5.rawsignal.bw A549 ChipSeq USF-1 Signal bigWig HudsonAlpha analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeHaibTfbsEcc1ControlV0416102Dmso2Aln_2Reps.norm5.rawsignal.bw ECC-1 ChipSeq Control Signal bigWig HudsonAlpha analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeHaibTfbsEcc1EralphaaV0416102Dmso2Aln_2Reps.norm5.rawsignal.bw ECC-1 ChipSeq ERalpha_a Signal bigWig HudsonAlpha analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeHaibTfbsEcc1EralphaaV0416102Estradia1hAln_2Reps.norm5.rawsignal.bw ECC-1 ChipSeq ERalpha_a Signal bigWig HudsonAlpha analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeHaibTfbsEcc1EralphaaV0416102Gen1hAln_2Reps.norm5.rawsignal.bw ECC-1 ChipSeq ERalpha_a Signal bigWig HudsonAlpha analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeHaibTfbsEcc1Foxa1c20V0416102Dmso2Aln_2Reps.norm5.rawsignal.bw ECC-1 ChipSeq FOXA1_(C-20) Signal bigWig HudsonAlpha analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeHaibTfbsEcc1GrV0416102DexaAln_2Reps.norm5.rawsignal.bw ECC-1 ChipSeq GR Signal bigWig HudsonAlpha analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeHaibTfbsEcc1GrV0416102Etoh02Aln_2Reps.norm5.rawsignal.bw ECC-1 ChipSeq GR Signal bigWig HudsonAlpha analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeHaibTfbsEcc1Pol2V0416102Dmso2Aln_2Reps.norm5.rawsignal.bw ECC-1 ChipSeq Pol2 Signal bigWig HudsonAlpha analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeHaibTfbsGm12878Atf3Pcr1xAln_2Reps.norm5.rawsignal.bw GM12878 ChipSeq ATF3 Signal bigWig HudsonAlpha analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeHaibTfbsGm12878BatfPcr1xAln_2Reps.norm5.rawsignal.bw GM12878 ChipSeq BATF Signal bigWig HudsonAlpha analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeHaibTfbsGm12878Bcl11aPcr1xAln_2Reps.norm5.rawsignal.bw GM12878 ChipSeq BCL11A Signal bigWig HudsonAlpha analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeHaibTfbsGm12878Bcl3Pcr1xAln_2Reps.norm5.rawsignal.bw GM12878 ChipSeq BCL3 Signal bigWig HudsonAlpha analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeHaibTfbsGm12878Bclaf1m33V0416101Aln_2Reps.norm5.rawsignal.bw GM12878 ChipSeq BCLAF1_(M33-P5B11) Signal bigWig HudsonAlpha analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeHaibTfbsGm12878ControlPcr1xAln_6Reps.norm5.rawsignal.bw GM12878 ChipSeq Control Signal bigWig HudsonAlpha analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeHaibTfbsGm12878ControlPcr2xAln_3Reps.norm5.rawsignal.bw GM12878 ChipSeq Control Signal bigWig HudsonAlpha analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeHaibTfbsGm12878Ebf1c8Pcr1xAln_2Reps.norm5.rawsignal.bw GM12878 ChipSeq EBF1_(C-8) Signal bigWig HudsonAlpha analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeHaibTfbsGm12878EbfPcr1xAln_2Reps.norm5.rawsignal.bw GM12878 ChipSeq EBF Signal bigWig HudsonAlpha analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeHaibTfbsGm12878Egr1Pcr2xAln_2Reps.norm5.rawsignal.bw GM12878 ChipSeq Egr-1 Signal bigWig HudsonAlpha analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeHaibTfbsGm12878Egr1V0416101Aln_2Reps.norm5.rawsignal.bw GM12878 ChipSeq Egr-1 Signal bigWig HudsonAlpha analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeHaibTfbsGm12878Elf1sc631V0416101Aln_2Reps.norm5.rawsignal.bw GM12878 ChipSeq ELF1_(SC-631) Signal bigWig HudsonAlpha analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeHaibTfbsGm12878Ets1Pcr1xAln_2Reps.norm5.rawsignal.bw GM12878 ChipSeq ETS1 Signal bigWig HudsonAlpha analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeHaibTfbsGm12878GabpPcr2xAln_2Reps.norm5.rawsignal.bw GM12878 ChipSeq GABP Signal bigWig HudsonAlpha analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeHaibTfbsGm12878Irf4m17Pcr1xAln_2Reps.norm5.rawsignal.bw GM12878 ChipSeq IRF4_(M-17) Signal bigWig HudsonAlpha analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeHaibTfbsGm12878Irf4Pcr1xAln_2Reps.norm5.rawsignal.bw GM12878 ChipSeq IRF4 Signal bigWig HudsonAlpha analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeHaibTfbsGm12878Mef2aPcr1xAln_2Reps.norm5.rawsignal.bw GM12878 ChipSeq MEF2A Signal bigWig HudsonAlpha analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeHaibTfbsGm12878Mef2csc13268Pcr1xAln_2Reps.norm5.rawsignal.bw GM12878 ChipSeq MEF2C_(SC-13268) Signal bigWig HudsonAlpha analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeHaibTfbsGm12878NrsfPcr2xAln_2Reps.norm5.rawsignal.bw GM12878 ChipSeq NRSF Signal bigWig HudsonAlpha analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeHaibTfbsGm12878Oct2Pcr1xAln_2Reps.norm5.rawsignal.bw GM12878 ChipSeq Oct-2 Signal bigWig HudsonAlpha analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeHaibTfbsGm12878P300Pcr1xAln_2Reps.norm5.rawsignal.bw GM12878 ChipSeq p300 Signal bigWig HudsonAlpha analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeHaibTfbsGm12878Pax5c20Pcr1xAln_2Reps.norm5.rawsignal.bw GM12878 ChipSeq PAX5-C20 Signal bigWig HudsonAlpha analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeHaibTfbsGm12878Pax5n19Pcr1xAln_2Reps.norm5.rawsignal.bw GM12878 ChipSeq PAX5-N19 Signal bigWig HudsonAlpha analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeHaibTfbsGm12878Pbx3Pcr1xAln_2Reps.norm5.rawsignal.bw GM12878 ChipSeq Pbx3 Signal bigWig HudsonAlpha analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeHaibTfbsGm12878Pol24h8Pcr1xAln_2Reps.norm5.rawsignal.bw GM12878 ChipSeq Pol2-4H8 Signal bigWig HudsonAlpha analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeHaibTfbsGm12878Pol2Pcr2xAln_2Reps.norm5.rawsignal.bw GM12878 ChipSeq Pol2 Signal bigWig HudsonAlpha analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeHaibTfbsGm12878Pou2f2Pcr1xAln_2Reps.norm5.rawsignal.bw GM12878 ChipSeq POU2F2 Signal bigWig HudsonAlpha analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeHaibTfbsGm12878Pu1Pcr1xAln_2Reps.norm5.rawsignal.bw GM12878 ChipSeq PU.1 Signal bigWig HudsonAlpha analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeHaibTfbsGm12878Rad21V0416101Aln_2Reps.norm5.rawsignal.bw GM12878 ChipSeq Rad21 Signal bigWig HudsonAlpha analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeHaibTfbsGm12878RxraPcr1xAln_2Reps.norm5.rawsignal.bw GM12878 ChipSeq RXRA Signal bigWig HudsonAlpha analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeHaibTfbsGm12878Sin3ak20Pcr1xAln_3Reps.norm5.rawsignal.bw GM12878 ChipSeq Sin3Ak-20 Signal bigWig HudsonAlpha analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeHaibTfbsGm12878Six5Pcr1xAln_2Reps.norm5.rawsignal.bw GM12878 ChipSeq SIX5 Signal bigWig HudsonAlpha analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeHaibTfbsGm12878Sp1Pcr1xAln_2Reps.norm5.rawsignal.bw GM12878 ChipSeq SP1 Signal bigWig HudsonAlpha analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeHaibTfbsGm12878SrfPcr2xAln_2Reps.norm5.rawsignal.bw GM12878 ChipSeq SRF Signal bigWig HudsonAlpha analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeHaibTfbsGm12878SrfV0416101Aln_2Reps.norm5.rawsignal.bw GM12878 ChipSeq SRF Signal bigWig HudsonAlpha analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeHaibTfbsGm12878Taf1Pcr1xAln_2Reps.norm5.rawsignal.bw GM12878 ChipSeq TAF1 Signal bigWig HudsonAlpha analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeHaibTfbsGm12878Tcf12Pcr1xAln_2Reps.norm5.rawsignal.bw GM12878 ChipSeq TCF12 Signal bigWig HudsonAlpha analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeHaibTfbsGm12878Usf1Pcr2xAln_2Reps.norm5.rawsignal.bw GM12878 ChipSeq USF-1 Signal bigWig HudsonAlpha analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeHaibTfbsGm12878Yy1V0416101Aln_2Reps.norm5.rawsignal.bw GM12878 ChipSeq YY1_(SC-281) Signal 1 bigWig HudsonAlpha analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeHaibTfbsGm12878Zbtb33Pcr1xAln_2Reps.norm5.rawsignal.bw GM12878 ChipSeq ZBTB33 Signal bigWig HudsonAlpha analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeHaibTfbsGm12878Zeb1sc25388V0416102Aln_2Reps.norm5.rawsignal.bw GM12878 ChipSeq ZEB1_(SC-25388) Signal bigWig HudsonAlpha analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeHaibTfbsGm12891ControlPcr1xAln_2Reps.norm5.rawsignal.bw GM12891 ChipSeq Control Signal bigWig HudsonAlpha analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeHaibTfbsGm12891Oct2Pcr1xAln_2Reps.norm5.rawsignal.bw GM12891 ChipSeq Oct-2 Signal bigWig HudsonAlpha analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeHaibTfbsGm12891Pax5c20Pcr1xAln_2Reps.norm5.rawsignal.bw GM12891 ChipSeq PAX5-C20 Signal bigWig HudsonAlpha analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeHaibTfbsGm12891Pol24h8Pcr1xAln_2Reps.norm5.rawsignal.bw GM12891 ChipSeq Pol2-4H8 Signal bigWig HudsonAlpha analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeHaibTfbsGm12891Pol2Pcr1xAln_2Reps.norm5.rawsignal.bw GM12891 ChipSeq Pol2 Signal bigWig HudsonAlpha analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeHaibTfbsGm12891Pou2f2Pcr1xAln_2Reps.norm5.rawsignal.bw GM12891 ChipSeq POU2F2 Signal bigWig HudsonAlpha analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeHaibTfbsGm12891Pu1Pcr1xAln_2Reps.norm5.rawsignal.bw GM12891 ChipSeq PU.1 Signal bigWig HudsonAlpha analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeHaibTfbsGm12891Taf1Pcr1xAln_2Reps.norm5.rawsignal.bw GM12891 ChipSeq TAF1 Signal bigWig HudsonAlpha analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeHaibTfbsGm12891Yy1c20V0416101Aln_2Reps.norm5.rawsignal.bw GM12891 ChipSeq YY1_(C-20) Signal bigWig HudsonAlpha analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeHaibTfbsGm12892ControlPcr1xAln_4Reps.norm5.rawsignal.bw GM12892 ChipSeq Control Signal bigWig HudsonAlpha analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeHaibTfbsGm12892Pax5c20Pcr1xAln_2Reps.norm5.rawsignal.bw GM12892 ChipSeq PAX5-C20 Signal bigWig HudsonAlpha analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeHaibTfbsGm12892Pol24h8Pcr1xAln_2Reps.norm5.rawsignal.bw GM12892 ChipSeq Pol2-4H8 Signal bigWig HudsonAlpha analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeHaibTfbsGm12892Pol24h8V0416102Aln_2Reps.norm5.rawsignal.bw GM12892 ChipSeq Pol2-4H8 Signal bigWig HudsonAlpha analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeHaibTfbsGm12892Pol2Pcr1xAln_2Reps.norm5.rawsignal.bw GM12892 ChipSeq Pol2 Signal bigWig HudsonAlpha analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeHaibTfbsGm12892Pol2V0416102Aln_2Reps.norm5.rawsignal.bw GM12892 ChipSeq Pol2 Signal bigWig HudsonAlpha analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeHaibTfbsGm12892Taf1Pcr1xAln_2Reps.norm5.rawsignal.bw GM12892 ChipSeq TAF1 Signal bigWig HudsonAlpha analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeHaibTfbsGm12892Taf1V0416102Aln_2Reps.norm5.rawsignal.bw GM12892 ChipSeq TAF1 Signal bigWig HudsonAlpha analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeHaibTfbsGm12892Yy1V0416101Aln_2Reps.norm5.rawsignal.bw GM12892 ChipSeq YY1 Signal bigWig HudsonAlpha analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeHaibTfbsH1hescAtf3Pcr1xAln_2Reps.norm5.rawsignal.bw H1-hESC ChipSeq ATF3 Signal bigWig HudsonAlpha analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeHaibTfbsH1hescBcl11aPcr1xAln_3Reps.norm5.rawsignal.bw H1-hESC ChipSeq BCL11A Signal bigWig HudsonAlpha analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeHaibTfbsH1hescBcl3Pcr1xAln_2Reps.norm5.rawsignal.bw H1-hESC ChipSeq BCL3 Signal bigWig HudsonAlpha analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeHaibTfbsH1hescControlPcr1xAln_2Reps.norm5.rawsignal.bw H1-hESC ChipSeq Control Signal bigWig HudsonAlpha analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeHaibTfbsH1hescCtcfsc5916V0416102Aln_2Reps.norm5.rawsignal.bw H1-hESC ChipSeq CTCF_(SC-5916) Signal bigWig HudsonAlpha analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeHaibTfbsH1hescEgr1V0416101Aln_2Reps.norm5.rawsignal.bw H1-hESC ChipSeq Egr-1 Signal bigWig HudsonAlpha analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeHaibTfbsH1hescEgr1V0416102Aln_2Reps.norm5.rawsignal.bw H1-hESC ChipSeq Egr-1 Signal bigWig HudsonAlpha analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeHaibTfbsH1hescGabpPcr1xAln_2Reps.norm5.rawsignal.bw H1-hESC ChipSeq GABP Signal bigWig HudsonAlpha analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeHaibTfbsH1hescHdac2sc6296V0416102Aln_2Reps.norm5.rawsignal.bw H1-hESC ChipSeq HDAC2_(SC-6296) Signal bigWig HudsonAlpha analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeHaibTfbsH1hescJundV0416102Aln_2Reps.norm5.rawsignal.bw H1-hESC ChipSeq JunD Signal bigWig HudsonAlpha analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeHaibTfbsH1hescNanogsc33759V0416102Aln_2Reps.norm5.rawsignal.bw H1-hESC ChipSeq NANOG_(SC-33759) Signal bigWig HudsonAlpha analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeHaibTfbsH1hescNrsfPcr1xAln_2Reps.norm5.rawsignal.bw H1-hESC ChipSeq NRSF Signal bigWig HudsonAlpha analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeHaibTfbsH1hescNrsfV0416102Aln_2Reps.norm5.rawsignal.bw H1-hESC ChipSeq NRSF Signal bigWig HudsonAlpha analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeHaibTfbsH1hescP300Pcr1xAln_2Reps.norm5.rawsignal.bw H1-hESC ChipSeq p300 Signal bigWig HudsonAlpha analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeHaibTfbsH1hescPol24h8Pcr1xAln_2Reps.norm5.rawsignal.bw H1-hESC ChipSeq Pol2-4H8 Signal bigWig HudsonAlpha analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeHaibTfbsH1hescPol24h8V0416102Aln_2Reps.norm5.rawsignal.bw H1-hESC ChipSeq Pol2-4H8 Signal bigWig HudsonAlpha analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeHaibTfbsH1hescPol2Pcr1xAln_2Reps.norm5.rawsignal.bw H1-hESC ChipSeq Pol2 Signal bigWig HudsonAlpha analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeHaibTfbsH1hescPol2V0416102Aln_2Reps.norm5.rawsignal.bw H1-hESC ChipSeq Pol2 Signal bigWig HudsonAlpha analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeHaibTfbsH1hescPou5f1sc9081V0416102Aln_2Reps.norm5.rawsignal.bw H1-hESC ChipSeq POU5F1_(SC-9081) Signal bigWig HudsonAlpha analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeHaibTfbsH1hescRad21V0416102Aln_2Reps.norm5.rawsignal.bw H1-hESC ChipSeq Rad21 Signal bigWig HudsonAlpha analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeHaibTfbsH1hescRxraV0416102Aln_2Reps.norm5.rawsignal.bw H1-hESC ChipSeq RXRA Signal bigWig HudsonAlpha analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeHaibTfbsH1hescSin3ak20Pcr1xAln_2Reps.norm5.rawsignal.bw H1-hESC ChipSeq Sin3Ak-20 Signal bigWig HudsonAlpha analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeHaibTfbsH1hescSix5Pcr1xAln_2Reps.norm5.rawsignal.bw H1-hESC ChipSeq SIX5 Signal bigWig HudsonAlpha analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeHaibTfbsH1hescSp1Pcr1xAln_2Reps.norm5.rawsignal.bw H1-hESC ChipSeq SP1 Signal bigWig HudsonAlpha analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeHaibTfbsH1hescSrfPcr1xAln_2Reps.norm5.rawsignal.bw H1-hESC ChipSeq SRF Signal bigWig HudsonAlpha analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeHaibTfbsH1hescTaf1Pcr1xAln_2Reps.norm5.rawsignal.bw H1-hESC ChipSeq TAF1 Signal bigWig HudsonAlpha analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeHaibTfbsH1hescTaf1V0416102Aln_2Reps.norm5.rawsignal.bw H1-hESC ChipSeq TAF1 Signal bigWig HudsonAlpha analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeHaibTfbsH1hescTaf7sq8V0416102Aln_2Reps.norm5.rawsignal.bw H1-hESC ChipSeq TAF7_(SQ-8) Signal bigWig HudsonAlpha analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeHaibTfbsH1hescTcf12Pcr1xAln_2Reps.norm5.rawsignal.bw H1-hESC ChipSeq TCF12 Signal bigWig HudsonAlpha analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeHaibTfbsH1hescUsf1Pcr1xAln_2Reps.norm5.rawsignal.bw H1-hESC ChipSeq USF-1 Signal bigWig HudsonAlpha analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeHaibTfbsH1hescYy1c20Pcr1xAln_2Reps.norm5.rawsignal.bw H1-hESC ChipSeq YY1_(C-20) Signal bigWig HudsonAlpha analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeHaibTfbsHct116ControlV0416101Aln_1Reps.norm5.rawsignal.bw HCT-116 ChipSeq Control Signal bigWig HudsonAlpha analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeHaibTfbsHct116Pol24h8V0416101Aln_2Reps.norm5.rawsignal.bw HCT-116 ChipSeq Pol2-4H8 Signal bigWig HudsonAlpha analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeHaibTfbsHelas3ControlPcr1xAln_2Reps.norm5.rawsignal.bw HeLa-S3 ChipSeq Control Signal bigWig HudsonAlpha analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeHaibTfbsHelas3GabpPcr1xAln_2Reps.norm5.rawsignal.bw HeLa-S3 ChipSeq GABP Signal bigWig HudsonAlpha analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeHaibTfbsHelas3NrsfPcr1xAln_2Reps.norm5.rawsignal.bw HeLa-S3 ChipSeq NRSF Signal bigWig HudsonAlpha analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeHaibTfbsHelas3Pol2Pcr1xAln_2Reps.norm5.rawsignal.bw HeLa-S3 ChipSeq Pol2 Signal bigWig HudsonAlpha analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeHaibTfbsHelas3Taf1Pcr1xAln_2Reps.norm5.rawsignal.bw HeLa-S3 ChipSeq TAF1 Signal bigWig HudsonAlpha analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeHaibTfbsHepg2Atf3Pcr1xAln_2Reps.norm5.rawsignal.bw HepG2 ChipSeq ATF3 Signal bigWig HudsonAlpha analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeHaibTfbsHepg2Bhlhe40V0416101Aln_3Reps.norm5.rawsignal.bw HepG2 ChipSeq BHLHE40 Signal bigWig HudsonAlpha analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeHaibTfbsHepg2ControlPcr1xAln_6Reps.norm5.rawsignal.bw HepG2 ChipSeq Control Signal bigWig HudsonAlpha analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeHaibTfbsHepg2ControlPcr2xAln_2Reps.norm5.rawsignal.bw HepG2 ChipSeq Control Signal bigWig HudsonAlpha analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeHaibTfbsHepg2CtcfV0416101Aln_2Reps.norm5.rawsignal.bw HepG2 ChipSeq CTCF Signal bigWig HudsonAlpha analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeHaibTfbsHepg2Elf1sc631V0416101Aln_2Reps.norm5.rawsignal.bw HepG2 ChipSeq ELF1_(SC-631) Signal bigWig HudsonAlpha analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeHaibTfbsHepg2Fosl2Pcr1xAln_2Reps.norm5.rawsignal.bw HepG2 ChipSeq FOSL2 Signal bigWig HudsonAlpha analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeHaibTfbsHepg2Foxa1c20Pcr1xAln_2Reps.norm5.rawsignal.bw HepG2 ChipSeq FOXA1_(C-20) Signal bigWig HudsonAlpha analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeHaibTfbsHepg2Foxa1sc101058Pcr1xAln_2Reps.norm5.rawsignal.bw HepG2 ChipSeq FOXA1_(SC-101058) Signal bigWig HudsonAlpha analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeHaibTfbsHepg2Foxa2sc6554V0416101Aln_2Reps.norm5.rawsignal.bw HepG2 ChipSeq FOXA2_(SC-6554) Signal bigWig HudsonAlpha analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeHaibTfbsHepg2GabpPcr2xAln_2Reps.norm5.rawsignal.bw HepG2 ChipSeq GABP Signal bigWig HudsonAlpha analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeHaibTfbsHepg2Hdac2sc6296V0416101Aln_2Reps.norm5.rawsignal.bw HepG2 ChipSeq HDAC2_(SC-6296) Signal bigWig HudsonAlpha analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeHaibTfbsHepg2Hey1V0416101Aln_2Reps.norm5.rawsignal.bw HepG2 ChipSeq HEY1 Signal bigWig HudsonAlpha analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeHaibTfbsHepg2Hnf4ah171Pcr1xAln_2Reps.norm5.rawsignal.bw HepG2 ChipSeq HNF4A_(H-171) Signal bigWig HudsonAlpha analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeHaibTfbsHepg2Hnf4gsc6558V0416101Aln_2Reps.norm5.rawsignal.bw HepG2 ChipSeq HNF4G_(SC-6558) Signal bigWig HudsonAlpha analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeHaibTfbsHepg2JundPcr1xAln_2Reps.norm5.rawsignal.bw HepG2 ChipSeq JunD Signal bigWig HudsonAlpha analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeHaibTfbsHepg2NrsfPcr2xAln_2Reps.norm5.rawsignal.bw HepG2 ChipSeq NRSF Signal bigWig HudsonAlpha analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeHaibTfbsHepg2P300Pcr1xAln_2Reps.norm5.rawsignal.bw HepG2 ChipSeq p300 Signal bigWig HudsonAlpha analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeHaibTfbsHepg2P300V0416101Aln_2Reps.norm5.rawsignal.bw HepG2 ChipSeq p300 Signal bigWig HudsonAlpha analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeHaibTfbsHepg2Pol2Pcr2xAln_2Reps.norm5.rawsignal.bw HepG2 ChipSeq Pol2 Signal bigWig HudsonAlpha analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeHaibTfbsHepg2Rad21V0416101Aln_2Reps.norm5.rawsignal.bw HepG2 ChipSeq Rad21 Signal bigWig HudsonAlpha analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeHaibTfbsHepg2RxraPcr1xAln_2Reps.norm5.rawsignal.bw HepG2 ChipSeq RXRA Signal bigWig HudsonAlpha analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeHaibTfbsHepg2Sin3ak20Pcr1xAln_2Reps.norm5.rawsignal.bw HepG2 ChipSeq Sin3Ak-20 Signal bigWig HudsonAlpha analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeHaibTfbsHepg2Sp1Pcr1xAln_2Reps.norm5.rawsignal.bw HepG2 ChipSeq SP1 Signal bigWig HudsonAlpha analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeHaibTfbsHepg2SrfV0416101Aln_2Reps.norm5.rawsignal.bw HepG2 ChipSeq SRF Signal bigWig HudsonAlpha analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeHaibTfbsHepg2Taf1Pcr2xAln_2Reps.norm5.rawsignal.bw HepG2 ChipSeq TAF1 Signal bigWig HudsonAlpha analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeHaibTfbsHepg2Tcf12Pcr1xAln_2Reps.norm5.rawsignal.bw HepG2 ChipSeq TCF12 Signal bigWig HudsonAlpha analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeHaibTfbsHepg2Usf1Pcr1xAln_2Reps.norm5.rawsignal.bw HepG2 ChipSeq USF-1 Signal bigWig HudsonAlpha analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeHaibTfbsHepg2Zbtb33Pcr1xAln_2Reps.norm5.rawsignal.bw HepG2 ChipSeq ZBTB33 Signal bigWig HudsonAlpha analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeHaibTfbsHepg2Zbtb33V0416101Aln_2Reps.norm5.rawsignal.bw HepG2 ChipSeq ZBTB33 Signal bigWig HudsonAlpha analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeHaibTfbsHtb11ControlPcr2xAln_2Reps.norm5.rawsignal.bw HTB-11 ChipSeq Control Signal bigWig HudsonAlpha analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeHaibTfbsHtb11NrsfPcr2xAln_2Reps.norm5.rawsignal.bw HTB-11 ChipSeq NRSF Signal bigWig HudsonAlpha analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeHaibTfbsK562Bcl3Pcr1xAln_2Reps.norm5.rawsignal.bw K562 ChipSeq BCL3 Signal bigWig HudsonAlpha analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeHaibTfbsK562Bclaf1m33Pcr1xAln_2Reps.norm5.rawsignal.bw K562 ChipSeq BCLAF1_(M33-P5B11) Signal bigWig HudsonAlpha analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeHaibTfbsK562ControlPcr1xAln_6Reps.norm5.rawsignal.bw K562 ChipSeq Control Signal bigWig HudsonAlpha analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeHaibTfbsK562Ctcflsc98982V0416101Aln_2Reps.norm5.rawsignal.bw K562 ChipSeq CTCFL_(SC-98982) Signal bigWig HudsonAlpha analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeHaibTfbsK562E2f6h50V0416102Aln_2Reps.norm5.rawsignal.bw K562 ChipSeq E2F6_(H-50) Signal bigWig HudsonAlpha analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeHaibTfbsK562Egr1V0416101Aln_2Reps.norm5.rawsignal.bw K562 ChipSeq Egr-1 Signal bigWig HudsonAlpha analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeHaibTfbsK562Elf1sc631V0416102Aln_2Reps.norm5.rawsignal.bw K562 ChipSeq ELF1_(SC-631) Signal bigWig HudsonAlpha analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeHaibTfbsK562Ets1V0416101Aln_2Reps.norm5.rawsignal.bw K562 ChipSeq ETS1 Signal bigWig HudsonAlpha analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeHaibTfbsK562Fosl1sc183V0416101Aln_2Reps.norm5.rawsignal.bw K562 ChipSeq FOSL1_(SC-183) Signal bigWig HudsonAlpha analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeHaibTfbsK562GabpV0416101Aln_2Reps.norm5.rawsignal.bw K562 ChipSeq GABP Signal bigWig HudsonAlpha analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeHaibTfbsK562Gata2cg2Pcr1xAln_2Reps.norm5.rawsignal.bw K562 ChipSeq GATA2_(CG2-96) Signal bigWig HudsonAlpha analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeHaibTfbsK562Hdac2sc6296V0416102Aln_2Reps.norm5.rawsignal.bw K562 ChipSeq HDAC2_(SC-6296) Signal bigWig HudsonAlpha analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeHaibTfbsK562Hey1Pcr1xAln_2Reps.norm5.rawsignal.bw K562 ChipSeq HEY1 Signal bigWig HudsonAlpha analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeHaibTfbsK562MaxV0416102Aln_2Reps.norm5.rawsignal.bw K562 ChipSeq Max Signal bigWig HudsonAlpha analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeHaibTfbsK562NrsfV0416102Aln_2Reps.norm5.rawsignal.bw K562 ChipSeq NRSF Signal bigWig HudsonAlpha analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeHaibTfbsK562Pol24h8Pcr1xAln_2Reps.norm5.rawsignal.bw K562 ChipSeq Pol2-4H8 Signal bigWig HudsonAlpha analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeHaibTfbsK562Pol24h8V0416101Aln_2Reps.norm5.rawsignal.bw K562 ChipSeq Pol2-4H8 Signal bigWig HudsonAlpha analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeHaibTfbsK562Pol2V0416101Aln_2Reps.norm5.rawsignal.bw K562 ChipSeq Pol2 Signal bigWig HudsonAlpha analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeHaibTfbsK562Pu1Pcr1xAln_2Reps.norm5.rawsignal.bw K562 ChipSeq PU.1 Signal bigWig HudsonAlpha analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeHaibTfbsK562Rad21V0416102Aln_2Reps.norm5.rawsignal.bw K562 ChipSeq Rad21 Signal bigWig HudsonAlpha analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeHaibTfbsK562Sin3ak20V0416101Aln_2Reps.norm5.rawsignal.bw K562 ChipSeq Sin3Ak-20 Signal bigWig HudsonAlpha analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeHaibTfbsK562Six5Pcr1xAln_2Reps.norm5.rawsignal.bw K562 ChipSeq SIX5 Signal bigWig HudsonAlpha analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeHaibTfbsK562Sp1Pcr1xAln_2Reps.norm5.rawsignal.bw K562 ChipSeq SP1 Signal bigWig HudsonAlpha analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeHaibTfbsK562Sp2sc643V0416102Aln_2Reps.norm5.rawsignal.bw K562 ChipSeq SP2_(SC-643) Signal bigWig HudsonAlpha analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeHaibTfbsK562SrfV0416101Aln_2Reps.norm5.rawsignal.bw K562 ChipSeq SRF Signal bigWig HudsonAlpha analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeHaibTfbsK562Taf1Pcr1xAln_2Reps.norm5.rawsignal.bw K562 ChipSeq TAF1 Signal bigWig HudsonAlpha analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeHaibTfbsK562Taf1V0416101Aln_2Reps.norm5.rawsignal.bw K562 ChipSeq TAF1 Signal bigWig HudsonAlpha analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeHaibTfbsK562Taf7sq8V0416101Aln_2Reps.norm5.rawsignal.bw K562 ChipSeq TAF7_(SQ-8) Signal bigWig HudsonAlpha analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeHaibTfbsK562Thap1sc98174V0416101Aln_2Reps.norm5.rawsignal.bw K562 ChipSeq THAP1_(SC-98174) Signal bigWig HudsonAlpha analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeHaibTfbsK562Usf1V0416101Aln_2Reps.norm5.rawsignal.bw K562 ChipSeq USF-1 Signal bigWig HudsonAlpha analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeHaibTfbsK562Yy1V0416101Aln_2Reps.norm5.rawsignal.bw K562 ChipSeq YY1 Signal bigWig HudsonAlpha analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeHaibTfbsK562Yy1V0416102Aln_2Reps.norm5.rawsignal.bw K562 ChipSeq YY1 Signal bigWig HudsonAlpha analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeHaibTfbsK562Zbtb33Pcr1xAln_2Reps.norm5.rawsignal.bw K562 ChipSeq ZBTB33 Signal bigWig HudsonAlpha analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeHaibTfbsK562Zbtb7asc34508V0416101Aln_2Reps.norm5.rawsignal.bw K562 ChipSeq ZBTB7A_(SC-34508) Signal bigWig HudsonAlpha analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeHaibTfbsPanc1ControlPcr2xAln_2Reps.norm5.rawsignal.bw PANC-1 ChipSeq Control Signal bigWig HudsonAlpha analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeHaibTfbsPanc1NrsfPcr2xAln_2Reps.norm5.rawsignal.bw PANC-1 ChipSeq NRSF Signal bigWig HudsonAlpha analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeHaibTfbsPfsk1ControlPcr2xAln_2Reps.norm5.rawsignal.bw PFSK-1 ChipSeq Control Signal bigWig HudsonAlpha analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeHaibTfbsPfsk1NrsfPcr2xAln_2Reps.norm5.rawsignal.bw PFSK-1 ChipSeq NRSF Signal bigWig HudsonAlpha analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeHaibTfbsSknmcControlV0416101Aln_1Reps.norm5.rawsignal.bw SK-N-MC ChipSeq Control Signal bigWig HudsonAlpha analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeHaibTfbsSknshraControlV0416102Aln_1Reps.norm5.rawsignal.bw SK-N-SH_RA ChipSeq Control Signal bigWig HudsonAlpha analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeHaibTfbsSknshraCtcfV0416102Aln_2Reps.norm5.rawsignal.bw SK-N-SH_RA ChipSeq CTCF Signal bigWig HudsonAlpha analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeHaibTfbsSknshraP300V0416102Aln_2Reps.norm5.rawsignal.bw SK-N-SH_RA ChipSeq p300 Signal bigWig HudsonAlpha analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeHaibTfbsSknshraRad21V0416102Aln_2Reps.norm5.rawsignal.bw SK-N-SH_RA ChipSeq Rad21 Signal bigWig HudsonAlpha analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeHaibTfbsSknshraUsf1sc8983V0416102Aln_2Reps.norm5.rawsignal.bw SK-N-SH_RA ChipSeq USF1_(SC-8983) Signal bigWig HudsonAlpha analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeHaibTfbsSknshraYy1c20V0416102Aln_2Reps.norm5.rawsignal.bw SK-N-SH_RA ChipSeq YY1_(C-20) Signal bigWig HudsonAlpha analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeHaibTfbsT47dControlV0416102Dmso2Aln_1Reps.norm5.rawsignal.bw T-47D ChipSeq Control Signal bigWig HudsonAlpha analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeHaibTfbsT47dCtcfsc5916V0416102Dmso2Aln_2Reps.norm5.rawsignal.bw T-47D ChipSeq CTCF_(SC-5916) Signal bigWig HudsonAlpha analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeHaibTfbsT47dEralphaaPcr2xGen1hAln_2Reps.norm5.rawsignal.bw T-47D ChipSeq ERalpha_a Signal bigWig HudsonAlpha analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeHaibTfbsT47dEralphaaV0416102Dmso2Aln_2Reps.norm5.rawsignal.bw T-47D ChipSeq ERalpha_a Signal bigWig HudsonAlpha analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeHaibTfbsT47dEralphaaV0416102Estradia1hAln_2Reps.norm5.rawsignal.bw T-47D ChipSeq ERalpha_a Signal bigWig HudsonAlpha analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeHaibTfbsT47dFoxa1c20V0416102Dmso2Aln_2Reps.norm5.rawsignal.bw T-47D ChipSeq FOXA1_(C-20) Signal bigWig HudsonAlpha analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeHaibTfbsT47dGata3sc268V0416102Dmso2Aln_2Reps.norm5.rawsignal.bw T-47D ChipSeq GATA3_(SC-268) Signal bigWig HudsonAlpha analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeHaibTfbsT47dP300V0416102Dmso2Aln_2Reps.norm5.rawsignal.bw T-47D ChipSeq p300 Signal bigWig HudsonAlpha analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeHaibTfbsU87ControlPcr2xAln_2Reps.norm5.rawsignal.bw U87 ChipSeq Control Signal bigWig HudsonAlpha analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeHaibTfbsU87NrsfPcr2xAln_2Reps.norm5.rawsignal.bw U87 ChipSeq NRSF Signal bigWig HudsonAlpha analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeOpenChromChipFibroblCtcfAln_2Reps.norm5.rawsignal.bw Fibrobl ChipSeq CTCF Signal bigWig UT-A analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeOpenChromChipFibroblInputAln_1Reps.norm5.rawsignal.bw Fibrobl ChipSeq Input Signal bigWig UT-A analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeOpenChromChipGlioblaCtcfAln_2Reps.norm5.rawsignal.bw Gliobla ChipSeq CTCF Signal bigWig UT-A analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeOpenChromChipGlioblaInputAln_1Reps.norm5.rawsignal.bw Gliobla ChipSeq Input Signal bigWig UT-A analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeOpenChromChipGlioblaPol2Aln_2Reps.norm5.rawsignal.bw Gliobla ChipSeq Pol2 Signal bigWig UT-A analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeOpenChromChipGm12878CmycAln_2Reps.norm5.rawsignal.bw GM12878 ChipSeq c-Myc Signal bigWig UT-A analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeOpenChromChipGm12878CtcfAln_3Reps.norm5.rawsignal.bw GM12878 ChipSeq CTCF Signal bigWig UT-A analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeOpenChromChipGm12878InputAln_1Reps.norm5.rawsignal.bw GM12878 ChipSeq Input Signal bigWig UT-A analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeOpenChromChipGm12878Pol2Aln_2Reps.norm5.rawsignal.bw GM12878 ChipSeq Pol2 Signal bigWig UT-A analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeOpenChromChipGm12891CtcfAln_2Reps.norm5.rawsignal.bw GM12891 ChipSeq CTCF Signal bigWig UT-A analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeOpenChromChipGm12892CtcfAln_2Reps.norm5.rawsignal.bw GM12892 ChipSeq CTCF Signal bigWig UT-A analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeOpenChromChipGm19238CtcfAln_2Reps.norm5.rawsignal.bw GM19238 ChipSeq CTCF Signal bigWig UT-A analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeOpenChromChipGm19239CtcfAln_2Reps.norm5.rawsignal.bw GM19239 ChipSeq CTCF Signal bigWig UT-A analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeOpenChromChipGm19240CtcfAln_2Reps.norm5.rawsignal.bw GM19240 ChipSeq CTCF Signal bigWig UT-A analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeOpenChromChipH1hescCmycAln_1Reps.norm5.rawsignal.bw H1-hESC ChipSeq c-Myc Signal bigWig UT-A analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeOpenChromChipH1hescCtcfAln_1Reps.norm5.rawsignal.bw H1-hESC ChipSeq CTCF Signal bigWig UT-A analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeOpenChromChipH1hescPol2Aln_1Reps.norm5.rawsignal.bw H1-hESC ChipSeq Pol2 Signal bigWig UT-A analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeOpenChromChipHelas3CmycAln_2Reps.norm5.rawsignal.bw HeLa-S3 ChipSeq c-Myc Signal bigWig UT-A analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeOpenChromChipHelas3CtcfAln_2Reps.norm5.rawsignal.bw HeLa-S3 ChipSeq CTCF Signal bigWig UT-A analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeOpenChromChipHelas3InputAln_1Reps.norm5.rawsignal.bw HeLa-S3 ChipSeq Input Signal bigWig UT-A analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeOpenChromChipHelas3Pol2Aln_2Reps.norm5.rawsignal.bw HeLa-S3 ChipSeq Pol2 Signal bigWig UT-A analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeOpenChromChipHepg2CmycAln_3Reps.norm5.rawsignal.bw HepG2 ChipSeq c-Myc Signal bigWig UT-A analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeOpenChromChipHepg2CtcfAln_2Reps.norm5.rawsignal.bw HepG2 ChipSeq CTCF Signal bigWig UT-A analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeOpenChromChipHepg2InputAln_1Reps.norm5.rawsignal.bw HepG2 ChipSeq Input Signal bigWig UT-A analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeOpenChromChipHepg2Pol2Aln_3Reps.norm5.rawsignal.bw HepG2 ChipSeq Pol2 Signal bigWig UT-A analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeOpenChromChipHuvecCmycAln_1Reps.norm5.rawsignal.bw HUVEC ChipSeq c-Myc Signal bigWig UT-A analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeOpenChromChipHuvecCtcfAln_2Reps.norm5.rawsignal.bw HUVEC ChipSeq CTCF Signal bigWig UT-A analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeOpenChromChipHuvecInputAln_1Reps.norm5.rawsignal.bw HUVEC ChipSeq Input Signal bigWig UT-A analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeOpenChromChipHuvecPol2Aln_2Reps.norm5.rawsignal.bw HUVEC ChipSeq Pol2 Signal bigWig UT-A analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeOpenChromChipK562CmycAln_3Reps.norm5.rawsignal.bw K562 ChipSeq c-Myc Signal bigWig UT-A analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeOpenChromChipK562CtcfAln_3Reps.norm5.rawsignal.bw K562 ChipSeq CTCF Signal bigWig UT-A analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeOpenChromChipK562InputAln_1Reps.norm5.rawsignal.bw K562 ChipSeq Input Signal bigWig UT-A analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeOpenChromChipK562Pol2Aln_2Reps.norm5.rawsignal.bw K562 ChipSeq Pol2 Signal bigWig UT-A analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeOpenChromChipMcf7CmycEstroAln_2Reps.norm5.rawsignal.bw MCF-7 ChipSeq c-Myc Signal bigWig UT-A analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeOpenChromChipMcf7CmycVehAln_2Reps.norm5.rawsignal.bw MCF-7 ChipSeq c-Myc Signal bigWig UT-A analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeOpenChromChipMcf7CtcfAln_2Reps.norm5.rawsignal.bw MCF-7 ChipSeq CTCF Signal bigWig UT-A analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeOpenChromChipMcf7CtcfEstroAln_2Reps.norm5.rawsignal.bw MCF-7 ChipSeq CTCF Signal bigWig UT-A analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeOpenChromChipMcf7CtcfVehAln_2Reps.norm5.rawsignal.bw MCF-7 ChipSeq CTCF Signal bigWig UT-A analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeOpenChromChipMcf7InputAln_1Reps.norm5.rawsignal.bw MCF-7 ChipSeq Input Signal bigWig UT-A analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeOpenChromChipMcf7Pol2Aln_2Reps.norm5.rawsignal.bw MCF-7 ChipSeq Pol2 Signal bigWig UT-A analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeOpenChromChipMonocd14InputAln_1Reps.norm5.rawsignal.bw Monocytes-CD14+ ChipSeq Input Signal bigWig UT-A analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeOpenChromChipNhekCtcfAln_2Reps.norm5.rawsignal.bw NHEK ChipSeq CTCF Signal bigWig UT-A analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeOpenChromChipProgfibCtcfAln_2Reps.norm5.rawsignal.bw ProgFib ChipSeq CTCF Signal bigWig UT-A analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeOpenChromChipProgfibInputAln_1Reps.norm5.rawsignal.bw ProgFib ChipSeq Input Signal bigWig UT-A analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeOpenChromChipProgfibPol2Aln_2Reps.norm5.rawsignal.bw ProgFib ChipSeq Pol2 Signal bigWig UT-A analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeOpenChromDnase8988tAln_2Reps.norm5.rawsignal.bw 8988T DnaseSeq Signal bigWig Duke analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeOpenChromDnaseA549Aln_2Reps.norm5.rawsignal.bw A549 DnaseSeq Signal bigWig Duke analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeOpenChromDnaseAosmcSerumfreeAln_2Reps.norm5.rawsignal.bw AoSMC DnaseSeq Signal bigWig Duke analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeOpenChromDnaseChorionAln_2Reps.norm5.rawsignal.bw Chorion DnaseSeq Signal bigWig Duke analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeOpenChromDnaseCllAln_3Reps.norm5.rawsignal.bw CLL DnaseSeq Signal bigWig Duke analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeOpenChromDnaseFibroblAln_2Reps.norm5.rawsignal.bw Fibrobl DnaseSeq Signal bigWig Duke analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeOpenChromDnaseFibropAln_3Reps.norm5.rawsignal.bw FibroP DnaseSeq Signal bigWig Duke analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeOpenChromDnaseGlioblaAln_2Reps.norm5.rawsignal.bw Gliobla DnaseSeq Signal bigWig Duke analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeOpenChromDnaseGm12878Aln_5Reps.norm5.rawsignal.bw GM12878 DnaseSeq Signal bigWig Duke analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeOpenChromDnaseGm12891Aln_2Reps.norm5.rawsignal.bw GM12891 DnaseSeq Signal bigWig Duke analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeOpenChromDnaseGm12892Aln_2Reps.norm5.rawsignal.bw GM12892 DnaseSeq Signal bigWig Duke analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeOpenChromDnaseGm18507Aln_3Reps.norm5.rawsignal.bw GM18507 DnaseSeq Signal bigWig Duke analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeOpenChromDnaseGm19238Aln_2Reps.norm5.rawsignal.bw GM19238 DnaseSeq Signal bigWig Duke analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeOpenChromDnaseGm19239Aln_2Reps.norm5.rawsignal.bw GM19239 DnaseSeq Signal bigWig Duke analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeOpenChromDnaseGm19240Aln_2Reps.norm5.rawsignal.bw GM19240 DnaseSeq Signal bigWig Duke analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeOpenChromDnaseH1hescAln_2Reps.norm5.rawsignal.bw H1-hESC DnaseSeq Signal bigWig Duke analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeOpenChromDnaseH9esAln_2Reps.norm5.rawsignal.bw H9ES DnaseSeq Signal bigWig Duke analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeOpenChromDnaseHelas3Aln_3Reps.norm5.rawsignal.bw HeLa-S3 DnaseSeq Signal bigWig Duke analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeOpenChromDnaseHelas3Ifna4hAln_2Reps.norm5.rawsignal.bw HeLa-S3 DnaseSeq Signal bigWig Duke analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeOpenChromDnaseHepatocytesAln_2Reps.norm5.rawsignal.bw Hepatocytes DnaseSeq Signal bigWig Duke analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeOpenChromDnaseHepg2Aln_3Reps.norm5.rawsignal.bw HepG2 DnaseSeq Signal bigWig Duke analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeOpenChromDnaseHmecAln_2Reps.norm5.rawsignal.bw HMEC DnaseSeq Signal bigWig Duke analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeOpenChromDnaseHpde6e6e7Aln_2Reps.norm5.rawsignal.bw HPDE6-E6E7 DnaseSeq Signal bigWig Duke analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeOpenChromDnaseHsmmAln_3Reps.norm5.rawsignal.bw HSMM DnaseSeq Signal bigWig Duke analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeOpenChromDnaseHsmmtAln_3Reps.norm5.rawsignal.bw HSMMtube DnaseSeq Signal bigWig Duke analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeOpenChromDnaseHtr8Aln_2Reps.norm5.rawsignal.bw HTR8svn DnaseSeq Signal bigWig Duke analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeOpenChromDnaseHuh75Aln_2Reps.norm5.rawsignal.bw Huh-7.5 DnaseSeq Signal bigWig Duke analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeOpenChromDnaseHuh7Aln_2Reps.norm5.rawsignal.bw Huh-7 DnaseSeq Signal bigWig Duke analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeOpenChromDnaseHuvecAln_2Reps.norm5.rawsignal.bw HUVEC DnaseSeq Signal bigWig Duke analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeOpenChromDnaseIpsAln_3Reps.norm5.rawsignal.bw iPS DnaseSeq Signal bigWig Duke analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeOpenChromDnaseK562Aln_2Reps.norm5.rawsignal.bw K562 DnaseSeq Signal bigWig Duke analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeOpenChromDnaseLncapAln_3Reps.norm5.rawsignal.bw LNCaP DnaseSeq Signal bigWig Duke analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeOpenChromDnaseLncapAndroAln_2Reps.norm5.rawsignal.bw LNCaP DnaseSeq Signal bigWig Duke analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeOpenChromDnaseMcf7Aln_2Reps.norm5.rawsignal.bw MCF-7 DnaseSeq Signal bigWig Duke analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeOpenChromDnaseMedulloAln_2Reps.norm5.rawsignal.bw Medullo DnaseSeq Signal bigWig Duke analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeOpenChromDnaseMelanoAln_2Reps.norm5.rawsignal.bw Melano DnaseSeq Signal bigWig Duke analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeOpenChromDnaseMyometrAln_2Reps.norm5.rawsignal.bw Myometr DnaseSeq Signal bigWig Duke analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeOpenChromDnaseNhekAln_2Reps.norm5.rawsignal.bw NHEK DnaseSeq Signal bigWig Duke analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeOpenChromDnaseOsteoblAln_3Reps.norm5.rawsignal.bw Osteobl DnaseSeq Signal bigWig Duke analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeOpenChromDnasePanisdAln_3Reps.norm5.rawsignal.bw PanIsletD DnaseSeq Signal bigWig Duke analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeOpenChromDnasePanisletsAln_3Reps.norm5.rawsignal.bw PanIslets DnaseSeq Signal bigWig Duke analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeOpenChromDnasePhteAln_2Reps.norm5.rawsignal.bw pHTE DnaseSeq Signal bigWig Duke analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeOpenChromDnaseProgfibAln_2Reps.norm5.rawsignal.bw ProgFib DnaseSeq Signal bigWig Duke analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeOpenChromDnaseStellateAln_2Reps.norm5.rawsignal.bw Stellate DnaseSeq Signal bigWig Duke analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeOpenChromDnaseT47dAln_2Reps.norm5.rawsignal.bw T-47D DnaseSeq Signal bigWig Duke analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeOpenChromDnaseUrotsaAln_2Reps.norm5.rawsignal.bw Urothelia DnaseSeq Signal bigWig Duke analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeOpenChromDnaseUrotsaUt189Aln_2Reps.norm5.rawsignal.bw Urothelia DnaseSeq Signal bigWig Duke analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeOpenChromFaireA549Aln_2Reps.norm5.rawsignal.bw A549 FaireSeq Signal bigWig UNC(Lieb) analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeOpenChromFaireAstrocyAln_2Reps.norm5.rawsignal.bw Astrocy FaireSeq Signal bigWig UNC analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeOpenChromFaireGlioblaAln_3Reps.norm5.rawsignal.bw Gliobla FaireSeq Signal bigWig UNC analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeOpenChromFaireGm12878Aln_3Reps.norm5.rawsignal.bw GM12878 FaireSeq Signal bigWig UNC analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeOpenChromFaireGm12891Aln_2Reps.norm5.rawsignal.bw GM12891 FaireSeq Signal bigWig UNC analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeOpenChromFaireGm12892Aln_2Reps.norm5.rawsignal.bw GM12892 FaireSeq Signal bigWig UNC analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeOpenChromFaireGm18507Aln_2Reps.norm5.rawsignal.bw GM18507 FaireSeq Signal bigWig UNC analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeOpenChromFaireGm19239Aln_2Reps.norm5.rawsignal.bw GM19239 FaireSeq Signal bigWig UNC analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeOpenChromFaireH1hescAln_2Reps.norm5.rawsignal.bw H1-hESC FaireSeq Signal bigWig UNC analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeOpenChromFaireHelas3Aln_2Reps.norm5.rawsignal.bw HeLa-S3 FaireSeq Signal bigWig UNC analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeOpenChromFaireHelas3Ifna4hAln_2Reps.norm5.rawsignal.bw HeLa-S3 FaireSeq Signal bigWig UNC analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeOpenChromFaireHelas3Ifng4hAln_2Reps.norm5.rawsignal.bw HeLa-S3 FaireSeq Signal bigWig UNC analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeOpenChromFaireHepg2Aln_3Reps.norm5.rawsignal.bw HepG2 FaireSeq Signal bigWig UNC analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeOpenChromFaireHtr8Aln_2Reps.norm5.rawsignal.bw HTR8svn FaireSeq Signal bigWig UNC analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeOpenChromFaireHuvecAln_2Reps.norm5.rawsignal.bw HUVEC FaireSeq Signal bigWig UNC analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeOpenChromFaireK562Aln_2Reps.norm5.rawsignal.bw K562 FaireSeq Signal bigWig UNC analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeOpenChromFaireK562NabutAln_2Reps.norm5.rawsignal.bw K562 FaireSeq Signal bigWig UNC analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeOpenChromFaireK562OhureaAln_2Reps.norm5.rawsignal.bw K562 FaireSeq Signal bigWig UNC analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeOpenChromFaireMcf7HypoxlacAln_2Reps.norm5.rawsignal.bw MCF-7 FaireSeq Signal bigWig UNC analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeOpenChromFaireMedulloAln_2Reps.norm5.rawsignal.bw Medullo FaireSeq Signal bigWig UNC analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeOpenChromFaireNhbeAln_2Reps.norm5.rawsignal.bw NHBE FaireSeq Signal bigWig UNC analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeOpenChromFaireNhekAln_2Reps.norm5.rawsignal.bw NHEK FaireSeq Signal bigWig UNC analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeOpenChromFairePanisletsAln_1Reps.norm5.rawsignal.bw PanIslets FaireSeq Signal bigWig UNC analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeOpenChromFaireUrotsaAln_2Reps.norm5.rawsignal.bw Urothelia FaireSeq Signal bigWig UNC analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeOpenChromFaireUrotsaUt189Aln_2Reps.norm5.rawsignal.bw Urothelia FaireSeq Signal bigWig UNC analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeSydhGm12878NucleosomeRep0.bw30.norm5.rawsignal.bw bw analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeSydhHistoneK562H3k27me3UcdAln_2Reps.norm5.rawsignal.bw K562 ChIP-seq H3K27me3 Signal bigWig UCD analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeSydhHistoneK562H3k4me1UcdAln_2Reps.norm5.rawsignal.bw K562 ChIP-seq H3K4me1 Signal bigWig UCD analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeSydhHistoneK562H3k4me3UcdAln_2Reps.norm5.rawsignal.bw K562 ChIP-seq H3K4me3 Signal bigWig UCD analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeSydhHistoneK562H3k9acbUcdAln_2Reps.norm5.rawsignal.bw K562 ChIP-seq H3K9acB Signal bigWig UCD analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeSydhHistoneNt2d1H3k27me3StdAln_2Reps.norm5.rawsignal.bw NT2-D1 ChIP-seq H3K27me3 Signal bigWig UCD analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeSydhHistoneNt2d1H3k36me3bUcdAln_2Reps.norm5.rawsignal.bw NT2-D1 ChIP-seq H3K36me3B Signal bigWig UCD analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeSydhHistoneNt2d1H3k4me1UcdAln_2Reps.norm5.rawsignal.bw NT2-D1 ChIP-seq H3K4me1 Signal bigWig UCD analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeSydhHistoneNt2d1H3k4me3StdAln_2Reps.norm5.rawsignal.bw NT2-D1 ChIP-seq H3K4me3 Signal bigWig UCD analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeSydhHistoneNt2d1H3k9acStdAln_2Reps.norm5.rawsignal.bw NT2-D1 ChIP-seq H3K9ac Signal bigWig UCD analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeSydhHistoneNt2d1H3k9me3UcdAln_2Reps.norm5.rawsignal.bw NT2-D1 ChIP-seq H3K9me3 Signal bigWig UCD analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeSydhHistoneNt2d1InputStdAln_1Reps.norm5.rawsignal.bw NT2-D1 ChIP-seq Input Signal bigWig UCD analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeSydhHistoneU2osH3k9me3UcdAln_2Reps.norm5.rawsignal.bw U2OS ChIP-seq H3K9me3 Signal bigWig UCD(Farnham) analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeSydhK562NucleosomeRep0.bw30.norm5.rawsignal.bw bw analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeSydhTfbsGm10847InputIggmusAln_2Reps.norm5.rawsignal.bw GM10847 ChipSeq Input Signal bigWig Stanford analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeSydhTfbsGm10847InputIggrabAln_2Reps.norm5.rawsignal.bw GM10847 ChipSeq Input Signal bigWig Stanford analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeSydhTfbsGm10847NfkbIggrabAln_5Reps.norm5.rawsignal.bw GM10847 ChipSeq NFKB Signal bigWig Stanford analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeSydhTfbsGm10847Pol2IggmusAln_1Reps.norm5.rawsignal.bw GM10847 ChipSeq Pol2 Signal bigWig Stanford analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeSydhTfbsGm12878Brca1cIggmusAln_2Reps.norm5.rawsignal.bw GM12878 ChipSeq BRCA1_(C-1863) Signal bigWig Stanford analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeSydhTfbsGm12878CfosStdAln_3Reps.norm5.rawsignal.bw GM12878 ChipSeq c-Fos Signal bigWig Stanford analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeSydhTfbsGm12878Chd21250IggmusAln_2Reps.norm5.rawsignal.bw GM12878 ChipSeq CHD2_(N-1250) Signal bigWig Stanford analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeSydhTfbsGm12878Ctcfc20StdAln_2Reps.norm5.rawsignal.bw GM12878 ChipSeq CTCF_(C-20) Signal bigWig Stanford analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeSydhTfbsGm12878EbfStdAln_2Reps.norm5.rawsignal.bw GM12878 ChipSeq EBF Signal bigWig Stanford analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeSydhTfbsGm12878Gcn5StdAln_2Reps.norm5.rawsignal.bw GM12878 ChipSeq GCN5 Signal bigWig Harvard(Weissman) analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeSydhTfbsGm12878InputIggmusAln_2Reps.norm5.rawsignal.bw GM12878 ChipSeq Input Signal bigWig Stanford analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeSydhTfbsGm12878InputIggrabAln_2Reps.norm5.rawsignal.bw GM12878 ChipSeq Input Signal bigWig Stanford analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeSydhTfbsGm12878InputStdAln_1Reps.norm5.rawsignal.bw GM12878 ChipSeq Input Signal bigWig Stanford analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeSydhTfbsGm12878Irf3StdAln_2Reps.norm5.rawsignal.bw GM12878 ChipSeq IRF3 Signal bigWig Stanford analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeSydhTfbsGm12878JundStdAln_2Reps.norm5.rawsignal.bw GM12878 ChipSeq JunD Signal bigWig Stanford analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeSydhTfbsGm12878MaxStdAln_2Reps.norm5.rawsignal.bw GM12878 ChipSeq Max Signal bigWig Stanford analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeSydhTfbsGm12878Nfe2hStdAln_2Reps.norm5.rawsignal.bw GM12878 ChipSeq NF-E2_(H-230) Signal bigWig Stanford analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeSydhTfbsGm12878NfkbIggrabAln_4Reps.norm5.rawsignal.bw GM12878 ChipSeq NFKB Signal bigWig Stanford analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeSydhTfbsGm12878NfkbTnfaStdAln_4Reps.norm5.rawsignal.bw GM12878 ChipSeq NFKB Signal bigWig Stanford analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeSydhTfbsGm12878Nrf1IggmusAln_2Reps.norm5.rawsignal.bw GM12878 ChipSeq Nrf1 Signal bigWig Stanford analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeSydhTfbsGm12878P300n15StdAln_2Reps.norm5.rawsignal.bw GM12878 ChipSeq p300_(N-15) Signal bigWig Stanford analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeSydhTfbsGm12878Pol2IggmusAln_7Reps.norm5.rawsignal.bw GM12878 ChipSeq Pol2 Signal bigWig Stanford analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeSydhTfbsGm12878Pol2StdAln_2Reps.norm5.rawsignal.bw GM12878 ChipSeq Pol2 Signal bigWig Stanford analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeSydhTfbsGm12878Pol3StdAln_2Reps.norm5.rawsignal.bw GM12878 ChipSeq Pol3 Signal bigWig Stanford analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeSydhTfbsGm12878Rad21IggrabAln_2Reps.norm5.rawsignal.bw GM12878 ChipSeq Rad21 Signal bigWig Stanford analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeSydhTfbsGm12878Rfx5n494IggmusAln_2Reps.norm5.rawsignal.bw GM12878 ChipSeq RFX5_(N-494) Signal bigWig Stanford analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeSydhTfbsGm12878Smc3ab9263IggmusAln_2Reps.norm5.rawsignal.bw GM12878 ChipSeq SMC3_(ab9263) Signal bigWig Stanford analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeSydhTfbsGm12878Spt20StdAln_2Reps.norm5.rawsignal.bw GM12878 ChipSeq SPT20 Signal bigWig Harvard(Weissman) analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeSydhTfbsGm12878Stat1StdAln_2Reps.norm5.rawsignal.bw GM12878 ChipSeq STAT1 Signal bigWig Stanford analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeSydhTfbsGm12878Stat3IggmusAln_2Reps.norm5.rawsignal.bw GM12878 ChipSeq STAT3 Signal bigWig Stanford analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeSydhTfbsGm12878TbpIggmusAln_2Reps.norm5.rawsignal.bw GM12878 ChipSeq TBP Signal bigWig Stanford analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeSydhTfbsGm12878Tr4StdAln_2Reps.norm5.rawsignal.bw GM12878 ChipSeq TR4 Signal bigWig Stanford analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeSydhTfbsGm12878Usf2IggmusAln_2Reps.norm5.rawsignal.bw GM12878 ChipSeq USF2 Signal bigWig Stanford analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeSydhTfbsGm12878WhipIggmusAln_2Reps.norm5.rawsignal.bw GM12878 ChipSeq WHIP Signal bigWig Stanford analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeSydhTfbsGm12878Yy1StdAln_2Reps.norm5.rawsignal.bw GM12878 ChipSeq YY1 Signal bigWig Stanford analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeSydhTfbsGm12878Znf143166181apStdAln_2Reps.norm5.rawsignal.bw GM12878 ChipSeq Znf143_(16618-1-AP) Signal bigWig Stanford analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeSydhTfbsGm12878Zzz3StdAln_2Reps.norm5.rawsignal.bw GM12878 ChipSeq ZZZ3 Signal bigWig Stanford analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeSydhTfbsGm12891InputIggmusAln_2Reps.norm5.rawsignal.bw GM12891 ChipSeq Input Signal bigWig Stanford analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeSydhTfbsGm12891InputIggrabAln_2Reps.norm5.rawsignal.bw GM12891 ChipSeq Input Signal bigWig Stanford analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeSydhTfbsGm12891NfkbIggrabAln_3Reps.norm5.rawsignal.bw GM12891 ChipSeq NFKB Signal bigWig Stanford analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeSydhTfbsGm12891Pol2IggmusAln_6Reps.norm5.rawsignal.bw GM12891 ChipSeq Pol2 Signal bigWig Stanford analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeSydhTfbsGm12892InputIggmusAln_2Reps.norm5.rawsignal.bw GM12892 ChipSeq Input Signal bigWig Stanford analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeSydhTfbsGm12892InputIggrabAln_2Reps.norm5.rawsignal.bw GM12892 ChipSeq Input Signal bigWig Stanford analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeSydhTfbsGm12892NfkbIggrabAln_3Reps.norm5.rawsignal.bw GM12892 ChipSeq NFKB Signal bigWig Stanford analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeSydhTfbsGm12892Pol2IggmusAln_3Reps.norm5.rawsignal.bw GM12892 ChipSeq Pol2 Signal bigWig Stanford analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeSydhTfbsGm15510InputIggmusAln_2Reps.norm5.rawsignal.bw GM15510 ChipSeq Input Signal bigWig Stanford analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeSydhTfbsGm15510InputIggrabAln_2Reps.norm5.rawsignal.bw GM15510 ChipSeq Input Signal bigWig Stanford analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeSydhTfbsGm15510NfkbIggrabAln_5Reps.norm5.rawsignal.bw GM15510 ChipSeq NFKB Signal bigWig Stanford analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeSydhTfbsGm15510Pol2IggmusAln_3Reps.norm5.rawsignal.bw GM15510 ChipSeq Pol2 Signal bigWig Stanford analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeSydhTfbsGm18505InputIggmusAln_2Reps.norm5.rawsignal.bw GM18505 ChipSeq Input Signal bigWig Stanford analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeSydhTfbsGm18505InputIggrabAln_2Reps.norm5.rawsignal.bw GM18505 ChipSeq Input Signal bigWig Stanford analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeSydhTfbsGm18505NfkbIggrabAln_5Reps.norm5.rawsignal.bw GM18505 ChipSeq NFKB Signal bigWig Stanford analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeSydhTfbsGm18505Pol2IggmusAln_4Reps.norm5.rawsignal.bw GM18505 ChipSeq Pol2 Signal bigWig Stanford analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeSydhTfbsGm18526InputIggmusAln_3Reps.norm5.rawsignal.bw GM18526 ChipSeq Input Signal bigWig Stanford analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeSydhTfbsGm18526InputIggrabAln_2Reps.norm5.rawsignal.bw GM18526 ChipSeq Input Signal bigWig Stanford analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeSydhTfbsGm18526NfkbIggrabAln_3Reps.norm5.rawsignal.bw GM18526 ChipSeq NFKB Signal bigWig Stanford analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeSydhTfbsGm18526Pol2IggmusAln_3Reps.norm5.rawsignal.bw GM18526 ChipSeq Pol2 Signal bigWig Stanford analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeSydhTfbsGm18951InputIggmusAln_1Reps.norm5.rawsignal.bw GM18951 ChipSeq Input Signal bigWig Stanford analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeSydhTfbsGm18951InputIggrabAln_2Reps.norm5.rawsignal.bw GM18951 ChipSeq Input Signal bigWig Stanford analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeSydhTfbsGm18951NfkbIggrabAln_4Reps.norm5.rawsignal.bw GM18951 ChipSeq NFKB Signal bigWig Stanford analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeSydhTfbsGm18951Pol2IggmusAln_4Reps.norm5.rawsignal.bw GM18951 ChipSeq Pol2 Signal bigWig Stanford analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeSydhTfbsGm19099InputIggmusAln_2Reps.norm5.rawsignal.bw GM19099 ChipSeq Input Signal bigWig Stanford analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeSydhTfbsGm19099InputIggrabAln_2Reps.norm5.rawsignal.bw GM19099 ChipSeq Input Signal bigWig Stanford analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeSydhTfbsGm19099NfkbIggrabAln_3Reps.norm5.rawsignal.bw GM19099 ChipSeq NFKB Signal bigWig Stanford analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeSydhTfbsGm19099Pol2IggmusAln_3Reps.norm5.rawsignal.bw GM19099 ChipSeq Pol2 Signal bigWig Stanford analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeSydhTfbsGm19193InputIggmusAln_2Reps.norm5.rawsignal.bw GM19193 ChipSeq Input Signal bigWig Stanford analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeSydhTfbsGm19193InputIggrabAln_2Reps.norm5.rawsignal.bw GM19193 ChipSeq Input Signal bigWig Stanford analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeSydhTfbsGm19193NfkbIggrabAln_3Reps.norm5.rawsignal.bw GM19193 ChipSeq NFKB Signal bigWig Stanford analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeSydhTfbsGm19193Pol2IggmusAln_4Reps.norm5.rawsignal.bw GM19193 ChipSeq Pol2 Signal bigWig Stanford analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeSydhTfbsH1hescCjunIggrabAln_2Reps.norm5.rawsignal.bw H1-hESC ChipSeq c-Jun Signal bigWig Stanford analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeSydhTfbsH1hescCtbp2UcdAln_2Reps.norm5.rawsignal.bw H1-hESC ChipSeq CtBP2 Signal bigWig UCD analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeSydhTfbsH1hescInputIggrabAln_1Reps.norm5.rawsignal.bw H1-hESC ChipSeq Input Signal bigWig Stanford analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeSydhTfbsH1hescInputStdAln_1Reps.norm5.rawsignal.bw H1-hESC ChipSeq Input Signal bigWig Stanford analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeSydhTfbsH1hescInputUcdAln_1Reps.norm5.rawsignal.bw H1-hESC ChipSeq Input Signal bigWig Stanford analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeSydhTfbsH1hescMaxUcdAln_2Reps.norm5.rawsignal.bw H1-hESC ChipSeq Max Signal bigWig Stanford analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeSydhTfbsH1hescNrf1IggrabAln_2Reps.norm5.rawsignal.bw H1-hESC ChipSeq Nrf1 Signal bigWig Stanford analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeSydhTfbsH1hescRad21IggrabAln_2Reps.norm5.rawsignal.bw H1-hESC ChipSeq Rad21 Signal bigWig Stanford analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeSydhTfbsH1hescRfx5n494IggrabAln_2Reps.norm5.rawsignal.bw H1-hESC ChipSeq RFX5_(N-494) Signal bigWig Stanford analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeSydhTfbsH1hescSuz12UcdAln_2Reps.norm5.rawsignal.bw H1-hESC ChipSeq SUZ12 Signal bigWig UCD analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeSydhTfbsH1hescTbpStdAln_2Reps.norm5.rawsignal.bw H1-hESC ChipSeq TBP Signal bigWig Stanford analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeSydhTfbsH1hescUsf2IggrabAln_2Reps.norm5.rawsignal.bw H1-hESC ChipSeq USF2 Signal bigWig Stanford analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeSydhTfbsHct116InputUcdAln_1Reps.norm5.rawsignal.bw HCT-116 ChipSeq Input Signal bigWig Stanford analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeSydhTfbsHct116Pol2UcdAln_2Reps.norm5.rawsignal.bw HCT-116 ChipSeq Pol2 Signal bigWig Stanford analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeSydhTfbsHct116Tcf4UcdAln_2Reps.norm5.rawsignal.bw HCT-116 ChipSeq TCF4 Signal bigWig Stanford analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeSydhTfbsHek293bElk4UcdAln_2Reps.norm5.rawsignal.bw HEK293(b) ChipSeq ELK4 Signal bigWig UCD analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeSydhTfbsHek293bInputStdAln_1Reps.norm5.rawsignal.bw HEK293(b) ChipSeq Input Signal bigWig Stanford analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeSydhTfbsHek293bKap1UcdAln_2Reps.norm5.rawsignal.bw HEK293(b) ChipSeq KAP1 Signal bigWig UCD analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeSydhTfbsHek293bPol2StdAln_3Reps.norm5.rawsignal.bw HEK293(b) ChipSeq Pol2 Signal bigWig Stanford analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeSydhTfbsHek293InputUcdAln_1Reps.norm5.rawsignal.bw HEK293(b) ChipSeq Input Signal bigWig UCD analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeSydhTfbsHelas3Ap2alphaStdAln_2Reps.norm5.rawsignal.bw HeLa-S3 ChipSeq AP-2alpha Signal bigWig Stanford analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeSydhTfbsHelas3Ap2gammaStdAln_2Reps.norm5.rawsignal.bw HeLa-S3 ChipSeq AP-2gamma Signal bigWig Stanford analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeSydhTfbsHelas3Baf155IggmusAln_3Reps.norm5.rawsignal.bw HeLa-S3 ChipSeq BAF155 Signal bigWig Stanford analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeSydhTfbsHelas3Baf170IggmusAln_3Reps.norm5.rawsignal.bw HeLa-S3 ChipSeq BAF170 Signal bigWig Stanford analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeSydhTfbsHelas3Bdp1StdAln_2Reps.norm5.rawsignal.bw HeLa-S3 ChipSeq BDP1 Signal bigWig Stanford analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeSydhTfbsHelas3Brca1cIggrabAln_2Reps.norm5.rawsignal.bw HeLa-S3 ChipSeq BRCA1_(C-1863) Signal bigWig Stanford analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeSydhTfbsHelas3Brf1StdAln_2Reps.norm5.rawsignal.bw HeLa-S3 ChipSeq BRF1 Signal bigWig Stanford analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeSydhTfbsHelas3Brf2StdAln_2Reps.norm5.rawsignal.bw HeLa-S3 ChipSeq BRF2 Signal bigWig Stanford analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeSydhTfbsHelas3Brg1IggmusAln_3Reps.norm5.rawsignal.bw HeLa-S3 ChipSeq Brg1 Signal bigWig Stanford analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeSydhTfbsHelas3CebpbIggrabAln_2Reps.norm5.rawsignal.bw HeLa-S3 ChipSeq CEBPB Signal bigWig Stanford analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeSydhTfbsHelas3CfosStdAln_2Reps.norm5.rawsignal.bw HeLa-S3 ChipSeq c-Fos Signal bigWig Stanford analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeSydhTfbsHelas3CjunIggrabAln_2Reps.norm5.rawsignal.bw HeLa-S3 ChipSeq c-Jun Signal bigWig Stanford analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeSydhTfbsHelas3CmycStdAln_2Reps.norm5.rawsignal.bw HeLa-S3 ChipSeq c-Myc Signal bigWig Stanford analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeSydhTfbsHelas3E2f1StdAln_2Reps.norm5.rawsignal.bw HeLa-S3 ChipSeq E2F1 Signal bigWig Stanford analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeSydhTfbsHelas3E2f4StdAln_2Reps.norm5.rawsignal.bw HeLa-S3 ChipSeq E2F4 Signal bigWig Stanford analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeSydhTfbsHelas3E2f6StdAln_2Reps.norm5.rawsignal.bw HeLa-S3 ChipSeq E2F6 Signal bigWig Stanford analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeSydhTfbsHelas3Elk4UcdAln_2Reps.norm5.rawsignal.bw HeLa-S3 ChipSeq ELK4 Signal bigWig UCD analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeSydhTfbsHelas3Gcn5StdAln_2Reps.norm5.rawsignal.bw HeLa-S3 ChipSeq GCN5 Signal bigWig Stanford analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeSydhTfbsHelas3Gtf2f1rapIggrabAln_2Reps.norm5.rawsignal.bw HeLa-S3 ChipSeq GTF2F1_(RAP-74) Signal bigWig Stanford analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeSydhTfbsHelas3Hae2f1StdAln_2Reps.norm5.rawsignal.bw HeLa-S3 ChipSeq HA-E2F1 Signal bigWig Stanford analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeSydhTfbsHelas3Ini1IggmusAln_3Reps.norm5.rawsignal.bw HeLa-S3 ChipSeq Ini1 Signal bigWig Stanford analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeSydhTfbsHelas3InputIfng30StdAln_1Reps.norm5.rawsignal.bw HeLa-S3 ChipSeq Input Signal bigWig Stanford analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeSydhTfbsHelas3InputIggmusAln_2Reps.norm5.rawsignal.bw HeLa-S3 ChipSeq Input Signal bigWig Stanford analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeSydhTfbsHelas3InputIggrabAln_1Reps.norm5.rawsignal.bw HeLa-S3 ChipSeq Input Signal bigWig Stanford analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeSydhTfbsHelas3InputLargefragmentAln_2Reps.norm5.rawsignal.bw HeLa-S3 ChipSeq Input Signal bigWig Stanford analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeSydhTfbsHelas3InputMnaseAln_2Reps.norm5.rawsignal.bw HeLa-S3 ChipSeq Input Signal bigWig Stanford analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeSydhTfbsHelas3InputNakeddnaAln_3Reps.norm5.rawsignal.bw HeLa-S3 ChipSeq Input Signal bigWig Stanford analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeSydhTfbsHelas3InputStdAln_1Reps.norm5.rawsignal.bw HeLa-S3 ChipSeq Input Signal bigWig Stanford analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeSydhTfbsHelas3InputUcdAln_1Reps.norm5.rawsignal.bw HeLa-S3 ChipSeq Input Signal bigWig Stanford analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeSydhTfbsHelas3Irf3IggrabAln_2Reps.norm5.rawsignal.bw HeLa-S3 ChipSeq IRF3 Signal bigWig Stanford analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeSydhTfbsHelas3JundIggrabAln_2Reps.norm5.rawsignal.bw HeLa-S3 ChipSeq JunD Signal bigWig Stanford analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeSydhTfbsHelas3MaxStdAln_2Reps.norm5.rawsignal.bw HeLa-S3 ChipSeq Max Signal bigWig Stanford analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeSydhTfbsHelas3Mxi1bhlhIggrabAln_2Reps.norm5.rawsignal.bw HeLa-S3 ChipSeq Mxi1_(bHLH) Signal bigWig Stanford analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeSydhTfbsHelas3Nrf1IggmusAln_2Reps.norm5.rawsignal.bw HeLa-S3 ChipSeq Nrf1 Signal bigWig Stanford analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeSydhTfbsHelas3P300n15IggrabAln_2Reps.norm5.rawsignal.bw HeLa-S3 ChipSeq p300_(N-15) Signal bigWig Stanford analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeSydhTfbsHelas3Pol2s2IggrabAln_2Reps.norm5.rawsignal.bw HeLa-S3 ChipSeq Pol2(phosphoS2) Signal bigWig Stanford analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeSydhTfbsHelas3Pol2StdAln_3Reps.norm5.rawsignal.bw HeLa-S3 ChipSeq Pol2 Signal bigWig Stanford analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeSydhTfbsHelas3Prdm1vIggrabAln_2Reps.norm5.rawsignal.bw HeLa-S3 ChipSeq PRDM1_(Val90) Signal bigWig Stanford analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeSydhTfbsHelas3Rad21IggrabAln_2Reps.norm5.rawsignal.bw HeLa-S3 ChipSeq Rad21 Signal bigWig Stanford analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeSydhTfbsHelas3Rfx5n494IggrabAln_2Reps.norm5.rawsignal.bw HeLa-S3 ChipSeq RFX5_(N-494) Signal bigWig Stanford analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeSydhTfbsHelas3Rpc155StdAln_2Reps.norm5.rawsignal.bw HeLa-S3 ChipSeq RPC155 Signal bigWig Stanford analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeSydhTfbsHelas3Smc3ab9263IggrabAln_2Reps.norm5.rawsignal.bw HeLa-S3 ChipSeq SMC3_(ab9263) Signal bigWig Stanford analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeSydhTfbsHelas3Spt20StdAln_2Reps.norm5.rawsignal.bw HeLa-S3 ChipSeq SPT20 Signal bigWig Stanford analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeSydhTfbsHelas3Stat1Ifng30StdAln_2Reps.norm5.rawsignal.bw HeLa-S3 ChipSeq STAT1 Signal bigWig Stanford analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeSydhTfbsHelas3Stat3IggrabAln_2Reps.norm5.rawsignal.bw HeLa-S3 ChipSeq STAT3 Signal bigWig Stanford analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeSydhTfbsHelas3TbpIggrabAln_2Reps.norm5.rawsignal.bw HeLa-S3 ChipSeq TBP Signal bigWig Stanford analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeSydhTfbsHelas3Tf3c110StdAln_2Reps.norm5.rawsignal.bw HeLa-S3 ChipSeq TFIIIC-110 Signal bigWig Stanford analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeSydhTfbsHelas3Tr4StdAln_2Reps.norm5.rawsignal.bw HeLa-S3 ChipSeq TR4 Signal bigWig Stanford analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeSydhTfbsHelas3Usf2IggmusAln_2Reps.norm5.rawsignal.bw HeLa-S3 ChipSeq USF2 Signal bigWig Stanford analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeSydhTfbsHelas3Znf274UcdAln_2Reps.norm5.rawsignal.bw HeLa-S3 ChipSeq ZNF274 Signal bigWig UCD analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeSydhTfbsHelas3Zzz3StdAln_2Reps.norm5.rawsignal.bw HeLa-S3 ChipSeq ZZZ3 Signal bigWig Harvard(Weissman) analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeSydhTfbsHepg2bInputUcdAln_1Reps.norm5.rawsignal.bw HepG2b ChipSeq Input Signal bigWig Stanford analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeSydhTfbsHepg2bTr4UcdAln_2Reps.norm5.rawsignal.bw HepG2b ChipSeq TR4 Signal bigWig Stanford analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeSydhTfbsHepg2bZnf274UcdAln_2Reps.norm5.rawsignal.bw HepG2b ChipSeq ZNF274 Signal bigWig UCD analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeSydhTfbsHepg2CebpbForsklnStdAln_2Reps.norm5.rawsignal.bw HepG2 ChipSeq CEBPB Signal bigWig Stanford analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeSydhTfbsHepg2CebpbIggrabAln_2Reps.norm5.rawsignal.bw HepG2 ChipSeq CEBPB Signal bigWig Stanford analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeSydhTfbsHepg2Chd21250IggrabAln_2Reps.norm5.rawsignal.bw HepG2 ChipSeq CHD2_(N-1250) Signal bigWig Stanford analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeSydhTfbsHepg2CjunIggrabAln_2Reps.norm5.rawsignal.bw HepG2 ChipSeq c-Jun Signal bigWig Stanford analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeSydhTfbsHepg2ErraForsklnStdAln_2Reps.norm5.rawsignal.bw HepG2 ChipSeq ERRA Signal bigWig Stanford analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeSydhTfbsHepg2Grp20ForsklnStdAln_2Reps.norm5.rawsignal.bw HepG2 ChipSeq GRp20 Signal bigWig Stanford analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeSydhTfbsHepg2Hnf4aForsklnStdAln_2Reps.norm5.rawsignal.bw HepG2 ChipSeq HNF4A Signal bigWig Stanford analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeSydhTfbsHepg2Hsf1ForsklnStdAln_2Reps.norm5.rawsignal.bw HepG2 ChipSeq HSF1 Signal bigWig Stanford analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeSydhTfbsHepg2InputForsklnStdAln_2Reps.norm5.rawsignal.bw HepG2 ChipSeq Input Signal bigWig Stanford analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeSydhTfbsHepg2InputIggrabAln_1Reps.norm5.rawsignal.bw HepG2 ChipSeq Input Signal bigWig Stanford analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeSydhTfbsHepg2InputInslnStdAln_2Reps.norm5.rawsignal.bw HepG2 ChipSeq Input Signal bigWig Stanford analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeSydhTfbsHepg2InputPravastStdAln_3Reps.norm5.rawsignal.bw HepG2 ChipSeq Input Signal bigWig Stanford analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeSydhTfbsHepg2Irf3IggrabAln_2Reps.norm5.rawsignal.bw HepG2 ChipSeq IRF3 Signal bigWig Stanford analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeSydhTfbsHepg2JundIggrabAln_2Reps.norm5.rawsignal.bw HepG2 ChipSeq JunD Signal bigWig Stanford analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeSydhTfbsHepg2Maffm8194IggrabAln_2Reps.norm5.rawsignal.bw HepG2 ChipSeq MafF_(M8194) Signal bigWig Stanford analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeSydhTfbsHepg2Mafkab50322IggrabAln_2Reps.norm5.rawsignal.bw HepG2 ChipSeq MafK_(ab50322) Signal bigWig Stanford analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeSydhTfbsHepg2Mafksc477IggrabAln_2Reps.norm5.rawsignal.bw HepG2 ChipSeq MafK_(SC-477) Signal bigWig Stanford analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeSydhTfbsHepg2Nrf1IggrabAln_2Reps.norm5.rawsignal.bw HepG2 ChipSeq Nrf1 Signal bigWig Stanford analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeSydhTfbsHepg2Pgc1aForsklnStdAln_2Reps.norm5.rawsignal.bw HepG2 ChipSeq PGC1A Signal bigWig Stanford analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeSydhTfbsHepg2Pol2ForsklnStdAln_2Reps.norm5.rawsignal.bw HepG2 ChipSeq Pol2 Signal bigWig Stanford analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeSydhTfbsHepg2Pol2IggrabAln_2Reps.norm5.rawsignal.bw HepG2 ChipSeq Pol2 Signal bigWig Stanford analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeSydhTfbsHepg2Pol2PravastStdAln_3Reps.norm5.rawsignal.bw HepG2 ChipSeq Pol2 Signal bigWig Stanford analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeSydhTfbsHepg2Rad21IggrabAln_2Reps.norm5.rawsignal.bw HepG2 ChipSeq Rad21 Signal bigWig Stanford analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeSydhTfbsHepg2Rfx5n494IggrabAln_2Reps.norm5.rawsignal.bw HepG2 ChipSeq RFX5_(N-494) Signal bigWig Stanford analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeSydhTfbsHepg2Srebp1InslnStdAln_3Reps.norm5.rawsignal.bw HepG2 ChipSeq SREBP1 Signal bigWig Stanford analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeSydhTfbsHepg2Srebp1PravastStdAln_3Reps.norm5.rawsignal.bw HepG2 ChipSeq SREBP1 Signal bigWig Stanford analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeSydhTfbsHepg2Srebp2PravastStdAln_3Reps.norm5.rawsignal.bw HepG2 ChipSeq SREBP2 Signal bigWig Stanford analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeSydhTfbsHepg2TbpIggrabAln_2Reps.norm5.rawsignal.bw HepG2 ChipSeq TBP Signal bigWig Stanford analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeSydhTfbsHepg2Tcf4UcdAln_2Reps.norm5.rawsignal.bw HepG2b ChipSeq TCF4 Signal bigWig UCD analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeSydhTfbsHepg2Usf2IggrabAln_2Reps.norm5.rawsignal.bw HepG2 ChipSeq USF2 Signal bigWig Stanford analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeSydhTfbsHuvecCfosUcdAln_2Reps.norm5.rawsignal.bw HUVEC ChipSeq c-Fos Signal bigWig UCD analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeSydhTfbsHuvecCjunStdAln_2Reps.norm5.rawsignal.bw HUVEC ChipSeq c-Jun Signal bigWig Stanford analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeSydhTfbsHuvecGata2UcdAln_2Reps.norm5.rawsignal.bw HUVEC ChipSeq GATA-2 Signal bigWig UCD analysis 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http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeSydhTfbsK562bZnf274UcdAln_2Reps.norm5.rawsignal.bw K562b ChipSeq ZNF274 Signal bigWig Stanford analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeSydhTfbsK562Ccnt2StdAln_2Reps.norm5.rawsignal.bw K562 ChipSeq CCNT2 Signal bigWig Harvard analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeSydhTfbsK562CebpbIggrabAln_2Reps.norm5.rawsignal.bw K562 ChipSeq CEBPB Signal bigWig Stanford analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeSydhTfbsK562CfosStdAln_3Reps.norm5.rawsignal.bw K562 ChipSeq c-Fos Signal bigWig Stanford analysis 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http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeSydhTfbsK562InputIfng30StdAln_1Reps.norm5.rawsignal.bw K562 ChipSeq Input Signal bigWig Stanford analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeSydhTfbsK562InputIfng6hStdAln_1Reps.norm5.rawsignal.bw K562 ChipSeq Input Signal bigWig Stanford analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeSydhTfbsK562InputIggmusAln_2Reps.norm5.rawsignal.bw K562 ChipSeq Input Signal bigWig Stanford analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeSydhTfbsK562InputIggrabAln_1Reps.norm5.rawsignal.bw K562 ChipSeq Input Signal bigWig Stanford analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeSydhTfbsK562InputStdAln_2Reps.norm5.rawsignal.bw K562 ChipSeq Input Signal bigWig Stanford analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeSydhTfbsK562Irf1Ifna30StdAln_2Reps.norm5.rawsignal.bw K562 ChipSeq IRF1 Signal bigWig Stanford analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeSydhTfbsK562Irf1Ifng6hStdAln_2Reps.norm5.rawsignal.bw K562 ChipSeq IRF1 Signal bigWig Stanford analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeSydhTfbsK562JundStdAln_2Reps.norm5.rawsignal.bw K562 ChipSeq JunD Signal bigWig Stanford analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeSydhTfbsK562Mafkab50322IggrabAln_2Reps.norm5.rawsignal.bw K562 ChipSeq MafK_(ab50322) Signal bigWig Stanford analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeSydhTfbsK562MaxStdAln_2Reps.norm5.rawsignal.bw K562 ChipSeq Max Signal bigWig Stanford analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeSydhTfbsK562Mxi1bhlhIggrabAln_2Reps.norm5.rawsignal.bw K562 ChipSeq Mxi1_(bHLH) Signal bigWig Stanford analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeSydhTfbsK562NelfeStdAln_2Reps.norm5.rawsignal.bw K562 ChipSeq NELFe Signal bigWig Stanford analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeSydhTfbsK562Nfe2StdAln_2Reps.norm5.rawsignal.bw K562 ChipSeq NF-E2 Signal bigWig Stanford analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeSydhTfbsK562NfyaStdAln_2Reps.norm5.rawsignal.bw K562 ChipSeq NF-YA Signal bigWig Stanford analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeSydhTfbsK562NfybStdAln_2Reps.norm5.rawsignal.bw K562 ChipSeq NF-YB Signal bigWig Stanford analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeSydhTfbsK562Nrf1IggrabAln_2Reps.norm5.rawsignal.bw K562 ChipSeq Nrf1 Signal bigWig Stanford analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeSydhTfbsK562P300f4IggrabAln_2Reps.norm5.rawsignal.bw K562 ChipSeq p300_(F-4) Signal bigWig Stanford analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeSydhTfbsK562Pol2Ifna30StdAln_2Reps.norm5.rawsignal.bw K562 ChipSeq Pol2 Signal bigWig Stanford analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeSydhTfbsK562Pol2Ifna6hStdAln_2Reps.norm5.rawsignal.bw K562 ChipSeq Pol2 Signal bigWig Stanford analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeSydhTfbsK562Pol2Ifng30StdAln_2Reps.norm5.rawsignal.bw K562 ChipSeq Pol2 Signal bigWig Stanford analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeSydhTfbsK562Pol2Ifng6hStdAln_2Reps.norm5.rawsignal.bw K562 ChipSeq Pol2 Signal bigWig Stanford analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeSydhTfbsK562Pol2IggmusAln_2Reps.norm5.rawsignal.bw K562 ChipSeq Pol2 Signal bigWig Stanford analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeSydhTfbsK562Pol2s2StdAln_2Reps.norm5.rawsignal.bw K562 ChipSeq Pol2(phosphoS2) Signal bigWig Stanford analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeSydhTfbsK562Pol2StdAln_2Reps.norm5.rawsignal.bw K562 ChipSeq Pol2 Signal bigWig Stanford analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeSydhTfbsK562Pol3StdAln_2Reps.norm5.rawsignal.bw K562 ChipSeq Pol3 Signal bigWig Stanford analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeSydhTfbsK562Rad21StdAln_2Reps.norm5.rawsignal.bw K562 ChipSeq Rad21 Signal bigWig Stanford analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeSydhTfbsK562Rpc155StdAln_2Reps.norm5.rawsignal.bw K562 ChipSeq RPC155 Signal bigWig Stanford analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeSydhTfbsK562Sirt6StdAln_2Reps.norm5.rawsignal.bw K562 ChipSeq SIRT6 Signal bigWig Stanford analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeSydhTfbsK562Smc3ab9263IggrabAln_2Reps.norm5.rawsignal.bw K562 ChipSeq SMC3_(ab9263) Signal bigWig Stanford analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeSydhTfbsK562Stat1Ifna30StdAln_2Reps.norm5.rawsignal.bw K562 ChipSeq STAT1 Signal bigWig Stanford analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeSydhTfbsK562Stat1Ifna6hStdAln_2Reps.norm5.rawsignal.bw K562 ChipSeq STAT1 Signal bigWig Stanford analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeSydhTfbsK562Stat1Ifng30StdAln_2Reps.norm5.rawsignal.bw K562 ChipSeq STAT1 Signal bigWig Stanford analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeSydhTfbsK562Stat1Ifng6hStdAln_2Reps.norm5.rawsignal.bw K562 ChipSeq STAT1 Signal bigWig Stanford analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeSydhTfbsK562Stat2Ifna30StdAln_2Reps.norm5.rawsignal.bw K562 ChipSeq STAT2 Signal bigWig Stanford analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeSydhTfbsK562Stat2Ifna6hStdAln_2Reps.norm5.rawsignal.bw K562 ChipSeq STAT2 Signal bigWig Stanford analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeSydhTfbsK562Tal1sc12984IggmusAln_2Reps.norm5.rawsignal.bw K562 ChipSeq TAL1_(SC-12984) Signal bigWig Stanford analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeSydhTfbsK562TbpIggmusAln_2Reps.norm5.rawsignal.bw K562 ChipSeq TBP Signal bigWig Stanford analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeSydhTfbsK562Tf3c110StdAln_3Reps.norm5.rawsignal.bw K562 ChipSeq TFIIIC-110 Signal bigWig Stanford analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeSydhTfbsK562Usf2StdAln_2Reps.norm5.rawsignal.bw K562 ChipSeq USF2 Signal bigWig Stanford analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeSydhTfbsK562Xrcc4StdAln_2Reps.norm5.rawsignal.bw K562 ChipSeq XRCC4 Signal bigWig Stanford analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeSydhTfbsMcf10aesInputEtoh01bStdAln_1Reps.norm5.rawsignal.bw MCF10A-Er-Src ChipSeq Input Signal bigWig Harvard(Weissman) analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeSydhTfbsMcf10aesInputEtoh01cStdAln_1Reps.norm5.rawsignal.bw MCF10A-Er-Src ChipSeq Input Signal bigWig Harvard(Weissman) analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeSydhTfbsMcf10aesInputUcdAln_1Reps.norm5.rawsignal.bw MCF10A-Er-Src ChipSeq Input Signal bigWig UCD(Farnham) analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeSydhTfbsMcf10aesPol2Etoh01StdAln_2Reps.norm5.rawsignal.bw MCF10A-Er-Src ChipSeq Pol2 Signal bigWig Stanford analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeSydhTfbsMcf10aesPol2TamStdAln_2Reps.norm5.rawsignal.bw MCF10A-Er-Src ChipSeq Pol2 Signal bigWig Harvard(Weissman) analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeSydhTfbsMcf10aesStat3Etoh01bStdAln_2Reps.norm5.rawsignal.bw MCF10A-Er-Src ChipSeq STAT3 Signal bigWig Harvard(Weissman) analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeSydhTfbsMcf10aesStat3Etoh01cStdAln_2Reps.norm5.rawsignal.bw MCF10A-Er-Src ChipSeq STAT3 Signal bigWig Stanford analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeSydhTfbsMcf10aesStat3Etoh01StdAln_2Reps.norm5.rawsignal.bw MCF10A-Er-Src ChipSeq STAT3 Signal bigWig Harvard(Weissman) analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeSydhTfbsMcf10aesStat3TamStdAln_2Reps.norm5.rawsignal.bw MCF10A-Er-Src ChipSeq STAT3 Signal bigWig Harvard(Weissman) analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeSydhTfbsMcf7Hae2f1UcdAln_2Reps.norm5.rawsignal.bw MCF-7 ChipSeq HA-E2F1 Signal bigWig Stanford analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeSydhTfbsMcf7InputUcdAln_2Reps.norm5.rawsignal.bw MCF-7 ChipSeq Input Signal bigWig Stanford analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeSydhTfbsNb4CmycStdAln_2Reps.norm5.rawsignal.bw NB4 ChipSeq c-Myc Signal bigWig Stanford analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeSydhTfbsNb4InputStdAln_1Reps.norm5.rawsignal.bw NB4 ChipSeq Input Signal bigWig Stanford analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeSydhTfbsNb4MaxStdAln_2Reps.norm5.rawsignal.bw NB4 ChipSeq Max Signal bigWig Stanford analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeSydhTfbsNb4Pol2StdAln_3Reps.norm5.rawsignal.bw NB4 ChipSeq Pol2 Signal bigWig Stanford analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeSydhTfbsNt2d1InputUcdAln_1Reps.norm5.rawsignal.bw NT2-D1 ChipSeq Input Signal bigWig Stanford analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeSydhTfbsNt2d1Suz12UcdAln_2Reps.norm5.rawsignal.bw NT2-D1 ChipSeq SUZ12 Signal bigWig Stanford analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeSydhTfbsNt2d1Yy1UcdAln_2Reps.norm5.rawsignal.bw NT2-D1 ChipSeq YY1 Signal bigWig Stanford analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeSydhTfbsNt2d1Znf274UcdAln_2Reps.norm5.rawsignal.bw NT2-D1 ChipSeq ZNF274 Signal bigWig UCD analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeSydhTfbsPbdeGata1UcdAln_2Reps.norm5.rawsignal.bw PBDE ChipSeq GATA-1 Signal bigWig UCD analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeSydhTfbsPbdeInputUcdAln_1Reps.norm5.rawsignal.bw PBDE ChipSeq Input Signal bigWig UCD analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeSydhTfbsPbdePol2UcdAln_2Reps.norm5.rawsignal.bw PBDE ChipSeq Pol2 Signal bigWig UCD analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeSydhTfbsRajiInputUcdAln_1Reps.norm5.rawsignal.bw Raji ChipSeq Input Signal bigWig Stanford analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeSydhTfbsRajiPol2UcdAln_2Reps.norm5.rawsignal.bw Raji ChipSeq Pol2 Signal bigWig UCD analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeSydhTfbsShsy5yGata2UcdAln_2Reps.norm5.rawsignal.bw SH-SY5Y ChipSeq GATA-2 Signal bigWig UCD analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeSydhTfbsShsy5yInputUcdAln_1Reps.norm5.rawsignal.bw SH-SY5Y ChipSeq Input Signal bigWig UCD(Farnham) analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeSydhTfbsThek293InputUcdAln_1Reps.norm5.rawsignal.bw T-REx-HEK293 ChipSeq Input Signal bigWig UCD(Farnham) analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeSydhTfbsTrexhek293Znf263UcdAln_2Reps.norm5.rawsignal.bw T-REx-HEK293 ChipSeq ZNF263 Signal bigWig UCD analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeSydhTfbsU2osInputUcdAln_1Reps.norm5.rawsignal.bw U2OS ChipSeq Input Signal bigWig Stanford analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeSydhTfbsU2osKap1UcdAln_2Reps.norm5.rawsignal.bw U2OS ChipSeq KAP1 Signal bigWig Stanford analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeSydhTfbsU2osSetdb1UcdAln_2Reps.norm5.rawsignal.bw U2OS ChipSeq SETDB1 Signal bigWig UCD analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeUchicagoTfbsK562EfosControlAln_3Reps.norm5.rawsignal.bw K562 ChipSeq eGFP-FOS Signal bigWig UChicago analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeUchicagoTfbsK562Egata2ControlAln_2Reps.norm5.rawsignal.bw K562 ChipSeq eGFP-GATA2 Signal bigWig UChicago analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeUchicagoTfbsK562Ehdac8ControlAln_2Reps.norm5.rawsignal.bw K562 ChipSeq eGFP-HDAC8 Signal bigWig UChicago analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeUchicagoTfbsK562EjunbControlAln_2Reps.norm5.rawsignal.bw K562 ChipSeq eGFP-JunB Signal bigWig UChicago analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeUchicagoTfbsK562EjundControlAln_3Reps.norm5.rawsignal.bw K562 ChipSeq eGFP-JunD Signal bigWig UChicago analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeUchicagoTfbsK562Enr4a1ControlAln_2Reps.norm5.rawsignal.bw K562 ChipSeq eGFP-NR4A1 Signal bigWig UChicago analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeUchicagoTfbsK562InputControlfosAln_3Reps.norm5.rawsignal.bw K562 ChipSeq Input Signal bigWig UChicago analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeUchicagoTfbsK562InputControlgata2Aln_2Reps.norm5.rawsignal.bw K562 ChipSeq Input Signal bigWig UChicago analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeUchicagoTfbsK562InputControlhdac8Aln_2Reps.norm5.rawsignal.bw K562 ChipSeq Input Signal bigWig UChicago analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeUchicagoTfbsK562InputControljunbAln_2Reps.norm5.rawsignal.bw K562 ChipSeq Input Signal bigWig UChicago analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeUchicagoTfbsK562InputControljundAln_3Reps.norm5.rawsignal.bw K562 ChipSeq Input Signal bigWig UChicago analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeUchicagoTfbsK562InputControlnr4a1Aln_2Reps.norm5.rawsignal.bw K562 ChipSeq Input Signal bigWig UChicago analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeUwDnaseA549Aln_2Reps.norm5.rawsignal.bw A549 DnaseSeq Signal bigWig UW analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeUwDnaseAg04449Aln_2Reps.norm5.rawsignal.bw AG04449 DnaseSeq Signal bigWig UW analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeUwDnaseAg04450Aln_2Reps.norm5.rawsignal.bw AG04450 DnaseSeq Signal bigWig UW analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeUwDnaseAg09309Aln_2Reps.norm5.rawsignal.bw AG09309 DnaseSeq Signal bigWig UW analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeUwDnaseAg09319Aln_2Reps.norm5.rawsignal.bw AG09319 DnaseSeq Signal bigWig UW analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeUwDnaseAg10803Aln_2Reps.norm5.rawsignal.bw AG10803 DnaseSeq Signal bigWig UW analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeUwDnaseAoafAln_2Reps.norm5.rawsignal.bw AoAF DnaseSeq Signal bigWig UW analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeUwDnaseBe2cAln_2Reps.norm5.rawsignal.bw BE2_C DnaseSeq Signal bigWig UW analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeUwDnaseBjAln_2Reps.norm5.rawsignal.bw BJ DnaseSeq Signal bigWig UW analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeUwDnaseCaco2Aln_2Reps.norm5.rawsignal.bw Caco-2 DnaseSeq Signal bigWig UW analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeUwDnaseCmkAln_1Reps.norm5.rawsignal.bw CMK DnaseSeq Signal bigWig UW analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeUwDnaseGm06990Aln_2Reps.norm5.rawsignal.bw GM06990 DnaseSeq Signal bigWig UW analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeUwDnaseGm12864Aln_1Reps.norm5.rawsignal.bw GM12864 DnaseSeq Signal bigWig UW analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeUwDnaseGm12865Aln_2Reps.norm5.rawsignal.bw GM12865 DnaseSeq Signal bigWig UW analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeUwDnaseGm12878Aln_2Reps.norm5.rawsignal.bw GM12878 DnaseSeq Signal bigWig UW analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeUwDnaseH1hescAln_1Reps.norm5.rawsignal.bw H1-hESC DnaseSeq Signal bigWig UW analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeUwDnaseH7esAln_2Reps.norm5.rawsignal.bw H7-hESC DnaseSeq Signal bigWig UW analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeUwDnaseHacAln_2Reps.norm5.rawsignal.bw HAc DnaseSeq Signal bigWig UW analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeUwDnaseHaeAln_2Reps.norm5.rawsignal.bw HAEpiC DnaseSeq Signal bigWig UW analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeUwDnaseHahAln_2Reps.norm5.rawsignal.bw HA-h DnaseSeq Signal bigWig UW analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeUwDnaseHaspAln_2Reps.norm5.rawsignal.bw HA-sp DnaseSeq Signal bigWig UW analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeUwDnaseHbmecAln_2Reps.norm5.rawsignal.bw HBMEC DnaseSeq Signal bigWig UW analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeUwDnaseHcfaaAln_2Reps.norm5.rawsignal.bw HCFaa DnaseSeq Signal bigWig UW analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeUwDnaseHcfAln_2Reps.norm5.rawsignal.bw HCF DnaseSeq Signal bigWig UW analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeUwDnaseHcmAln_2Reps.norm5.rawsignal.bw HCM DnaseSeq Signal bigWig UW analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeUwDnaseHconfAln_2Reps.norm5.rawsignal.bw HConF DnaseSeq Signal bigWig UW analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeUwDnaseHcpeAln_2Reps.norm5.rawsignal.bw HCPEpiC DnaseSeq Signal bigWig UW analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeUwDnaseHct116Aln_2Reps.norm5.rawsignal.bw HCT-116 DnaseSeq Signal bigWig UW analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeUwDnaseHeeAln_2Reps.norm5.rawsignal.bw HEEpiC DnaseSeq Signal bigWig UW analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeUwDnaseHelas3Aln_2Reps.norm5.rawsignal.bw HeLa-S3 DnaseSeq Signal bigWig UW analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeUwDnaseHepg2Aln_2Reps.norm5.rawsignal.bw HepG2 DnaseSeq Signal bigWig UW analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeUwDnaseHffAln_2Reps.norm5.rawsignal.bw HFF DnaseSeq Signal bigWig UW analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeUwDnaseHffmycAln_2Reps.norm5.rawsignal.bw HFF-Myc DnaseSeq Signal bigWig UW analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeUwDnaseHgfAln_2Reps.norm5.rawsignal.bw HGF DnaseSeq Signal bigWig UW analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeUwDnaseHipeAln_2Reps.norm5.rawsignal.bw HIPEpiC DnaseSeq Signal bigWig UW analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeUwDnaseHl60Aln_2Reps.norm5.rawsignal.bw HL-60 DnaseSeq Signal bigWig UW analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeUwDnaseHmecAln_2Reps.norm5.rawsignal.bw HMEC DnaseSeq Signal bigWig UW analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeUwDnaseHmfAln_2Reps.norm5.rawsignal.bw HMF DnaseSeq Signal bigWig UW analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeUwDnaseHmvecdbladAln_2Reps.norm5.rawsignal.bw HMVEC-dBl-Ad DnaseSeq Signal bigWig UW analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeUwDnaseHmvecdblneoAln_2Reps.norm5.rawsignal.bw HMVEC-dBl-Neo DnaseSeq Signal bigWig UW analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeUwDnaseHmvecdlyadAln_2Reps.norm5.rawsignal.bw HMVEC-dLy-Ad DnaseSeq Signal bigWig UW analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeUwDnaseHmvecdlyneoAln_2Reps.norm5.rawsignal.bw HMVEC-dLy-Neo DnaseSeq Signal bigWig UW analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeUwDnaseHmvecdneoAln_2Reps.norm5.rawsignal.bw HMVEC-dNeo DnaseSeq Signal bigWig UW analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeUwDnaseHmveclblAln_2Reps.norm5.rawsignal.bw HMVEC-LBl DnaseSeq Signal bigWig UW analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeUwDnaseHmvecllyAln_2Reps.norm5.rawsignal.bw HMVEC-LLy DnaseSeq Signal bigWig UW analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeUwDnaseHnpceAln_2Reps.norm5.rawsignal.bw HNPCEpiC DnaseSeq Signal bigWig UW analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeUwDnaseHpafAln_2Reps.norm5.rawsignal.bw HPAF DnaseSeq Signal bigWig UW analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeUwDnaseHpdlfAln_2Reps.norm5.rawsignal.bw HPdLF DnaseSeq Signal bigWig UW analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeUwDnaseHpfAln_2Reps.norm5.rawsignal.bw HPF DnaseSeq Signal bigWig UW analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeUwDnaseHrceAln_2Reps.norm5.rawsignal.bw HRCEpiC DnaseSeq Signal bigWig UW analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeUwDnaseHreAln_2Reps.norm5.rawsignal.bw HRE DnaseSeq Signal bigWig UW analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeUwDnaseHrgecAln_2Reps.norm5.rawsignal.bw HRGEC DnaseSeq Signal bigWig UW analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeUwDnaseHrpeAln_2Reps.norm5.rawsignal.bw HRPEpiC DnaseSeq Signal bigWig UW analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeUwDnaseHsmmAln_2Reps.norm5.rawsignal.bw HSMM DnaseSeq Signal bigWig UW analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeUwDnaseHsmmtAln_1Reps.norm5.rawsignal.bw HSMMtube DnaseSeq Signal bigWig UW analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeUwDnaseHuvecAln_2Reps.norm5.rawsignal.bw HUVEC DnaseSeq Signal bigWig UW analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeUwDnaseHvmfAln_2Reps.norm5.rawsignal.bw HVMF DnaseSeq Signal bigWig UW analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeUwDnaseJurkatAln_2Reps.norm5.rawsignal.bw Jurkat DnaseSeq Signal bigWig UW analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeUwDnaseK562Aln_2Reps.norm5.rawsignal.bw K562 DnaseSeq Signal bigWig UW analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeUwDnaseLncapAln_2Reps.norm5.rawsignal.bw LNCaP DnaseSeq Signal bigWig UW analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeUwDnaseMcf7Aln_2Reps.norm5.rawsignal.bw MCF-7 DnaseSeq Signal bigWig UW analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeUwDnaseMonocd14Aln_1Reps.norm5.rawsignal.bw Monocytes-CD14+ DnaseSeq Signal bigWig UW analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeUwDnaseNb4Aln_2Reps.norm5.rawsignal.bw NB4 DnaseSeq Signal bigWig UW analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeUwDnaseNhaAln_2Reps.norm5.rawsignal.bw NH-A DnaseSeq Signal bigWig UW analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeUwDnaseNhdfadAln_2Reps.norm5.rawsignal.bw NHDF-Ad DnaseSeq Signal bigWig UW analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeUwDnaseNhdfneoAln_2Reps.norm5.rawsignal.bw NHDF-neo DnaseSeq Signal bigWig UW analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeUwDnaseNhekAln_2Reps.norm5.rawsignal.bw NHEK DnaseSeq Signal bigWig UW analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeUwDnaseNhlfAln_2Reps.norm5.rawsignal.bw NHLF DnaseSeq Signal bigWig UW analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeUwDnasePanc1Aln_2Reps.norm5.rawsignal.bw PANC-1 DnaseSeq Signal bigWig UW analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeUwDnaseRptecAln_2Reps.norm5.rawsignal.bw RPTEC DnaseSeq Signal bigWig UW analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeUwDnaseSaecAln_2Reps.norm5.rawsignal.bw SAEC DnaseSeq Signal bigWig UW analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeUwDnaseSkmcAln_2Reps.norm5.rawsignal.bw SKMC DnaseSeq Signal bigWig UW analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeUwDnaseSknmcAln_2Reps.norm5.rawsignal.bw SK-N-MC DnaseSeq Signal bigWig UW analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeUwDnaseSknshraAln_2Reps.norm5.rawsignal.bw SK-N-SH_RA DnaseSeq Signal bigWig UW analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeUwDnaseTh1Aln_1Reps.norm5.rawsignal.bw Th1 DnaseSeq Signal bigWig UW analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeUwDnaseTh2Aln_1Reps.norm5.rawsignal.bw Th2 DnaseSeq Signal bigWig UW analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeUwDnaseWerirb1Aln_2Reps.norm5.rawsignal.bw WERI-Rb-1 DnaseSeq Signal bigWig UW analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeUwDnaseWi38Aln_2Reps.norm5.rawsignal.bw WI-38 DnaseSeq Signal bigWig UW analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeUwDnaseWi38OhtamAln_2Reps.norm5.rawsignal.bw WI-38 DnaseSeq Signal bigWig UW analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeUwHistoneAg04449H3k4me3StdAln_2Reps.norm5.rawsignal.bw AG04449 ChipSeq H3K4me3 Signal 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http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeUwHistoneAg09309InputStdAln_1Reps.norm5.rawsignal.bw AG09309 ChipSeq Input Signal bigWig UW analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeUwHistoneAg09319H3k4me3StdAln_2Reps.norm5.rawsignal.bw AG09319 ChipSeq H3K4me3 Signal bigWig UW analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeUwHistoneAg09319InputStdAln_1Reps.norm5.rawsignal.bw AG09319 ChipSeq Input Signal bigWig UW analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeUwHistoneAg10803H3k4me3StdAln_2Reps.norm5.rawsignal.bw AG10803 ChipSeq H3K4me3 Signal bigWig UW analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeUwHistoneAg10803InputStdAln_1Reps.norm5.rawsignal.bw AG10803 ChipSeq Input Signal bigWig UW analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeUwHistoneAoafH3k4me3StdAln_2Reps.norm5.rawsignal.bw AoAF ChipSeq H3K4me3 Signal bigWig UW analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeUwHistoneAoafInputStdAln_1Reps.norm5.rawsignal.bw AoAF ChipSeq Input Signal bigWig UW analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeUwHistoneBjH3k27me3StdAln_2Reps.norm5.rawsignal.bw BJ ChipSeq H3K27me3 Signal bigWig UW analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeUwHistoneBjH3k36me3StdAln_2Reps.norm5.rawsignal.bw BJ ChipSeq H3K36me3 Signal bigWig UW analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeUwHistoneBjH3k4me3StdAln_2Reps.norm5.rawsignal.bw BJ ChipSeq H3K4me3 Signal bigWig UW analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeUwHistoneBjInputStdAln_1Reps.norm5.rawsignal.bw BJ ChipSeq Input Signal bigWig UW analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeUwHistoneCaco2H3k27me3StdAln_2Reps.norm5.rawsignal.bw Caco-2 ChipSeq H3K27me3 Signal bigWig UW analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeUwHistoneCaco2H3k36me3StdAln_2Reps.norm5.rawsignal.bw Caco-2 ChipSeq H3K36me3 Signal bigWig UW analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeUwHistoneCaco2H3k4me3StdAln_2Reps.norm5.rawsignal.bw Caco-2 ChipSeq H3K4me3 Signal bigWig UW analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeUwHistoneCaco2InputStdAln_1Reps.norm5.rawsignal.bw Caco-2 ChipSeq Input Signal bigWig UW analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeUwHistoneGm06990H3k27me3StdAln_2Reps.norm5.rawsignal.bw GM06990 ChipSeq H3K27me3 Signal bigWig UW analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeUwHistoneGm06990H3k36me3StdAln_2Reps.norm5.rawsignal.bw GM06990 ChipSeq H3K36me3 Signal bigWig UW analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeUwHistoneGm06990H3k4me3StdAln_2Reps.norm5.rawsignal.bw GM06990 ChipSeq H3K4me3 Signal bigWig UW analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeUwHistoneGm06990InputStdAln_1Reps.norm5.rawsignal.bw GM06990 ChipSeq Input Signal bigWig UW analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeUwHistoneGm12878H3k27me3StdAln_2Reps.norm5.rawsignal.bw GM12878 ChipSeq H3K27me3 Signal bigWig UW analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeUwHistoneGm12878H3k36me3StdAln_2Reps.norm5.rawsignal.bw GM12878 ChipSeq H3K36me3 Signal bigWig UW analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeUwHistoneGm12878H3k4me3StdAln_2Reps.norm5.rawsignal.bw GM12878 ChipSeq H3K4me3 Signal bigWig UW analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeUwHistoneGm12878InputStdAln_1Reps.norm5.rawsignal.bw GM12878 ChipSeq Input Signal bigWig UW analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeUwHistoneH7esH3k27me3StdAln_2Reps.norm5.rawsignal.bw H7-hESC ChipSeq H3K27me3 Signal bigWig UW analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeUwHistoneH7esH3k36me3StdAln_2Reps.norm5.rawsignal.bw H7-hESC ChipSeq H3K36me3 Signal bigWig UW analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeUwHistoneH7esH3k4me3StdAln_2Reps.norm5.rawsignal.bw H7-hESC ChipSeq H3K4me3 Signal bigWig UW analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeUwHistoneH7esInputStdAln_1Reps.norm5.rawsignal.bw H7-hESC ChipSeq Input Signal bigWig UW analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeUwHistoneHaspH3k4me3StdAln_2Reps.norm5.rawsignal.bw HA-sp ChipSeq H3K4me3 Signal bigWig UW analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeUwHistoneHaspInputStdAln_1Reps.norm5.rawsignal.bw HA-sp ChipSeq Input Signal bigWig UW analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeUwHistoneHbmecH3k4me3StdAln_2Reps.norm5.rawsignal.bw HBMEC ChipSeq H3K4me3 Signal bigWig UW analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeUwHistoneHbmecInputStdAln_1Reps.norm5.rawsignal.bw HBMEC ChipSeq Input Signal bigWig UW analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeUwHistoneHcfaaH3k4me3StdAln_1Reps.norm5.rawsignal.bw HCFaa ChipSeq H3K4me3 Signal bigWig UW analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeUwHistoneHcfaaInputStdAln_1Reps.norm5.rawsignal.bw HCFaa ChipSeq Input Signal bigWig UW analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeUwHistoneHcfH3k4me3StdAln_2Reps.norm5.rawsignal.bw HCF ChipSeq H3K4me3 Signal bigWig UW analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeUwHistoneHcfInputStdAln_1Reps.norm5.rawsignal.bw HCF ChipSeq Input Signal bigWig UW analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeUwHistoneHcmH3k4me3StdAln_2Reps.norm5.rawsignal.bw HCM ChipSeq H3K4me3 Signal bigWig UW analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeUwHistoneHcmInputStdAln_1Reps.norm5.rawsignal.bw HCM ChipSeq Input Signal bigWig UW analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeUwHistoneHcpeH3k4me3StdAln_2Reps.norm5.rawsignal.bw HCPEpiC ChipSeq H3K4me3 Signal bigWig UW analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeUwHistoneHcpeInputStdAln_1Reps.norm5.rawsignal.bw HCPEpiC ChipSeq Input Signal bigWig UW analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeUwHistoneHct116H3k4me3StdAln_2Reps.norm5.rawsignal.bw HCT-116 ChipSeq H3K4me3 Signal bigWig UW analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeUwHistoneHct116InputStdAln_1Reps.norm5.rawsignal.bw HCT-116 ChipSeq Input Signal bigWig UW analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeUwHistoneHeeH3k4me3StdAln_2Reps.norm5.rawsignal.bw HEEpiC ChipSeq H3K4me3 Signal bigWig UW analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeUwHistoneHeeInputStdAln_1Reps.norm5.rawsignal.bw HEEpiC ChipSeq Input Signal bigWig UW analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeUwHistoneHek293H3k4me3StdAln_2Reps.norm5.rawsignal.bw HEK293 ChipSeq H3K4me3 Signal bigWig UW analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeUwHistoneHek293InputStdAln_1Reps.norm5.rawsignal.bw HEK293 ChipSeq Input Signal bigWig UW analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeUwHistoneHelas3H3k27me3StdAln_2Reps.norm5.rawsignal.bw HeLa-S3 ChipSeq H3K27me3 Signal bigWig UW analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeUwHistoneHelas3H3k36me3StdAln_2Reps.norm5.rawsignal.bw HeLa-S3 ChipSeq H3K36me3 Signal bigWig UW analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeUwHistoneHelas3H3k4me3StdAln_2Reps.norm5.rawsignal.bw HeLa-S3 ChipSeq H3K4me3 Signal bigWig UW analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeUwHistoneHelas3InputStdAln_1Reps.norm5.rawsignal.bw HeLa-S3 ChipSeq Input Signal bigWig UW analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeUwHistoneHepg2H3k27me3StdAln_2Reps.norm5.rawsignal.bw HepG2 ChipSeq H3K27me3 Signal bigWig UW analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeUwHistoneHepg2H3k36me3StdAln_2Reps.norm5.rawsignal.bw HepG2 ChipSeq H3K36me3 Signal bigWig UW analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeUwHistoneHepg2H3k4me3StdAln_2Reps.norm5.rawsignal.bw HepG2 ChipSeq H3K4me3 Signal bigWig UW analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeUwHistoneHepg2InputStdAln_1Reps.norm5.rawsignal.bw HepG2 ChipSeq Input Signal bigWig UW analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeUwHistoneHl60H3k4me3StdAln_2Reps.norm5.rawsignal.bw HL-60 ChipSeq H3K4me3 Signal bigWig UW analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeUwHistoneHl60InputStdAln_1Reps.norm5.rawsignal.bw HL-60 ChipSeq Input Signal bigWig UW analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeUwHistoneHmecH3k27me3StdAln_1Reps.norm5.rawsignal.bw HMEC ChipSeq H3K27me3 Signal bigWig UW analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeUwHistoneHmecH3k4me3StdAln_2Reps.norm5.rawsignal.bw HMEC ChipSeq H3K4me3 Signal bigWig UW analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeUwHistoneHmecInputStdAln_1Reps.norm5.rawsignal.bw HMEC ChipSeq Input Signal bigWig UW analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeUwHistoneHmfH3k4me3StdAln_2Reps.norm5.rawsignal.bw HMF ChipSeq H3K4me3 Signal bigWig UW analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeUwHistoneHmfInputStdAln_1Reps.norm5.rawsignal.bw HMF ChipSeq Input Signal bigWig UW analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeUwHistoneHpafH3k4me3StdAln_2Reps.norm5.rawsignal.bw HPAF ChipSeq H3K4me3 Signal bigWig UW analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeUwHistoneHpafInputStdAln_1Reps.norm5.rawsignal.bw HPAF ChipSeq Input Signal bigWig UW analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeUwHistoneHpfH3k4me3StdAln_2Reps.norm5.rawsignal.bw HPF ChipSeq H3K4me3 Signal bigWig UW analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeUwHistoneHpfInputStdAln_1Reps.norm5.rawsignal.bw HPF ChipSeq Input Signal bigWig UW analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeUwHistoneHreH3k27me3StdAln_2Reps.norm5.rawsignal.bw HRE ChipSeq H3K27me3 Signal bigWig UW analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeUwHistoneHreH3k36me3StdAln_2Reps.norm5.rawsignal.bw HRE ChipSeq H3K36me3 Signal bigWig UW analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeUwHistoneHreH3k4me3StdAln_2Reps.norm5.rawsignal.bw HRE ChipSeq H3K4me3 Signal bigWig UW analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeUwHistoneHreInputStdAln_1Reps.norm5.rawsignal.bw HRE ChipSeq Input Signal bigWig UW analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeUwHistoneHrpeH3k4me3StdAln_2Reps.norm5.rawsignal.bw HRPEpiC ChipSeq H3K4me3 Signal bigWig UW analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeUwHistoneHrpeInputStdAln_1Reps.norm5.rawsignal.bw HRPEpiC ChipSeq Input Signal bigWig UW analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeUwHistoneHuvecH3k27me3StdAln_2Reps.norm5.rawsignal.bw HUVEC ChipSeq H3K27me3 Signal bigWig UW analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeUwHistoneHuvecH3k36me3StdAln_2Reps.norm5.rawsignal.bw HUVEC ChipSeq H3K36me3 Signal bigWig UW analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeUwHistoneHuvecH3k4me3StdAln_2Reps.norm5.rawsignal.bw HUVEC ChipSeq H3K4me3 Signal bigWig UW analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeUwHistoneHuvecInputStdAln_1Reps.norm5.rawsignal.bw HUVEC ChipSeq Input Signal bigWig UW analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeUwHistoneHvmfH3k4me3StdAln_2Reps.norm5.rawsignal.bw HVMF ChipSeq H3K4me3 Signal bigWig UW analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeUwHistoneHvmfInputStdAln_1Reps.norm5.rawsignal.bw HVMF ChipSeq Input Signal bigWig UW analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeUwHistoneJurkatH3k4me3StdAln_2Reps.norm5.rawsignal.bw Jurkat ChipSeq H3K4me3 Signal bigWig UW analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeUwHistoneJurkatInputStdAln_1Reps.norm5.rawsignal.bw Jurkat ChipSeq Input Signal bigWig UW analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeUwHistoneK562H3k27me3StdAln_2Reps.norm5.rawsignal.bw K562 ChipSeq H3K27me3 Signal bigWig UW analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeUwHistoneK562H3k36me3StdAln_2Reps.norm5.rawsignal.bw K562 ChipSeq H3K36me3 Signal bigWig UW analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeUwHistoneK562H3k4me3StdAln_2Reps.norm5.rawsignal.bw K562 ChipSeq H3K4me3 Signal bigWig UW analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeUwHistoneK562InputStdAln_1Reps.norm5.rawsignal.bw K562 ChipSeq Input Signal bigWig UW analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeUwHistoneMcf7H3k4me3StdAln_1Reps.norm5.rawsignal.bw MCF-7 ChipSeq H3K4me3 Signal bigWig UW analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeUwHistoneMcf7InputStdAln_1Reps.norm5.rawsignal.bw MCF-7 ChipSeq Input Signal bigWig UW analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeUwHistoneNb4H3k4me3StdAln_1Reps.norm5.rawsignal.bw NB4 ChipSeq H3K4me3 Signal bigWig UW analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeUwHistoneNb4InputStdAln_1Reps.norm5.rawsignal.bw NB4 ChipSeq Input Signal bigWig UW analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeUwHistoneNhdfneoH3k4me3StdAln_2Reps.norm5.rawsignal.bw NHDF-neo ChipSeq H3K4me3 Signal bigWig UW analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeUwHistoneNhdfneoInputStdAln_1Reps.norm5.rawsignal.bw NHDF-neo ChipSeq Input Signal bigWig UW analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeUwHistoneNhekH3k27me3StdAln_2Reps.norm5.rawsignal.bw NHEK ChipSeq H3K27me3 Signal bigWig UW analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeUwHistoneNhekH3k36me3StdAln_2Reps.norm5.rawsignal.bw NHEK ChipSeq H3K36me3 Signal bigWig UW analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeUwHistoneNhekH3k4me3StdAln_2Reps.norm5.rawsignal.bw NHEK ChipSeq H3K4me3 Signal bigWig UW analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeUwHistoneNhekInputStdAln_1Reps.norm5.rawsignal.bw NHEK ChipSeq Input Signal bigWig UW analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeUwHistoneSaecH3k27me3StdAln_2Reps.norm5.rawsignal.bw SAEC ChipSeq H3K27me3 Signal bigWig UW analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeUwHistoneSaecH3k36me3StdAln_2Reps.norm5.rawsignal.bw SAEC ChipSeq H3K36me3 Signal bigWig UW analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeUwHistoneSaecH3k4me3StdAln_2Reps.norm5.rawsignal.bw SAEC ChipSeq H3K4me3 Signal bigWig UW analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeUwHistoneSaecInputStdAln_1Reps.norm5.rawsignal.bw SAEC ChipSeq Input Signal bigWig UW analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeUwHistoneSknshraH3k27me3StdAln_2Reps.norm5.rawsignal.bw SK-N-SH_RA ChipSeq H3K27me3 Signal bigWig UW analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeUwHistoneSknshraH3k36me3StdAln_2Reps.norm5.rawsignal.bw SK-N-SH_RA ChipSeq H3K36me3 Signal bigWig UW analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeUwHistoneSknshraH3k4me3StdAln_2Reps.norm5.rawsignal.bw SK-N-SH_RA ChipSeq H3K4me3 Signal bigWig UW analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeUwHistoneSknshraInputStdAln_1Reps.norm5.rawsignal.bw SK-N-SH_RA ChipSeq Input Signal bigWig UW analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeUwTfbsAg04449CtcfStdAln_2Reps.norm5.rawsignal.bw AG04449 ChipSeq CTCF Signal bigWig UW analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeUwTfbsAg04449InputStdAln_1Reps.norm5.rawsignal.bw AG04449 ChipSeq Input Signal bigWig UW analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeUwTfbsAg04450CtcfStdAln_1Reps.norm5.rawsignal.bw AG04450 ChipSeq CTCF Signal bigWig UW analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeUwTfbsAg04450InputStdAln_1Reps.norm5.rawsignal.bw AG04450 ChipSeq Input Signal bigWig UW analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeUwTfbsAg09309CtcfStdAln_2Reps.norm5.rawsignal.bw AG09309 ChipSeq CTCF Signal bigWig UW analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeUwTfbsAg09309InputStdAln_1Reps.norm5.rawsignal.bw AG09309 ChipSeq Input Signal bigWig UW analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeUwTfbsAg09319CtcfStdAln_2Reps.norm5.rawsignal.bw AG09319 ChipSeq CTCF Signal bigWig UW analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeUwTfbsAg09319InputStdAln_1Reps.norm5.rawsignal.bw AG09319 ChipSeq Input Signal bigWig UW analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeUwTfbsAg10803CtcfStdAln_2Reps.norm5.rawsignal.bw AG10803 ChipSeq CTCF Signal bigWig UW analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeUwTfbsAg10803InputStdAln_1Reps.norm5.rawsignal.bw AG10803 ChipSeq Input Signal bigWig UW analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeUwTfbsAoafCtcfStdAln_2Reps.norm5.rawsignal.bw AoAF ChipSeq CTCF Signal bigWig UW analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeUwTfbsAoafInputStdAln_1Reps.norm5.rawsignal.bw AoAF ChipSeq Input Signal bigWig UW analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeUwTfbsBjCtcfStdAln_2Reps.norm5.rawsignal.bw BJ ChipSeq CTCF Signal bigWig UW analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeUwTfbsBjInputStdAln_1Reps.norm5.rawsignal.bw BJ ChipSeq Input Signal bigWig UW analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeUwTfbsCaco2CtcfStdAln_2Reps.norm5.rawsignal.bw Caco-2 ChipSeq CTCF Signal bigWig UW analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeUwTfbsCaco2InputStdAln_1Reps.norm5.rawsignal.bw Caco-2 ChipSeq Input Signal bigWig UW analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeUwTfbsGm06990CtcfStdAln_2Reps.norm5.rawsignal.bw GM06990 ChipSeq CTCF Signal bigWig UW analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeUwTfbsGm06990InputStdAln_1Reps.norm5.rawsignal.bw GM06990 ChipSeq Input Signal bigWig UW analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeUwTfbsGm12801CtcfStdAln_1Reps.norm5.rawsignal.bw GM12801 ChipSeq CTCF Signal bigWig UW analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeUwTfbsGm12801InputStdAln_1Reps.norm5.rawsignal.bw GM12801 ChipSeq Input Signal bigWig UW analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeUwTfbsGm12864CtcfStdAln_2Reps.norm5.rawsignal.bw GM12864 ChipSeq CTCF Signal bigWig UW analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeUwTfbsGm12864InputStdAln_1Reps.norm5.rawsignal.bw GM12864 ChipSeq Input Signal bigWig UW analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeUwTfbsGm12865CtcfStdAln_2Reps.norm5.rawsignal.bw GM12865 ChipSeq CTCF Signal bigWig UW analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeUwTfbsGm12865InputStdAln_1Reps.norm5.rawsignal.bw GM12865 ChipSeq Input Signal bigWig UW analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeUwTfbsGm12872CtcfStdAln_2Reps.norm5.rawsignal.bw GM12872 ChipSeq CTCF Signal bigWig UW analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeUwTfbsGm12872InputStdAln_1Reps.norm5.rawsignal.bw GM12872 ChipSeq Input Signal bigWig UW analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeUwTfbsGm12873CtcfStdAln_2Reps.norm5.rawsignal.bw GM12873 ChipSeq CTCF Signal bigWig UW analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeUwTfbsGm12873InputStdAln_1Reps.norm5.rawsignal.bw GM12873 ChipSeq Input Signal bigWig UW analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeUwTfbsGm12874CtcfStdAln_2Reps.norm5.rawsignal.bw GM12874 ChipSeq CTCF Signal bigWig UW analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeUwTfbsGm12874InputStdAln_1Reps.norm5.rawsignal.bw GM12874 ChipSeq Input Signal bigWig UW analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeUwTfbsGm12875CtcfStdAln_2Reps.norm5.rawsignal.bw GM12875 ChipSeq CTCF Signal bigWig UW analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeUwTfbsGm12875InputStdAln_1Reps.norm5.rawsignal.bw GM12875 ChipSeq Input Signal bigWig UW analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeUwTfbsGm12878CtcfStdAln_2Reps.norm5.rawsignal.bw GM12878 ChipSeq CTCF Signal bigWig UW analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeUwTfbsGm12878InputStdAln_1Reps.norm5.rawsignal.bw GM12878 ChipSeq Input Signal bigWig UW analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeUwTfbsHaspCtcfStdAln_1Reps.norm5.rawsignal.bw HA-sp ChipSeq CTCF Signal bigWig UW analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeUwTfbsHaspInputStdAln_1Reps.norm5.rawsignal.bw HA-sp ChipSeq Input Signal bigWig UW analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeUwTfbsHbmecCtcfStdAln_2Reps.norm5.rawsignal.bw HBMEC ChipSeq CTCF Signal bigWig UW analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeUwTfbsHbmecInputStdAln_1Reps.norm5.rawsignal.bw HBMEC ChipSeq Input Signal bigWig UW analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeUwTfbsHcfaaCtcfStdAln_1Reps.norm5.rawsignal.bw HCFaa ChipSeq CTCF Signal bigWig UW analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeUwTfbsHcfaaInputStdAln_1Reps.norm5.rawsignal.bw HCFaa ChipSeq Input Signal bigWig UW analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeUwTfbsHcfInputStdAln_1Reps.norm5.rawsignal.bw HCF ChipSeq Input Signal bigWig UW analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeUwTfbsHcmInputStdAln_1Reps.norm5.rawsignal.bw HCM ChipSeq Input Signal bigWig UW analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeUwTfbsHcpeCtcfStdAln_2Reps.norm5.rawsignal.bw HCPEpiC ChipSeq CTCF Signal bigWig UW analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeUwTfbsHcpeInputStdAln_1Reps.norm5.rawsignal.bw HCPEpiC ChipSeq Input Signal bigWig UW analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeUwTfbsHct116InputStdAln_1Reps.norm5.rawsignal.bw HCT-116 ChipSeq Input Signal bigWig UW analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeUwTfbsHeeCtcfStdAln_2Reps.norm5.rawsignal.bw HEEpiC ChipSeq CTCF Signal bigWig UW analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeUwTfbsHeeInputStdAln_1Reps.norm5.rawsignal.bw HEEpiC ChipSeq Input Signal bigWig UW analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeUwTfbsHek293CtcfStdAln_2Reps.norm5.rawsignal.bw HEK293 ChipSeq CTCF Signal bigWig UW analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeUwTfbsHek293InputStdAln_1Reps.norm5.rawsignal.bw HEK293 ChipSeq Input Signal bigWig UW analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeUwTfbsHelas3CtcfStdAln_2Reps.norm5.rawsignal.bw HeLa-S3 ChipSeq CTCF Signal bigWig UW analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeUwTfbsHelas3InputStdAln_1Reps.norm5.rawsignal.bw HeLa-S3 ChipSeq Input Signal bigWig UW analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeUwTfbsHepg2CtcfStdAln_2Reps.norm5.rawsignal.bw HepG2 ChipSeq CTCF Signal bigWig UW analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeUwTfbsHepg2InputStdAln_1Reps.norm5.rawsignal.bw HepG2 ChipSeq Input Signal bigWig UW analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeUwTfbsHl60CtcfStdAln_1Reps.norm5.rawsignal.bw HL-60 ChipSeq CTCF Signal bigWig UW analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeUwTfbsHl60InputStdAln_1Reps.norm5.rawsignal.bw HL-60 ChipSeq Input Signal bigWig UW analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeUwTfbsHmecCtcfStdAln_1Reps.norm5.rawsignal.bw HMEC ChipSeq CTCF Signal bigWig UW analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeUwTfbsHmecInputStdAln_1Reps.norm5.rawsignal.bw HMEC ChipSeq Input Signal bigWig UW analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeUwTfbsHmfCtcfStdAln_2Reps.norm5.rawsignal.bw HMF ChipSeq CTCF Signal bigWig UW analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeUwTfbsHmfInputStdAln_1Reps.norm5.rawsignal.bw HMF ChipSeq Input Signal bigWig UW analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeUwTfbsHpafCtcfStdAln_2Reps.norm5.rawsignal.bw HPAF ChipSeq CTCF Signal bigWig UW analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeUwTfbsHpafInputStdAln_1Reps.norm5.rawsignal.bw HPAF ChipSeq Input Signal bigWig UW analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeUwTfbsHpfCtcfStdAln_2Reps.norm5.rawsignal.bw HPF ChipSeq CTCF Signal bigWig UW analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeUwTfbsHpfInputStdAln_1Reps.norm5.rawsignal.bw HPF ChipSeq Input Signal bigWig UW analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeUwTfbsHreCtcfStdAln_2Reps.norm5.rawsignal.bw HRE ChipSeq CTCF Signal bigWig UW analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeUwTfbsHreInputStdAln_1Reps.norm5.rawsignal.bw HRE ChipSeq Input Signal bigWig UW analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeUwTfbsHrpeCtcfStdAln_1Reps.norm5.rawsignal.bw HRPEpiC ChipSeq CTCF Signal bigWig UW analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeUwTfbsHrpeInputStdAln_1Reps.norm5.rawsignal.bw HRPEpiC ChipSeq Input Signal bigWig UW analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeUwTfbsHuvecCtcfStdAln_2Reps.norm5.rawsignal.bw HUVEC ChipSeq CTCF Signal bigWig UW analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeUwTfbsHuvecInputStdAln_1Reps.norm5.rawsignal.bw HUVEC ChipSeq Input Signal bigWig UW analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeUwTfbsHvmfInputStdAln_1Reps.norm5.rawsignal.bw HVMF ChipSeq Input Signal bigWig UW analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeUwTfbsJurkatInputStdAln_1Reps.norm5.rawsignal.bw Jurkat ChipSeq Input Signal bigWig UW analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeUwTfbsK562CtcfStdAln_2Reps.norm5.rawsignal.bw K562 ChipSeq CTCF Signal bigWig UW analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeUwTfbsK562InputStdAln_1Reps.norm5.rawsignal.bw K562 ChipSeq Input Signal bigWig UW analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeUwTfbsMcf7InputStdAln_1Reps.norm5.rawsignal.bw MCF-7 ChipSeq Input Signal bigWig UW analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeUwTfbsNb4InputStdAln_1Reps.norm5.rawsignal.bw NB4 ChipSeq Input Signal bigWig UW analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeUwTfbsNhdfneoInputStdAln_1Reps.norm5.rawsignal.bw NHDF-neo ChipSeq Input Signal bigWig UW analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeUwTfbsNhekCtcfStdAln_2Reps.norm5.rawsignal.bw NHEK ChipSeq CTCF Signal bigWig UW analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeUwTfbsNhekInputStdAln_1Reps.norm5.rawsignal.bw NHEK ChipSeq Input Signal bigWig UW analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeUwTfbsSaecCtcfStdAln_2Reps.norm5.rawsignal.bw SAEC ChipSeq CTCF Signal bigWig UW analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeUwTfbsSaecInputStdAln_1Reps.norm5.rawsignal.bw SAEC ChipSeq Input Signal bigWig UW analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeUwTfbsSknshraCtcfStdAln_2Reps.norm5.rawsignal.bw SK-N-SH_RA ChipSeq CTCF Signal bigWig UW analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeUwTfbsSknshraInputStdAln_1Reps.norm5.rawsignal.bw SK-N-SH_RA ChipSeq Input Signal bigWig UW analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeUwTfbsWerirb1CtcfStdAln_2Reps.norm5.rawsignal.bw WERI-Rb-1 ChipSeq CTCF Signal bigWig UW analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/signal/jan2011/bigwig/wgEncodeUwTfbsWerirb1InputStdAln_1Reps.norm5.rawsignal.bw WERI-Rb-1 ChipSeq Input Signal bigWig UW analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/rna_signal/jan2011/hub/wgEncodeCshlLongRnaSeqA549CellLongnonpolyaMinusRawSigRep1.bigWig A549 RnaSeq MinusSignal 1 bigWig CSHL analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/rna_signal/jan2011/hub/wgEncodeCshlLongRnaSeqA549CellLongnonpolyaMinusRawSigRep2.bigWig A549 RnaSeq MinusSignal 2 bigWig CSHL analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/rna_signal/jan2011/hub/wgEncodeCshlLongRnaSeqA549CellLongnonpolyaPlusRawSigRep1.bigWig A549 RnaSeq PlusSignal 1 bigWig CSHL analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/rna_signal/jan2011/hub/wgEncodeCshlLongRnaSeqA549CellLongnonpolyaPlusRawSigRep2.bigWig A549 RnaSeq PlusSignal 2 bigWig CSHL analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/rna_signal/jan2011/hub/wgEncodeCshlLongRnaSeqA549CellPapMinusRawSigRep1.bigWig A549 RnaSeq MinusSignal 1 bigWig CSHL analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/rna_signal/jan2011/hub/wgEncodeCshlLongRnaSeqA549CellPapMinusRawSigRep2.bigWig A549 RnaSeq MinusSignal 2 bigWig CSHL analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/rna_signal/jan2011/hub/wgEncodeCshlLongRnaSeqA549CellPapPlusRawSigRep1.bigWig A549 RnaSeq PlusSignal 1 bigWig CSHL analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/rna_signal/jan2011/hub/wgEncodeCshlLongRnaSeqA549CellPapPlusRawSigRep2.bigWig A549 RnaSeq PlusSignal 2 bigWig CSHL analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/rna_signal/jan2011/hub/wgEncodeCshlLongRnaSeqAg04450CellLongnonpolyaMinusRawSigRep1.bigWig AG04450 RnaSeq MinusSignal 1 bigWig CSHL analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/rna_signal/jan2011/hub/wgEncodeCshlLongRnaSeqAg04450CellLongnonpolyaMinusRawSigRep2.bigWig AG04450 RnaSeq MinusSignal 2 bigWig CSHL analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/rna_signal/jan2011/hub/wgEncodeCshlLongRnaSeqAg04450CellLongnonpolyaPlusRawSigRep1.bigWig AG04450 RnaSeq PlusSignal 1 bigWig CSHL analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/rna_signal/jan2011/hub/wgEncodeCshlLongRnaSeqAg04450CellLongnonpolyaPlusRawSigRep2.bigWig AG04450 RnaSeq PlusSignal 2 bigWig CSHL analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/rna_signal/jan2011/hub/wgEncodeCshlLongRnaSeqAg04450CellPapMinusRawSigRep1.bigWig AG04450 RnaSeq MinusSignal 1 bigWig CSHL analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/rna_signal/jan2011/hub/wgEncodeCshlLongRnaSeqAg04450CellPapMinusRawSigRep2.bigWig AG04450 RnaSeq MinusSignal 2 bigWig CSHL analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/rna_signal/jan2011/hub/wgEncodeCshlLongRnaSeqAg04450CellPapPlusRawSigRep1.bigWig AG04450 RnaSeq PlusSignal 1 bigWig CSHL analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/rna_signal/jan2011/hub/wgEncodeCshlLongRnaSeqAg04450CellPapPlusRawSigRep2.bigWig AG04450 RnaSeq PlusSignal 2 bigWig CSHL analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/rna_signal/jan2011/hub/wgEncodeCshlLongRnaSeqBjCellLongnonpolyaMinusRawSigRep1.bigWig BJ RnaSeq MinusSignal 1 bigWig CSHL analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/rna_signal/jan2011/hub/wgEncodeCshlLongRnaSeqBjCellLongnonpolyaMinusRawSigRep2.bigWig BJ RnaSeq MinusSignal 2 bigWig CSHL analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/rna_signal/jan2011/hub/wgEncodeCshlLongRnaSeqBjCellLongnonpolyaPlusRawSigRep1.bigWig BJ RnaSeq PlusSignal 1 bigWig CSHL analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/rna_signal/jan2011/hub/wgEncodeCshlLongRnaSeqBjCellLongnonpolyaPlusRawSigRep2.bigWig BJ RnaSeq PlusSignal 2 bigWig CSHL analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/rna_signal/jan2011/hub/wgEncodeCshlLongRnaSeqBjCellPapMinusRawSigRep1.bigWig BJ RnaSeq MinusSignal 1 bigWig CSHL analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/rna_signal/jan2011/hub/wgEncodeCshlLongRnaSeqBjCellPapMinusRawSigRep2.bigWig BJ RnaSeq MinusSignal 2 bigWig CSHL analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/rna_signal/jan2011/hub/wgEncodeCshlLongRnaSeqBjCellPapPlusRawSigRep1.bigWig BJ RnaSeq PlusSignal 1 bigWig CSHL analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/rna_signal/jan2011/hub/wgEncodeCshlLongRnaSeqBjCellPapPlusRawSigRep2.bigWig BJ RnaSeq PlusSignal 2 bigWig CSHL analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/rna_signal/jan2011/hub/wgEncodeCshlLongRnaSeqGm12878CellLongnonpolyaMinusRawSigRep1.bigWig GM12878 RnaSeq MinusSignal 1 bigWig CSHL analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/rna_signal/jan2011/hub/wgEncodeCshlLongRnaSeqGm12878CellLongnonpolyaMinusRawSigRep2.bigWig GM12878 RnaSeq MinusSignal 2 bigWig CSHL analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/rna_signal/jan2011/hub/wgEncodeCshlLongRnaSeqGm12878CellLongnonpolyaPlusRawSigRep1.bigWig GM12878 RnaSeq PlusSignal 1 bigWig CSHL analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/rna_signal/jan2011/hub/wgEncodeCshlLongRnaSeqGm12878CellLongnonpolyaPlusRawSigRep2.bigWig GM12878 RnaSeq PlusSignal 2 bigWig CSHL analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/rna_signal/jan2011/hub/wgEncodeCshlLongRnaSeqGm12878CellPapMinusRawSigRep1.bigWig GM12878 RnaSeq MinusSignal 1 bigWig CSHL analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/rna_signal/jan2011/hub/wgEncodeCshlLongRnaSeqGm12878CellPapMinusRawSigRep2.bigWig GM12878 RnaSeq MinusSignal 2 bigWig CSHL analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/rna_signal/jan2011/hub/wgEncodeCshlLongRnaSeqGm12878CellPapPlusRawSigRep1.bigWig GM12878 RnaSeq PlusSignal 1 bigWig CSHL analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/rna_signal/jan2011/hub/wgEncodeCshlLongRnaSeqGm12878CellPapPlusRawSigRep2.bigWig GM12878 RnaSeq PlusSignal 2 bigWig CSHL analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/rna_signal/jan2011/hub/wgEncodeCshlLongRnaSeqGm12878CellTotalMinusRawSigRep1.bigWig GM12878 RnaSeq MinusSignal 1 bigWig CSHL analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/rna_signal/jan2011/hub/wgEncodeCshlLongRnaSeqGm12878CellTotalMinusRawSigRep2.bigWig GM12878 RnaSeq MinusSignal 2 bigWig CSHL analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/rna_signal/jan2011/hub/wgEncodeCshlLongRnaSeqGm12878CellTotalPlusRawSigRep1.bigWig GM12878 RnaSeq PlusSignal 1 bigWig CSHL analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/rna_signal/jan2011/hub/wgEncodeCshlLongRnaSeqGm12878CellTotalPlusRawSigRep2.bigWig GM12878 RnaSeq PlusSignal 2 bigWig CSHL analysis http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/rna_signal/jan2011/hub/wgEncodeCshlLongRnaSeqGm12878CytosolLongnonpolyaMinusRawSigRep1.bigWig GM12878 RnaSeq MinusSignal 1 bigWig CSHL analysis 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ChipSeq CHD1_(A301-218A) Peaks narrowPeak Stanford Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeAwgTfbsUniform//wgEncodeAwgTfbsSydhGm12878Chd2ab68301IggmusUniPk.narrowPeak.gz GM12878 ChipSeq CHD2_(AB68301) Peaks narrowPeak Stanford Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeAwgTfbsUniform//wgEncodeAwgTfbsBroadGm12878CtcfUniPk.narrowPeak.gz GM12878 ChipSeq CTCF Peaks narrowPeak Broad Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeAwgTfbsUniform//wgEncodeAwgTfbsSydhGm12878Ctcfsc15914c20UniPk.narrowPeak.gz GM12878 ChipSeq CTCF_(SC-15914) Peaks narrowPeak Stanford Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeAwgTfbsUniform//wgEncodeAwgTfbsUtaGm12878CtcfUniPk.narrowPeak.gz GM12878 ChipSeq CTCF Peaks narrowPeak UT-A Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeAwgTfbsUniform//wgEncodeAwgTfbsUwGm12878CtcfUniPk.narrowPeak.gz GM12878 ChipSeq CTCF Peaks narrowPeak UW Data 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Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeAwgTfbsUniform//wgEncodeAwgTfbsHaibGm12878P300Pcr1xUniPk.narrowPeak.gz GM12878 ChipSeq p300 Peaks narrowPeak HudsonAlpha Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeAwgTfbsUniform//wgEncodeAwgTfbsHaibGm12878Ets1Pcr1xUniPk.narrowPeak.gz GM12878 ChipSeq ETS1 Peaks narrowPeak HudsonAlpha Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeAwgTfbsUniform//wgEncodeAwgTfbsBroadGm12878Ezh239875UniPk.narrowPeak.gz GM12878 ChipSeq EZH2_(39875) Peaks narrowPeak Broad Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeAwgTfbsUniform//wgEncodeAwgTfbsSydhGm12878CfosUniPk.narrowPeak.gz GM12878 ChipSeq c-Fos Peaks narrowPeak Yale Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeAwgTfbsUniform//wgEncodeAwgTfbsHaibGm12878Foxm1sc502V0422111UniPk.narrowPeak.gz GM12878 ChipSeq FOXM1_(SC-502) Peaks narrowPeak HudsonAlpha Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeAwgTfbsUniform//wgEncodeAwgTfbsHaibGm12878GabpPcr2xUniPk.narrowPeak.gz GM12878 ChipSeq GABP Peaks narrowPeak HudsonAlpha Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeAwgTfbsUniform//wgEncodeAwgTfbsSydhGm12878Ikzf1iknuclaUniPk.narrowPeak.gz GM12878 ChipSeq IKZF1_(IkN)_(UCLA) Peaks narrowPeak USC Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeAwgTfbsUniform//wgEncodeAwgTfbsHaibGm12878Irf4sc6059Pcr1xUniPk.narrowPeak.gz GM12878 ChipSeq IRF4_(SC-6059) Peaks narrowPeak HudsonAlpha Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeAwgTfbsUniform//wgEncodeAwgTfbsSydhGm12878JundUniPk.narrowPeak.gz GM12878 ChipSeq JunD Peaks narrowPeak Yale Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeAwgTfbsUniform//wgEncodeAwgTfbsSydhGm12878MaxIggmusUniPk.narrowPeak.gz GM12878 ChipSeq Max Peaks narrowPeak Stanford Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeAwgTfbsUniform//wgEncodeAwgTfbsSydhGm12878Mazab85725IggmusUniPk.narrowPeak.gz GM12878 ChipSeq MAZ_(ab85725) Peaks narrowPeak Stanford Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeAwgTfbsUniform//wgEncodeAwgTfbsHaibGm12878Mef2aPcr1xUniPk.narrowPeak.gz GM12878 ChipSeq MEF2A Peaks narrowPeak HudsonAlpha Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeAwgTfbsUniform//wgEncodeAwgTfbsHaibGm12878Mef2csc13268V0416101UniPk.narrowPeak.gz GM12878 ChipSeq MEF2C_(SC-13268) Peaks narrowPeak HudsonAlpha Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeAwgTfbsUniform//wgEncodeAwgTfbsHaibGm12878Mta3sc81325V0422111UniPk.narrowPeak.gz GM12878 ChipSeq MTA3_(SC-81325) Peaks narrowPeak HudsonAlpha Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeAwgTfbsUniform//wgEncodeAwgTfbsSydhGm12878Mxi1IggmusUniPk.narrowPeak.gz GM12878 ChipSeq Mxi1_(AF4185) Peaks narrowPeak Stanford Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeAwgTfbsUniform//wgEncodeAwgTfbsUtaGm12878CmycUniPk.narrowPeak.gz GM12878 ChipSeq c-Myc Peaks narrowPeak UT-A Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeAwgTfbsUniform//wgEncodeAwgTfbsHaibGm12878Nfatc1sc17834V0422111UniPk.narrowPeak.gz GM12878 ChipSeq NFATC1_(SC-17834) Peaks narrowPeak HudsonAlpha Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeAwgTfbsUniform//wgEncodeAwgTfbsSydhGm12878Nfe2sc22827UniPk.narrowPeak.gz GM12878 ChipSeq NF-E2_(SC-22827) Peaks narrowPeak Stanford Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeAwgTfbsUniform//wgEncodeAwgTfbsHaibGm12878Nficsc81335V0422111UniPk.narrowPeak.gz GM12878 ChipSeq NFIC_(SC-81335) Peaks narrowPeak HudsonAlpha Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeAwgTfbsUniform//wgEncodeAwgTfbsSydhGm12878NfyaIggmusUniPk.narrowPeak.gz GM12878 ChipSeq NF-YA Peaks narrowPeak Harvard Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeAwgTfbsUniform//wgEncodeAwgTfbsSydhGm12878NfybIggmusUniPk.narrowPeak.gz GM12878 ChipSeq NF-YB Peaks narrowPeak Harvard Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeAwgTfbsUniform//wgEncodeAwgTfbsSydhGm12878Tr4UniPk.narrowPeak.gz GM12878 ChipSeq TR4 Peaks narrowPeak USC Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeAwgTfbsUniform//wgEncodeAwgTfbsSydhGm12878Nrf1IggmusUniPk.narrowPeak.gz GM12878 ChipSeq Nrf1 Peaks narrowPeak Stanford Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeAwgTfbsUniform//wgEncodeAwgTfbsHaibGm12878Pax5c20Pcr1xUniPk.narrowPeak.gz GM12878 ChipSeq PAX5-C20 Peaks narrowPeak HudsonAlpha Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeAwgTfbsUniform//wgEncodeAwgTfbsHaibGm12878Pax5n19Pcr1xUniPk.narrowPeak.gz GM12878 ChipSeq PAX5-N19 Peaks narrowPeak HudsonAlpha Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeAwgTfbsUniform//wgEncodeAwgTfbsHaibGm12878Pbx3Pcr1xUniPk.narrowPeak.gz GM12878 ChipSeq Pbx3 Peaks narrowPeak HudsonAlpha Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeAwgTfbsUniform//wgEncodeAwgTfbsHaibGm12878Pmlsc71910V0422111UniPk.narrowPeak.gz GM12878 ChipSeq PML_(SC-71910) Peaks narrowPeak HudsonAlpha Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeAwgTfbsUniform//wgEncodeAwgTfbsHaibGm12878Pol24h8Pcr1xUniPk.narrowPeak.gz GM12878 ChipSeq Pol2-4H8 Peaks narrowPeak HudsonAlpha Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeAwgTfbsUniform//wgEncodeAwgTfbsHaibGm12878Pol2Pcr2xUniPk.narrowPeak.gz GM12878 ChipSeq Pol2 Peaks narrowPeak HudsonAlpha Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeAwgTfbsUniform//wgEncodeAwgTfbsSydhGm12878Pol2IggmusUniPk.narrowPeak.gz GM12878 ChipSeq Pol2 Peaks narrowPeak Stanford Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeAwgTfbsUniform//wgEncodeAwgTfbsUtaGm12878Pol2UniPk.narrowPeak.gz GM12878 ChipSeq Pol2 Peaks narrowPeak UT-A Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeAwgTfbsUniform//wgEncodeAwgTfbsSydhGm12878Pol2UniPk.narrowPeak.gz GM12878 ChipSeq Pol2 Peaks narrowPeak Yale Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeAwgTfbsUniform//wgEncodeAwgTfbsSydhGm12878Pol2s2IggmusUniPk.narrowPeak.gz GM12878 ChipSeq Pol2(phosphoS2) Peaks narrowPeak Stanford Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeAwgTfbsUniform//wgEncodeAwgTfbsSydhGm12878Pol3UniPk.narrowPeak.gz GM12878 ChipSeq Pol3 Peaks narrowPeak Yale Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeAwgTfbsUniform//wgEncodeAwgTfbsHaibGm12878Pou2f2Pcr1xUniPk.narrowPeak.gz GM12878 ChipSeq POU2F2 Peaks narrowPeak HudsonAlpha Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeAwgTfbsUniform//wgEncodeAwgTfbsHaibGm12878Rad21V0416101UniPk.narrowPeak.gz GM12878 ChipSeq Rad21 Peaks narrowPeak HudsonAlpha Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeAwgTfbsUniform//wgEncodeAwgTfbsSydhGm12878Rad21IggrabUniPk.narrowPeak.gz GM12878 ChipSeq Rad21 Peaks narrowPeak Stanford Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeAwgTfbsUniform//wgEncodeAwgTfbsSydhGm12878Corestsc30189IggmusUniPk.narrowPeak.gz GM12878 ChipSeq COREST_(sc-30189) Peaks narrowPeak Stanford Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeAwgTfbsUniform//wgEncodeAwgTfbsSydhGm12878NfkbTnfaIggrabUniPk.narrowPeak.gz GM12878 ChipSeq NFKB Peaks narrowPeak Stanford Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeAwgTfbsUniform//wgEncodeAwgTfbsHaibGm12878NrsfPcr1xUniPk.narrowPeak.gz GM12878 ChipSeq NRSF Peaks narrowPeak HudsonAlpha Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeAwgTfbsUniform//wgEncodeAwgTfbsSydhGm12878Rfx5200401194IggmusUniPk.narrowPeak.gz GM12878 ChipSeq RFX5_(200-401-194) Peaks narrowPeak Stanford Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeAwgTfbsUniform//wgEncodeAwgTfbsHaibGm12878Runx3sc101553V0422111UniPk.narrowPeak.gz GM12878 ChipSeq RUNX3_(SC-101553) Peaks narrowPeak HudsonAlpha Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeAwgTfbsUniform//wgEncodeAwgTfbsHaibGm12878RxraPcr1xUniPk.narrowPeak.gz GM12878 ChipSeq RXRA Peaks narrowPeak HudsonAlpha Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeAwgTfbsUniform//wgEncodeAwgTfbsSydhGm12878Sin3anb6001263IggmusUniPk.narrowPeak.gz GM12878 ChipSeq SIN3A_(NB600-1263) Peaks narrowPeak Stanford Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeAwgTfbsUniform//wgEncodeAwgTfbsHaibGm12878Six5Pcr1xUniPk.narrowPeak.gz GM12878 ChipSeq SIX5 Peaks narrowPeak HudsonAlpha Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeAwgTfbsUniform//wgEncodeAwgTfbsSydhGm12878Smc3ab9263IggmusUniPk.narrowPeak.gz GM12878 ChipSeq SMC3_(ab9263) Peaks narrowPeak Stanford Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeAwgTfbsUniform//wgEncodeAwgTfbsHaibGm12878Sp1Pcr1xUniPk.narrowPeak.gz GM12878 ChipSeq SP1 Peaks narrowPeak HudsonAlpha Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeAwgTfbsUniform//wgEncodeAwgTfbsHaibGm12878Pu1Pcr1xUniPk.narrowPeak.gz GM12878 ChipSeq PU.1 Peaks narrowPeak HudsonAlpha Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeAwgTfbsUniform//wgEncodeAwgTfbsHaibGm12878SrfPcr2xUniPk.narrowPeak.gz GM12878 ChipSeq SRF Peaks narrowPeak HudsonAlpha Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeAwgTfbsUniform//wgEncodeAwgTfbsSydhGm12878Stat1UniPk.narrowPeak.gz GM12878 ChipSeq STAT1 Peaks narrowPeak Stanford Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeAwgTfbsUniform//wgEncodeAwgTfbsSydhGm12878Stat3IggmusUniPk.narrowPeak.gz GM12878 ChipSeq STAT3 Peaks narrowPeak Stanford Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeAwgTfbsUniform//wgEncodeAwgTfbsHaibGm12878Stat5asc74442V0422111UniPk.narrowPeak.gz GM12878 ChipSeq STAT5A_(SC-74442) Peaks narrowPeak HudsonAlpha Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeAwgTfbsUniform//wgEncodeAwgTfbsHaibGm12878Taf1Pcr1xUniPk.narrowPeak.gz GM12878 ChipSeq TAF1 Peaks narrowPeak HudsonAlpha Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeAwgTfbsUniform//wgEncodeAwgTfbsSydhGm12878Tblr1ab24550IggmusUniPk.narrowPeak.gz GM12878 ChipSeq TBLR1_(ab24550) Peaks narrowPeak Stanford Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeAwgTfbsUniform//wgEncodeAwgTfbsSydhGm12878TbpIggmusUniPk.narrowPeak.gz GM12878 ChipSeq TBP Peaks narrowPeak Stanford Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeAwgTfbsUniform//wgEncodeAwgTfbsHaibGm12878Tcf12Pcr1xUniPk.narrowPeak.gz GM12878 ChipSeq TCF12 Peaks narrowPeak HudsonAlpha Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeAwgTfbsUniform//wgEncodeAwgTfbsHaibGm12878Tcf3Pcr1xUniPk.narrowPeak.gz GM12878 ChipSeq TCF3_(SC-349) Peaks narrowPeak HudsonAlpha Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeAwgTfbsUniform//wgEncodeAwgTfbsHaibGm12878Usf1Pcr2xUniPk.narrowPeak.gz GM12878 ChipSeq USF-1 Peaks narrowPeak HudsonAlpha Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeAwgTfbsUniform//wgEncodeAwgTfbsSydhGm12878Usf2IggmusUniPk.narrowPeak.gz GM12878 ChipSeq USF2 Peaks narrowPeak Stanford Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeAwgTfbsUniform//wgEncodeAwgTfbsSydhGm12878WhipIggmusUniPk.narrowPeak.gz GM12878 ChipSeq WHIP Peaks narrowPeak Stanford Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeAwgTfbsUniform//wgEncodeAwgTfbsHaibGm12878Yy1sc281Pcr1xUniPk.narrowPeak.gz GM12878 ChipSeq YY1_(SC-281) Peaks narrowPeak HudsonAlpha Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeAwgTfbsUniform//wgEncodeAwgTfbsSydhGm12878Yy1UniPk.narrowPeak.gz GM12878 ChipSeq YY1 Peaks narrowPeak USC Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeAwgTfbsUniform//wgEncodeAwgTfbsHaibGm12878Zbtb33Pcr1xUniPk.narrowPeak.gz GM12878 ChipSeq ZBTB33 Peaks narrowPeak HudsonAlpha Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeAwgTfbsUniform//wgEncodeAwgTfbsHaibGm12878Zeb1sc25388V0416102UniPk.narrowPeak.gz GM12878 ChipSeq ZEB1_(SC-25388) Peaks narrowPeak HudsonAlpha Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeAwgTfbsUniform//wgEncodeAwgTfbsSydhGm12878Znf143166181apUniPk.narrowPeak.gz GM12878 ChipSeq Znf143_(16618-1-AP) Peaks narrowPeak Stanford Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeAwgTfbsUniform//wgEncodeAwgTfbsSydhGm12878Znf274UniPk.narrowPeak.gz GM12878 ChipSeq ZNF274 Peaks narrowPeak USC Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeAwgTfbsUniform//wgEncodeAwgTfbsSydhGm12878Zzz3UniPk.narrowPeak.gz GM12878 ChipSeq ZZZ3 Peaks narrowPeak Harvard Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeAwgTfbsUniform//wgEncodeAwgTfbsBroadHmecCtcfUniPk.narrowPeak.gz HMEC ChipSeq CTCF Peaks narrowPeak Broad Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeAwgTfbsUniform//wgEncodeAwgTfbsBroadHmecEzh239875UniPk.narrowPeak.gz HMEC ChipSeq EZH2_(39875) Peaks narrowPeak Broad Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeAwgTfbsUniform//wgEncodeAwgTfbsSydhImr90CebpbIggrabUniPk.narrowPeak.gz IMR90 ChipSeq CEBPB Peaks narrowPeak Stanford Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeAwgTfbsUniform//wgEncodeAwgTfbsSydhImr90CtcfbIggrabUniPk.narrowPeak.gz IMR90 ChipSeq CTCF_(SC-15914) Peaks narrowPeak Stanford Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeAwgTfbsUniform//wgEncodeAwgTfbsSydhImr90MafkIggrabUniPk.narrowPeak.gz IMR90 ChipSeq MafK_(ab50322) Peaks narrowPeak Stanford Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeAwgTfbsUniform//wgEncodeAwgTfbsSydhImr90Pol2IggrabUniPk.narrowPeak.gz IMR90 ChipSeq Pol2 Peaks narrowPeak Stanford Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeAwgTfbsUniform//wgEncodeAwgTfbsSydhImr90Rad21IggrabUniPk.narrowPeak.gz IMR90 ChipSeq Rad21 Peaks narrowPeak Stanford Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeAwgTfbsUniform//wgEncodeAwgTfbsSydhK562Arid3asc8821IggrabUniPk.narrowPeak.gz K562 ChipSeq ARID3A_(sc-8821) Peaks narrowPeak Stanford Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeAwgTfbsUniform//wgEncodeAwgTfbsSydhK562Atf106325UniPk.narrowPeak.gz K562 ChipSeq ATF1_(06-325) Peaks narrowPeak Harvard Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeAwgTfbsUniform//wgEncodeAwgTfbsHaibK562Atf3V0416101UniPk.narrowPeak.gz K562 ChipSeq ATF3 Peaks narrowPeak HudsonAlpha Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeAwgTfbsUniform//wgEncodeAwgTfbsSydhK562Atf3UniPk.narrowPeak.gz K562 ChipSeq ATF3 Peaks narrowPeak Harvard Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeAwgTfbsUniform//wgEncodeAwgTfbsSydhK562Bach1sc14700IggrabUniPk.narrowPeak.gz K562 ChipSeq Bach1_(sc-14700) Peaks narrowPeak Stanford Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeAwgTfbsUniform//wgEncodeAwgTfbsHaibK562Bcl3Pcr1xUniPk.narrowPeak.gz K562 ChipSeq BCL3 Peaks narrowPeak HudsonAlpha Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeAwgTfbsUniform//wgEncodeAwgTfbsHaibK562Bclaf101388Pcr1xUniPk.narrowPeak.gz K562 ChipSeq BCLAF1_(SC-101388) Peaks narrowPeak HudsonAlpha Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeAwgTfbsUniform//wgEncodeAwgTfbsSydhK562Bdp1UniPk.narrowPeak.gz K562 ChipSeq BDP1 Peaks narrowPeak Harvard Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeAwgTfbsUniform//wgEncodeAwgTfbsSydhK562Bhlhe40nb100IggrabUniPk.narrowPeak.gz K562 ChipSeq BHLHE40_(NB100-1800) Peaks narrowPeak Stanford Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeAwgTfbsUniform//wgEncodeAwgTfbsSydhK562Brf1UniPk.narrowPeak.gz K562 ChipSeq BRF1 Peaks narrowPeak Harvard Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeAwgTfbsUniform//wgEncodeAwgTfbsSydhK562Brf2UniPk.narrowPeak.gz K562 ChipSeq BRF2 Peaks narrowPeak Harvard Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeAwgTfbsUniform//wgEncodeAwgTfbsSydhK562Brg1IggmusUniPk.narrowPeak.gz K562 ChipSeq Brg1 Peaks narrowPeak Stanford Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeAwgTfbsUniform//wgEncodeAwgTfbsHaibK562Cbx3sc101004V0422111UniPk.narrowPeak.gz K562 ChipSeq CBX3_(SC-101004) Peaks narrowPeak HudsonAlpha Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeAwgTfbsUniform//wgEncodeAwgTfbsSydhK562Ccnt2UniPk.narrowPeak.gz K562 ChipSeq CCNT2 Peaks narrowPeak Harvard Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeAwgTfbsUniform//wgEncodeAwgTfbsHaibK562Cebpbsc150V0422111UniPk.narrowPeak.gz K562 ChipSeq CEBPB_(SC-150) Peaks narrowPeak HudsonAlpha Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeAwgTfbsUniform//wgEncodeAwgTfbsSydhK562CebpbIggrabUniPk.narrowPeak.gz K562 ChipSeq CEBPB Peaks narrowPeak Stanford Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeAwgTfbsUniform//wgEncodeAwgTfbsBroadK562Chd1a301218aUniPk.narrowPeak.gz K562 ChipSeq CHD1_(A301-218A) Peaks narrowPeak Broad Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeAwgTfbsUniform//wgEncodeAwgTfbsSydhK562Chd2ab68301IggrabUniPk.narrowPeak.gz K562 ChipSeq CHD2_(AB68301) Peaks narrowPeak Stanford Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeAwgTfbsUniform//wgEncodeAwgTfbsBroadK562CtcfUniPk.narrowPeak.gz K562 ChipSeq CTCF Peaks narrowPeak Broad Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeAwgTfbsUniform//wgEncodeAwgTfbsHaibK562CtcfcPcr1xUniPk.narrowPeak.gz K562 ChipSeq CTCF_(SC-5916) Peaks narrowPeak HudsonAlpha Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeAwgTfbsUniform//wgEncodeAwgTfbsSydhK562CtcfbIggrabUniPk.narrowPeak.gz K562 ChipSeq CTCF_(SC-15914) Peaks narrowPeak Stanford Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeAwgTfbsUniform//wgEncodeAwgTfbsUtaK562CtcfUniPk.narrowPeak.gz K562 ChipSeq CTCF Peaks narrowPeak UT-A Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeAwgTfbsUniform//wgEncodeAwgTfbsUwK562CtcfUniPk.narrowPeak.gz K562 ChipSeq CTCF Peaks narrowPeak UW Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeAwgTfbsUniform//wgEncodeAwgTfbsHaibK562Ctcflsc98982V0416101UniPk.narrowPeak.gz K562 ChipSeq CTCFL_(SC-98982) Peaks narrowPeak HudsonAlpha Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeAwgTfbsUniform//wgEncodeAwgTfbsSydhK562E2f4UcdUniPk.narrowPeak.gz K562 ChipSeq E2F4 Peaks narrowPeak USC Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeAwgTfbsUniform//wgEncodeAwgTfbsHaibK562E2f6V0416102UniPk.narrowPeak.gz K562 ChipSeq E2F6 Peaks narrowPeak HudsonAlpha Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeAwgTfbsUniform//wgEncodeAwgTfbsSydhK562E2f6UcdUniPk.narrowPeak.gz K562 ChipSeq E2F6 Peaks narrowPeak USC Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeAwgTfbsUniform//wgEncodeAwgTfbsHaibK562Egr1V0416101UniPk.narrowPeak.gz K562 ChipSeq Egr-1 Peaks narrowPeak HudsonAlpha Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeAwgTfbsUniform//wgEncodeAwgTfbsHaibK562Elf1sc631V0416102UniPk.narrowPeak.gz K562 ChipSeq ELF1_(SC-631) Peaks narrowPeak HudsonAlpha Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeAwgTfbsUniform//wgEncodeAwgTfbsSydhK562Elk112771IggrabUniPk.narrowPeak.gz K562 ChipSeq ELK1_(1277-1) Peaks narrowPeak Stanford Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeAwgTfbsUniform//wgEncodeAwgTfbsBroadK562P300UniPk.narrowPeak.gz K562 ChipSeq p300 Peaks narrowPeak Broad Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeAwgTfbsUniform//wgEncodeAwgTfbsSydhK562P300IggrabUniPk.narrowPeak.gz K562 ChipSeq p300 Peaks narrowPeak Stanford Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeAwgTfbsUniform//wgEncodeAwgTfbsHaibK562Ets1V0416101UniPk.narrowPeak.gz K562 ChipSeq ETS1 Peaks narrowPeak HudsonAlpha Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeAwgTfbsUniform//wgEncodeAwgTfbsBroadK562Ezh239875UniPk.narrowPeak.gz K562 ChipSeq EZH2_(39875) Peaks narrowPeak Broad Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeAwgTfbsUniform//wgEncodeAwgTfbsSydhK562CfosUniPk.narrowPeak.gz K562 ChipSeq c-Fos Peaks narrowPeak Yale Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeAwgTfbsUniform//wgEncodeAwgTfbsHaibK562Fosl1sc183V0416101UniPk.narrowPeak.gz K562 ChipSeq FOSL1_(SC-183) Peaks narrowPeak HudsonAlpha Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeAwgTfbsUniform//wgEncodeAwgTfbsHaibK562GabpV0416101UniPk.narrowPeak.gz K562 ChipSeq GABP Peaks narrowPeak HudsonAlpha Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeAwgTfbsUniform//wgEncodeAwgTfbsSydhK562Gata1UcdUniPk.narrowPeak.gz K562 ChipSeq GATA-1 Peaks narrowPeak USC Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeAwgTfbsUniform//wgEncodeAwgTfbsHaibK562Gata2sc267Pcr1xUniPk.narrowPeak.gz K562 ChipSeq GATA2_(SC-267) Peaks narrowPeak HudsonAlpha Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeAwgTfbsUniform//wgEncodeAwgTfbsSydhK562Gata2UcdUniPk.narrowPeak.gz K562 ChipSeq GATA-2 Peaks narrowPeak USC Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeAwgTfbsUniform//wgEncodeAwgTfbsSydhK562Gtf2bUniPk.narrowPeak.gz K562 ChipSeq GTF2B Peaks narrowPeak Harvard Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeAwgTfbsUniform//wgEncodeAwgTfbsSydhK562Gtf2f1ab28179IggrabUniPk.narrowPeak.gz K562 ChipSeq GTF2F1_(AB28179) Peaks narrowPeak Stanford Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeAwgTfbsUniform//wgEncodeAwgTfbsSydhK562Tf3c110UniPk.narrowPeak.gz K562 ChipSeq TFIIIC-110 Peaks narrowPeak Harvard Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeAwgTfbsUniform//wgEncodeAwgTfbsBroadK562Hdac1sc6298UniPk.narrowPeak.gz K562 ChipSeq HDAC1_(SC-6298) Peaks narrowPeak Broad Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeAwgTfbsUniform//wgEncodeAwgTfbsBroadK562Hdac2a300705aUniPk.narrowPeak.gz K562 ChipSeq HDAC2_(A300-705A) Peaks narrowPeak Broad Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeAwgTfbsUniform//wgEncodeAwgTfbsBroadK562Hdac6a301341aUniPk.narrowPeak.gz K562 ChipSeq HDAC6_(A301-341A) Peaks narrowPeak Broad Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeAwgTfbsUniform//wgEncodeAwgTfbsSydhK562Hmgn3UniPk.narrowPeak.gz K562 ChipSeq HMGN3 Peaks narrowPeak Harvard Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeAwgTfbsUniform//wgEncodeAwgTfbsSydhK562Irf1Ifna30UniPk.narrowPeak.gz K562 ChipSeq IRF1 Peaks narrowPeak Stanford Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeAwgTfbsUniform//wgEncodeAwgTfbsSydhK562CjunIfna30UniPk.narrowPeak.gz K562 ChipSeq c-Jun Peaks narrowPeak Stanford Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeAwgTfbsUniform//wgEncodeAwgTfbsSydhK562JundIggrabUniPk.narrowPeak.gz K562 ChipSeq JunD Peaks narrowPeak Stanford Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeAwgTfbsUniform//wgEncodeAwgTfbsSydhK562Kap1UcdUniPk.narrowPeak.gz K562 ChipSeq KAP1 Peaks narrowPeak USC Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeAwgTfbsUniform//wgEncodeAwgTfbsBroadK562Plu1UniPk.narrowPeak.gz K562 ChipSeq PLU1 Peaks narrowPeak Broad Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeAwgTfbsUniform//wgEncodeAwgTfbsSydhK562MaffIggrabUniPk.narrowPeak.gz K562 ChipSeq MafF_(M8194) Peaks narrowPeak Stanford Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeAwgTfbsUniform//wgEncodeAwgTfbsSydhK562Mafkab50322IggrabUniPk.narrowPeak.gz K562 ChipSeq MafK_(ab50322) Peaks narrowPeak Stanford Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeAwgTfbsUniform//wgEncodeAwgTfbsHaibK562MaxV0416102UniPk.narrowPeak.gz K562 ChipSeq Max Peaks narrowPeak HudsonAlpha Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeAwgTfbsUniform//wgEncodeAwgTfbsSydhK562Mazab85725IggrabUniPk.narrowPeak.gz K562 ChipSeq MAZ_(ab85725) Peaks narrowPeak Stanford Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeAwgTfbsUniform//wgEncodeAwgTfbsHaibK562Mef2aV0416101UniPk.narrowPeak.gz K562 ChipSeq MEF2A Peaks narrowPeak HudsonAlpha Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeAwgTfbsUniform//wgEncodeAwgTfbsSydhK562Mxi1af4185IggrabUniPk.narrowPeak.gz K562 ChipSeq Mxi1_(AF4185) Peaks narrowPeak Stanford Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeAwgTfbsUniform//wgEncodeAwgTfbsSydhK562CmycIfna30UniPk.narrowPeak.gz K562 ChipSeq c-Myc Peaks narrowPeak Yale Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeAwgTfbsUniform//wgEncodeAwgTfbsSydhK562Nfe2UniPk.narrowPeak.gz K562 ChipSeq NF-E2 Peaks narrowPeak Yale Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeAwgTfbsUniform//wgEncodeAwgTfbsSydhK562NfyaUniPk.narrowPeak.gz K562 ChipSeq NF-YA Peaks narrowPeak Stanford Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeAwgTfbsUniform//wgEncodeAwgTfbsSydhK562NfybUniPk.narrowPeak.gz K562 ChipSeq NF-YB Peaks narrowPeak Stanford Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeAwgTfbsUniform//wgEncodeAwgTfbsSydhK562Tr4UcdUniPk.narrowPeak.gz K562 ChipSeq TR4 Peaks narrowPeak USC Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeAwgTfbsUniform//wgEncodeAwgTfbsHaibK562Nr2f2sc271940V0422111UniPk.narrowPeak.gz K562 ChipSeq NR2F2_(SC-271940) Peaks narrowPeak HudsonAlpha Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeAwgTfbsUniform//wgEncodeAwgTfbsSydhK562Nrf1IggrabUniPk.narrowPeak.gz K562 ChipSeq Nrf1 Peaks narrowPeak Stanford Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeAwgTfbsUniform//wgEncodeAwgTfbsBroadK562Phf8a301772aUniPk.narrowPeak.gz K562 ChipSeq PHF8_(A301-772A) Peaks narrowPeak Broad Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeAwgTfbsUniform//wgEncodeAwgTfbsHaibK562Pmlsc71910V0422111UniPk.narrowPeak.gz K562 ChipSeq PML_(SC-71910) Peaks narrowPeak HudsonAlpha Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeAwgTfbsUniform//wgEncodeAwgTfbsBroadK562Pol2bUniPk.narrowPeak.gz K562 ChipSeq Pol2(b) Peaks narrowPeak Broad Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeAwgTfbsUniform//wgEncodeAwgTfbsSydhK562Pol3UniPk.narrowPeak.gz K562 ChipSeq Pol3 Peaks narrowPeak Stanford Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeAwgTfbsUniform//wgEncodeAwgTfbsHaibK562Rad21V0416102UniPk.narrowPeak.gz K562 ChipSeq Rad21 Peaks narrowPeak HudsonAlpha Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeAwgTfbsUniform//wgEncodeAwgTfbsBroadK562Rbbp5a300109aUniPk.narrowPeak.gz K562 ChipSeq RBBP5_(A300-109A) Peaks narrowPeak Broad Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeAwgTfbsUniform//wgEncodeAwgTfbsSydhK562Corestab24166IggrabUniPk.narrowPeak.gz K562 ChipSeq COREST_(ab24166) Peaks narrowPeak Stanford Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeAwgTfbsUniform//wgEncodeAwgTfbsSydhK562Corestsc30189IggrabUniPk.narrowPeak.gz K562 ChipSeq COREST_(sc-30189) Peaks narrowPeak Stanford Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeAwgTfbsUniform//wgEncodeAwgTfbsSydhK562NelfeUniPk.narrowPeak.gz K562 ChipSeq NELFe Peaks narrowPeak Harvard Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeAwgTfbsUniform//wgEncodeAwgTfbsHaibK562NrsfV0416102UniPk.narrowPeak.gz K562 ChipSeq NRSF Peaks narrowPeak HudsonAlpha Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeAwgTfbsUniform//wgEncodeAwgTfbsSydhK562Rfx5IggrabUniPk.narrowPeak.gz K562 ChipSeq RFX5_(200-401-194) Peaks narrowPeak Stanford Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeAwgTfbsUniform//wgEncodeAwgTfbsSydhK562Rpc155UniPk.narrowPeak.gz K562 ChipSeq RPC155 Peaks narrowPeak Harvard Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeAwgTfbsUniform//wgEncodeAwgTfbsBroadK562Sap3039731UniPk.narrowPeak.gz K562 ChipSeq SAP30_(39731) Peaks narrowPeak Broad Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeAwgTfbsUniform//wgEncodeAwgTfbsSydhK562Setdb1MnasedUcdUniPk.narrowPeak.gz K562 ChipSeq SETDB1 Peaks narrowPeak USC Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeAwgTfbsUniform//wgEncodeAwgTfbsHaibK562Sin3ak20V0416101UniPk.narrowPeak.gz K562 ChipSeq Sin3Ak-20 Peaks narrowPeak HudsonAlpha Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeAwgTfbsUniform//wgEncodeAwgTfbsSydhK562Sirt6UniPk.narrowPeak.gz K562 ChipSeq SIRT6 Peaks narrowPeak Harvard Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeAwgTfbsUniform//wgEncodeAwgTfbsHaibK562Six5Pcr1xUniPk.narrowPeak.gz K562 ChipSeq SIX5 Peaks narrowPeak HudsonAlpha Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeAwgTfbsUniform//wgEncodeAwgTfbsSydhK562Ini1IggmusUniPk.narrowPeak.gz K562 ChipSeq Ini1 Peaks narrowPeak Stanford Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeAwgTfbsUniform//wgEncodeAwgTfbsSydhK562Smc3ab9263IggrabUniPk.narrowPeak.gz K562 ChipSeq SMC3_(ab9263) Peaks narrowPeak Stanford Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeAwgTfbsUniform//wgEncodeAwgTfbsHaibK562Sp1Pcr1xUniPk.narrowPeak.gz K562 ChipSeq SP1 Peaks narrowPeak HudsonAlpha Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeAwgTfbsUniform//wgEncodeAwgTfbsHaibK562Sp2sc643V0416102UniPk.narrowPeak.gz K562 ChipSeq SP2_(SC-643) Peaks narrowPeak HudsonAlpha Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeAwgTfbsUniform//wgEncodeAwgTfbsHaibK562Pu1Pcr1xUniPk.narrowPeak.gz K562 ChipSeq PU.1 Peaks narrowPeak HudsonAlpha Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeAwgTfbsUniform//wgEncodeAwgTfbsHaibK562SrfV0416101UniPk.narrowPeak.gz K562 ChipSeq SRF Peaks narrowPeak HudsonAlpha Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeAwgTfbsUniform//wgEncodeAwgTfbsSydhK562Stat1Ifna30UniPk.narrowPeak.gz K562 ChipSeq STAT1 Peaks narrowPeak Yale Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeAwgTfbsUniform//wgEncodeAwgTfbsSydhK562Stat2Ifna30UniPk.narrowPeak.gz K562 ChipSeq STAT2 Peaks narrowPeak Yale Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeAwgTfbsUniform//wgEncodeAwgTfbsHaibK562Stat5asc74442V0422111UniPk.narrowPeak.gz K562 ChipSeq STAT5A_(SC-74442) Peaks narrowPeak HudsonAlpha Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeAwgTfbsUniform//wgEncodeAwgTfbsHaibK562Taf1V0416101UniPk.narrowPeak.gz K562 ChipSeq TAF1 Peaks narrowPeak HudsonAlpha Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeAwgTfbsUniform//wgEncodeAwgTfbsHaibK562Taf7sc101167V0416101UniPk.narrowPeak.gz K562 ChipSeq TAF7_(SC-101167) Peaks narrowPeak HudsonAlpha Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeAwgTfbsUniform//wgEncodeAwgTfbsSydhK562Tal1sc12984IggmusUniPk.narrowPeak.gz K562 ChipSeq TAL1_(SC-12984) Peaks narrowPeak Stanford Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeAwgTfbsUniform//wgEncodeAwgTfbsSydhK562Tblr1ab24550IggrabUniPk.narrowPeak.gz K562 ChipSeq TBLR1_(ab24550) Peaks narrowPeak Stanford Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeAwgTfbsUniform//wgEncodeAwgTfbsSydhK562TbpIggmusUniPk.narrowPeak.gz K562 ChipSeq TBP Peaks narrowPeak Stanford Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeAwgTfbsUniform//wgEncodeAwgTfbsHaibK562Tead4sc101184V0422111UniPk.narrowPeak.gz K562 ChipSeq TEAD4_(SC-101184) Peaks narrowPeak HudsonAlpha Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeAwgTfbsUniform//wgEncodeAwgTfbsHaibK562Thap1sc98174V0416101UniPk.narrowPeak.gz K562 ChipSeq THAP1_(SC-98174) Peaks narrowPeak HudsonAlpha Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeAwgTfbsUniform//wgEncodeAwgTfbsHaibK562Trim28sc81411V0422111UniPk.narrowPeak.gz K562 ChipSeq TRIM28_(SC-81411) Peaks narrowPeak HudsonAlpha Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeAwgTfbsUniform//wgEncodeAwgTfbsSydhK562Ubfsc13125IggmusUniPk.narrowPeak.gz K562 ChipSeq UBF_(sc-13125) Peaks narrowPeak Stanford Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeAwgTfbsUniform//wgEncodeAwgTfbsSydhK562Ubtfsab1404509IggmusUniPk.narrowPeak.gz K562 ChipSeq UBTF_(SAB1404509) Peaks narrowPeak Stanford Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeAwgTfbsUniform//wgEncodeAwgTfbsHaibK562Usf1V0416101UniPk.narrowPeak.gz K562 ChipSeq USF-1 Peaks narrowPeak HudsonAlpha Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeAwgTfbsUniform//wgEncodeAwgTfbsSydhK562Usf2IggrabUniPk.narrowPeak.gz K562 ChipSeq USF2 Peaks narrowPeak Stanford Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeAwgTfbsUniform//wgEncodeAwgTfbsHaibK562Yy1V0416101UniPk.narrowPeak.gz K562 ChipSeq YY1_(SC-281) Peaks narrowPeak HudsonAlpha Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeAwgTfbsUniform//wgEncodeAwgTfbsHaibK562Zbtb33Pcr1xUniPk.narrowPeak.gz K562 ChipSeq ZBTB33 Peaks narrowPeak HudsonAlpha Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeAwgTfbsUniform//wgEncodeAwgTfbsHaibK562Zbtb7asc34508V0416101UniPk.narrowPeak.gz K562 ChipSeq ZBTB7A_(SC-34508) Peaks narrowPeak HudsonAlpha Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeAwgTfbsUniform//wgEncodeAwgTfbsSydhK562Znf143IggrabUniPk.narrowPeak.gz K562 ChipSeq Znf143_(16618-1-AP) Peaks narrowPeak Stanford Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeAwgTfbsUniform//wgEncodeAwgTfbsSydhK562Znf263UcdUniPk.narrowPeak.gz K562 ChipSeq ZNF263 Peaks narrowPeak USC Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeAwgTfbsUniform//wgEncodeAwgTfbsSydhK562Znf274UcdUniPk.narrowPeak.gz K562 ChipSeq ZNF274 Peaks narrowPeak USC Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeAwgTfbsUniform//wgEncodeAwgTfbsBroadNhekCtcfUniPk.narrowPeak.gz NHEK ChipSeq CTCF Peaks narrowPeak Broad Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeAwgTfbsUniform//wgEncodeAwgTfbsBroadNhekEzh239875UniPk.narrowPeak.gz NHEK ChipSeq EZH2_(39875) Peaks narrowPeak Broad Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeAwgDnaseUniform//wgEncodeAwgDnaseUwdukeGm12878UniPk.narrowPeak.gz GM12878 DnaseSeq Peaks narrowPeak AWG Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeAwgDnaseUniform//wgEncodeAwgDnaseUwdukeHmecUniPk.narrowPeak.gz HMEC DnaseSeq Peaks narrowPeak AWG Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeAwgDnaseUniform//wgEncodeAwgDnaseUwNhlfUniPk.narrowPeak.gz NHLF DnaseSeq Peaks narrowPeak UW Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeAwgDnaseUniform//wgEncodeAwgDnaseUwdukeK562UniPk.narrowPeak.gz K562 DnaseSeq Peaks narrowPeak AWG Data http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeAwgDnaseUniform//wgEncodeAwgDnaseUwdukeNhekUniPk.narrowPeak.gz NHEK DnaseSeq Peaks narrowPeak AWG Data 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http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeCaltechTfbs/wgEncodeCaltechTfbsC2c12NrsfFCntrl32bE2p60hPcr2xPkRep1.narrowPeak.gz C2C12 ChipSeq NRSF Peaks 1 narrowPeak Caltech-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeCaltechTfbs/wgEncodeCaltechTfbsC2c12NrsfFCntrl32bE2p60hPcr2xSigRep1.bigWig C2C12 ChipSeq NRSF Signal 1 bigWig Caltech-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeCaltechTfbs/wgEncodeCaltechTfbsC2c12Pol2FCntrl32bE2p60hPcr2xAlnRep1.bam C2C12 ChipSeq Pol2 Alignments 1 bam Caltech-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeCaltechTfbs/wgEncodeCaltechTfbsC2c12Pol2FCntrl32bE2p60hPcr2xPkRep1.narrowPeak.gz C2C12 ChipSeq Pol2 Peaks 1 narrowPeak Caltech-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeCaltechTfbs/wgEncodeCaltechTfbsC2c12Pol2FCntrl32bE2p60hPcr2xSigRep1.bigWig C2C12 ChipSeq Pol2 Signal 1 bigWig Caltech-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeCaltechTfbs/wgEncodeCaltechTfbsC2c12Pol2s2FCntrl32bE2p60hPcr2xAlnRep1.bam C2C12 ChipSeq Pol2(phosphoS2) Alignments 1 bam Caltech-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeCaltechTfbs/wgEncodeCaltechTfbsC2c12Pol2s2FCntrl32bE2p60hPcr2xPkRep1.narrowPeak.gz C2C12 ChipSeq Pol2(phosphoS2) Peaks 1 narrowPeak Caltech-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeCaltechTfbs/wgEncodeCaltechTfbsC2c12Pol2s2FCntrl32bE2p60hPcr2xSigRep1.bigWig C2C12 ChipSeq Pol2(phosphoS2) Signal 1 bigWig Caltech-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeCaltechTfbs/wgEncodeCaltechTfbsC2c12Sc12732FCntrl32bE2p24hPcr2xPkRep1.narrowPeak.gz C2C12 ChipSeq Myogenin_(sc-12732) Peaks 1 narrowPeak Caltech-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeCaltechTfbs/wgEncodeCaltechTfbsC2c12Sc12732FCntrl32bE2p24hPcr2xSigRep1.bigWig C2C12 ChipSeq Myogenin_(sc-12732) Signal 1 bigWig Caltech-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeCaltechTfbs/wgEncodeCaltechTfbsC2c12Sc12732FCntrl32bE2p60hPcr2xAlnRep1.bam C2C12 ChipSeq Myogenin_(sc-12732) Alignments 1 bam Caltech-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeCaltechTfbs/wgEncodeCaltechTfbsC2c12Sc12732FCntrl32bE2p60hPcr2xPkRep1.narrowPeak.gz C2C12 ChipSeq Myogenin_(sc-12732) Peaks 1 narrowPeak Caltech-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeCaltechTfbs/wgEncodeCaltechTfbsC2c12Sc12732FCntrl32bE2p60hPcr2xSigRep1.bigWig C2C12 ChipSeq Myogenin_(sc-12732) Signal 1 bigWig Caltech-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeCaltechTfbs/wgEncodeCaltechTfbsC2c12Sc12732FCntrl32bPcr2xAlnRep1.bam C2C12 ChipSeq Myogenin_(sc-12732) Alignments 1 bam Caltech-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeCaltechTfbs/wgEncodeCaltechTfbsC2c12Sc12732FCntrl32bPcr2xPkRep1.narrowPeak.gz C2C12 ChipSeq Myogenin_(sc-12732) Peaks 1 narrowPeak Caltech-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeCaltechTfbs/wgEncodeCaltechTfbsC2c12Sc12732FCntrl32bPcr2xSigRep1.bigWig C2C12 ChipSeq Myogenin_(sc-12732) Signal 1 bigWig Caltech-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeCaltechTfbs/wgEncodeCaltechTfbsC2c12Sc12732FCntrl50bE2p7dPcr1xAlnRep1.bam C2C12 ChipSeq Myogenin_(sc-12732) Alignments 1 bam Caltech-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeCaltechTfbs/wgEncodeCaltechTfbsC2c12Sc12732FCntrl50bE2p7dPcr1xPkRep1.narrowPeak.gz C2C12 ChipSeq Myogenin_(sc-12732) Peaks 1 narrowPeak Caltech-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeCaltechTfbs/wgEncodeCaltechTfbsC2c12Sc12732FCntrl50bE2p7dPcr1xSigRep1.bigWig C2C12 ChipSeq Myogenin_(sc-12732) Signal 1 bigWig Caltech-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeCaltechTfbs/wgEncodeCaltechTfbsC2c12Sc32758FCntrl32bE2p24hPcr2xAlnRep1.bam C2C12 ChipSeq MyoD_(sc-32758) Alignments 1 bam Caltech-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeCaltechTfbs/wgEncodeCaltechTfbsC2c12Sc32758FCntrl32bE2p24hPcr2xPkRep1.narrowPeak.gz C2C12 ChipSeq MyoD_(sc-32758) Peaks 1 narrowPeak Caltech-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeCaltechTfbs/wgEncodeCaltechTfbsC2c12Sc32758FCntrl32bE2p24hPcr2xSigRep1.bigWig C2C12 ChipSeq MyoD_(sc-32758) Signal 1 bigWig Caltech-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeCaltechTfbs/wgEncodeCaltechTfbsC2c12Sc32758FCntrl32bE2p60hPcr2xAlnRep1.bam C2C12 ChipSeq MyoD_(sc-32758) Alignments 1 bam Caltech-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeCaltechTfbs/wgEncodeCaltechTfbsC2c12Sc32758FCntrl32bE2p60hPcr2xPkRep1.narrowPeak.gz C2C12 ChipSeq MyoD_(sc-32758) Peaks 1 narrowPeak Caltech-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeCaltechTfbs/wgEncodeCaltechTfbsC2c12Sc32758FCntrl32bE2p60hPcr2xSigRep1.bigWig C2C12 ChipSeq MyoD_(sc-32758) Signal 1 bigWig Caltech-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeCaltechTfbs/wgEncodeCaltechTfbsC2c12Sc32758FCntrl32bPcr2xAlnRep1.bam C2C12 ChipSeq MyoD_(sc-32758) Alignments 1 bam Caltech-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeCaltechTfbs/wgEncodeCaltechTfbsC2c12Sc32758FCntrl32bPcr2xPkRep1.narrowPeak.gz C2C12 ChipSeq MyoD_(sc-32758) Peaks 1 narrowPeak Caltech-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeCaltechTfbs/wgEncodeCaltechTfbsC2c12Sc32758FCntrl32bPcr2xSigRep1.bigWig C2C12 ChipSeq MyoD_(sc-32758) Signal 1 bigWig Caltech-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeCaltechTfbs/wgEncodeCaltechTfbsC2c12Sc32758FCntrl50bE2p7dPcr1xAlnRep1.bam C2C12 ChipSeq MyoD_(sc-32758) Alignments 1 bam Caltech-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeCaltechTfbs/wgEncodeCaltechTfbsC2c12Sc32758FCntrl50bE2p7dPcr1xPkRep1.narrowPeak.gz C2C12 ChipSeq MyoD_(sc-32758) Peaks 1 narrowPeak Caltech-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeCaltechTfbs/wgEncodeCaltechTfbsC2c12Sc32758FCntrl50bE2p7dPcr1xSigRep1.bigWig C2C12 ChipSeq MyoD_(sc-32758) Signal 1 bigWig Caltech-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeCaltechTfbs/wgEncodeCaltechTfbsC2c12SrfFCntrl32bE2p24hPcr2xAlnRep1.bam C2C12 ChipSeq SRF Alignments 1 bam Caltech-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeCaltechTfbs/wgEncodeCaltechTfbsC2c12SrfFCntrl32bE2p24hPcr2xPkRep1.narrowPeak.gz C2C12 ChipSeq SRF Peaks 1 narrowPeak Caltech-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeCaltechTfbs/wgEncodeCaltechTfbsC2c12SrfFCntrl32bE2p24hPcr2xSigRep1.bigWig C2C12 ChipSeq SRF Signal 1 bigWig Caltech-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeCaltechTfbs/wgEncodeCaltechTfbsC2c12Tcf12FCntrl50bE2p60hPcr1xAlnRep1.bam C2C12 ChipSeq TCF12 Alignments 1 bam Caltech-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeCaltechTfbs/wgEncodeCaltechTfbsC2c12Tcf12FCntrl50bE2p60hPcr1xPkRep1.narrowPeak.gz C2C12 ChipSeq TCF12 Peaks 1 narrowPeak Caltech-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeCaltechTfbs/wgEncodeCaltechTfbsC2c12Tcf12FCntrl50bE2p60hPcr1xSigRep1.bigWig C2C12 ChipSeq TCF12 Signal 1 bigWig Caltech-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeCaltechTfbs/wgEncodeCaltechTfbsC2c12Tcf3FCntrl32bE2p5dPcr2xAlnRep1.bam C2C12 ChipSeq TCF3_(SC-349) Alignments 1 bam Caltech-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeCaltechTfbs/wgEncodeCaltechTfbsC2c12Tcf3FCntrl32bE2p5dPcr2xPkRep1.narrowPeak.gz C2C12 ChipSeq TCF3_(SC-349) Peaks 1 narrowPeak Caltech-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeCaltechTfbs/wgEncodeCaltechTfbsC2c12Tcf3FCntrl32bE2p5dPcr2xSigRep1.bigWig C2C12 ChipSeq TCF3_(SC-349) Signal 1 bigWig Caltech-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeCaltechTfbs/wgEncodeCaltechTfbsC2c12Usf1FCntrl50bE2p60hPcr1xAlnRep1.bam C2C12 ChipSeq USF-1 Alignments 1 bam Caltech-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeCaltechTfbs/wgEncodeCaltechTfbsC2c12Usf1FCntrl50bE2p60hPcr1xPkRep1.narrowPeak.gz C2C12 ChipSeq USF-1 Peaks 1 narrowPeak Caltech-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeCaltechTfbs/wgEncodeCaltechTfbsC2c12Usf1FCntrl50bE2p60hPcr1xSigRep1.bigWig C2C12 ChipSeq USF-1 Signal 1 bigWig Caltech-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeCaltechTfbs/wgEncodeCaltechTfbsC2c12Usf1FCntrl50bPcr1xAlnRep1.bam C2C12 ChipSeq USF-1 Alignments 1 bam Caltech-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeCaltechTfbs/wgEncodeCaltechTfbsC2c12Usf1FCntrl50bPcr1xPkRep1.narrowPeak.gz C2C12 ChipSeq USF-1 Peaks 1 narrowPeak Caltech-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeCaltechTfbs/wgEncodeCaltechTfbsC2c12Usf1FCntrl50bPcr1xSigRep1.bigWig C2C12 ChipSeq USF-1 Signal 1 bigWig Caltech-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeCshlLongRnaSeq/wgEncodeCshlLongRnaSeqAdrenalAdult8wksAlnRep1.bam Adrenal RnaSeq Alignments 1 bam CSHL-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeCshlLongRnaSeq/wgEncodeCshlLongRnaSeqAdrenalAdult8wksAlnRep1V2.bam Adrenal RnaSeq Alignments 1 bam CSHL-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeCshlLongRnaSeq/wgEncodeCshlLongRnaSeqAdrenalAdult8wksAlnRep2.bam Adrenal RnaSeq Alignments 2 bam CSHL-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeCshlLongRnaSeq/wgEncodeCshlLongRnaSeqAdrenalAdult8wksAlnRep2V2.bam Adrenal RnaSeq Alignments 2 bam CSHL-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeCshlLongRnaSeq/wgEncodeCshlLongRnaSeqAdrenalAdult8wksExonsDeNovo.gtf.gz Adrenal RnaSeq ExonsDeNovo gtf CSHL-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeCshlLongRnaSeq/wgEncodeCshlLongRnaSeqAdrenalAdult8wksExonsEnsV65IAcuff.gtf.gz Adrenal RnaSeq ExonsEnsV65IAcuff gtf CSHL-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeCshlLongRnaSeq/wgEncodeCshlLongRnaSeqAdrenalAdult8wksGeneDeNovo.gtf.gz Adrenal RnaSeq GeneDeNovo gtf CSHL-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeCshlLongRnaSeq/wgEncodeCshlLongRnaSeqAdrenalAdult8wksGeneEnsV65IAcuff.gtf.gz Adrenal RnaSeq GeneEnsV65IAcuff gtf CSHL-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeCshlLongRnaSeq/wgEncodeCshlLongRnaSeqAdrenalAdult8wksMinusRawRep1.bigWig Adrenal RnaSeq MinusRawSignal 1 bigWig CSHL-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeCshlLongRnaSeq/wgEncodeCshlLongRnaSeqAdrenalAdult8wksMinusRawRep2.bigWig Adrenal RnaSeq MinusRawSignal 2 bigWig CSHL-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeCshlLongRnaSeq/wgEncodeCshlLongRnaSeqAdrenalAdult8wksPlusRawRep1.bigWig Adrenal RnaSeq PlusRawSignal 1 bigWig CSHL-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeCshlLongRnaSeq/wgEncodeCshlLongRnaSeqAdrenalAdult8wksPlusRawRep2.bigWig Adrenal RnaSeq PlusRawSignal 2 bigWig CSHL-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeCshlLongRnaSeq/wgEncodeCshlLongRnaSeqAdrenalAdult8wksSpikeinsRep1.spikeins.CL.bam.gz Adrenal RnaSeq Spikeins 1 bam CSHL-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeCshlLongRnaSeq/wgEncodeCshlLongRnaSeqAdrenalAdult8wksSpikeinsRep2.spikeins.CL.bam.gz Adrenal RnaSeq Spikeins 2 bam CSHL-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeCshlLongRnaSeq/wgEncodeCshlLongRnaSeqAdrenalAdult8wksTranscriptDeNovo.gtf.gz Adrenal RnaSeq TranscriptDeNovo gtf CSHL-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeCshlLongRnaSeq/wgEncodeCshlLongRnaSeqAdrenalAdult8wksTranscriptEnsV65IAcuff.gtf.gz Adrenal RnaSeq TranscriptEnsV65IAcuff gtf CSHL-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeCshlLongRnaSeq/wgEncodeCshlLongRnaSeqBladderAdult8wksAlnRep1.bam Bladder RnaSeq Alignments 1 bam CSHL-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeCshlLongRnaSeq/wgEncodeCshlLongRnaSeqBladderAdult8wksAlnRep2.bam Bladder RnaSeq Alignments 2 bam CSHL-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeCshlLongRnaSeq/wgEncodeCshlLongRnaSeqBladderAdult8wksExonsDeNovo.gtf.gz Bladder RnaSeq ExonsDeNovo gtf CSHL-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeCshlLongRnaSeq/wgEncodeCshlLongRnaSeqBladderAdult8wksExonsEnsV65IAcuff.gtf.gz Bladder RnaSeq ExonsEnsV65IAcuff gtf CSHL-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeCshlLongRnaSeq/wgEncodeCshlLongRnaSeqBladderAdult8wksGeneDeNovo.gtf.gz Bladder RnaSeq GeneDeNovo gtf CSHL-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeCshlLongRnaSeq/wgEncodeCshlLongRnaSeqBladderAdult8wksGeneEnsV65IAcuff.gtf.gz Bladder RnaSeq GeneEnsV65IAcuff gtf CSHL-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeCshlLongRnaSeq/wgEncodeCshlLongRnaSeqBladderAdult8wksMinusRawRep1.bigWig Bladder RnaSeq MinusRawSignal 1 bigWig CSHL-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeCshlLongRnaSeq/wgEncodeCshlLongRnaSeqBladderAdult8wksMinusRawRep2.bigWig Bladder RnaSeq MinusRawSignal 2 bigWig CSHL-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeCshlLongRnaSeq/wgEncodeCshlLongRnaSeqBladderAdult8wksPlusRawRep1.bigWig Bladder RnaSeq PlusRawSignal 1 bigWig CSHL-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeCshlLongRnaSeq/wgEncodeCshlLongRnaSeqBladderAdult8wksPlusRawRep2.bigWig Bladder RnaSeq PlusRawSignal 2 bigWig CSHL-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeCshlLongRnaSeq/wgEncodeCshlLongRnaSeqBladderAdult8wksTranscriptDeNovo.gtf.gz Bladder RnaSeq TranscriptDeNovo gtf CSHL-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeCshlLongRnaSeq/wgEncodeCshlLongRnaSeqBladderAdult8wksTranscriptEnsV65IAcuff.gtf.gz Bladder RnaSeq TranscriptEnsV65IAcuff gtf CSHL-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeCshlLongRnaSeq/wgEncodeCshlLongRnaSeqCbellumAdult8wksAlnRep1.bam Cerebellum RnaSeq Alignments 1 bam CSHL-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeCshlLongRnaSeq/wgEncodeCshlLongRnaSeqCbellumAdult8wksAlnRep2.bam Cerebellum RnaSeq Alignments 2 bam CSHL-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeCshlLongRnaSeq/wgEncodeCshlLongRnaSeqCbellumAdult8wksExonsDeNovo.gtf.gz Cerebellum RnaSeq ExonsDeNovo gtf CSHL-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeCshlLongRnaSeq/wgEncodeCshlLongRnaSeqCbellumAdult8wksExonsEnsV65IAcuff.gtf.gz Cerebellum RnaSeq ExonsEnsV65IAcuff gtf CSHL-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeCshlLongRnaSeq/wgEncodeCshlLongRnaSeqCbellumAdult8wksGeneDeNovo.gtf.gz Cerebellum RnaSeq GeneDeNovo gtf CSHL-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeCshlLongRnaSeq/wgEncodeCshlLongRnaSeqCbellumAdult8wksGeneEnsV65IAcuff.gtf.gz Cerebellum RnaSeq GeneEnsV65IAcuff gtf CSHL-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeCshlLongRnaSeq/wgEncodeCshlLongRnaSeqCbellumAdult8wksMinusRawRep1.bigWig Cerebellum RnaSeq MinusRawSignal 1 bigWig CSHL-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeCshlLongRnaSeq/wgEncodeCshlLongRnaSeqCbellumAdult8wksMinusRawRep2.bigWig Cerebellum RnaSeq MinusRawSignal 2 bigWig CSHL-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeCshlLongRnaSeq/wgEncodeCshlLongRnaSeqCbellumAdult8wksPlusRawRep1.bigWig Cerebellum RnaSeq PlusRawSignal 1 bigWig CSHL-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeCshlLongRnaSeq/wgEncodeCshlLongRnaSeqCbellumAdult8wksPlusRawRep2.bigWig Cerebellum RnaSeq PlusRawSignal 2 bigWig CSHL-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeCshlLongRnaSeq/wgEncodeCshlLongRnaSeqCbellumAdult8wksTranscriptDeNovo.gtf.gz Cerebellum RnaSeq TranscriptDeNovo gtf CSHL-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeCshlLongRnaSeq/wgEncodeCshlLongRnaSeqCbellumAdult8wksTranscriptEnsV65IAcuff.gtf.gz Cerebellum RnaSeq TranscriptEnsV65IAcuff gtf CSHL-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeCshlLongRnaSeq/wgEncodeCshlLongRnaSeqCnsE11halfAlnRep1.bam CNS RnaSeq Alignments 1 bam CSHL-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeCshlLongRnaSeq/wgEncodeCshlLongRnaSeqCnsE11halfAlnRep2.bam CNS RnaSeq Alignments 2 bam CSHL-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeCshlLongRnaSeq/wgEncodeCshlLongRnaSeqCnsE11halfExonsDeNovo.gtf.gz CNS RnaSeq ExonsDeNovo gtf CSHL-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeCshlLongRnaSeq/wgEncodeCshlLongRnaSeqCnsE11halfExonsEnsV65IAcuff.gtf.gz CNS RnaSeq ExonsEnsV65IAcuff gtf CSHL-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeCshlLongRnaSeq/wgEncodeCshlLongRnaSeqCnsE11halfGeneDeNovo.gtf.gz CNS RnaSeq GeneDeNovo gtf CSHL-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeCshlLongRnaSeq/wgEncodeCshlLongRnaSeqCnsE11halfGeneEnsV65IAcuff.gtf.gz CNS RnaSeq GeneEnsV65IAcuff gtf CSHL-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeCshlLongRnaSeq/wgEncodeCshlLongRnaSeqCnsE11halfMinusRawRep1.bigWig CNS RnaSeq MinusRawSignal 1 bigWig CSHL-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeCshlLongRnaSeq/wgEncodeCshlLongRnaSeqCnsE11halfMinusRawRep2.bigWig CNS RnaSeq MinusRawSignal 2 bigWig CSHL-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeCshlLongRnaSeq/wgEncodeCshlLongRnaSeqCnsE11halfPlusRawRep1.bigWig CNS RnaSeq PlusRawSignal 1 bigWig CSHL-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeCshlLongRnaSeq/wgEncodeCshlLongRnaSeqCnsE11halfPlusRawRep2.bigWig CNS RnaSeq PlusRawSignal 2 bigWig CSHL-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeCshlLongRnaSeq/wgEncodeCshlLongRnaSeqCnsE11halfTranscriptDeNovo.gtf.gz CNS RnaSeq TranscriptDeNovo gtf CSHL-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeCshlLongRnaSeq/wgEncodeCshlLongRnaSeqCnsE11halfTranscriptEnsV65IAcuff.gtf.gz CNS RnaSeq TranscriptEnsV65IAcuff gtf CSHL-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeCshlLongRnaSeq/wgEncodeCshlLongRnaSeqCnsE14AlnRep1.bam CNS RnaSeq Alignments 1 bam CSHL-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeCshlLongRnaSeq/wgEncodeCshlLongRnaSeqCnsE14AlnRep2.bam CNS RnaSeq Alignments 2 bam CSHL-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeCshlLongRnaSeq/wgEncodeCshlLongRnaSeqCnsE14ExonsDeNovo.gtf.gz CNS RnaSeq ExonsDeNovo gtf CSHL-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeCshlLongRnaSeq/wgEncodeCshlLongRnaSeqCnsE14ExonsEnsV65IAcuff.gtf.gz CNS RnaSeq ExonsEnsV65IAcuff gtf CSHL-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeCshlLongRnaSeq/wgEncodeCshlLongRnaSeqCnsE14GeneDeNovo.gtf.gz CNS RnaSeq GeneDeNovo gtf CSHL-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeCshlLongRnaSeq/wgEncodeCshlLongRnaSeqCnsE14GeneEnsV65IAcuff.gtf.gz CNS RnaSeq GeneEnsV65IAcuff gtf CSHL-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeCshlLongRnaSeq/wgEncodeCshlLongRnaSeqCnsE14MinusRawRep1.bigWig CNS RnaSeq MinusRawSignal 1 bigWig CSHL-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeCshlLongRnaSeq/wgEncodeCshlLongRnaSeqCnsE14MinusRawRep2.bigWig CNS RnaSeq MinusRawSignal 2 bigWig CSHL-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeCshlLongRnaSeq/wgEncodeCshlLongRnaSeqCnsE14PlusRawRep1.bigWig CNS RnaSeq PlusRawSignal 1 bigWig CSHL-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeCshlLongRnaSeq/wgEncodeCshlLongRnaSeqCnsE14PlusRawRep2.bigWig CNS RnaSeq PlusRawSignal 2 bigWig CSHL-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeCshlLongRnaSeq/wgEncodeCshlLongRnaSeqCnsE14TranscriptDeNovo.gtf.gz CNS RnaSeq TranscriptDeNovo gtf CSHL-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeCshlLongRnaSeq/wgEncodeCshlLongRnaSeqCnsE14TranscriptEnsV65IAcuff.gtf.gz CNS RnaSeq TranscriptEnsV65IAcuff gtf CSHL-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeCshlLongRnaSeq/wgEncodeCshlLongRnaSeqCnsE18AlnRep1.bam CNS RnaSeq Alignments 1 bam CSHL-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeCshlLongRnaSeq/wgEncodeCshlLongRnaSeqCnsE18AlnRep2.bam CNS RnaSeq Alignments 2 bam CSHL-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeCshlLongRnaSeq/wgEncodeCshlLongRnaSeqCnsE18ExonsDeNovo.gtf.gz CNS RnaSeq ExonsDeNovo gtf CSHL-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeCshlLongRnaSeq/wgEncodeCshlLongRnaSeqCnsE18ExonsEnsV65IAcuff.gtf.gz CNS RnaSeq ExonsEnsV65IAcuff gtf CSHL-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeCshlLongRnaSeq/wgEncodeCshlLongRnaSeqCnsE18GeneDeNovo.gtf.gz CNS RnaSeq GeneDeNovo gtf CSHL-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeCshlLongRnaSeq/wgEncodeCshlLongRnaSeqCnsE18GeneEnsV65IAcuff.gtf.gz CNS RnaSeq GeneEnsV65IAcuff gtf CSHL-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeCshlLongRnaSeq/wgEncodeCshlLongRnaSeqCnsE18MinusRawRep1.bigWig CNS RnaSeq MinusRawSignal 1 bigWig CSHL-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeCshlLongRnaSeq/wgEncodeCshlLongRnaSeqCnsE18MinusRawRep2.bigWig CNS RnaSeq MinusRawSignal 2 bigWig CSHL-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeCshlLongRnaSeq/wgEncodeCshlLongRnaSeqCnsE18PlusRawRep1.bigWig CNS RnaSeq PlusRawSignal 1 bigWig CSHL-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeCshlLongRnaSeq/wgEncodeCshlLongRnaSeqCnsE18PlusRawRep2.bigWig CNS RnaSeq PlusRawSignal 2 bigWig CSHL-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeCshlLongRnaSeq/wgEncodeCshlLongRnaSeqCnsE18TranscriptDeNovo.gtf.gz CNS RnaSeq TranscriptDeNovo gtf CSHL-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeCshlLongRnaSeq/wgEncodeCshlLongRnaSeqCnsE18TranscriptEnsV65IAcuff.gtf.gz CNS RnaSeq TranscriptEnsV65IAcuff gtf CSHL-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeCshlLongRnaSeq/wgEncodeCshlLongRnaSeqColonAdult8wksAlnRep1.bam Colon RnaSeq Alignments 1 bam CSHL-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeCshlLongRnaSeq/wgEncodeCshlLongRnaSeqColonAdult8wksAlnRep1V2.bam Colon RnaSeq Alignments 1 bam CSHL-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeCshlLongRnaSeq/wgEncodeCshlLongRnaSeqColonAdult8wksAlnRep2.bam Colon RnaSeq Alignments 2 bam CSHL-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeCshlLongRnaSeq/wgEncodeCshlLongRnaSeqColonAdult8wksAlnRep2V2.bam Colon RnaSeq Alignments 2 bam CSHL-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeCshlLongRnaSeq/wgEncodeCshlLongRnaSeqColonAdult8wksExonsDeNovo.gtf.gz Colon RnaSeq ExonsDeNovo gtf CSHL-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeCshlLongRnaSeq/wgEncodeCshlLongRnaSeqColonAdult8wksExonsEnsV65IAcuff.gtf.gz Colon RnaSeq ExonsEnsV65IAcuff gtf CSHL-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeCshlLongRnaSeq/wgEncodeCshlLongRnaSeqColonAdult8wksGeneDeNovo.gtf.gz Colon RnaSeq GeneDeNovo gtf CSHL-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeCshlLongRnaSeq/wgEncodeCshlLongRnaSeqColonAdult8wksGeneEnsV65IAcuff.gtf.gz Colon RnaSeq GeneEnsV65IAcuff gtf CSHL-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeCshlLongRnaSeq/wgEncodeCshlLongRnaSeqColonAdult8wksMinusRawRep1.bigWig Colon RnaSeq MinusRawSignal 1 bigWig CSHL-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeCshlLongRnaSeq/wgEncodeCshlLongRnaSeqColonAdult8wksMinusRawRep2.bigWig Colon RnaSeq MinusRawSignal 2 bigWig CSHL-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeCshlLongRnaSeq/wgEncodeCshlLongRnaSeqColonAdult8wksPlusRawRep1.bigWig Colon RnaSeq PlusRawSignal 1 bigWig CSHL-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeCshlLongRnaSeq/wgEncodeCshlLongRnaSeqColonAdult8wksPlusRawRep2.bigWig Colon RnaSeq PlusRawSignal 2 bigWig CSHL-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeCshlLongRnaSeq/wgEncodeCshlLongRnaSeqColonAdult8wksSpikeinsRep1.spikeins.CL.bam.gz Colon RnaSeq Spikeins 1 bam CSHL-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeCshlLongRnaSeq/wgEncodeCshlLongRnaSeqColonAdult8wksSpikeinsRep2.spikeins.CL.bam.gz Colon RnaSeq Spikeins 2 bam CSHL-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeCshlLongRnaSeq/wgEncodeCshlLongRnaSeqColonAdult8wksTranscriptDeNovo.gtf.gz Colon RnaSeq TranscriptDeNovo gtf CSHL-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeCshlLongRnaSeq/wgEncodeCshlLongRnaSeqColonAdult8wksTranscriptEnsV65IAcuff.gtf.gz Colon RnaSeq TranscriptEnsV65IAcuff gtf CSHL-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeCshlLongRnaSeq/wgEncodeCshlLongRnaSeqCortexAdult8wksAlnRep1.bam Cortex RnaSeq Alignments 1 bam CSHL-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeCshlLongRnaSeq/wgEncodeCshlLongRnaSeqCortexAdult8wksAlnRep2.bam Cortex RnaSeq Alignments 2 bam CSHL-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeCshlLongRnaSeq/wgEncodeCshlLongRnaSeqCortexAdult8wksExonsDeNovo.gtf.gz Cortex RnaSeq ExonsDeNovo gtf CSHL-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeCshlLongRnaSeq/wgEncodeCshlLongRnaSeqCortexAdult8wksExonsEnsV65IAcuff.gtf.gz Cortex RnaSeq ExonsEnsV65IAcuff gtf CSHL-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeCshlLongRnaSeq/wgEncodeCshlLongRnaSeqCortexAdult8wksGeneDeNovo.gtf.gz Cortex RnaSeq GeneDeNovo gtf CSHL-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeCshlLongRnaSeq/wgEncodeCshlLongRnaSeqCortexAdult8wksGeneEnsV65IAcuff.gtf.gz Cortex RnaSeq GeneEnsV65IAcuff gtf CSHL-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeCshlLongRnaSeq/wgEncodeCshlLongRnaSeqCortexAdult8wksMinusRawRep1.bigWig Cortex RnaSeq MinusRawSignal 1 bigWig CSHL-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeCshlLongRnaSeq/wgEncodeCshlLongRnaSeqCortexAdult8wksMinusRawRep2.bigWig Cortex RnaSeq MinusRawSignal 2 bigWig CSHL-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeCshlLongRnaSeq/wgEncodeCshlLongRnaSeqCortexAdult8wksPlusRawRep1.bigWig Cortex RnaSeq PlusRawSignal 1 bigWig CSHL-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeCshlLongRnaSeq/wgEncodeCshlLongRnaSeqCortexAdult8wksPlusRawRep2.bigWig Cortex RnaSeq PlusRawSignal 2 bigWig CSHL-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeCshlLongRnaSeq/wgEncodeCshlLongRnaSeqCortexAdult8wksTranscriptDeNovo.gtf.gz Cortex RnaSeq TranscriptDeNovo gtf CSHL-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeCshlLongRnaSeq/wgEncodeCshlLongRnaSeqCortexAdult8wksTranscriptEnsV65IAcuff.gtf.gz Cortex RnaSeq TranscriptEnsV65IAcuff gtf CSHL-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeCshlLongRnaSeq/wgEncodeCshlLongRnaSeqDuodAdult8wksAlnRep1.bam Duodenum RnaSeq Alignments 1 bam CSHL-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeCshlLongRnaSeq/wgEncodeCshlLongRnaSeqDuodAdult8wksAlnRep1V2.bam Duodenum RnaSeq Alignments 1 bam CSHL-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeCshlLongRnaSeq/wgEncodeCshlLongRnaSeqDuodAdult8wksAlnRep2.bam Duodenum RnaSeq Alignments 2 bam CSHL-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeCshlLongRnaSeq/wgEncodeCshlLongRnaSeqDuodAdult8wksAlnRep2V2.bam Duodenum RnaSeq Alignments 2 bam CSHL-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeCshlLongRnaSeq/wgEncodeCshlLongRnaSeqDuodAdult8wksExonsDeNovo.gtf.gz Duodenum RnaSeq ExonsDeNovo gtf CSHL-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeCshlLongRnaSeq/wgEncodeCshlLongRnaSeqDuodAdult8wksExonsEnsV65IAcuff.gtf.gz Duodenum RnaSeq ExonsEnsV65IAcuff gtf CSHL-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeCshlLongRnaSeq/wgEncodeCshlLongRnaSeqDuodAdult8wksGeneDeNovo.gtf.gz Duodenum RnaSeq GeneDeNovo gtf CSHL-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeCshlLongRnaSeq/wgEncodeCshlLongRnaSeqDuodAdult8wksGeneEnsV65IAcuff.gtf.gz Duodenum RnaSeq GeneEnsV65IAcuff gtf CSHL-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeCshlLongRnaSeq/wgEncodeCshlLongRnaSeqDuodAdult8wksMinusRawRep1.bigWig Duodenum RnaSeq MinusRawSignal 1 bigWig CSHL-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeCshlLongRnaSeq/wgEncodeCshlLongRnaSeqDuodAdult8wksMinusRawRep2.bigWig Duodenum RnaSeq MinusRawSignal 2 bigWig CSHL-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeCshlLongRnaSeq/wgEncodeCshlLongRnaSeqDuodAdult8wksPlusRawRep1.bigWig Duodenum RnaSeq PlusRawSignal 1 bigWig CSHL-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeCshlLongRnaSeq/wgEncodeCshlLongRnaSeqDuodAdult8wksPlusRawRep2.bigWig Duodenum RnaSeq PlusRawSignal 2 bigWig CSHL-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeCshlLongRnaSeq/wgEncodeCshlLongRnaSeqDuodAdult8wksSpikeinsRep1.spikeins.CL.bam.gz Duodenum RnaSeq Spikeins 1 bam CSHL-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeCshlLongRnaSeq/wgEncodeCshlLongRnaSeqDuodAdult8wksSpikeinsRep2.spikeins.CL.bam.gz Duodenum RnaSeq Spikeins 2 bam CSHL-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeCshlLongRnaSeq/wgEncodeCshlLongRnaSeqDuodAdult8wksTranscriptDeNovo.gtf.gz Duodenum RnaSeq TranscriptDeNovo gtf CSHL-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeCshlLongRnaSeq/wgEncodeCshlLongRnaSeqDuodAdult8wksTranscriptEnsV65IAcuff.gtf.gz Duodenum RnaSeq TranscriptEnsV65IAcuff gtf CSHL-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeCshlLongRnaSeq/wgEncodeCshlLongRnaSeqFlobeAdult8wksAlnRep1.bam FrontalLobe RnaSeq Alignments 1 bam CSHL-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeCshlLongRnaSeq/wgEncodeCshlLongRnaSeqFlobeAdult8wksAlnRep2.bam FrontalLobe RnaSeq Alignments 2 bam CSHL-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeCshlLongRnaSeq/wgEncodeCshlLongRnaSeqFlobeAdult8wksExonsDeNovo.gtf.gz FrontalLobe RnaSeq ExonsDeNovo gtf CSHL-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeCshlLongRnaSeq/wgEncodeCshlLongRnaSeqFlobeAdult8wksExonsEnsV65IAcuff.gtf.gz FrontalLobe RnaSeq ExonsEnsV65IAcuff gtf CSHL-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeCshlLongRnaSeq/wgEncodeCshlLongRnaSeqFlobeAdult8wksGeneDeNovo.gtf.gz FrontalLobe RnaSeq GeneDeNovo gtf CSHL-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeCshlLongRnaSeq/wgEncodeCshlLongRnaSeqFlobeAdult8wksGeneEnsV65IAcuff.gtf.gz FrontalLobe RnaSeq GeneEnsV65IAcuff gtf CSHL-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeCshlLongRnaSeq/wgEncodeCshlLongRnaSeqFlobeAdult8wksMinusRawRep1.bigWig FrontalLobe RnaSeq MinusRawSignal 1 bigWig CSHL-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeCshlLongRnaSeq/wgEncodeCshlLongRnaSeqFlobeAdult8wksMinusRawRep2.bigWig FrontalLobe RnaSeq MinusRawSignal 2 bigWig CSHL-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeCshlLongRnaSeq/wgEncodeCshlLongRnaSeqFlobeAdult8wksPlusRawRep1.bigWig FrontalLobe RnaSeq PlusRawSignal 1 bigWig CSHL-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeCshlLongRnaSeq/wgEncodeCshlLongRnaSeqFlobeAdult8wksPlusRawRep2.bigWig FrontalLobe RnaSeq PlusRawSignal 2 bigWig CSHL-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeCshlLongRnaSeq/wgEncodeCshlLongRnaSeqFlobeAdult8wksTranscriptDeNovo.gtf.gz FrontalLobe RnaSeq TranscriptDeNovo gtf CSHL-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeCshlLongRnaSeq/wgEncodeCshlLongRnaSeqFlobeAdult8wksTranscriptEnsV65IAcuff.gtf.gz FrontalLobe RnaSeq TranscriptEnsV65IAcuff gtf CSHL-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeCshlLongRnaSeq/wgEncodeCshlLongRnaSeqGfatAdult8wksAlnRep1.bam GenitalFatPad RnaSeq Alignments 1 bam CSHL-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeCshlLongRnaSeq/wgEncodeCshlLongRnaSeqGfatAdult8wksAlnRep1V2.bam GenitalFatPad RnaSeq Alignments 1 bam CSHL-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeCshlLongRnaSeq/wgEncodeCshlLongRnaSeqGfatAdult8wksAlnRep2.bam GenitalFatPad RnaSeq Alignments 2 bam CSHL-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeCshlLongRnaSeq/wgEncodeCshlLongRnaSeqGfatAdult8wksAlnRep2V2.bam GenitalFatPad RnaSeq Alignments 2 bam CSHL-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeCshlLongRnaSeq/wgEncodeCshlLongRnaSeqGfatAdult8wksExonsDeNovo.gtf.gz GenitalFatPad RnaSeq ExonsDeNovo gtf CSHL-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeCshlLongRnaSeq/wgEncodeCshlLongRnaSeqGfatAdult8wksExonsEnsV65IAcuff.gtf.gz GenitalFatPad RnaSeq ExonsEnsV65IAcuff gtf CSHL-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeCshlLongRnaSeq/wgEncodeCshlLongRnaSeqGfatAdult8wksGeneDeNovo.gtf.gz GenitalFatPad RnaSeq GeneDeNovo gtf CSHL-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeCshlLongRnaSeq/wgEncodeCshlLongRnaSeqGfatAdult8wksGeneEnsV65IAcuff.gtf.gz GenitalFatPad RnaSeq GeneEnsV65IAcuff gtf CSHL-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeCshlLongRnaSeq/wgEncodeCshlLongRnaSeqGfatAdult8wksMinusRawRep1.bigWig GenitalFatPad RnaSeq MinusRawSignal 1 bigWig CSHL-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeCshlLongRnaSeq/wgEncodeCshlLongRnaSeqGfatAdult8wksMinusRawRep2.bigWig GenitalFatPad RnaSeq MinusRawSignal 2 bigWig CSHL-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeCshlLongRnaSeq/wgEncodeCshlLongRnaSeqGfatAdult8wksPlusRawRep1.bigWig GenitalFatPad RnaSeq PlusRawSignal 1 bigWig CSHL-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeCshlLongRnaSeq/wgEncodeCshlLongRnaSeqGfatAdult8wksPlusRawRep2.bigWig GenitalFatPad RnaSeq PlusRawSignal 2 bigWig CSHL-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeCshlLongRnaSeq/wgEncodeCshlLongRnaSeqGfatAdult8wksSpikeinsRep1.spikeins.CL.bam.gz GenitalFatPad RnaSeq Spikeins 1 bam CSHL-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeCshlLongRnaSeq/wgEncodeCshlLongRnaSeqGfatAdult8wksSpikeinsRep2.spikeins.CL.bam.gz GenitalFatPad RnaSeq Spikeins 2 bam CSHL-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeCshlLongRnaSeq/wgEncodeCshlLongRnaSeqGfatAdult8wksTranscriptDeNovo.gtf.gz GenitalFatPad RnaSeq TranscriptDeNovo gtf CSHL-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeCshlLongRnaSeq/wgEncodeCshlLongRnaSeqGfatAdult8wksTranscriptEnsV65IAcuff.gtf.gz GenitalFatPad RnaSeq TranscriptEnsV65IAcuff gtf CSHL-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeCshlLongRnaSeq/wgEncodeCshlLongRnaSeqHeartAdult8wksAlnRep1.bam Heart RnaSeq Alignments 1 bam CSHL-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeCshlLongRnaSeq/wgEncodeCshlLongRnaSeqHeartAdult8wksAlnRep1V2.bam Heart RnaSeq Alignments 1 bam CSHL-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeCshlLongRnaSeq/wgEncodeCshlLongRnaSeqHeartAdult8wksAlnRep2.bam Heart RnaSeq Alignments 2 bam CSHL-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeCshlLongRnaSeq/wgEncodeCshlLongRnaSeqHeartAdult8wksAlnRep2V2.bam Heart RnaSeq Alignments 2 bam CSHL-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeCshlLongRnaSeq/wgEncodeCshlLongRnaSeqHeartAdult8wksExonsDeNovo.gtf.gz Heart RnaSeq ExonsDeNovo gtf CSHL-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeCshlLongRnaSeq/wgEncodeCshlLongRnaSeqHeartAdult8wksExonsEnsV65IAcuff.gtf.gz Heart RnaSeq ExonsEnsV65IAcuff gtf CSHL-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeCshlLongRnaSeq/wgEncodeCshlLongRnaSeqHeartAdult8wksGeneDeNovo.gtf.gz Heart RnaSeq GeneDeNovo gtf CSHL-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeCshlLongRnaSeq/wgEncodeCshlLongRnaSeqHeartAdult8wksGeneEnsV65IAcuff.gtf.gz Heart RnaSeq GeneEnsV65IAcuff gtf CSHL-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeCshlLongRnaSeq/wgEncodeCshlLongRnaSeqHeartAdult8wksMinusRawRep1.bigWig Heart RnaSeq MinusRawSignal 1 bigWig CSHL-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeCshlLongRnaSeq/wgEncodeCshlLongRnaSeqHeartAdult8wksMinusRawRep2.bigWig Heart RnaSeq MinusRawSignal 2 bigWig CSHL-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeCshlLongRnaSeq/wgEncodeCshlLongRnaSeqHeartAdult8wksPlusRawRep1.bigWig Heart RnaSeq PlusRawSignal 1 bigWig CSHL-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeCshlLongRnaSeq/wgEncodeCshlLongRnaSeqHeartAdult8wksPlusRawRep2.bigWig Heart RnaSeq PlusRawSignal 2 bigWig CSHL-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeCshlLongRnaSeq/wgEncodeCshlLongRnaSeqHeartAdult8wksSpikeinsRep1.spikeins.CL.bam.gz Heart RnaSeq Spikeins 1 bam CSHL-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeCshlLongRnaSeq/wgEncodeCshlLongRnaSeqHeartAdult8wksSpikeinsRep2.spikeins.CL.bam.gz Heart RnaSeq Spikeins 2 bam CSHL-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeCshlLongRnaSeq/wgEncodeCshlLongRnaSeqHeartAdult8wksTranscriptDeNovo.gtf.gz Heart RnaSeq TranscriptDeNovo gtf CSHL-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeCshlLongRnaSeq/wgEncodeCshlLongRnaSeqHeartAdult8wksTranscriptEnsV65IAcuff.gtf.gz Heart RnaSeq TranscriptEnsV65IAcuff gtf CSHL-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeCshlLongRnaSeq/wgEncodeCshlLongRnaSeqKidneyAdult8wksAlnRep1.bam Kidney RnaSeq Alignments 1 bam CSHL-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeCshlLongRnaSeq/wgEncodeCshlLongRnaSeqKidneyAdult8wksAlnRep1V2.bam Kidney RnaSeq Alignments 1 bam CSHL-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeCshlLongRnaSeq/wgEncodeCshlLongRnaSeqKidneyAdult8wksAlnRep2.bam Kidney RnaSeq Alignments 2 bam CSHL-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeCshlLongRnaSeq/wgEncodeCshlLongRnaSeqKidneyAdult8wksAlnRep2V2.bam Kidney RnaSeq Alignments 2 bam CSHL-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeCshlLongRnaSeq/wgEncodeCshlLongRnaSeqKidneyAdult8wksExonsDeNovo.gtf.gz Kidney RnaSeq ExonsDeNovo gtf CSHL-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeCshlLongRnaSeq/wgEncodeCshlLongRnaSeqKidneyAdult8wksExonsEnsV65IAcuff.gtf.gz Kidney RnaSeq ExonsEnsV65IAcuff gtf CSHL-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeCshlLongRnaSeq/wgEncodeCshlLongRnaSeqKidneyAdult8wksGeneDeNovo.gtf.gz Kidney RnaSeq GeneDeNovo gtf CSHL-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeCshlLongRnaSeq/wgEncodeCshlLongRnaSeqKidneyAdult8wksGeneEnsV65IAcuff.gtf.gz Kidney RnaSeq GeneEnsV65IAcuff gtf CSHL-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeCshlLongRnaSeq/wgEncodeCshlLongRnaSeqKidneyAdult8wksMinusRawRep1.bigWig Kidney RnaSeq MinusRawSignal 1 bigWig CSHL-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeCshlLongRnaSeq/wgEncodeCshlLongRnaSeqKidneyAdult8wksMinusRawRep2.bigWig Kidney RnaSeq MinusRawSignal 2 bigWig CSHL-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeCshlLongRnaSeq/wgEncodeCshlLongRnaSeqKidneyAdult8wksPlusRawRep1.bigWig Kidney RnaSeq PlusRawSignal 1 bigWig CSHL-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeCshlLongRnaSeq/wgEncodeCshlLongRnaSeqKidneyAdult8wksPlusRawRep2.bigWig Kidney RnaSeq PlusRawSignal 2 bigWig CSHL-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeCshlLongRnaSeq/wgEncodeCshlLongRnaSeqKidneyAdult8wksSpikeinsRep1.spikeins.CL.bam.gz Kidney RnaSeq Spikeins 1 bam CSHL-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeCshlLongRnaSeq/wgEncodeCshlLongRnaSeqKidneyAdult8wksSpikeinsRep2.spikeins.CL.bam.gz Kidney RnaSeq Spikeins 2 bam CSHL-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeCshlLongRnaSeq/wgEncodeCshlLongRnaSeqKidneyAdult8wksTranscriptDeNovo.gtf.gz Kidney RnaSeq TranscriptDeNovo gtf CSHL-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeCshlLongRnaSeq/wgEncodeCshlLongRnaSeqKidneyAdult8wksTranscriptEnsV65IAcuff.gtf.gz Kidney RnaSeq TranscriptEnsV65IAcuff gtf CSHL-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeCshlLongRnaSeq/wgEncodeCshlLongRnaSeqLgintAdult8wksAlnRep1.bam LgIntestine RnaSeq Alignments 1 bam CSHL-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeCshlLongRnaSeq/wgEncodeCshlLongRnaSeqLgintAdult8wksAlnRep1V2.bam LgIntestine RnaSeq Alignments 1 bam CSHL-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeCshlLongRnaSeq/wgEncodeCshlLongRnaSeqLgintAdult8wksAlnRep2.bam LgIntestine RnaSeq Alignments 2 bam CSHL-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeCshlLongRnaSeq/wgEncodeCshlLongRnaSeqLgintAdult8wksAlnRep2V2.bam LgIntestine RnaSeq Alignments 2 bam CSHL-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeCshlLongRnaSeq/wgEncodeCshlLongRnaSeqLgintAdult8wksExonsDeNovo.gtf.gz LgIntestine RnaSeq ExonsDeNovo gtf CSHL-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeCshlLongRnaSeq/wgEncodeCshlLongRnaSeqLgintAdult8wksExonsEnsV65IAcuff.gtf.gz LgIntestine RnaSeq ExonsEnsV65IAcuff gtf CSHL-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeCshlLongRnaSeq/wgEncodeCshlLongRnaSeqLgintAdult8wksGeneDeNovo.gtf.gz LgIntestine RnaSeq GeneDeNovo gtf CSHL-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeCshlLongRnaSeq/wgEncodeCshlLongRnaSeqLgintAdult8wksGeneEnsV65IAcuff.gtf.gz LgIntestine RnaSeq GeneEnsV65IAcuff gtf CSHL-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeCshlLongRnaSeq/wgEncodeCshlLongRnaSeqLgintAdult8wksMinusRawRep1.bigWig LgIntestine RnaSeq MinusRawSignal 1 bigWig CSHL-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeCshlLongRnaSeq/wgEncodeCshlLongRnaSeqLgintAdult8wksMinusRawRep2.bigWig LgIntestine RnaSeq MinusRawSignal 2 bigWig CSHL-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeCshlLongRnaSeq/wgEncodeCshlLongRnaSeqLgintAdult8wksPlusRawRep1.bigWig LgIntestine RnaSeq PlusRawSignal 1 bigWig CSHL-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeCshlLongRnaSeq/wgEncodeCshlLongRnaSeqLgintAdult8wksPlusRawRep2.bigWig LgIntestine RnaSeq PlusRawSignal 2 bigWig CSHL-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeCshlLongRnaSeq/wgEncodeCshlLongRnaSeqLgintAdult8wksSpikeinsRep1.spikeins.CL.bam.gz LgIntestine RnaSeq Spikeins 1 bam CSHL-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeCshlLongRnaSeq/wgEncodeCshlLongRnaSeqLgintAdult8wksSpikeinsRep2.spikeins.CL.bam.gz LgIntestine RnaSeq Spikeins 2 bam CSHL-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeCshlLongRnaSeq/wgEncodeCshlLongRnaSeqLgintAdult8wksTranscriptDeNovo.gtf.gz LgIntestine RnaSeq TranscriptDeNovo gtf CSHL-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeCshlLongRnaSeq/wgEncodeCshlLongRnaSeqLgintAdult8wksTranscriptEnsV65IAcuff.gtf.gz LgIntestine RnaSeq TranscriptEnsV65IAcuff gtf CSHL-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeCshlLongRnaSeq/wgEncodeCshlLongRnaSeqLimbE14halfAlnRep1.bam Limb RnaSeq Alignments 1 bam CSHL-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeCshlLongRnaSeq/wgEncodeCshlLongRnaSeqLimbE14halfAlnRep2.bam Limb RnaSeq Alignments 2 bam CSHL-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeCshlLongRnaSeq/wgEncodeCshlLongRnaSeqLimbE14halfExonsDeNovo.gtf.gz Limb RnaSeq ExonsDeNovo gtf CSHL-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeCshlLongRnaSeq/wgEncodeCshlLongRnaSeqLimbE14halfExonsEnsV65IAcuff.gtf.gz Limb RnaSeq ExonsEnsV65IAcuff gtf CSHL-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeCshlLongRnaSeq/wgEncodeCshlLongRnaSeqLimbE14halfGeneDeNovo.gtf.gz Limb RnaSeq GeneDeNovo gtf CSHL-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeCshlLongRnaSeq/wgEncodeCshlLongRnaSeqLimbE14halfGeneEnsV65IAcuff.gtf.gz Limb RnaSeq GeneEnsV65IAcuff gtf CSHL-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeCshlLongRnaSeq/wgEncodeCshlLongRnaSeqLimbE14halfMinusRawRep1.bigWig Limb RnaSeq MinusRawSignal 1 bigWig CSHL-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeCshlLongRnaSeq/wgEncodeCshlLongRnaSeqLimbE14halfMinusRawRep2.bigWig Limb RnaSeq MinusRawSignal 2 bigWig CSHL-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeCshlLongRnaSeq/wgEncodeCshlLongRnaSeqLimbE14halfPlusRawRep1.bigWig Limb RnaSeq PlusRawSignal 1 bigWig CSHL-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeCshlLongRnaSeq/wgEncodeCshlLongRnaSeqLimbE14halfPlusRawRep2.bigWig Limb RnaSeq PlusRawSignal 2 bigWig CSHL-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeCshlLongRnaSeq/wgEncodeCshlLongRnaSeqLimbE14halfTranscriptDeNovo.gtf.gz Limb RnaSeq TranscriptDeNovo gtf CSHL-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeCshlLongRnaSeq/wgEncodeCshlLongRnaSeqLimbE14halfTranscriptEnsV65IAcuff.gtf.gz Limb RnaSeq TranscriptEnsV65IAcuff gtf CSHL-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeCshlLongRnaSeq/wgEncodeCshlLongRnaSeqLiverAdult8wksAlnRep1.bam Liver RnaSeq Alignments 1 bam CSHL-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeCshlLongRnaSeq/wgEncodeCshlLongRnaSeqLiverAdult8wksAlnRep1V2.bam Liver RnaSeq Alignments 1 bam CSHL-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeCshlLongRnaSeq/wgEncodeCshlLongRnaSeqLiverAdult8wksAlnRep2.bam Liver RnaSeq Alignments 2 bam CSHL-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeCshlLongRnaSeq/wgEncodeCshlLongRnaSeqLiverAdult8wksAlnRep2V2.bam Liver RnaSeq Alignments 2 bam CSHL-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeCshlLongRnaSeq/wgEncodeCshlLongRnaSeqLiverAdult8wksExonsDeNovo.gtf.gz Liver RnaSeq ExonsDeNovo gtf CSHL-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeCshlLongRnaSeq/wgEncodeCshlLongRnaSeqLiverAdult8wksExonsEnsV65IAcuff.gtf.gz Liver RnaSeq ExonsEnsV65IAcuff gtf CSHL-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeCshlLongRnaSeq/wgEncodeCshlLongRnaSeqLiverAdult8wksGeneDeNovo.gtf.gz Liver RnaSeq GeneDeNovo gtf CSHL-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeCshlLongRnaSeq/wgEncodeCshlLongRnaSeqLiverAdult8wksGeneEnsV65IAcuff.gtf.gz Liver RnaSeq GeneEnsV65IAcuff gtf CSHL-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeCshlLongRnaSeq/wgEncodeCshlLongRnaSeqLiverAdult8wksMinusRawRep1.bigWig Liver RnaSeq MinusRawSignal 1 bigWig CSHL-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeCshlLongRnaSeq/wgEncodeCshlLongRnaSeqLiverAdult8wksMinusRawRep2.bigWig Liver RnaSeq MinusRawSignal 2 bigWig CSHL-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeCshlLongRnaSeq/wgEncodeCshlLongRnaSeqLiverAdult8wksPlusRawRep1.bigWig Liver RnaSeq PlusRawSignal 1 bigWig CSHL-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeCshlLongRnaSeq/wgEncodeCshlLongRnaSeqLiverAdult8wksPlusRawRep2.bigWig Liver RnaSeq PlusRawSignal 2 bigWig CSHL-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeCshlLongRnaSeq/wgEncodeCshlLongRnaSeqLiverAdult8wksSpikeinsRep1.spikeins.CL.bam.gz Liver RnaSeq Spikeins 1 bam CSHL-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeCshlLongRnaSeq/wgEncodeCshlLongRnaSeqLiverAdult8wksSpikeinsRep2.spikeins.CL.bam.gz Liver RnaSeq Spikeins 2 bam CSHL-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeCshlLongRnaSeq/wgEncodeCshlLongRnaSeqLiverAdult8wksTranscriptDeNovo.gtf.gz Liver RnaSeq TranscriptDeNovo gtf CSHL-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeCshlLongRnaSeq/wgEncodeCshlLongRnaSeqLiverAdult8wksTranscriptEnsV65IAcuff.gtf.gz Liver RnaSeq TranscriptEnsV65IAcuff gtf CSHL-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeCshlLongRnaSeq/wgEncodeCshlLongRnaSeqLiverE14AlnRep1.bam Liver RnaSeq Alignments 1 bam CSHL-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeCshlLongRnaSeq/wgEncodeCshlLongRnaSeqLiverE14AlnRep2.bam Liver RnaSeq Alignments 2 bam CSHL-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeCshlLongRnaSeq/wgEncodeCshlLongRnaSeqLiverE14ExonsDeNovo.gtf.gz Liver RnaSeq ExonsDeNovo gtf CSHL-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeCshlLongRnaSeq/wgEncodeCshlLongRnaSeqLiverE14ExonsEnsV65IAcuff.gtf.gz Liver RnaSeq ExonsEnsV65IAcuff gtf CSHL-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeCshlLongRnaSeq/wgEncodeCshlLongRnaSeqLiverE14GeneDeNovo.gtf.gz Liver RnaSeq GeneDeNovo gtf CSHL-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeCshlLongRnaSeq/wgEncodeCshlLongRnaSeqLiverE14GeneEnsV65IAcuff.gtf.gz Liver RnaSeq GeneEnsV65IAcuff gtf CSHL-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeCshlLongRnaSeq/wgEncodeCshlLongRnaSeqLiverE14MinusRawRep1.bigWig Liver RnaSeq MinusRawSignal 1 bigWig CSHL-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeCshlLongRnaSeq/wgEncodeCshlLongRnaSeqLiverE14MinusRawRep2.bigWig Liver RnaSeq MinusRawSignal 2 bigWig CSHL-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeCshlLongRnaSeq/wgEncodeCshlLongRnaSeqLiverE14PlusRawRep1.bigWig Liver RnaSeq PlusRawSignal 1 bigWig CSHL-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeCshlLongRnaSeq/wgEncodeCshlLongRnaSeqLiverE14PlusRawRep2.bigWig Liver RnaSeq PlusRawSignal 2 bigWig CSHL-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeCshlLongRnaSeq/wgEncodeCshlLongRnaSeqLiverE14TranscriptDeNovo.gtf.gz Liver RnaSeq TranscriptDeNovo gtf CSHL-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeCshlLongRnaSeq/wgEncodeCshlLongRnaSeqLiverE14TranscriptEnsV65IAcuff.gtf.gz Liver RnaSeq TranscriptEnsV65IAcuff gtf CSHL-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeCshlLongRnaSeq/wgEncodeCshlLongRnaSeqLiverE14halfAlnRep1.bam Liver RnaSeq Alignments 1 bam CSHL-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeCshlLongRnaSeq/wgEncodeCshlLongRnaSeqLiverE14halfAlnRep2.bam Liver RnaSeq Alignments 2 bam CSHL-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeCshlLongRnaSeq/wgEncodeCshlLongRnaSeqLiverE14halfExonsDeNovo.gtf.gz Liver RnaSeq ExonsDeNovo gtf CSHL-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeCshlLongRnaSeq/wgEncodeCshlLongRnaSeqLiverE14halfExonsEnsV65IAcuff.gtf.gz Liver RnaSeq ExonsEnsV65IAcuff gtf CSHL-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeCshlLongRnaSeq/wgEncodeCshlLongRnaSeqLiverE14halfGeneDeNovo.gtf.gz Liver RnaSeq GeneDeNovo gtf CSHL-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeCshlLongRnaSeq/wgEncodeCshlLongRnaSeqLiverE14halfGeneEnsV65IAcuff.gtf.gz Liver RnaSeq GeneEnsV65IAcuff gtf CSHL-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeCshlLongRnaSeq/wgEncodeCshlLongRnaSeqLiverE14halfMinusRawRep1.bigWig Liver RnaSeq MinusRawSignal 1 bigWig CSHL-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeCshlLongRnaSeq/wgEncodeCshlLongRnaSeqLiverE14halfMinusRawRep2.bigWig Liver RnaSeq MinusRawSignal 2 bigWig CSHL-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeCshlLongRnaSeq/wgEncodeCshlLongRnaSeqLiverE14halfPlusRawRep1.bigWig Liver RnaSeq PlusRawSignal 1 bigWig CSHL-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeCshlLongRnaSeq/wgEncodeCshlLongRnaSeqLiverE14halfPlusRawRep2.bigWig Liver RnaSeq PlusRawSignal 2 bigWig CSHL-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeCshlLongRnaSeq/wgEncodeCshlLongRnaSeqLiverE14halfTranscriptDeNovo.gtf.gz Liver RnaSeq TranscriptDeNovo gtf CSHL-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeCshlLongRnaSeq/wgEncodeCshlLongRnaSeqLiverE14halfTranscriptEnsV65IAcuff.gtf.gz Liver RnaSeq TranscriptEnsV65IAcuff gtf CSHL-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeCshlLongRnaSeq/wgEncodeCshlLongRnaSeqLiverE18AlnRep1.bam Liver RnaSeq Alignments 1 bam CSHL-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeCshlLongRnaSeq/wgEncodeCshlLongRnaSeqLiverE18AlnRep2.bam Liver RnaSeq Alignments 2 bam CSHL-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeCshlLongRnaSeq/wgEncodeCshlLongRnaSeqLiverE18ExonsDeNovo.gtf.gz Liver RnaSeq ExonsDeNovo gtf CSHL-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeCshlLongRnaSeq/wgEncodeCshlLongRnaSeqLiverE18ExonsEnsV65IAcuff.gtf.gz Liver RnaSeq ExonsEnsV65IAcuff gtf CSHL-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeCshlLongRnaSeq/wgEncodeCshlLongRnaSeqLiverE18GeneDeNovo.gtf.gz Liver RnaSeq GeneDeNovo gtf CSHL-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeCshlLongRnaSeq/wgEncodeCshlLongRnaSeqLiverE18GeneEnsV65IAcuff.gtf.gz Liver RnaSeq GeneEnsV65IAcuff gtf CSHL-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeCshlLongRnaSeq/wgEncodeCshlLongRnaSeqLiverE18MinusRawRep1.bigWig Liver RnaSeq MinusRawSignal 1 bigWig CSHL-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeCshlLongRnaSeq/wgEncodeCshlLongRnaSeqLiverE18MinusRawRep2.bigWig Liver RnaSeq MinusRawSignal 2 bigWig CSHL-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeCshlLongRnaSeq/wgEncodeCshlLongRnaSeqLiverE18PlusRawRep1.bigWig Liver RnaSeq PlusRawSignal 1 bigWig CSHL-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeCshlLongRnaSeq/wgEncodeCshlLongRnaSeqLiverE18PlusRawRep2.bigWig Liver RnaSeq PlusRawSignal 2 bigWig CSHL-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeCshlLongRnaSeq/wgEncodeCshlLongRnaSeqLiverE18TranscriptDeNovo.gtf.gz Liver RnaSeq TranscriptDeNovo gtf CSHL-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeCshlLongRnaSeq/wgEncodeCshlLongRnaSeqLiverE18TranscriptEnsV65IAcuff.gtf.gz Liver RnaSeq TranscriptEnsV65IAcuff gtf CSHL-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeCshlLongRnaSeq/wgEncodeCshlLongRnaSeqLungAdult8wksAlnRep1.bam Lung RnaSeq Alignments 1 bam CSHL-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeCshlLongRnaSeq/wgEncodeCshlLongRnaSeqLungAdult8wksAlnRep1V2.bam Lung RnaSeq Alignments 1 bam CSHL-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeCshlLongRnaSeq/wgEncodeCshlLongRnaSeqLungAdult8wksAlnRep2.bam Lung RnaSeq Alignments 2 bam CSHL-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeCshlLongRnaSeq/wgEncodeCshlLongRnaSeqLungAdult8wksAlnRep2V2.bam Lung RnaSeq Alignments 2 bam CSHL-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeCshlLongRnaSeq/wgEncodeCshlLongRnaSeqLungAdult8wksExonsDeNovo.gtf.gz Lung RnaSeq ExonsDeNovo gtf CSHL-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeCshlLongRnaSeq/wgEncodeCshlLongRnaSeqLungAdult8wksExonsEnsV65IAcuff.gtf.gz Lung RnaSeq ExonsEnsV65IAcuff gtf CSHL-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeCshlLongRnaSeq/wgEncodeCshlLongRnaSeqLungAdult8wksGeneDeNovo.gtf.gz Lung RnaSeq GeneDeNovo gtf CSHL-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeCshlLongRnaSeq/wgEncodeCshlLongRnaSeqLungAdult8wksGeneEnsV65IAcuff.gtf.gz Lung RnaSeq GeneEnsV65IAcuff gtf CSHL-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeCshlLongRnaSeq/wgEncodeCshlLongRnaSeqLungAdult8wksMinusRawRep1.bigWig Lung RnaSeq MinusRawSignal 1 bigWig CSHL-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeCshlLongRnaSeq/wgEncodeCshlLongRnaSeqLungAdult8wksMinusRawRep2.bigWig Lung RnaSeq MinusRawSignal 2 bigWig CSHL-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeCshlLongRnaSeq/wgEncodeCshlLongRnaSeqLungAdult8wksPlusRawRep1.bigWig Lung RnaSeq PlusRawSignal 1 bigWig CSHL-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeCshlLongRnaSeq/wgEncodeCshlLongRnaSeqLungAdult8wksPlusRawRep2.bigWig Lung RnaSeq PlusRawSignal 2 bigWig CSHL-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeCshlLongRnaSeq/wgEncodeCshlLongRnaSeqLungAdult8wksSpikeinsRep1.spikeins.CL.bam.gz Lung RnaSeq Spikeins 1 bam CSHL-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeCshlLongRnaSeq/wgEncodeCshlLongRnaSeqLungAdult8wksSpikeinsRep2.spikeins.CL.bam.gz Lung RnaSeq Spikeins 2 bam CSHL-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeCshlLongRnaSeq/wgEncodeCshlLongRnaSeqLungAdult8wksTranscriptDeNovo.gtf.gz Lung RnaSeq TranscriptDeNovo gtf CSHL-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeCshlLongRnaSeq/wgEncodeCshlLongRnaSeqLungAdult8wksTranscriptEnsV65IAcuff.gtf.gz Lung RnaSeq TranscriptEnsV65IAcuff gtf CSHL-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeCshlLongRnaSeq/wgEncodeCshlLongRnaSeqMamgAdult8wksAlnRep1.bam MammaryGland RnaSeq Alignments 1 bam CSHL-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeCshlLongRnaSeq/wgEncodeCshlLongRnaSeqMamgAdult8wksAlnRep1V2.bam MammaryGland RnaSeq Alignments 1 bam CSHL-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeCshlLongRnaSeq/wgEncodeCshlLongRnaSeqMamgAdult8wksAlnRep2.bam MammaryGland RnaSeq Alignments 2 bam CSHL-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeCshlLongRnaSeq/wgEncodeCshlLongRnaSeqMamgAdult8wksAlnRep2V2.bam MammaryGland RnaSeq Alignments 2 bam CSHL-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeCshlLongRnaSeq/wgEncodeCshlLongRnaSeqMamgAdult8wksExonsDeNovo.gtf.gz MammaryGland RnaSeq ExonsDeNovo gtf CSHL-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeCshlLongRnaSeq/wgEncodeCshlLongRnaSeqMamgAdult8wksExonsEnsV65IAcuff.gtf.gz MammaryGland RnaSeq ExonsEnsV65IAcuff gtf CSHL-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeCshlLongRnaSeq/wgEncodeCshlLongRnaSeqMamgAdult8wksGeneDeNovo.gtf.gz MammaryGland RnaSeq GeneDeNovo gtf CSHL-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeCshlLongRnaSeq/wgEncodeCshlLongRnaSeqMamgAdult8wksGeneEnsV65IAcuff.gtf.gz MammaryGland RnaSeq GeneEnsV65IAcuff gtf CSHL-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeCshlLongRnaSeq/wgEncodeCshlLongRnaSeqMamgAdult8wksMinusRawRep1.bigWig MammaryGland RnaSeq MinusRawSignal 1 bigWig CSHL-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeCshlLongRnaSeq/wgEncodeCshlLongRnaSeqMamgAdult8wksMinusRawRep2.bigWig MammaryGland RnaSeq MinusRawSignal 2 bigWig CSHL-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeCshlLongRnaSeq/wgEncodeCshlLongRnaSeqMamgAdult8wksPlusRawRep1.bigWig MammaryGland RnaSeq PlusRawSignal 1 bigWig CSHL-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeCshlLongRnaSeq/wgEncodeCshlLongRnaSeqMamgAdult8wksPlusRawRep2.bigWig MammaryGland RnaSeq PlusRawSignal 2 bigWig CSHL-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeCshlLongRnaSeq/wgEncodeCshlLongRnaSeqMamgAdult8wksSpikeinsRep1.spikeins.CL.bam.gz MammaryGland RnaSeq Spikeins 1 bam CSHL-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeCshlLongRnaSeq/wgEncodeCshlLongRnaSeqMamgAdult8wksSpikeinsRep2.spikeins.CL.bam.gz MammaryGland RnaSeq Spikeins 2 bam CSHL-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeCshlLongRnaSeq/wgEncodeCshlLongRnaSeqMamgAdult8wksTranscriptDeNovo.gtf.gz MammaryGland RnaSeq TranscriptDeNovo gtf CSHL-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeCshlLongRnaSeq/wgEncodeCshlLongRnaSeqMamgAdult8wksTranscriptEnsV65IAcuff.gtf.gz MammaryGland RnaSeq TranscriptEnsV65IAcuff gtf CSHL-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeCshlLongRnaSeq/wgEncodeCshlLongRnaSeqOvaryAdult8wksAlnRep1.bam Ovary RnaSeq Alignments 1 bam CSHL-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeCshlLongRnaSeq/wgEncodeCshlLongRnaSeqOvaryAdult8wksAlnRep1V2.bam Ovary RnaSeq Alignments 1 bam CSHL-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeCshlLongRnaSeq/wgEncodeCshlLongRnaSeqOvaryAdult8wksAlnRep2.bam Ovary RnaSeq Alignments 2 bam CSHL-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeCshlLongRnaSeq/wgEncodeCshlLongRnaSeqOvaryAdult8wksAlnRep2V2.bam Ovary RnaSeq Alignments 2 bam CSHL-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeCshlLongRnaSeq/wgEncodeCshlLongRnaSeqOvaryAdult8wksExonsDeNovo.gtf.gz Ovary RnaSeq ExonsDeNovo gtf CSHL-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeCshlLongRnaSeq/wgEncodeCshlLongRnaSeqOvaryAdult8wksExonsEnsV65IAcuff.gtf.gz Ovary RnaSeq ExonsEnsV65IAcuff gtf CSHL-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeCshlLongRnaSeq/wgEncodeCshlLongRnaSeqOvaryAdult8wksGeneDeNovo.gtf.gz Ovary RnaSeq GeneDeNovo gtf CSHL-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeCshlLongRnaSeq/wgEncodeCshlLongRnaSeqOvaryAdult8wksGeneEnsV65IAcuff.gtf.gz Ovary RnaSeq GeneEnsV65IAcuff gtf CSHL-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeCshlLongRnaSeq/wgEncodeCshlLongRnaSeqOvaryAdult8wksMinusRawRep1.bigWig Ovary RnaSeq MinusRawSignal 1 bigWig CSHL-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeCshlLongRnaSeq/wgEncodeCshlLongRnaSeqOvaryAdult8wksMinusRawRep2.bigWig Ovary RnaSeq MinusRawSignal 2 bigWig CSHL-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeCshlLongRnaSeq/wgEncodeCshlLongRnaSeqOvaryAdult8wksPlusRawRep1.bigWig Ovary RnaSeq PlusRawSignal 1 bigWig CSHL-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeCshlLongRnaSeq/wgEncodeCshlLongRnaSeqOvaryAdult8wksPlusRawRep2.bigWig Ovary RnaSeq PlusRawSignal 2 bigWig CSHL-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeCshlLongRnaSeq/wgEncodeCshlLongRnaSeqOvaryAdult8wksSpikeinsRep1.spikeins.CL.bam.gz Ovary RnaSeq Spikeins 1 bam CSHL-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeCshlLongRnaSeq/wgEncodeCshlLongRnaSeqOvaryAdult8wksSpikeinsRep2.spikeins.CL.bam.gz Ovary RnaSeq Spikeins 2 bam CSHL-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeCshlLongRnaSeq/wgEncodeCshlLongRnaSeqOvaryAdult8wksTranscriptDeNovo.gtf.gz Ovary RnaSeq TranscriptDeNovo gtf CSHL-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeCshlLongRnaSeq/wgEncodeCshlLongRnaSeqOvaryAdult8wksTranscriptEnsV65IAcuff.gtf.gz Ovary RnaSeq TranscriptEnsV65IAcuff gtf CSHL-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeCshlLongRnaSeq/wgEncodeCshlLongRnaSeqPlacAdult8wksAlnRep1.bam Placenta RnaSeq Alignments 1 bam CSHL-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeCshlLongRnaSeq/wgEncodeCshlLongRnaSeqPlacAdult8wksAlnRep2.bam Placenta RnaSeq Alignments 2 bam CSHL-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeCshlLongRnaSeq/wgEncodeCshlLongRnaSeqPlacAdult8wksExonsDeNovo.gtf.gz Placenta RnaSeq ExonsDeNovo gtf CSHL-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeCshlLongRnaSeq/wgEncodeCshlLongRnaSeqPlacAdult8wksExonsEnsV65IAcuff.gtf.gz Placenta RnaSeq ExonsEnsV65IAcuff gtf CSHL-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeCshlLongRnaSeq/wgEncodeCshlLongRnaSeqPlacAdult8wksGeneDeNovo.gtf.gz Placenta RnaSeq GeneDeNovo gtf CSHL-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeCshlLongRnaSeq/wgEncodeCshlLongRnaSeqPlacAdult8wksGeneEnsV65IAcuff.gtf.gz Placenta RnaSeq GeneEnsV65IAcuff gtf CSHL-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeCshlLongRnaSeq/wgEncodeCshlLongRnaSeqPlacAdult8wksMinusRawRep1.bigWig Placenta RnaSeq MinusRawSignal 1 bigWig CSHL-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeCshlLongRnaSeq/wgEncodeCshlLongRnaSeqPlacAdult8wksMinusRawRep2.bigWig Placenta RnaSeq MinusRawSignal 2 bigWig CSHL-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeCshlLongRnaSeq/wgEncodeCshlLongRnaSeqPlacAdult8wksPlusRawRep1.bigWig Placenta RnaSeq PlusRawSignal 1 bigWig CSHL-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeCshlLongRnaSeq/wgEncodeCshlLongRnaSeqPlacAdult8wksPlusRawRep2.bigWig Placenta RnaSeq PlusRawSignal 2 bigWig CSHL-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeCshlLongRnaSeq/wgEncodeCshlLongRnaSeqPlacAdult8wksTranscriptDeNovo.gtf.gz Placenta RnaSeq TranscriptDeNovo gtf CSHL-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeCshlLongRnaSeq/wgEncodeCshlLongRnaSeqPlacAdult8wksTranscriptEnsV65IAcuff.gtf.gz Placenta RnaSeq TranscriptEnsV65IAcuff gtf CSHL-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeCshlLongRnaSeq/wgEncodeCshlLongRnaSeqSfatAdult8wksAlnRep1.bam SubcFatPad RnaSeq Alignments 1 bam CSHL-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeCshlLongRnaSeq/wgEncodeCshlLongRnaSeqSfatAdult8wksAlnRep1V2.bam SubcFatPad RnaSeq Alignments 1 bam CSHL-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeCshlLongRnaSeq/wgEncodeCshlLongRnaSeqSfatAdult8wksAlnRep2.bam SubcFatPad RnaSeq Alignments 2 bam CSHL-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeCshlLongRnaSeq/wgEncodeCshlLongRnaSeqSfatAdult8wksAlnRep2V2.bam SubcFatPad RnaSeq Alignments 2 bam CSHL-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeCshlLongRnaSeq/wgEncodeCshlLongRnaSeqSfatAdult8wksExonsDeNovo.gtf.gz SubcFatPad RnaSeq ExonsDeNovo gtf CSHL-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeCshlLongRnaSeq/wgEncodeCshlLongRnaSeqSfatAdult8wksExonsEnsV65IAcuff.gtf.gz SubcFatPad RnaSeq ExonsEnsV65IAcuff gtf CSHL-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeCshlLongRnaSeq/wgEncodeCshlLongRnaSeqSfatAdult8wksGeneDeNovo.gtf.gz SubcFatPad RnaSeq GeneDeNovo gtf CSHL-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeCshlLongRnaSeq/wgEncodeCshlLongRnaSeqSfatAdult8wksGeneEnsV65IAcuff.gtf.gz SubcFatPad RnaSeq GeneEnsV65IAcuff gtf CSHL-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeCshlLongRnaSeq/wgEncodeCshlLongRnaSeqSfatAdult8wksMinusRawRep1.bigWig SubcFatPad RnaSeq MinusRawSignal 1 bigWig CSHL-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeCshlLongRnaSeq/wgEncodeCshlLongRnaSeqSfatAdult8wksMinusRawRep2.bigWig SubcFatPad RnaSeq MinusRawSignal 2 bigWig CSHL-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeCshlLongRnaSeq/wgEncodeCshlLongRnaSeqSfatAdult8wksPlusRawRep1.bigWig SubcFatPad RnaSeq PlusRawSignal 1 bigWig CSHL-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeCshlLongRnaSeq/wgEncodeCshlLongRnaSeqSfatAdult8wksPlusRawRep2.bigWig SubcFatPad RnaSeq PlusRawSignal 2 bigWig CSHL-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeCshlLongRnaSeq/wgEncodeCshlLongRnaSeqSfatAdult8wksSpikeinsRep1.spikeins.CL.bam.gz SubcFatPad RnaSeq Spikeins 1 bam CSHL-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeCshlLongRnaSeq/wgEncodeCshlLongRnaSeqSfatAdult8wksSpikeinsRep2.spikeins.CL.bam.gz SubcFatPad RnaSeq Spikeins 2 bam CSHL-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeCshlLongRnaSeq/wgEncodeCshlLongRnaSeqSfatAdult8wksTranscriptDeNovo.gtf.gz SubcFatPad RnaSeq TranscriptDeNovo gtf CSHL-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeCshlLongRnaSeq/wgEncodeCshlLongRnaSeqSfatAdult8wksTranscriptEnsV65IAcuff.gtf.gz SubcFatPad RnaSeq TranscriptEnsV65IAcuff gtf CSHL-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeCshlLongRnaSeq/wgEncodeCshlLongRnaSeqSmintAdult8wksAlnRep1.bam SmIntestine RnaSeq Alignments 1 bam CSHL-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeCshlLongRnaSeq/wgEncodeCshlLongRnaSeqSmintAdult8wksAlnRep1V2.bam SmIntestine RnaSeq Alignments 1 bam CSHL-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeCshlLongRnaSeq/wgEncodeCshlLongRnaSeqSmintAdult8wksAlnRep2.bam SmIntestine RnaSeq Alignments 2 bam CSHL-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeCshlLongRnaSeq/wgEncodeCshlLongRnaSeqSmintAdult8wksAlnRep2V2.bam SmIntestine RnaSeq Alignments 2 bam CSHL-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeCshlLongRnaSeq/wgEncodeCshlLongRnaSeqSmintAdult8wksExonsDeNovo.gtf.gz SmIntestine RnaSeq ExonsDeNovo gtf CSHL-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeCshlLongRnaSeq/wgEncodeCshlLongRnaSeqSmintAdult8wksExonsEnsV65IAcuff.gtf.gz SmIntestine RnaSeq ExonsEnsV65IAcuff gtf CSHL-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeCshlLongRnaSeq/wgEncodeCshlLongRnaSeqSmintAdult8wksGeneDeNovo.gtf.gz SmIntestine RnaSeq GeneDeNovo gtf CSHL-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeCshlLongRnaSeq/wgEncodeCshlLongRnaSeqSmintAdult8wksGeneEnsV65IAcuff.gtf.gz SmIntestine RnaSeq GeneEnsV65IAcuff gtf CSHL-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeCshlLongRnaSeq/wgEncodeCshlLongRnaSeqSmintAdult8wksMinusRawRep1.bigWig SmIntestine RnaSeq MinusRawSignal 1 bigWig CSHL-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeCshlLongRnaSeq/wgEncodeCshlLongRnaSeqSmintAdult8wksMinusRawRep2.bigWig SmIntestine RnaSeq MinusRawSignal 2 bigWig CSHL-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeCshlLongRnaSeq/wgEncodeCshlLongRnaSeqSmintAdult8wksPlusRawRep1.bigWig SmIntestine RnaSeq PlusRawSignal 1 bigWig CSHL-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeCshlLongRnaSeq/wgEncodeCshlLongRnaSeqSmintAdult8wksPlusRawRep2.bigWig SmIntestine RnaSeq PlusRawSignal 2 bigWig CSHL-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeCshlLongRnaSeq/wgEncodeCshlLongRnaSeqSmintAdult8wksSpikeinsRep1.spikeins.CL.bam.gz SmIntestine RnaSeq Spikeins 1 bam CSHL-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeCshlLongRnaSeq/wgEncodeCshlLongRnaSeqSmintAdult8wksSpikeinsRep2.spikeins.CL.bam.gz SmIntestine RnaSeq Spikeins 2 bam CSHL-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeCshlLongRnaSeq/wgEncodeCshlLongRnaSeqSmintAdult8wksTranscriptDeNovo.gtf.gz SmIntestine RnaSeq TranscriptDeNovo gtf CSHL-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeCshlLongRnaSeq/wgEncodeCshlLongRnaSeqSmintAdult8wksTranscriptEnsV65IAcuff.gtf.gz SmIntestine RnaSeq TranscriptEnsV65IAcuff gtf CSHL-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeCshlLongRnaSeq/wgEncodeCshlLongRnaSeqSplAdult8wksAlnRep1V2.bam Spleen RnaSeq Alignments 1 bam CSHL-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeCshlLongRnaSeq/wgEncodeCshlLongRnaSeqSplAdult8wksAlnRep2V2.bam Spleen RnaSeq Alignments 2 bam CSHL-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeCshlLongRnaSeq/wgEncodeCshlLongRnaSeqSplAdult8wksExonsDeNovo.gtf.gz Spleen RnaSeq ExonsDeNovo gtf CSHL-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeCshlLongRnaSeq/wgEncodeCshlLongRnaSeqSplAdult8wksGeneDeNovo.gtf.gz Spleen RnaSeq GeneDeNovo gtf CSHL-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeCshlLongRnaSeq/wgEncodeCshlLongRnaSeqSpleenAdult8wksAlnRep1.bam Spleen RnaSeq Alignments 1 bam CSHL-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeCshlLongRnaSeq/wgEncodeCshlLongRnaSeqSpleenAdult8wksAlnRep2.bam Spleen RnaSeq Alignments 2 bam CSHL-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeCshlLongRnaSeq/wgEncodeCshlLongRnaSeqSpleenAdult8wksExonsEnsV65IAcuff.gtf.gz Spleen RnaSeq ExonsEnsV65IAcuff gtf CSHL-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeCshlLongRnaSeq/wgEncodeCshlLongRnaSeqSpleenAdult8wksGeneEnsV65IAcuff.gtf.gz Spleen RnaSeq GeneEnsV65IAcuff gtf CSHL-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeCshlLongRnaSeq/wgEncodeCshlLongRnaSeqSpleenAdult8wksMinusRawRep1.bigWig Spleen RnaSeq MinusRawSignal 1 bigWig CSHL-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeCshlLongRnaSeq/wgEncodeCshlLongRnaSeqSpleenAdult8wksMinusRawRep2.bigWig Spleen RnaSeq MinusRawSignal 2 bigWig CSHL-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeCshlLongRnaSeq/wgEncodeCshlLongRnaSeqSpleenAdult8wksPlusRawRep1.bigWig Spleen RnaSeq PlusRawSignal 1 bigWig CSHL-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeCshlLongRnaSeq/wgEncodeCshlLongRnaSeqSpleenAdult8wksPlusRawRep2.bigWig Spleen RnaSeq PlusRawSignal 2 bigWig CSHL-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeCshlLongRnaSeq/wgEncodeCshlLongRnaSeqSpleenAdult8wksSpikeinsRep1.spikeins.CL.bam.gz Spleen RnaSeq Spikeins 1 bam CSHL-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeCshlLongRnaSeq/wgEncodeCshlLongRnaSeqSpleenAdult8wksSpikeinsRep2.spikeins.CL.bam.gz Spleen RnaSeq Spikeins 2 bam CSHL-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeCshlLongRnaSeq/wgEncodeCshlLongRnaSeqSpleenAdult8wksTranscriptDeNovo.gtf.gz Spleen RnaSeq TranscriptDeNovo gtf CSHL-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeCshlLongRnaSeq/wgEncodeCshlLongRnaSeqSpleenAdult8wksTranscriptEnsV65IAcuff.gtf.gz Spleen RnaSeq TranscriptEnsV65IAcuff gtf CSHL-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeCshlLongRnaSeq/wgEncodeCshlLongRnaSeqStomAdult8wksAlnRep1.bam Stomach RnaSeq Alignments 1 bam CSHL-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeCshlLongRnaSeq/wgEncodeCshlLongRnaSeqStomAdult8wksAlnRep1V2.bam Stomach RnaSeq Alignments 1 bam CSHL-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeCshlLongRnaSeq/wgEncodeCshlLongRnaSeqStomAdult8wksAlnRep2.bam Stomach RnaSeq Alignments 2 bam CSHL-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeCshlLongRnaSeq/wgEncodeCshlLongRnaSeqStomAdult8wksAlnRep2V2.bam Stomach RnaSeq Alignments 2 bam CSHL-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeCshlLongRnaSeq/wgEncodeCshlLongRnaSeqStomAdult8wksExonsDeNovo.gtf.gz Stomach RnaSeq ExonsDeNovo gtf CSHL-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeCshlLongRnaSeq/wgEncodeCshlLongRnaSeqStomAdult8wksExonsEnsV65IAcuff.gtf.gz Stomach RnaSeq ExonsEnsV65IAcuff gtf CSHL-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeCshlLongRnaSeq/wgEncodeCshlLongRnaSeqStomAdult8wksGeneDeNovo.gtf.gz Stomach RnaSeq GeneDeNovo gtf CSHL-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeCshlLongRnaSeq/wgEncodeCshlLongRnaSeqStomAdult8wksGeneEnsV65IAcuff.gtf.gz Stomach RnaSeq GeneEnsV65IAcuff gtf CSHL-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeCshlLongRnaSeq/wgEncodeCshlLongRnaSeqStomAdult8wksMinusRawRep1.bigWig Stomach RnaSeq MinusRawSignal 1 bigWig CSHL-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeCshlLongRnaSeq/wgEncodeCshlLongRnaSeqStomAdult8wksMinusRawRep2.bigWig Stomach RnaSeq MinusRawSignal 2 bigWig CSHL-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeCshlLongRnaSeq/wgEncodeCshlLongRnaSeqStomAdult8wksPlusRawRep1.bigWig Stomach RnaSeq PlusRawSignal 1 bigWig CSHL-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeCshlLongRnaSeq/wgEncodeCshlLongRnaSeqStomAdult8wksPlusRawRep2.bigWig Stomach RnaSeq PlusRawSignal 2 bigWig CSHL-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeCshlLongRnaSeq/wgEncodeCshlLongRnaSeqStomAdult8wksSpikeinsRep1.spikeins.CL.bam.gz Stomach RnaSeq Spikeins 1 bam CSHL-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeCshlLongRnaSeq/wgEncodeCshlLongRnaSeqStomAdult8wksSpikeinsRep2.spikeins.CL.bam.gz Stomach RnaSeq Spikeins 2 bam CSHL-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeCshlLongRnaSeq/wgEncodeCshlLongRnaSeqStomAdult8wksTranscriptDeNovo.gtf.gz Stomach RnaSeq TranscriptDeNovo gtf CSHL-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeCshlLongRnaSeq/wgEncodeCshlLongRnaSeqStomAdult8wksTranscriptEnsV65IAcuff.gtf.gz Stomach RnaSeq TranscriptEnsV65IAcuff gtf CSHL-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeCshlLongRnaSeq/wgEncodeCshlLongRnaSeqTestisAdult8wksAlnRep1.bam Testis RnaSeq Alignments 1 bam CSHL-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeCshlLongRnaSeq/wgEncodeCshlLongRnaSeqTestisAdult8wksAlnRep1V2.bam Testis RnaSeq Alignments 1 bam CSHL-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeCshlLongRnaSeq/wgEncodeCshlLongRnaSeqTestisAdult8wksAlnRep2.bam Testis RnaSeq Alignments 2 bam CSHL-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeCshlLongRnaSeq/wgEncodeCshlLongRnaSeqTestisAdult8wksAlnRep2V2.bam Testis RnaSeq Alignments 2 bam CSHL-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeCshlLongRnaSeq/wgEncodeCshlLongRnaSeqTestisAdult8wksExonsDeNovo.gtf.gz Testis RnaSeq ExonsDeNovo gtf CSHL-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeCshlLongRnaSeq/wgEncodeCshlLongRnaSeqTestisAdult8wksExonsEnsV65IAcuff.gtf.gz Testis RnaSeq ExonsEnsV65IAcuff gtf CSHL-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeCshlLongRnaSeq/wgEncodeCshlLongRnaSeqTestisAdult8wksGeneDeNovo.gtf.gz Testis RnaSeq GeneDeNovo gtf CSHL-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeCshlLongRnaSeq/wgEncodeCshlLongRnaSeqTestisAdult8wksGeneEnsV65IAcuff.gtf.gz Testis RnaSeq GeneEnsV65IAcuff gtf CSHL-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeCshlLongRnaSeq/wgEncodeCshlLongRnaSeqTestisAdult8wksMinusRawRep1.bigWig Testis RnaSeq MinusRawSignal 1 bigWig CSHL-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeCshlLongRnaSeq/wgEncodeCshlLongRnaSeqTestisAdult8wksMinusRawRep2.bigWig Testis RnaSeq MinusRawSignal 2 bigWig CSHL-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeCshlLongRnaSeq/wgEncodeCshlLongRnaSeqTestisAdult8wksPlusRawRep1.bigWig Testis RnaSeq PlusRawSignal 1 bigWig CSHL-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeCshlLongRnaSeq/wgEncodeCshlLongRnaSeqTestisAdult8wksPlusRawRep2.bigWig Testis RnaSeq PlusRawSignal 2 bigWig CSHL-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeCshlLongRnaSeq/wgEncodeCshlLongRnaSeqTestisAdult8wksSpikeinsRep1.spikeins.CL.bam.gz Testis RnaSeq Spikeins 1 bam CSHL-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeCshlLongRnaSeq/wgEncodeCshlLongRnaSeqTestisAdult8wksSpikeinsRep2.spikeins.CL.bam.gz Testis RnaSeq Spikeins 2 bam CSHL-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeCshlLongRnaSeq/wgEncodeCshlLongRnaSeqTestisAdult8wksTranscriptDeNovo.gtf.gz Testis RnaSeq TranscriptDeNovo gtf CSHL-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeCshlLongRnaSeq/wgEncodeCshlLongRnaSeqTestisAdult8wksTranscriptEnsV65IAcuff.gtf.gz Testis RnaSeq TranscriptEnsV65IAcuff gtf CSHL-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeCshlLongRnaSeq/wgEncodeCshlLongRnaSeqThymusAdult8wksAlnRep1.bam Thymus RnaSeq Alignments 1 bam CSHL-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeCshlLongRnaSeq/wgEncodeCshlLongRnaSeqThymusAdult8wksAlnRep1V2.bam Thymus RnaSeq Alignments 1 bam CSHL-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeCshlLongRnaSeq/wgEncodeCshlLongRnaSeqThymusAdult8wksAlnRep2.bam Thymus RnaSeq Alignments 2 bam CSHL-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeCshlLongRnaSeq/wgEncodeCshlLongRnaSeqThymusAdult8wksAlnRep2V2.bam Thymus RnaSeq Alignments 2 bam CSHL-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeCshlLongRnaSeq/wgEncodeCshlLongRnaSeqThymusAdult8wksExonsDeNovo.gtf.gz Thymus RnaSeq ExonsDeNovo gtf CSHL-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeCshlLongRnaSeq/wgEncodeCshlLongRnaSeqThymusAdult8wksExonsEnsV65IAcuff.gtf.gz Thymus RnaSeq ExonsEnsV65IAcuff gtf CSHL-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeCshlLongRnaSeq/wgEncodeCshlLongRnaSeqThymusAdult8wksGeneDeNovo.gtf.gz Thymus RnaSeq GeneDeNovo gtf CSHL-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeCshlLongRnaSeq/wgEncodeCshlLongRnaSeqThymusAdult8wksGeneEnsV65IAcuff.gtf.gz Thymus RnaSeq GeneEnsV65IAcuff gtf CSHL-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeCshlLongRnaSeq/wgEncodeCshlLongRnaSeqThymusAdult8wksMinusRawRep1.bigWig Thymus RnaSeq MinusRawSignal 1 bigWig CSHL-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeCshlLongRnaSeq/wgEncodeCshlLongRnaSeqThymusAdult8wksMinusRawRep2.bigWig Thymus RnaSeq MinusRawSignal 2 bigWig CSHL-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeCshlLongRnaSeq/wgEncodeCshlLongRnaSeqThymusAdult8wksPlusRawRep1.bigWig Thymus RnaSeq PlusRawSignal 1 bigWig CSHL-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeCshlLongRnaSeq/wgEncodeCshlLongRnaSeqThymusAdult8wksPlusRawRep2.bigWig Thymus RnaSeq PlusRawSignal 2 bigWig CSHL-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeCshlLongRnaSeq/wgEncodeCshlLongRnaSeqThymusAdult8wksSpikeinsRep1.spikeins.CL.bam.gz Thymus RnaSeq Spikeins 1 bam CSHL-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeCshlLongRnaSeq/wgEncodeCshlLongRnaSeqThymusAdult8wksSpikeinsRep2.spikeins.CL.bam.gz Thymus RnaSeq Spikeins 2 bam CSHL-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeCshlLongRnaSeq/wgEncodeCshlLongRnaSeqThymusAdult8wksTranscriptDeNovo.gtf.gz Thymus RnaSeq TranscriptDeNovo gtf CSHL-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeCshlLongRnaSeq/wgEncodeCshlLongRnaSeqThymusAdult8wksTranscriptEnsV65IAcuff.gtf.gz Thymus RnaSeq TranscriptEnsV65IAcuff gtf CSHL-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeCshlLongRnaSeq/wgEncodeCshlLongRnaSeqWbrainE14halfAlnRep1.bam WholeBrain RnaSeq Alignments 1 bam CSHL-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeCshlLongRnaSeq/wgEncodeCshlLongRnaSeqWbrainE14halfAlnRep2.bam WholeBrain RnaSeq Alignments 2 bam CSHL-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeCshlLongRnaSeq/wgEncodeCshlLongRnaSeqWbrainE14halfExonsDeNovo.gtf.gz WholeBrain RnaSeq ExonsDeNovo gtf CSHL-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeCshlLongRnaSeq/wgEncodeCshlLongRnaSeqWbrainE14halfExonsEnsV65IAcuff.gtf.gz WholeBrain RnaSeq ExonsEnsV65IAcuff gtf CSHL-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeCshlLongRnaSeq/wgEncodeCshlLongRnaSeqWbrainE14halfGeneDeNovo.gtf.gz WholeBrain RnaSeq GeneDeNovo gtf CSHL-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeCshlLongRnaSeq/wgEncodeCshlLongRnaSeqWbrainE14halfGeneEnsV65IAcuff.gtf.gz WholeBrain RnaSeq GeneEnsV65IAcuff gtf CSHL-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeCshlLongRnaSeq/wgEncodeCshlLongRnaSeqWbrainE14halfMinusRawRep1.bigWig WholeBrain RnaSeq MinusRawSignal 1 bigWig CSHL-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeCshlLongRnaSeq/wgEncodeCshlLongRnaSeqWbrainE14halfMinusRawRep2.bigWig WholeBrain RnaSeq MinusRawSignal 2 bigWig CSHL-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeCshlLongRnaSeq/wgEncodeCshlLongRnaSeqWbrainE14halfPlusRawRep1.bigWig WholeBrain RnaSeq PlusRawSignal 1 bigWig CSHL-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeCshlLongRnaSeq/wgEncodeCshlLongRnaSeqWbrainE14halfPlusRawRep2.bigWig WholeBrain RnaSeq PlusRawSignal 2 bigWig CSHL-m 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http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeLicrHistone/wgEncodeLicrHistoneCh12H3k36me3FImmortalC57bl6StdSig.bigWig CH12 ChipSeq H3K36me3 Signal bigWig LICR-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeLicrHistone/wgEncodeLicrHistoneCh12H3k79me2FImmortalC57bl6StdAlnRep1.bam CH12 ChipSeq H3K79me2 Alignments 1 bam LICR-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeLicrHistone/wgEncodeLicrHistoneCh12H3k79me2FImmortalC57bl6StdAlnRep2.bam CH12 ChipSeq H3K79me2 Alignments 2 bam LICR-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeLicrHistone/wgEncodeLicrHistoneCh12H3k79me2FImmortalC57bl6StdPk.broadPeak.gz CH12 ChipSeq H3K79me2 Peaks broadPeak LICR-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeLicrHistone/wgEncodeLicrHistoneCh12H3k79me2FImmortalC57bl6StdSig.bigWig CH12 ChipSeq H3K79me2 Signal bigWig LICR-m 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http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeLicrHistone/wgEncodeLicrHistoneLimbH3k04me3UE14halfC57bl6StdSig.bigWig Limb ChipSeq H3K4me3 Signal bigWig LICR-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeLicrHistone/wgEncodeLicrHistoneLimbH3k27acUE14halfC57bl6StdAlnRep1.bam Limb ChipSeq H3K27ac Alignments 1 bam LICR-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeLicrHistone/wgEncodeLicrHistoneLimbH3k27acUE14halfC57bl6StdAlnRep2.bam Limb ChipSeq H3K27ac Alignments 2 bam LICR-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeLicrHistone/wgEncodeLicrHistoneLimbH3k27acUE14halfC57bl6StdPk.broadPeak.gz Limb ChipSeq H3K27ac Peaks broadPeak LICR-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeLicrHistone/wgEncodeLicrHistoneLimbH3k27acUE14halfC57bl6StdSig.bigWig Limb ChipSeq H3K27ac Signal bigWig LICR-m 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http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeLicrHistone/wgEncodeLicrHistoneLiverH3k4me1MAdult8wksC57bl6StdSig.bigWig Liver ChipSeq H3K4me1 Signal bigWig LICR-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeLicrHistone/wgEncodeLicrHistoneLiverH3k4me3MAdult8wksC57bl6StdAlnRep1.bam Liver ChipSeq H3K4me3 Alignments 1 bam LICR-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeLicrHistone/wgEncodeLicrHistoneLiverH3k4me3MAdult8wksC57bl6StdAlnRep2.bam Liver ChipSeq H3K4me3 Alignments 2 bam LICR-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeLicrHistone/wgEncodeLicrHistoneLiverH3k4me3MAdult8wksC57bl6StdPk.broadPeak.gz Liver ChipSeq H3K4me3 Peaks broadPeak LICR-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeLicrHistone/wgEncodeLicrHistoneLiverH3k4me3MAdult8wksC57bl6StdSig.bigWig Liver ChipSeq H3K4me3 Signal bigWig LICR-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeLicrHistone/wgEncodeLicrHistoneLiverH3k79me2MAdult8wksC57bl6StdAlnRep1.bam Liver ChipSeq H3K79me2 Alignments 1 bam LICR-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeLicrHistone/wgEncodeLicrHistoneLiverH3k79me2MAdult8wksC57bl6StdAlnRep2.bam Liver ChipSeq H3K79me2 Alignments 2 bam LICR-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeLicrHistone/wgEncodeLicrHistoneLiverH3k79me2MAdult8wksC57bl6StdPk.broadPeak.gz Liver ChipSeq H3K79me2 Peaks broadPeak LICR-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeLicrHistone/wgEncodeLicrHistoneLiverH3k79me2MAdult8wksC57bl6StdSig.bigWig Liver ChipSeq H3K79me2 Signal bigWig LICR-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeLicrHistone/wgEncodeLicrHistoneLiverInputMAdult8wksC57bl6StdAlnRep1.bam Liver ChipSeq Input Alignments 1 bam LICR-m 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http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeLicrHistone/wgEncodeLicrHistoneLungH3k4me1MAdult8wksC57bl6StdAlnRep1.bam Lung ChipSeq H3K4me1 Alignments 1 bam LICR-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeLicrHistone/wgEncodeLicrHistoneLungH3k4me1MAdult8wksC57bl6StdAlnRep2.bam Lung ChipSeq H3K4me1 Alignments 2 bam LICR-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeLicrHistone/wgEncodeLicrHistoneLungH3k4me1MAdult8wksC57bl6StdPk.broadPeak.gz Lung ChipSeq H3K4me1 Peaks broadPeak LICR-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeLicrHistone/wgEncodeLicrHistoneLungH3k4me1MAdult8wksC57bl6StdSig.bigWig Lung ChipSeq H3K4me1 Signal bigWig LICR-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeLicrHistone/wgEncodeLicrHistoneLungH3k4me3MAdult8wksC57bl6StdAlnRep1.bam Lung ChipSeq H3K4me3 Alignments 1 bam LICR-m 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http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeLicrHistone/wgEncodeLicrHistoneWbrainH3k09me3ME14halfC57bl6StdAlnRep1.bam WholeBrain ChipSeq H3K9me3 Alignments 1 bam LICR-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeLicrHistone/wgEncodeLicrHistoneWbrainH3k09me3ME14halfC57bl6StdAlnRep2.bam WholeBrain ChipSeq H3K9me3 Alignments 2 bam LICR-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeLicrHistone/wgEncodeLicrHistoneWbrainH3k09me3ME14halfC57bl6StdPk.broadPeak.gz WholeBrain ChipSeq H3K9me3 Peaks broadPeak LICR-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeLicrHistone/wgEncodeLicrHistoneWbrainH3k09me3ME14halfC57bl6StdSig.bigWig WholeBrain ChipSeq H3K9me3 Signal bigWig LICR-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeLicrHistone/wgEncodeLicrHistoneWbrainH3k27acUE14halfC57bl6StdAlnRep1.bam WholeBrain ChipSeq H3K27ac Alignments 1 bam LICR-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeLicrHistone/wgEncodeLicrHistoneWbrainH3k27acUE14halfC57bl6StdAlnRep2.bam WholeBrain ChipSeq H3K27ac Alignments 2 bam LICR-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeLicrHistone/wgEncodeLicrHistoneWbrainH3k27acUE14halfC57bl6StdPk.broadPeak.gz WholeBrain ChipSeq H3K27ac Peaks broadPeak LICR-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeLicrHistone/wgEncodeLicrHistoneWbrainH3k27acUE14halfC57bl6StdSig.bigWig WholeBrain ChipSeq H3K27ac Signal bigWig LICR-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeLicrHistone/wgEncodeLicrHistoneWbrainH3k27me3ME14halfC57bl6StdAlnRep1.bam WholeBrain ChipSeq H3K27me3 Alignments 1 bam LICR-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeLicrHistone/wgEncodeLicrHistoneWbrainH3k27me3ME14halfC57bl6StdAlnRep2.bam WholeBrain ChipSeq H3K27me3 Alignments 2 bam LICR-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeLicrHistone/wgEncodeLicrHistoneWbrainH3k27me3ME14halfC57bl6StdPk.broadPeak.gz WholeBrain ChipSeq H3K27me3 Peaks broadPeak LICR-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeLicrHistone/wgEncodeLicrHistoneWbrainH3k27me3ME14halfC57bl6StdSig.bigWig WholeBrain ChipSeq H3K27me3 Signal bigWig LICR-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeLicrHistone/wgEncodeLicrHistoneWbrainH3k36me3ME14halfC57bl6StdAlnRep1.bam WholeBrain ChipSeq H3K36me3 Alignments 1 bam LICR-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeLicrHistone/wgEncodeLicrHistoneWbrainH3k36me3ME14halfC57bl6StdAlnRep2.bam WholeBrain ChipSeq H3K36me3 Alignments 2 bam LICR-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeLicrHistone/wgEncodeLicrHistoneWbrainH3k36me3ME14halfC57bl6StdPk.broadPeak.gz WholeBrain ChipSeq H3K36me3 Peaks broadPeak LICR-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeLicrHistone/wgEncodeLicrHistoneWbrainH3k36me3ME14halfC57bl6StdSig.bigWig WholeBrain ChipSeq H3K36me3 Signal bigWig LICR-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeLicrHistone/wgEncodeLicrHistoneWbrainInputUE14halfC57bl6StdAlnRep1.bam WholeBrain ChipSeq Input Alignments 1 bam LICR-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeLicrHistone/wgEncodeLicrHistoneWbrainInputUE14halfC57bl6StdAlnRep2.bam WholeBrain ChipSeq Input Alignments 2 bam LICR-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeLicrHistone/wgEncodeLicrHistoneWbrainInputUE14halfC57bl6StdAlnRep2V2.bam WholeBrain ChipSeq Input Alignments 2 bam LICR-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeLicrHistone/wgEncodeLicrHistoneWbrainInputUE14halfC57bl6StdSig.bigWig WholeBrain ChipSeq Input Signal bigWig LICR-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeLicrRnaSeq/wgEncodeLicrRnaSeqBatCellPapMAdult24wksC57bl6AlnRep1.bam BAT RnaSeq Alignments 1 bam LICR-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeLicrRnaSeq/wgEncodeLicrRnaSeqBatCellPapMAdult24wksC57bl6AlnRep2.bam BAT RnaSeq Alignments 2 bam LICR-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeLicrRnaSeq/wgEncodeLicrRnaSeqBatCellPapMAdult24wksC57bl6SigRep1.bigWig BAT RnaSeq Signal 1 bigWig LICR-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeLicrRnaSeq/wgEncodeLicrRnaSeqBatCellPapMAdult24wksC57bl6SigRep2.bigWig BAT RnaSeq Signal 2 bigWig LICR-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeLicrRnaSeq/wgEncodeLicrRnaSeqBmarrowCellPapMAdult8wksC57bl6AlnRep1.bam BoneMarrow RnaSeq Alignments 1 bam LICR-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeLicrRnaSeq/wgEncodeLicrRnaSeqBmarrowCellPapMAdult8wksC57bl6AlnRep2.bam BoneMarrow RnaSeq Alignments 2 bam LICR-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeLicrRnaSeq/wgEncodeLicrRnaSeqBmarrowCellPapMAdult8wksC57bl6SigRep1.bigWig BoneMarrow RnaSeq Signal 1 bigWig LICR-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeLicrRnaSeq/wgEncodeLicrRnaSeqBmarrowCellPapMAdult8wksC57bl6SigRep2.bigWig BoneMarrow RnaSeq Signal 2 bigWig LICR-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeLicrRnaSeq/wgEncodeLicrRnaSeqBmdmCellPapFAdult8wksC57bl6AlnRep1.bam BMDM RnaSeq Alignments 1 bam LICR-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeLicrRnaSeq/wgEncodeLicrRnaSeqBmdmCellPapFAdult8wksC57bl6AlnRep2.bam BMDM RnaSeq Alignments 2 bam LICR-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeLicrRnaSeq/wgEncodeLicrRnaSeqBmdmCellPapFAdult8wksC57bl6SigRep1.bigWig BMDM RnaSeq Signal 1 bigWig LICR-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeLicrRnaSeq/wgEncodeLicrRnaSeqBmdmCellPapFAdult8wksC57bl6SigRep2.bigWig BMDM RnaSeq Signal 2 bigWig LICR-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeLicrRnaSeq/wgEncodeLicrRnaSeqCbellumCellPapMAdult8wksC57bl6AlnRep1.bam Cerebellum RnaSeq Alignments 1 bam LICR-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeLicrRnaSeq/wgEncodeLicrRnaSeqCbellumCellPapMAdult8wksC57bl6AlnRep2.bam Cerebellum RnaSeq Alignments 2 bam LICR-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeLicrRnaSeq/wgEncodeLicrRnaSeqCbellumCellPapMAdult8wksC57bl6SigRep1.bigWig Cerebellum RnaSeq Signal 1 bigWig LICR-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeLicrRnaSeq/wgEncodeLicrRnaSeqCbellumCellPapMAdult8wksC57bl6SigRep2.bigWig Cerebellum RnaSeq Signal 2 bigWig LICR-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeLicrRnaSeq/wgEncodeLicrRnaSeqCortexCellPapMAdult8wksC57bl6AlnRep1.bam Cortex RnaSeq Alignments 1 bam LICR-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeLicrRnaSeq/wgEncodeLicrRnaSeqCortexCellPapMAdult8wksC57bl6AlnRep2.bam Cortex RnaSeq Alignments 2 bam LICR-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeLicrRnaSeq/wgEncodeLicrRnaSeqCortexCellPapMAdult8wksC57bl6SigRep1.bigWig Cortex RnaSeq Signal 1 bigWig LICR-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeLicrRnaSeq/wgEncodeLicrRnaSeqCortexCellPapMAdult8wksC57bl6SigRep2.bigWig Cortex RnaSeq Signal 2 bigWig LICR-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeLicrRnaSeq/wgEncodeLicrRnaSeqEsb4CellPapME0C57bl6AlnRep1.bam ES-Bruce4 RnaSeq Alignments 1 bam LICR-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeLicrRnaSeq/wgEncodeLicrRnaSeqEsb4CellPapME0C57bl6AlnRep2.bam ES-Bruce4 RnaSeq Alignments 2 bam LICR-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeLicrRnaSeq/wgEncodeLicrRnaSeqEsb4CellPapME0C57bl6SigRep1.bigWig ES-Bruce4 RnaSeq Signal 1 bigWig LICR-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeLicrRnaSeq/wgEncodeLicrRnaSeqEsb4CellPapME0C57bl6SigRep2.bigWig ES-Bruce4 RnaSeq Signal 2 bigWig LICR-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeLicrRnaSeq/wgEncodeLicrRnaSeqHeartCellPapMAdult8wksC57bl6AlnRep1.bam Heart RnaSeq Alignments 1 bam LICR-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeLicrRnaSeq/wgEncodeLicrRnaSeqHeartCellPapMAdult8wksC57bl6AlnRep2.bam Heart RnaSeq Alignments 2 bam LICR-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeLicrRnaSeq/wgEncodeLicrRnaSeqHeartCellPapMAdult8wksC57bl6SigRep1.bigWig Heart RnaSeq Signal 1 bigWig LICR-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeLicrRnaSeq/wgEncodeLicrRnaSeqHeartCellPapMAdult8wksC57bl6SigRep2.bigWig Heart RnaSeq Signal 2 bigWig LICR-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeLicrRnaSeq/wgEncodeLicrRnaSeqHeartCellPapUE14halfC57bl6AlnRep1.bam Heart RnaSeq Alignments 1 bam LICR-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeLicrRnaSeq/wgEncodeLicrRnaSeqHeartCellPapUE14halfC57bl6AlnRep2.bam Heart RnaSeq Alignments 2 bam LICR-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeLicrRnaSeq/wgEncodeLicrRnaSeqHeartCellPapUE14halfC57bl6SigRep1.bigWig Heart RnaSeq Signal 1 bigWig LICR-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeLicrRnaSeq/wgEncodeLicrRnaSeqHeartCellPapUE14halfC57bl6SigRep2.bigWig Heart RnaSeq Signal 2 bigWig LICR-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeLicrRnaSeq/wgEncodeLicrRnaSeqKidneyCellPapMAdult8wksC57bl6AlnRep1.bam Kidney RnaSeq Alignments 1 bam LICR-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeLicrRnaSeq/wgEncodeLicrRnaSeqKidneyCellPapMAdult8wksC57bl6AlnRep2.bam Kidney RnaSeq Alignments 2 bam LICR-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeLicrRnaSeq/wgEncodeLicrRnaSeqKidneyCellPapMAdult8wksC57bl6SigRep1.bigWig Kidney RnaSeq Signal 1 bigWig LICR-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeLicrRnaSeq/wgEncodeLicrRnaSeqKidneyCellPapMAdult8wksC57bl6SigRep2.bigWig Kidney RnaSeq Signal 2 bigWig LICR-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeLicrRnaSeq/wgEncodeLicrRnaSeqLimbCellPapUE14halfC57bl6AlnRep1.bam Limb RnaSeq Alignments 1 bam LICR-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeLicrRnaSeq/wgEncodeLicrRnaSeqLimbCellPapUE14halfC57bl6AlnRep2.bam Limb RnaSeq Alignments 2 bam LICR-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeLicrRnaSeq/wgEncodeLicrRnaSeqLimbCellPapUE14halfC57bl6SigRep1.bigWig Limb RnaSeq Signal 1 bigWig LICR-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeLicrRnaSeq/wgEncodeLicrRnaSeqLimbCellPapUE14halfC57bl6SigRep2.bigWig Limb RnaSeq Signal 2 bigWig LICR-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeLicrRnaSeq/wgEncodeLicrRnaSeqLiverCellPapMAdult8wksC57bl6AlnRep1.bam Liver RnaSeq Alignments 1 bam LICR-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeLicrRnaSeq/wgEncodeLicrRnaSeqLiverCellPapMAdult8wksC57bl6AlnRep2.bam Liver RnaSeq Alignments 2 bam LICR-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeLicrRnaSeq/wgEncodeLicrRnaSeqLiverCellPapMAdult8wksC57bl6SigRep1.bigWig Liver RnaSeq Signal 1 bigWig LICR-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeLicrRnaSeq/wgEncodeLicrRnaSeqLiverCellPapMAdult8wksC57bl6SigRep2.bigWig Liver RnaSeq Signal 2 bigWig LICR-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeLicrRnaSeq/wgEncodeLicrRnaSeqLiverCellPapUE14halfC57bl6AlnRep1.bam Liver RnaSeq Alignments 1 bam LICR-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeLicrRnaSeq/wgEncodeLicrRnaSeqLiverCellPapUE14halfC57bl6AlnRep2.bam Liver RnaSeq Alignments 2 bam LICR-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeLicrRnaSeq/wgEncodeLicrRnaSeqLiverCellPapUE14halfC57bl6SigRep1.bigWig Liver RnaSeq Signal 1 bigWig LICR-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeLicrRnaSeq/wgEncodeLicrRnaSeqLiverCellPapUE14halfC57bl6SigRep2.bigWig Liver RnaSeq Signal 2 bigWig LICR-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeLicrRnaSeq/wgEncodeLicrRnaSeqLungCellPapMAdult8wksC57bl6AlnRep1.bam Lung RnaSeq Alignments 1 bam LICR-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeLicrRnaSeq/wgEncodeLicrRnaSeqLungCellPapMAdult8wksC57bl6AlnRep2.bam Lung RnaSeq Alignments 2 bam LICR-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeLicrRnaSeq/wgEncodeLicrRnaSeqLungCellPapMAdult8wksC57bl6SigRep1.bigWig Lung RnaSeq Signal 1 bigWig LICR-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeLicrRnaSeq/wgEncodeLicrRnaSeqLungCellPapMAdult8wksC57bl6SigRep2.bigWig Lung RnaSeq Signal 2 bigWig LICR-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeLicrRnaSeq/wgEncodeLicrRnaSeqMefCellPapMAdult8wksC57bl6AlnRep1.bam MEF RnaSeq Alignments 1 bam LICR-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeLicrRnaSeq/wgEncodeLicrRnaSeqMefCellPapMAdult8wksC57bl6AlnRep2.bam MEF RnaSeq Alignments 2 bam LICR-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeLicrRnaSeq/wgEncodeLicrRnaSeqMefCellPapMAdult8wksC57bl6SigRep1.bigWig MEF RnaSeq Signal 1 bigWig LICR-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeLicrRnaSeq/wgEncodeLicrRnaSeqMefCellPapMAdult8wksC57bl6SigRep2.bigWig MEF RnaSeq Signal 2 bigWig LICR-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeLicrRnaSeq/wgEncodeLicrRnaSeqMelCellPapMImmortalC57bl6AlnRep1.bam MEL RnaSeq Alignments 1 bam LICR-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeLicrRnaSeq/wgEncodeLicrRnaSeqMelCellPapMImmortalC57bl6AlnRep2.bam MEL RnaSeq Alignments 2 bam LICR-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeLicrRnaSeq/wgEncodeLicrRnaSeqMelCellPapMImmortalC57bl6SigRep1.bigWig MEL RnaSeq Signal 1 bigWig LICR-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeLicrRnaSeq/wgEncodeLicrRnaSeqMelCellPapMImmortalC57bl6SigRep2.bigWig MEL RnaSeq Signal 2 bigWig LICR-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeLicrRnaSeq/wgEncodeLicrRnaSeqOlfactCellPapMAdult8wksC57bl6AlnRep1.bam OlfactBulb RnaSeq Alignments 1 bam LICR-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeLicrRnaSeq/wgEncodeLicrRnaSeqOlfactCellPapMAdult8wksC57bl6AlnRep2.bam OlfactBulb RnaSeq Alignments 2 bam LICR-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeLicrRnaSeq/wgEncodeLicrRnaSeqOlfactCellPapMAdult8wksC57bl6SigRep1.bigWig OlfactBulb RnaSeq Signal 1 bigWig LICR-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeLicrRnaSeq/wgEncodeLicrRnaSeqOlfactCellPapMAdult8wksC57bl6SigRep2.bigWig OlfactBulb RnaSeq Signal 2 bigWig LICR-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeLicrRnaSeq/wgEncodeLicrRnaSeqPlacCellPapFAdult8wksC57bl6AlnRep1.bam Placenta RnaSeq Alignments 1 bam LICR-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeLicrRnaSeq/wgEncodeLicrRnaSeqPlacCellPapFAdult8wksC57bl6AlnRep2.bam Placenta RnaSeq Alignments 2 bam LICR-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeLicrRnaSeq/wgEncodeLicrRnaSeqPlacCellPapFAdult8wksC57bl6SigRep1.bigWig Placenta RnaSeq Signal 1 bigWig LICR-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeLicrRnaSeq/wgEncodeLicrRnaSeqPlacCellPapFAdult8wksC57bl6SigRep2.bigWig Placenta RnaSeq Signal 2 bigWig LICR-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeLicrRnaSeq/wgEncodeLicrRnaSeqSmintCellPapMAdult8wksC57bl6AlnRep1.bam SmIntestine RnaSeq Alignments 1 bam LICR-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeLicrRnaSeq/wgEncodeLicrRnaSeqSmintCellPapMAdult8wksC57bl6AlnRep2.bam SmIntestine RnaSeq Alignments 2 bam LICR-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeLicrRnaSeq/wgEncodeLicrRnaSeqSmintCellPapMAdult8wksC57bl6SigRep1.bigWig SmIntestine RnaSeq Signal 1 bigWig LICR-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeLicrRnaSeq/wgEncodeLicrRnaSeqSmintCellPapMAdult8wksC57bl6SigRep2.bigWig SmIntestine RnaSeq Signal 2 bigWig LICR-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeLicrRnaSeq/wgEncodeLicrRnaSeqSpleenCellPapMAdult8wksC57bl6AlnRep1.bam Spleen RnaSeq Alignments 1 bam LICR-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeLicrRnaSeq/wgEncodeLicrRnaSeqSpleenCellPapMAdult8wksC57bl6AlnRep2.bam Spleen RnaSeq Alignments 2 bam LICR-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeLicrRnaSeq/wgEncodeLicrRnaSeqSpleenCellPapMAdult8wksC57bl6SigRep1.bigWig Spleen RnaSeq Signal 1 bigWig LICR-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeLicrRnaSeq/wgEncodeLicrRnaSeqSpleenCellPapMAdult8wksC57bl6SigRep2.bigWig Spleen RnaSeq Signal 2 bigWig LICR-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeLicrRnaSeq/wgEncodeLicrRnaSeqTestisCellPapMAdult8wksC57bl6AlnRep1.bam Testis RnaSeq Alignments 1 bam LICR-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeLicrRnaSeq/wgEncodeLicrRnaSeqTestisCellPapMAdult8wksC57bl6AlnRep2.bam Testis RnaSeq Alignments 2 bam LICR-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeLicrRnaSeq/wgEncodeLicrRnaSeqTestisCellPapMAdult8wksC57bl6SigRep1.bigWig Testis RnaSeq Signal 1 bigWig LICR-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeLicrRnaSeq/wgEncodeLicrRnaSeqTestisCellPapMAdult8wksC57bl6SigRep2.bigWig Testis RnaSeq Signal 2 bigWig LICR-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeLicrRnaSeq/wgEncodeLicrRnaSeqThymusCellPapMAdult8wksC57bl6AlnRep1.bam Thymus RnaSeq Alignments 1 bam LICR-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeLicrRnaSeq/wgEncodeLicrRnaSeqThymusCellPapMAdult8wksC57bl6AlnRep2.bam Thymus RnaSeq Alignments 2 bam LICR-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeLicrRnaSeq/wgEncodeLicrRnaSeqThymusCellPapMAdult8wksC57bl6SigRep1.bigWig Thymus RnaSeq Signal 1 bigWig LICR-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeLicrRnaSeq/wgEncodeLicrRnaSeqThymusCellPapMAdult8wksC57bl6SigRep2.bigWig Thymus RnaSeq Signal 2 bigWig LICR-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeLicrRnaSeq/wgEncodeLicrRnaSeqWbrainCellPapUE14halfC57bl6AlnRep1.bam WholeBrain RnaSeq Alignments 1 bam LICR-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeLicrRnaSeq/wgEncodeLicrRnaSeqWbrainCellPapUE14halfC57bl6AlnRep2.bam WholeBrain RnaSeq Alignments 2 bam LICR-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeLicrRnaSeq/wgEncodeLicrRnaSeqWbrainCellPapUE14halfC57bl6SigRep1.bigWig WholeBrain RnaSeq Signal 1 bigWig LICR-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeLicrRnaSeq/wgEncodeLicrRnaSeqWbrainCellPapUE14halfC57bl6SigRep2.bigWig WholeBrain RnaSeq Signal 2 bigWig LICR-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeLicrTfbs/wgEncodeLicrTfbsBatInputMAdult24wksC57bl6StdAlnRep1.bam BAT ChipSeq Input Alignments 1 bam LICR-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeLicrTfbs/wgEncodeLicrTfbsBatInputMAdult24wksC57bl6StdAlnRep2.bam BAT ChipSeq Input Alignments 2 bam LICR-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeLicrTfbs/wgEncodeLicrTfbsBatInputMAdult24wksC57bl6StdSig.bigWig BAT ChipSeq Input Signal bigWig LICR-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeLicrTfbs/wgEncodeLicrTfbsBmarrowCtcfMAdult8wksC57bl6StdAlnRep1.bam BoneMarrow ChipSeq CTCF Alignments 1 bam LICR-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeLicrTfbs/wgEncodeLicrTfbsBmarrowCtcfMAdult8wksC57bl6StdAlnRep2.bam BoneMarrow ChipSeq CTCF Alignments 2 bam LICR-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeLicrTfbs/wgEncodeLicrTfbsBmarrowCtcfMAdult8wksC57bl6StdAlnRep2V2.bam BoneMarrow ChipSeq CTCF Alignments 2 bam LICR-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeLicrTfbs/wgEncodeLicrTfbsBmarrowCtcfMAdult8wksC57bl6StdPk.broadPeak.gz BoneMarrow ChipSeq CTCF Peaks broadPeak LICR-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeLicrTfbs/wgEncodeLicrTfbsBmarrowCtcfMAdult8wksC57bl6StdSig.bigWig BoneMarrow ChipSeq CTCF Signal bigWig LICR-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeLicrTfbs/wgEncodeLicrTfbsBmarrowInputMAdult8wksC57bl6StdAlnRep1.bam BoneMarrow ChipSeq Input Alignments 1 bam LICR-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeLicrTfbs/wgEncodeLicrTfbsBmarrowInputMAdult8wksC57bl6StdAlnRep2.bam BoneMarrow ChipSeq Input Alignments 2 bam LICR-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeLicrTfbs/wgEncodeLicrTfbsBmarrowInputMAdult8wksC57bl6StdSig.bigWig BoneMarrow ChipSeq Input Signal bigWig LICR-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeLicrTfbs/wgEncodeLicrTfbsBmarrowPol2MAdult8wksC57bl6StdAlnRep1.bam BoneMarrow ChipSeq Pol2 Alignments 1 bam LICR-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeLicrTfbs/wgEncodeLicrTfbsBmarrowPol2MAdult8wksC57bl6StdAlnRep1V2.bam BoneMarrow ChipSeq Pol2 Alignments 1 bam LICR-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeLicrTfbs/wgEncodeLicrTfbsBmarrowPol2MAdult8wksC57bl6StdAlnRep2.bam BoneMarrow ChipSeq Pol2 Alignments 2 bam LICR-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeLicrTfbs/wgEncodeLicrTfbsBmarrowPol2MAdult8wksC57bl6StdPk.broadPeak.gz BoneMarrow ChipSeq Pol2 Peaks broadPeak LICR-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeLicrTfbs/wgEncodeLicrTfbsBmarrowPol2MAdult8wksC57bl6StdSig.bigWig BoneMarrow ChipSeq Pol2 Signal bigWig LICR-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeLicrTfbs/wgEncodeLicrTfbsBmdmCtcfFAdult8wksC57bl6StdAlnRep1.bam BMDM ChipSeq CTCF Alignments 1 bam LICR-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeLicrTfbs/wgEncodeLicrTfbsBmdmCtcfFAdult8wksC57bl6StdAlnRep2.bam BMDM ChipSeq CTCF Alignments 2 bam LICR-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeLicrTfbs/wgEncodeLicrTfbsBmdmCtcfFAdult8wksC57bl6StdPk.broadPeak.gz BMDM ChipSeq CTCF Peaks broadPeak LICR-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeLicrTfbs/wgEncodeLicrTfbsBmdmCtcfFAdult8wksC57bl6StdSig.bigWig BMDM ChipSeq CTCF Signal bigWig LICR-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeLicrTfbs/wgEncodeLicrTfbsBmdmInputFAdult8wksC57bl6StdAlnRep1.bam BMDM ChipSeq Input Alignments 1 bam LICR-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeLicrTfbs/wgEncodeLicrTfbsBmdmInputFAdult8wksC57bl6StdAlnRep2.bam BMDM ChipSeq Input Alignments 2 bam LICR-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeLicrTfbs/wgEncodeLicrTfbsBmdmInputFAdult8wksC57bl6StdSig.bigWig BMDM ChipSeq Input Signal bigWig LICR-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeLicrTfbs/wgEncodeLicrTfbsBmdmPol2FAdult8wksC57bl6StdAlnRep1.bam BMDM ChipSeq Pol2 Alignments 1 bam LICR-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeLicrTfbs/wgEncodeLicrTfbsBmdmPol2FAdult8wksC57bl6StdAlnRep2.bam BMDM ChipSeq Pol2 Alignments 2 bam LICR-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeLicrTfbs/wgEncodeLicrTfbsBmdmPol2FAdult8wksC57bl6StdPk.broadPeak.gz BMDM ChipSeq Pol2 Peaks broadPeak LICR-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeLicrTfbs/wgEncodeLicrTfbsBmdmPol2FAdult8wksC57bl6StdSig.bigWig BMDM ChipSeq Pol2 Signal bigWig LICR-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeLicrTfbs/wgEncodeLicrTfbsCbellumCtcfMAdult8wksC57bl6StdAlnRep1.bam Cerebellum ChipSeq CTCF Alignments 1 bam LICR-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeLicrTfbs/wgEncodeLicrTfbsCbellumCtcfMAdult8wksC57bl6StdAlnRep2.bam Cerebellum ChipSeq CTCF Alignments 2 bam LICR-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeLicrTfbs/wgEncodeLicrTfbsCbellumCtcfMAdult8wksC57bl6StdAlnRep2V2.bam Cerebellum ChipSeq CTCF Alignments 2 bam LICR-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeLicrTfbs/wgEncodeLicrTfbsCbellumCtcfMAdult8wksC57bl6StdPk.broadPeak.gz Cerebellum ChipSeq CTCF Peaks broadPeak LICR-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeLicrTfbs/wgEncodeLicrTfbsCbellumCtcfMAdult8wksC57bl6StdSig.bigWig Cerebellum ChipSeq CTCF Signal bigWig LICR-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeLicrTfbs/wgEncodeLicrTfbsCbellumInputMAdult8wksC57bl6StdAlnRep1.bam Cerebellum ChipSeq Input Alignments 1 bam LICR-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeLicrTfbs/wgEncodeLicrTfbsCbellumInputMAdult8wksC57bl6StdAlnRep2.bam Cerebellum ChipSeq Input Alignments 2 bam LICR-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeLicrTfbs/wgEncodeLicrTfbsCbellumInputMAdult8wksC57bl6StdSig.bigWig Cerebellum ChipSeq Input Signal bigWig LICR-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeLicrTfbs/wgEncodeLicrTfbsCbellumPol2MAdult8wksC57bl6StdAlnRep1.bam Cerebellum ChipSeq Pol2 Alignments 1 bam LICR-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeLicrTfbs/wgEncodeLicrTfbsCbellumPol2MAdult8wksC57bl6StdAlnRep2.bam Cerebellum ChipSeq Pol2 Alignments 2 bam LICR-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeLicrTfbs/wgEncodeLicrTfbsCbellumPol2MAdult8wksC57bl6StdPk.broadPeak.gz Cerebellum ChipSeq Pol2 Peaks broadPeak LICR-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeLicrTfbs/wgEncodeLicrTfbsCbellumPol2MAdult8wksC57bl6StdSig.bigWig Cerebellum ChipSeq Pol2 Signal bigWig LICR-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeLicrTfbs/wgEncodeLicrTfbsCerebellumInputMAdult8wksC57bl6StdAlnRep1.bam Cerebellum ChipSeq Input Alignments 1 bam LICR-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeLicrTfbs/wgEncodeLicrTfbsCortexCtcfMAdult8wksC57bl6StdAlnRep1.bam Cortex ChipSeq CTCF Alignments 1 bam LICR-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeLicrTfbs/wgEncodeLicrTfbsCortexCtcfMAdult8wksC57bl6StdAlnRep2.bam Cortex ChipSeq CTCF Alignments 2 bam LICR-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeLicrTfbs/wgEncodeLicrTfbsCortexCtcfMAdult8wksC57bl6StdPk.broadPeak.gz Cortex ChipSeq CTCF Peaks broadPeak LICR-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeLicrTfbs/wgEncodeLicrTfbsCortexCtcfMAdult8wksC57bl6StdSig.bigWig Cortex ChipSeq CTCF Signal bigWig LICR-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeLicrTfbs/wgEncodeLicrTfbsCortexInputMAdult8wksC57bl6StdAlnRep1.bam Cortex ChipSeq Input Alignments 1 bam LICR-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeLicrTfbs/wgEncodeLicrTfbsCortexInputMAdult8wksC57bl6StdAlnRep2.bam Cortex ChipSeq Input Alignments 2 bam LICR-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeLicrTfbs/wgEncodeLicrTfbsCortexInputMAdult8wksC57bl6StdSig.bigWig Cortex ChipSeq Input Signal bigWig LICR-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeLicrTfbs/wgEncodeLicrTfbsCortexPol2MAdult8wksC57bl6StdAlnRep1.bam Cortex ChipSeq Pol2 Alignments 1 bam LICR-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeLicrTfbs/wgEncodeLicrTfbsCortexPol2MAdult8wksC57bl6StdAlnRep2.bam Cortex ChipSeq Pol2 Alignments 2 bam LICR-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeLicrTfbs/wgEncodeLicrTfbsCortexPol2MAdult8wksC57bl6StdPk.broadPeak.gz Cortex ChipSeq Pol2 Peaks broadPeak LICR-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeLicrTfbs/wgEncodeLicrTfbsCortexPol2MAdult8wksC57bl6StdSig.bigWig Cortex ChipSeq Pol2 Signal bigWig LICR-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeLicrTfbs/wgEncodeLicrTfbsEsb4CtcfME0C57bl6StdAlnRep1.bam ES-Bruce4 ChipSeq CTCF Alignments 1 bam LICR-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeLicrTfbs/wgEncodeLicrTfbsEsb4CtcfME0C57bl6StdAlnRep2.bam ES-Bruce4 ChipSeq CTCF Alignments 2 bam LICR-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeLicrTfbs/wgEncodeLicrTfbsEsb4CtcfME0C57bl6StdPk.broadPeak.gz ES-Bruce4 ChipSeq CTCF Peaks broadPeak LICR-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeLicrTfbs/wgEncodeLicrTfbsEsb4CtcfME0C57bl6StdSig.bigWig ES-Bruce4 ChipSeq CTCF Signal bigWig LICR-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeLicrTfbs/wgEncodeLicrTfbsEsb4InputME0C57bl6StdAlnRep1.bam ES-Bruce4 ChipSeq Input Alignments 1 bam LICR-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeLicrTfbs/wgEncodeLicrTfbsEsb4InputME0C57bl6StdAlnRep2.bam ES-Bruce4 ChipSeq Input Alignments 2 bam LICR-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeLicrTfbs/wgEncodeLicrTfbsEsb4InputME0C57bl6StdSig.bigWig ES-Bruce4 ChipSeq Input Signal bigWig LICR-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeLicrTfbs/wgEncodeLicrTfbsEsb4P300ME0C57bl6StdAlnRep1.bam ES-Bruce4 ChipSeq p300 Alignments 1 bam LICR-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeLicrTfbs/wgEncodeLicrTfbsEsb4P300ME0C57bl6StdAlnRep2.bam ES-Bruce4 ChipSeq p300 Alignments 2 bam LICR-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeLicrTfbs/wgEncodeLicrTfbsEsb4P300ME0C57bl6StdPk.broadPeak.gz ES-Bruce4 ChipSeq p300 Peaks broadPeak LICR-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeLicrTfbs/wgEncodeLicrTfbsEsb4P300ME0C57bl6StdSig.bigWig ES-Bruce4 ChipSeq p300 Signal bigWig LICR-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeLicrTfbs/wgEncodeLicrTfbsEsb4Pol2ME0C57bl6StdAlnRep1.bam ES-Bruce4 ChipSeq Pol2 Alignments 1 bam LICR-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeLicrTfbs/wgEncodeLicrTfbsEsb4Pol2ME0C57bl6StdAlnRep2.bam ES-Bruce4 ChipSeq Pol2 Alignments 2 bam LICR-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeLicrTfbs/wgEncodeLicrTfbsEsb4Pol2ME0C57bl6StdPk.broadPeak.gz ES-Bruce4 ChipSeq Pol2 Peaks broadPeak LICR-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeLicrTfbs/wgEncodeLicrTfbsEsb4Pol2ME0C57bl6StdSig.bigWig ES-Bruce4 ChipSeq Pol2 Signal bigWig LICR-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeLicrTfbs/wgEncodeLicrTfbsHeartCtcfMAdult8wksC57bl6StdAlnRep1.bam Heart ChipSeq CTCF Alignments 1 bam LICR-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeLicrTfbs/wgEncodeLicrTfbsHeartCtcfMAdult8wksC57bl6StdAlnRep2.bam Heart ChipSeq CTCF Alignments 2 bam LICR-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeLicrTfbs/wgEncodeLicrTfbsHeartCtcfMAdult8wksC57bl6StdPk.broadPeak.gz Heart ChipSeq CTCF Peaks broadPeak LICR-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeLicrTfbs/wgEncodeLicrTfbsHeartCtcfMAdult8wksC57bl6StdSig.bigWig Heart ChipSeq CTCF Signal bigWig LICR-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeLicrTfbs/wgEncodeLicrTfbsHeartInputMAdult8wksC57bl6StdAlnRep1.bam Heart ChipSeq Input Alignments 1 bam LICR-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeLicrTfbs/wgEncodeLicrTfbsHeartInputMAdult8wksC57bl6StdAlnRep1V2.bam Heart ChipSeq Input Alignments 1 bam LICR-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeLicrTfbs/wgEncodeLicrTfbsHeartInputMAdult8wksC57bl6StdAlnRep2.bam Heart ChipSeq Input Alignments 2 bam LICR-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeLicrTfbs/wgEncodeLicrTfbsHeartInputMAdult8wksC57bl6StdSig.bigWig Heart ChipSeq Input Signal bigWig LICR-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeLicrTfbs/wgEncodeLicrTfbsHeartInputUE14halfC57bl6StdAlnRep1.bam Heart ChipSeq Input Alignments 1 bam LICR-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeLicrTfbs/wgEncodeLicrTfbsHeartInputUE14halfC57bl6StdAlnRep2.bam Heart ChipSeq Input Alignments 2 bam LICR-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeLicrTfbs/wgEncodeLicrTfbsHeartInputUE14halfC57bl6StdSig.bigWig Heart ChipSeq Input Signal bigWig LICR-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeLicrTfbs/wgEncodeLicrTfbsHeartP300MAdult8wksC57bl6StdAlnRep1.bam Heart ChipSeq p300 Alignments 1 bam LICR-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeLicrTfbs/wgEncodeLicrTfbsHeartP300MAdult8wksC57bl6StdAlnRep2.bam Heart ChipSeq p300 Alignments 2 bam LICR-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeLicrTfbs/wgEncodeLicrTfbsHeartP300MAdult8wksC57bl6StdPk.broadPeak.gz Heart ChipSeq p300 Peaks broadPeak LICR-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeLicrTfbs/wgEncodeLicrTfbsHeartP300MAdult8wksC57bl6StdSig.bigWig Heart ChipSeq p300 Signal bigWig LICR-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeLicrTfbs/wgEncodeLicrTfbsHeartPol2MAdult8wksC57bl6StdAlnRep1.bam Heart ChipSeq Pol2 Alignments 1 bam LICR-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeLicrTfbs/wgEncodeLicrTfbsHeartPol2MAdult8wksC57bl6StdAlnRep2.bam Heart ChipSeq Pol2 Alignments 2 bam LICR-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeLicrTfbs/wgEncodeLicrTfbsHeartPol2MAdult8wksC57bl6StdPk.broadPeak.gz Heart ChipSeq Pol2 Peaks broadPeak LICR-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeLicrTfbs/wgEncodeLicrTfbsHeartPol2MAdult8wksC57bl6StdSig.bigWig Heart ChipSeq Pol2 Signal bigWig LICR-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeLicrTfbs/wgEncodeLicrTfbsKidneyCtcfMAdult8wksC57bl6StdAlnRep1.bam Kidney ChipSeq CTCF Alignments 1 bam LICR-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeLicrTfbs/wgEncodeLicrTfbsKidneyCtcfMAdult8wksC57bl6StdAlnRep2.bam Kidney ChipSeq CTCF Alignments 2 bam LICR-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeLicrTfbs/wgEncodeLicrTfbsKidneyCtcfMAdult8wksC57bl6StdPk.broadPeak.gz Kidney ChipSeq CTCF Peaks broadPeak LICR-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeLicrTfbs/wgEncodeLicrTfbsKidneyCtcfMAdult8wksC57bl6StdSig.bigWig Kidney ChipSeq CTCF Signal bigWig LICR-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeLicrTfbs/wgEncodeLicrTfbsKidneyInputMAdult8wksC57bl6StdAlnRep1.bam Kidney ChipSeq Input Alignments 1 bam LICR-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeLicrTfbs/wgEncodeLicrTfbsKidneyInputMAdult8wksC57bl6StdAlnRep1V2.bam Kidney ChipSeq Input Alignments 1 bam LICR-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeLicrTfbs/wgEncodeLicrTfbsKidneyInputMAdult8wksC57bl6StdAlnRep2.bam Kidney ChipSeq Input Alignments 2 bam LICR-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeLicrTfbs/wgEncodeLicrTfbsKidneyInputMAdult8wksC57bl6StdSig.bigWig Kidney ChipSeq Input Signal bigWig LICR-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeLicrTfbs/wgEncodeLicrTfbsKidneyPol2MAdult8wksC57bl6StdAlnRep1.bam Kidney ChipSeq Pol2 Alignments 1 bam LICR-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeLicrTfbs/wgEncodeLicrTfbsKidneyPol2MAdult8wksC57bl6StdAlnRep1V2.bam Kidney ChipSeq Pol2 Alignments 1 bam LICR-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeLicrTfbs/wgEncodeLicrTfbsKidneyPol2MAdult8wksC57bl6StdAlnRep2.bam Kidney ChipSeq Pol2 Alignments 2 bam LICR-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeLicrTfbs/wgEncodeLicrTfbsKidneyPol2MAdult8wksC57bl6StdAlnRep2V2.bam Kidney ChipSeq Pol2 Alignments 2 bam LICR-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeLicrTfbs/wgEncodeLicrTfbsKidneyPol2MAdult8wksC57bl6StdAlnRep3.bam Kidney ChipSeq Pol2 Alignments 3 bam LICR-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeLicrTfbs/wgEncodeLicrTfbsKidneyPol2MAdult8wksC57bl6StdPk.broadPeak.gz Kidney ChipSeq Pol2 Peaks broadPeak LICR-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeLicrTfbs/wgEncodeLicrTfbsKidneyPol2MAdult8wksC57bl6StdSig.bigWig Kidney ChipSeq Pol2 Signal bigWig LICR-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeLicrTfbs/wgEncodeLicrTfbsLimbCtcfUE14halfC57bl6StdAlnRep1.bam Limb ChipSeq CTCF Alignments 1 bam LICR-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeLicrTfbs/wgEncodeLicrTfbsLimbCtcfUE14halfC57bl6StdAlnRep1V2.bam Limb ChipSeq CTCF Alignments 1 bam LICR-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeLicrTfbs/wgEncodeLicrTfbsLimbCtcfUE14halfC57bl6StdAlnRep2.bam Limb ChipSeq CTCF Alignments 2 bam LICR-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeLicrTfbs/wgEncodeLicrTfbsLimbCtcfUE14halfC57bl6StdAlnRep2V2.bam Limb ChipSeq CTCF Alignments 2 bam LICR-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeLicrTfbs/wgEncodeLicrTfbsLimbCtcfUE14halfC57bl6StdPk.broadPeak.gz Limb ChipSeq CTCF Peaks broadPeak LICR-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeLicrTfbs/wgEncodeLicrTfbsLimbCtcfUE14halfC57bl6StdSig.bigWig Limb ChipSeq CTCF Signal bigWig LICR-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeLicrTfbs/wgEncodeLicrTfbsLimbInputUE14halfC57bl6StdAlnRep1.bam Limb ChipSeq Input Alignments 1 bam LICR-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeLicrTfbs/wgEncodeLicrTfbsLimbInputUE14halfC57bl6StdAlnRep2.bam Limb ChipSeq Input Alignments 2 bam LICR-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeLicrTfbs/wgEncodeLicrTfbsLimbInputUE14halfC57bl6StdAlnRep2V2.bam Limb ChipSeq Input Alignments 2 bam LICR-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeLicrTfbs/wgEncodeLicrTfbsLimbInputUE14halfC57bl6StdSig.bigWig Limb ChipSeq Input Signal bigWig LICR-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeLicrTfbs/wgEncodeLicrTfbsLimbPol2UE14halfC57bl6StdAlnRep1.bam Limb ChipSeq Pol2 Alignments 1 bam LICR-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeLicrTfbs/wgEncodeLicrTfbsLimbPol2UE14halfC57bl6StdAlnRep1V2.bam Limb ChipSeq Pol2 Alignments 1 bam LICR-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeLicrTfbs/wgEncodeLicrTfbsLimbPol2UE14halfC57bl6StdAlnRep2.bam Limb ChipSeq Pol2 Alignments 2 bam LICR-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeLicrTfbs/wgEncodeLicrTfbsLimbPol2UE14halfC57bl6StdAlnRep2V2.bam Limb ChipSeq Pol2 Alignments 2 bam LICR-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeLicrTfbs/wgEncodeLicrTfbsLimbPol2UE14halfC57bl6StdPk.broadPeak.gz Limb ChipSeq Pol2 Peaks broadPeak LICR-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeLicrTfbs/wgEncodeLicrTfbsLimbPol2UE14halfC57bl6StdSig.bigWig Limb ChipSeq Pol2 Signal bigWig LICR-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeLicrTfbs/wgEncodeLicrTfbsLiverCtcfMAdult8wksC57bl6StdAlnRep1.bam Liver ChipSeq CTCF Alignments 1 bam LICR-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeLicrTfbs/wgEncodeLicrTfbsLiverCtcfMAdult8wksC57bl6StdAlnRep2.bam Liver ChipSeq CTCF Alignments 2 bam LICR-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeLicrTfbs/wgEncodeLicrTfbsLiverCtcfMAdult8wksC57bl6StdPk.broadPeak.gz Liver ChipSeq CTCF Peaks broadPeak LICR-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeLicrTfbs/wgEncodeLicrTfbsLiverCtcfMAdult8wksC57bl6StdSig.bigWig Liver ChipSeq CTCF Signal bigWig LICR-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeLicrTfbs/wgEncodeLicrTfbsLiverInputMAdult8wksC57bl6StdAlnRep1.bam Liver ChipSeq Input Alignments 1 bam LICR-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeLicrTfbs/wgEncodeLicrTfbsLiverInputMAdult8wksC57bl6StdAlnRep2.bam Liver ChipSeq Input Alignments 2 bam LICR-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeLicrTfbs/wgEncodeLicrTfbsLiverInputMAdult8wksC57bl6StdSig.bigWig Liver ChipSeq Input Signal bigWig LICR-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeLicrTfbs/wgEncodeLicrTfbsLiverInputUE14halfC57bl6StdAlnRep1.bam Liver ChipSeq Input Alignments 1 bam LICR-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeLicrTfbs/wgEncodeLicrTfbsLiverInputUE14halfC57bl6StdAlnRep2.bam Liver ChipSeq Input Alignments 2 bam LICR-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeLicrTfbs/wgEncodeLicrTfbsLiverInputUE14halfC57bl6StdSig.bigWig Liver ChipSeq Input Signal bigWig LICR-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeLicrTfbs/wgEncodeLicrTfbsLiverPol2MAdult8wksC57bl6StdAlnRep1.bam Liver ChipSeq Pol2 Alignments 1 bam LICR-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeLicrTfbs/wgEncodeLicrTfbsLiverPol2MAdult8wksC57bl6StdAlnRep2.bam Liver ChipSeq Pol2 Alignments 2 bam LICR-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeLicrTfbs/wgEncodeLicrTfbsLiverPol2MAdult8wksC57bl6StdPk.broadPeak.gz Liver ChipSeq Pol2 Peaks broadPeak LICR-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeLicrTfbs/wgEncodeLicrTfbsLiverPol2MAdult8wksC57bl6StdSig.bigWig Liver ChipSeq Pol2 Signal bigWig LICR-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeLicrTfbs/wgEncodeLicrTfbsLungCtcfMAdult8wksC57bl6StdAlnRep1.bam Lung ChipSeq CTCF Alignments 1 bam LICR-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeLicrTfbs/wgEncodeLicrTfbsLungCtcfMAdult8wksC57bl6StdAlnRep2.bam Lung ChipSeq CTCF Alignments 2 bam LICR-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeLicrTfbs/wgEncodeLicrTfbsLungCtcfMAdult8wksC57bl6StdPk.broadPeak.gz Lung ChipSeq CTCF Peaks broadPeak LICR-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeLicrTfbs/wgEncodeLicrTfbsLungCtcfMAdult8wksC57bl6StdSig.bigWig Lung ChipSeq CTCF Signal bigWig LICR-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeLicrTfbs/wgEncodeLicrTfbsLungInputMAdult8wksC57bl6StdAlnRep1.bam Lung ChipSeq Input Alignments 1 bam LICR-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeLicrTfbs/wgEncodeLicrTfbsLungInputMAdult8wksC57bl6StdAlnRep2.bam Lung ChipSeq Input Alignments 2 bam LICR-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeLicrTfbs/wgEncodeLicrTfbsLungInputMAdult8wksC57bl6StdSig.bigWig Lung ChipSeq Input Signal bigWig LICR-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeLicrTfbs/wgEncodeLicrTfbsLungPol2MAdult8wksC57bl6StdAlnRep1.bam Lung ChipSeq Pol2 Alignments 1 bam LICR-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeLicrTfbs/wgEncodeLicrTfbsLungPol2MAdult8wksC57bl6StdAlnRep2.bam Lung ChipSeq Pol2 Alignments 2 bam LICR-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeLicrTfbs/wgEncodeLicrTfbsLungPol2MAdult8wksC57bl6StdPk.broadPeak.gz Lung ChipSeq Pol2 Peaks broadPeak LICR-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeLicrTfbs/wgEncodeLicrTfbsLungPol2MAdult8wksC57bl6StdSig.bigWig Lung ChipSeq Pol2 Signal bigWig LICR-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeLicrTfbs/wgEncodeLicrTfbsMefCtcfMAdult8wksC57bl6StdAlnRep1.bam MEF ChipSeq CTCF Alignments 1 bam LICR-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeLicrTfbs/wgEncodeLicrTfbsMefCtcfMAdult8wksC57bl6StdAlnRep2.bam MEF ChipSeq CTCF Alignments 2 bam LICR-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeLicrTfbs/wgEncodeLicrTfbsMefCtcfMAdult8wksC57bl6StdPk.broadPeak.gz MEF ChipSeq CTCF Peaks broadPeak LICR-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeLicrTfbs/wgEncodeLicrTfbsMefCtcfMAdult8wksC57bl6StdSig.bigWig MEF ChipSeq CTCF Signal bigWig LICR-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeLicrTfbs/wgEncodeLicrTfbsMefInputMAdult8wksC57bl6StdAlnRep1.bam MEF ChipSeq Input Alignments 1 bam LICR-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeLicrTfbs/wgEncodeLicrTfbsMefInputMAdult8wksC57bl6StdAlnRep2.bam MEF ChipSeq Input Alignments 2 bam LICR-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeLicrTfbs/wgEncodeLicrTfbsMefInputMAdult8wksC57bl6StdSig.bigWig MEF ChipSeq Input Signal bigWig LICR-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeLicrTfbs/wgEncodeLicrTfbsMefPol2MAdult8wksC57bl6StdAlnRep1.bam MEF ChipSeq Pol2 Alignments 1 bam LICR-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeLicrTfbs/wgEncodeLicrTfbsMefPol2MAdult8wksC57bl6StdAlnRep2.bam MEF ChipSeq Pol2 Alignments 2 bam LICR-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeLicrTfbs/wgEncodeLicrTfbsMefPol2MAdult8wksC57bl6StdPk.broadPeak.gz MEF ChipSeq Pol2 Peaks broadPeak LICR-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeLicrTfbs/wgEncodeLicrTfbsMefPol2MAdult8wksC57bl6StdSig.bigWig MEF ChipSeq Pol2 Signal bigWig LICR-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeLicrTfbs/wgEncodeLicrTfbsMelCtcfMImmortalC57bl6StdAlnRep1.bam MEL ChipSeq CTCF Alignments 1 bam LICR-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeLicrTfbs/wgEncodeLicrTfbsMelCtcfMImmortalC57bl6StdAlnRep2.bam MEL ChipSeq CTCF Alignments 2 bam LICR-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeLicrTfbs/wgEncodeLicrTfbsMelCtcfMImmortalC57bl6StdPk.broadPeak.gz MEL ChipSeq CTCF Peaks broadPeak LICR-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeLicrTfbs/wgEncodeLicrTfbsMelCtcfMImmortalC57bl6StdSig.bigWig MEL ChipSeq CTCF Signal bigWig LICR-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeLicrTfbs/wgEncodeLicrTfbsMelInputMImmortalC57bl6StdAlnRep1.bam MEL ChipSeq Input Alignments 1 bam LICR-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeLicrTfbs/wgEncodeLicrTfbsMelInputMImmortalC57bl6StdAlnRep2.bam MEL ChipSeq Input Alignments 2 bam LICR-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeLicrTfbs/wgEncodeLicrTfbsMelInputMImmortalC57bl6StdSig.bigWig MEL ChipSeq Input Signal bigWig LICR-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeLicrTfbs/wgEncodeLicrTfbsMelPol2MImmortalC57bl6StdAlnRep1.bam MEL ChipSeq Pol2 Alignments 1 bam LICR-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeLicrTfbs/wgEncodeLicrTfbsMelPol2MImmortalC57bl6StdAlnRep2.bam MEL ChipSeq Pol2 Alignments 2 bam LICR-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeLicrTfbs/wgEncodeLicrTfbsMelPol2MImmortalC57bl6StdPk.broadPeak.gz MEL ChipSeq Pol2 Peaks broadPeak LICR-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeLicrTfbs/wgEncodeLicrTfbsMelPol2MImmortalC57bl6StdSig.bigWig MEL ChipSeq Pol2 Signal bigWig LICR-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeLicrTfbs/wgEncodeLicrTfbsOlfactCtcfMAdult8wksC57bl6StdAlnRep1.bam OlfactBulb ChipSeq CTCF Alignments 1 bam LICR-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeLicrTfbs/wgEncodeLicrTfbsOlfactCtcfMAdult8wksC57bl6StdAlnRep2.bam OlfactBulb ChipSeq CTCF Alignments 2 bam LICR-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeLicrTfbs/wgEncodeLicrTfbsOlfactCtcfMAdult8wksC57bl6StdPk.broadPeak.gz OlfactBulb ChipSeq CTCF Peaks broadPeak LICR-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeLicrTfbs/wgEncodeLicrTfbsOlfactCtcfMAdult8wksC57bl6StdSig.bigWig OlfactBulb ChipSeq CTCF Signal bigWig LICR-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeLicrTfbs/wgEncodeLicrTfbsOlfactInputMAdult8wksC57bl6StdAlnRep1.bam OlfactBulb ChipSeq Input Alignments 1 bam LICR-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeLicrTfbs/wgEncodeLicrTfbsOlfactInputMAdult8wksC57bl6StdAlnRep2.bam OlfactBulb ChipSeq Input Alignments 2 bam LICR-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeLicrTfbs/wgEncodeLicrTfbsOlfactInputMAdult8wksC57bl6StdSig.bigWig OlfactBulb ChipSeq Input Signal bigWig LICR-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeLicrTfbs/wgEncodeLicrTfbsOlfactPol2MAdult8wksC57bl6StdAlnRep1.bam OlfactBulb ChipSeq Pol2 Alignments 1 bam LICR-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeLicrTfbs/wgEncodeLicrTfbsOlfactPol2MAdult8wksC57bl6StdAlnRep2.bam OlfactBulb ChipSeq Pol2 Alignments 2 bam LICR-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeLicrTfbs/wgEncodeLicrTfbsOlfactPol2MAdult8wksC57bl6StdPk.broadPeak.gz OlfactBulb ChipSeq Pol2 Peaks broadPeak LICR-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeLicrTfbs/wgEncodeLicrTfbsOlfactPol2MAdult8wksC57bl6StdSig.bigWig OlfactBulb ChipSeq Pol2 Signal bigWig LICR-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeLicrTfbs/wgEncodeLicrTfbsSmintCtcfMAdult8wksC57bl6StdAlnRep1.bam SmIntestine ChipSeq CTCF Alignments 1 bam LICR-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeLicrTfbs/wgEncodeLicrTfbsSmintCtcfMAdult8wksC57bl6StdAlnRep2.bam SmIntestine ChipSeq CTCF Alignments 2 bam LICR-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeLicrTfbs/wgEncodeLicrTfbsSmintCtcfMAdult8wksC57bl6StdPk.broadPeak.gz SmIntestine ChipSeq CTCF Peaks broadPeak LICR-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeLicrTfbs/wgEncodeLicrTfbsSmintCtcfMAdult8wksC57bl6StdSig.bigWig SmIntestine ChipSeq CTCF Signal bigWig LICR-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeLicrTfbs/wgEncodeLicrTfbsSmintInputMAdult8wksC57bl6StdAlnRep1.bam SmIntestine ChipSeq Input Alignments 1 bam LICR-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeLicrTfbs/wgEncodeLicrTfbsSmintInputMAdult8wksC57bl6StdAlnRep2.bam SmIntestine ChipSeq Input Alignments 2 bam LICR-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeLicrTfbs/wgEncodeLicrTfbsSmintInputMAdult8wksC57bl6StdSig.bigWig SmIntestine ChipSeq Input Signal bigWig LICR-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeLicrTfbs/wgEncodeLicrTfbsSmintPol2MAdult8wksC57bl6StdAlnRep1.bam SmIntestine ChipSeq Pol2 Alignments 1 bam LICR-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeLicrTfbs/wgEncodeLicrTfbsSmintPol2MAdult8wksC57bl6StdAlnRep2.bam SmIntestine ChipSeq Pol2 Alignments 2 bam LICR-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeLicrTfbs/wgEncodeLicrTfbsSmintPol2MAdult8wksC57bl6StdPk.broadPeak.gz SmIntestine ChipSeq Pol2 Peaks broadPeak LICR-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeLicrTfbs/wgEncodeLicrTfbsSmintPol2MAdult8wksC57bl6StdSig.bigWig SmIntestine ChipSeq Pol2 Signal bigWig LICR-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeLicrTfbs/wgEncodeLicrTfbsSpleenCtcfMAdult8wksC57bl6StdAlnRep1.bam Spleen ChipSeq CTCF Alignments 1 bam LICR-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeLicrTfbs/wgEncodeLicrTfbsSpleenCtcfMAdult8wksC57bl6StdAlnRep2.bam Spleen ChipSeq CTCF Alignments 2 bam LICR-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeLicrTfbs/wgEncodeLicrTfbsSpleenCtcfMAdult8wksC57bl6StdAlnRep2V2.bam Spleen ChipSeq CTCF Alignments 2 bam LICR-m 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Testis ChipSeq Pol2 Alignments 1 bam LICR-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeLicrTfbs/wgEncodeLicrTfbsTestisPol2MAdult8wksC57bl6StdAlnRep2.bam Testis ChipSeq Pol2 Alignments 2 bam LICR-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeLicrTfbs/wgEncodeLicrTfbsTestisPol2MAdult8wksC57bl6StdPk.broadPeak.gz Testis ChipSeq Pol2 Peaks broadPeak LICR-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeLicrTfbs/wgEncodeLicrTfbsTestisPol2MAdult8wksC57bl6StdSig.bigWig Testis ChipSeq Pol2 Signal bigWig LICR-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeLicrTfbs/wgEncodeLicrTfbsThymusCtcfMAdult8wksC57bl6StdAlnRep1.bam Thymus ChipSeq CTCF Alignments 1 bam LICR-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeLicrTfbs/wgEncodeLicrTfbsThymusCtcfMAdult8wksC57bl6StdAlnRep2.bam Thymus ChipSeq CTCF Alignments 2 bam LICR-m 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http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodePsuDnase/wgEncodePsuDnaseG1eS129ME0PkRep2.narrowPeak.gz G1E DnaseSeq Peaks 2 narrowPeak PSU-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodePsuDnase/wgEncodePsuDnaseG1eS129ME0SigRep1.bigWig G1E DnaseSeq Signal 1 bigWig PSU-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodePsuDnase/wgEncodePsuDnaseG1eS129ME0SigRep2.bigWig G1E DnaseSeq Signal 2 bigWig PSU-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodePsuDnase/wgEncodePsuDnaseG1eer4S129ME0Diffd24hAlnRep1.bam G1E-ER4 DnaseSeq Alignments 1 bam PSU-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodePsuDnase/wgEncodePsuDnaseG1eer4S129ME0Diffd24hAlnRep2.bam G1E-ER4 DnaseSeq Alignments 2 bam PSU-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodePsuDnase/wgEncodePsuDnaseG1eer4S129ME0Diffd24hPkRep1.narrowPeak.gz G1E-ER4 DnaseSeq Peaks 1 narrowPeak PSU-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodePsuDnase/wgEncodePsuDnaseG1eer4S129ME0Diffd24hPkRep2.narrowPeak.gz G1E-ER4 DnaseSeq Peaks 2 narrowPeak PSU-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodePsuDnase/wgEncodePsuDnaseG1eer4S129ME0Diffd24hSigRep1.bigWig G1E-ER4 DnaseSeq Signal 1 bigWig PSU-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodePsuDnase/wgEncodePsuDnaseG1eer4S129ME0Diffd24hSigRep2.bigWig G1E-ER4 DnaseSeq Signal 2 bigWig PSU-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodePsuHistone/wgEncodePsuHistoneCh12H3k04me1FImmortal2a4bInputAlnRep1.bam CH12 ChipSeq H3K4me1 Alignments 1 bam PSU-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodePsuHistone/wgEncodePsuHistoneCh12H3k04me1FImmortal2a4bInputAlnRep2.bam CH12 ChipSeq H3K4me1 Alignments 2 bam PSU-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodePsuHistone/wgEncodePsuHistoneCh12H3k04me1FImmortal2a4bInputPk.broadPeak.gz 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http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodePsuHistone/wgEncodePsuHistoneCh12H3k04me3FImmortal2a4bInputRepSignalRep1.bigWig CH12 ChipSeq H3K4me3 RepSignal 1 bigWig PSU-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodePsuHistone/wgEncodePsuHistoneCh12H3k04me3FImmortal2a4bInputRepSignalRep2.bigWig CH12 ChipSeq H3K4me3 RepSignal 2 bigWig PSU-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodePsuHistone/wgEncodePsuHistoneCh12H3k04me3FImmortal2a4bInputSig.bigWig CH12 ChipSeq H3K4me3 Signal bigWig PSU-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodePsuHistone/wgEncodePsuHistoneCh12H3k09me3FImmortal2a4bAlnRep1.bam CH12 ChipSeq H3K9me3 Alignments 1 bam PSU-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodePsuHistone/wgEncodePsuHistoneCh12H3k09me3FImmortal2a4bAlnRep2.bam CH12 ChipSeq H3K9me3 Alignments 2 bam PSU-m 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http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodePsuRnaSeq/wgEncodePsuRnaSeqG1eer4ME0S129R2x99dDiffd7hMinusRawRep1.bigWig G1E-ER4 RnaSeq MinusRawSignal 1 bigWig PSU-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodePsuRnaSeq/wgEncodePsuRnaSeqG1eer4ME0S129R2x99dDiffd7hMinusRawRep2.bigWig G1E-ER4 RnaSeq MinusRawSignal 2 bigWig PSU-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodePsuRnaSeq/wgEncodePsuRnaSeqG1eer4ME0S129R2x99dDiffd7hPlusRawRep1.bigWig G1E-ER4 RnaSeq PlusRawSignal 1 bigWig PSU-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodePsuRnaSeq/wgEncodePsuRnaSeqG1eer4ME0S129R2x99dDiffd7hPlusRawRep2.bigWig G1E-ER4 RnaSeq PlusRawSignal 2 bigWig PSU-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodePsuRnaSeq/wgEncodePsuRnaSeqG1eer4ME0S129R2x99dMinusRawRep1.bigWig G1E-ER4 RnaSeq MinusRawSignal 1 bigWig PSU-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodePsuRnaSeq/wgEncodePsuRnaSeqG1eer4ME0S129R2x99dMinusRawRep2.bigWig G1E-ER4 RnaSeq MinusRawSignal 2 bigWig PSU-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodePsuRnaSeq/wgEncodePsuRnaSeqG1eer4ME0S129R2x99dPlusRawRep1.bigWig G1E-ER4 RnaSeq PlusRawSignal 1 bigWig PSU-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodePsuRnaSeq/wgEncodePsuRnaSeqG1eer4ME0S129R2x99dPlusRawRep2.bigWig G1E-ER4 RnaSeq PlusRawSignal 2 bigWig PSU-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodePsuRnaSeq/wgEncodePsuRnaSeqMegakaryoBE14halfCd1R2x99dAlnRep1.bam Megakaryo RnaSeq Alignments 1 bam PSU-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodePsuRnaSeq/wgEncodePsuRnaSeqMegakaryoBE14halfCd1R2x99dAlnRep2.bam Megakaryo RnaSeq Alignments 2 bam PSU-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodePsuRnaSeq/wgEncodePsuRnaSeqMegakaryoBE14halfCd1R2x99dMinusRawRep1.bigWig Megakaryo RnaSeq MinusRawSignal 1 bigWig PSU-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodePsuRnaSeq/wgEncodePsuRnaSeqMegakaryoBE14halfCd1R2x99dMinusRawRep2.bigWig Megakaryo RnaSeq MinusRawSignal 2 bigWig PSU-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodePsuRnaSeq/wgEncodePsuRnaSeqMegakaryoBE14halfCd1R2x99dPlusRawRep1.bigWig Megakaryo RnaSeq PlusRawSignal 1 bigWig PSU-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodePsuRnaSeq/wgEncodePsuRnaSeqMegakaryoBE14halfCd1R2x99dPlusRawRep2.bigWig Megakaryo RnaSeq PlusRawSignal 2 bigWig PSU-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodePsuRnaSeq/wgEncodePsuRnaSeqMelMImmortalUknR1x45AlnRep1.bam MEL RnaSeq Alignments 1 bam PSU-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodePsuRnaSeq/wgEncodePsuRnaSeqMelMImmortalUknR1x45AlnRep2.bam MEL RnaSeq Alignments 2 bam PSU-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodePsuRnaSeq/wgEncodePsuRnaSeqMelMImmortalUknR1x45Dm2p5dAlnRep1.bam MEL RnaSeq Alignments 1 bam PSU-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodePsuRnaSeq/wgEncodePsuRnaSeqMelMImmortalUknR1x45Dm2p5dAlnRep2.bam MEL RnaSeq Alignments 2 bam PSU-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodePsuRnaSeq/wgEncodePsuRnaSeqMelMImmortalUknR1x45Dm2p5dSigRep1.bigWig MEL RnaSeq Signal 1 bigWig PSU-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodePsuRnaSeq/wgEncodePsuRnaSeqMelMImmortalUknR1x45Dm2p5dSigRep2.bigWig MEL RnaSeq Signal 2 bigWig PSU-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodePsuRnaSeq/wgEncodePsuRnaSeqMelMImmortalUknR1x45SigRep1.bigWig MEL RnaSeq Signal 1 bigWig PSU-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodePsuRnaSeq/wgEncodePsuRnaSeqMelMImmortalUknR1x45SigRep2.bigWig MEL RnaSeq Signal 2 bigWig PSU-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodePsuRnaSeq/wgEncodePsuRnaSeqMepFAdult5wksC57bl6jR2x99dAlnRep1.bam MEP RnaSeq Alignments 1 bam PSU-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodePsuRnaSeq/wgEncodePsuRnaSeqMepFAdult5wksC57bl6jR2x99dAlnRep2.bam MEP RnaSeq Alignments 2 bam PSU-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodePsuRnaSeq/wgEncodePsuRnaSeqMepFAdult5wksC57bl6jR2x99dMinusRawRep1.bigWig MEP RnaSeq MinusRawSignal 1 bigWig PSU-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodePsuRnaSeq/wgEncodePsuRnaSeqMepFAdult5wksC57bl6jR2x99dMinusRawRep2.bigWig MEP RnaSeq MinusRawSignal 2 bigWig PSU-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodePsuRnaSeq/wgEncodePsuRnaSeqMepFAdult5wksC57bl6jR2x99dPlusRawRep1.bigWig MEP RnaSeq PlusRawSignal 1 bigWig PSU-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodePsuRnaSeq/wgEncodePsuRnaSeqMepFAdult5wksC57bl6jR2x99dPlusRawRep2.bigWig MEP RnaSeq PlusRawSignal 2 bigWig PSU-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodePsuTfbs/wgEncodePsuTfbsCh12CtcfFImmortal2a4bInputAlnRep1.bam CH12 ChipSeq CTCF Alignments 1 bam PSU-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodePsuTfbs/wgEncodePsuTfbsCh12CtcfFImmortal2a4bInputAlnRep2.bam CH12 ChipSeq CTCF Alignments 2 bam PSU-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodePsuTfbs/wgEncodePsuTfbsCh12CtcfFImmortal2a4bInputPk.broadPeak.gz CH12 ChipSeq CTCF Peaks broadPeak PSU-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodePsuTfbs/wgEncodePsuTfbsCh12CtcfFImmortal2a4bInputRepPeaksRep1.broadPeak.gz CH12 ChipSeq CTCF RepPeaks 1 broadPeak PSU-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodePsuTfbs/wgEncodePsuTfbsCh12CtcfFImmortal2a4bInputRepPeaksRep2.broadPeak.gz CH12 ChipSeq CTCF RepPeaks 2 broadPeak PSU-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodePsuTfbs/wgEncodePsuTfbsCh12CtcfFImmortal2a4bInputRepSignalRep1.bigWig CH12 ChipSeq CTCF RepSignal 1 bigWig PSU-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodePsuTfbs/wgEncodePsuTfbsCh12CtcfFImmortal2a4bInputRepSignalRep2.bigWig CH12 ChipSeq CTCF RepSignal 2 bigWig PSU-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodePsuTfbs/wgEncodePsuTfbsCh12CtcfFImmortal2a4bInputSig.bigWig CH12 ChipSeq CTCF Signal bigWig PSU-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodePsuTfbs/wgEncodePsuTfbsCh12InputFImmortal2a4bInputAlnRep1.bam CH12 ChipSeq Input Alignments 1 bam PSU-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodePsuTfbs/wgEncodePsuTfbsCh12InputFImmortal2a4bInputAlnRep2.bam CH12 ChipSeq Input Alignments 2 bam PSU-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodePsuTfbs/wgEncodePsuTfbsCh12InputFImmortal2a4bInputRepSignalRep1.bigWig CH12 ChipSeq Input RepSignal 1 bigWig PSU-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodePsuTfbs/wgEncodePsuTfbsCh12InputFImmortal2a4bInputRepSignalRep2.bigWig CH12 ChipSeq Input RepSignal 2 bigWig PSU-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodePsuTfbs/wgEncodePsuTfbsCh12InputFImmortal2a4bInputSig.bigWig CH12 ChipSeq Input Signal bigWig PSU-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodePsuTfbs/wgEncodePsuTfbsCh12Pax5cFImmortal2a4bInputAlnRep1.bam CH12 ChipSeq PAX5_(N-15) Alignments 1 bam PSU-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodePsuTfbs/wgEncodePsuTfbsCh12Pax5cFImmortal2a4bInputAlnRep2.bam CH12 ChipSeq PAX5_(N-15) Alignments 2 bam PSU-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodePsuTfbs/wgEncodePsuTfbsCh12Pax5cFImmortal2a4bInputPk.broadPeak.gz CH12 ChipSeq PAX5_(N-15) Peaks broadPeak PSU-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodePsuTfbs/wgEncodePsuTfbsCh12Pax5cFImmortal2a4bInputRepPeaksRep1.broadPeak.gz CH12 ChipSeq PAX5_(N-15) RepPeaks 1 broadPeak PSU-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodePsuTfbs/wgEncodePsuTfbsCh12Pax5cFImmortal2a4bInputRepPeaksRep2.broadPeak.gz CH12 ChipSeq PAX5_(N-15) RepPeaks 2 broadPeak PSU-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodePsuTfbs/wgEncodePsuTfbsCh12Pax5cFImmortal2a4bInputRepSignalRep1.bigWig CH12 ChipSeq PAX5_(N-15) RepSignal 1 bigWig PSU-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodePsuTfbs/wgEncodePsuTfbsCh12Pax5cFImmortal2a4bInputRepSignalRep2.bigWig CH12 ChipSeq PAX5_(N-15) RepSignal 2 bigWig PSU-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodePsuTfbs/wgEncodePsuTfbsCh12Pax5cFImmortal2a4bInputSig.bigWig CH12 ChipSeq PAX5_(N-15) Signal bigWig PSU-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodePsuTfbs/wgEncodePsuTfbsErythroblGata1aBE14halfCd1InputAlnRep1.bam Erythrobl ChipSeq GATA1_(SC-265) Alignments 1 bam PSU-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodePsuTfbs/wgEncodePsuTfbsErythroblGata1aBE14halfCd1InputAlnRep2.bam Erythrobl ChipSeq GATA1_(SC-265) Alignments 2 bam PSU-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodePsuTfbs/wgEncodePsuTfbsErythroblGata1aBE14halfCd1InputPk.broadPeak.gz Erythrobl ChipSeq GATA1_(SC-265) Peaks broadPeak PSU-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodePsuTfbs/wgEncodePsuTfbsErythroblGata1aBE14halfCd1InputRepPeaksRep1.broadPeak.gz Erythrobl ChipSeq GATA1_(SC-265) RepPeaks 1 broadPeak PSU-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodePsuTfbs/wgEncodePsuTfbsErythroblGata1aBE14halfCd1InputRepPeaksRep2.broadPeak.gz Erythrobl ChipSeq GATA1_(SC-265) RepPeaks 2 broadPeak PSU-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodePsuTfbs/wgEncodePsuTfbsErythroblGata1aBE14halfCd1InputRepSignalRep1.bigWig Erythrobl ChipSeq GATA1_(SC-265) RepSignal 1 bigWig PSU-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodePsuTfbs/wgEncodePsuTfbsErythroblGata1aBE14halfCd1InputRepSignalRep2.bigWig Erythrobl ChipSeq GATA1_(SC-265) RepSignal 2 bigWig PSU-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodePsuTfbs/wgEncodePsuTfbsErythroblGata1aBE14halfCd1InputSig.bigWig Erythrobl ChipSeq GATA1_(SC-265) Signal bigWig PSU-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodePsuTfbs/wgEncodePsuTfbsErythroblInputBE14halfCd1InputAlnRep1.bam Erythrobl ChipSeq Input Alignments 1 bam PSU-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodePsuTfbs/wgEncodePsuTfbsErythroblInputBE14halfCd1InputAlnRep2.bam Erythrobl ChipSeq Input Alignments 2 bam PSU-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodePsuTfbs/wgEncodePsuTfbsErythroblInputBE14halfCd1InputRepSignalRep1.bigWig Erythrobl ChipSeq Input RepSignal 1 bigWig PSU-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodePsuTfbs/wgEncodePsuTfbsErythroblInputBE14halfCd1InputRepSignalRep2.bigWig Erythrobl ChipSeq Input RepSignal 2 bigWig PSU-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodePsuTfbs/wgEncodePsuTfbsErythroblInputBE14halfCd1InputSig.bigWig Erythrobl ChipSeq Input Signal bigWig PSU-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodePsuTfbs/wgEncodePsuTfbsErythroblTal1BE14halfCd1InputAlnRep1.bam Erythrobl ChipSeq TAL1_(SC-12984) Alignments 1 bam PSU-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodePsuTfbs/wgEncodePsuTfbsErythroblTal1BE14halfCd1InputAlnRep2.bam Erythrobl ChipSeq TAL1_(SC-12984) Alignments 2 bam PSU-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodePsuTfbs/wgEncodePsuTfbsErythroblTal1BE14halfCd1InputAlnRep3.bam Erythrobl ChipSeq TAL1_(SC-12984) Alignments 3 bam PSU-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodePsuTfbs/wgEncodePsuTfbsErythroblTal1BE14halfCd1InputPk.broadPeak.gz Erythrobl ChipSeq TAL1_(SC-12984) Peaks broadPeak PSU-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodePsuTfbs/wgEncodePsuTfbsErythroblTal1BE14halfCd1InputRepPeaksRep1.broadPeak.gz Erythrobl ChipSeq TAL1_(SC-12984) RepPeaks 1 broadPeak PSU-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodePsuTfbs/wgEncodePsuTfbsErythroblTal1BE14halfCd1InputRepPeaksRep2.broadPeak.gz Erythrobl ChipSeq TAL1_(SC-12984) RepPeaks 2 broadPeak PSU-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodePsuTfbs/wgEncodePsuTfbsErythroblTal1BE14halfCd1InputRepPeaksRep3.broadPeak.gz Erythrobl ChipSeq TAL1_(SC-12984) RepPeaks 3 broadPeak PSU-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodePsuTfbs/wgEncodePsuTfbsErythroblTal1BE14halfCd1InputRepSignalRep1.bigWig Erythrobl ChipSeq TAL1_(SC-12984) RepSignal 1 bigWig PSU-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodePsuTfbs/wgEncodePsuTfbsErythroblTal1BE14halfCd1InputRepSignalRep2.bigWig Erythrobl ChipSeq TAL1_(SC-12984) RepSignal 2 bigWig PSU-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodePsuTfbs/wgEncodePsuTfbsErythroblTal1BE14halfCd1InputRepSignalRep3.bigWig Erythrobl ChipSeq TAL1_(SC-12984) RepSignal 3 bigWig PSU-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodePsuTfbs/wgEncodePsuTfbsErythroblTal1BE14halfCd1InputSig.bigWig Erythrobl ChipSeq TAL1_(SC-12984) Signal bigWig PSU-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodePsuTfbs/wgEncodePsuTfbsG1eCtcfME0S129InputAlnRep1.bam G1E ChipSeq CTCF Alignments 1 bam PSU-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodePsuTfbs/wgEncodePsuTfbsG1eCtcfME0S129InputAlnRep2.bam G1E ChipSeq CTCF Alignments 2 bam PSU-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodePsuTfbs/wgEncodePsuTfbsG1eCtcfME0S129InputPk.broadPeak.gz G1E ChipSeq CTCF Peaks broadPeak PSU-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodePsuTfbs/wgEncodePsuTfbsG1eCtcfME0S129InputRepPeaksRep1.broadPeak.gz G1E ChipSeq CTCF RepPeaks 1 broadPeak PSU-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodePsuTfbs/wgEncodePsuTfbsG1eCtcfME0S129InputRepPeaksRep2.broadPeak.gz G1E ChipSeq CTCF RepPeaks 2 broadPeak PSU-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodePsuTfbs/wgEncodePsuTfbsG1eCtcfME0S129InputRepSignalRep1.bigWig G1E ChipSeq CTCF RepSignal 1 bigWig PSU-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodePsuTfbs/wgEncodePsuTfbsG1eCtcfME0S129InputRepSignalRep2.bigWig G1E ChipSeq CTCF RepSignal 2 bigWig PSU-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodePsuTfbs/wgEncodePsuTfbsG1eCtcfME0S129InputSig.bigWig G1E ChipSeq CTCF Signal bigWig PSU-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodePsuTfbs/wgEncodePsuTfbsG1eGata1aME0S129InputAlnRep1.bam G1E ChipSeq GATA1_(SC-265) Alignments 1 bam PSU-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodePsuTfbs/wgEncodePsuTfbsG1eGata1aME0S129InputAlnRep2.bam G1E ChipSeq GATA1_(SC-265) Alignments 2 bam PSU-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodePsuTfbs/wgEncodePsuTfbsG1eGata1aME0S129InputPk.broadPeak.gz G1E ChipSeq GATA1_(SC-265) Peaks broadPeak PSU-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodePsuTfbs/wgEncodePsuTfbsG1eGata1aME0S129InputRepPeaksRep1.broadPeak.gz G1E ChipSeq GATA1_(SC-265) RepPeaks 1 broadPeak PSU-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodePsuTfbs/wgEncodePsuTfbsG1eGata1aME0S129InputRepPeaksRep2.broadPeak.gz G1E ChipSeq GATA1_(SC-265) RepPeaks 2 broadPeak PSU-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodePsuTfbs/wgEncodePsuTfbsG1eGata1aME0S129InputRepSignalRep1.bigWig G1E ChipSeq GATA1_(SC-265) RepSignal 1 bigWig PSU-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodePsuTfbs/wgEncodePsuTfbsG1eGata1aME0S129InputRepSignalRep2.bigWig G1E ChipSeq GATA1_(SC-265) RepSignal 2 bigWig PSU-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodePsuTfbs/wgEncodePsuTfbsG1eGata1aME0S129InputSig.bigWig G1E ChipSeq GATA1_(SC-265) Signal bigWig PSU-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodePsuTfbs/wgEncodePsuTfbsG1eGata2sc9008ME0S129InputAlnRep1.bam G1E ChipSeq GATA2_(SC-9008) Alignments 1 bam PSU-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodePsuTfbs/wgEncodePsuTfbsG1eGata2sc9008ME0S129InputAlnRep2.bam G1E ChipSeq GATA2_(SC-9008) Alignments 2 bam PSU-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodePsuTfbs/wgEncodePsuTfbsG1eGata2sc9008ME0S129InputPk.broadPeak.gz G1E ChipSeq GATA2_(SC-9008) Peaks broadPeak PSU-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodePsuTfbs/wgEncodePsuTfbsG1eGata2sc9008ME0S129InputRepPeaksRep1.broadPeak.gz G1E ChipSeq GATA2_(SC-9008) RepPeaks 1 broadPeak PSU-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodePsuTfbs/wgEncodePsuTfbsG1eGata2sc9008ME0S129InputRepPeaksRep2.broadPeak.gz G1E ChipSeq GATA2_(SC-9008) RepPeaks 2 broadPeak PSU-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodePsuTfbs/wgEncodePsuTfbsG1eGata2sc9008ME0S129InputRepSignalRep1.bigWig G1E ChipSeq GATA2_(SC-9008) RepSignal 1 bigWig PSU-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodePsuTfbs/wgEncodePsuTfbsG1eGata2sc9008ME0S129InputRepSignalRep2.bigWig G1E ChipSeq GATA2_(SC-9008) RepSignal 2 bigWig PSU-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodePsuTfbs/wgEncodePsuTfbsG1eGata2sc9008ME0S129InputSig.bigWig G1E ChipSeq GATA2_(SC-9008) Signal bigWig PSU-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodePsuTfbs/wgEncodePsuTfbsG1eInputME0S129InputAlnRep1.bam G1E ChipSeq Input Alignments 1 bam PSU-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodePsuTfbs/wgEncodePsuTfbsG1eInputME0S129InputAlnRep2.bam G1E ChipSeq Input Alignments 2 bam PSU-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodePsuTfbs/wgEncodePsuTfbsG1eInputME0S129InputRepSignalRep1.bigWig G1E ChipSeq Input RepSignal 1 bigWig PSU-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodePsuTfbs/wgEncodePsuTfbsG1eInputME0S129InputRepSignalRep2.bigWig G1E ChipSeq Input RepSignal 2 bigWig PSU-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodePsuTfbs/wgEncodePsuTfbsG1eInputME0S129InputSig.bigWig G1E ChipSeq Input Signal bigWig PSU-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodePsuTfbs/wgEncodePsuTfbsG1ePol24h8ME0S129InputAlnRep1.bam G1E ChipSeq Pol2-4H8 Alignments 1 bam PSU-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodePsuTfbs/wgEncodePsuTfbsG1ePol24h8ME0S129InputAlnRep2.bam G1E ChipSeq Pol2-4H8 Alignments 2 bam PSU-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodePsuTfbs/wgEncodePsuTfbsG1ePol24h8ME0S129InputPk.broadPeak.gz G1E ChipSeq Pol2-4H8 Peaks broadPeak PSU-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodePsuTfbs/wgEncodePsuTfbsG1ePol24h8ME0S129InputRepPeaksRep1.broadPeak.gz G1E ChipSeq Pol2-4H8 RepPeaks 1 broadPeak PSU-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodePsuTfbs/wgEncodePsuTfbsG1ePol24h8ME0S129InputRepPeaksRep2.broadPeak.gz G1E ChipSeq Pol2-4H8 RepPeaks 2 broadPeak PSU-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodePsuTfbs/wgEncodePsuTfbsG1ePol24h8ME0S129InputRepSignalRep1.bigWig G1E ChipSeq Pol2-4H8 RepSignal 1 bigWig PSU-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodePsuTfbs/wgEncodePsuTfbsG1ePol24h8ME0S129InputRepSignalRep2.bigWig G1E ChipSeq Pol2-4H8 RepSignal 2 bigWig PSU-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodePsuTfbs/wgEncodePsuTfbsG1ePol24h8ME0S129InputSig.bigWig G1E ChipSeq Pol2-4H8 Signal bigWig PSU-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodePsuTfbs/wgEncodePsuTfbsG1eTal1ME0S129InputAlnRep1.bam G1E ChipSeq TAL1_(SC-12984) Alignments 1 bam PSU-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodePsuTfbs/wgEncodePsuTfbsG1eTal1ME0S129InputAlnRep2.bam G1E ChipSeq TAL1_(SC-12984) Alignments 2 bam PSU-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodePsuTfbs/wgEncodePsuTfbsG1eTal1ME0S129InputPk.broadPeak.gz G1E ChipSeq TAL1_(SC-12984) Peaks broadPeak PSU-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodePsuTfbs/wgEncodePsuTfbsG1eTal1ME0S129InputRepPeaksRep1.broadPeak.gz G1E ChipSeq TAL1_(SC-12984) RepPeaks 1 broadPeak PSU-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodePsuTfbs/wgEncodePsuTfbsG1eTal1ME0S129InputRepPeaksRep2.broadPeak.gz G1E ChipSeq TAL1_(SC-12984) RepPeaks 2 broadPeak PSU-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodePsuTfbs/wgEncodePsuTfbsG1eTal1ME0S129InputRepSignalRep1.bigWig G1E ChipSeq TAL1_(SC-12984) RepSignal 1 bigWig PSU-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodePsuTfbs/wgEncodePsuTfbsG1eTal1ME0S129InputRepSignalRep2.bigWig G1E ChipSeq TAL1_(SC-12984) RepSignal 2 bigWig PSU-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodePsuTfbs/wgEncodePsuTfbsG1eTal1ME0S129InputSig.bigWig G1E ChipSeq TAL1_(SC-12984) Signal bigWig PSU-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodePsuTfbs/wgEncodePsuTfbsG1eer4Gata1aME0S129InputAlnRep1.bam G1E-ER4 ChipSeq GATA1_(SC-265) Alignments 1 bam PSU-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodePsuTfbs/wgEncodePsuTfbsG1eer4Gata1aME0S129InputDiffd14hAlnRep1.bam G1E-ER4 ChipSeq GATA1_(SC-265) Alignments 1 bam PSU-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodePsuTfbs/wgEncodePsuTfbsG1eer4Gata1aME0S129InputDiffd14hPkRep1.broadPeak.gz G1E-ER4 ChipSeq GATA1_(SC-265) Peaks 1 broadPeak PSU-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodePsuTfbs/wgEncodePsuTfbsG1eer4Gata1aME0S129InputDiffd14hSigRep1.bigWig G1E-ER4 ChipSeq GATA1_(SC-265) Signal 1 bigWig PSU-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodePsuTfbs/wgEncodePsuTfbsG1eer4Gata1aME0S129InputDiffd24hAlnRep1.bam G1E-ER4 ChipSeq GATA1_(SC-265) Alignments 1 bam PSU-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodePsuTfbs/wgEncodePsuTfbsG1eer4Gata1aME0S129InputDiffd24hPkRep1.broadPeak.gz G1E-ER4 ChipSeq GATA1_(SC-265) Peaks 1 broadPeak PSU-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodePsuTfbs/wgEncodePsuTfbsG1eer4Gata1aME0S129InputDiffd24hSigRep1.bigWig G1E-ER4 ChipSeq GATA1_(SC-265) Signal 1 bigWig PSU-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodePsuTfbs/wgEncodePsuTfbsG1eer4Gata1aME0S129InputDiffd30hAlnRep1.bam G1E-ER4 ChipSeq GATA1_(SC-265) Alignments 1 bam PSU-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodePsuTfbs/wgEncodePsuTfbsG1eer4Gata1aME0S129InputDiffd30hPkRep1.broadPeak.gz G1E-ER4 ChipSeq GATA1_(SC-265) Peaks 1 broadPeak PSU-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodePsuTfbs/wgEncodePsuTfbsG1eer4Gata1aME0S129InputDiffd30hSigRep1.bigWig G1E-ER4 ChipSeq GATA1_(SC-265) Signal 1 bigWig PSU-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodePsuTfbs/wgEncodePsuTfbsG1eer4Gata1aME0S129InputDiffd3hAlnRep1.bam G1E-ER4 ChipSeq GATA1_(SC-265) Alignments 1 bam PSU-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodePsuTfbs/wgEncodePsuTfbsG1eer4Gata1aME0S129InputDiffd3hPkRep1.broadPeak.gz G1E-ER4 ChipSeq GATA1_(SC-265) Peaks 1 broadPeak PSU-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodePsuTfbs/wgEncodePsuTfbsG1eer4Gata1aME0S129InputDiffd3hSigRep1.bigWig G1E-ER4 ChipSeq GATA1_(SC-265) Signal 1 bigWig PSU-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodePsuTfbs/wgEncodePsuTfbsG1eer4Gata1aME0S129InputDiffd7hAlnRep1.bam G1E-ER4 ChipSeq GATA1_(SC-265) Alignments 1 bam PSU-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodePsuTfbs/wgEncodePsuTfbsG1eer4Gata1aME0S129InputDiffd7hPkRep1.broadPeak.gz G1E-ER4 ChipSeq GATA1_(SC-265) Peaks 1 broadPeak PSU-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodePsuTfbs/wgEncodePsuTfbsG1eer4Gata1aME0S129InputDiffd7hSigRep1.bigWig G1E-ER4 ChipSeq GATA1_(SC-265) Signal 1 bigWig PSU-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodePsuTfbs/wgEncodePsuTfbsG1eer4Gata1aME0S129InputPkRep1.broadPeak.gz G1E-ER4 ChipSeq GATA1_(SC-265) Peaks 1 broadPeak PSU-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodePsuTfbs/wgEncodePsuTfbsG1eer4Gata1aME0S129InputSigRep1.bigWig G1E-ER4 ChipSeq GATA1_(SC-265) Signal 1 bigWig PSU-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodePsuTfbs/wgEncodePsuTfbsG1eer4InputME0S129InputAlnRep1.bam G1E-ER4 ChipSeq Input Alignments 1 bam PSU-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodePsuTfbs/wgEncodePsuTfbsG1eer4InputME0S129InputDiffd14hAlnRep1.bam G1E-ER4 ChipSeq Input Alignments 1 bam PSU-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodePsuTfbs/wgEncodePsuTfbsG1eer4InputME0S129InputDiffd14hSigRep1.bigWig G1E-ER4 ChipSeq Input Signal 1 bigWig PSU-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodePsuTfbs/wgEncodePsuTfbsG1eer4InputME0S129InputDiffd24hAlnRep1.bam G1E-ER4 ChipSeq Input Alignments 1 bam PSU-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodePsuTfbs/wgEncodePsuTfbsG1eer4InputME0S129InputDiffd24hSigRep1.bigWig G1E-ER4 ChipSeq Input Signal 1 bigWig PSU-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodePsuTfbs/wgEncodePsuTfbsG1eer4InputME0S129InputDiffd30hAlnRep1.bam G1E-ER4 ChipSeq Input Alignments 1 bam PSU-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodePsuTfbs/wgEncodePsuTfbsG1eer4InputME0S129InputDiffd30hSigRep1.bigWig G1E-ER4 ChipSeq Input Signal 1 bigWig PSU-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodePsuTfbs/wgEncodePsuTfbsG1eer4InputME0S129InputDiffd3hAlnRep1.bam G1E-ER4 ChipSeq Input Alignments 1 bam PSU-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodePsuTfbs/wgEncodePsuTfbsG1eer4InputME0S129InputDiffd3hSigRep1.bigWig G1E-ER4 ChipSeq Input Signal 1 bigWig PSU-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodePsuTfbs/wgEncodePsuTfbsG1eer4InputME0S129InputDiffd7hAlnRep1.bam G1E-ER4 ChipSeq Input Alignments 1 bam PSU-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodePsuTfbs/wgEncodePsuTfbsG1eer4InputME0S129InputDiffd7hSigRep1.bigWig G1E-ER4 ChipSeq Input Signal 1 bigWig PSU-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodePsuTfbs/wgEncodePsuTfbsG1eer4InputME0S129InputSigRep1.bigWig G1E-ER4 ChipSeq Input Signal 1 bigWig PSU-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodePsuTfbs/wgEncodePsuTfbsG1eer4e2CtcfME0S129InputAlnRep1.bam G1E-ER4 ChipSeq CTCF Alignments 1 bam PSU-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodePsuTfbs/wgEncodePsuTfbsG1eer4e2CtcfME0S129InputAlnRep2.bam G1E-ER4 ChipSeq CTCF Alignments 2 bam PSU-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodePsuTfbs/wgEncodePsuTfbsG1eer4e2CtcfME0S129InputPk.broadPeak.gz G1E-ER4 ChipSeq CTCF Peaks broadPeak PSU-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodePsuTfbs/wgEncodePsuTfbsG1eer4e2CtcfME0S129InputRepPeaksRep1.broadPeak.gz G1E-ER4 ChipSeq CTCF RepPeaks 1 broadPeak PSU-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodePsuTfbs/wgEncodePsuTfbsG1eer4e2CtcfME0S129InputRepPeaksRep2.broadPeak.gz G1E-ER4 ChipSeq CTCF RepPeaks 2 broadPeak PSU-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodePsuTfbs/wgEncodePsuTfbsG1eer4e2CtcfME0S129InputRepSignalRep1.bigWig G1E-ER4 ChipSeq CTCF RepSignal 1 bigWig PSU-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodePsuTfbs/wgEncodePsuTfbsG1eer4e2CtcfME0S129InputRepSignalRep2.bigWig G1E-ER4 ChipSeq CTCF RepSignal 2 bigWig PSU-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodePsuTfbs/wgEncodePsuTfbsG1eer4e2CtcfME0S129InputSig.bigWig G1E-ER4 ChipSeq CTCF Signal bigWig PSU-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodePsuTfbs/wgEncodePsuTfbsG1eer4e2Gata1aME0S129InputAlnRep1.bam G1E-ER4 ChipSeq GATA1_(SC-265) Alignments 1 bam PSU-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodePsuTfbs/wgEncodePsuTfbsG1eer4e2Gata1aME0S129InputAlnRep2.bam G1E-ER4 ChipSeq GATA1_(SC-265) Alignments 2 bam PSU-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodePsuTfbs/wgEncodePsuTfbsG1eer4e2Gata1aME0S129InputPk.broadPeak.gz G1E-ER4 ChipSeq GATA1_(SC-265) Peaks broadPeak PSU-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodePsuTfbs/wgEncodePsuTfbsG1eer4e2Gata1aME0S129InputRepPeaksRep1.broadPeak.gz G1E-ER4 ChipSeq GATA1_(SC-265) RepPeaks 1 broadPeak PSU-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodePsuTfbs/wgEncodePsuTfbsG1eer4e2Gata1aME0S129InputRepPeaksRep2.broadPeak.gz G1E-ER4 ChipSeq GATA1_(SC-265) RepPeaks 2 broadPeak PSU-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodePsuTfbs/wgEncodePsuTfbsG1eer4e2Gata1aME0S129InputRepSignalRep1.bigWig G1E-ER4 ChipSeq GATA1_(SC-265) RepSignal 1 bigWig PSU-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodePsuTfbs/wgEncodePsuTfbsG1eer4e2Gata1aME0S129InputRepSignalRep2.bigWig G1E-ER4 ChipSeq GATA1_(SC-265) RepSignal 2 bigWig PSU-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodePsuTfbs/wgEncodePsuTfbsG1eer4e2Gata1aME0S129InputSig.bigWig G1E-ER4 ChipSeq GATA1_(SC-265) Signal bigWig PSU-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodePsuTfbs/wgEncodePsuTfbsG1eer4e2Gata2sc9008ME0S129InputAlnRep1.bam G1E-ER4 ChipSeq GATA2_(SC-9008) Alignments 1 bam PSU-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodePsuTfbs/wgEncodePsuTfbsG1eer4e2Gata2sc9008ME0S129InputAlnRep2.bam G1E-ER4 ChipSeq GATA2_(SC-9008) Alignments 2 bam PSU-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodePsuTfbs/wgEncodePsuTfbsG1eer4e2Gata2sc9008ME0S129InputPk.broadPeak.gz G1E-ER4 ChipSeq GATA2_(SC-9008) Peaks broadPeak PSU-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodePsuTfbs/wgEncodePsuTfbsG1eer4e2Gata2sc9008ME0S129InputRepPeaksRep1.broadPeak.gz G1E-ER4 ChipSeq GATA2_(SC-9008) RepPeaks 1 broadPeak PSU-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodePsuTfbs/wgEncodePsuTfbsG1eer4e2Gata2sc9008ME0S129InputRepPeaksRep2.broadPeak.gz G1E-ER4 ChipSeq GATA2_(SC-9008) RepPeaks 2 broadPeak PSU-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodePsuTfbs/wgEncodePsuTfbsG1eer4e2Gata2sc9008ME0S129InputRepSignalRep1.bigWig G1E-ER4 ChipSeq GATA2_(SC-9008) RepSignal 1 bigWig PSU-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodePsuTfbs/wgEncodePsuTfbsG1eer4e2Gata2sc9008ME0S129InputRepSignalRep2.bigWig G1E-ER4 ChipSeq GATA2_(SC-9008) RepSignal 2 bigWig PSU-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodePsuTfbs/wgEncodePsuTfbsG1eer4e2Gata2sc9008ME0S129InputSig.bigWig G1E-ER4 ChipSeq GATA2_(SC-9008) Signal bigWig PSU-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodePsuTfbs/wgEncodePsuTfbsG1eer4e2InputME0S129InputAlnRep1.bam G1E-ER4 ChipSeq Input Alignments 1 bam PSU-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodePsuTfbs/wgEncodePsuTfbsG1eer4e2InputME0S129InputAlnRep2.bam G1E-ER4 ChipSeq Input Alignments 2 bam PSU-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodePsuTfbs/wgEncodePsuTfbsG1eer4e2InputME0S129InputRepSignalRep1.bigWig G1E-ER4 ChipSeq Input RepSignal 1 bigWig PSU-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodePsuTfbs/wgEncodePsuTfbsG1eer4e2InputME0S129InputRepSignalRep2.bigWig G1E-ER4 ChipSeq Input RepSignal 2 bigWig PSU-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodePsuTfbs/wgEncodePsuTfbsG1eer4e2InputME0S129InputSig.bigWig G1E-ER4 ChipSeq Input Signal bigWig PSU-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodePsuTfbs/wgEncodePsuTfbsG1eer4e2Pol24h8ME0S129InputAlnRep1.bam G1E-ER4 ChipSeq Pol2-4H8 Alignments 1 bam PSU-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodePsuTfbs/wgEncodePsuTfbsG1eer4e2Pol24h8ME0S129InputAlnRep2.bam G1E-ER4 ChipSeq Pol2-4H8 Alignments 2 bam PSU-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodePsuTfbs/wgEncodePsuTfbsG1eer4e2Pol24h8ME0S129InputAlnRep3.bam G1E-ER4 ChipSeq Pol2-4H8 Alignments 3 bam PSU-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodePsuTfbs/wgEncodePsuTfbsG1eer4e2Pol24h8ME0S129InputPk.broadPeak.gz G1E-ER4 ChipSeq Pol2-4H8 Peaks broadPeak PSU-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodePsuTfbs/wgEncodePsuTfbsG1eer4e2Pol24h8ME0S129InputRepPeaksRep1.broadPeak.gz G1E-ER4 ChipSeq Pol2-4H8 RepPeaks 1 broadPeak PSU-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodePsuTfbs/wgEncodePsuTfbsG1eer4e2Pol24h8ME0S129InputRepPeaksRep2.broadPeak.gz G1E-ER4 ChipSeq Pol2-4H8 RepPeaks 2 broadPeak PSU-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodePsuTfbs/wgEncodePsuTfbsG1eer4e2Pol24h8ME0S129InputRepPeaksRep3.broadPeak.gz G1E-ER4 ChipSeq Pol2-4H8 RepPeaks 3 broadPeak PSU-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodePsuTfbs/wgEncodePsuTfbsG1eer4e2Pol24h8ME0S129InputRepSignalRep1.bigWig G1E-ER4 ChipSeq Pol2-4H8 RepSignal 1 bigWig PSU-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodePsuTfbs/wgEncodePsuTfbsG1eer4e2Pol24h8ME0S129InputRepSignalRep2.bigWig G1E-ER4 ChipSeq Pol2-4H8 RepSignal 2 bigWig PSU-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodePsuTfbs/wgEncodePsuTfbsG1eer4e2Pol24h8ME0S129InputRepSignalRep3.bigWig G1E-ER4 ChipSeq Pol2-4H8 RepSignal 3 bigWig PSU-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodePsuTfbs/wgEncodePsuTfbsG1eer4e2Pol24h8ME0S129InputSig.bigWig G1E-ER4 ChipSeq Pol2-4H8 Signal bigWig PSU-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodePsuTfbs/wgEncodePsuTfbsG1eer4e2Tal1ME0S129InputAlnRep1.bam G1E-ER4 ChipSeq TAL1_(SC-12984) Alignments 1 bam PSU-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodePsuTfbs/wgEncodePsuTfbsG1eer4e2Tal1ME0S129InputAlnRep2.bam G1E-ER4 ChipSeq TAL1_(SC-12984) Alignments 2 bam PSU-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodePsuTfbs/wgEncodePsuTfbsG1eer4e2Tal1ME0S129InputPk.broadPeak.gz G1E-ER4 ChipSeq TAL1_(SC-12984) Peaks broadPeak PSU-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodePsuTfbs/wgEncodePsuTfbsG1eer4e2Tal1ME0S129InputRepPeaksRep1.broadPeak.gz G1E-ER4 ChipSeq TAL1_(SC-12984) RepPeaks 1 broadPeak PSU-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodePsuTfbs/wgEncodePsuTfbsG1eer4e2Tal1ME0S129InputRepPeaksRep2.broadPeak.gz G1E-ER4 ChipSeq TAL1_(SC-12984) RepPeaks 2 broadPeak PSU-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodePsuTfbs/wgEncodePsuTfbsG1eer4e2Tal1ME0S129InputRepSignalRep1.bigWig G1E-ER4 ChipSeq TAL1_(SC-12984) RepSignal 1 bigWig PSU-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodePsuTfbs/wgEncodePsuTfbsG1eer4e2Tal1ME0S129InputRepSignalRep2.bigWig G1E-ER4 ChipSeq TAL1_(SC-12984) RepSignal 2 bigWig PSU-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodePsuTfbs/wgEncodePsuTfbsG1eer4e2Tal1ME0S129InputSig.bigWig G1E-ER4 ChipSeq TAL1_(SC-12984) Signal bigWig PSU-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodePsuTfbs/wgEncodePsuTfbsMegakaryoFli1sc356BE14halfCd1InputAlnRep1.bam Megakaryo ChipSeq FLI1_(sc-356) Alignments 1 bam PSU-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodePsuTfbs/wgEncodePsuTfbsMegakaryoFli1sc356BE14halfCd1InputAlnRep2.bam Megakaryo ChipSeq FLI1_(sc-356) Alignments 2 bam PSU-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodePsuTfbs/wgEncodePsuTfbsMegakaryoFli1sc356BE14halfCd1InputPk.broadPeak.gz Megakaryo ChipSeq FLI1_(sc-356) Peaks broadPeak PSU-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodePsuTfbs/wgEncodePsuTfbsMegakaryoFli1sc356BE14halfCd1InputRepPeaksRep1.broadPeak.gz Megakaryo ChipSeq FLI1_(sc-356) RepPeaks 1 broadPeak PSU-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodePsuTfbs/wgEncodePsuTfbsMegakaryoFli1sc356BE14halfCd1InputRepPeaksRep2.broadPeak.gz Megakaryo ChipSeq FLI1_(sc-356) RepPeaks 2 broadPeak PSU-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodePsuTfbs/wgEncodePsuTfbsMegakaryoFli1sc356BE14halfCd1InputRepSignalRep1.bigWig Megakaryo ChipSeq FLI1_(sc-356) RepSignal 1 bigWig PSU-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodePsuTfbs/wgEncodePsuTfbsMegakaryoFli1sc356BE14halfCd1InputRepSignalRep2.bigWig Megakaryo ChipSeq FLI1_(sc-356) RepSignal 2 bigWig PSU-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodePsuTfbs/wgEncodePsuTfbsMegakaryoFli1sc356BE14halfCd1InputSig.bigWig Megakaryo ChipSeq FLI1_(sc-356) Signal bigWig PSU-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodePsuTfbs/wgEncodePsuTfbsMegakaryoGata1aBE14halfCd1InputAlnRep1.bam Megakaryo ChipSeq GATA1_(SC-265) Alignments 1 bam PSU-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodePsuTfbs/wgEncodePsuTfbsMegakaryoGata1aBE14halfCd1InputAlnRep2.bam Megakaryo ChipSeq GATA1_(SC-265) Alignments 2 bam PSU-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodePsuTfbs/wgEncodePsuTfbsMegakaryoGata1aBE14halfCd1InputAlnRep3.bam Megakaryo ChipSeq GATA1_(SC-265) Alignments 3 bam PSU-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodePsuTfbs/wgEncodePsuTfbsMegakaryoGata1aBE14halfCd1InputPk.broadPeak.gz Megakaryo ChipSeq GATA1_(SC-265) Peaks broadPeak PSU-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodePsuTfbs/wgEncodePsuTfbsMegakaryoGata1aBE14halfCd1InputPkV2.broadPeak.gz Megakaryo ChipSeq GATA1_(SC-265) Peaks broadPeak PSU-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodePsuTfbs/wgEncodePsuTfbsMegakaryoGata1aBE14halfCd1InputRepPeaksRep1.broadPeak.gz Megakaryo ChipSeq GATA1_(SC-265) RepPeaks 1 broadPeak PSU-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodePsuTfbs/wgEncodePsuTfbsMegakaryoGata1aBE14halfCd1InputRepPeaksRep2.broadPeak.gz Megakaryo ChipSeq GATA1_(SC-265) RepPeaks 2 broadPeak PSU-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodePsuTfbs/wgEncodePsuTfbsMegakaryoGata1aBE14halfCd1InputRepPeaksRep3.broadPeak.gz Megakaryo ChipSeq GATA1_(SC-265) RepPeaks 3 broadPeak PSU-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodePsuTfbs/wgEncodePsuTfbsMegakaryoGata1aBE14halfCd1InputRepSignalRep1.bigWig Megakaryo ChipSeq GATA1_(SC-265) RepSignal 1 bigWig PSU-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodePsuTfbs/wgEncodePsuTfbsMegakaryoGata1aBE14halfCd1InputRepSignalRep2.bigWig Megakaryo ChipSeq GATA1_(SC-265) RepSignal 2 bigWig PSU-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodePsuTfbs/wgEncodePsuTfbsMegakaryoGata1aBE14halfCd1InputRepSignalRep3.bigWig Megakaryo ChipSeq GATA1_(SC-265) RepSignal 3 bigWig PSU-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodePsuTfbs/wgEncodePsuTfbsMegakaryoGata1aBE14halfCd1InputSig.bigWig Megakaryo ChipSeq GATA1_(SC-265) Signal bigWig PSU-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodePsuTfbs/wgEncodePsuTfbsMegakaryoGata1aBE14halfCd1InputSigV2.bigWig Megakaryo ChipSeq GATA1_(SC-265) Signal bigWig PSU-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodePsuTfbs/wgEncodePsuTfbsMegakaryoInputBE14halfCd1InputAlnRep1.bam Megakaryo ChipSeq Input Alignments 1 bam PSU-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodePsuTfbs/wgEncodePsuTfbsMegakaryoInputBE14halfCd1InputAlnRep2.bam Megakaryo ChipSeq Input Alignments 2 bam PSU-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodePsuTfbs/wgEncodePsuTfbsMegakaryoInputBE14halfCd1InputRepSignalRep1.bigWig Megakaryo ChipSeq Input RepSignal 1 bigWig PSU-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodePsuTfbs/wgEncodePsuTfbsMegakaryoInputBE14halfCd1InputRepSignalRep2.bigWig Megakaryo ChipSeq Input RepSignal 2 bigWig PSU-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodePsuTfbs/wgEncodePsuTfbsMegakaryoInputBE14halfCd1InputSig.bigWig Megakaryo ChipSeq Input Signal bigWig PSU-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodePsuTfbs/wgEncodePsuTfbsMegakaryoTal1BE14halfCd1InputAlnRep1.bam Megakaryo ChipSeq TAL1_(SC-12984) Alignments 1 bam PSU-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodePsuTfbs/wgEncodePsuTfbsMegakaryoTal1BE14halfCd1InputAlnRep2.bam Megakaryo ChipSeq TAL1_(SC-12984) Alignments 2 bam PSU-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodePsuTfbs/wgEncodePsuTfbsMegakaryoTal1BE14halfCd1InputAlnRep3.bam Megakaryo ChipSeq TAL1_(SC-12984) Alignments 3 bam PSU-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodePsuTfbs/wgEncodePsuTfbsMegakaryoTal1BE14halfCd1InputAlnRep4.bam Megakaryo ChipSeq TAL1_(SC-12984) Alignments 4 bam PSU-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodePsuTfbs/wgEncodePsuTfbsMegakaryoTal1BE14halfCd1InputPk.broadPeak.gz Megakaryo ChipSeq TAL1_(SC-12984) Peaks broadPeak PSU-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodePsuTfbs/wgEncodePsuTfbsMegakaryoTal1BE14halfCd1InputRepPeaksRep1.broadPeak.gz Megakaryo ChipSeq TAL1_(SC-12984) RepPeaks 1 broadPeak PSU-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodePsuTfbs/wgEncodePsuTfbsMegakaryoTal1BE14halfCd1InputRepPeaksRep2.broadPeak.gz Megakaryo ChipSeq TAL1_(SC-12984) RepPeaks 2 broadPeak PSU-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodePsuTfbs/wgEncodePsuTfbsMegakaryoTal1BE14halfCd1InputRepPeaksRep3.broadPeak.gz Megakaryo ChipSeq TAL1_(SC-12984) RepPeaks 3 broadPeak PSU-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodePsuTfbs/wgEncodePsuTfbsMegakaryoTal1BE14halfCd1InputRepPeaksRep4.broadPeak.gz Megakaryo ChipSeq TAL1_(SC-12984) RepPeaks 4 broadPeak PSU-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodePsuTfbs/wgEncodePsuTfbsMegakaryoTal1BE14halfCd1InputRepSignalRep1.bigWig Megakaryo ChipSeq TAL1_(SC-12984) RepSignal 1 bigWig PSU-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodePsuTfbs/wgEncodePsuTfbsMegakaryoTal1BE14halfCd1InputRepSignalRep2.bigWig Megakaryo ChipSeq TAL1_(SC-12984) RepSignal 2 bigWig PSU-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodePsuTfbs/wgEncodePsuTfbsMegakaryoTal1BE14halfCd1InputRepSignalRep3.bigWig Megakaryo ChipSeq TAL1_(SC-12984) RepSignal 3 bigWig PSU-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodePsuTfbs/wgEncodePsuTfbsMegakaryoTal1BE14halfCd1InputRepSignalRep4.bigWig Megakaryo ChipSeq TAL1_(SC-12984) RepSignal 4 bigWig PSU-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodePsuTfbs/wgEncodePsuTfbsMegakaryoTal1BE14halfCd1InputSig.bigWig Megakaryo ChipSeq TAL1_(SC-12984) Signal bigWig PSU-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodePsuTfbs/wgEncodePsuTfbsMelCtcfMImmortalC57bl6InputAlnRep1.bam MEL ChipSeq CTCF Alignments 1 bam PSU-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodePsuTfbs/wgEncodePsuTfbsMelCtcfMImmortalC57bl6InputAlnRep2.bam MEL ChipSeq CTCF Alignments 2 bam PSU-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodePsuTfbs/wgEncodePsuTfbsMelCtcfMImmortalC57bl6InputPk.broadPeak.gz MEL ChipSeq CTCF Peaks broadPeak PSU-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodePsuTfbs/wgEncodePsuTfbsMelCtcfMImmortalC57bl6InputRepPeaksRep1.broadPeak.gz MEL ChipSeq CTCF RepPeaks 1 broadPeak PSU-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodePsuTfbs/wgEncodePsuTfbsMelCtcfMImmortalC57bl6InputRepPeaksRep2.broadPeak.gz MEL ChipSeq CTCF RepPeaks 2 broadPeak PSU-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodePsuTfbs/wgEncodePsuTfbsMelCtcfMImmortalC57bl6InputRepSignalRep1.bigWig MEL ChipSeq CTCF RepSignal 1 bigWig PSU-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodePsuTfbs/wgEncodePsuTfbsMelCtcfMImmortalC57bl6InputRepSignalRep2.bigWig MEL ChipSeq CTCF RepSignal 2 bigWig PSU-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodePsuTfbs/wgEncodePsuTfbsMelCtcfMImmortalC57bl6InputSig.bigWig MEL ChipSeq CTCF Signal bigWig PSU-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodePsuTfbs/wgEncodePsuTfbsMelInputUImmortalC57bl6InputAlnRep1.bam MEL ChipSeq Input Alignments 1 bam PSU-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodePsuTfbs/wgEncodePsuTfbsMelInputUImmortalC57bl6InputAlnRep2.bam MEL ChipSeq Input Alignments 2 bam PSU-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodePsuTfbs/wgEncodePsuTfbsMelInputUImmortalC57bl6InputRepSignalRep1.bigWig MEL ChipSeq Input RepSignal 1 bigWig PSU-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodePsuTfbs/wgEncodePsuTfbsMelInputUImmortalC57bl6InputRepSignalRep2.bigWig MEL ChipSeq Input RepSignal 2 bigWig PSU-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodePsuTfbs/wgEncodePsuTfbsMelInputUImmortalC57bl6InputSig.bigWig MEL ChipSeq Input Signal bigWig PSU-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodePsuTfbs/wgEncodePsuTfbsMelPol24h8UImmortalC57bl6InputAlnRep1.bam MEL ChipSeq Pol2-4H8 Alignments 1 bam PSU-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodePsuTfbs/wgEncodePsuTfbsMelPol24h8UImmortalC57bl6InputAlnRep2.bam MEL ChipSeq Pol2-4H8 Alignments 2 bam PSU-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodePsuTfbs/wgEncodePsuTfbsMelPol24h8UImmortalC57bl6InputPk.broadPeak.gz MEL ChipSeq Pol2-4H8 Peaks broadPeak PSU-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodePsuTfbs/wgEncodePsuTfbsMelPol24h8UImmortalC57bl6InputRepPeaksRep1.broadPeak.gz MEL ChipSeq Pol2-4H8 RepPeaks 1 broadPeak PSU-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodePsuTfbs/wgEncodePsuTfbsMelPol24h8UImmortalC57bl6InputRepPeaksRep2.broadPeak.gz MEL ChipSeq Pol2-4H8 RepPeaks 2 broadPeak PSU-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodePsuTfbs/wgEncodePsuTfbsMelPol24h8UImmortalC57bl6InputRepSignalRep1.bigWig MEL ChipSeq Pol2-4H8 RepSignal 1 bigWig PSU-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodePsuTfbs/wgEncodePsuTfbsMelPol24h8UImmortalC57bl6InputRepSignalRep2.bigWig MEL ChipSeq Pol2-4H8 RepSignal 2 bigWig PSU-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodePsuTfbs/wgEncodePsuTfbsMelPol24h8UImmortalC57bl6InputSig.bigWig MEL ChipSeq Pol2-4H8 Signal bigWig PSU-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodePsuTfbs/wgEncodePsuTfbsMelTal1UImmortalC57bl6InputAlnRep1.bam MEL ChipSeq TAL1_(SC-12984) Alignments 1 bam PSU-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodePsuTfbs/wgEncodePsuTfbsMelTal1UImmortalC57bl6InputAlnRep2.bam MEL ChipSeq TAL1_(SC-12984) Alignments 2 bam PSU-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodePsuTfbs/wgEncodePsuTfbsMelTal1UImmortalC57bl6InputPk.broadPeak.gz MEL ChipSeq TAL1_(SC-12984) Peaks broadPeak PSU-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodePsuTfbs/wgEncodePsuTfbsMelTal1UImmortalC57bl6InputRepPeaksRep1.broadPeak.gz MEL ChipSeq TAL1_(SC-12984) RepPeaks 1 broadPeak PSU-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodePsuTfbs/wgEncodePsuTfbsMelTal1UImmortalC57bl6InputRepPeaksRep2.broadPeak.gz MEL ChipSeq TAL1_(SC-12984) RepPeaks 2 broadPeak PSU-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodePsuTfbs/wgEncodePsuTfbsMelTal1UImmortalC57bl6InputRepSignalRep1.bigWig MEL ChipSeq TAL1_(SC-12984) RepSignal 1 bigWig PSU-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodePsuTfbs/wgEncodePsuTfbsMelTal1UImmortalC57bl6InputRepSignalRep2.bigWig MEL ChipSeq TAL1_(SC-12984) RepSignal 2 bigWig PSU-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodePsuTfbs/wgEncodePsuTfbsMelTal1UImmortalC57bl6InputSig.bigWig MEL ChipSeq TAL1_(SC-12984) Signal bigWig PSU-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeSydhHist/wgEncodeSydhHistCh12H3k04me3IggyaleAlnRep1.bam CH12 ChipSeq H3K4me3 Alignments 1 bam Yale-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeSydhHist/wgEncodeSydhHistCh12H3k04me3IggyaleAlnRep2.bam CH12 ChipSeq H3K4me3 Alignments 2 bam Yale-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeSydhHist/wgEncodeSydhHistCh12H3k4me3IggyalePk.narrowPeak.gz CH12 ChipSeq H3K4me3 Peaks narrowPeak Yale-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeSydhHist/wgEncodeSydhHistCh12H3k4me3IggyaleSig.bigWig CH12 ChipSeq H3K4me3 Signal bigWig Yale-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeSydhHist/wgEncodeSydhHistCh12InputIggyaleAlnRep1.bam CH12 ChipSeq Input Alignments 1 bam Yale-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeSydhHist/wgEncodeSydhHistCh12InputIggyaleSig.bigWig CH12 ChipSeq Input Signal bigWig Yale-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeSydhHist/wgEncodeSydhHistEse14H3k04me1StdAlnRep1.bam ES-E14 ChipSeq H3K4me1 Alignments 1 bam Stanford-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeSydhHist/wgEncodeSydhHistEse14H3k04me1StdAlnRep2.bam ES-E14 ChipSeq H3K4me1 Alignments 2 bam Stanford-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeSydhHist/wgEncodeSydhHistEse14H3k04me1StdPk.narrowPeak.gz ES-E14 ChipSeq H3K4me1 Peaks narrowPeak Stanford-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeSydhHist/wgEncodeSydhHistEse14H3k04me1StdSig.bigWig ES-E14 ChipSeq H3K4me1 Signal bigWig Stanford-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeSydhHist/wgEncodeSydhHistEse14H3k04me3StdAlnRep1.bam ES-E14 ChipSeq H3K4me3 Alignments 1 bam Stanford-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeSydhHist/wgEncodeSydhHistEse14H3k04me3StdAlnRep2.bam ES-E14 ChipSeq H3K4me3 Alignments 2 bam Stanford-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeSydhHist/wgEncodeSydhHistEse14H3k04me3StdPk.narrowPeak.gz ES-E14 ChipSeq H3K4me3 Peaks narrowPeak Stanford-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeSydhHist/wgEncodeSydhHistEse14H3k04me3StdSig.bigWig ES-E14 ChipSeq H3K4me3 Signal bigWig Stanford-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeSydhHist/wgEncodeSydhHistEse14H3k09me3StdAlnRep1.bam ES-E14 ChipSeq H3K9me3 Alignments 1 bam Stanford-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeSydhHist/wgEncodeSydhHistEse14H3k09me3StdAlnRep2.bam ES-E14 ChipSeq H3K9me3 Alignments 2 bam Stanford-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeSydhHist/wgEncodeSydhHistEse14H3k09me3StdPk.narrowPeak.gz ES-E14 ChipSeq H3K9me3 Peaks narrowPeak Stanford-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeSydhHist/wgEncodeSydhHistEse14H3k09me3StdSig.bigWig ES-E14 ChipSeq H3K9me3 Signal bigWig Stanford-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeSydhHist/wgEncodeSydhHistEse14InputStdAlnRep1.bam ES-E14 ChipSeq Input Alignments 1 bam Stanford-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeSydhHist/wgEncodeSydhHistEse14InputStdSig.bigWig ES-E14 ChipSeq Input Signal bigWig Stanford-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeSydhHist/wgEncodeSydhHistMelH3k04me1Dm2p5dStdAlnRep1.bam MEL ChipSeq H3K4me1 Alignments 1 bam Stanford-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeSydhHist/wgEncodeSydhHistMelH3k04me1Dm2p5dStdAlnRep2.bam MEL ChipSeq H3K4me1 Alignments 2 bam Stanford-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeSydhHist/wgEncodeSydhHistMelH3k04me1Dm2p5dStdPk.narrowPeak.gz MEL ChipSeq H3K4me1 Peaks narrowPeak Stanford-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeSydhHist/wgEncodeSydhHistMelH3k04me1Dm2p5dStdSig.bigWig MEL ChipSeq H3K4me1 Signal bigWig Stanford-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeSydhHist/wgEncodeSydhHistMelH3k04me1IggrabAlnRep1.bam MEL ChipSeq H3K4me1 Alignments 1 bam Stanford-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeSydhHist/wgEncodeSydhHistMelH3k04me1IggrabAlnRep2.bam MEL ChipSeq H3K4me1 Alignments 2 bam Stanford-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeSydhHist/wgEncodeSydhHistMelH3k04me1IggrabPk.narrowPeak.gz MEL ChipSeq H3K4me1 Peaks narrowPeak Stanford-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeSydhHist/wgEncodeSydhHistMelH3k04me1IggrabSig.bigWig MEL ChipSeq H3K4me1 Signal bigWig Stanford-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeSydhHist/wgEncodeSydhHistMelH3k04me3Dm2p5dIggyaleAlnRep1.bam MEL ChipSeq H3K4me3 Alignments 1 bam Yale-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeSydhHist/wgEncodeSydhHistMelH3k04me3Dm2p5dIggyaleAlnRep2.bam MEL ChipSeq H3K4me3 Alignments 2 bam Yale-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeSydhHist/wgEncodeSydhHistMelH3k04me3Dm2p5dIggyalePk.narrowPeak.gz MEL ChipSeq H3K4me3 Peaks narrowPeak Yale-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeSydhHist/wgEncodeSydhHistMelH3k04me3Dm2p5dIggyaleSig.bigWig MEL ChipSeq H3K4me3 Signal bigWig Yale-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeSydhHist/wgEncodeSydhHistMelH3k04me3Dm2p5dStdAlnRep1.bam MEL ChipSeq H3K4me3 Alignments 1 bam Stanford-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeSydhHist/wgEncodeSydhHistMelH3k04me3Dm2p5dStdAlnRep2.bam MEL ChipSeq H3K4me3 Alignments 2 bam Stanford-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeSydhHist/wgEncodeSydhHistMelH3k04me3Dm2p5dStdPk.narrowPeak.gz MEL ChipSeq H3K4me3 Peaks narrowPeak Stanford-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeSydhHist/wgEncodeSydhHistMelH3k04me3Dm2p5dStdSig.bigWig MEL ChipSeq H3K4me3 Signal bigWig Stanford-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeSydhHist/wgEncodeSydhHistMelH3k04me3IggrabAlnRep1.bam MEL ChipSeq H3K4me3 Alignments 1 bam Stanford-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeSydhHist/wgEncodeSydhHistMelH3k04me3IggrabAlnRep2.bam MEL ChipSeq H3K4me3 Alignments 2 bam Stanford-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeSydhHist/wgEncodeSydhHistMelH3k04me3IggrabPk.narrowPeak.gz MEL ChipSeq H3K4me3 Peaks narrowPeak Stanford-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeSydhHist/wgEncodeSydhHistMelH3k04me3IggrabSig.bigWig MEL ChipSeq H3K4me3 Signal bigWig Stanford-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeSydhHist/wgEncodeSydhHistMelH3k04me3IggyaleAlnRep1.bam MEL ChipSeq H3K4me3 Alignments 1 bam Yale-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeSydhHist/wgEncodeSydhHistMelH3k04me3IggyaleAlnRep2.bam MEL ChipSeq H3K4me3 Alignments 2 bam Yale-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeSydhHist/wgEncodeSydhHistMelH3k04me3IggyalePk.narrowPeak.gz MEL ChipSeq H3K4me3 Peaks narrowPeak Yale-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeSydhHist/wgEncodeSydhHistMelH3k09me3Dm2p5dStdAlnRep1.bam MEL ChipSeq H3K9me3 Alignments 1 bam Stanford-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeSydhHist/wgEncodeSydhHistMelH3k09me3Dm2p5dStdAlnRep2.bam MEL ChipSeq H3K9me3 Alignments 2 bam Stanford-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeSydhHist/wgEncodeSydhHistMelH3k09me3Dm2p5dStdPk.narrowPeak.gz MEL ChipSeq H3K9me3 Peaks narrowPeak Stanford-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeSydhHist/wgEncodeSydhHistMelH3k09me3Dm2p5dStdSig.bigWig MEL ChipSeq H3K9me3 Signal bigWig Stanford-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeSydhHist/wgEncodeSydhHistMelH3k09me3IggrabAlnRep1.bam MEL ChipSeq H3K9me3 Alignments 1 bam Stanford-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeSydhHist/wgEncodeSydhHistMelH3k09me3IggrabAlnRep2.bam MEL ChipSeq H3K9me3 Alignments 2 bam Stanford-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeSydhHist/wgEncodeSydhHistMelH3k09me3IggrabPk.narrowPeak.gz MEL ChipSeq H3K9me3 Peaks narrowPeak Stanford-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeSydhHist/wgEncodeSydhHistMelH3k09me3IggrabSig.bigWig MEL ChipSeq H3K9me3 Signal bigWig Stanford-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeSydhHist/wgEncodeSydhHistMelH3k27acIggrabAlnRep1.bam MEL ChipSeq H3K27ac Alignments 1 bam Stanford-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeSydhHist/wgEncodeSydhHistMelH3k27acIggrabAlnRep2.bam MEL ChipSeq H3K27ac Alignments 2 bam Stanford-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeSydhHist/wgEncodeSydhHistMelH3k27acIggrabPk.narrowPeak.gz MEL ChipSeq H3K27ac Peaks narrowPeak Stanford-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeSydhHist/wgEncodeSydhHistMelH3k27acIggrabSig.bigWig MEL ChipSeq H3K27ac Signal bigWig Stanford-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeSydhHist/wgEncodeSydhHistMelH3k27me3bDm2p5dStdAlnRep1.bam MEL ChipSeq H3K27me3B Alignments 1 bam Stanford-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeSydhHist/wgEncodeSydhHistMelH3k27me3bDm2p5dStdAlnRep2.bam MEL ChipSeq H3K27me3B Alignments 2 bam Stanford-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeSydhHist/wgEncodeSydhHistMelH3k27me3bDm2p5dStdPk.narrowPeak.gz MEL ChipSeq H3K27me3B Peaks narrowPeak Stanford-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeSydhHist/wgEncodeSydhHistMelH3k27me3bDm2p5dStdSig.bigWig MEL ChipSeq H3K27me3B Signal bigWig Stanford-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeSydhHist/wgEncodeSydhHistMelH3k36me3bDm2p5dStdAlnRep1.bam MEL ChipSeq H3K36me3B Alignments 1 bam Stanford-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeSydhHist/wgEncodeSydhHistMelH3k36me3bDm2p5dStdAlnRep2.bam MEL ChipSeq H3K36me3B Alignments 2 bam Stanford-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeSydhHist/wgEncodeSydhHistMelH3k36me3bDm2p5dStdPk.narrowPeak.gz MEL ChipSeq H3K36me3B Peaks narrowPeak Stanford-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeSydhHist/wgEncodeSydhHistMelH3k36me3bDm2p5dStdSig.bigWig MEL ChipSeq H3K36me3B Signal bigWig Stanford-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeSydhHist/wgEncodeSydhHistMelH3k4me3IggyaleSig.bigWig MEL ChipSeq H3K4me3 Signal bigWig Yale-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeSydhHist/wgEncodeSydhHistMelInputDm2p5dIggyaleAlnRep1.bam MEL ChipSeq Input Alignments 1 bam Yale-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeSydhHist/wgEncodeSydhHistMelInputDm2p5dIggyaleSig.bigWig MEL ChipSeq Input Signal bigWig Yale-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeSydhHist/wgEncodeSydhHistMelInputDm2p5dStdAlnRep1.bam MEL ChipSeq Input Alignments 1 bam Stanford-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeSydhHist/wgEncodeSydhHistMelInputDm2p5dStdSig.bigWig MEL ChipSeq Input Signal bigWig Stanford-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeSydhHist/wgEncodeSydhHistMelInputIggrabAlnRep1.bam MEL ChipSeq Input Alignments 1 bam Stanford-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeSydhHist/wgEncodeSydhHistMelInputIggrabSig.bigWig MEL ChipSeq Input Signal bigWig Stanford-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeSydhHist/wgEncodeSydhHistMelInputIggyaleAlnRep1.bam MEL ChipSeq Input Alignments 1 bam Yale-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeSydhHist/wgEncodeSydhHistMelInputIggyaleSig.bigWig MEL ChipSeq Input Signal bigWig Yale-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeSydhRnaSeq/wgEncodeSydhRnaSeqCh12RibozerogR2x101dAlnRep1.bam CH12 RnaSeq Alignments 1 bam Stanford-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeSydhRnaSeq/wgEncodeSydhRnaSeqCh12RibozerogR2x101dAlnRep2.bam CH12 RnaSeq Alignments 2 bam Stanford-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeSydhRnaSeq/wgEncodeSydhRnaSeqEse14RibozerogR2x101dAlnRep1.bam ES-E14 RnaSeq Alignments 1 bam Stanford-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeSydhRnaSeq/wgEncodeSydhRnaSeqEse14RibozerogR2x101dAlnRep2.bam ES-E14 RnaSeq Alignments 2 bam Stanford-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeSydhRnaSeq/wgEncodeSydhRnaSeqMelDm2p5dRibozerogR2x101dAlnRep1.bam MEL RnaSeq Alignments 1 bam Stanford-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeSydhRnaSeq/wgEncodeSydhRnaSeqMelDm2p5dRibozerogR2x101dAlnRep2.bam MEL RnaSeq Alignments 2 bam Stanford-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeSydhRnaSeq/wgEncodeSydhRnaSeqMelRibozerogR2x101dAlnRep1.bam MEL RnaSeq Alignments 1 bam Stanford-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeSydhRnaSeq/wgEncodeSydhRnaSeqMelRibozerogR2x101dAlnRep2.bam MEL RnaSeq Alignments 2 bam Stanford-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeSydhTfbs/wgEncodeSydhTfbsCh12Bhlhe40nb100IggrabAlnRep1.bam CH12 ChipSeq BHLHE40_(NB100-1800) Alignments 1 bam Stanford-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeSydhTfbs/wgEncodeSydhTfbsCh12Bhlhe40nb100IggrabAlnRep2.bam CH12 ChipSeq BHLHE40_(NB100-1800) Alignments 2 bam Stanford-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeSydhTfbs/wgEncodeSydhTfbsCh12Bhlhe40nb100IggrabPk.narrowPeak.gz CH12 ChipSeq BHLHE40_(NB100-1800) Peaks narrowPeak Stanford-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeSydhTfbs/wgEncodeSydhTfbsCh12Bhlhe40nb100IggrabSig.bigWig CH12 ChipSeq BHLHE40_(NB100-1800) Signal bigWig Stanford-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeSydhTfbs/wgEncodeSydhTfbsCh12Chd1nb10060411IggrabAlnRep1.bam CH12 ChipSeq CHD1_(NB100-60411) Alignments 1 bam Stanford-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeSydhTfbs/wgEncodeSydhTfbsCh12Chd1nb10060411IggrabAlnRep2.bam CH12 ChipSeq CHD1_(NB100-60411) Alignments 2 bam Stanford-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeSydhTfbs/wgEncodeSydhTfbsCh12Chd1nb10060411IggrabPk.narrowPeak.gz CH12 ChipSeq CHD1_(NB100-60411) Peaks narrowPeak Stanford-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeSydhTfbs/wgEncodeSydhTfbsCh12Chd1nb10060411IggrabSig.bigWig CH12 ChipSeq CHD1_(NB100-60411) Signal bigWig Stanford-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeSydhTfbs/wgEncodeSydhTfbsCh12Chd2ab68301IggrabAlnRep1.bam CH12 ChipSeq CHD2_(AB68301) Alignments 1 bam Stanford-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeSydhTfbs/wgEncodeSydhTfbsCh12Chd2ab68301IggrabAlnRep2.bam CH12 ChipSeq CHD2_(AB68301) Alignments 2 bam Stanford-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeSydhTfbs/wgEncodeSydhTfbsCh12Chd2ab68301IggrabPk.narrowPeak.gz CH12 ChipSeq CHD2_(AB68301) Peaks narrowPeak Stanford-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeSydhTfbs/wgEncodeSydhTfbsCh12Chd2ab68301IggrabSig.bigWig CH12 ChipSeq CHD2_(AB68301) Signal bigWig Stanford-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeSydhTfbs/wgEncodeSydhTfbsCh12CjunIggrabAlnRep1.bam CH12 ChipSeq c-Jun Alignments 1 bam Stanford-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeSydhTfbs/wgEncodeSydhTfbsCh12CjunIggrabAlnRep2.bam CH12 ChipSeq c-Jun Alignments 2 bam Stanford-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeSydhTfbs/wgEncodeSydhTfbsCh12CjunIggrabPk.narrowPeak.gz CH12 ChipSeq c-Jun Peaks narrowPeak Stanford-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeSydhTfbs/wgEncodeSydhTfbsCh12CjunIggrabSig.bigWig CH12 ChipSeq c-Jun Signal bigWig Stanford-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeSydhTfbs/wgEncodeSydhTfbsCh12CmycIggrabAlnRep1.bam CH12 ChipSeq c-Myc Alignments 1 bam Stanford-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeSydhTfbs/wgEncodeSydhTfbsCh12CmycIggrabAlnRep2.bam CH12 ChipSeq c-Myc Alignments 2 bam Stanford-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeSydhTfbs/wgEncodeSydhTfbsCh12CmycIggrabPk.narrowPeak.gz CH12 ChipSeq c-Myc Peaks narrowPeak Stanford-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeSydhTfbs/wgEncodeSydhTfbsCh12CmycIggrabSig.bigWig CH12 ChipSeq c-Myc Signal bigWig Stanford-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeSydhTfbs/wgEncodeSydhTfbsCh12Corestsc30189IggrabAlnRep1.bam CH12 ChipSeq COREST_(sc-30189) Alignments 1 bam Stanford-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeSydhTfbs/wgEncodeSydhTfbsCh12Corestsc30189IggrabAlnRep2.bam CH12 ChipSeq COREST_(sc-30189) Alignments 2 bam Stanford-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeSydhTfbs/wgEncodeSydhTfbsCh12Corestsc30189IggrabPk.narrowPeak.gz CH12 ChipSeq COREST_(sc-30189) Peaks narrowPeak Stanford-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeSydhTfbs/wgEncodeSydhTfbsCh12Corestsc30189IggrabSig.bigWig CH12 ChipSeq COREST_(sc-30189) Signal bigWig Stanford-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeSydhTfbs/wgEncodeSydhTfbsCh12CtcfbIggrabAlnRep1.bam CH12 ChipSeq CTCF_(SC-15914) Alignments 1 bam Stanford-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeSydhTfbs/wgEncodeSydhTfbsCh12CtcfbIggrabAlnRep2.bam CH12 ChipSeq CTCF_(SC-15914) Alignments 2 bam Stanford-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeSydhTfbs/wgEncodeSydhTfbsCh12CtcfbIggrabPk.narrowPeak.gz CH12 ChipSeq CTCF_(SC-15914) Peaks narrowPeak Stanford-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeSydhTfbs/wgEncodeSydhTfbsCh12CtcfbIggrabSig.bigWig CH12 ChipSeq CTCF_(SC-15914) Signal bigWig Stanford-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeSydhTfbs/wgEncodeSydhTfbsCh12E2f4IggrabAlnRep1.bam CH12 ChipSeq E2F4 Alignments 1 bam Stanford-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeSydhTfbs/wgEncodeSydhTfbsCh12E2f4IggrabAlnRep2.bam CH12 ChipSeq E2F4 Alignments 2 bam Stanford-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeSydhTfbs/wgEncodeSydhTfbsCh12E2f4IggrabPk.narrowPeak.gz CH12 ChipSeq E2F4 Peaks narrowPeak Stanford-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeSydhTfbs/wgEncodeSydhTfbsCh12E2f4IggrabSig.bigWig CH12 ChipSeq E2F4 Signal bigWig Stanford-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeSydhTfbs/wgEncodeSydhTfbsCh12Ets1IggrabAlnRep1.bam CH12 ChipSeq ETS1 Alignments 1 bam Stanford-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeSydhTfbs/wgEncodeSydhTfbsCh12Ets1IggrabAlnRep2.bam CH12 ChipSeq ETS1 Alignments 2 bam Stanford-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeSydhTfbs/wgEncodeSydhTfbsCh12Ets1IggrabPk.narrowPeak.gz CH12 ChipSeq ETS1 Peaks narrowPeak Stanford-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeSydhTfbs/wgEncodeSydhTfbsCh12Ets1IggrabSig.bigWig CH12 ChipSeq ETS1 Signal bigWig Stanford-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeSydhTfbs/wgEncodeSydhTfbsCh12Gcn5IggrabAlnRep1.bam CH12 ChipSeq GCN5 Alignments 1 bam Stanford-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeSydhTfbs/wgEncodeSydhTfbsCh12Gcn5IggrabAlnRep2.bam CH12 ChipSeq GCN5 Alignments 2 bam Stanford-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeSydhTfbs/wgEncodeSydhTfbsCh12Gcn5IggrabPk.narrowPeak.gz CH12 ChipSeq GCN5 Peaks narrowPeak Stanford-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeSydhTfbs/wgEncodeSydhTfbsCh12Gcn5IggrabSig.bigWig CH12 ChipSeq GCN5 Signal bigWig Stanford-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeSydhTfbs/wgEncodeSydhTfbsCh12Hcfc1nb10068209IggrabAlnRep1.bam CH12 ChipSeq HCFC1_(NB100-68209) Alignments 1 bam Stanford-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeSydhTfbs/wgEncodeSydhTfbsCh12Hcfc1nb10068209IggrabAlnRep2.bam CH12 ChipSeq HCFC1_(NB100-68209) Alignments 2 bam Stanford-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeSydhTfbs/wgEncodeSydhTfbsCh12Hcfc1nb10068209IggrabPk.narrowPeak.gz CH12 ChipSeq HCFC1_(NB100-68209) Peaks narrowPeak Stanford-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeSydhTfbs/wgEncodeSydhTfbsCh12Hcfc1nb10068209IggrabSig.bigWig CH12 ChipSeq HCFC1_(NB100-68209) Signal bigWig Stanford-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeSydhTfbs/wgEncodeSydhTfbsCh12InputIggmusAlnRep1.bam CH12 ChipSeq Input Alignments 1 bam Stanford-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeSydhTfbs/wgEncodeSydhTfbsCh12InputIggmusSig.bigWig CH12 ChipSeq Input Signal bigWig Stanford-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeSydhTfbs/wgEncodeSydhTfbsCh12InputIggrabAlnRep1.bam CH12 ChipSeq Input Alignments 1 bam Stanford-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeSydhTfbs/wgEncodeSydhTfbsCh12InputIggrabSig.bigWig CH12 ChipSeq Input Signal bigWig Stanford-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeSydhTfbs/wgEncodeSydhTfbsCh12JundIggrabAlnRep1.bam CH12 ChipSeq JunD Alignments 1 bam Stanford-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeSydhTfbs/wgEncodeSydhTfbsCh12JundIggrabAlnRep2.bam CH12 ChipSeq JunD Alignments 2 bam Stanford-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeSydhTfbs/wgEncodeSydhTfbsCh12JundIggrabPk.narrowPeak.gz CH12 ChipSeq JunD Peaks narrowPeak Stanford-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeSydhTfbs/wgEncodeSydhTfbsCh12JundIggrabSig.bigWig CH12 ChipSeq JunD Signal bigWig Stanford-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeSydhTfbs/wgEncodeSydhTfbsCh12Mafkab50322IggrabAlnRep1.bam CH12 ChipSeq MafK_(ab50322) Alignments 1 bam Stanford-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeSydhTfbs/wgEncodeSydhTfbsCh12Mafkab50322IggrabAlnRep2.bam CH12 ChipSeq MafK_(ab50322) Alignments 2 bam Stanford-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeSydhTfbs/wgEncodeSydhTfbsCh12Mafkab50322IggrabPk.narrowPeak.gz CH12 ChipSeq MafK_(ab50322) Peaks narrowPeak Stanford-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeSydhTfbs/wgEncodeSydhTfbsCh12Mafkab50322IggrabSig.bigWig CH12 ChipSeq MafK_(ab50322) Signal bigWig Stanford-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeSydhTfbs/wgEncodeSydhTfbsCh12MaxIggrabAlnRep1.bam CH12 ChipSeq Max Alignments 1 bam Stanford-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeSydhTfbs/wgEncodeSydhTfbsCh12MaxIggrabAlnRep2.bam CH12 ChipSeq Max Alignments 2 bam Stanford-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeSydhTfbs/wgEncodeSydhTfbsCh12MaxIggrabPk.narrowPeak.gz CH12 ChipSeq Max Peaks narrowPeak Stanford-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeSydhTfbs/wgEncodeSydhTfbsCh12MaxIggrabSig.bigWig CH12 ChipSeq Max Signal bigWig Stanford-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeSydhTfbs/wgEncodeSydhTfbsCh12Mazab85725IggrabAlnRep1.bam CH12 ChipSeq MAZ_(ab85725) Alignments 1 bam Stanford-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeSydhTfbs/wgEncodeSydhTfbsCh12Mazab85725IggrabAlnRep2.bam CH12 ChipSeq MAZ_(ab85725) Alignments 2 bam Stanford-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeSydhTfbs/wgEncodeSydhTfbsCh12Mazab85725IggrabPk.narrowPeak.gz CH12 ChipSeq MAZ_(ab85725) Peaks narrowPeak Stanford-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeSydhTfbs/wgEncodeSydhTfbsCh12Mazab85725IggrabSig.bigWig CH12 ChipSeq MAZ_(ab85725) Signal bigWig Stanford-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeSydhTfbs/wgEncodeSydhTfbsCh12Mxi1af4185IggrabAlnRep1.bam CH12 ChipSeq Mxi1_(AF4185) Alignments 1 bam Stanford-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeSydhTfbs/wgEncodeSydhTfbsCh12Mxi1af4185IggrabAlnRep2.bam CH12 ChipSeq Mxi1_(AF4185) Alignments 2 bam Stanford-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeSydhTfbs/wgEncodeSydhTfbsCh12Mxi1af4185IggrabPk.narrowPeak.gz CH12 ChipSeq Mxi1_(AF4185) Peaks narrowPeak Stanford-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeSydhTfbs/wgEncodeSydhTfbsCh12Mxi1af4185IggrabSig.bigWig CH12 ChipSeq Mxi1_(AF4185) Signal bigWig Stanford-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeSydhTfbs/wgEncodeSydhTfbsCh12NelfeIggrabAlnRep1.bam CH12 ChipSeq NELFe Alignments 1 bam Stanford-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeSydhTfbs/wgEncodeSydhTfbsCh12NelfeIggrabAlnRep2.bam CH12 ChipSeq NELFe Alignments 2 bam Stanford-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeSydhTfbs/wgEncodeSydhTfbsCh12NelfeIggrabPk.narrowPeak.gz CH12 ChipSeq NELFe Peaks narrowPeak Stanford-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeSydhTfbs/wgEncodeSydhTfbsCh12NelfeIggrabSig.bigWig CH12 ChipSeq NELFe Signal bigWig Stanford-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeSydhTfbs/wgEncodeSydhTfbsCh12Nrf2IggrabAlnRep1.bam CH12 ChipSeq Nrf2 Alignments 1 bam Stanford-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeSydhTfbs/wgEncodeSydhTfbsCh12Nrf2IggrabAlnRep2.bam CH12 ChipSeq Nrf2 Alignments 2 bam Stanford-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeSydhTfbs/wgEncodeSydhTfbsCh12Nrf2IggrabPk.narrowPeak.gz CH12 ChipSeq Nrf2 Peaks narrowPeak Stanford-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeSydhTfbs/wgEncodeSydhTfbsCh12Nrf2IggrabSig.bigWig CH12 ChipSeq Nrf2 Signal bigWig Stanford-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeSydhTfbs/wgEncodeSydhTfbsCh12P300sc584IggrabAlnRep1.bam CH12 ChipSeq p300_(SC-584) Alignments 1 bam Stanford-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeSydhTfbs/wgEncodeSydhTfbsCh12P300sc584IggrabAlnRep2.bam CH12 ChipSeq p300_(SC-584) Alignments 2 bam Stanford-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeSydhTfbs/wgEncodeSydhTfbsCh12P300sc584IggrabPk.narrowPeak.gz CH12 ChipSeq p300_(SC-584) Peaks narrowPeak Stanford-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeSydhTfbs/wgEncodeSydhTfbsCh12P300sc584IggrabSig.bigWig CH12 ChipSeq p300_(SC-584) Signal bigWig Stanford-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeSydhTfbs/wgEncodeSydhTfbsCh12Pol2IggmusAlnRep1.bam CH12 ChipSeq Pol2 Alignments 1 bam Stanford-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeSydhTfbs/wgEncodeSydhTfbsCh12Pol2IggmusAlnRep2.bam CH12 ChipSeq Pol2 Alignments 2 bam Stanford-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeSydhTfbs/wgEncodeSydhTfbsCh12Pol2IggmusPk.narrowPeak.gz CH12 ChipSeq Pol2 Peaks narrowPeak Stanford-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeSydhTfbs/wgEncodeSydhTfbsCh12Pol2IggmusSig.bigWig CH12 ChipSeq Pol2 Signal bigWig Stanford-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeSydhTfbs/wgEncodeSydhTfbsCh12Pol2s2IggrabAlnRep1.bam CH12 ChipSeq Pol2(phosphoS2) Alignments 1 bam Stanford-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeSydhTfbs/wgEncodeSydhTfbsCh12Pol2s2IggrabAlnRep2.bam CH12 ChipSeq Pol2(phosphoS2) Alignments 2 bam Stanford-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeSydhTfbs/wgEncodeSydhTfbsCh12Pol2s2IggrabPk.narrowPeak.gz CH12 ChipSeq Pol2(phosphoS2) Peaks narrowPeak Stanford-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeSydhTfbs/wgEncodeSydhTfbsCh12Pol2s2IggrabSig.bigWig CH12 ChipSeq Pol2(phosphoS2) Signal bigWig Stanford-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeSydhTfbs/wgEncodeSydhTfbsCh12Rad21IggrabAlnRep1.bam CH12 ChipSeq Rad21 Alignments 1 bam Stanford-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeSydhTfbs/wgEncodeSydhTfbsCh12Rad21IggrabAlnRep2.bam CH12 ChipSeq Rad21 Alignments 2 bam Stanford-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeSydhTfbs/wgEncodeSydhTfbsCh12Rad21IggrabPk.narrowPeak.gz CH12 ChipSeq Rad21 Peaks narrowPeak Stanford-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeSydhTfbs/wgEncodeSydhTfbsCh12Rad21IggrabSig.bigWig CH12 ChipSeq Rad21 Signal bigWig Stanford-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeSydhTfbs/wgEncodeSydhTfbsCh12Sin3anb6001263IggrabAlnRep1.bam CH12 ChipSeq SIN3A_(NB600-1263) Alignments 1 bam Stanford-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeSydhTfbs/wgEncodeSydhTfbsCh12Sin3anb6001263IggrabAlnRep2.bam CH12 ChipSeq SIN3A_(NB600-1263) Alignments 2 bam Stanford-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeSydhTfbs/wgEncodeSydhTfbsCh12Sin3anb6001263IggrabPk.narrowPeak.gz CH12 ChipSeq SIN3A_(NB600-1263) Peaks narrowPeak Stanford-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeSydhTfbs/wgEncodeSydhTfbsCh12Sin3anb6001263IggrabSig.bigWig CH12 ChipSeq SIN3A_(NB600-1263) Signal bigWig Stanford-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeSydhTfbs/wgEncodeSydhTfbsCh12Smc3ab9263IggrabAlnRep1.bam CH12 ChipSeq SMC3_(ab9263) Alignments 1 bam Stanford-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeSydhTfbs/wgEncodeSydhTfbsCh12Smc3ab9263IggrabAlnRep2.bam CH12 ChipSeq SMC3_(ab9263) Alignments 2 bam Stanford-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeSydhTfbs/wgEncodeSydhTfbsCh12Smc3ab9263IggrabPk.narrowPeak.gz CH12 ChipSeq SMC3_(ab9263) Peaks narrowPeak Stanford-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeSydhTfbs/wgEncodeSydhTfbsCh12Smc3ab9263IggrabSig.bigWig CH12 ChipSeq SMC3_(ab9263) Signal bigWig Stanford-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeSydhTfbs/wgEncodeSydhTfbsCh12TbpIggmusAlnRep1.bam CH12 ChipSeq TBP Alignments 1 bam Stanford-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeSydhTfbs/wgEncodeSydhTfbsCh12TbpIggmusAlnRep2.bam CH12 ChipSeq TBP Alignments 2 bam Stanford-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeSydhTfbs/wgEncodeSydhTfbsCh12TbpIggmusPk.narrowPeak.gz CH12 ChipSeq TBP Peaks narrowPeak Stanford-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeSydhTfbs/wgEncodeSydhTfbsCh12TbpIggmusSig.bigWig CH12 ChipSeq TBP Signal bigWig Stanford-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeSydhTfbs/wgEncodeSydhTfbsCh12Ubfsc13125IggrabAlnRep1.bam CH12 ChipSeq UBF_(sc-13125) Alignments 1 bam Stanford-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeSydhTfbs/wgEncodeSydhTfbsCh12Ubfsc13125IggrabAlnRep2.bam CH12 ChipSeq UBF_(sc-13125) Alignments 2 bam Stanford-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeSydhTfbs/wgEncodeSydhTfbsCh12Ubfsc13125IggrabPk.narrowPeak.gz CH12 ChipSeq UBF_(sc-13125) Peaks narrowPeak Stanford-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeSydhTfbs/wgEncodeSydhTfbsCh12Ubfsc13125IggrabSig.bigWig CH12 ChipSeq UBF_(sc-13125) Signal bigWig Stanford-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeSydhTfbs/wgEncodeSydhTfbsCh12Usf2IggmusAlnRep1.bam CH12 ChipSeq USF2 Alignments 1 bam Stanford-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeSydhTfbs/wgEncodeSydhTfbsCh12Usf2IggmusAlnRep2.bam CH12 ChipSeq USF2 Alignments 2 bam Stanford-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeSydhTfbs/wgEncodeSydhTfbsCh12Usf2IggmusPk.narrowPeak.gz CH12 ChipSeq USF2 Peaks narrowPeak Stanford-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeSydhTfbs/wgEncodeSydhTfbsCh12Usf2IggmusSig.bigWig CH12 ChipSeq USF2 Signal bigWig Stanford-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeSydhTfbs/wgEncodeSydhTfbsCh12Zc3h11anb10074650IggrabAlnRep1.bam CH12 ChipSeq ZC3H11A_(NB100-74650) Alignments 1 bam Stanford-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeSydhTfbs/wgEncodeSydhTfbsCh12Zc3h11anb10074650IggrabAlnRep2.bam CH12 ChipSeq ZC3H11A_(NB100-74650) Alignments 2 bam Stanford-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeSydhTfbs/wgEncodeSydhTfbsCh12Zc3h11anb10074650IggrabPk.narrowPeak.gz CH12 ChipSeq ZC3H11A_(NB100-74650) Peaks narrowPeak Stanford-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeSydhTfbs/wgEncodeSydhTfbsCh12Zc3h11anb10074650IggrabSig.bigWig CH12 ChipSeq ZC3H11A_(NB100-74650) Signal bigWig Stanford-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeSydhTfbs/wgEncodeSydhTfbsCh12Zkscan1hpa006672IggrabAlnRep1.bam CH12 ChipSeq ZKSCAN1_(HPA006672) Alignments 1 bam Stanford-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeSydhTfbs/wgEncodeSydhTfbsCh12Zkscan1hpa006672IggrabAlnRep2.bam CH12 ChipSeq ZKSCAN1_(HPA006672) Alignments 2 bam Stanford-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeSydhTfbs/wgEncodeSydhTfbsCh12Zkscan1hpa006672IggrabPk.narrowPeak.gz CH12 ChipSeq ZKSCAN1_(HPA006672) Peaks narrowPeak Stanford-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeSydhTfbs/wgEncodeSydhTfbsCh12Zkscan1hpa006672IggrabSig.bigWig CH12 ChipSeq ZKSCAN1_(HPA006672) Signal bigWig Stanford-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeSydhTfbs/wgEncodeSydhTfbsCh12Znf384hpa004051IggrabAlnRep1.bam CH12 ChipSeq ZNF384_(HPA004051) Alignments 1 bam Stanford-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeSydhTfbs/wgEncodeSydhTfbsCh12Znf384hpa004051IggrabAlnRep2.bam CH12 ChipSeq ZNF384_(HPA004051) Alignments 2 bam Stanford-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeSydhTfbs/wgEncodeSydhTfbsCh12Znf384hpa004051IggrabPk.narrowPeak.gz CH12 ChipSeq ZNF384_(HPA004051) Peaks narrowPeak Stanford-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeSydhTfbs/wgEncodeSydhTfbsCh12Znf384hpa004051IggrabSig.bigWig CH12 ChipSeq ZNF384_(HPA004051) Signal bigWig Stanford-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeSydhTfbs/wgEncodeSydhTfbsCh12Znfmizdcp1ab65767IggrabAlnRep1.bam CH12 ChipSeq ZNF-MIZD-CP1_(ab65767) Alignments 1 bam Stanford-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeSydhTfbs/wgEncodeSydhTfbsCh12Znfmizdcp1ab65767IggrabAlnRep2.bam CH12 ChipSeq ZNF-MIZD-CP1_(ab65767) Alignments 2 bam Stanford-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeSydhTfbs/wgEncodeSydhTfbsCh12Znfmizdcp1ab65767IggrabPk.narrowPeak.gz CH12 ChipSeq ZNF-MIZD-CP1_(ab65767) Peaks narrowPeak Stanford-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeSydhTfbs/wgEncodeSydhTfbsCh12Znfmizdcp1ab65767IggrabSig.bigWig CH12 ChipSeq ZNF-MIZD-CP1_(ab65767) Signal bigWig Stanford-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeSydhTfbs/wgEncodeSydhTfbsEse14Hcfc1nb10068209StdAlnRep1.bam ES-E14 ChipSeq HCFC1_(NB100-68209) Alignments 1 bam Stanford-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeSydhTfbs/wgEncodeSydhTfbsEse14Hcfc1nb10068209StdAlnRep2.bam ES-E14 ChipSeq HCFC1_(NB100-68209) Alignments 2 bam Stanford-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeSydhTfbs/wgEncodeSydhTfbsEse14Hcfc1nb10068209StdPk.narrowPeak.gz ES-E14 ChipSeq HCFC1_(NB100-68209) Peaks narrowPeak Stanford-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeSydhTfbs/wgEncodeSydhTfbsEse14Hcfc1nb10068209StdSig.bigWig ES-E14 ChipSeq HCFC1_(NB100-68209) Signal bigWig Stanford-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeSydhTfbs/wgEncodeSydhTfbsEse14InputStdAlnRep1.bam ES-E14 ChipSeq Input Alignments 1 bam Stanford-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeSydhTfbs/wgEncodeSydhTfbsEse14InputStdSig.bigWig ES-E14 ChipSeq Input Signal bigWig Stanford-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeSydhTfbs/wgEncodeSydhTfbsEse14MafkStdAlnRep1.bam ES-E14 ChipSeq MafK_(ab50322) Alignments 1 bam Stanford-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeSydhTfbs/wgEncodeSydhTfbsEse14MafkStdAlnRep2.bam ES-E14 ChipSeq MafK_(ab50322) Alignments 2 bam Stanford-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeSydhTfbs/wgEncodeSydhTfbsEse14MafkStdPk.narrowPeak.gz ES-E14 ChipSeq MafK_(ab50322) Peaks narrowPeak Stanford-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeSydhTfbs/wgEncodeSydhTfbsEse14MafkStdSig.bigWig ES-E14 ChipSeq MafK_(ab50322) Signal bigWig Stanford-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeSydhTfbs/wgEncodeSydhTfbsEse14Zc3h11anb10074650StdAlnRep1.bam ES-E14 ChipSeq ZC3H11A_(NB100-74650) Alignments 1 bam Stanford-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeSydhTfbs/wgEncodeSydhTfbsEse14Zc3h11anb10074650StdAlnRep2.bam ES-E14 ChipSeq ZC3H11A_(NB100-74650) Alignments 2 bam Stanford-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeSydhTfbs/wgEncodeSydhTfbsEse14Zc3h11anb10074650StdPk.narrowPeak.gz ES-E14 ChipSeq ZC3H11A_(NB100-74650) Peaks narrowPeak Stanford-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeSydhTfbs/wgEncodeSydhTfbsEse14Zc3h11anb10074650StdSig.bigWig ES-E14 ChipSeq ZC3H11A_(NB100-74650) Signal bigWig Stanford-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeSydhTfbs/wgEncodeSydhTfbsEse14Znf384hpa004051StdAlnRep1.bam ES-E14 ChipSeq ZNF384_(HPA004051) Alignments 1 bam Stanford-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeSydhTfbs/wgEncodeSydhTfbsEse14Znf384hpa004051StdAlnRep2.bam ES-E14 ChipSeq ZNF384_(HPA004051) Alignments 2 bam Stanford-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeSydhTfbs/wgEncodeSydhTfbsEse14Znf384hpa004051StdPk.narrowPeak.gz ES-E14 ChipSeq ZNF384_(HPA004051) Peaks narrowPeak Stanford-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeSydhTfbs/wgEncodeSydhTfbsEse14Znf384hpa004051StdSig.bigWig ES-E14 ChipSeq ZNF384_(HPA004051) Signal bigWig Stanford-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeSydhTfbs/wgEncodeSydhTfbsMelBhlhe40cIggrabAlnRep1.bam MEL ChipSeq BHLHE40_(NB100-1800) Alignments 1 bam Stanford-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeSydhTfbs/wgEncodeSydhTfbsMelBhlhe40cIggrabAlnRep2.bam MEL ChipSeq BHLHE40_(NB100-1800) Alignments 2 bam Stanford-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeSydhTfbs/wgEncodeSydhTfbsMelBhlhe40cIggrabPk.narrowPeak.gz MEL ChipSeq BHLHE40_(NB100-1800) Peaks narrowPeak Stanford-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeSydhTfbs/wgEncodeSydhTfbsMelBhlhe40cIggrabSig.bigWig MEL ChipSeq BHLHE40_(NB100-1800) Signal bigWig Stanford-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeSydhTfbs/wgEncodeSydhTfbsMelChd1nb10060411IggrabAlnRep1.bam MEL ChipSeq CHD1_(NB100-60411) Alignments 1 bam Stanford-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeSydhTfbs/wgEncodeSydhTfbsMelChd1nb10060411IggrabAlnRep2.bam MEL ChipSeq CHD1_(NB100-60411) Alignments 2 bam Stanford-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeSydhTfbs/wgEncodeSydhTfbsMelChd1nb10060411IggrabPk.narrowPeak.gz MEL ChipSeq CHD1_(NB100-60411) Peaks narrowPeak Stanford-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeSydhTfbs/wgEncodeSydhTfbsMelChd1nb10060411IggrabSig.bigWig MEL ChipSeq CHD1_(NB100-60411) Signal bigWig Stanford-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeSydhTfbs/wgEncodeSydhTfbsMelChd2ab68301IggrabAlnRep1.bam MEL ChipSeq CHD2_(AB68301) Alignments 1 bam Stanford-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeSydhTfbs/wgEncodeSydhTfbsMelChd2ab68301IggrabAlnRep2.bam MEL ChipSeq CHD2_(AB68301) Alignments 2 bam Stanford-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeSydhTfbs/wgEncodeSydhTfbsMelChd2ab68301IggrabPk.narrowPeak.gz MEL ChipSeq CHD2_(AB68301) Peaks narrowPeak Stanford-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeSydhTfbs/wgEncodeSydhTfbsMelChd2ab68301IggrabSig.bigWig MEL ChipSeq CHD2_(AB68301) Signal bigWig Stanford-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeSydhTfbs/wgEncodeSydhTfbsMelCmybh141IggrabAlnRep1.bam MEL ChipSeq c-Myb_(SC-7874) Alignments 1 bam Stanford-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeSydhTfbs/wgEncodeSydhTfbsMelCmybh141IggrabAlnRep2.bam MEL ChipSeq c-Myb_(SC-7874) Alignments 2 bam Stanford-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeSydhTfbs/wgEncodeSydhTfbsMelCmybh141IggrabPk.narrowPeak.gz MEL ChipSeq c-Myb_(SC-7874) Peaks narrowPeak Stanford-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeSydhTfbs/wgEncodeSydhTfbsMelCmybh141IggrabSig.bigWig MEL ChipSeq c-Myb_(SC-7874) Signal bigWig Stanford-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeSydhTfbs/wgEncodeSydhTfbsMelCmybsc7874IggrabAlnRep1.bam MEL ChipSeq c-Myb_(SC-7874) Alignments 1 bam Stanford-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeSydhTfbs/wgEncodeSydhTfbsMelCmybsc7874IggrabAlnRep2.bam MEL ChipSeq c-Myb_(SC-7874) Alignments 2 bam Stanford-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeSydhTfbs/wgEncodeSydhTfbsMelCmybsc7874IggrabPk.narrowPeak.gz MEL ChipSeq c-Myb_(SC-7874) Peaks narrowPeak Stanford-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeSydhTfbs/wgEncodeSydhTfbsMelCmybsc7874IggrabSig.bigWig MEL ChipSeq c-Myb_(SC-7874) Signal bigWig Stanford-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeSydhTfbs/wgEncodeSydhTfbsMelCmycIggrabAlnRep1.bam MEL ChipSeq c-Myc Alignments 1 bam Stanford-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeSydhTfbs/wgEncodeSydhTfbsMelCmycIggrabAlnRep2.bam MEL ChipSeq c-Myc Alignments 2 bam Stanford-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeSydhTfbs/wgEncodeSydhTfbsMelCmycIggrabPk.narrowPeak.gz MEL ChipSeq c-Myc Peaks narrowPeak Stanford-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeSydhTfbs/wgEncodeSydhTfbsMelCmycIggrabSig.bigWig MEL ChipSeq c-Myc Signal bigWig Stanford-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeSydhTfbs/wgEncodeSydhTfbsMelCorestsc30189IggrabAlnRep1.bam MEL ChipSeq COREST_(sc-30189) Alignments 1 bam Stanford-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeSydhTfbs/wgEncodeSydhTfbsMelCorestsc30189IggrabAlnRep2.bam MEL ChipSeq COREST_(sc-30189) Alignments 2 bam Stanford-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeSydhTfbs/wgEncodeSydhTfbsMelCorestsc30189IggrabPk.narrowPeak.gz MEL ChipSeq COREST_(sc-30189) Peaks narrowPeak Stanford-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeSydhTfbs/wgEncodeSydhTfbsMelCorestsc30189IggrabSig.bigWig MEL ChipSeq COREST_(sc-30189) Signal bigWig Stanford-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeSydhTfbs/wgEncodeSydhTfbsMelCtcfDmso20IggyaleAlnRep1.bam MEL ChipSeq CTCF_(SC-15914) Alignments 1 bam Stanford-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeSydhTfbs/wgEncodeSydhTfbsMelCtcfDmso20IggyaleAlnRep2.bam MEL ChipSeq CTCF_(SC-15914) Alignments 2 bam Stanford-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeSydhTfbs/wgEncodeSydhTfbsMelCtcfDmso20IggyalePk.narrowPeak.gz MEL ChipSeq CTCF_(SC-15914) Peaks narrowPeak Stanford-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeSydhTfbs/wgEncodeSydhTfbsMelCtcfDmso20IggyaleSig.bigWig MEL ChipSeq CTCF_(SC-15914) Signal bigWig Stanford-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeSydhTfbs/wgEncodeSydhTfbsMelCtcfbDm2p5dStdAlnRep1.bam MEL ChipSeq CTCF_(SC-15914) Alignments 1 bam Stanford-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeSydhTfbs/wgEncodeSydhTfbsMelCtcfbDm2p5dStdAlnRep2.bam MEL ChipSeq CTCF_(SC-15914) Alignments 2 bam Stanford-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeSydhTfbs/wgEncodeSydhTfbsMelCtcfbDm2p5dStdPk.narrowPeak.gz MEL ChipSeq CTCF_(SC-15914) Peaks narrowPeak Stanford-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeSydhTfbs/wgEncodeSydhTfbsMelCtcfbDm2p5dStdSig.bigWig MEL ChipSeq CTCF_(SC-15914) Signal bigWig Stanford-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeSydhTfbs/wgEncodeSydhTfbsMelCtcfbIggrabPk.narrowPeak.gz MEL ChipSeq CTCF_(SC-15914) Peaks narrowPeak Stanford-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeSydhTfbs/wgEncodeSydhTfbsMelCtcfsc15914Dm2p5dIggyaleAlnRep1.bam MEL ChipSeq CTCF_(SC-15914) Alignments 1 bam Yale-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeSydhTfbs/wgEncodeSydhTfbsMelCtcfsc15914Dm2p5dIggyaleAlnRep2.bam MEL ChipSeq CTCF_(SC-15914) Alignments 2 bam Yale-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeSydhTfbs/wgEncodeSydhTfbsMelCtcfsc15914Dm2p5dIggyalePk.narrowPeak.gz MEL ChipSeq CTCF_(SC-15914) Peaks narrowPeak Yale-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeSydhTfbs/wgEncodeSydhTfbsMelCtcfsc15914Dm2p5dIggyaleSig.bigWig MEL ChipSeq CTCF_(SC-15914) Signal bigWig Yale-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeSydhTfbs/wgEncodeSydhTfbsMelCtcfsc15914IggrabAlnRep1.bam MEL ChipSeq CTCF_(SC-15914) Alignments 1 bam Stanford-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeSydhTfbs/wgEncodeSydhTfbsMelCtcfsc15914IggrabAlnRep2.bam MEL ChipSeq CTCF_(SC-15914) Alignments 2 bam Stanford-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeSydhTfbs/wgEncodeSydhTfbsMelCtcfsc15914IggrabSig.bigWig MEL ChipSeq CTCF_(SC-15914) Signal bigWig Stanford-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeSydhTfbs/wgEncodeSydhTfbsMelE2f4IggrabAlnRep1.bam MEL ChipSeq E2F4 Alignments 1 bam Stanford-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeSydhTfbs/wgEncodeSydhTfbsMelE2f4IggrabAlnRep2.bam MEL ChipSeq E2F4 Alignments 2 bam Stanford-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeSydhTfbs/wgEncodeSydhTfbsMelE2f4IggrabPk.narrowPeak.gz MEL ChipSeq E2F4 Peaks narrowPeak Stanford-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeSydhTfbs/wgEncodeSydhTfbsMelE2f4IggrabSig.bigWig MEL ChipSeq E2F4 Signal bigWig Stanford-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeSydhTfbs/wgEncodeSydhTfbsMelEts1IggrabAlnRep1.bam MEL ChipSeq ETS1 Alignments 1 bam Stanford-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeSydhTfbs/wgEncodeSydhTfbsMelEts1IggrabAlnRep2.bam MEL ChipSeq ETS1 Alignments 2 bam Stanford-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeSydhTfbs/wgEncodeSydhTfbsMelEts1IggrabPk.narrowPeak.gz MEL ChipSeq ETS1 Peaks narrowPeak Stanford-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeSydhTfbs/wgEncodeSydhTfbsMelEts1IggrabSig.bigWig MEL ChipSeq ETS1 Signal bigWig Stanford-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeSydhTfbs/wgEncodeSydhTfbsMelGata1Dm2p5dStdAlnRep1.bam MEL ChipSeq GATA-1 Alignments 1 bam Stanford-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeSydhTfbs/wgEncodeSydhTfbsMelGata1Dm2p5dStdAlnRep2.bam MEL ChipSeq GATA-1 Alignments 2 bam Stanford-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeSydhTfbs/wgEncodeSydhTfbsMelGata1Dm2p5dStdPk.narrowPeak.gz MEL ChipSeq GATA-1 Peaks narrowPeak Stanford-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeSydhTfbs/wgEncodeSydhTfbsMelGata1Dm2p5dStdSig.bigWig MEL ChipSeq GATA-1 Signal bigWig Stanford-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeSydhTfbs/wgEncodeSydhTfbsMelGata1IggratAlnRep1.bam MEL ChipSeq GATA-1 Alignments 1 bam Stanford-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeSydhTfbs/wgEncodeSydhTfbsMelGata1IggratAlnRep2.bam MEL ChipSeq GATA-1 Alignments 2 bam Stanford-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeSydhTfbs/wgEncodeSydhTfbsMelGata1IggratPk.narrowPeak.gz MEL ChipSeq GATA-1 Peaks narrowPeak Stanford-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeSydhTfbs/wgEncodeSydhTfbsMelGata1IggratSig.bigWig MEL ChipSeq GATA-1 Signal bigWig Stanford-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeSydhTfbs/wgEncodeSydhTfbsMelGcn5IggrabAlnRep1.bam MEL ChipSeq GCN5 Alignments 1 bam Stanford-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeSydhTfbs/wgEncodeSydhTfbsMelGcn5IggrabAlnRep2.bam MEL ChipSeq GCN5 Alignments 2 bam Stanford-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeSydhTfbs/wgEncodeSydhTfbsMelGcn5IggrabPk.narrowPeak.gz MEL ChipSeq GCN5 Peaks narrowPeak Stanford-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeSydhTfbs/wgEncodeSydhTfbsMelGcn5IggrabSig.bigWig MEL ChipSeq GCN5 Signal bigWig Stanford-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeSydhTfbs/wgEncodeSydhTfbsMelHcfc1nb10068209IggrabAlnRep1.bam MEL ChipSeq HCFC1_(NB100-68209) Alignments 1 bam Stanford-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeSydhTfbs/wgEncodeSydhTfbsMelHcfc1nb10068209IggrabAlnRep2.bam MEL ChipSeq HCFC1_(NB100-68209) Alignments 2 bam Stanford-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeSydhTfbs/wgEncodeSydhTfbsMelHcfc1nb10068209IggrabPk.narrowPeak.gz MEL ChipSeq HCFC1_(NB100-68209) Peaks narrowPeak Stanford-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeSydhTfbs/wgEncodeSydhTfbsMelHcfc1nb10068209IggrabSig.bigWig MEL ChipSeq HCFC1_(NB100-68209) Signal bigWig Stanford-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeSydhTfbs/wgEncodeSydhTfbsMelInputDm2p5dIggratAlnRep1.bam MEL ChipSeq Input Alignments 1 bam Stanford-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeSydhTfbs/wgEncodeSydhTfbsMelInputDm2p5dIggratSig.bigWig MEL ChipSeq Input Signal bigWig Stanford-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeSydhTfbs/wgEncodeSydhTfbsMelInputDm2p5dIggyaleAln.bam MEL ChipSeq Input Alignments bam Yale-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeSydhTfbs/wgEncodeSydhTfbsMelInputDm2p5dIggyaleSig.bigWig MEL ChipSeq Input Signal bigWig Yale-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeSydhTfbs/wgEncodeSydhTfbsMelInputDm2p5dStdAlnRep1.bam MEL ChipSeq Input Alignments 1 bam Yale-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeSydhTfbs/wgEncodeSydhTfbsMelInputDm2p5dStdAlnRep1V2.bam MEL ChipSeq Input Alignments 1 bam Stanford-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeSydhTfbs/wgEncodeSydhTfbsMelInputDm2p5dStdSig.bigWig MEL ChipSeq Input Signal bigWig Yale-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeSydhTfbs/wgEncodeSydhTfbsMelInputDm2p5dStdSigV2.bigWig MEL ChipSeq Input Signal bigWig Stanford-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeSydhTfbs/wgEncodeSydhTfbsMelInputDmso20IggyaleAln.bam MEL ChipSeq Input Alignments bam Stanford-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeSydhTfbs/wgEncodeSydhTfbsMelInputDmso20IggyaleSig.bigWig MEL ChipSeq Input Signal bigWig Stanford-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeSydhTfbs/wgEncodeSydhTfbsMelInputIggmusAlnRep1.bam MEL ChipSeq Input Alignments 1 bam Stanford-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeSydhTfbs/wgEncodeSydhTfbsMelInputIggmusSig.bigWig MEL ChipSeq Input Signal bigWig Stanford-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeSydhTfbs/wgEncodeSydhTfbsMelInputIggrabAlnRep1.bam MEL ChipSeq Input Alignments 1 bam Stanford-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeSydhTfbs/wgEncodeSydhTfbsMelInputIggrabSig.bigWig MEL ChipSeq Input Signal bigWig Stanford-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeSydhTfbs/wgEncodeSydhTfbsMelInputIggratAlnRep1.bam MEL ChipSeq Input Alignments 1 bam Stanford-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeSydhTfbs/wgEncodeSydhTfbsMelInputIggratSig.bigWig MEL ChipSeq Input Signal bigWig Stanford-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeSydhTfbs/wgEncodeSydhTfbsMelInputStdAlnRep1.bam MEL ChipSeq Input Alignments 1 bam Stanford-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeSydhTfbs/wgEncodeSydhTfbsMelInputStdSig.bigWig MEL ChipSeq Input Signal bigWig Stanford-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeSydhTfbs/wgEncodeSydhTfbsMelJundIggrabAlnRep1.bam MEL ChipSeq JunD Alignments 1 bam Stanford-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeSydhTfbs/wgEncodeSydhTfbsMelJundIggrabAlnRep2.bam MEL ChipSeq JunD Alignments 2 bam Stanford-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeSydhTfbs/wgEncodeSydhTfbsMelJundIggrabPk.narrowPeak.gz MEL ChipSeq JunD Peaks narrowPeak Stanford-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeSydhTfbs/wgEncodeSydhTfbsMelJundIggrabSig.bigWig MEL ChipSeq JunD Signal bigWig Stanford-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeSydhTfbs/wgEncodeSydhTfbsMelMafkDm2p5dStdAlnRep1.bam MEL ChipSeq MafK_(ab50322) Alignments 1 bam Stanford-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeSydhTfbs/wgEncodeSydhTfbsMelMafkDm2p5dStdAlnRep2.bam MEL ChipSeq MafK_(ab50322) Alignments 2 bam Stanford-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeSydhTfbs/wgEncodeSydhTfbsMelMafkDm2p5dStdPk.narrowPeak.gz MEL ChipSeq MafK_(ab50322) Peaks narrowPeak Stanford-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeSydhTfbs/wgEncodeSydhTfbsMelMafkDm2p5dStdSig.bigWig MEL ChipSeq MafK_(ab50322) Signal bigWig Stanford-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeSydhTfbs/wgEncodeSydhTfbsMelMafkab50322IggrabAlnRep1.bam MEL ChipSeq MafK_(ab50322) Alignments 1 bam Stanford-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeSydhTfbs/wgEncodeSydhTfbsMelMafkab50322IggrabAlnRep2.bam MEL ChipSeq MafK_(ab50322) Alignments 2 bam Stanford-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeSydhTfbs/wgEncodeSydhTfbsMelMafkab50322IggrabPk.narrowPeak.gz MEL ChipSeq MafK_(ab50322) Peaks narrowPeak Stanford-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeSydhTfbs/wgEncodeSydhTfbsMelMafkab50322IggrabSig.bigWig MEL ChipSeq MafK_(ab50322) Signal bigWig Stanford-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeSydhTfbs/wgEncodeSydhTfbsMelMaxIggrabAlnRep1.bam MEL ChipSeq Max Alignments 1 bam Stanford-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeSydhTfbs/wgEncodeSydhTfbsMelMaxIggrabAlnRep1V2.bam MEL ChipSeq Max Alignments 1 bam Stanford-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeSydhTfbs/wgEncodeSydhTfbsMelMaxIggrabAlnRep2.bam MEL ChipSeq Max Alignments 2 bam Stanford-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeSydhTfbs/wgEncodeSydhTfbsMelMaxIggrabAlnRep2V2.bam MEL ChipSeq Max Alignments 2 bam Stanford-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeSydhTfbs/wgEncodeSydhTfbsMelMaxIggrabPk.narrowPeak.gz MEL ChipSeq Max Peaks narrowPeak Stanford-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeSydhTfbs/wgEncodeSydhTfbsMelMaxIggrabSig.bigWig MEL ChipSeq Max Signal bigWig Stanford-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeSydhTfbs/wgEncodeSydhTfbsMelMazab85725IggrabAlnRep1.bam MEL ChipSeq MAZ_(ab85725) Alignments 1 bam Stanford-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeSydhTfbs/wgEncodeSydhTfbsMelMazab85725IggrabAlnRep2.bam MEL ChipSeq MAZ_(ab85725) Alignments 2 bam Stanford-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeSydhTfbs/wgEncodeSydhTfbsMelMazab85725IggrabPk.narrowPeak.gz MEL ChipSeq MAZ_(ab85725) Peaks narrowPeak Stanford-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeSydhTfbs/wgEncodeSydhTfbsMelMazab85725IggrabSig.bigWig MEL ChipSeq MAZ_(ab85725) Signal bigWig Stanford-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeSydhTfbs/wgEncodeSydhTfbsMelMxi1af4185IggrabAlnRep1.bam MEL ChipSeq Mxi1_(AF4185) Alignments 1 bam Stanford-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeSydhTfbs/wgEncodeSydhTfbsMelMxi1af4185IggrabAlnRep2.bam MEL ChipSeq Mxi1_(AF4185) Alignments 2 bam Stanford-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeSydhTfbs/wgEncodeSydhTfbsMelMxi1af4185IggrabPk.narrowPeak.gz MEL ChipSeq Mxi1_(AF4185) Peaks narrowPeak Stanford-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeSydhTfbs/wgEncodeSydhTfbsMelMxi1af4185IggrabSig.bigWig MEL ChipSeq Mxi1_(AF4185) Signal bigWig Stanford-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeSydhTfbs/wgEncodeSydhTfbsMelNelfeIggrabAlnRep1.bam MEL ChipSeq NELFe Alignments 1 bam Stanford-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeSydhTfbs/wgEncodeSydhTfbsMelNelfeIggrabAlnRep2.bam MEL ChipSeq NELFe Alignments 2 bam Stanford-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeSydhTfbs/wgEncodeSydhTfbsMelNelfeIggrabPk.narrowPeak.gz MEL ChipSeq NELFe Peaks narrowPeak Stanford-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeSydhTfbs/wgEncodeSydhTfbsMelNelfeIggrabSig.bigWig MEL ChipSeq NELFe Signal bigWig Stanford-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeSydhTfbs/wgEncodeSydhTfbsMelNrf2IggrabAlnRep1.bam MEL ChipSeq Nrf2 Alignments 1 bam Stanford-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeSydhTfbs/wgEncodeSydhTfbsMelNrf2IggrabAlnRep2.bam MEL ChipSeq Nrf2 Alignments 2 bam Stanford-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeSydhTfbs/wgEncodeSydhTfbsMelNrf2IggrabPk.narrowPeak.gz MEL ChipSeq Nrf2 Peaks narrowPeak Stanford-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeSydhTfbs/wgEncodeSydhTfbsMelNrf2IggrabSig.bigWig MEL ChipSeq Nrf2 Signal bigWig Stanford-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeSydhTfbs/wgEncodeSydhTfbsMelP300IggrabAlnRep1.bam MEL ChipSeq p300_(SC-584) Alignments 1 bam Stanford-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeSydhTfbs/wgEncodeSydhTfbsMelP300IggrabAlnRep1V2.bam MEL ChipSeq p300 Alignments 1 bam Stanford-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeSydhTfbs/wgEncodeSydhTfbsMelP300IggrabAlnRep2.bam MEL ChipSeq p300_(SC-584) Alignments 2 bam Stanford-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeSydhTfbs/wgEncodeSydhTfbsMelP300IggrabAlnRep2V2.bam MEL ChipSeq p300 Alignments 2 bam Stanford-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeSydhTfbs/wgEncodeSydhTfbsMelP300IggrabPk.narrowPeak.gz MEL ChipSeq p300_(SC-584) Peaks narrowPeak Stanford-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeSydhTfbs/wgEncodeSydhTfbsMelP300IggrabPkV2.narrowPeak.gz MEL ChipSeq p300 Peaks narrowPeak Stanford-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeSydhTfbs/wgEncodeSydhTfbsMelP300IggrabSig.bigWig MEL ChipSeq p300_(SC-584) Signal bigWig Stanford-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeSydhTfbs/wgEncodeSydhTfbsMelP300IggrabSigV2.bigWig MEL ChipSeq p300 Signal bigWig Stanford-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeSydhTfbs/wgEncodeSydhTfbsMelP300sc584IggrabAlnRep1.bam MEL ChipSeq p300_(SC-584) Alignments 1 bam Stanford-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeSydhTfbs/wgEncodeSydhTfbsMelP300sc584IggrabAlnRep2.bam MEL ChipSeq p300_(SC-584) Alignments 2 bam Stanford-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeSydhTfbs/wgEncodeSydhTfbsMelP300sc584IggrabPk.narrowPeak.gz MEL ChipSeq p300_(SC-584) Peaks narrowPeak Stanford-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeSydhTfbs/wgEncodeSydhTfbsMelP300sc584IggrabSig.bigWig MEL ChipSeq p300_(SC-584) Signal bigWig Stanford-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeSydhTfbs/wgEncodeSydhTfbsMelPol2Dm2p5dIggrabAlnRep1.bam MEL ChipSeq Pol2 Alignments 1 bam Stanford-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeSydhTfbs/wgEncodeSydhTfbsMelPol2Dm2p5dIggrabAlnRep2.bam MEL ChipSeq Pol2 Alignments 2 bam Stanford-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeSydhTfbs/wgEncodeSydhTfbsMelPol2Dm2p5dIggrabPk.narrowPeak.gz MEL ChipSeq Pol2 Peaks narrowPeak Stanford-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeSydhTfbs/wgEncodeSydhTfbsMelPol2Dm2p5dIggrabSig.bigWig MEL ChipSeq Pol2 Signal bigWig Stanford-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeSydhTfbs/wgEncodeSydhTfbsMelPol2IggmusAlnRep1.bam MEL ChipSeq Pol2 Alignments 1 bam Stanford-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeSydhTfbs/wgEncodeSydhTfbsMelPol2IggmusAlnRep2.bam MEL ChipSeq Pol2 Alignments 2 bam Stanford-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeSydhTfbs/wgEncodeSydhTfbsMelPol2IggmusPk.narrowPeak.gz MEL ChipSeq Pol2 Peaks narrowPeak Stanford-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeSydhTfbs/wgEncodeSydhTfbsMelPol2IggmusSig.bigWig MEL ChipSeq Pol2 Signal bigWig Stanford-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeSydhTfbs/wgEncodeSydhTfbsMelPol2s2IggrabAlnRep1.bam MEL ChipSeq Pol2(phosphoS2) Alignments 1 bam Stanford-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeSydhTfbs/wgEncodeSydhTfbsMelPol2s2IggrabAlnRep2.bam MEL ChipSeq Pol2(phosphoS2) Alignments 2 bam Stanford-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeSydhTfbs/wgEncodeSydhTfbsMelPol2s2IggrabPk.narrowPeak.gz MEL ChipSeq Pol2(phosphoS2) Peaks narrowPeak Stanford-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeSydhTfbs/wgEncodeSydhTfbsMelPol2s2IggrabSig.bigWig MEL ChipSeq Pol2(phosphoS2) Signal bigWig Stanford-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeSydhTfbs/wgEncodeSydhTfbsMelRad21Dm2p5dIggrabAlnRep1.bam MEL ChipSeq Rad21 Alignments 1 bam Stanford-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeSydhTfbs/wgEncodeSydhTfbsMelRad21Dm2p5dIggrabAlnRep2.bam MEL ChipSeq Rad21 Alignments 2 bam Stanford-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeSydhTfbs/wgEncodeSydhTfbsMelRad21Dm2p5dIggrabPk.narrowPeak.gz MEL ChipSeq Rad21 Peaks narrowPeak Stanford-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeSydhTfbs/wgEncodeSydhTfbsMelRad21Dm2p5dIggrabSig.bigWig MEL ChipSeq Rad21 Signal bigWig Stanford-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeSydhTfbs/wgEncodeSydhTfbsMelRad21Dmso20IggrabAlnRep1.bam MEL ChipSeq Rad21 Alignments 1 bam Stanford-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeSydhTfbs/wgEncodeSydhTfbsMelRad21Dmso20IggrabAlnRep2.bam MEL ChipSeq Rad21 Alignments 2 bam Stanford-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeSydhTfbs/wgEncodeSydhTfbsMelRad21Dmso20IggrabPk.narrowPeak.gz MEL ChipSeq Rad21 Peaks narrowPeak Stanford-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeSydhTfbs/wgEncodeSydhTfbsMelRad21Dmso20IggrabSig.bigWig MEL ChipSeq Rad21 Signal bigWig Stanford-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeSydhTfbs/wgEncodeSydhTfbsMelRad21IggrabAlnRep1.bam MEL ChipSeq Rad21 Alignments 1 bam Stanford-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeSydhTfbs/wgEncodeSydhTfbsMelRad21IggrabAlnRep2.bam MEL ChipSeq Rad21 Alignments 2 bam Stanford-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeSydhTfbs/wgEncodeSydhTfbsMelRad21IggrabPk.narrowPeak.gz MEL ChipSeq Rad21 Peaks narrowPeak Stanford-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeSydhTfbs/wgEncodeSydhTfbsMelRad21IggrabSig.bigWig MEL ChipSeq Rad21 Signal bigWig Stanford-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeSydhTfbs/wgEncodeSydhTfbsMelSin3anb6001263IggrabAlnRep1.bam MEL ChipSeq SIN3A_(NB600-1263) Alignments 1 bam Stanford-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeSydhTfbs/wgEncodeSydhTfbsMelSin3anb6001263IggrabAlnRep2.bam MEL ChipSeq SIN3A_(NB600-1263) Alignments 2 bam Stanford-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeSydhTfbs/wgEncodeSydhTfbsMelSin3anb6001263IggrabPk.narrowPeak.gz MEL ChipSeq SIN3A_(NB600-1263) Peaks narrowPeak Stanford-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeSydhTfbs/wgEncodeSydhTfbsMelSin3anb6001263IggrabSig.bigWig MEL ChipSeq SIN3A_(NB600-1263) Signal bigWig Stanford-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeSydhTfbs/wgEncodeSydhTfbsMelSmc3ab9263IggrabAlnRep1.bam MEL ChipSeq SMC3_(ab9263) Alignments 1 bam Stanford-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeSydhTfbs/wgEncodeSydhTfbsMelSmc3ab9263IggrabAlnRep2.bam MEL ChipSeq SMC3_(ab9263) Alignments 2 bam Stanford-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeSydhTfbs/wgEncodeSydhTfbsMelSmc3ab9263IggrabPk.narrowPeak.gz MEL ChipSeq SMC3_(ab9263) Peaks narrowPeak Stanford-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeSydhTfbs/wgEncodeSydhTfbsMelSmc3ab9263IggrabSig.bigWig MEL ChipSeq SMC3_(ab9263) Signal bigWig Stanford-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeSydhTfbs/wgEncodeSydhTfbsMelTbpIggmusAlnRep1.bam MEL ChipSeq TBP Alignments 1 bam Stanford-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeSydhTfbs/wgEncodeSydhTfbsMelTbpIggmusAlnRep2.bam MEL ChipSeq TBP Alignments 2 bam Stanford-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeSydhTfbs/wgEncodeSydhTfbsMelTbpIggmusPk.narrowPeak.gz MEL ChipSeq TBP Peaks narrowPeak Stanford-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeSydhTfbs/wgEncodeSydhTfbsMelTbpIggmusSig.bigWig MEL ChipSeq TBP Signal bigWig Stanford-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeSydhTfbs/wgEncodeSydhTfbsMelUbfsc13125IggmusAlnRep1.bam MEL ChipSeq UBF_(sc-13125) Alignments 1 bam Stanford-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeSydhTfbs/wgEncodeSydhTfbsMelUbfsc13125IggmusAlnRep2.bam MEL ChipSeq UBF_(sc-13125) Alignments 2 bam Stanford-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeSydhTfbs/wgEncodeSydhTfbsMelUbfsc13125IggmusPk.narrowPeak.gz MEL ChipSeq UBF_(sc-13125) Peaks narrowPeak Stanford-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeSydhTfbs/wgEncodeSydhTfbsMelUbfsc13125IggmusSig.bigWig MEL ChipSeq UBF_(sc-13125) Signal bigWig Stanford-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeSydhTfbs/wgEncodeSydhTfbsMelUsf2IggmusAlnRep1.bam MEL ChipSeq USF2 Alignments 1 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http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeUwDgf/wgEncodeUwDgfLungC57bl6MAdult8wksSigRep1.bigWig Lung DnaseDgf Signal 1 bigWig UW-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeUwDgf/wgEncodeUwDgfMelUknImmortalAlnRep1.bam MEL DnaseDgf Alignments 1 bam UW-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeUwDgf/wgEncodeUwDgfMelUknImmortalHotspotsRep1.broadPeak.gz MEL DnaseDgf Hotspots 1 broadPeak UW-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeUwDgf/wgEncodeUwDgfMelUknImmortalPkRep1.narrowPeak.gz MEL DnaseDgf Peaks 1 narrowPeak UW-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeUwDgf/wgEncodeUwDgfMelUknImmortalRawRep1.bigWig MEL DnaseDgf RawSignal 1 bigWig UW-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeUwDgf/wgEncodeUwDgfMelUknImmortalSigRep1.bigWig MEL DnaseDgf Signal 1 bigWig UW-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeUwDgf/wgEncodeUwDgfNih3t3NihsMImmortalAlnRep1.bam NIH-3T3 DnaseDgf Alignments 1 bam UW-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeUwDgf/wgEncodeUwDgfNih3t3NihsMImmortalHotspotsRep1.broadPeak.gz NIH-3T3 DnaseDgf Hotspots 1 broadPeak UW-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeUwDgf/wgEncodeUwDgfNih3t3NihsMImmortalPkRep1.narrowPeak.gz NIH-3T3 DnaseDgf Peaks 1 narrowPeak UW-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeUwDgf/wgEncodeUwDgfNih3t3NihsMImmortalRawRep1.bigWig NIH-3T3 DnaseDgf RawSignal 1 bigWig UW-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeUwDgf/wgEncodeUwDgfNih3t3NihsMImmortalSigRep1.bigWig NIH-3T3 DnaseDgf Signal 1 bigWig UW-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeUwDgf/wgEncodeUwDgfRetinaC57bl6MNew1daysAlnRep1.bam Retina DnaseDgf Alignments 1 bam UW-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeUwDgf/wgEncodeUwDgfRetinaC57bl6MNew1daysHotspotsRep1.broadPeak.gz Retina DnaseDgf Hotspots 1 broadPeak UW-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeUwDgf/wgEncodeUwDgfRetinaC57bl6MNew1daysPkRep1.narrowPeak.gz Retina DnaseDgf Peaks 1 narrowPeak UW-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeUwDgf/wgEncodeUwDgfRetinaC57bl6MNew1daysRawRep1.bigWig Retina DnaseDgf RawSignal 1 bigWig UW-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeUwDgf/wgEncodeUwDgfRetinaC57bl6MNew1daysSigRep1.bigWig Retina DnaseDgf Signal 1 bigWig UW-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeUwDgf/wgEncodeUwDgfThelpaC57bl6MAdult8wksAlnRep1.bam THelper-Activated DnaseDgf Alignments 1 bam UW-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeUwDgf/wgEncodeUwDgfThelpaC57bl6MAdult8wksHotspotsRep1.broadPeak.gz THelper-Activated DnaseDgf Hotspots 1 broadPeak 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http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeUwDgf/wgEncodeUwDgfTnaiveC57bl6MAdult8wksPkRep1.narrowPeak.gz T-Naive DnaseDgf Peaks 1 narrowPeak UW-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeUwDgf/wgEncodeUwDgfTnaiveC57bl6MAdult8wksPkRep2.narrowPeak.gz T-Naive DnaseDgf Peaks 2 narrowPeak UW-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeUwDgf/wgEncodeUwDgfTnaiveC57bl6MAdult8wksRawRep1.bigWig T-Naive DnaseDgf RawSignal 1 bigWig UW-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeUwDgf/wgEncodeUwDgfTnaiveC57bl6MAdult8wksRawRep2.bigWig T-Naive DnaseDgf RawSignal 2 bigWig UW-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeUwDgf/wgEncodeUwDgfTnaiveC57bl6MAdult8wksSigRep1.bigWig T-Naive DnaseDgf Signal 1 bigWig UW-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeUwDgf/wgEncodeUwDgfTnaiveC57bl6MAdult8wksSigRep2.bigWig T-Naive DnaseDgf Signal 2 bigWig UW-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeUwDgf/wgEncodeUwDgfTregC57bl6MAdult8wksAlnRep1.bam TReg DnaseDgf Alignments 1 bam UW-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeUwDgf/wgEncodeUwDgfTregC57bl6MAdult8wksHotspotsRep1.broadPeak.gz TReg DnaseDgf Hotspots 1 broadPeak UW-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeUwDgf/wgEncodeUwDgfTregC57bl6MAdult8wksPkRep1.narrowPeak.gz TReg DnaseDgf Peaks 1 narrowPeak UW-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeUwDgf/wgEncodeUwDgfTregC57bl6MAdult8wksRawRep1.bigWig TReg DnaseDgf RawSignal 1 bigWig UW-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeUwDgf/wgEncodeUwDgfTregC57bl6MAdult8wksSigRep1.bigWig TReg DnaseDgf Signal 1 bigWig UW-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeUwDgf/wgEncodeUwDgfTregaC57bl6MAdult8wksAlnRep1.bam TReg-Activated DnaseDgf Alignments 1 bam UW-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeUwDgf/wgEncodeUwDgfTregaC57bl6MAdult8wksHotspotsRep1.broadPeak.gz TReg-Activated DnaseDgf Hotspots 1 broadPeak UW-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeUwDgf/wgEncodeUwDgfTregaC57bl6MAdult8wksPkRep1.narrowPeak.gz TReg-Activated DnaseDgf Peaks 1 narrowPeak UW-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeUwDgf/wgEncodeUwDgfTregaC57bl6MAdult8wksRawRep1.bigWig TReg-Activated DnaseDgf RawSignal 1 bigWig UW-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeUwDgf/wgEncodeUwDgfTregaC57bl6MAdult8wksSigRep1.bigWig TReg-Activated DnaseDgf Signal 1 bigWig UW-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeUwDgf/wgEncodeUwDgfWbrainC57bl6MAdult8wksAlnRep1.bam WholeBrain DnaseDgf Alignments 1 bam UW-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeUwDgf/wgEncodeUwDgfWbrainC57bl6MAdult8wksHotspotsRep1.broadPeak.gz WholeBrain DnaseDgf Hotspots 1 broadPeak UW-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeUwDgf/wgEncodeUwDgfWbrainC57bl6MAdult8wksPkRep1.narrowPeak.gz WholeBrain DnaseDgf Peaks 1 narrowPeak UW-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeUwDgf/wgEncodeUwDgfWbrainC57bl6MAdult8wksRawRep1.bigWig WholeBrain DnaseDgf RawSignal 1 bigWig UW-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeUwDgf/wgEncodeUwDgfWbrainC57bl6MAdult8wksSigRep1.bigWig WholeBrain DnaseDgf Signal 1 bigWig UW-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeUwDgf/wgEncodeUwDgfWbrainC57bl6ME14halfAlnRep1.bam WholeBrain DnaseDgf Alignments 1 bam UW-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeUwDgf/wgEncodeUwDgfWbrainC57bl6ME14halfHotspotsRep1.broadPeak.gz WholeBrain DnaseDgf Hotspots 1 broadPeak UW-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeUwDgf/wgEncodeUwDgfWbrainC57bl6ME14halfPkRep1.narrowPeak.gz WholeBrain DnaseDgf Peaks 1 narrowPeak UW-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeUwDgf/wgEncodeUwDgfWbrainC57bl6ME14halfRawRep1.bigWig WholeBrain DnaseDgf RawSignal 1 bigWig UW-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeUwDgf/wgEncodeUwDgfWbrainC57bl6ME14halfSigRep1.bigWig WholeBrain DnaseDgf Signal 1 bigWig UW-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeUwDgf/wgEncodeUwDgfZhbtc4129olaME0AlnRep1.bam ZhBTc4 DnaseDgf Alignments 1 bam UW-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeUwDgf/wgEncodeUwDgfZhbtc4129olaME0Diffb24hAlnRep1.bam ZhBTc4 DnaseDgf Alignments 1 bam UW-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeUwDgf/wgEncodeUwDgfZhbtc4129olaME0Diffb24hHotspotsRep1.broadPeak.gz ZhBTc4 DnaseDgf Hotspots 1 broadPeak UW-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeUwDgf/wgEncodeUwDgfZhbtc4129olaME0Diffb24hPkRep1.narrowPeak.gz ZhBTc4 DnaseDgf Peaks 1 narrowPeak UW-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeUwDgf/wgEncodeUwDgfZhbtc4129olaME0Diffb24hRawRep1.bigWig ZhBTc4 DnaseDgf RawSignal 1 bigWig UW-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeUwDgf/wgEncodeUwDgfZhbtc4129olaME0Diffb24hSigRep1.bigWig ZhBTc4 DnaseDgf Signal 1 bigWig UW-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeUwDgf/wgEncodeUwDgfZhbtc4129olaME0HotspotsRep1.broadPeak.gz ZhBTc4 DnaseDgf Hotspots 1 broadPeak UW-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeUwDgf/wgEncodeUwDgfZhbtc4129olaME0PkRep1.narrowPeak.gz ZhBTc4 DnaseDgf Peaks 1 narrowPeak UW-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeUwDgf/wgEncodeUwDgfZhbtc4129olaME0RawRep1.bigWig ZhBTc4 DnaseDgf RawSignal 1 bigWig UW-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeUwDgf/wgEncodeUwDgfZhbtc4129olaME0SigRep1.bigWig ZhBTc4 DnaseDgf Signal 1 bigWig UW-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeUwDnase/wgEncodeUwDnase3134RiiiMImmortalAlnRep1.bam 3134 DnaseSeq Alignments 1 bam UW-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeUwDnase/wgEncodeUwDnase3134RiiiMImmortalAlnRep2.bam 3134 DnaseSeq Alignments 2 bam UW-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeUwDnase/wgEncodeUwDnase3134RiiiMImmortalHotspotsRep1.broadPeak.gz 3134 DnaseSeq Hotspots 1 broadPeak UW-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeUwDnase/wgEncodeUwDnase3134RiiiMImmortalHotspotsRep2.broadPeak.gz 3134 DnaseSeq Hotspots 2 broadPeak UW-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeUwDnase/wgEncodeUwDnase3134RiiiMImmortalPkRep1.narrowPeak.gz 3134 DnaseSeq Peaks 1 narrowPeak UW-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeUwDnase/wgEncodeUwDnase3134RiiiMImmortalPkRep2.narrowPeak.gz 3134 DnaseSeq Peaks 2 narrowPeak UW-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeUwDnase/wgEncodeUwDnase3134RiiiMImmortalSigRep1.bigWig 3134 DnaseSeq Signal 1 bigWig UW-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeUwDnase/wgEncodeUwDnase3134RiiiMImmortalSigRep2.bigWig 3134 DnaseSeq Signal 2 bigWig UW-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeUwDnase/wgEncodeUwDnase416bC57bl6MAdult8wksAlnRep1.bam 416B DnaseSeq Alignments 1 bam UW-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeUwDnase/wgEncodeUwDnase416bC57bl6MAdult8wksAlnRep2.bam 416B DnaseSeq Alignments 2 bam UW-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeUwDnase/wgEncodeUwDnase416bC57bl6MAdult8wksHotspotsRep1.broadPeak.gz 416B DnaseSeq Hotspots 1 broadPeak UW-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeUwDnase/wgEncodeUwDnase416bC57bl6MAdult8wksHotspotsRep2.broadPeak.gz 416B DnaseSeq Hotspots 2 broadPeak UW-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeUwDnase/wgEncodeUwDnase416bC57bl6MAdult8wksPkRep1.narrowPeak.gz 416B DnaseSeq Peaks 1 narrowPeak UW-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeUwDnase/wgEncodeUwDnase416bC57bl6MAdult8wksPkRep2.narrowPeak.gz 416B DnaseSeq Peaks 2 narrowPeak UW-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeUwDnase/wgEncodeUwDnase416bC57bl6MAdult8wksSigRep1.bigWig 416B DnaseSeq Signal 1 bigWig UW-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeUwDnase/wgEncodeUwDnase416bC57bl6MAdult8wksSigRep2.bigWig 416B DnaseSeq Signal 2 bigWig UW-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeUwDnase/wgEncodeUwDnaseA20BalbcannMAdult8wksAlnRep1.bam A20 DnaseSeq Alignments 1 bam UW-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeUwDnase/wgEncodeUwDnaseA20BalbcannMAdult8wksAlnRep2.bam A20 DnaseSeq Alignments 2 bam UW-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeUwDnase/wgEncodeUwDnaseA20BalbcannMAdult8wksHotspotsRep1.broadPeak.gz A20 DnaseSeq Hotspots 1 broadPeak UW-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeUwDnase/wgEncodeUwDnaseA20BalbcannMAdult8wksHotspotsRep2.broadPeak.gz A20 DnaseSeq Hotspots 2 broadPeak UW-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeUwDnase/wgEncodeUwDnaseA20BalbcannMAdult8wksPkRep1.narrowPeak.gz A20 DnaseSeq Peaks 1 narrowPeak UW-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeUwDnase/wgEncodeUwDnaseA20BalbcannMAdult8wksPkRep2.narrowPeak.gz A20 DnaseSeq Peaks 2 narrowPeak UW-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeUwDnase/wgEncodeUwDnaseA20BalbcannMAdult8wksSigRep1.bigWig A20 DnaseSeq Signal 1 bigWig UW-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeUwDnase/wgEncodeUwDnaseA20BalbcannMAdult8wksSigRep2.bigWig A20 DnaseSeq Signal 2 bigWig UW-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeUwDnase/wgEncodeUwDnaseBcellcd19pC57bl6MAdult8wksAlnRep1.bam B-cell_(CD19+) DnaseSeq Alignments 1 bam UW-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeUwDnase/wgEncodeUwDnaseBcellcd19pC57bl6MAdult8wksAlnRep2.bam B-cell_(CD19+) DnaseSeq Alignments 2 bam UW-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeUwDnase/wgEncodeUwDnaseBcellcd19pC57bl6MAdult8wksHotspotsRep1.broadPeak.gz B-cell_(CD19+) DnaseSeq Hotspots 1 broadPeak UW-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeUwDnase/wgEncodeUwDnaseBcellcd19pC57bl6MAdult8wksHotspotsRep2.broadPeak.gz B-cell_(CD19+) DnaseSeq Hotspots 2 broadPeak UW-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeUwDnase/wgEncodeUwDnaseBcellcd19pC57bl6MAdult8wksPkRep1.narrowPeak.gz B-cell_(CD19+) DnaseSeq Peaks 1 narrowPeak UW-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeUwDnase/wgEncodeUwDnaseBcellcd19pC57bl6MAdult8wksPkRep2.narrowPeak.gz B-cell_(CD19+) DnaseSeq Peaks 2 narrowPeak UW-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeUwDnase/wgEncodeUwDnaseBcellcd19pC57bl6MAdult8wksSigRep1.bigWig B-cell_(CD19+) DnaseSeq Signal 1 bigWig UW-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeUwDnase/wgEncodeUwDnaseBcellcd19pC57bl6MAdult8wksSigRep2.bigWig B-cell_(CD19+) DnaseSeq Signal 2 bigWig UW-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeUwDnase/wgEncodeUwDnaseBcellcd43nC57bl6MAdult8wksAlnRep1.bam B-cell_(CD43-) DnaseSeq Alignments 1 bam UW-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeUwDnase/wgEncodeUwDnaseBcellcd43nC57bl6MAdult8wksAlnRep2.bam B-cell_(CD43-) DnaseSeq Alignments 2 bam UW-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeUwDnase/wgEncodeUwDnaseBcellcd43nC57bl6MAdult8wksAlnRep3.bam B-cell_(CD43-) DnaseSeq Alignments 3 bam UW-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeUwDnase/wgEncodeUwDnaseBcellcd43nC57bl6MAdult8wksAlnRep4.bam B-cell_(CD43-) DnaseSeq Alignments 4 bam UW-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeUwDnase/wgEncodeUwDnaseBcellcd43nC57bl6MAdult8wksHotspotsRep1.broadPeak.gz B-cell_(CD43-) DnaseSeq Hotspots 1 broadPeak UW-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeUwDnase/wgEncodeUwDnaseBcellcd43nC57bl6MAdult8wksHotspotsRep2.broadPeak.gz B-cell_(CD43-) DnaseSeq Hotspots 2 broadPeak UW-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeUwDnase/wgEncodeUwDnaseBcellcd43nC57bl6MAdult8wksHotspotsRep3.broadPeak.gz B-cell_(CD43-) DnaseSeq Hotspots 3 broadPeak UW-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeUwDnase/wgEncodeUwDnaseBcellcd43nC57bl6MAdult8wksHotspotsRep4.broadPeak.gz B-cell_(CD43-) DnaseSeq Hotspots 4 broadPeak UW-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeUwDnase/wgEncodeUwDnaseBcellcd43nC57bl6MAdult8wksPkRep1.narrowPeak.gz B-cell_(CD43-) DnaseSeq Peaks 1 narrowPeak UW-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeUwDnase/wgEncodeUwDnaseBcellcd43nC57bl6MAdult8wksPkRep2.narrowPeak.gz B-cell_(CD43-) DnaseSeq Peaks 2 narrowPeak UW-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeUwDnase/wgEncodeUwDnaseBcellcd43nC57bl6MAdult8wksPkRep3.narrowPeak.gz B-cell_(CD43-) DnaseSeq Peaks 3 narrowPeak UW-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeUwDnase/wgEncodeUwDnaseBcellcd43nC57bl6MAdult8wksPkRep4.narrowPeak.gz B-cell_(CD43-) DnaseSeq Peaks 4 narrowPeak UW-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeUwDnase/wgEncodeUwDnaseBcellcd43nC57bl6MAdult8wksSigRep1.bigWig B-cell_(CD43-) DnaseSeq Signal 1 bigWig UW-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeUwDnase/wgEncodeUwDnaseBcellcd43nC57bl6MAdult8wksSigRep2.bigWig B-cell_(CD43-) DnaseSeq Signal 2 bigWig UW-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeUwDnase/wgEncodeUwDnaseBcellcd43nC57bl6MAdult8wksSigRep3.bigWig B-cell_(CD43-) DnaseSeq Signal 3 bigWig UW-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeUwDnase/wgEncodeUwDnaseBcellcd43nC57bl6MAdult8wksSigRep4.bigWig B-cell_(CD43-) DnaseSeq Signal 4 bigWig UW-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeUwDnase/wgEncodeUwDnaseCbellumC57bl6MAdult8wksAlnRep2.bam Cerebellum DnaseSeq Alignments 2 bam UW-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeUwDnase/wgEncodeUwDnaseCbellumC57bl6MAdult8wksAlnRep3.bam Cerebellum DnaseSeq Alignments 3 bam UW-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeUwDnase/wgEncodeUwDnaseCbellumC57bl6MAdult8wksHotspotsRep2.broadPeak.gz Cerebellum DnaseSeq Hotspots 2 broadPeak UW-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeUwDnase/wgEncodeUwDnaseCbellumC57bl6MAdult8wksHotspotsRep3.broadPeak.gz Cerebellum DnaseSeq Hotspots 3 broadPeak UW-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeUwDnase/wgEncodeUwDnaseCbellumC57bl6MAdult8wksPkRep2.narrowPeak.gz Cerebellum DnaseSeq Peaks 2 narrowPeak UW-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeUwDnase/wgEncodeUwDnaseCbellumC57bl6MAdult8wksPkRep3.narrowPeak.gz Cerebellum DnaseSeq Peaks 3 narrowPeak UW-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeUwDnase/wgEncodeUwDnaseCbellumC57bl6MAdult8wksSigRep2.bigWig Cerebellum DnaseSeq Signal 2 bigWig UW-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeUwDnase/wgEncodeUwDnaseCbellumC57bl6MAdult8wksSigRep3.bigWig Cerebellum DnaseSeq Signal 3 bigWig UW-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeUwDnase/wgEncodeUwDnaseCerebellumC57bl6MAdult8wksAlnRep1.bam Cerebellum DnaseSeq Alignments 1 bam UW-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeUwDnase/wgEncodeUwDnaseCerebellumC57bl6MAdult8wksHotspotsRep1.broadPeak.gz Cerebellum DnaseSeq Hotspots 1 broadPeak UW-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeUwDnase/wgEncodeUwDnaseCerebellumC57bl6MAdult8wksPkRep1.narrowPeak.gz Cerebellum DnaseSeq Peaks 1 narrowPeak UW-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeUwDnase/wgEncodeUwDnaseCerebellumC57bl6MAdult8wksSigRep1.bigWig Cerebellum DnaseSeq Signal 1 bigWig UW-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeUwDnase/wgEncodeUwDnaseCerebrumC57bl6MAdult8wksAlnRep1.bam Cerebrum DnaseSeq Alignments 1 bam UW-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeUwDnase/wgEncodeUwDnaseCerebrumC57bl6MAdult8wksAlnRep2.bam Cerebrum DnaseSeq Alignments 2 bam UW-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeUwDnase/wgEncodeUwDnaseCerebrumC57bl6MAdult8wksAlnRep3.bam Cerebrum DnaseSeq Alignments 3 bam UW-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeUwDnase/wgEncodeUwDnaseCerebrumC57bl6MAdult8wksHotspotsRep1.broadPeak.gz Cerebrum DnaseSeq Hotspots 1 broadPeak UW-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeUwDnase/wgEncodeUwDnaseCerebrumC57bl6MAdult8wksHotspotsRep2.broadPeak.gz Cerebrum DnaseSeq Hotspots 2 broadPeak UW-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeUwDnase/wgEncodeUwDnaseCerebrumC57bl6MAdult8wksHotspotsRep3.broadPeak.gz Cerebrum DnaseSeq Hotspots 3 broadPeak UW-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeUwDnase/wgEncodeUwDnaseCerebrumC57bl6MAdult8wksPkRep1.narrowPeak.gz Cerebrum DnaseSeq Peaks 1 narrowPeak UW-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeUwDnase/wgEncodeUwDnaseCerebrumC57bl6MAdult8wksPkRep2.narrowPeak.gz Cerebrum DnaseSeq Peaks 2 narrowPeak UW-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeUwDnase/wgEncodeUwDnaseCerebrumC57bl6MAdult8wksPkRep3.narrowPeak.gz Cerebrum DnaseSeq Peaks 3 narrowPeak UW-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeUwDnase/wgEncodeUwDnaseCerebrumC57bl6MAdult8wksSigRep1.bigWig Cerebrum DnaseSeq Signal 1 bigWig UW-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeUwDnase/wgEncodeUwDnaseCerebrumC57bl6MAdult8wksSigRep2.bigWig Cerebrum DnaseSeq Signal 2 bigWig UW-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeUwDnase/wgEncodeUwDnaseCerebrumC57bl6MAdult8wksSigRep3.bigWig Cerebrum DnaseSeq Signal 3 bigWig UW-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeUwDnase/wgEncodeUwDnaseCh122a4bFImmortalAlnRep1.bam CH12 DnaseSeq Alignments 1 bam UW-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeUwDnase/wgEncodeUwDnaseCh122a4bFImmortalAlnRep2.bam CH12 DnaseSeq Alignments 2 bam UW-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeUwDnase/wgEncodeUwDnaseCh122a4bFImmortalHotspotsRep1.broadPeak.gz CH12 DnaseSeq Hotspots 1 broadPeak UW-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeUwDnase/wgEncodeUwDnaseCh122a4bFImmortalHotspotsRep2.broadPeak.gz CH12 DnaseSeq Hotspots 2 broadPeak UW-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeUwDnase/wgEncodeUwDnaseCh122a4bFImmortalPkRep1.narrowPeak.gz CH12 DnaseSeq Peaks 1 narrowPeak UW-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeUwDnase/wgEncodeUwDnaseCh122a4bFImmortalPkRep2.narrowPeak.gz CH12 DnaseSeq Peaks 2 narrowPeak UW-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeUwDnase/wgEncodeUwDnaseCh122a4bFImmortalSigRep1.bigWig CH12 DnaseSeq Signal 1 bigWig UW-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeUwDnase/wgEncodeUwDnaseCh122a4bFImmortalSigRep2.bigWig CH12 DnaseSeq Signal 2 bigWig UW-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeUwDnase/wgEncodeUwDnaseEpcmppCd1ME14halfAlnRep1.bam EPC_(CD117-_CD71+_TER119+) DnaseSeq Alignments 1 bam UW-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeUwDnase/wgEncodeUwDnaseEpcmppCd1ME14halfHotspotsRep1.broadPeak.gz EPC_(CD117-_CD71+_TER119+) DnaseSeq Hotspots 1 broadPeak UW-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeUwDnase/wgEncodeUwDnaseEpcmppCd1ME14halfPkRep1.narrowPeak.gz EPC_(CD117-_CD71+_TER119+) DnaseSeq Peaks 1 narrowPeak UW-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeUwDnase/wgEncodeUwDnaseEpcmppCd1ME14halfSigRep1.bigWig EPC_(CD117-_CD71+_TER119+) DnaseSeq Signal 1 bigWig UW-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeUwDnase/wgEncodeUwDnaseEpcpmmCd1ME14halfAlnRep1.bam EPC_(CD117+_CD71-_TER119-) DnaseSeq Alignments 1 bam UW-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeUwDnase/wgEncodeUwDnaseEpcpmmCd1ME14halfHotspotsRep1.broadPeak.gz EPC_(CD117+_CD71-_TER119-) DnaseSeq Hotspots 1 broadPeak UW-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeUwDnase/wgEncodeUwDnaseEpcpmmCd1ME14halfPkRep1.narrowPeak.gz EPC_(CD117+_CD71-_TER119-) DnaseSeq Peaks 1 narrowPeak UW-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeUwDnase/wgEncodeUwDnaseEpcpmmCd1ME14halfSigRep1.bigWig EPC_(CD117+_CD71-_TER119-) DnaseSeq Signal 1 bigWig UW-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeUwDnase/wgEncodeUwDnaseEpcppmCd1ME14halfAlnRep1.bam EPC_(CD117+_CD71+_TER119-) DnaseSeq Alignments 1 bam UW-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeUwDnase/wgEncodeUwDnaseEpcppmCd1ME14halfHotspotsRep1.broadPeak.gz EPC_(CD117+_CD71+_TER119-) DnaseSeq Hotspots 1 broadPeak UW-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeUwDnase/wgEncodeUwDnaseEpcppmCd1ME14halfPkRep1.narrowPeak.gz EPC_(CD117+_CD71+_TER119-) DnaseSeq Peaks 1 narrowPeak UW-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeUwDnase/wgEncodeUwDnaseEpcppmCd1ME14halfSigRep1.bigWig EPC_(CD117+_CD71+_TER119-) DnaseSeq Signal 1 bigWig UW-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeUwDnase/wgEncodeUwDnaseEpcpppCd1ME14halfAlnRep1.bam EPC_(CD117+_CD71+_TER119+) DnaseSeq Alignments 1 bam UW-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeUwDnase/wgEncodeUwDnaseEpcpppCd1ME14halfHotspotsRep1.broadPeak.gz EPC_(CD117+_CD71+_TER119+) DnaseSeq Hotspots 1 broadPeak UW-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeUwDnase/wgEncodeUwDnaseEpcpppCd1ME14halfPkRep1.narrowPeak.gz EPC_(CD117+_CD71+_TER119+) DnaseSeq Peaks 1 narrowPeak UW-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeUwDnase/wgEncodeUwDnaseEpcpppCd1ME14halfSigRep1.bigWig EPC_(CD117+_CD71+_TER119+) DnaseSeq Signal 1 bigWig UW-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeUwDnase/wgEncodeUwDnaseEscj7S129ME0AlnRep1.bam ES-CJ7 DnaseSeq Alignments 1 bam UW-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeUwDnase/wgEncodeUwDnaseEscj7S129ME0AlnRep2.bam ES-CJ7 DnaseSeq Alignments 2 bam UW-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeUwDnase/wgEncodeUwDnaseEscj7S129ME0HotspotsRep1.broadPeak.gz ES-CJ7 DnaseSeq Hotspots 1 broadPeak UW-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeUwDnase/wgEncodeUwDnaseEscj7S129ME0HotspotsRep2.broadPeak.gz ES-CJ7 DnaseSeq Hotspots 2 broadPeak UW-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeUwDnase/wgEncodeUwDnaseEscj7S129ME0PkRep1.narrowPeak.gz ES-CJ7 DnaseSeq Peaks 1 narrowPeak UW-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeUwDnase/wgEncodeUwDnaseEscj7S129ME0PkRep2.narrowPeak.gz ES-CJ7 DnaseSeq Peaks 2 narrowPeak UW-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeUwDnase/wgEncodeUwDnaseEscj7S129ME0SigRep1.bigWig ES-CJ7 DnaseSeq Signal 1 bigWig UW-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeUwDnase/wgEncodeUwDnaseEscj7S129ME0SigRep2.bigWig ES-CJ7 DnaseSeq Signal 2 bigWig UW-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeUwDnase/wgEncodeUwDnaseEse14129olaME0AlnRep1.bam ES-E14 DnaseSeq Alignments 1 bam UW-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeUwDnase/wgEncodeUwDnaseEse14129olaME0AlnRep2.bam ES-E14 DnaseSeq Alignments 2 bam UW-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeUwDnase/wgEncodeUwDnaseEse14129olaME0HotspotsRep1.broadPeak.gz ES-E14 DnaseSeq Hotspots 1 broadPeak UW-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeUwDnase/wgEncodeUwDnaseEse14129olaME0HotspotsRep2.broadPeak.gz ES-E14 DnaseSeq Hotspots 2 broadPeak UW-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeUwDnase/wgEncodeUwDnaseEse14129olaME0PkRep1.narrowPeak.gz ES-E14 DnaseSeq Peaks 1 narrowPeak UW-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeUwDnase/wgEncodeUwDnaseEse14129olaME0PkRep2.narrowPeak.gz ES-E14 DnaseSeq Peaks 2 narrowPeak UW-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeUwDnase/wgEncodeUwDnaseEse14129olaME0SigRep1.bigWig ES-E14 DnaseSeq Signal 1 bigWig UW-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeUwDnase/wgEncodeUwDnaseEse14129olaME0SigRep2.bigWig ES-E14 DnaseSeq Signal 2 bigWig UW-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeUwDnase/wgEncodeUwDnaseEsww6UknME0AlnRep1.bam ES-WW6 DnaseSeq Alignments 1 bam UW-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeUwDnase/wgEncodeUwDnaseEsww6UknME0AlnRep2.bam ES-WW6 DnaseSeq Alignments 2 bam UW-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeUwDnase/wgEncodeUwDnaseEsww6UknME0HotspotsRep1.broadPeak.gz ES-WW6 DnaseSeq Hotspots 1 broadPeak UW-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeUwDnase/wgEncodeUwDnaseEsww6UknME0HotspotsRep2.broadPeak.gz ES-WW6 DnaseSeq Hotspots 2 broadPeak UW-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeUwDnase/wgEncodeUwDnaseEsww6UknME0PkRep1.narrowPeak.gz ES-WW6 DnaseSeq Peaks 1 narrowPeak UW-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeUwDnase/wgEncodeUwDnaseEsww6UknME0PkRep2.narrowPeak.gz ES-WW6 DnaseSeq Peaks 2 narrowPeak UW-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeUwDnase/wgEncodeUwDnaseEsww6UknME0SigRep1.bigWig ES-WW6 DnaseSeq Signal 1 bigWig UW-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeUwDnase/wgEncodeUwDnaseEsww6UknME0SigRep2.bigWig ES-WW6 DnaseSeq Signal 2 bigWig UW-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeUwDnase/wgEncodeUwDnaseEsww6koUknME0AlnRep1.bam ES-WW6_F1KO DnaseSeq Alignments 1 bam UW-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeUwDnase/wgEncodeUwDnaseEsww6koUknME0AlnRep2.bam ES-WW6_F1KO DnaseSeq Alignments 2 bam UW-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeUwDnase/wgEncodeUwDnaseEsww6koUknME0HotspotsRep1.broadPeak.gz ES-WW6_F1KO DnaseSeq Hotspots 1 broadPeak UW-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeUwDnase/wgEncodeUwDnaseEsww6koUknME0HotspotsRep2.broadPeak.gz ES-WW6_F1KO DnaseSeq Hotspots 2 broadPeak UW-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeUwDnase/wgEncodeUwDnaseEsww6koUknME0PkRep1.narrowPeak.gz ES-WW6_F1KO DnaseSeq Peaks 1 narrowPeak UW-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeUwDnase/wgEncodeUwDnaseEsww6koUknME0PkRep2.narrowPeak.gz ES-WW6_F1KO DnaseSeq Peaks 2 narrowPeak UW-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeUwDnase/wgEncodeUwDnaseEsww6koUknME0SigRep1.bigWig ES-WW6_F1KO DnaseSeq Signal 1 bigWig UW-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeUwDnase/wgEncodeUwDnaseEsww6koUknME0SigRep2.bigWig ES-WW6_F1KO DnaseSeq Signal 2 bigWig UW-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeUwDnase/wgEncodeUwDnaseFatC57bl6MAdult8wksAlnRep1.bam FatPad DnaseSeq Alignments 1 bam UW-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeUwDnase/wgEncodeUwDnaseFatC57bl6MAdult8wksAlnRep2.bam FatPad DnaseSeq Alignments 2 bam UW-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeUwDnase/wgEncodeUwDnaseFatC57bl6MAdult8wksHotspotsRep1.broadPeak.gz FatPad DnaseSeq Hotspots 1 broadPeak UW-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeUwDnase/wgEncodeUwDnaseFatC57bl6MAdult8wksHotspotsRep2.broadPeak.gz FatPad DnaseSeq Hotspots 2 broadPeak UW-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeUwDnase/wgEncodeUwDnaseFatC57bl6MAdult8wksPkRep1.narrowPeak.gz FatPad DnaseSeq Peaks 1 narrowPeak UW-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeUwDnase/wgEncodeUwDnaseFatC57bl6MAdult8wksPkRep2.narrowPeak.gz FatPad DnaseSeq Peaks 2 narrowPeak UW-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeUwDnase/wgEncodeUwDnaseFatC57bl6MAdult8wksSigRep1.bigWig FatPad DnaseSeq Signal 1 bigWig UW-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeUwDnase/wgEncodeUwDnaseFatC57bl6MAdult8wksSigRep2.bigWig FatPad DnaseSeq Signal 2 bigWig UW-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeUwDnase/wgEncodeUwDnaseFibroblastC57bl6MAdult8wksAlnRep1.bam Fibroblast DnaseSeq Alignments 1 bam UW-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeUwDnase/wgEncodeUwDnaseFibroblastC57bl6MAdult8wksAlnRep2.bam Fibroblast DnaseSeq Alignments 2 bam UW-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeUwDnase/wgEncodeUwDnaseFibroblastC57bl6MAdult8wksHotspotsRep1.broadPeak.gz Fibroblast DnaseSeq Hotspots 1 broadPeak UW-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeUwDnase/wgEncodeUwDnaseFibroblastC57bl6MAdult8wksHotspotsRep2.broadPeak.gz Fibroblast DnaseSeq Hotspots 2 broadPeak UW-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeUwDnase/wgEncodeUwDnaseFibroblastC57bl6MAdult8wksPkRep1.narrowPeak.gz Fibroblast DnaseSeq Peaks 1 narrowPeak UW-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeUwDnase/wgEncodeUwDnaseFibroblastC57bl6MAdult8wksPkRep2.narrowPeak.gz Fibroblast DnaseSeq Peaks 2 narrowPeak UW-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeUwDnase/wgEncodeUwDnaseFibroblastC57bl6MAdult8wksSigRep1.bigWig Fibroblast DnaseSeq Signal 1 bigWig UW-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeUwDnase/wgEncodeUwDnaseFibroblastC57bl6MAdult8wksSigRep2.bigWig Fibroblast DnaseSeq Signal 2 bigWig UW-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeUwDnase/wgEncodeUwDnaseFlbudCd1ME11halfAlnRep1.bam ForelimbBud DnaseSeq Alignments 1 bam UW-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeUwDnase/wgEncodeUwDnaseFlbudCd1ME11halfAlnRep2.bam ForelimbBud DnaseSeq Alignments 2 bam UW-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeUwDnase/wgEncodeUwDnaseFlbudCd1ME11halfHotspotsRep1.broadPeak.gz ForelimbBud DnaseSeq Hotspots 1 broadPeak UW-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeUwDnase/wgEncodeUwDnaseFlbudCd1ME11halfHotspotsRep2.broadPeak.gz ForelimbBud DnaseSeq Hotspots 2 broadPeak UW-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeUwDnase/wgEncodeUwDnaseFlbudCd1ME11halfPkRep1.narrowPeak.gz ForelimbBud DnaseSeq Peaks 1 narrowPeak UW-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeUwDnase/wgEncodeUwDnaseFlbudCd1ME11halfPkRep2.narrowPeak.gz ForelimbBud DnaseSeq Peaks 2 narrowPeak UW-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeUwDnase/wgEncodeUwDnaseFlbudCd1ME11halfSigRep1.bigWig ForelimbBud DnaseSeq Signal 1 bigWig UW-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeUwDnase/wgEncodeUwDnaseFlbudCd1ME11halfSigRep2.bigWig ForelimbBud DnaseSeq Signal 2 bigWig UW-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeUwDnase/wgEncodeUwDnaseGfatC57bl6MAdult8wksAlnRep1.bam GenitalFatPad DnaseSeq Alignments 1 bam UW-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeUwDnase/wgEncodeUwDnaseGfatC57bl6MAdult8wksAlnRep2.bam GenitalFatPad DnaseSeq Alignments 2 bam UW-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeUwDnase/wgEncodeUwDnaseGfatC57bl6MAdult8wksHotspotsRep1.broadPeak.gz GenitalFatPad DnaseSeq Hotspots 1 broadPeak UW-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeUwDnase/wgEncodeUwDnaseGfatC57bl6MAdult8wksHotspotsRep2.broadPeak.gz GenitalFatPad DnaseSeq Hotspots 2 broadPeak UW-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeUwDnase/wgEncodeUwDnaseGfatC57bl6MAdult8wksPkRep1.narrowPeak.gz GenitalFatPad DnaseSeq Peaks 1 narrowPeak UW-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeUwDnase/wgEncodeUwDnaseGfatC57bl6MAdult8wksPkRep2.narrowPeak.gz GenitalFatPad DnaseSeq Peaks 2 narrowPeak UW-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeUwDnase/wgEncodeUwDnaseGfatC57bl6MAdult8wksSigRep1.bigWig GenitalFatPad DnaseSeq Signal 1 bigWig UW-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeUwDnase/wgEncodeUwDnaseGfatC57bl6MAdult8wksSigRep2.bigWig GenitalFatPad DnaseSeq Signal 2 bigWig UW-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeUwDnase/wgEncodeUwDnaseHeartC57bl6MAdult8wksAlnRep1.bam Heart DnaseSeq Alignments 1 bam UW-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeUwDnase/wgEncodeUwDnaseHeartC57bl6MAdult8wksAlnRep2.bam Heart DnaseSeq Alignments 2 bam UW-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeUwDnase/wgEncodeUwDnaseHeartC57bl6MAdult8wksHotspotsRep1.broadPeak.gz Heart DnaseSeq Hotspots 1 broadPeak UW-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeUwDnase/wgEncodeUwDnaseHeartC57bl6MAdult8wksHotspotsRep2.broadPeak.gz Heart DnaseSeq Hotspots 2 broadPeak UW-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeUwDnase/wgEncodeUwDnaseHeartC57bl6MAdult8wksPkRep1.narrowPeak.gz Heart DnaseSeq Peaks 1 narrowPeak UW-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeUwDnase/wgEncodeUwDnaseHeartC57bl6MAdult8wksPkRep2.narrowPeak.gz Heart DnaseSeq Peaks 2 narrowPeak UW-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeUwDnase/wgEncodeUwDnaseHeartC57bl6MAdult8wksSigRep1.bigWig Heart DnaseSeq Signal 1 bigWig UW-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeUwDnase/wgEncodeUwDnaseHeartC57bl6MAdult8wksSigRep2.bigWig Heart DnaseSeq Signal 2 bigWig UW-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeUwDnase/wgEncodeUwDnaseHlbudCd1ME11halfAlnRep1.bam HindlimbBud DnaseSeq Alignments 1 bam UW-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeUwDnase/wgEncodeUwDnaseHlbudCd1ME11halfAlnRep2.bam HindlimbBud DnaseSeq Alignments 2 bam UW-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeUwDnase/wgEncodeUwDnaseHlbudCd1ME11halfHotspotsRep1.broadPeak.gz HindlimbBud DnaseSeq Hotspots 1 broadPeak UW-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeUwDnase/wgEncodeUwDnaseHlbudCd1ME11halfHotspotsRep2.broadPeak.gz HindlimbBud DnaseSeq Hotspots 2 broadPeak UW-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeUwDnase/wgEncodeUwDnaseHlbudCd1ME11halfPkRep1.narrowPeak.gz HindlimbBud DnaseSeq Peaks 1 narrowPeak UW-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeUwDnase/wgEncodeUwDnaseHlbudCd1ME11halfPkRep2.narrowPeak.gz HindlimbBud DnaseSeq Peaks 2 narrowPeak UW-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeUwDnase/wgEncodeUwDnaseHlbudCd1ME11halfSigRep1.bigWig HindlimbBud DnaseSeq Signal 1 bigWig UW-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeUwDnase/wgEncodeUwDnaseHlbudCd1ME11halfSigRep2.bigWig HindlimbBud DnaseSeq Signal 2 bigWig UW-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeUwDnase/wgEncodeUwDnaseHlembryoCd1ME11halfAlnRep1.bam HeadlessEmbryo DnaseSeq Alignments 1 bam UW-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeUwDnase/wgEncodeUwDnaseHlembryoCd1ME11halfAlnRep2.bam HeadlessEmbryo DnaseSeq Alignments 2 bam UW-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeUwDnase/wgEncodeUwDnaseHlembryoCd1ME11halfHotspotsRep1.broadPeak.gz HeadlessEmbryo DnaseSeq Hotspots 1 broadPeak UW-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeUwDnase/wgEncodeUwDnaseHlembryoCd1ME11halfHotspotsRep2.broadPeak.gz HeadlessEmbryo DnaseSeq Hotspots 2 broadPeak UW-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeUwDnase/wgEncodeUwDnaseHlembryoCd1ME11halfPkRep1.narrowPeak.gz HeadlessEmbryo DnaseSeq Peaks 1 narrowPeak UW-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeUwDnase/wgEncodeUwDnaseHlembryoCd1ME11halfPkRep2.narrowPeak.gz HeadlessEmbryo DnaseSeq Peaks 2 narrowPeak UW-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeUwDnase/wgEncodeUwDnaseHlembryoCd1ME11halfSigRep1.bigWig HeadlessEmbryo DnaseSeq Signal 1 bigWig UW-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeUwDnase/wgEncodeUwDnaseHlembryoCd1ME11halfSigRep2.bigWig HeadlessEmbryo DnaseSeq Signal 2 bigWig UW-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeUwDnase/wgEncodeUwDnaseKidneyC57bl6MAdult8wksAlnRep1.bam Kidney DnaseSeq Alignments 1 bam UW-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeUwDnase/wgEncodeUwDnaseKidneyC57bl6MAdult8wksAlnRep2.bam Kidney DnaseSeq Alignments 2 bam UW-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeUwDnase/wgEncodeUwDnaseKidneyC57bl6MAdult8wksHotspotsRep1.broadPeak.gz Kidney DnaseSeq Hotspots 1 broadPeak UW-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeUwDnase/wgEncodeUwDnaseKidneyC57bl6MAdult8wksHotspotsRep2.broadPeak.gz Kidney DnaseSeq Hotspots 2 broadPeak UW-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeUwDnase/wgEncodeUwDnaseKidneyC57bl6MAdult8wksPkRep1.narrowPeak.gz Kidney DnaseSeq Peaks 1 narrowPeak UW-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeUwDnase/wgEncodeUwDnaseKidneyC57bl6MAdult8wksPkRep2.narrowPeak.gz Kidney DnaseSeq Peaks 2 narrowPeak UW-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeUwDnase/wgEncodeUwDnaseKidneyC57bl6MAdult8wksSigRep1.bigWig Kidney DnaseSeq Signal 1 bigWig UW-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeUwDnase/wgEncodeUwDnaseKidneyC57bl6MAdult8wksSigRep2.bigWig Kidney DnaseSeq Signal 2 bigWig UW-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeUwDnase/wgEncodeUwDnaseLgintC57bl6MAdult8wksAlnRep1.bam LgIntestine DnaseSeq Alignments 1 bam UW-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeUwDnase/wgEncodeUwDnaseLgintC57bl6MAdult8wksAlnRep2.bam LgIntestine DnaseSeq Alignments 2 bam UW-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeUwDnase/wgEncodeUwDnaseLgintC57bl6MAdult8wksHotspotsRep1.broadPeak.gz LgIntestine DnaseSeq Hotspots 1 broadPeak UW-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeUwDnase/wgEncodeUwDnaseLgintC57bl6MAdult8wksHotspotsRep2.broadPeak.gz LgIntestine DnaseSeq Hotspots 2 broadPeak UW-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeUwDnase/wgEncodeUwDnaseLgintC57bl6MAdult8wksPkRep1.narrowPeak.gz LgIntestine DnaseSeq Peaks 1 narrowPeak UW-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeUwDnase/wgEncodeUwDnaseLgintC57bl6MAdult8wksPkRep2.narrowPeak.gz LgIntestine DnaseSeq Peaks 2 narrowPeak UW-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeUwDnase/wgEncodeUwDnaseLgintC57bl6MAdult8wksSigRep1.bigWig LgIntestine DnaseSeq Signal 1 bigWig UW-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeUwDnase/wgEncodeUwDnaseLgintC57bl6MAdult8wksSigRep2.bigWig LgIntestine DnaseSeq Signal 2 bigWig UW-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeUwDnase/wgEncodeUwDnaseLiver129dlcrME14halfAlnRep1.bam Liver DnaseSeq Alignments 1 bam UW-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeUwDnase/wgEncodeUwDnaseLiver129dlcrME14halfAlnRep2.bam Liver DnaseSeq Alignments 2 bam UW-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeUwDnase/wgEncodeUwDnaseLiver129dlcrME14halfHotspotsRep1.broadPeak.gz Liver DnaseSeq Hotspots 1 broadPeak UW-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeUwDnase/wgEncodeUwDnaseLiver129dlcrME14halfHotspotsRep2.broadPeak.gz Liver DnaseSeq Hotspots 2 broadPeak UW-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeUwDnase/wgEncodeUwDnaseLiver129dlcrME14halfPkRep1.narrowPeak.gz Liver DnaseSeq Peaks 1 narrowPeak UW-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeUwDnase/wgEncodeUwDnaseLiver129dlcrME14halfPkRep2.narrowPeak.gz Liver DnaseSeq Peaks 2 narrowPeak UW-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeUwDnase/wgEncodeUwDnaseLiver129dlcrME14halfSigRep1.bigWig Liver DnaseSeq Signal 1 bigWig UW-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeUwDnase/wgEncodeUwDnaseLiver129dlcrME14halfSigRep2.bigWig Liver DnaseSeq Signal 2 bigWig UW-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeUwDnase/wgEncodeUwDnaseLiverC57bl6MAdult8wksAlnRep1.bam Liver DnaseSeq Alignments 1 bam UW-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeUwDnase/wgEncodeUwDnaseLiverC57bl6MAdult8wksAlnRep10.bam Liver DnaseSeq Alignments 10 bam UW-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeUwDnase/wgEncodeUwDnaseLiverC57bl6MAdult8wksAlnRep11.bam Liver DnaseSeq Alignments 11 bam UW-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeUwDnase/wgEncodeUwDnaseLiverC57bl6MAdult8wksAlnRep12.bam Liver DnaseSeq Alignments 12 bam UW-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeUwDnase/wgEncodeUwDnaseLiverC57bl6MAdult8wksAlnRep13.bam Liver DnaseSeq Alignments 13 bam UW-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeUwDnase/wgEncodeUwDnaseLiverC57bl6MAdult8wksAlnRep14.bam Liver DnaseSeq Alignments 14 bam UW-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeUwDnase/wgEncodeUwDnaseLiverC57bl6MAdult8wksAlnRep2.bam Liver DnaseSeq Alignments 2 bam UW-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeUwDnase/wgEncodeUwDnaseLiverC57bl6MAdult8wksAlnRep3.bam Liver DnaseSeq Alignments 3 bam UW-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeUwDnase/wgEncodeUwDnaseLiverC57bl6MAdult8wksAlnRep4.bam Liver DnaseSeq Alignments 4 bam UW-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeUwDnase/wgEncodeUwDnaseLiverC57bl6MAdult8wksAlnRep5.bam Liver DnaseSeq Alignments 5 bam UW-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeUwDnase/wgEncodeUwDnaseLiverC57bl6MAdult8wksAlnRep6.bam Liver DnaseSeq Alignments 6 bam UW-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeUwDnase/wgEncodeUwDnaseLiverC57bl6MAdult8wksAlnRep7.bam Liver DnaseSeq Alignments 7 bam UW-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeUwDnase/wgEncodeUwDnaseLiverC57bl6MAdult8wksAlnRep8.bam Liver DnaseSeq Alignments 8 bam UW-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeUwDnase/wgEncodeUwDnaseLiverC57bl6MAdult8wksAlnRep9.bam Liver DnaseSeq Alignments 9 bam UW-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeUwDnase/wgEncodeUwDnaseLiverC57bl6MAdult8wksHotspotsRep1.broadPeak.gz Liver DnaseSeq Hotspots 1 broadPeak UW-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeUwDnase/wgEncodeUwDnaseLiverC57bl6MAdult8wksHotspotsRep10.broadPeak.gz Liver DnaseSeq Hotspots 10 broadPeak UW-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeUwDnase/wgEncodeUwDnaseLiverC57bl6MAdult8wksHotspotsRep11.broadPeak.gz Liver DnaseSeq Hotspots 11 broadPeak UW-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeUwDnase/wgEncodeUwDnaseLiverC57bl6MAdult8wksHotspotsRep12.broadPeak.gz Liver DnaseSeq Hotspots 12 broadPeak UW-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeUwDnase/wgEncodeUwDnaseLiverC57bl6MAdult8wksHotspotsRep13.broadPeak.gz Liver DnaseSeq Hotspots 13 broadPeak UW-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeUwDnase/wgEncodeUwDnaseLiverC57bl6MAdult8wksHotspotsRep14.broadPeak.gz Liver DnaseSeq Hotspots 14 broadPeak UW-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeUwDnase/wgEncodeUwDnaseLiverC57bl6MAdult8wksHotspotsRep2.broadPeak.gz Liver DnaseSeq Hotspots 2 broadPeak UW-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeUwDnase/wgEncodeUwDnaseLiverC57bl6MAdult8wksHotspotsRep3.broadPeak.gz Liver DnaseSeq Hotspots 3 broadPeak UW-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeUwDnase/wgEncodeUwDnaseLiverC57bl6MAdult8wksHotspotsRep4.broadPeak.gz Liver DnaseSeq Hotspots 4 broadPeak UW-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeUwDnase/wgEncodeUwDnaseLiverC57bl6MAdult8wksHotspotsRep5.broadPeak.gz Liver DnaseSeq Hotspots 5 broadPeak UW-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeUwDnase/wgEncodeUwDnaseLiverC57bl6MAdult8wksHotspotsRep6.broadPeak.gz Liver DnaseSeq Hotspots 6 broadPeak UW-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeUwDnase/wgEncodeUwDnaseLiverC57bl6MAdult8wksHotspotsRep7.broadPeak.gz Liver DnaseSeq Hotspots 7 broadPeak UW-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeUwDnase/wgEncodeUwDnaseLiverC57bl6MAdult8wksHotspotsRep8.broadPeak.gz Liver DnaseSeq Hotspots 8 broadPeak UW-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeUwDnase/wgEncodeUwDnaseLiverC57bl6MAdult8wksHotspotsRep9.broadPeak.gz Liver DnaseSeq Hotspots 9 broadPeak UW-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeUwDnase/wgEncodeUwDnaseLiverC57bl6MAdult8wksPkRep1.narrowPeak.gz Liver DnaseSeq Peaks 1 narrowPeak UW-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeUwDnase/wgEncodeUwDnaseLiverC57bl6MAdult8wksPkRep10.narrowPeak.gz Liver DnaseSeq Peaks 10 narrowPeak UW-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeUwDnase/wgEncodeUwDnaseLiverC57bl6MAdult8wksPkRep11.narrowPeak.gz Liver DnaseSeq Peaks 11 narrowPeak UW-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeUwDnase/wgEncodeUwDnaseLiverC57bl6MAdult8wksPkRep12.narrowPeak.gz Liver DnaseSeq Peaks 12 narrowPeak UW-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeUwDnase/wgEncodeUwDnaseLiverC57bl6MAdult8wksPkRep13.narrowPeak.gz Liver DnaseSeq Peaks 13 narrowPeak UW-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeUwDnase/wgEncodeUwDnaseLiverC57bl6MAdult8wksPkRep14.narrowPeak.gz Liver DnaseSeq Peaks 14 narrowPeak UW-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeUwDnase/wgEncodeUwDnaseLiverC57bl6MAdult8wksPkRep2.narrowPeak.gz Liver DnaseSeq Peaks 2 narrowPeak UW-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeUwDnase/wgEncodeUwDnaseLiverC57bl6MAdult8wksPkRep3.narrowPeak.gz Liver DnaseSeq Peaks 3 narrowPeak UW-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeUwDnase/wgEncodeUwDnaseLiverC57bl6MAdult8wksPkRep4.narrowPeak.gz Liver DnaseSeq Peaks 4 narrowPeak UW-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeUwDnase/wgEncodeUwDnaseLiverC57bl6MAdult8wksPkRep5.narrowPeak.gz Liver DnaseSeq Peaks 5 narrowPeak UW-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeUwDnase/wgEncodeUwDnaseLiverC57bl6MAdult8wksPkRep6.narrowPeak.gz Liver DnaseSeq Peaks 6 narrowPeak UW-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeUwDnase/wgEncodeUwDnaseLiverC57bl6MAdult8wksPkRep7.narrowPeak.gz Liver DnaseSeq Peaks 7 narrowPeak UW-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeUwDnase/wgEncodeUwDnaseLiverC57bl6MAdult8wksPkRep8.narrowPeak.gz Liver DnaseSeq Peaks 8 narrowPeak UW-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeUwDnase/wgEncodeUwDnaseLiverC57bl6MAdult8wksPkRep9.narrowPeak.gz Liver DnaseSeq Peaks 9 narrowPeak UW-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeUwDnase/wgEncodeUwDnaseLiverC57bl6MAdult8wksSigRep1.bigWig Liver DnaseSeq Signal 1 bigWig UW-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeUwDnase/wgEncodeUwDnaseLiverC57bl6MAdult8wksSigRep10.bigWig Liver DnaseSeq Signal 10 bigWig UW-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeUwDnase/wgEncodeUwDnaseLiverC57bl6MAdult8wksSigRep11.bigWig Liver DnaseSeq Signal 11 bigWig UW-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeUwDnase/wgEncodeUwDnaseLiverC57bl6MAdult8wksSigRep12.bigWig Liver DnaseSeq Signal 12 bigWig UW-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeUwDnase/wgEncodeUwDnaseLiverC57bl6MAdult8wksSigRep13.bigWig Liver DnaseSeq Signal 13 bigWig UW-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeUwDnase/wgEncodeUwDnaseLiverC57bl6MAdult8wksSigRep14.bigWig Liver DnaseSeq Signal 14 bigWig UW-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeUwDnase/wgEncodeUwDnaseLiverC57bl6MAdult8wksSigRep2.bigWig Liver DnaseSeq Signal 2 bigWig UW-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeUwDnase/wgEncodeUwDnaseLiverC57bl6MAdult8wksSigRep3.bigWig Liver DnaseSeq Signal 3 bigWig UW-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeUwDnase/wgEncodeUwDnaseLiverC57bl6MAdult8wksSigRep4.bigWig Liver DnaseSeq Signal 4 bigWig UW-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeUwDnase/wgEncodeUwDnaseLiverC57bl6MAdult8wksSigRep5.bigWig Liver DnaseSeq Signal 5 bigWig UW-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeUwDnase/wgEncodeUwDnaseLiverC57bl6MAdult8wksSigRep6.bigWig Liver DnaseSeq Signal 6 bigWig UW-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeUwDnase/wgEncodeUwDnaseLiverC57bl6MAdult8wksSigRep7.bigWig Liver DnaseSeq Signal 7 bigWig UW-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeUwDnase/wgEncodeUwDnaseLiverC57bl6MAdult8wksSigRep8.bigWig Liver DnaseSeq Signal 8 bigWig UW-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeUwDnase/wgEncodeUwDnaseLiverC57bl6MAdult8wksSigRep9.bigWig Liver DnaseSeq Signal 9 bigWig UW-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeUwDnase/wgEncodeUwDnaseLiverC57bl6ME14halfAlnRep1.bam Liver DnaseSeq Alignments 1 bam UW-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeUwDnase/wgEncodeUwDnaseLiverC57bl6ME14halfHotspotsRep1.broadPeak.gz Liver DnaseSeq Hotspots 1 broadPeak UW-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeUwDnase/wgEncodeUwDnaseLiverC57bl6ME14halfPkRep1.narrowPeak.gz Liver DnaseSeq Peaks 1 narrowPeak UW-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeUwDnase/wgEncodeUwDnaseLiverC57bl6ME14halfSigRep1.bigWig Liver DnaseSeq Signal 1 bigWig UW-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeUwDnase/wgEncodeUwDnaseLiverS129ME14halfAlnRep1.bam Liver DnaseSeq Alignments 1 bam UW-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeUwDnase/wgEncodeUwDnaseLiverS129ME14halfHotspotsRep1.broadPeak.gz Liver DnaseSeq Hotspots 1 broadPeak UW-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeUwDnase/wgEncodeUwDnaseLiverS129ME14halfPkRep1.narrowPeak.gz Liver DnaseSeq Peaks 1 narrowPeak UW-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeUwDnase/wgEncodeUwDnaseLiverS129ME14halfSigRep1.bigWig Liver DnaseSeq Signal 1 bigWig UW-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeUwDnase/wgEncodeUwDnaseLungC57bl6MAdult8wksAlnRep1.bam Lung DnaseSeq Alignments 1 bam UW-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeUwDnase/wgEncodeUwDnaseLungC57bl6MAdult8wksAlnRep2.bam Lung DnaseSeq Alignments 2 bam UW-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeUwDnase/wgEncodeUwDnaseLungC57bl6MAdult8wksAlnRep3.bam Lung DnaseSeq Alignments 3 bam UW-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeUwDnase/wgEncodeUwDnaseLungC57bl6MAdult8wksHotspotsRep1.broadPeak.gz Lung DnaseSeq Hotspots 1 broadPeak UW-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeUwDnase/wgEncodeUwDnaseLungC57bl6MAdult8wksHotspotsRep2.broadPeak.gz Lung DnaseSeq Hotspots 2 broadPeak UW-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeUwDnase/wgEncodeUwDnaseLungC57bl6MAdult8wksHotspotsRep3.broadPeak.gz Lung DnaseSeq Hotspots 3 broadPeak UW-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeUwDnase/wgEncodeUwDnaseLungC57bl6MAdult8wksPkRep1.narrowPeak.gz Lung DnaseSeq Peaks 1 narrowPeak UW-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeUwDnase/wgEncodeUwDnaseLungC57bl6MAdult8wksPkRep2.narrowPeak.gz Lung DnaseSeq Peaks 2 narrowPeak UW-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeUwDnase/wgEncodeUwDnaseLungC57bl6MAdult8wksPkRep3.narrowPeak.gz Lung DnaseSeq Peaks 3 narrowPeak UW-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeUwDnase/wgEncodeUwDnaseLungC57bl6MAdult8wksSigRep1.bigWig Lung DnaseSeq Signal 1 bigWig UW-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeUwDnase/wgEncodeUwDnaseLungC57bl6MAdult8wksSigRep2.bigWig Lung DnaseSeq Signal 2 bigWig UW-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeUwDnase/wgEncodeUwDnaseLungC57bl6MAdult8wksSigRep3.bigWig Lung DnaseSeq Signal 3 bigWig UW-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeUwDnase/wgEncodeUwDnaseMelC57bl6MAdult8wksAlnRep1.bam MEL DnaseSeq Alignments 1 bam UW-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeUwDnase/wgEncodeUwDnaseMelC57bl6MAdult8wksAlnRep2.bam MEL DnaseSeq Alignments 2 bam UW-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeUwDnase/wgEncodeUwDnaseMelC57bl6MAdult8wksAlnRep3.bam MEL DnaseSeq Alignments 3 bam UW-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeUwDnase/wgEncodeUwDnaseMelC57bl6MAdult8wksHotspotsRep1.broadPeak.gz MEL DnaseSeq Hotspots 1 broadPeak UW-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeUwDnase/wgEncodeUwDnaseMelC57bl6MAdult8wksHotspotsRep2.broadPeak.gz MEL DnaseSeq Hotspots 2 broadPeak UW-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeUwDnase/wgEncodeUwDnaseMelC57bl6MAdult8wksHotspotsRep3.broadPeak.gz MEL DnaseSeq Hotspots 3 broadPeak UW-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeUwDnase/wgEncodeUwDnaseMelC57bl6MAdult8wksPkRep1.narrowPeak.gz MEL DnaseSeq Peaks 1 narrowPeak UW-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeUwDnase/wgEncodeUwDnaseMelC57bl6MAdult8wksPkRep2.narrowPeak.gz MEL DnaseSeq Peaks 2 narrowPeak UW-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeUwDnase/wgEncodeUwDnaseMelC57bl6MAdult8wksPkRep3.narrowPeak.gz MEL DnaseSeq Peaks 3 narrowPeak UW-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeUwDnase/wgEncodeUwDnaseMelC57bl6MAdult8wksSigRep1.bigWig MEL DnaseSeq Signal 1 bigWig UW-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeUwDnase/wgEncodeUwDnaseMelC57bl6MAdult8wksSigRep2.bigWig MEL DnaseSeq Signal 2 bigWig UW-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeUwDnase/wgEncodeUwDnaseMelC57bl6MAdult8wksSigRep3.bigWig MEL DnaseSeq Signal 3 bigWig UW-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeUwDnase/wgEncodeUwDnaseMesodermCd1ME11halfAlnRep1.bam Mesoderm DnaseSeq Alignments 1 bam UW-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeUwDnase/wgEncodeUwDnaseMesodermCd1ME11halfAlnRep2.bam Mesoderm DnaseSeq Alignments 2 bam UW-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeUwDnase/wgEncodeUwDnaseMesodermCd1ME11halfHotspotsRep1.broadPeak.gz Mesoderm DnaseSeq Hotspots 1 broadPeak UW-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeUwDnase/wgEncodeUwDnaseMesodermCd1ME11halfHotspotsRep2.broadPeak.gz Mesoderm DnaseSeq Hotspots 2 broadPeak UW-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeUwDnase/wgEncodeUwDnaseMesodermCd1ME11halfPkRep1.narrowPeak.gz Mesoderm DnaseSeq Peaks 1 narrowPeak UW-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeUwDnase/wgEncodeUwDnaseMesodermCd1ME11halfPkRep2.narrowPeak.gz Mesoderm DnaseSeq Peaks 2 narrowPeak UW-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeUwDnase/wgEncodeUwDnaseMesodermCd1ME11halfSigRep1.bigWig Mesoderm DnaseSeq Signal 1 bigWig UW-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeUwDnase/wgEncodeUwDnaseMesodermCd1ME11halfSigRep2.bigWig Mesoderm DnaseSeq Signal 2 bigWig UW-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeUwDnase/wgEncodeUwDnaseMgerUknImmortalAlnRep1.bam mG/ER DnaseSeq Alignments 1 bam UW-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeUwDnase/wgEncodeUwDnaseMgerUknImmortalAlnRep2.bam mG/ER DnaseSeq Alignments 2 bam UW-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeUwDnase/wgEncodeUwDnaseMgerUknImmortalDiffc24hAlnRep1.bam mG/ER DnaseSeq Alignments 1 bam UW-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeUwDnase/wgEncodeUwDnaseMgerUknImmortalDiffc24hAlnRep2.bam mG/ER DnaseSeq Alignments 2 bam UW-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeUwDnase/wgEncodeUwDnaseMgerUknImmortalDiffc24hHotspotsRep1.broadPeak.gz mG/ER DnaseSeq Hotspots 1 broadPeak UW-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeUwDnase/wgEncodeUwDnaseMgerUknImmortalDiffc24hHotspotsRep2.broadPeak.gz mG/ER DnaseSeq Hotspots 2 broadPeak UW-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeUwDnase/wgEncodeUwDnaseMgerUknImmortalDiffc24hPkRep1.narrowPeak.gz mG/ER DnaseSeq Peaks 1 narrowPeak UW-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeUwDnase/wgEncodeUwDnaseMgerUknImmortalDiffc24hPkRep2.narrowPeak.gz mG/ER DnaseSeq Peaks 2 narrowPeak UW-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeUwDnase/wgEncodeUwDnaseMgerUknImmortalDiffc24hSigRep1.bigWig mG/ER DnaseSeq Signal 1 bigWig UW-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeUwDnase/wgEncodeUwDnaseMgerUknImmortalDiffc24hSigRep2.bigWig mG/ER DnaseSeq Signal 2 bigWig UW-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeUwDnase/wgEncodeUwDnaseMgerUknImmortalDiffc48hAlnRep1.bam mG/ER DnaseSeq Alignments 1 bam UW-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeUwDnase/wgEncodeUwDnaseMgerUknImmortalDiffc48hAlnRep2.bam mG/ER DnaseSeq Alignments 2 bam UW-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeUwDnase/wgEncodeUwDnaseMgerUknImmortalDiffc48hHotspotsRep1.broadPeak.gz mG/ER DnaseSeq Hotspots 1 broadPeak UW-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeUwDnase/wgEncodeUwDnaseMgerUknImmortalDiffc48hHotspotsRep2.broadPeak.gz mG/ER DnaseSeq Hotspots 2 broadPeak UW-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeUwDnase/wgEncodeUwDnaseMgerUknImmortalDiffc48hPkRep1.narrowPeak.gz mG/ER DnaseSeq Peaks 1 narrowPeak UW-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeUwDnase/wgEncodeUwDnaseMgerUknImmortalDiffc48hPkRep2.narrowPeak.gz mG/ER DnaseSeq Peaks 2 narrowPeak UW-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeUwDnase/wgEncodeUwDnaseMgerUknImmortalDiffc48hSigRep1.bigWig mG/ER DnaseSeq Signal 1 bigWig UW-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeUwDnase/wgEncodeUwDnaseMgerUknImmortalDiffc48hSigRep2.bigWig mG/ER DnaseSeq Signal 2 bigWig UW-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeUwDnase/wgEncodeUwDnaseMgerUknImmortalHotspotsRep1.broadPeak.gz mG/ER DnaseSeq Hotspots 1 broadPeak UW-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeUwDnase/wgEncodeUwDnaseMgerUknImmortalHotspotsRep2.broadPeak.gz mG/ER DnaseSeq Hotspots 2 broadPeak UW-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeUwDnase/wgEncodeUwDnaseMgerUknImmortalPkRep1.narrowPeak.gz mG/ER DnaseSeq Peaks 1 narrowPeak UW-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeUwDnase/wgEncodeUwDnaseMgerUknImmortalPkRep2.narrowPeak.gz mG/ER DnaseSeq Peaks 2 narrowPeak UW-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeUwDnase/wgEncodeUwDnaseMgerUknImmortalSigRep1.bigWig mG/ER DnaseSeq Signal 1 bigWig UW-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeUwDnase/wgEncodeUwDnaseMgerUknImmortalSigRep2.bigWig mG/ER DnaseSeq Signal 2 bigWig UW-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeUwDnase/wgEncodeUwDnaseNih3t3NihsMImmortalAlnRep1.bam NIH-3T3 DnaseSeq Alignments 1 bam UW-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeUwDnase/wgEncodeUwDnaseNih3t3NihsMImmortalAlnRep2.bam NIH-3T3 DnaseSeq Alignments 2 bam UW-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeUwDnase/wgEncodeUwDnaseNih3t3NihsMImmortalHotspotsRep1.broadPeak.gz NIH-3T3 DnaseSeq Hotspots 1 broadPeak UW-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeUwDnase/wgEncodeUwDnaseNih3t3NihsMImmortalHotspotsRep2.broadPeak.gz NIH-3T3 DnaseSeq Hotspots 2 broadPeak UW-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeUwDnase/wgEncodeUwDnaseNih3t3NihsMImmortalPkRep1.narrowPeak.gz NIH-3T3 DnaseSeq Peaks 1 narrowPeak UW-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeUwDnase/wgEncodeUwDnaseNih3t3NihsMImmortalPkRep2.narrowPeak.gz NIH-3T3 DnaseSeq Peaks 2 narrowPeak UW-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeUwDnase/wgEncodeUwDnaseNih3t3NihsMImmortalSigRep1.bigWig NIH-3T3 DnaseSeq Signal 1 bigWig UW-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeUwDnase/wgEncodeUwDnaseNih3t3NihsMImmortalSigRep2.bigWig NIH-3T3 DnaseSeq Signal 2 bigWig UW-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeUwDnase/wgEncodeUwDnasePatskiSpbl6MImmortalAlnRep1.bam Patski DnaseSeq Alignments 1 bam UW-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeUwDnase/wgEncodeUwDnasePatskiSpbl6MImmortalAlnRep2.bam Patski DnaseSeq Alignments 2 bam UW-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeUwDnase/wgEncodeUwDnasePatskiSpbl6MImmortalHotspotsRep1.broadPeak.gz Patski DnaseSeq Hotspots 1 broadPeak UW-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeUwDnase/wgEncodeUwDnasePatskiSpbl6MImmortalHotspotsRep2.broadPeak.gz Patski DnaseSeq Hotspots 2 broadPeak UW-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeUwDnase/wgEncodeUwDnasePatskiSpbl6MImmortalPkRep1.narrowPeak.gz Patski DnaseSeq Peaks 1 narrowPeak UW-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeUwDnase/wgEncodeUwDnasePatskiSpbl6MImmortalPkRep2.narrowPeak.gz Patski DnaseSeq Peaks 2 narrowPeak UW-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeUwDnase/wgEncodeUwDnasePatskiSpbl6MImmortalSigRep1.bigWig Patski DnaseSeq Signal 1 bigWig UW-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeUwDnase/wgEncodeUwDnasePatskiSpbl6MImmortalSigRep2.bigWig Patski DnaseSeq Signal 2 bigWig UW-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeUwDnase/wgEncodeUwDnaseRetinaC57bl6MAdult1wksAlnRep1.bam Retina DnaseSeq Alignments 1 bam UW-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeUwDnase/wgEncodeUwDnaseRetinaC57bl6MAdult1wksHotspotsRep1.broadPeak.gz Retina DnaseSeq Hotspots 1 broadPeak UW-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeUwDnase/wgEncodeUwDnaseRetinaC57bl6MAdult1wksPkRep1.narrowPeak.gz Retina DnaseSeq Peaks 1 narrowPeak UW-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeUwDnase/wgEncodeUwDnaseRetinaC57bl6MAdult1wksSigRep1.bigWig Retina DnaseSeq Signal 1 bigWig UW-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeUwDnase/wgEncodeUwDnaseRetinaC57bl6MAdult8wksAlnRep1.bam Retina DnaseSeq Alignments 1 bam UW-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeUwDnase/wgEncodeUwDnaseRetinaC57bl6MAdult8wksHotspotsRep1.broadPeak.gz Retina DnaseSeq Hotspots 1 broadPeak UW-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeUwDnase/wgEncodeUwDnaseRetinaC57bl6MAdult8wksPkRep1.narrowPeak.gz Retina DnaseSeq Peaks 1 narrowPeak UW-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeUwDnase/wgEncodeUwDnaseRetinaC57bl6MAdult8wksSigRep1.bigWig Retina DnaseSeq Signal 1 bigWig UW-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeUwDnase/wgEncodeUwDnaseRetinaC57bl6MNew1daysAlnRep1.bam Retina DnaseSeq Alignments 1 bam UW-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeUwDnase/wgEncodeUwDnaseRetinaC57bl6MNew1daysHotspotsRep1.broadPeak.gz Retina DnaseSeq Hotspots 1 broadPeak UW-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeUwDnase/wgEncodeUwDnaseRetinaC57bl6MNew1daysPkRep1.narrowPeak.gz Retina DnaseSeq Peaks 1 narrowPeak UW-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeUwDnase/wgEncodeUwDnaseRetinaC57bl6MNew1daysSigRep1.bigWig Retina DnaseSeq Signal 1 bigWig UW-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeUwDnase/wgEncodeUwDnaseSkmuscleC57bl6MAdult8wksAlnRep1.bam SkMuscle DnaseSeq Alignments 1 bam UW-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeUwDnase/wgEncodeUwDnaseSkmuscleC57bl6MAdult8wksAlnRep2.bam SkMuscle DnaseSeq Alignments 2 bam UW-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeUwDnase/wgEncodeUwDnaseSkmuscleC57bl6MAdult8wksHotspotsRep1.broadPeak.gz SkMuscle DnaseSeq Hotspots 1 broadPeak UW-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeUwDnase/wgEncodeUwDnaseSkmuscleC57bl6MAdult8wksHotspotsRep2.broadPeak.gz SkMuscle DnaseSeq Hotspots 2 broadPeak UW-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeUwDnase/wgEncodeUwDnaseSkmuscleC57bl6MAdult8wksPkRep1.narrowPeak.gz SkMuscle DnaseSeq Peaks 1 narrowPeak UW-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeUwDnase/wgEncodeUwDnaseSkmuscleC57bl6MAdult8wksPkRep2.narrowPeak.gz SkMuscle DnaseSeq Peaks 2 narrowPeak UW-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeUwDnase/wgEncodeUwDnaseSkmuscleC57bl6MAdult8wksSigRep1.bigWig SkMuscle DnaseSeq Signal 1 bigWig UW-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeUwDnase/wgEncodeUwDnaseSkmuscleC57bl6MAdult8wksSigRep2.bigWig SkMuscle DnaseSeq Signal 2 bigWig UW-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeUwDnase/wgEncodeUwDnaseSpleenC57bl6MAdult8wksAlnRep1.bam Spleen DnaseSeq Alignments 1 bam UW-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeUwDnase/wgEncodeUwDnaseSpleenC57bl6MAdult8wksAlnRep2.bam Spleen DnaseSeq Alignments 2 bam UW-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeUwDnase/wgEncodeUwDnaseSpleenC57bl6MAdult8wksHotspotsRep1.broadPeak.gz Spleen DnaseSeq Hotspots 1 broadPeak UW-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeUwDnase/wgEncodeUwDnaseSpleenC57bl6MAdult8wksHotspotsRep2.broadPeak.gz Spleen DnaseSeq Hotspots 2 broadPeak UW-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeUwDnase/wgEncodeUwDnaseSpleenC57bl6MAdult8wksPkRep1.narrowPeak.gz Spleen DnaseSeq Peaks 1 narrowPeak UW-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeUwDnase/wgEncodeUwDnaseSpleenC57bl6MAdult8wksPkRep2.narrowPeak.gz Spleen DnaseSeq Peaks 2 narrowPeak UW-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeUwDnase/wgEncodeUwDnaseSpleenC57bl6MAdult8wksSigRep1.bigWig Spleen DnaseSeq Signal 1 bigWig UW-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeUwDnase/wgEncodeUwDnaseSpleenC57bl6MAdult8wksSigRep2.bigWig Spleen DnaseSeq Signal 2 bigWig UW-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeUwDnase/wgEncodeUwDnaseThelpaC57bl6MAdult8wksAlnRep1.bam THelper-Activated DnaseSeq Alignments 1 bam UW-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeUwDnase/wgEncodeUwDnaseThelpaC57bl6MAdult8wksAlnRep2.bam THelper-Activated DnaseSeq Alignments 2 bam UW-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeUwDnase/wgEncodeUwDnaseThelpaC57bl6MAdult8wksHotspotsRep1.broadPeak.gz THelper-Activated DnaseSeq Hotspots 1 broadPeak UW-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeUwDnase/wgEncodeUwDnaseThelpaC57bl6MAdult8wksHotspotsRep2.broadPeak.gz THelper-Activated DnaseSeq Hotspots 2 broadPeak UW-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeUwDnase/wgEncodeUwDnaseThelpaC57bl6MAdult8wksPkRep1.narrowPeak.gz THelper-Activated DnaseSeq Peaks 1 narrowPeak UW-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeUwDnase/wgEncodeUwDnaseThelpaC57bl6MAdult8wksPkRep2.narrowPeak.gz THelper-Activated DnaseSeq Peaks 2 narrowPeak UW-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeUwDnase/wgEncodeUwDnaseThelpaC57bl6MAdult8wksSigRep1.bigWig THelper-Activated DnaseSeq Signal 1 bigWig UW-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeUwDnase/wgEncodeUwDnaseThelpaC57bl6MAdult8wksSigRep2.bigWig THelper-Activated DnaseSeq Signal 2 bigWig UW-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeUwDnase/wgEncodeUwDnaseThymusC57bl6MAdult8wksAlnRep1.bam Thymus DnaseSeq Alignments 1 bam UW-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeUwDnase/wgEncodeUwDnaseThymusC57bl6MAdult8wksAlnRep2.bam Thymus DnaseSeq Alignments 2 bam UW-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeUwDnase/wgEncodeUwDnaseThymusC57bl6MAdult8wksHotspotsRep1.broadPeak.gz Thymus DnaseSeq Hotspots 1 broadPeak UW-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeUwDnase/wgEncodeUwDnaseThymusC57bl6MAdult8wksHotspotsRep2.broadPeak.gz Thymus DnaseSeq Hotspots 2 broadPeak UW-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeUwDnase/wgEncodeUwDnaseThymusC57bl6MAdult8wksPkRep1.narrowPeak.gz Thymus DnaseSeq Peaks 1 narrowPeak UW-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeUwDnase/wgEncodeUwDnaseThymusC57bl6MAdult8wksPkRep2.narrowPeak.gz Thymus DnaseSeq Peaks 2 narrowPeak UW-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeUwDnase/wgEncodeUwDnaseThymusC57bl6MAdult8wksSigRep1.bigWig Thymus DnaseSeq Signal 1 bigWig UW-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeUwDnase/wgEncodeUwDnaseThymusC57bl6MAdult8wksSigRep2.bigWig Thymus DnaseSeq Signal 2 bigWig UW-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeUwDnase/wgEncodeUwDnaseTnaiveC57bl6MAdult8wksAlnRep1.bam T-Naive DnaseSeq Alignments 1 bam UW-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeUwDnase/wgEncodeUwDnaseTnaiveC57bl6MAdult8wksAlnRep2.bam T-Naive DnaseSeq Alignments 2 bam UW-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeUwDnase/wgEncodeUwDnaseTnaiveC57bl6MAdult8wksAlnRep3.bam T-Naive DnaseSeq Alignments 3 bam UW-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeUwDnase/wgEncodeUwDnaseTnaiveC57bl6MAdult8wksAlnRep4.bam T-Naive DnaseSeq Alignments 4 bam UW-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeUwDnase/wgEncodeUwDnaseTnaiveC57bl6MAdult8wksHotspotsRep1.broadPeak.gz T-Naive DnaseSeq Hotspots 1 broadPeak UW-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeUwDnase/wgEncodeUwDnaseTnaiveC57bl6MAdult8wksHotspotsRep2.broadPeak.gz T-Naive DnaseSeq Hotspots 2 broadPeak UW-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeUwDnase/wgEncodeUwDnaseTnaiveC57bl6MAdult8wksHotspotsRep3.broadPeak.gz T-Naive DnaseSeq Hotspots 3 broadPeak UW-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeUwDnase/wgEncodeUwDnaseTnaiveC57bl6MAdult8wksHotspotsRep4.broadPeak.gz T-Naive DnaseSeq Hotspots 4 broadPeak UW-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeUwDnase/wgEncodeUwDnaseTnaiveC57bl6MAdult8wksPkRep1.narrowPeak.gz T-Naive DnaseSeq Peaks 1 narrowPeak UW-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeUwDnase/wgEncodeUwDnaseTnaiveC57bl6MAdult8wksPkRep2.narrowPeak.gz T-Naive DnaseSeq Peaks 2 narrowPeak UW-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeUwDnase/wgEncodeUwDnaseTnaiveC57bl6MAdult8wksPkRep3.narrowPeak.gz T-Naive DnaseSeq Peaks 3 narrowPeak UW-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeUwDnase/wgEncodeUwDnaseTnaiveC57bl6MAdult8wksPkRep4.narrowPeak.gz T-Naive DnaseSeq Peaks 4 narrowPeak UW-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeUwDnase/wgEncodeUwDnaseTnaiveC57bl6MAdult8wksSigRep1.bigWig T-Naive DnaseSeq Signal 1 bigWig UW-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeUwDnase/wgEncodeUwDnaseTnaiveC57bl6MAdult8wksSigRep2.bigWig T-Naive DnaseSeq Signal 2 bigWig UW-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeUwDnase/wgEncodeUwDnaseTnaiveC57bl6MAdult8wksSigRep3.bigWig T-Naive DnaseSeq Signal 3 bigWig UW-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeUwDnase/wgEncodeUwDnaseTnaiveC57bl6MAdult8wksSigRep4.bigWig T-Naive DnaseSeq Signal 4 bigWig UW-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeUwDnase/wgEncodeUwDnaseTregC57bl6MAdult8wksAlnRep1.bam TReg DnaseSeq Alignments 1 bam UW-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeUwDnase/wgEncodeUwDnaseTregC57bl6MAdult8wksAlnRep2.bam TReg DnaseSeq Alignments 2 bam UW-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeUwDnase/wgEncodeUwDnaseTregC57bl6MAdult8wksAlnRep3.bam TReg DnaseSeq Alignments 3 bam UW-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeUwDnase/wgEncodeUwDnaseTregC57bl6MAdult8wksHotspotsRep1.broadPeak.gz TReg DnaseSeq Hotspots 1 broadPeak UW-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeUwDnase/wgEncodeUwDnaseTregC57bl6MAdult8wksHotspotsRep2.broadPeak.gz TReg DnaseSeq Hotspots 2 broadPeak UW-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeUwDnase/wgEncodeUwDnaseTregC57bl6MAdult8wksHotspotsRep3.broadPeak.gz TReg DnaseSeq Hotspots 3 broadPeak UW-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeUwDnase/wgEncodeUwDnaseTregC57bl6MAdult8wksPkRep1.narrowPeak.gz TReg DnaseSeq Peaks 1 narrowPeak UW-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeUwDnase/wgEncodeUwDnaseTregC57bl6MAdult8wksPkRep2.narrowPeak.gz TReg DnaseSeq Peaks 2 narrowPeak UW-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeUwDnase/wgEncodeUwDnaseTregC57bl6MAdult8wksPkRep3.narrowPeak.gz TReg DnaseSeq Peaks 3 narrowPeak UW-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeUwDnase/wgEncodeUwDnaseTregC57bl6MAdult8wksSigRep1.bigWig TReg DnaseSeq Signal 1 bigWig UW-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeUwDnase/wgEncodeUwDnaseTregC57bl6MAdult8wksSigRep2.bigWig TReg DnaseSeq Signal 2 bigWig UW-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeUwDnase/wgEncodeUwDnaseTregC57bl6MAdult8wksSigRep3.bigWig TReg DnaseSeq Signal 3 bigWig UW-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeUwDnase/wgEncodeUwDnaseTregaC57bl6MAdult8wksAlnRep1.bam TReg-Activated DnaseSeq Alignments 1 bam UW-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeUwDnase/wgEncodeUwDnaseTregaC57bl6MAdult8wksAlnRep2.bam TReg-Activated DnaseSeq Alignments 2 bam UW-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeUwDnase/wgEncodeUwDnaseTregaC57bl6MAdult8wksHotspotsRep1.broadPeak.gz TReg-Activated DnaseSeq Hotspots 1 broadPeak UW-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeUwDnase/wgEncodeUwDnaseTregaC57bl6MAdult8wksHotspotsRep2.broadPeak.gz TReg-Activated DnaseSeq Hotspots 2 broadPeak UW-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeUwDnase/wgEncodeUwDnaseTregaC57bl6MAdult8wksPkRep1.narrowPeak.gz TReg-Activated DnaseSeq Peaks 1 narrowPeak UW-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeUwDnase/wgEncodeUwDnaseTregaC57bl6MAdult8wksPkRep2.narrowPeak.gz TReg-Activated DnaseSeq Peaks 2 narrowPeak UW-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeUwDnase/wgEncodeUwDnaseTregaC57bl6MAdult8wksSigRep1.bigWig TReg-Activated DnaseSeq Signal 1 bigWig UW-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeUwDnase/wgEncodeUwDnaseTregaC57bl6MAdult8wksSigRep2.bigWig TReg-Activated DnaseSeq Signal 2 bigWig UW-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeUwDnase/wgEncodeUwDnaseWbrainC57bl6MAdult8wksAlnRep1.bam WholeBrain DnaseSeq Alignments 1 bam UW-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeUwDnase/wgEncodeUwDnaseWbrainC57bl6MAdult8wksAlnRep2.bam WholeBrain DnaseSeq Alignments 2 bam UW-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeUwDnase/wgEncodeUwDnaseWbrainC57bl6MAdult8wksAlnRep3.bam WholeBrain DnaseSeq Alignments 3 bam UW-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeUwDnase/wgEncodeUwDnaseWbrainC57bl6MAdult8wksAlnRep4.bam WholeBrain DnaseSeq Alignments 4 bam UW-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeUwDnase/wgEncodeUwDnaseWbrainC57bl6MAdult8wksAlnRep5.bam WholeBrain DnaseSeq Alignments 5 bam UW-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeUwDnase/wgEncodeUwDnaseWbrainC57bl6MAdult8wksAlnRep6.bam WholeBrain DnaseSeq Alignments 6 bam UW-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeUwDnase/wgEncodeUwDnaseWbrainC57bl6MAdult8wksAlnRep7.bam WholeBrain DnaseSeq Alignments 7 bam UW-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeUwDnase/wgEncodeUwDnaseWbrainC57bl6MAdult8wksHotspotsRep1.broadPeak.gz WholeBrain DnaseSeq Hotspots 1 broadPeak UW-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeUwDnase/wgEncodeUwDnaseWbrainC57bl6MAdult8wksHotspotsRep2.broadPeak.gz WholeBrain DnaseSeq Hotspots 2 broadPeak UW-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeUwDnase/wgEncodeUwDnaseWbrainC57bl6MAdult8wksHotspotsRep3.broadPeak.gz WholeBrain DnaseSeq Hotspots 3 broadPeak UW-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeUwDnase/wgEncodeUwDnaseWbrainC57bl6MAdult8wksHotspotsRep4.broadPeak.gz WholeBrain DnaseSeq Hotspots 4 broadPeak UW-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeUwDnase/wgEncodeUwDnaseWbrainC57bl6MAdult8wksHotspotsRep5.broadPeak.gz WholeBrain DnaseSeq Hotspots 5 broadPeak UW-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeUwDnase/wgEncodeUwDnaseWbrainC57bl6MAdult8wksHotspotsRep6.broadPeak.gz WholeBrain DnaseSeq Hotspots 6 broadPeak UW-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeUwDnase/wgEncodeUwDnaseWbrainC57bl6MAdult8wksHotspotsRep7.broadPeak.gz WholeBrain DnaseSeq Hotspots 7 broadPeak UW-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeUwDnase/wgEncodeUwDnaseWbrainC57bl6MAdult8wksPkRep1.narrowPeak.gz WholeBrain DnaseSeq Peaks 1 narrowPeak UW-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeUwDnase/wgEncodeUwDnaseWbrainC57bl6MAdult8wksPkRep2.narrowPeak.gz WholeBrain DnaseSeq Peaks 2 narrowPeak UW-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeUwDnase/wgEncodeUwDnaseWbrainC57bl6MAdult8wksPkRep3.narrowPeak.gz WholeBrain DnaseSeq Peaks 3 narrowPeak UW-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeUwDnase/wgEncodeUwDnaseWbrainC57bl6MAdult8wksPkRep4.narrowPeak.gz WholeBrain DnaseSeq Peaks 4 narrowPeak UW-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeUwDnase/wgEncodeUwDnaseWbrainC57bl6MAdult8wksPkRep5.narrowPeak.gz WholeBrain DnaseSeq Peaks 5 narrowPeak UW-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeUwDnase/wgEncodeUwDnaseWbrainC57bl6MAdult8wksPkRep6.narrowPeak.gz WholeBrain DnaseSeq Peaks 6 narrowPeak UW-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeUwDnase/wgEncodeUwDnaseWbrainC57bl6MAdult8wksPkRep7.narrowPeak.gz WholeBrain DnaseSeq Peaks 7 narrowPeak UW-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeUwDnase/wgEncodeUwDnaseWbrainC57bl6MAdult8wksSigRep1.bigWig WholeBrain DnaseSeq Signal 1 bigWig UW-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeUwDnase/wgEncodeUwDnaseWbrainC57bl6MAdult8wksSigRep2.bigWig WholeBrain DnaseSeq Signal 2 bigWig UW-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeUwDnase/wgEncodeUwDnaseWbrainC57bl6MAdult8wksSigRep3.bigWig WholeBrain DnaseSeq Signal 3 bigWig UW-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeUwDnase/wgEncodeUwDnaseWbrainC57bl6MAdult8wksSigRep4.bigWig WholeBrain DnaseSeq Signal 4 bigWig UW-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeUwDnase/wgEncodeUwDnaseWbrainC57bl6MAdult8wksSigRep5.bigWig WholeBrain DnaseSeq Signal 5 bigWig UW-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeUwDnase/wgEncodeUwDnaseWbrainC57bl6MAdult8wksSigRep6.bigWig WholeBrain DnaseSeq Signal 6 bigWig UW-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeUwDnase/wgEncodeUwDnaseWbrainC57bl6MAdult8wksSigRep7.bigWig WholeBrain DnaseSeq Signal 7 bigWig UW-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeUwDnase/wgEncodeUwDnaseWbrainC57bl6ME14halfAlnRep1.bam WholeBrain DnaseSeq Alignments 1 bam UW-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeUwDnase/wgEncodeUwDnaseWbrainC57bl6ME14halfAlnRep2.bam WholeBrain DnaseSeq Alignments 2 bam UW-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeUwDnase/wgEncodeUwDnaseWbrainC57bl6ME14halfHotspotsRep1.broadPeak.gz WholeBrain DnaseSeq Hotspots 1 broadPeak UW-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeUwDnase/wgEncodeUwDnaseWbrainC57bl6ME14halfHotspotsRep2.broadPeak.gz WholeBrain DnaseSeq Hotspots 2 broadPeak UW-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeUwDnase/wgEncodeUwDnaseWbrainC57bl6ME14halfPkRep1.narrowPeak.gz WholeBrain DnaseSeq Peaks 1 narrowPeak UW-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeUwDnase/wgEncodeUwDnaseWbrainC57bl6ME14halfPkRep2.narrowPeak.gz WholeBrain DnaseSeq Peaks 2 narrowPeak UW-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeUwDnase/wgEncodeUwDnaseWbrainC57bl6ME14halfSigRep1.bigWig WholeBrain DnaseSeq Signal 1 bigWig UW-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeUwDnase/wgEncodeUwDnaseWbrainC57bl6ME14halfSigRep2.bigWig WholeBrain DnaseSeq Signal 2 bigWig UW-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeUwDnase/wgEncodeUwDnaseWbrainC57bl6ME18halfAlnRep1.bam WholeBrain DnaseSeq Alignments 1 bam UW-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeUwDnase/wgEncodeUwDnaseWbrainC57bl6ME18halfAlnRep2.bam WholeBrain DnaseSeq Alignments 2 bam UW-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeUwDnase/wgEncodeUwDnaseWbrainC57bl6ME18halfHotspotsRep1.broadPeak.gz WholeBrain DnaseSeq Hotspots 1 broadPeak UW-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeUwDnase/wgEncodeUwDnaseWbrainC57bl6ME18halfHotspotsRep2.broadPeak.gz WholeBrain DnaseSeq Hotspots 2 broadPeak UW-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeUwDnase/wgEncodeUwDnaseWbrainC57bl6ME18halfPkRep1.narrowPeak.gz WholeBrain DnaseSeq Peaks 1 narrowPeak UW-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeUwDnase/wgEncodeUwDnaseWbrainC57bl6ME18halfPkRep2.narrowPeak.gz WholeBrain DnaseSeq Peaks 2 narrowPeak UW-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeUwDnase/wgEncodeUwDnaseWbrainC57bl6ME18halfSigRep1.bigWig WholeBrain DnaseSeq Signal 1 bigWig UW-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeUwDnase/wgEncodeUwDnaseWbrainC57bl6ME18halfSigRep2.bigWig WholeBrain DnaseSeq Signal 2 bigWig UW-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeUwDnase/wgEncodeUwDnaseWholebrainC57bl6MAdult8wksAlnRep1.bam WholeBrain DnaseSeq Alignments 1 bam UW-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeUwDnase/wgEncodeUwDnaseWholebrainC57bl6MAdult8wksAlnRep2.bam WholeBrain DnaseSeq Alignments 2 bam UW-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeUwDnase/wgEncodeUwDnaseWholebrainC57bl6MAdult8wksAlnRep3.bam WholeBrain DnaseSeq Alignments 3 bam UW-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeUwDnase/wgEncodeUwDnaseWholebrainC57bl6MAdult8wksAlnRep4.bam WholeBrain DnaseSeq Alignments 4 bam UW-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeUwDnase/wgEncodeUwDnaseWholebrainC57bl6MAdult8wksAlnRep5.bam WholeBrain DnaseSeq Alignments 5 bam UW-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeUwDnase/wgEncodeUwDnaseWholebrainC57bl6MAdult8wksAlnRep6.bam WholeBrain DnaseSeq Alignments 6 bam UW-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeUwDnase/wgEncodeUwDnaseWholebrainC57bl6MAdult8wksAlnRep7.bam WholeBrain DnaseSeq Alignments 7 bam UW-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeUwDnase/wgEncodeUwDnaseWholebrainC57bl6MAdult8wksHotspotsRep1.broadPeak.gz WholeBrain DnaseSeq Hotspots 1 broadPeak UW-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeUwDnase/wgEncodeUwDnaseWholebrainC57bl6MAdult8wksHotspotsRep2.broadPeak.gz WholeBrain DnaseSeq Hotspots 2 broadPeak UW-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeUwDnase/wgEncodeUwDnaseWholebrainC57bl6MAdult8wksHotspotsRep3.broadPeak.gz WholeBrain DnaseSeq Hotspots 3 broadPeak UW-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeUwDnase/wgEncodeUwDnaseWholebrainC57bl6MAdult8wksHotspotsRep4.broadPeak.gz WholeBrain DnaseSeq Hotspots 4 broadPeak UW-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeUwDnase/wgEncodeUwDnaseWholebrainC57bl6MAdult8wksHotspotsRep5.broadPeak.gz WholeBrain DnaseSeq Hotspots 5 broadPeak UW-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeUwDnase/wgEncodeUwDnaseWholebrainC57bl6MAdult8wksHotspotsRep6.broadPeak.gz WholeBrain DnaseSeq Hotspots 6 broadPeak UW-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeUwDnase/wgEncodeUwDnaseWholebrainC57bl6MAdult8wksHotspotsRep7.broadPeak.gz WholeBrain DnaseSeq Hotspots 7 broadPeak UW-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeUwDnase/wgEncodeUwDnaseWholebrainC57bl6MAdult8wksPkRep1.narrowPeak.gz WholeBrain DnaseSeq Peaks 1 narrowPeak UW-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeUwDnase/wgEncodeUwDnaseWholebrainC57bl6MAdult8wksPkRep2.narrowPeak.gz WholeBrain DnaseSeq Peaks 2 narrowPeak UW-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeUwDnase/wgEncodeUwDnaseWholebrainC57bl6MAdult8wksPkRep3.narrowPeak.gz WholeBrain DnaseSeq Peaks 3 narrowPeak UW-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeUwDnase/wgEncodeUwDnaseWholebrainC57bl6MAdult8wksPkRep4.narrowPeak.gz WholeBrain DnaseSeq Peaks 4 narrowPeak UW-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeUwDnase/wgEncodeUwDnaseWholebrainC57bl6MAdult8wksPkRep5.narrowPeak.gz WholeBrain DnaseSeq Peaks 5 narrowPeak UW-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeUwDnase/wgEncodeUwDnaseWholebrainC57bl6MAdult8wksPkRep6.narrowPeak.gz WholeBrain DnaseSeq Peaks 6 narrowPeak UW-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeUwDnase/wgEncodeUwDnaseWholebrainC57bl6MAdult8wksPkRep7.narrowPeak.gz WholeBrain DnaseSeq Peaks 7 narrowPeak UW-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeUwDnase/wgEncodeUwDnaseWholebrainC57bl6MAdult8wksSigRep1.bigWig WholeBrain DnaseSeq Signal 1 bigWig UW-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeUwDnase/wgEncodeUwDnaseWholebrainC57bl6MAdult8wksSigRep2.bigWig WholeBrain DnaseSeq Signal 2 bigWig UW-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeUwDnase/wgEncodeUwDnaseWholebrainC57bl6MAdult8wksSigRep3.bigWig WholeBrain DnaseSeq Signal 3 bigWig UW-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeUwDnase/wgEncodeUwDnaseWholebrainC57bl6MAdult8wksSigRep4.bigWig WholeBrain DnaseSeq Signal 4 bigWig UW-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeUwDnase/wgEncodeUwDnaseWholebrainC57bl6MAdult8wksSigRep5.bigWig WholeBrain DnaseSeq Signal 5 bigWig UW-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeUwDnase/wgEncodeUwDnaseWholebrainC57bl6MAdult8wksSigRep6.bigWig WholeBrain DnaseSeq Signal 6 bigWig UW-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeUwDnase/wgEncodeUwDnaseWholebrainC57bl6MAdult8wksSigRep7.bigWig WholeBrain DnaseSeq Signal 7 bigWig UW-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeUwDnase/wgEncodeUwDnaseWholebrainC57bl6ME14halfAlnRep1.bam WholeBrain DnaseSeq Alignments 1 bam UW-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeUwDnase/wgEncodeUwDnaseWholebrainC57bl6ME14halfAlnRep2.bam WholeBrain DnaseSeq Alignments 2 bam UW-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeUwDnase/wgEncodeUwDnaseWholebrainC57bl6ME14halfHotspotsRep1.broadPeak.gz WholeBrain DnaseSeq Hotspots 1 broadPeak UW-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeUwDnase/wgEncodeUwDnaseWholebrainC57bl6ME14halfHotspotsRep2.broadPeak.gz WholeBrain DnaseSeq Hotspots 2 broadPeak UW-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeUwDnase/wgEncodeUwDnaseWholebrainC57bl6ME14halfPkRep1.narrowPeak.gz WholeBrain DnaseSeq Peaks 1 narrowPeak UW-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeUwDnase/wgEncodeUwDnaseWholebrainC57bl6ME14halfPkRep2.narrowPeak.gz WholeBrain DnaseSeq Peaks 2 narrowPeak UW-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeUwDnase/wgEncodeUwDnaseWholebrainC57bl6ME14halfSigRep1.bigWig WholeBrain DnaseSeq Signal 1 bigWig UW-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeUwDnase/wgEncodeUwDnaseWholebrainC57bl6ME14halfSigRep2.bigWig WholeBrain DnaseSeq Signal 2 bigWig UW-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeUwDnase/wgEncodeUwDnaseZhbtc4129olaME0AlnRep1.bam ZhBTc4 DnaseSeq Alignments 1 bam UW-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeUwDnase/wgEncodeUwDnaseZhbtc4129olaME0AlnRep1V2.bam ZhBTc4 DnaseSeq Alignments 1 bam UW-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeUwDnase/wgEncodeUwDnaseZhbtc4129olaME0AlnRep2.bam ZhBTc4 DnaseSeq Alignments 2 bam UW-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeUwDnase/wgEncodeUwDnaseZhbtc4129olaME0Diffb24hAlnRep1.bam ZhBTc4 DnaseSeq Alignments 1 bam UW-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeUwDnase/wgEncodeUwDnaseZhbtc4129olaME0Diffb24hAlnRep2.bam ZhBTc4 DnaseSeq Alignments 2 bam UW-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeUwDnase/wgEncodeUwDnaseZhbtc4129olaME0Diffb24hHotspotsRep1.broadPeak.gz ZhBTc4 DnaseSeq Hotspots 1 broadPeak UW-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeUwDnase/wgEncodeUwDnaseZhbtc4129olaME0Diffb24hHotspotsRep2.broadPeak.gz ZhBTc4 DnaseSeq Hotspots 2 broadPeak UW-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeUwDnase/wgEncodeUwDnaseZhbtc4129olaME0Diffb24hPkRep1.narrowPeak.gz ZhBTc4 DnaseSeq Peaks 1 narrowPeak UW-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeUwDnase/wgEncodeUwDnaseZhbtc4129olaME0Diffb24hPkRep2.narrowPeak.gz ZhBTc4 DnaseSeq Peaks 2 narrowPeak UW-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeUwDnase/wgEncodeUwDnaseZhbtc4129olaME0Diffb24hSigRep1.bigWig ZhBTc4 DnaseSeq Signal 1 bigWig UW-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeUwDnase/wgEncodeUwDnaseZhbtc4129olaME0Diffb24hSigRep2.bigWig ZhBTc4 DnaseSeq Signal 2 bigWig UW-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeUwDnase/wgEncodeUwDnaseZhbtc4129olaME0Diffb6hAlnRep1.bam ZhBTc4 DnaseSeq Alignments 1 bam UW-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeUwDnase/wgEncodeUwDnaseZhbtc4129olaME0Diffb6hAlnRep2.bam ZhBTc4 DnaseSeq Alignments 2 bam UW-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeUwDnase/wgEncodeUwDnaseZhbtc4129olaME0Diffb6hHotspotsRep1.broadPeak.gz ZhBTc4 DnaseSeq Hotspots 1 broadPeak UW-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeUwDnase/wgEncodeUwDnaseZhbtc4129olaME0Diffb6hHotspotsRep2.broadPeak.gz ZhBTc4 DnaseSeq Hotspots 2 broadPeak UW-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeUwDnase/wgEncodeUwDnaseZhbtc4129olaME0Diffb6hPkRep1.narrowPeak.gz ZhBTc4 DnaseSeq Peaks 1 narrowPeak UW-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeUwDnase/wgEncodeUwDnaseZhbtc4129olaME0Diffb6hPkRep2.narrowPeak.gz ZhBTc4 DnaseSeq Peaks 2 narrowPeak UW-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeUwDnase/wgEncodeUwDnaseZhbtc4129olaME0Diffb6hSigRep1.bigWig ZhBTc4 DnaseSeq Signal 1 bigWig UW-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeUwDnase/wgEncodeUwDnaseZhbtc4129olaME0Diffb6hSigRep2.bigWig ZhBTc4 DnaseSeq Signal 2 bigWig UW-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeUwDnase/wgEncodeUwDnaseZhbtc4129olaME0HotspotsRep1.broadPeak.gz ZhBTc4 DnaseSeq Hotspots 1 broadPeak UW-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeUwDnase/wgEncodeUwDnaseZhbtc4129olaME0HotspotsRep1V2.broadPeak.gz ZhBTc4 DnaseSeq Hotspots 1 broadPeak UW-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeUwDnase/wgEncodeUwDnaseZhbtc4129olaME0HotspotsRep2.broadPeak.gz ZhBTc4 DnaseSeq Hotspots 2 broadPeak UW-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeUwDnase/wgEncodeUwDnaseZhbtc4129olaME0PkRep1.narrowPeak.gz ZhBTc4 DnaseSeq Peaks 1 narrowPeak UW-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeUwDnase/wgEncodeUwDnaseZhbtc4129olaME0PkRep1V2.narrowPeak.gz ZhBTc4 DnaseSeq Peaks 1 narrowPeak UW-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeUwDnase/wgEncodeUwDnaseZhbtc4129olaME0PkRep2.narrowPeak.gz ZhBTc4 DnaseSeq Peaks 2 narrowPeak UW-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeUwDnase/wgEncodeUwDnaseZhbtc4129olaME0SigRep1.bigWig ZhBTc4 DnaseSeq Signal 1 bigWig UW-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeUwDnase/wgEncodeUwDnaseZhbtc4129olaME0SigRep1V2.bigWig ZhBTc4 DnaseSeq Signal 1 bigWig UW-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeUwDnase/wgEncodeUwDnaseZhbtc4129olaME0SigRep2.bigWig ZhBTc4 DnaseSeq Signal 2 bigWig UW-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeUwRnaSeq/wgEncodeUwRnaSeq416bCellPolyaMImmortalB6d2f1jAlnRep1.bam 416B RnaSeq Alignments 1 bam UW-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeUwRnaSeq/wgEncodeUwRnaSeq416bCellPolyaMImmortalB6d2f1jAlnRep2.bam 416B RnaSeq Alignments 2 bam UW-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeUwRnaSeq/wgEncodeUwRnaSeq416bCellPolyaMImmortalB6d2f1jMinusRawRep1.bigWig 416B RnaSeq MinusRawSignal 1 bigWig UW-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeUwRnaSeq/wgEncodeUwRnaSeq416bCellPolyaMImmortalB6d2f1jMinusRawRep2.bigWig 416B RnaSeq MinusRawSignal 2 bigWig UW-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeUwRnaSeq/wgEncodeUwRnaSeq416bCellPolyaMImmortalB6d2f1jPlusRawRep1.bigWig 416B RnaSeq PlusRawSignal 1 bigWig UW-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeUwRnaSeq/wgEncodeUwRnaSeq416bCellPolyaMImmortalB6d2f1jPlusRawRep2.bigWig 416B RnaSeq PlusRawSignal 2 bigWig UW-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeUwRnaSeq/wgEncodeUwRnaSeq416bCellPolyaMImmortalB6d2f1jSigRep1.bigWig 416B RnaSeq Signal 1 bigWig UW-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeUwRnaSeq/wgEncodeUwRnaSeq416bCellPolyaMImmortalB6d2f1jSigRep2.bigWig 416B RnaSeq Signal 2 bigWig UW-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeUwRnaSeq/wgEncodeUwRnaSeqA20CellPolyaMImmortalBalbcannAlnRep1.bam A20 RnaSeq Alignments 1 bam UW-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeUwRnaSeq/wgEncodeUwRnaSeqA20CellPolyaMImmortalBalbcannAlnRep2.bam A20 RnaSeq Alignments 2 bam UW-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeUwRnaSeq/wgEncodeUwRnaSeqA20CellPolyaMImmortalBalbcannMinusRawRep1.bigWig A20 RnaSeq MinusRawSignal 1 bigWig UW-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeUwRnaSeq/wgEncodeUwRnaSeqA20CellPolyaMImmortalBalbcannMinusRawRep2.bigWig A20 RnaSeq MinusRawSignal 2 bigWig UW-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeUwRnaSeq/wgEncodeUwRnaSeqA20CellPolyaMImmortalBalbcannPlusRawRep1.bigWig A20 RnaSeq PlusRawSignal 1 bigWig UW-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeUwRnaSeq/wgEncodeUwRnaSeqA20CellPolyaMImmortalBalbcannPlusRawRep2.bigWig A20 RnaSeq PlusRawSignal 2 bigWig UW-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeUwRnaSeq/wgEncodeUwRnaSeqA20CellPolyaMImmortalBalbcannSigRep1.bigWig A20 RnaSeq Signal 1 bigWig UW-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeUwRnaSeq/wgEncodeUwRnaSeqA20CellPolyaMImmortalBalbcannSigRep2.bigWig A20 RnaSeq Signal 2 bigWig UW-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeUwRnaSeq/wgEncodeUwRnaSeqBcellcd19pCellPolyaMAdult8wksC57bl6AlnRep1.bam B-cell_(CD19+) RnaSeq Alignments 1 bam UW-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeUwRnaSeq/wgEncodeUwRnaSeqBcellcd19pCellPolyaMAdult8wksC57bl6MinusRawRep1.bigWig B-cell_(CD19+) RnaSeq MinusRawSignal 1 bigWig UW-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeUwRnaSeq/wgEncodeUwRnaSeqBcellcd19pCellPolyaMAdult8wksC57bl6PlusRawRep1.bigWig B-cell_(CD19+) RnaSeq PlusRawSignal 1 bigWig UW-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeUwRnaSeq/wgEncodeUwRnaSeqBcellcd19pCellPolyaMAdult8wksC57bl6SigRep1.bigWig B-cell_(CD19+) RnaSeq Signal 1 bigWig UW-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeUwRnaSeq/wgEncodeUwRnaSeqBcellcd43nCellPolyaMAdult8wksC57bl6AlnRep1.bam B-cell_(CD43-) RnaSeq Alignments 1 bam UW-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeUwRnaSeq/wgEncodeUwRnaSeqBcellcd43nCellPolyaMAdult8wksC57bl6AlnRep2.bam B-cell_(CD43-) RnaSeq Alignments 2 bam UW-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeUwRnaSeq/wgEncodeUwRnaSeqBcellcd43nCellPolyaMAdult8wksC57bl6MinusRawRep1.bigWig B-cell_(CD43-) RnaSeq MinusRawSignal 1 bigWig UW-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeUwRnaSeq/wgEncodeUwRnaSeqBcellcd43nCellPolyaMAdult8wksC57bl6MinusRawRep2.bigWig B-cell_(CD43-) RnaSeq MinusRawSignal 2 bigWig UW-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeUwRnaSeq/wgEncodeUwRnaSeqBcellcd43nCellPolyaMAdult8wksC57bl6PlusRawRep1.bigWig B-cell_(CD43-) RnaSeq PlusRawSignal 1 bigWig UW-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeUwRnaSeq/wgEncodeUwRnaSeqBcellcd43nCellPolyaMAdult8wksC57bl6PlusRawRep2.bigWig B-cell_(CD43-) RnaSeq PlusRawSignal 2 bigWig UW-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeUwRnaSeq/wgEncodeUwRnaSeqBcellcd43nCellPolyaMAdult8wksC57bl6SigRep1.bigWig B-cell_(CD43-) RnaSeq Signal 1 bigWig UW-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeUwRnaSeq/wgEncodeUwRnaSeqBcellcd43nCellPolyaMAdult8wksC57bl6SigRep2.bigWig B-cell_(CD43-) RnaSeq Signal 2 bigWig UW-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeUwRnaSeq/wgEncodeUwRnaSeqCbellumCellPolyaMAdult8wksC57bl6AlnRep1.bam Cerebellum RnaSeq Alignments 1 bam UW-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeUwRnaSeq/wgEncodeUwRnaSeqCbellumCellPolyaMAdult8wksC57bl6AlnRep2.bam Cerebellum RnaSeq Alignments 2 bam UW-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeUwRnaSeq/wgEncodeUwRnaSeqCbellumCellPolyaMAdult8wksC57bl6MinusRawRep1.bigWig Cerebellum RnaSeq MinusRawSignal 1 bigWig UW-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeUwRnaSeq/wgEncodeUwRnaSeqCbellumCellPolyaMAdult8wksC57bl6MinusRawRep2.bigWig Cerebellum RnaSeq MinusRawSignal 2 bigWig UW-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeUwRnaSeq/wgEncodeUwRnaSeqCbellumCellPolyaMAdult8wksC57bl6PlusRawRep1.bigWig Cerebellum RnaSeq PlusRawSignal 1 bigWig UW-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeUwRnaSeq/wgEncodeUwRnaSeqCbellumCellPolyaMAdult8wksC57bl6PlusRawRep2.bigWig Cerebellum RnaSeq PlusRawSignal 2 bigWig UW-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeUwRnaSeq/wgEncodeUwRnaSeqCbellumCellPolyaMAdult8wksC57bl6SigRep1.bigWig Cerebellum RnaSeq Signal 1 bigWig UW-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeUwRnaSeq/wgEncodeUwRnaSeqCbellumCellPolyaMAdult8wksC57bl6SigRep2.bigWig Cerebellum RnaSeq Signal 2 bigWig UW-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeUwRnaSeq/wgEncodeUwRnaSeqCerebrumCellPolyaMAdult8wksC57bl6AlnRep1.bam Cerebrum RnaSeq Alignments 1 bam UW-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeUwRnaSeq/wgEncodeUwRnaSeqCerebrumCellPolyaMAdult8wksC57bl6AlnRep2.bam Cerebrum RnaSeq Alignments 2 bam UW-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeUwRnaSeq/wgEncodeUwRnaSeqCerebrumCellPolyaMAdult8wksC57bl6MinusRawRep1.bigWig Cerebrum RnaSeq MinusRawSignal 1 bigWig UW-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeUwRnaSeq/wgEncodeUwRnaSeqCerebrumCellPolyaMAdult8wksC57bl6MinusRawRep2.bigWig Cerebrum RnaSeq MinusRawSignal 2 bigWig UW-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeUwRnaSeq/wgEncodeUwRnaSeqCerebrumCellPolyaMAdult8wksC57bl6PlusRawRep1.bigWig Cerebrum RnaSeq PlusRawSignal 1 bigWig UW-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeUwRnaSeq/wgEncodeUwRnaSeqCerebrumCellPolyaMAdult8wksC57bl6PlusRawRep2.bigWig Cerebrum RnaSeq PlusRawSignal 2 bigWig UW-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeUwRnaSeq/wgEncodeUwRnaSeqCerebrumCellPolyaMAdult8wksC57bl6SigRep1.bigWig Cerebrum RnaSeq Signal 1 bigWig UW-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeUwRnaSeq/wgEncodeUwRnaSeqCerebrumCellPolyaMAdult8wksC57bl6SigRep2.bigWig Cerebrum RnaSeq Signal 2 bigWig UW-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeUwRnaSeq/wgEncodeUwRnaSeqFatCellPolyaMAdult8wksC57bl6AlnRep1.bam FatPad RnaSeq Alignments 1 bam UW-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeUwRnaSeq/wgEncodeUwRnaSeqFatCellPolyaMAdult8wksC57bl6MinusRawRep1.bigWig FatPad RnaSeq MinusRawSignal 1 bigWig UW-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeUwRnaSeq/wgEncodeUwRnaSeqFatCellPolyaMAdult8wksC57bl6PlusRawRep1.bigWig FatPad RnaSeq PlusRawSignal 1 bigWig UW-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeUwRnaSeq/wgEncodeUwRnaSeqFatCellPolyaMAdult8wksC57bl6SigRep1.bigWig FatPad RnaSeq Signal 1 bigWig UW-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeUwRnaSeq/wgEncodeUwRnaSeqGfatCellPolyaMAdult8wksC57bl6AlnRep1.bam GenitalFatPad RnaSeq Alignments 1 bam UW-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeUwRnaSeq/wgEncodeUwRnaSeqGfatCellPolyaMAdult8wksC57bl6AlnRep2.bam GenitalFatPad RnaSeq Alignments 2 bam UW-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeUwRnaSeq/wgEncodeUwRnaSeqGfatCellPolyaMAdult8wksC57bl6MinusRawRep1.bigWig GenitalFatPad RnaSeq MinusRawSignal 1 bigWig UW-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeUwRnaSeq/wgEncodeUwRnaSeqGfatCellPolyaMAdult8wksC57bl6MinusRawRep2.bigWig GenitalFatPad RnaSeq MinusRawSignal 2 bigWig UW-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeUwRnaSeq/wgEncodeUwRnaSeqGfatCellPolyaMAdult8wksC57bl6PlusRawRep1.bigWig GenitalFatPad RnaSeq PlusRawSignal 1 bigWig UW-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeUwRnaSeq/wgEncodeUwRnaSeqGfatCellPolyaMAdult8wksC57bl6PlusRawRep2.bigWig GenitalFatPad RnaSeq PlusRawSignal 2 bigWig UW-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeUwRnaSeq/wgEncodeUwRnaSeqGfatCellPolyaMAdult8wksC57bl6SigRep1.bigWig GenitalFatPad RnaSeq Signal 1 bigWig UW-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeUwRnaSeq/wgEncodeUwRnaSeqGfatCellPolyaMAdult8wksC57bl6SigRep2.bigWig GenitalFatPad RnaSeq Signal 2 bigWig UW-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeUwRnaSeq/wgEncodeUwRnaSeqHeartCellPolyaMAdult8wksC57bl6AlnRep1.bam Heart RnaSeq Alignments 1 bam UW-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeUwRnaSeq/wgEncodeUwRnaSeqHeartCellPolyaMAdult8wksC57bl6AlnRep2.bam Heart RnaSeq Alignments 2 bam UW-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeUwRnaSeq/wgEncodeUwRnaSeqHeartCellPolyaMAdult8wksC57bl6MinusRawRep1.bigWig Heart RnaSeq MinusRawSignal 1 bigWig UW-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeUwRnaSeq/wgEncodeUwRnaSeqHeartCellPolyaMAdult8wksC57bl6MinusRawRep2.bigWig Heart RnaSeq MinusRawSignal 2 bigWig UW-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeUwRnaSeq/wgEncodeUwRnaSeqHeartCellPolyaMAdult8wksC57bl6PlusRawRep1.bigWig Heart RnaSeq PlusRawSignal 1 bigWig UW-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeUwRnaSeq/wgEncodeUwRnaSeqHeartCellPolyaMAdult8wksC57bl6PlusRawRep2.bigWig Heart RnaSeq PlusRawSignal 2 bigWig UW-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeUwRnaSeq/wgEncodeUwRnaSeqHeartCellPolyaMAdult8wksC57bl6SigRep1.bigWig Heart RnaSeq Signal 1 bigWig UW-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeUwRnaSeq/wgEncodeUwRnaSeqHeartCellPolyaMAdult8wksC57bl6SigRep2.bigWig Heart RnaSeq Signal 2 bigWig UW-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeUwRnaSeq/wgEncodeUwRnaSeqHlembryoCellPolyaME11halfCd1AlnRep1.bam HeadlessEmbryo RnaSeq Alignments 1 bam UW-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeUwRnaSeq/wgEncodeUwRnaSeqHlembryoCellPolyaME11halfCd1MinusRawRep1.bigWig HeadlessEmbryo RnaSeq MinusRawSignal 1 bigWig UW-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeUwRnaSeq/wgEncodeUwRnaSeqHlembryoCellPolyaME11halfCd1PlusRawRep1.bigWig HeadlessEmbryo RnaSeq PlusRawSignal 1 bigWig UW-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeUwRnaSeq/wgEncodeUwRnaSeqHlembryoCellPolyaME11halfCd1SigRep1.bigWig HeadlessEmbryo RnaSeq Signal 1 bigWig UW-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeUwRnaSeq/wgEncodeUwRnaSeqKidneyCellPolyaMAdult8wksC57bl6AlnRep1.bam Kidney RnaSeq Alignments 1 bam UW-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeUwRnaSeq/wgEncodeUwRnaSeqKidneyCellPolyaMAdult8wksC57bl6MinusRawRep1.bigWig Kidney RnaSeq MinusRawSignal 1 bigWig UW-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeUwRnaSeq/wgEncodeUwRnaSeqKidneyCellPolyaMAdult8wksC57bl6PlusRawRep1.bigWig Kidney RnaSeq PlusRawSignal 1 bigWig UW-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeUwRnaSeq/wgEncodeUwRnaSeqKidneyCellPolyaMAdult8wksC57bl6SigRep1.bigWig Kidney RnaSeq Signal 1 bigWig UW-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeUwRnaSeq/wgEncodeUwRnaSeqLgintCellPolyaMAdult8wksC57bl6AlnRep1.bam LgIntestine RnaSeq Alignments 1 bam UW-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeUwRnaSeq/wgEncodeUwRnaSeqLgintCellPolyaMAdult8wksC57bl6AlnRep2.bam LgIntestine RnaSeq Alignments 2 bam UW-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeUwRnaSeq/wgEncodeUwRnaSeqLgintCellPolyaMAdult8wksC57bl6MinusRawRep1.bigWig LgIntestine RnaSeq MinusRawSignal 1 bigWig UW-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeUwRnaSeq/wgEncodeUwRnaSeqLgintCellPolyaMAdult8wksC57bl6MinusRawRep2.bigWig LgIntestine RnaSeq MinusRawSignal 2 bigWig UW-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeUwRnaSeq/wgEncodeUwRnaSeqLgintCellPolyaMAdult8wksC57bl6PlusRawRep1.bigWig LgIntestine RnaSeq PlusRawSignal 1 bigWig UW-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeUwRnaSeq/wgEncodeUwRnaSeqLgintCellPolyaMAdult8wksC57bl6PlusRawRep2.bigWig LgIntestine RnaSeq PlusRawSignal 2 bigWig UW-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeUwRnaSeq/wgEncodeUwRnaSeqLgintCellPolyaMAdult8wksC57bl6SigRep1.bigWig LgIntestine RnaSeq Signal 1 bigWig UW-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeUwRnaSeq/wgEncodeUwRnaSeqLgintCellPolyaMAdult8wksC57bl6SigRep2.bigWig LgIntestine RnaSeq Signal 2 bigWig UW-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeUwRnaSeq/wgEncodeUwRnaSeqLiverCellPolyaMAdult8wksC57bl6AlnRep1.bam Liver RnaSeq Alignments 1 bam UW-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeUwRnaSeq/wgEncodeUwRnaSeqLiverCellPolyaMAdult8wksC57bl6AlnRep2.bam Liver RnaSeq Alignments 2 bam UW-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeUwRnaSeq/wgEncodeUwRnaSeqLiverCellPolyaMAdult8wksC57bl6AlnRep3.bam Liver RnaSeq Alignments 3 bam UW-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeUwRnaSeq/wgEncodeUwRnaSeqLiverCellPolyaMAdult8wksC57bl6AlnRep4.bam Liver RnaSeq Alignments 4 bam UW-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeUwRnaSeq/wgEncodeUwRnaSeqLiverCellPolyaMAdult8wksC57bl6MinusRawRep1.bigWig Liver RnaSeq MinusRawSignal 1 bigWig UW-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeUwRnaSeq/wgEncodeUwRnaSeqLiverCellPolyaMAdult8wksC57bl6MinusRawRep2.bigWig Liver RnaSeq MinusRawSignal 2 bigWig UW-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeUwRnaSeq/wgEncodeUwRnaSeqLiverCellPolyaMAdult8wksC57bl6MinusRawRep3.bigWig Liver RnaSeq MinusRawSignal 3 bigWig UW-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeUwRnaSeq/wgEncodeUwRnaSeqLiverCellPolyaMAdult8wksC57bl6MinusRawRep4.bigWig Liver RnaSeq MinusRawSignal 4 bigWig UW-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeUwRnaSeq/wgEncodeUwRnaSeqLiverCellPolyaMAdult8wksC57bl6PlusRawRep1.bigWig Liver RnaSeq PlusRawSignal 1 bigWig UW-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeUwRnaSeq/wgEncodeUwRnaSeqLiverCellPolyaMAdult8wksC57bl6PlusRawRep2.bigWig Liver RnaSeq PlusRawSignal 2 bigWig UW-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeUwRnaSeq/wgEncodeUwRnaSeqLiverCellPolyaMAdult8wksC57bl6PlusRawRep3.bigWig Liver RnaSeq PlusRawSignal 3 bigWig UW-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeUwRnaSeq/wgEncodeUwRnaSeqLiverCellPolyaMAdult8wksC57bl6PlusRawRep4.bigWig Liver RnaSeq PlusRawSignal 4 bigWig UW-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeUwRnaSeq/wgEncodeUwRnaSeqLiverCellPolyaMAdult8wksC57bl6SigRep1.bigWig Liver RnaSeq Signal 1 bigWig UW-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeUwRnaSeq/wgEncodeUwRnaSeqLiverCellPolyaMAdult8wksC57bl6SigRep2.bigWig Liver RnaSeq Signal 2 bigWig UW-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeUwRnaSeq/wgEncodeUwRnaSeqLiverCellPolyaMAdult8wksC57bl6SigRep3.bigWig Liver RnaSeq Signal 3 bigWig UW-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeUwRnaSeq/wgEncodeUwRnaSeqLiverCellPolyaMAdult8wksC57bl6SigRep4.bigWig Liver RnaSeq Signal 4 bigWig UW-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeUwRnaSeq/wgEncodeUwRnaSeqLiverCellPolyaME14halfC57bl6AlnRep1.bam Liver RnaSeq Alignments 1 bam UW-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeUwRnaSeq/wgEncodeUwRnaSeqLiverCellPolyaME14halfC57bl6MinusRawRep1.bigWig Liver RnaSeq MinusRawSignal 1 bigWig UW-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeUwRnaSeq/wgEncodeUwRnaSeqLiverCellPolyaME14halfC57bl6PlusRawRep1.bigWig Liver RnaSeq PlusRawSignal 1 bigWig UW-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeUwRnaSeq/wgEncodeUwRnaSeqLiverCellPolyaME14halfC57bl6SigRep1.bigWig Liver RnaSeq Signal 1 bigWig UW-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeUwRnaSeq/wgEncodeUwRnaSeqLiverCellPolyaME14halfS129AlnRep1.bam Liver RnaSeq Alignments 1 bam UW-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeUwRnaSeq/wgEncodeUwRnaSeqLiverCellPolyaME14halfS129MinusRawRep1.bigWig Liver RnaSeq MinusRawSignal 1 bigWig UW-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeUwRnaSeq/wgEncodeUwRnaSeqLiverCellPolyaME14halfS129PlusRawRep1.bigWig Liver RnaSeq PlusRawSignal 1 bigWig UW-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeUwRnaSeq/wgEncodeUwRnaSeqLiverCellPolyaME14halfS129SigRep1.bigWig Liver RnaSeq Signal 1 bigWig UW-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeUwRnaSeq/wgEncodeUwRnaSeqLungCellPolyaMAdult8wksC57bl6AlnRep1.bam Lung RnaSeq Alignments 1 bam UW-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeUwRnaSeq/wgEncodeUwRnaSeqLungCellPolyaMAdult8wksC57bl6MinusRawRep1.bigWig Lung RnaSeq MinusRawSignal 1 bigWig UW-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeUwRnaSeq/wgEncodeUwRnaSeqLungCellPolyaMAdult8wksC57bl6PlusRawRep1.bigWig Lung RnaSeq PlusRawSignal 1 bigWig UW-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeUwRnaSeq/wgEncodeUwRnaSeqLungCellPolyaMAdult8wksC57bl6SigRep1.bigWig Lung RnaSeq Signal 1 bigWig UW-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeUwRnaSeq/wgEncodeUwRnaSeqMelCellPolyaMImmortalUknAlnRep1.bam MEL RnaSeq Alignments 1 bam UW-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeUwRnaSeq/wgEncodeUwRnaSeqMelCellPolyaMImmortalUknAlnRep2.bam MEL RnaSeq Alignments 2 bam UW-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeUwRnaSeq/wgEncodeUwRnaSeqMelCellPolyaMImmortalUknMinusRawRep1.bigWig MEL RnaSeq MinusRawSignal 1 bigWig UW-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeUwRnaSeq/wgEncodeUwRnaSeqMelCellPolyaMImmortalUknMinusRawRep2.bigWig MEL RnaSeq MinusRawSignal 2 bigWig UW-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeUwRnaSeq/wgEncodeUwRnaSeqMelCellPolyaMImmortalUknPlusRawRep1.bigWig MEL RnaSeq PlusRawSignal 1 bigWig UW-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeUwRnaSeq/wgEncodeUwRnaSeqMelCellPolyaMImmortalUknPlusRawRep2.bigWig MEL RnaSeq PlusRawSignal 2 bigWig UW-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeUwRnaSeq/wgEncodeUwRnaSeqMelCellPolyaMImmortalUknSigRep1.bigWig MEL RnaSeq Signal 1 bigWig UW-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeUwRnaSeq/wgEncodeUwRnaSeqMelCellPolyaMImmortalUknSigRep2.bigWig MEL RnaSeq Signal 2 bigWig UW-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeUwRnaSeq/wgEncodeUwRnaSeqNih3t3CellPolyaMImmortalNihsAlnRep1.bam NIH-3T3 RnaSeq Alignments 1 bam UW-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeUwRnaSeq/wgEncodeUwRnaSeqNih3t3CellPolyaMImmortalNihsAlnRep2.bam NIH-3T3 RnaSeq Alignments 2 bam UW-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeUwRnaSeq/wgEncodeUwRnaSeqNih3t3CellPolyaMImmortalNihsMinusRawRep1.bigWig NIH-3T3 RnaSeq MinusRawSignal 1 bigWig UW-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeUwRnaSeq/wgEncodeUwRnaSeqNih3t3CellPolyaMImmortalNihsMinusRawRep2.bigWig NIH-3T3 RnaSeq MinusRawSignal 2 bigWig UW-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeUwRnaSeq/wgEncodeUwRnaSeqNih3t3CellPolyaMImmortalNihsPlusRawRep1.bigWig NIH-3T3 RnaSeq PlusRawSignal 1 bigWig UW-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeUwRnaSeq/wgEncodeUwRnaSeqNih3t3CellPolyaMImmortalNihsPlusRawRep2.bigWig NIH-3T3 RnaSeq PlusRawSignal 2 bigWig UW-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeUwRnaSeq/wgEncodeUwRnaSeqNih3t3CellPolyaMImmortalNihsSigRep1.bigWig NIH-3T3 RnaSeq Signal 1 bigWig UW-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeUwRnaSeq/wgEncodeUwRnaSeqNih3t3CellPolyaMImmortalNihsSigRep2.bigWig NIH-3T3 RnaSeq Signal 2 bigWig UW-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeUwRnaSeq/wgEncodeUwRnaSeqPatskiCellPolyaFImmortalSpbl6AlnRep1.bam Patski RnaSeq Alignments 1 bam UW-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeUwRnaSeq/wgEncodeUwRnaSeqPatskiCellPolyaFImmortalSpbl6AlnRep2.bam Patski RnaSeq Alignments 2 bam UW-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeUwRnaSeq/wgEncodeUwRnaSeqPatskiCellPolyaFImmortalSpbl6MinusRawRep1.bigWig Patski RnaSeq MinusRawSignal 1 bigWig UW-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeUwRnaSeq/wgEncodeUwRnaSeqPatskiCellPolyaFImmortalSpbl6MinusRawRep2.bigWig Patski RnaSeq MinusRawSignal 2 bigWig UW-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeUwRnaSeq/wgEncodeUwRnaSeqPatskiCellPolyaFImmortalSpbl6PlusRawRep1.bigWig Patski RnaSeq PlusRawSignal 1 bigWig UW-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeUwRnaSeq/wgEncodeUwRnaSeqPatskiCellPolyaFImmortalSpbl6PlusRawRep2.bigWig Patski RnaSeq PlusRawSignal 2 bigWig UW-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeUwRnaSeq/wgEncodeUwRnaSeqPatskiCellPolyaFImmortalSpbl6SigRep1.bigWig Patski RnaSeq Signal 1 bigWig UW-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeUwRnaSeq/wgEncodeUwRnaSeqPatskiCellPolyaFImmortalSpbl6SigRep2.bigWig Patski RnaSeq Signal 2 bigWig UW-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeUwRnaSeq/wgEncodeUwRnaSeqSkmuscleCellPolyaMAdult8wksC57bl6AlnRep1.bam SkMuscle RnaSeq Alignments 1 bam UW-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeUwRnaSeq/wgEncodeUwRnaSeqSkmuscleCellPolyaMAdult8wksC57bl6AlnRep2.bam SkMuscle RnaSeq Alignments 2 bam UW-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeUwRnaSeq/wgEncodeUwRnaSeqSkmuscleCellPolyaMAdult8wksC57bl6MinusRawRep1.bigWig SkMuscle RnaSeq MinusRawSignal 1 bigWig UW-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeUwRnaSeq/wgEncodeUwRnaSeqSkmuscleCellPolyaMAdult8wksC57bl6MinusRawRep2.bigWig SkMuscle RnaSeq MinusRawSignal 2 bigWig UW-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeUwRnaSeq/wgEncodeUwRnaSeqSkmuscleCellPolyaMAdult8wksC57bl6PlusRawRep1.bigWig SkMuscle RnaSeq PlusRawSignal 1 bigWig UW-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeUwRnaSeq/wgEncodeUwRnaSeqSkmuscleCellPolyaMAdult8wksC57bl6PlusRawRep2.bigWig SkMuscle RnaSeq PlusRawSignal 2 bigWig UW-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeUwRnaSeq/wgEncodeUwRnaSeqSkmuscleCellPolyaMAdult8wksC57bl6SigRep1.bigWig SkMuscle RnaSeq Signal 1 bigWig UW-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeUwRnaSeq/wgEncodeUwRnaSeqSkmuscleCellPolyaMAdult8wksC57bl6SigRep2.bigWig SkMuscle RnaSeq Signal 2 bigWig UW-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeUwRnaSeq/wgEncodeUwRnaSeqSpleenCellPolyaMAdult8wksC57bl6AlnRep1.bam Spleen RnaSeq Alignments 1 bam UW-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeUwRnaSeq/wgEncodeUwRnaSeqSpleenCellPolyaMAdult8wksC57bl6MinusRawRep1.bigWig Spleen RnaSeq MinusRawSignal 1 bigWig UW-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeUwRnaSeq/wgEncodeUwRnaSeqSpleenCellPolyaMAdult8wksC57bl6PlusRawRep1.bigWig Spleen RnaSeq PlusRawSignal 1 bigWig UW-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeUwRnaSeq/wgEncodeUwRnaSeqSpleenCellPolyaMAdult8wksC57bl6SigRep1.bigWig Spleen RnaSeq Signal 1 bigWig UW-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeUwRnaSeq/wgEncodeUwRnaSeqThymusCellPolyaMAdult8wksC57bl6AlnRep1.bam Thymus RnaSeq Alignments 1 bam UW-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeUwRnaSeq/wgEncodeUwRnaSeqThymusCellPolyaMAdult8wksC57bl6AlnRep2.bam Thymus RnaSeq Alignments 2 bam UW-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeUwRnaSeq/wgEncodeUwRnaSeqThymusCellPolyaMAdult8wksC57bl6MinusRawRep1.bigWig Thymus RnaSeq MinusRawSignal 1 bigWig UW-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeUwRnaSeq/wgEncodeUwRnaSeqThymusCellPolyaMAdult8wksC57bl6MinusRawRep2.bigWig Thymus RnaSeq MinusRawSignal 2 bigWig UW-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeUwRnaSeq/wgEncodeUwRnaSeqThymusCellPolyaMAdult8wksC57bl6PlusRawRep1.bigWig Thymus RnaSeq PlusRawSignal 1 bigWig UW-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeUwRnaSeq/wgEncodeUwRnaSeqThymusCellPolyaMAdult8wksC57bl6PlusRawRep2.bigWig Thymus RnaSeq PlusRawSignal 2 bigWig UW-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeUwRnaSeq/wgEncodeUwRnaSeqThymusCellPolyaMAdult8wksC57bl6SigRep1.bigWig Thymus RnaSeq Signal 1 bigWig UW-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeUwRnaSeq/wgEncodeUwRnaSeqThymusCellPolyaMAdult8wksC57bl6SigRep2.bigWig Thymus RnaSeq Signal 2 bigWig UW-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeUwRnaSeq/wgEncodeUwRnaSeqTnaiveCellPolyaMAdult8wksC57bl6AlnRep1.bam T-Naive RnaSeq Alignments 1 bam UW-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeUwRnaSeq/wgEncodeUwRnaSeqTnaiveCellPolyaMAdult8wksC57bl6MinusRawRep1.bigWig T-Naive RnaSeq MinusRawSignal 1 bigWig UW-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeUwRnaSeq/wgEncodeUwRnaSeqTnaiveCellPolyaMAdult8wksC57bl6PlusRawRep1.bigWig T-Naive RnaSeq PlusRawSignal 1 bigWig UW-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeUwRnaSeq/wgEncodeUwRnaSeqTnaiveCellPolyaMAdult8wksC57bl6SigRep1.bigWig T-Naive RnaSeq Signal 1 bigWig UW-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeUwRnaSeq/wgEncodeUwRnaSeqWbrainCellPolyaME14halfC57bl6AlnRep1.bam WholeBrain RnaSeq Alignments 1 bam UW-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeUwRnaSeq/wgEncodeUwRnaSeqWbrainCellPolyaME14halfC57bl6AlnRep2.bam WholeBrain RnaSeq Alignments 2 bam UW-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeUwRnaSeq/wgEncodeUwRnaSeqWbrainCellPolyaME14halfC57bl6MinusRawRep1.bigWig WholeBrain RnaSeq MinusRawSignal 1 bigWig UW-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeUwRnaSeq/wgEncodeUwRnaSeqWbrainCellPolyaME14halfC57bl6MinusRawRep2.bigWig WholeBrain RnaSeq MinusRawSignal 2 bigWig UW-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeUwRnaSeq/wgEncodeUwRnaSeqWbrainCellPolyaME14halfC57bl6PlusRawRep1.bigWig WholeBrain RnaSeq PlusRawSignal 1 bigWig UW-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeUwRnaSeq/wgEncodeUwRnaSeqWbrainCellPolyaME14halfC57bl6PlusRawRep2.bigWig WholeBrain RnaSeq PlusRawSignal 2 bigWig UW-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeUwRnaSeq/wgEncodeUwRnaSeqWbrainCellPolyaME14halfC57bl6SigRep1.bigWig WholeBrain RnaSeq Signal 1 bigWig UW-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeUwRnaSeq/wgEncodeUwRnaSeqWbrainCellPolyaME14halfC57bl6SigRep2.bigWig WholeBrain RnaSeq Signal 2 bigWig UW-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeUwRnaSeq/wgEncodeUwRnaSeqWbrainCellPolyaME18halfC57bl6AlnRep1.bam WholeBrain RnaSeq Alignments 1 bam UW-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeUwRnaSeq/wgEncodeUwRnaSeqWbrainCellPolyaME18halfC57bl6AlnRep2.bam WholeBrain RnaSeq Alignments 2 bam UW-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeUwRnaSeq/wgEncodeUwRnaSeqWbrainCellPolyaME18halfC57bl6MinusRawRep1.bigWig WholeBrain RnaSeq MinusRawSignal 1 bigWig UW-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeUwRnaSeq/wgEncodeUwRnaSeqWbrainCellPolyaME18halfC57bl6MinusRawRep2.bigWig WholeBrain RnaSeq MinusRawSignal 2 bigWig UW-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeUwRnaSeq/wgEncodeUwRnaSeqWbrainCellPolyaME18halfC57bl6PlusRawRep1.bigWig WholeBrain RnaSeq PlusRawSignal 1 bigWig UW-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeUwRnaSeq/wgEncodeUwRnaSeqWbrainCellPolyaME18halfC57bl6PlusRawRep2.bigWig WholeBrain RnaSeq PlusRawSignal 2 bigWig UW-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeUwRnaSeq/wgEncodeUwRnaSeqWbrainCellPolyaME18halfC57bl6SigRep1.bigWig WholeBrain RnaSeq Signal 1 bigWig UW-m http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeUwRnaSeq/wgEncodeUwRnaSeqWbrainCellPolyaME18halfC57bl6SigRep2.bigWig WholeBrain RnaSeq Signal 2 bigWig UW-m ================================================ FILE: src/juicebox/encode/rnaChip.txt ================================================ antibodyAliases.put("Gm12878CellTotal", "Gm12878CellTotal"); antibodyAliases.put("Gm12878CytosolLongnonpolya", "Gm12878CytosolLongnonpolya"); antibodyAliases.put("Gm12878CytosolLongpolya", "Gm12878CytosolLongpolya"); antibodyAliases.put("Gm12878NucleolusTotal", "Gm12878NucleolusTotal"); antibodyAliases.put("Gm12878NucleusLongnonpolya", "Gm12878NucleusLongnonpolya"); antibodyAliases.put("Gm12878NucleusLongpolya", "Gm12878NucleusLongpolya"); antibodyAliases.put("Hepg2CytosolLongnonpolya", "Hepg2CytosolLongnonpolya"); antibodyAliases.put("Hepg2CytosolLongpolya", "Hepg2CytosolLongpolya"); antibodyAliases.put("Hepg2NucleolusTotal", "Hepg2NucleolusTotal"); antibodyAliases.put("Hepg2NucleusLongnonpolya", "Hepg2NucleusLongnonpolya"); antibodyAliases.put("Hepg2NucleusLongpolya", "Hepg2NucleusLongpolya"); antibodyAliases.put("K562CellTotal", "K562CellTotal"); antibodyAliases.put("K562ChromatinTotal", "K562ChromatinTotal"); antibodyAliases.put("K562CytosolLongnonpolya", "K562CytosolLongnonpolya"); antibodyAliases.put("K562CytosolLongpolya", "K562CytosolLongpolya"); antibodyAliases.put("K562NucleolusTotal", "K562NucleolusTotal"); antibodyAliases.put("K562NucleoplasmTotal", "K562NucleoplasmTotal"); antibodyAliases.put("K562NucleusLongnonpolya", "K562NucleusLongnonpolya"); antibodyAliases.put("K562NucleusLongpolya", "K562NucleusLongpolya"); antibodyAliases.put("K562PolysomeLongnonpolya", "K562PolysomeLongnonpolya"); antibodyAliases.put("KeratinocyteCytosolLongnonpolya", "KeratinocyteCytosolLongnonpolya"); antibodyAliases.put("KeratinocyteCytosolLongpolya", "KeratinocyteCytosolLongpolya"); antibodyAliases.put("KeratinocyteNucleusLongnonpolya", "KeratinocyteNucleusLongnonpolya"); antibodyAliases.put("KeratinocyteNucleusLongpolya", "KeratinocyteNucleusLongpolya"); antibodyAliases.put("ProstateCellLongnonpolya", "ProstateCellLongnonpolya"); antibodyAliases.put("ProstateCellLongpolya", "ProstateCellLongpolya"); ================================================ FILE: src/juicebox/gui/BoundsPopupMenuListener.java ================================================ /* * The MIT License (MIT) * * Copyright (c) 2011-2020 Broad Institute, Aiden Lab, Rice University, Baylor College of Medicine * * Permission is hereby granted, free of charge, to any person obtaining a copy * of this software and associated documentation files (the "Software"), to deal * in the Software without restriction, including without limitation the rights * to use, copy, modify, merge, publish, distribute, sublicense, and/or sell * copies of the Software, and to permit persons to whom the Software is * furnished to do so, subject to the following conditions: * * The above copyright notice and this permission notice shall be included in * all copies or substantial portions of the Software. * * THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR * IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, * FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE * AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER * LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, * OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN * THE SOFTWARE. */ package juicebox.gui; import javax.swing.*; import javax.swing.event.PopupMenuEvent; import javax.swing.event.PopupMenuListener; import javax.swing.plaf.basic.BasicComboPopup; import java.awt.*; /** * http://www.camick.com/java/source/BoundsPopupMenuListener.java * This class will change the bounds of the JComboBox popup menu to support * different functionality. It will support the following features: * - a horizontal scrollbar can be displayed when necessary * - the popup can be wider than the combo box * - the popup can be displayed above the combo box *

* Class will only work for a JComboBox that uses a BasicComboPop. */ class BoundsPopupMenuListener implements PopupMenuListener { private boolean scrollBarRequired = true; private boolean popupWider; private int maximumWidth = -1; private boolean popupAbove; private JScrollPane scrollPane; /** * Convenience constructore to allow the display of a horizontal scrollbar * when required. */ public BoundsPopupMenuListener() { this(true, false, -1, false); } /** * Convenience constructor that allows you to display the popup * wider and/or above the combo box. * * @param popupWider when true, popup width is based on the popup * preferred width * @param popupAbove when true, popup is displayed above the combobox */ public BoundsPopupMenuListener(boolean popupWider, boolean popupAbove) { this(true, popupWider, -1, popupAbove); } /** * Convenience constructor that allows you to display the popup * wider than the combo box and to specify the maximum width * * @param maximumWidth the maximum width of the popup. The * popupAbove value is set to "true". */ public BoundsPopupMenuListener(int maximumWidth) { this(true, true, maximumWidth, false); } /** * General purpose constructor to set all popup properties at once. * * @param scrollBarRequired display a horizontal scrollbar when the * preferred width of popup is greater than width of scrollPane. * @param popupWider display the popup at its preferred with * @param maximumWidth limit the popup width to the value specified * (minimum size will be the width of the combo box) * @param popupAbove display the popup above the combo box */ private BoundsPopupMenuListener( boolean scrollBarRequired, boolean popupWider, int maximumWidth, boolean popupAbove) { setScrollBarRequired(scrollBarRequired); setPopupWider(popupWider); setMaximumWidth(maximumWidth); setPopupAbove(popupAbove); } /** * Return the maximum width of the popup. * * @return the maximumWidth value */ public int getMaximumWidth() { return maximumWidth; } /** * Set the maximum width for the popup. This value is only used when * setPopupWider( true ) has been specified. A value of -1 indicates * that there is no maximum. * * @param maximumWidth the maximum width of the popup */ private void setMaximumWidth(int maximumWidth) { this.maximumWidth = maximumWidth; } /** * Determine if the popup should be displayed above the combo box. * * @return the popupAbove value */ public boolean isPopupAbove() { return popupAbove; } /** * Change the location of the popup relative to the combo box. * * @param popupAbove true display popup above the combo box, * false display popup below the combo box. */ private void setPopupAbove(boolean popupAbove) { this.popupAbove = popupAbove; } /** * Determine if the popup might be displayed wider than the combo box * * @return the popupWider value */ public boolean isPopupWider() { return popupWider; } /** * Change the width of the popup to be the greater of the width of the * combo box or the preferred width of the popup. Normally the popup width * is always the same size as the combo box width. * * @param popupWider true adjust the width as required. */ private void setPopupWider(boolean popupWider) { this.popupWider = popupWider; } /** * Determine if the horizontal scroll bar might be required for the popup * * @return the scrollBarRequired value */ public boolean isScrollBarRequired() { return scrollBarRequired; } /** * For some reason the default implementation of the popup removes the * horizontal scrollBar from the popup scroll pane which can result in * the truncation of the rendered items in the popop. Adding a scrollBar * back to the scrollPane will allow horizontal scrolling if necessary. * * @param scrollBarRequired true add horizontal scrollBar to scrollPane * false remove the horizontal scrollBar */ private void setScrollBarRequired(boolean scrollBarRequired) { this.scrollBarRequired = scrollBarRequired; } /** * Alter the bounds of the popup just before it is made visible. */ @Override public void popupMenuWillBecomeVisible(PopupMenuEvent e) { @SuppressWarnings("unchecked") JComboBox comboBox = (JComboBox) e.getSource(); if (comboBox.getItemCount() == 0) return; final Object child = comboBox.getAccessibleContext().getAccessibleChild(0); if (child instanceof BasicComboPopup) { SwingUtilities.invokeLater(new Runnable() { public void run() { customizePopup((BasicComboPopup) child); } }); } } private void customizePopup(BasicComboPopup popup) { scrollPane = getScrollPane(popup); if (popupWider) popupWider(popup); checkHorizontalScrollBar(popup); // For some reason in JDK7 the popup will not display at its preferred // width unless its location has been changed from its default // (ie. for normal "pop down" shift the popup and reset) Component comboBox = popup.getInvoker(); Point location = comboBox.getLocationOnScreen(); if (popupAbove) { int height = popup.getPreferredSize().height; popup.setLocation(location.x, location.y - height); } else { //int height = comboBox.getPreferredSize().height; //popup.setLocation(location.x, location.y + height - 1); //popup.setLocation(location.x, location.y + height); //TODO should not be hardcoded popup.setLocation(location.x + 5, location.y + 35); } } /* * Adjust the width of the scrollpane used by the popup */ private void popupWider(BasicComboPopup popup) { @SuppressWarnings("unchecked") JList list = (JList) popup.getList(); // Determine the maximimum width to use: // a) determine the popup preferred width // b) limit width to the maximum if specified // c) ensure width is not less than the scroll pane width int popupWidth = list.getPreferredSize().width + 5 // make sure horizontal scrollbar doesn't appear + getScrollBarWidth(popup, scrollPane); if (maximumWidth != -1) { popupWidth = Math.min(popupWidth, maximumWidth); } Dimension scrollPaneSize = scrollPane.getPreferredSize(); popupWidth = Math.max(popupWidth, scrollPaneSize.width); // Adjust the width scrollPaneSize.width = popupWidth; scrollPane.setPreferredSize(scrollPaneSize); scrollPane.setMaximumSize(scrollPaneSize); } /* * This method is called every time: * - to make sure the viewport is returned to its default position * - to remove the horizontal scrollbar when it is not wanted */ private void checkHorizontalScrollBar(BasicComboPopup popup) { // Reset the viewport to the left JViewport viewport = scrollPane.getViewport(); Point p = viewport.getViewPosition(); p.x = 0; viewport.setViewPosition(p); // Remove the scrollbar so it is never painted if (!scrollBarRequired) { scrollPane.setHorizontalScrollBar(null); return; } // Make sure a horizontal scrollbar exists in the scrollpane JScrollBar horizontal = scrollPane.getHorizontalScrollBar(); if (horizontal == null) { horizontal = new JScrollBar(JScrollBar.HORIZONTAL); scrollPane.setHorizontalScrollBar(horizontal); scrollPane.setHorizontalScrollBarPolicy(JScrollPane.HORIZONTAL_SCROLLBAR_AS_NEEDED); } // Potentially increase height of scroll pane to display the scrollbar if (horizontalScrollBarWillBeVisible(popup, scrollPane)) { Dimension scrollPaneSize = scrollPane.getPreferredSize(); scrollPaneSize.height += horizontal.getPreferredSize().height; scrollPane.setPreferredSize(scrollPaneSize); scrollPane.setMaximumSize(scrollPaneSize); scrollPane.revalidate(); } } /* * Get the scroll pane used by the popup so its bounds can be adjusted */ private JScrollPane getScrollPane(BasicComboPopup popup) { @SuppressWarnings("unchecked") JList list = (JList) popup.getList(); Container c = SwingUtilities.getAncestorOfClass(JScrollPane.class, list); return (JScrollPane) c; } /* * I can't find any property on the scrollBar to determine if it will be * displayed or not so use brute force to determine this. */ private int getScrollBarWidth(BasicComboPopup popup, JScrollPane scrollPane) { int scrollBarWidth = 0; @SuppressWarnings("unchecked") JComboBox comboBox = (JComboBox) popup.getInvoker(); if (comboBox.getItemCount() > comboBox.getMaximumRowCount()) { JScrollBar vertical = scrollPane.getVerticalScrollBar(); scrollBarWidth = vertical.getPreferredSize().width; } return scrollBarWidth; } /* * I can't find any property on the scrollBar to determine if it will be * displayed or not so use brute force to determine this. */ private boolean horizontalScrollBarWillBeVisible(BasicComboPopup popup, JScrollPane scrollPane) { @SuppressWarnings("unchecked") JList list = (JList) popup.getList(); int scrollBarWidth = getScrollBarWidth(popup, scrollPane); int popupWidth = list.getPreferredSize().width + scrollBarWidth; return popupWidth > scrollPane.getPreferredSize().width; } @Override public void popupMenuCanceled(PopupMenuEvent e) { } @Override public void popupMenuWillBecomeInvisible(PopupMenuEvent e) { // In its normal state the scrollpane does not have a scrollbar if (scrollPane != null) { scrollPane.setHorizontalScrollBar(null); } } } ================================================ FILE: src/juicebox/gui/MainMenuBar.java ================================================ /* * The MIT License (MIT) * * Copyright (c) 2011-2021 Broad Institute, Aiden Lab, Rice University, Baylor College of Medicine * * Permission is hereby granted, free of charge, to any person obtaining a copy * of this software and associated documentation files (the "Software"), to deal * in the Software without restriction, including without limitation the rights * to use, copy, modify, merge, publish, distribute, sublicense, and/or sell * copies of the Software, and to permit persons to whom the Software is * furnished to do so, subject to the following conditions: * * The above copyright notice and this permission notice shall be included in * all copies or substantial portions of the Software. * * THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR * IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, * FITNESS FOR A PARTICULAR PURPOSE AND NON-INFRINGEMENT. IN NO EVENT SHALL THE * AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER * LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, * OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN * THE SOFTWARE. */ package juicebox.gui; import juicebox.DirectoryManager; import juicebox.HiCGlobals; import juicebox.ProcessHelper; import juicebox.assembly.AssemblyFileImporter; import juicebox.assembly.IGVFeatureCopy; import juicebox.mapcolorui.ColorScaleHandler; import juicebox.mapcolorui.Feature2DHandler; import juicebox.state.SaveFileDialog; import juicebox.tools.dev.Private; import juicebox.windowui.*; import org.broad.igv.ui.util.MessageUtils; import javax.swing.*; import java.awt.*; import java.awt.event.ActionEvent; import java.awt.event.ActionListener; import java.io.File; import java.io.IOException; /** * Created by muhammadsaadshamim on 8/4/15. */ public class MainMenuBar extends JMenuBar { private static final long serialVersionUID = 9000025; private static final int recentMapListMaxItems = 10; private static final int recentLocationMaxItems = 20; private static final String recentMapEntityNode = "hicMapRecent"; private static final String recentLocationEntityNode = "hicLocationRecent"; private static final String recentStateEntityNode = "hicStateRecent"; //private static JMenuItem loadOldAnnotationsMI; private static RecentMenu recentMapMenu, recentControlMapMenu; private static RecentMenu recentLocationMenu; private static JMenuItem saveLocationList; private static JMenuItem saveStateForReload; private static RecentMenu previousStates; private static JMenuItem exportSavedStateMenuItem; private static JMenuItem importMapAsFile; private static JMenuItem slideShow; private static JMenuItem showStats, showControlStats; private static JMenuItem renameGenome; //private static JMenu annotationsMenu; private static JMenu viewMenu; private static JMenu bookmarksMenu; private static JMenu assemblyMenu; private static JMenu devMenu; private static JMenuItem exportAssembly; private static JMenuItem resetAssembly; private static JMenuItem exitAssembly; private static JCheckBoxMenuItem enableAssembly; private static JMenuItem setScale; private static JMenuItem importModifiedAssembly; private final JCheckBoxMenuItem layersItem = new JCheckBoxMenuItem("Show Annotation Panel"); // created separately because it will be enabled after an initial map is loaded private final JMenuItem loadControlFromList = new JMenuItem(); public MainMenuBar(SuperAdapter superAdapter) { createMenuBar(superAdapter); } public static void exitAssemblyMode() { resetAssembly.setEnabled(false); exportAssembly.setEnabled(false); // setScale.setEnabled(false); importModifiedAssembly.setEnabled(false); exitAssembly.setEnabled(false); } public boolean unsavedEditsExist() { File unsavedSampleFile = new File(DirectoryManager.getHiCDirectory(), HiCGlobals.BACKUP_FILE_STEM + "0.bedpe"); return unsavedSampleFile.exists(); } public void addRecentMapMenuEntry(String title, boolean status) { recentMapMenu.addEntry(title, status); recentControlMapMenu.addEntry(title, status); } private void addRecentStateMenuEntry(String title, boolean status) { recentLocationMenu.addEntry(title, status); } private void createMenuBar(final SuperAdapter superAdapter) { //======== fileMenu ======== JMenu fileMenu = new JMenu("File"); fileMenu.setMnemonic('F'); JMenuItem newWindow = new JMenuItem("New Window"); newWindow.addActionListener(new ActionListener() { public void actionPerformed(ActionEvent e) { ProcessHelper p = new ProcessHelper(); try { p.startNewJavaProcess(); } catch (IOException error) { superAdapter.launchGenericMessageDialog(error.getMessage(), "Error", JOptionPane.ERROR_MESSAGE); } } }); fileMenu.add(newWindow); //---- openMenuItem ---- // create control first because it is enabled by regular open loadControlFromList.setText("Open as Control..."); loadControlFromList.addActionListener(new ActionListener() { public void actionPerformed(ActionEvent e) { superAdapter.loadFromListActionPerformed(true); } }); loadControlFromList.setEnabled(false); JMenuItem openItem = new JMenuItem("Open..."); openItem.addActionListener(new ActionListener() { public void actionPerformed(ActionEvent e) { superAdapter.loadFromListActionPerformed(false); } }); fileMenu.add(openItem); fileMenu.add(loadControlFromList); recentMapMenu = new RecentMenu("Open Recent", recentMapListMaxItems, recentMapEntityNode, HiCGlobals.menuType.MAP) { private static final long serialVersionUID = 9000021; public void onSelectPosition(String mapPath) { String[] temp = encodeSafeDelimeterSplit(mapPath); superAdapter.loadFromRecentActionPerformed((temp[1]), (temp[0]), false); } }; recentMapMenu.setMnemonic('R'); fileMenu.add(recentMapMenu); recentControlMapMenu = new RecentMenu("Open Recent as Control", recentMapListMaxItems, recentMapEntityNode, HiCGlobals.menuType.MAP) { private static final long serialVersionUID = 9000022; public void onSelectPosition(String mapPath) { String[] temp = encodeSafeDelimeterSplit(mapPath); superAdapter.loadFromRecentActionPerformed((temp[1]), (temp[0]), true); } }; //recentControlMapMenu.setMnemonic('r'); recentControlMapMenu.setEnabled(false); fileMenu.add(recentControlMapMenu); fileMenu.addSeparator(); showStats = new JMenuItem("Show Dataset Metrics"); showStats.addActionListener(new ActionListener() { @Override public void actionPerformed(ActionEvent actionEvent) { superAdapter.showDataSetMetrics(false); } }); showStats.setEnabled(false); showControlStats = new JMenuItem("Show Control Dataset Metrics"); showControlStats.addActionListener(new ActionListener() { @Override public void actionPerformed(ActionEvent actionEvent) { superAdapter.showDataSetMetrics(true); } }); showControlStats.setEnabled(false); fileMenu.add(showStats); fileMenu.add(showControlStats); fileMenu.addSeparator(); // TODO: make this an export of the data on screen instead of a GUI for CLT JMenuItem dump = new JMenuItem("Export Data..."); dump.addActionListener(new ActionListener() { @Override public void actionPerformed(ActionEvent actionEvent) { superAdapter.exportDataLauncher(); } }); fileMenu.add(dump); JMenuItem creditsMenu = new JMenuItem(); creditsMenu.setText("About"); creditsMenu.addActionListener(new ActionListener() { public void actionPerformed(ActionEvent e) { ImageIcon icon = new ImageIcon(getClass().getResource("/images/juicebox.png")); JLabel iconLabel = new JLabel(icon); JPanel iconPanel = new JPanel(new GridBagLayout()); iconPanel.add(iconLabel); JPanel textPanel = new JPanel(new GridLayout(0, 1)); textPanel.add(new JLabel("

" + "

" + "Juicebox with Assembly Tools

" + "
" + "

" + "Juicebox is the Aiden Lab's software for visualizing data from proximity ligation experiments, " + "such as Hi-C. Juicebox was created by Jim Robinson, Neva C. Durand, and Erez Aiden.

" + "Ongoing development work is carried out by Muhammad S. Shamim, Neva Durand, Olga Dudchenko, " + "Suhas Rao, and other members of the Aiden Lab.

" + "Current version: " + HiCGlobals.versionNum + "
" + "Copyright © 2014-2021. Broad Institute and Aiden Lab" + "

" + "" + "If you use Juicebox or Assembly Tools in your research, please cite:

" + "" + "Neva C. Durand*, James T. Robinson*, et al. " + "\"Juicebox provides a visualization system for Hi-C contact maps " + "with unlimited zoom.\" Cell Systems 2016." + "

" + "Olga Dudchenko, et al. " + "\"The Juicebox Assembly Tools module facilitates de novo assembly of " + "mammalian genomes with chromosome-length scaffolds for under $1000.\" " + "Biorxiv 2018." + "

" + "Suhas S.P. Rao*, Miriam H. Huntley*, et al. \"A 3D Map of the Human Genome at Kilobase " + "Resolution Reveals Principles of Chromatin Looping.\" Cell 2014.
" + "* contributed equally" + "

")); JPanel mainPanel = new JPanel(new BorderLayout()); mainPanel.add(textPanel); mainPanel.add(iconPanel, BorderLayout.WEST); JOptionPane.showMessageDialog(superAdapter.getMainWindow(), mainPanel, "About", JOptionPane.PLAIN_MESSAGE);//INFORMATION_MESSAGE } }); fileMenu.add(creditsMenu); //---- exit ---- JMenuItem exit = new JMenuItem(); exit.setText("Exit"); exit.addActionListener(new ActionListener() { public void actionPerformed(ActionEvent e) { superAdapter.exitActionPerformed(); } }); fileMenu.add(exit); bookmarksMenu = new JMenu("Bookmarks"); //---- Save location ---- saveLocationList = new JMenuItem("Save Current Location"); saveLocationList.addActionListener(new ActionListener() { public void actionPerformed(ActionEvent e) { //code to add a recent location to the menu String stateString = superAdapter.getLocationDescription(); String stateDescription = superAdapter.getDescription("location"); if (stateDescription != null && stateDescription.length() > 0) { addRecentStateMenuEntry(stateDescription + RecentMenu.delimiter + stateString, true); recentLocationMenu.setEnabled(true); } } }); bookmarksMenu.add(saveLocationList); saveLocationList.setEnabled(false); //---Save State test----- saveStateForReload = new JMenuItem(); saveStateForReload.setText("Save Current State"); saveStateForReload.addActionListener(new ActionListener() { public void actionPerformed(ActionEvent e) { //code to add a recent location to the menu try { String stateDescription = superAdapter.getDescription("state"); if (stateDescription != null && stateDescription.length() > 0) { stateDescription = previousStates.checkForDuplicateNames(stateDescription); if (stateDescription == null || stateDescription.length() < 0) { return; } previousStates.addEntry(stateDescription, true); superAdapter.addNewStateToXML(stateDescription); previousStates.setEnabled(true); } } catch (Exception e1) { e1.printStackTrace(); } } }); saveStateForReload.setEnabled(false); //bookmarksMenu.add(saveStateForReload); recentLocationMenu = new RecentMenu("Restore Saved Location", recentLocationMaxItems, recentLocationEntityNode, HiCGlobals.menuType.LOCATION) { private static final long serialVersionUID = 9000023; public void onSelectPosition(String mapPath) { String[] temp = encodeSafeDelimeterSplit(mapPath); superAdapter.restoreLocation(temp[1]); superAdapter.setNormalizationDisplayState(); } }; recentLocationMenu.setMnemonic('S'); recentLocationMenu.setEnabled(false); bookmarksMenu.add(recentLocationMenu); bookmarksMenu.setEnabled(false); //---Export States---- exportSavedStateMenuItem = new JMenuItem(); exportSavedStateMenuItem.setText("Export Saved States"); exportSavedStateMenuItem.addActionListener(new ActionListener() { @Override public void actionPerformed(ActionEvent e) { new SaveFileDialog(HiCGlobals.xmlSavedStatesFile); } }); // restore recent saved states previousStates = new RecentMenu("Restore Previous States", recentLocationMaxItems, recentStateEntityNode, HiCGlobals.menuType.STATE) { private static final long serialVersionUID = 9000024; public void onSelectPosition(String mapPath) { superAdapter.launchLoadStateFromXML(mapPath); } @Override public void setEnabled(boolean b) { super.setEnabled(b); exportSavedStateMenuItem.setEnabled(b); } }; //bookmarksMenu.add(previousStates); //---Import States---- importMapAsFile = new JMenuItem(); importMapAsFile.setText("Import State From File"); importMapAsFile.addActionListener(new ActionListener() { @Override public void actionPerformed(ActionEvent e) { superAdapter.launchImportState(HiCGlobals.xmlSavedStatesFile); importMapAsFile.setSelected(true); } }); //---Slideshow---- slideShow = new JMenuItem(); slideShow.setText("View Slideshow"); slideShow.addActionListener(new ActionListener() { @Override public void actionPerformed(ActionEvent e) { superAdapter.launchSlideShow(); HiCGlobals.slideshowEnabled = true; } }); //bookmarksMenu.add(slideShow); // todo replace with a save state URL //bookmarksMenu.addSeparator(); //bookmarksMenu.add(exportSavedStateMenuItem); //bookmarksMenu.add(importMapAsFile); //---View Menu----- viewMenu = new JMenu("View"); layersItem.addActionListener(new ActionListener() { @Override public void actionPerformed(ActionEvent e) { superAdapter.setLayersPanelVisible(layersItem.isSelected()); } }); viewMenu.add(layersItem); viewMenu.setEnabled(false); final JMenuItem colorItem = new JMenuItem("Change Heatmap Color"); colorItem.addActionListener(new ActionListener() { @Override public void actionPerformed(ActionEvent e) { JColorChooser colorChooser = new JColorChooser(ColorScaleHandler.HIC_MAP_COLOR); JDialog dialog = JColorChooser.createDialog(MainMenuBar.this, "Select Heatmap Color", true, colorChooser, null, null); dialog.setVisible(true); Color color = colorChooser.getColor(); if (color != null) { ColorScaleHandler.HIC_MAP_COLOR = color; superAdapter.getMainViewPanel().resetAllColors(); superAdapter.refresh(); } } }); viewMenu.add(colorItem); final JCheckBoxMenuItem darkulaMode = new JCheckBoxMenuItem("Darkula Mode"); darkulaMode.addActionListener(new ActionListener() { @Override public void actionPerformed(ActionEvent e) { HiCGlobals.isDarkulaModeEnabled = !HiCGlobals.isDarkulaModeEnabled; superAdapter.getMainViewPanel().resetAllColors(); //superAdapter.safeClearAllMZDCache(); superAdapter.refresh(); } }); darkulaMode.setSelected(HiCGlobals.isDarkulaModeEnabled); viewMenu.add(darkulaMode); final JCheckBoxMenuItem advancedViewsMode = new JCheckBoxMenuItem("Advanced Views Mode"); advancedViewsMode.addActionListener(new ActionListener() { @Override public void actionPerformed(ActionEvent e) { MatrixType.toggleAdvancedViews(); //superAdapter.getMainViewPanel().resetAllColors(); //superAdapter.refresh(); } }); advancedViewsMode.setSelected(MatrixType.getAdvancedViewEnabled()); viewMenu.add(advancedViewsMode); JMenuItem addCustomChromosome = new JMenuItem("Make Custom Chromosome (from .bed)..."); addCustomChromosome.addActionListener(new ActionListener() { public void actionPerformed(ActionEvent e) { superAdapter.createCustomChromosomesFromBED(); } }); JMenuItem addGWChromosome = new JMenuItem("Make Genomewide Chromosome"); addGWChromosome.addActionListener(new ActionListener() { public void actionPerformed(ActionEvent e) { superAdapter.createGenomewideChromosomeFromChromDotSizes(); } }); if (HiCGlobals.isDevCustomChromosomesAllowedPublic) { //viewMenu.add(addGWChromosome); viewMenu.add(addCustomChromosome); } viewMenu.addSeparator(); //---Axis Layout mode----- final JCheckBoxMenuItem axisEndpoint = new JCheckBoxMenuItem("Axis Endpoints Only"); axisEndpoint.setSelected(HiCRulerPanel.getShowOnlyEndPts()); axisEndpoint.addActionListener(new ActionListener() { @Override public void actionPerformed(ActionEvent e) { HiCRulerPanel.setShowOnlyEndPts(axisEndpoint.isSelected()); superAdapter.repaint(); } }); viewMenu.add(axisEndpoint); //---ShowChromosomeFig mode----- //drawLine, drawArc or draw polygon// draw round rect // fill Rect according to the chormsome location. final JCheckBoxMenuItem showChromosomeFig = new JCheckBoxMenuItem("Chromosome Context"); showChromosomeFig.setSelected(HiCRulerPanel.getShowChromosomeFigure()); showChromosomeFig.addActionListener(new ActionListener() { @Override public void actionPerformed(ActionEvent e) { superAdapter.setShowChromosomeFig(showChromosomeFig.isSelected()); superAdapter.repaint(); } }); viewMenu.add(showChromosomeFig); //---Grids mode----- // turn grids on/off final JCheckBoxMenuItem showGrids = new JCheckBoxMenuItem("Gridlines"); showGrids.setSelected(superAdapter.getShowGridLines()); showGrids.addActionListener(new ActionListener() { @Override public void actionPerformed(ActionEvent e) { superAdapter.setShowGridLines(showGrids.isSelected()); superAdapter.repaint(); } }); viewMenu.add(showGrids); viewMenu.addSeparator(); //---Export Image Menu----- JMenuItem saveToPDF = new JMenuItem("Export PDF Figure..."); saveToPDF.addActionListener(new ActionListener() { public void actionPerformed(ActionEvent e) { superAdapter.launchExportPDF(); } }); viewMenu.add(saveToPDF); JMenuItem saveToSVG = new JMenuItem("Export SVG Figure..."); saveToSVG.addActionListener(new ActionListener() { public void actionPerformed(ActionEvent e) { superAdapter.launchExportSVG(); } }); viewMenu.add(saveToSVG); devMenu = new JMenu("Dev"); devMenu.setEnabled(false); final JMenuItem addRainbowTrack = new JMenuItem("Add a rainbow track..."); addRainbowTrack.addActionListener(new ActionListener() { @Override public void actionPerformed(ActionEvent e) { superAdapter.getHiC().generateRainbowBed(); } }); if (HiCGlobals.isDevAssemblyToolsAllowedPublic) { devMenu.add(addRainbowTrack); } final JCheckBoxMenuItem skipSortInPhase = new JCheckBoxMenuItem("Skip variant sorting in phase mode"); skipSortInPhase.addActionListener(new ActionListener() { @Override public void actionPerformed(ActionEvent e) { HiCGlobals.noSortInPhasing = !HiCGlobals.noSortInPhasing; superAdapter.getHeatmapPanel().repaint(); } }); skipSortInPhase.setSelected(HiCGlobals.noSortInPhasing); if (HiCGlobals.isDevAssemblyToolsAllowedPublic) { devMenu.add(skipSortInPhase); } final JMenuItem addCustomNormsObs = new JMenuItem("Add Custom Norms to Observed..."); addCustomNormsObs.addActionListener(new ActionListener() { @Override public void actionPerformed(ActionEvent e) { superAdapter.safeLaunchImportNormalizations(false); } }); final JMenuItem addCustomNormsCtrl = new JMenuItem("Add Custom Norms to Control..."); addCustomNormsCtrl.addActionListener(new ActionListener() { @Override public void actionPerformed(ActionEvent e) { superAdapter.safeLaunchImportNormalizations(true); } }); final JMenuItem addResolutionToDatasets = new JMenuItem("Add Custom Resolution..."); addResolutionToDatasets.addActionListener(new ActionListener() { @Override public void actionPerformed(ActionEvent e) { superAdapter.safeLaunchCreateNewResolution(); } }); if (HiCGlobals.isDevAssemblyToolsAllowedPublic) { devMenu.add(addCustomNormsObs); devMenu.add(addCustomNormsCtrl); devMenu.add(addResolutionToDatasets); } final JCheckBoxMenuItem displayTiles = new JCheckBoxMenuItem("Display Tiles"); displayTiles.addActionListener(new ActionListener() { @Override public void actionPerformed(ActionEvent e) { HiCGlobals.displayTiles = !HiCGlobals.displayTiles; superAdapter.getHeatmapPanel().repaint(); } }); final JCheckBoxMenuItem hackLinearColorScale = new JCheckBoxMenuItem("Hack linear color scale"); hackLinearColorScale.addActionListener(new ActionListener() { @Override public void actionPerformed(ActionEvent e) { HiCGlobals.HACK_COLORSCALE_LINEAR = !HiCGlobals.HACK_COLORSCALE_LINEAR; superAdapter.getHeatmapPanel().repaint(); } }); final JCheckBoxMenuItem hackColorScale = new JCheckBoxMenuItem("Hack color scale"); hackColorScale.addActionListener(new ActionListener() { @Override public void actionPerformed(ActionEvent e) { HiCGlobals.HACK_COLORSCALE = !HiCGlobals.HACK_COLORSCALE; superAdapter.getHeatmapPanel().repaint(); } }); final JCheckBoxMenuItem hackColorScaleEqual = new JCheckBoxMenuItem("Hack color scale equally"); hackColorScaleEqual.addActionListener(new ActionListener() { @Override public void actionPerformed(ActionEvent e) { HiCGlobals.HACK_COLORSCALE_EQUAL = !HiCGlobals.HACK_COLORSCALE_EQUAL; superAdapter.getHeatmapPanel().repaint(); } }); displayTiles.setSelected(HiCGlobals.displayTiles); if (HiCGlobals.isDevAssemblyToolsAllowedPublic) { devMenu.add(displayTiles); devMenu.add(hackColorScaleEqual); devMenu.add(hackColorScale); devMenu.add(hackLinearColorScale); } final JCheckBoxMenuItem colorFeatures = new JCheckBoxMenuItem("Recolor 1D Annotations in Assembly Mode"); colorFeatures.addActionListener(new ActionListener() { @Override public void actionPerformed(ActionEvent e) { IGVFeatureCopy.invertColorFeaturesChk(); repaint(); } }); colorFeatures.setSelected(IGVFeatureCopy.colorFeaturesChk); if (HiCGlobals.isDevAssemblyToolsAllowedPublic) { devMenu.add(colorFeatures); } // todo MSS and Santiago - is this to be deleted? final JCheckBoxMenuItem useAssemblyMatrix = new JCheckBoxMenuItem("Use Assembly Chromosome Matrix"); useAssemblyMatrix.setEnabled(!SuperAdapter.assemblyModeCurrentlyActive); useAssemblyMatrix.addActionListener(new ActionListener() { @Override public void actionPerformed(ActionEvent e) { MainViewPanel.invertAssemblyMatCheck(); superAdapter.createAssemblyChromosome(); AssemblyFileImporter assemblyFileImporter; assemblyFileImporter = new AssemblyFileImporter(superAdapter); assemblyFileImporter.importAssembly(); // superAdapter.assemblyModeCurrentlyActive = true; System.out.println(assemblyFileImporter.getAssemblyScaffoldHandler().toString()); } }); useAssemblyMatrix.setSelected(HiCGlobals.isAssemblyMatCheck); if (HiCGlobals.isDevAssemblyToolsAllowedPublic) { devMenu.add(useAssemblyMatrix); } renameGenome = new JMenuItem("Rename genome..."); renameGenome.addActionListener(new ActionListener() { @Override public void actionPerformed(ActionEvent e) { String curr_genome = superAdapter.getHiC().getDataset().getGenomeId(); String response = JOptionPane.showInputDialog("Current genome is " + curr_genome + "\nEnter another genome name or press cancel to exit"); if (response != null) { superAdapter.getHiC().getDataset().setGenomeId(response); } } }); renameGenome.setEnabled(false); fileMenu.add(renameGenome); fileMenu.addSeparator(); JMenuItem editPearsonsColorItem = new JMenuItem("Edit Pearson's Color Scale"); editPearsonsColorItem.addActionListener(new ActionListener() { @Override public void actionPerformed(ActionEvent e) { superAdapter.launchPearsonColorScaleEditor(); } }); devMenu.add(editPearsonsColorItem); JMenuItem editPseudoCounts = new JMenuItem("Change Pseudocount"); editPseudoCounts.addActionListener(new ActionListener() { @Override public void actionPerformed(ActionEvent e) { superAdapter.launchSetPseudoCountEditor(); } }); devMenu.add(editPseudoCounts); JMenuItem mapSubset = new JMenuItem("Select Map Subset..."); mapSubset.addActionListener(new ActionListener() { @Override public void actionPerformed(ActionEvent e) { Private.launchMapSubsetGUI(superAdapter); } }); devMenu.add(mapSubset); final JTextField numSparse = new JTextField("" + Feature2DHandler.numberOfLoopsToFind); numSparse.setEnabled(true); numSparse.isEditable(); numSparse.setToolTipText("Set how many 2D annotations to plot at a time."); final JButton updateSparseOptions = new JButton("Update"); updateSparseOptions.addActionListener(new ActionListener() { @Override public void actionPerformed(ActionEvent e) { if (numSparse.getText().length() > 0) { Feature2DHandler.numberOfLoopsToFind = Integer.parseInt(numSparse.getText()); } } }); updateSparseOptions.setToolTipText("Set how many 2D annotations to plot at a time."); final JPanel sparseOptions = new JPanel(); sparseOptions.setLayout(new GridLayout(0, 2)); sparseOptions.add(numSparse); sparseOptions.add(updateSparseOptions); sparseOptions.setToolTipText("Set how many 2D annotations to plot at a time."); devMenu.addSeparator(); devMenu.add(sparseOptions); /** Assembly Menu **/ assemblyMenu = new JMenu("Assembly"); assemblyMenu.setEnabled(false); enableAssembly = new JCheckBoxMenuItem("Enable Edits"); enableAssembly.addActionListener(new ActionListener() { @Override public void actionPerformed(ActionEvent e) { if (enableAssembly.isSelected()) { superAdapter.getHeatmapPanel().enableAssemblyEditing(); } else { superAdapter.getHeatmapPanel().disableAssemblyEditing(); } } }); resetAssembly = new JMenuItem("Reset Assembly"); resetAssembly.addActionListener(new ActionListener() { @Override public void actionPerformed(ActionEvent e) { int option = JOptionPane.showConfirmDialog(null, "Are you sure you want to reset?", "warning", JOptionPane.YES_NO_OPTION); if (option == 0) { //The ISSUE is here superAdapter.getAssemblyStateTracker().resetState(); superAdapter.refresh(); } } }); exitAssembly = new JMenuItem("Exit Assembly"); exitAssembly.addActionListener(new ActionListener() { @Override public void actionPerformed(ActionEvent e) { int option = JOptionPane.showConfirmDialog(null, "Are you sure you want to exit?", "warning", JOptionPane.YES_NO_OPTION); if (option == 0) { superAdapter.exitAssemblyMode(); } } }); exportAssembly = new JMenuItem("Export Assembly"); exportAssembly.addActionListener(new ActionListener() { @Override public void actionPerformed(ActionEvent e) { String mapName = SuperAdapter.getDatasetTitle(); new SaveAssemblyDialog(superAdapter.getAssemblyStateTracker().getAssemblyHandler(), mapName.substring(0, mapName.lastIndexOf("."))); //find how to get HiC filename } }); final JMenuItem importMapAssembly = new JMenuItem("Import Map Assembly"); importMapAssembly.addActionListener(new ActionListener() { @Override public void actionPerformed(ActionEvent e) { if (superAdapter.getLayersPanel() == null) { superAdapter.intializeLayersPanel(); } new LoadAssemblyAnnotationsDialog(superAdapter); } }); importModifiedAssembly = new JMenuItem("Import Modified Assembly"); importModifiedAssembly.addActionListener(new ActionListener() { //TODO: add warning if changes are present @Override public void actionPerformed(ActionEvent e) { if (superAdapter.getLayersPanel() == null) { superAdapter.intializeLayersPanel(); } new LoadModifiedAssemblyAnnotationsDialog(superAdapter); } }); setScale = new JMenuItem("Set Scale"); setScale.addActionListener(new ActionListener() { @Override public void actionPerformed(ActionEvent e) { double scale; String newScale = MessageUtils.showInputDialog("Specify a scale", Double.toString(HiCGlobals.hicMapScale)); try { scale = Double.parseDouble(newScale); if (scale == 0.0) { // scale cannot be zero scale = 1.0; } HiCGlobals.hicMapScale = scale; // Rescale resolution slider labels superAdapter.getMainViewPanel().getResolutionSlider().reset(); // Rescale axis tick labels superAdapter.getMainViewPanel().getRulerPanelX().repaint(); superAdapter.getMainViewPanel().getRulerPanelY().repaint(); // Rescale and redraw assembly annotations if (superAdapter.getAssemblyStateTracker() != null) { superAdapter.getAssemblyStateTracker().resetState(); } } catch (NumberFormatException t) { JOptionPane.showMessageDialog(null, "Value must be an integer!"); } } }); boolean enabled = superAdapter.getAssemblyStateTracker() != null && superAdapter.getAssemblyStateTracker().getAssemblyHandler() != null; exportAssembly.setEnabled(enabled); resetAssembly.setEnabled(enabled); enableAssembly.setEnabled(enabled); setScale.setEnabled(superAdapter.getHiC() != null && !superAdapter.getHiC().isWholeGenome()); importModifiedAssembly.setEnabled(enabled); exitAssembly.setEnabled(enabled); assemblyMenu.add(importMapAssembly); assemblyMenu.add(importModifiedAssembly); assemblyMenu.add(exportAssembly); assemblyMenu.add(resetAssembly); assemblyMenu.add(resetAssembly); setScale.setEnabled(true); assemblyMenu.add(setScale); assemblyMenu.add(exitAssembly); // assemblyMenu.add(enableAssembly); add(fileMenu); // add(annotationsMenu); add(viewMenu); add(bookmarksMenu); if (HiCGlobals.isDevAssemblyToolsAllowedPublic) { add(assemblyMenu); } add(devMenu); } public RecentMenu getRecentLocationMenu() { return recentLocationMenu; } public void setEnableForAllElements(boolean status) { //annotationsMenu.setEnabled(status); viewMenu.setEnabled(status); bookmarksMenu.setEnabled(status); assemblyMenu.setEnabled(status); saveLocationList.setEnabled(status); saveStateForReload.setEnabled(status); saveLocationList.setEnabled(status); devMenu.setEnabled(status); } public void setEnableAssemblyMenuOptions(boolean status) { resetAssembly.setEnabled(status); exportAssembly.setEnabled(status); enableAssembly.setEnabled(status); setScale.setEnabled(status); importModifiedAssembly.setEnabled(status); exitAssembly.setEnabled(status); devMenu.setEnabled(status); } public void enableAssemblyEditsOnImport(SuperAdapter superAdapter) { enableAssembly.setState(true); superAdapter.getHeatmapPanel().enableAssemblyEditing(); } public void updatePrevStateNameFromImport(String path) { previousStates.updateNamesFromImport(path); } public void updateMainMapHasBeenLoaded(boolean status) { loadControlFromList.setEnabled(status); recentControlMapMenu.setEnabled(status); // if a control map can be loaded, that means main is loaded and its stats can be viewed showStats.setEnabled(status); } public void updateControlMapHasBeenLoaded(boolean status) { showControlStats.setEnabled(status); } public void setAnnotationPanelMenuItemSelected(boolean status) { layersItem.setSelected(status); } } ================================================ FILE: src/juicebox/gui/MainViewPanel.java ================================================ /* * The MIT License (MIT) * * Copyright (c) 2011-2021 Broad Institute, Aiden Lab, Rice University, Baylor College of Medicine * * Permission is hereby granted, free of charge, to any person obtaining a copy * of this software and associated documentation files (the "Software"), to deal * in the Software without restriction, including without limitation the rights * to use, copy, modify, merge, publish, distribute, sublicense, and/or sell * copies of the Software, and to permit persons to whom the Software is * furnished to do so, subject to the following conditions: * * The above copyright notice and this permission notice shall be included in * all copies or substantial portions of the Software. * * THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR * IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, * FITNESS FOR A PARTICULAR PURPOSE AND NON-INFRINGEMENT. IN NO EVENT SHALL THE * AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER * LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, * OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN * THE SOFTWARE. */ package juicebox.gui; import com.jidesoft.swing.JideButton; import juicebox.Context; import juicebox.HiC; import juicebox.HiCGlobals; import juicebox.data.ChromosomeHandler; import juicebox.data.MatrixZoomData; import juicebox.data.basics.Chromosome; import juicebox.mapcolorui.HeatmapPanel; import juicebox.mapcolorui.JColorRangePanel; import juicebox.mapcolorui.ResolutionControl; import juicebox.mapcolorui.ThumbnailPanel; import juicebox.track.TrackLabelPanel; import juicebox.track.TrackPanel; import juicebox.windowui.*; import juicebox.windowui.layers.MiniAnnotationsLayerPanel; import javax.swing.*; import javax.swing.border.EmptyBorder; import javax.swing.border.LineBorder; import javax.swing.event.ChangeEvent; import javax.swing.event.ChangeListener; import java.awt.*; import java.awt.event.ActionEvent; import java.awt.event.ActionListener; /** * Created by muhammadsaadshamim on 8/4/15. */ public class MainViewPanel { private final JideButton refreshButton = new JideButton(); private final JPanel hiCPanel = new JPanel(new HiCLayout()); private final JPanel bottomChromosomeFigPanel = new JPanel(new BorderLayout()); private final JPanel chrSidePanel = new JPanel(new BorderLayout()); private final JPanel chrSidePanel3 = new JPanel(new BorderLayout()); private JComboBox chrBox1; private JComboBox chrBox2; private JComboBox observedNormalizationComboBox, controlNormalizationComboBox; private JComboBox displayOptionComboBox; private JColorRangePanel colorRangePanel; private ResolutionControl resolutionSlider; private TrackPanel trackPanelX; private TrackPanel trackPanelY; private TrackLabelPanel trackLabelPanel; private HiCRulerPanel rulerPanelX; private HeatmapPanel heatmapPanel; private HiCRulerPanel rulerPanelY; private ThumbnailPanel thumbnailPanel; private JEditorPane mouseHoverTextPanel; private GoToPanel goPanel; private HiCChromosomeFigPanel chromosomePanelX; private HiCChromosomeFigPanel chromosomePanelY; private MainMenuBar menuBar; private final JToggleButton annotationsPanelToggleButton = new JToggleButton("Show Annotation Panel"); private final JPanel annotationsPanel = new JPanel(new BorderLayout()); private final JPanel mainPanel = new JPanel(new BorderLayout()); private final JPanel bigPanel = new JPanel(new BorderLayout()); private final JPanel toolbarPanel = new JPanel(new GridBagLayout()); //private final JPanel bottomPanel = new JPanel(); private final JPanel chrSelectionPanel = new JPanel(new BorderLayout()); private final JPanel wrapGapPanel = new JPanel(); private final JPanel topPanel = new JPanel(new BorderLayout()); private final JPanel leftPanel = new JPanel(new BorderLayout()); private final JPanel chrSidePanel2 = new JPanel(); private final JPanel wrapHeatmapPanel = new JPanel(new BorderLayout()); private final JPanel rightSidePanel = new JPanel(); private final JPanel normalizationPanel = new JPanel(new BorderLayout()); private final JPanel normalizationLabelPanel = new JPanel(new BorderLayout()); private final JPanel topCenterPanel = new JPanel(new BorderLayout()); private final JPanel displayOptionPanel = new JPanel(new BorderLayout()); private final JPanel displayOptionLabelPanel = new JPanel(new BorderLayout()); private final JPanel chrButtonPanel = new JPanel(); private final JPanel chrLabelPanel = new JPanel(new BorderLayout()); private final JLabel chrLabel = new JLabel("Chromosomes"); private final JLabel normalizationLabel = new JLabel("Normalization (Obs | Ctrl)"); private final JLabel displayOptionLabel = new JLabel("Show"); private MiniAnnotationsLayerPanel miniAnnotationsLayerPanel; private boolean tooltipAllowedToUpdate = true; private boolean ignoreUpdateThumbnail = false; private final JPanel tooltipPanel = new JPanel(new BorderLayout()); private boolean controlIsLoaded = false; public void setIgnoreUpdateThumbnail(boolean flag) { ignoreUpdateThumbnail = flag; } public JComboBox getChrBox2() { return chrBox2; } public JComboBox getChrBox1() { return chrBox1; } public MainMenuBar getMenuBar() { return menuBar; } public void initializeMainView(final SuperAdapter superAdapter, Container contentPane, Dimension screenSize, int taskBarHeight) { Dimension bigPanelDim = new Dimension((int) (screenSize.width * .85), (int) ((screenSize.height - taskBarHeight) * .9)); Dimension panelDim = new Dimension((int) (screenSize.width * .75), screenSize.height - taskBarHeight); Dimension chrBoxDim = new Dimension(95, 70); contentPane.setLayout(new BorderLayout()); contentPane.add(mainPanel, BorderLayout.CENTER); toolbarPanel.setBorder(null); mainPanel.add(toolbarPanel, BorderLayout.NORTH); bigPanel.setPreferredSize(new Dimension(bigPanelDim)); bigPanel.setMaximumSize(new Dimension(bigPanelDim)); bigPanel.setMinimumSize(new Dimension(bigPanelDim)); menuBar = new MainMenuBar(superAdapter); contentPane.add(menuBar, BorderLayout.NORTH); GridBagConstraints toolbarConstraints = new GridBagConstraints(0, 0, 1, 1, 0.1, 0, GridBagConstraints.LINE_START, GridBagConstraints.HORIZONTAL, new Insets(0, 0, 0, 0), 0, 0); // --- Chromosome panel --- toolbarPanel.add(chrSelectionPanel, toolbarConstraints); chrSelectionPanel.setBorder(LineBorder.createGrayLineBorder()); chrLabel.setHorizontalAlignment(SwingConstants.CENTER); chrLabelPanel.add(chrLabel, BorderLayout.CENTER); chrSelectionPanel.add(chrLabelPanel, BorderLayout.PAGE_START); chrButtonPanel.setLayout(new BoxLayout(chrButtonPanel, BoxLayout.X_AXIS)); //---- chrBox1 ---- chrBox1 = new JComboBox<>(); //new Chromosome[]{new Chromosome(0, Globals.CHR_ALL, 0)}); chrBox1.addPopupMenuListener(new BoundsPopupMenuListener(true, false)); chrBox1.addActionListener(new ActionListener() { public void actionPerformed(ActionEvent e) { chrBox1ActionPerformed(e); } }); chrBox1.setPreferredSize(chrBoxDim); chrButtonPanel.add(chrBox1); //---- chrBox2 ---- chrBox2 = new JComboBox<>(); //new Chromosome[]{new Chromosome(0, Globals.CHR_ALL, 0)}); chrBox2.addPopupMenuListener(new BoundsPopupMenuListener(true, false)); chrBox2.addActionListener(new ActionListener() { public void actionPerformed(ActionEvent e) { chrBox2ActionPerformed(e); } }); chrBox2.setPreferredSize(chrBoxDim); chrButtonPanel.add(chrBox2); //---- refreshButton ---- refreshButton.setIcon(new ImageIcon(getClass().getResource("/toolbarButtonGraphics/general/Refresh24.gif"))); refreshButton.addActionListener(new ActionListener() { public void actionPerformed(ActionEvent e) { superAdapter.safeRefreshButtonActionPerformed(); } }); refreshButton.setPreferredSize(new Dimension(24, 24)); chrButtonPanel.add(refreshButton); chrSelectionPanel.add(chrButtonPanel, BorderLayout.CENTER); chrSelectionPanel.setMinimumSize(new Dimension(200, 70)); chrSelectionPanel.setPreferredSize(new Dimension(210, 70)); //======== Display Option Panel ======== displayOptionLabel.setHorizontalAlignment(SwingConstants.CENTER); displayOptionLabelPanel.add(displayOptionLabel, BorderLayout.CENTER); displayOptionPanel.add(displayOptionLabelPanel, BorderLayout.PAGE_START); JPanel displayOptionButtonPanel = new JPanel(); displayOptionButtonPanel.setBorder(new EmptyBorder(0, 10, 0, 10)); displayOptionButtonPanel.setLayout(new GridLayout(1, 0, 20, 0)); displayOptionComboBox = new JComboBox<>(new MatrixType[]{MatrixType.OBSERVED}); displayOptionComboBox.setPreferredSize(new Dimension(500, 30)); displayOptionComboBox.addPopupMenuListener(new BoundsPopupMenuListener(true, false)); displayOptionComboBox.addActionListener(new ActionListener() { public void actionPerformed(ActionEvent e) { superAdapter.safeDisplayOptionComboBoxActionPerformed(); observedNormalizationComboBox.setEnabled(!isWholeGenome()); controlNormalizationComboBox.setEnabled(!isWholeGenome() && ifControlIsLoaded()); } }); displayOptionButtonPanel.add(displayOptionComboBox); displayOptionPanel.add(displayOptionButtonPanel, BorderLayout.CENTER); displayOptionPanel.setMinimumSize(new Dimension(140, 70)); displayOptionPanel.setPreferredSize(new Dimension(140, 70)); displayOptionPanel.setMaximumSize(new Dimension(140, 70)); toolbarConstraints.gridx = 1; toolbarConstraints.weightx = 0.1; toolbarPanel.add(displayOptionPanel, toolbarConstraints); //======== Normalization Panel ======== normalizationPanel.setBorder(LineBorder.createGrayLineBorder()); normalizationLabel.setHorizontalAlignment(SwingConstants.CENTER); normalizationLabelPanel.add(normalizationLabel, BorderLayout.CENTER); normalizationPanel.add(normalizationLabelPanel, BorderLayout.PAGE_START); JPanel normalizationButtonPanel = new JPanel(); normalizationButtonPanel.setBorder(new EmptyBorder(0, 10, 0, 10)); normalizationButtonPanel.setLayout(new GridLayout(1, 0, 20, 0)); observedNormalizationComboBox = new JComboBox<>(new String[]{NormalizationHandler.NONE.getDescription()}); observedNormalizationComboBox.addPopupMenuListener(new BoundsPopupMenuListener(true, false)); observedNormalizationComboBox.addActionListener(new ActionListener() { public void actionPerformed(ActionEvent e) { superAdapter.safeNormalizationComboBoxActionPerformed(e, false); } }); controlNormalizationComboBox = new JComboBox<>(new String[]{NormalizationHandler.NONE.getDescription()}); controlNormalizationComboBox.addPopupMenuListener(new BoundsPopupMenuListener(true, false)); controlNormalizationComboBox.addActionListener(new ActionListener() { public void actionPerformed(ActionEvent e) { superAdapter.safeNormalizationComboBoxActionPerformed(e, true); } }); normalizationButtonPanel.add(observedNormalizationComboBox); normalizationButtonPanel.add(controlNormalizationComboBox); normalizationPanel.add(normalizationButtonPanel, BorderLayout.CENTER); normalizationPanel.setPreferredSize(new Dimension(180, 70)); normalizationPanel.setMinimumSize(new Dimension(140, 70)); toolbarConstraints.gridx = 2; toolbarConstraints.weightx = 0.1; toolbarPanel.add(normalizationPanel, toolbarConstraints); bigPanel.add(hiCPanel, BorderLayout.CENTER); wrapGapPanel.setMaximumSize(new Dimension(5, 5)); wrapGapPanel.setMinimumSize(new Dimension(5, 5)); wrapGapPanel.setPreferredSize(new Dimension(5, 5)); wrapGapPanel.setBorder(LineBorder.createBlackLineBorder()); bigPanel.add(wrapGapPanel, BorderLayout.EAST); hiCPanel.add(topPanel, BorderLayout.NORTH); trackLabelPanel = new TrackLabelPanel(superAdapter.getHiC()); hiCPanel.add(trackLabelPanel, HiCLayout.NORTH_WEST); topPanel.add(topCenterPanel, BorderLayout.CENTER); trackPanelX = new TrackPanel(superAdapter, superAdapter.getHiC(), TrackPanel.Orientation.X); trackPanelX.setMaximumSize(new Dimension(4000, 50)); trackPanelX.setPreferredSize(new Dimension(1, 50)); trackPanelX.setMinimumSize(new Dimension(1, 50)); trackPanelX.setVisible(false); topCenterPanel.add(trackPanelX, BorderLayout.NORTH); rulerPanelX = new HiCRulerPanel(superAdapter.getHiC()); rulerPanelX.setMaximumSize(new Dimension(4000, 50)); rulerPanelX.setMinimumSize(new Dimension(1, 50)); rulerPanelX.setPreferredSize(new Dimension(1, 50)); rulerPanelX.setBorder(null); topCenterPanel.add(rulerPanelX, BorderLayout.SOUTH); //---- rulerPanel1 ---- hiCPanel.add(leftPanel, BorderLayout.WEST); trackPanelY = new TrackPanel(superAdapter, superAdapter.getHiC(), TrackPanel.Orientation.Y); trackPanelY.setMaximumSize(new Dimension(50, 4000)); trackPanelY.setPreferredSize(new Dimension(50, 1)); trackPanelY.setMinimumSize(new Dimension(50, 1)); trackPanelY.setVisible(false); leftPanel.add(trackPanelY, BorderLayout.WEST); rulerPanelY = new HiCRulerPanel(superAdapter.getHiC()); rulerPanelY.setMaximumSize(new Dimension(50, 4000)); rulerPanelY.setPreferredSize(new Dimension(50, 800)); rulerPanelY.setBorder(null); rulerPanelY.setMinimumSize(new Dimension(50, 1)); leftPanel.add(rulerPanelY, BorderLayout.EAST); //---- chromosomeSidePanel ---- chrSidePanel.setMaximumSize(new Dimension(4000, 50)); chrSidePanel.setPreferredSize(new Dimension(50, 50)); chrSidePanel.setMinimumSize(new Dimension(50, 50)); chrSidePanel.setVisible(true); chrSidePanel2.setMaximumSize(new Dimension(50, 50)); chrSidePanel2.setPreferredSize(new Dimension(50, 50)); chrSidePanel2.setMinimumSize(new Dimension(50, 50)); chrSidePanel3.setMaximumSize(new Dimension(50, 4000)); chrSidePanel3.setPreferredSize(new Dimension(50, 50)); chrSidePanel3.setMinimumSize(new Dimension(50, 50)); chrSidePanel3.setVisible(true); chromosomePanelX = new HiCChromosomeFigPanel(superAdapter.getHiC()); chromosomePanelX.setMaximumSize(new Dimension(4000, 50)); chromosomePanelX.setPreferredSize(new Dimension(1, 50)); chromosomePanelX.setMinimumSize(new Dimension(1, 50)); bottomChromosomeFigPanel.add(chromosomePanelX, BorderLayout.CENTER); bottomChromosomeFigPanel.add(chrSidePanel2, BorderLayout.EAST); bottomChromosomeFigPanel.setVisible(true); leftPanel.add(chrSidePanel, BorderLayout.SOUTH); topPanel.add(chrSidePanel3, BorderLayout.EAST); //---- chromosomeFigPanel1 ---- chromosomePanelY = new HiCChromosomeFigPanel(superAdapter.getHiC()); chromosomePanelY.setMaximumSize(new Dimension(50, 4000)); chromosomePanelY.setPreferredSize(new Dimension(50, 1)); chromosomePanelY.setMinimumSize(new Dimension(50, 1)); chromosomePanelY.setVisible(true); int panelWidth = (int) panelDim.getWidth(); int panelHeight = (int) panelDim.getHeight(); System.err.println("Window W: " + panelWidth + " H" + panelHeight); wrapHeatmapPanel.setMaximumSize(new Dimension(panelDim)); wrapHeatmapPanel.setMinimumSize(new Dimension(panelDim)); wrapHeatmapPanel.setPreferredSize(new Dimension(panelDim)); wrapHeatmapPanel.setVisible(true); heatmapPanel = new HeatmapPanel(superAdapter); heatmapPanel.setMaximumSize(new Dimension(panelWidth - 5, panelHeight - 5)); heatmapPanel.setMinimumSize(new Dimension(panelWidth - 5, panelHeight - 5)); heatmapPanel.setPreferredSize(new Dimension(panelWidth - 5, panelHeight - 5)); wrapHeatmapPanel.add(heatmapPanel, BorderLayout.CENTER); wrapHeatmapPanel.add(bottomChromosomeFigPanel, BorderLayout.SOUTH); wrapHeatmapPanel.add(chromosomePanelY, BorderLayout.EAST); hiCPanel.add(wrapHeatmapPanel, BorderLayout.CENTER); //======== Resolution Slider Panel ======== resolutionSlider = new ResolutionControl(superAdapter); resolutionSlider.setPreferredSize(new Dimension(200, 70)); resolutionSlider.setMinimumSize(new Dimension(150, 70)); toolbarConstraints.gridx = 3; toolbarConstraints.weightx = 0.1; toolbarPanel.add(resolutionSlider, toolbarConstraints); //======== Color Range Panel ======== colorRangePanel = new JColorRangePanel(superAdapter, heatmapPanel); toolbarConstraints.gridx = 4; toolbarConstraints.weightx = 0.5; toolbarPanel.add(colorRangePanel, toolbarConstraints); goPanel = new GoToPanel(superAdapter); toolbarConstraints.gridx = 5; toolbarConstraints.weightx = 0.25; toolbarPanel.add(goPanel, toolbarConstraints); // not sure this is working //toolbarPanel.setPreferredSize(new Dimension(panelHeight,100)); //======== Right side panel ======== int prefRightSideWidth = (int) (screenSize.width * .15); rightSidePanel.setLayout(new BoxLayout(rightSidePanel, BoxLayout.Y_AXIS)); rightSidePanel.setMinimumSize(new Dimension((int) (screenSize.width * .15), screenSize.height)); rightSidePanel.setPreferredSize(new Dimension(prefRightSideWidth, screenSize.height)); rightSidePanel.setMaximumSize(new Dimension((int) (screenSize.width * .21), screenSize.height)); //======== Bird's view mini map ======== Dimension thumbNailDim = new Dimension(prefRightSideWidth, prefRightSideWidth); thumbnailPanel = new ThumbnailPanel(superAdapter); thumbnailPanel.setMaximumSize(thumbNailDim); thumbnailPanel.setMinimumSize(thumbNailDim); thumbnailPanel.setPreferredSize(thumbNailDim); // todo eliminate thumbpanel - redundant container? rightSidePanel.add(thumbnailPanel, BorderLayout.NORTH); //========= mini-annotations panel ====== int maxMiniAnnotHeight = (screenSize.height - toolbarPanel.getHeight() - taskBarHeight) / 5; miniAnnotationsLayerPanel = new MiniAnnotationsLayerPanel(superAdapter, prefRightSideWidth, maxMiniAnnotHeight); //========= mouse hover text ====== int leftoverHeight = screenSize.height - toolbarPanel.getHeight() - taskBarHeight - miniAnnotationsLayerPanel.getDynamicHeight() - annotationsPanelToggleButton.getHeight(); mouseHoverTextPanel = new JEditorPane(); mouseHoverTextPanel.setEditable(false); mouseHoverTextPanel.setContentType("text/html"); mouseHoverTextPanel.setFont(new Font("sans-serif", Font.PLAIN, 20)); mouseHoverTextPanel.setBorder(null); int mouseTextY = rightSidePanel.getBounds().y + rightSidePanel.getBounds().height; Dimension prefTextPanelSize = new Dimension(prefRightSideWidth, leftoverHeight); mouseHoverTextPanel.setPreferredSize(prefTextPanelSize); tooltipPanel.setPreferredSize(prefTextPanelSize); JScrollPane tooltipScroller = new JScrollPane(mouseHoverTextPanel, JScrollPane.VERTICAL_SCROLLBAR_AS_NEEDED, JScrollPane.HORIZONTAL_SCROLLBAR_NEVER); tooltipScroller.setBorder(null); tooltipScroller.setMaximumSize(prefTextPanelSize); tooltipPanel.add(tooltipScroller); tooltipPanel.setBounds(new Rectangle(new Point(0, mouseTextY), prefTextPanelSize)); tooltipPanel.setBorder(null); rightSidePanel.add(tooltipPanel, BorderLayout.CENTER); annotationsPanelToggleButton.addChangeListener(new ChangeListener() { @Override public void stateChanged(ChangeEvent e) { if (annotationsPanelToggleButton.isSelected()) { annotationsPanelToggleButton.setText("Hide Annotation Panel"); } else { annotationsPanelToggleButton.setText("Show Annotation Panel"); } } }); annotationsPanelToggleButton.addActionListener(new ActionListener() { @Override public void actionPerformed(ActionEvent e) { if (annotationsPanelToggleButton.isSelected()) { superAdapter.setLayersPanelVisible(true); annotationsPanelToggleButton.setText("Hide Annotation Panel"); } else { superAdapter.setLayersPanelVisible(false); annotationsPanelToggleButton.setText("Show Annotation Panel"); } } }); annotationsPanelToggleButton.setSelected(false); annotationsPanel.add(miniAnnotationsLayerPanel, BorderLayout.NORTH); miniAnnotationsLayerPanel.setAlignmentX(Component.CENTER_ALIGNMENT); annotationsPanel.add(annotationsPanelToggleButton, BorderLayout.SOUTH); annotationsPanelToggleButton.setAlignmentX(Component.CENTER_ALIGNMENT); rightSidePanel.add(annotationsPanel, BorderLayout.SOUTH); annotationsPanel.setAlignmentX(Component.CENTER_ALIGNMENT); mainPanel.add(bigPanel, BorderLayout.CENTER); mainPanel.add(rightSidePanel, BorderLayout.EAST); resetAllColors(); initialSetToFalse(); } private void initialSetToFalse() { JComponent[] comps = new JComponent[]{chrBox1, chrBox2, refreshButton, displayOptionComboBox, observedNormalizationComboBox, controlNormalizationComboBox, toolbarPanel, miniAnnotationsLayerPanel, annotationsPanelToggleButton}; for (JComponent comp : comps) { comp.setEnabled(false); } } public void resetAllColors() { Color mainBackgroundColor = HiCGlobals.isDarkulaModeEnabled ? Color.darkGray : Color.WHITE; JComponent[] components = new JComponent[]{mainPanel, bigPanel, topPanel, trackLabelPanel, leftPanel, chrSidePanel, chrSidePanel2, chrSidePanel3, bottomChromosomeFigPanel, wrapHeatmapPanel, heatmapPanel, wrapGapPanel, hiCPanel, trackPanelX, trackPanelY, rulerPanelX, rulerPanelY, chromosomePanelX, chromosomePanelY, topCenterPanel}; //annotationsPanelToggleButton for (JComponent component : components) { component.setBackground(mainBackgroundColor); } topCenterPanel.setBackground(Color.BLUE); normalizationLabelPanel.setBackground(HiCGlobals.backgroundColor); chrLabelPanel.setBackground(HiCGlobals.backgroundColor); displayOptionLabelPanel.setBackground(HiCGlobals.backgroundColor); normalizationPanel.setBackground(HiCGlobals.diffGrayColor); displayOptionPanel.setBackground(HiCGlobals.diffGrayColor); chrButtonPanel.setBackground(HiCGlobals.diffGrayColor); displayOptionPanel.setBorder(LineBorder.createGrayLineBorder()); heatmapPanel.reset(); } public JPanel getHiCPanel() { return hiCPanel; } public void updateToolTipText(String s) { if (tooltipAllowedToUpdate) mouseHoverTextPanel.setText(s); mouseHoverTextPanel.setCaretPosition(0); } public boolean isResolutionLocked() { return resolutionSlider.isResolutionLocked(); } public HeatmapPanel getHeatmapPanel() { return heatmapPanel; } public void updateZoom(HiCZoom newZoom) { resolutionSlider.setZoom(newZoom); } public void updateAndResetZoom(HiCZoom newZoom) { resolutionSlider.setZoom(newZoom); //resolutionSlider.reset(); } /* * Only accessed from within another unsafe method in Heatmap Panel class, * which in turn is encapsulated (i.e. made safe) */ public void unsafeSetSelectedChromosomes(SuperAdapter superAdapter, Chromosome xChrom, Chromosome yChrom) { chrBox1.setSelectedIndex(yChrom.getIndex()); chrBox2.setSelectedIndex(xChrom.getIndex()); unsafeRefreshChromosomes(superAdapter); } public void unsafeRefreshChromosomes(SuperAdapter superAdapter) { Chromosome chr1 = (Chromosome) chrBox1.getSelectedItem(); Chromosome chr2 = (Chromosome) chrBox2.getSelectedItem(); if (ChromosomeHandler.isAllByAll(chr1) || ChromosomeHandler.isAllByAll(chr2)) { chrBox1.setSelectedIndex(0); chrBox2.setSelectedIndex(0); MatrixType matrixType = (MatrixType) displayOptionComboBox.getSelectedItem(); if (MatrixType.isPearsonType(matrixType)) { // can't do pearson's genomewide displayOptionComboBox.setSelectedIndex(0); superAdapter.unsafeDisplayOptionComboBoxActionPerformed(); } } chr1 = (Chromosome) chrBox1.getSelectedItem(); chr2 = (Chromosome) chrBox2.getSelectedItem(); Chromosome chrX = chr1.getIndex() < chr2.getIndex() ? chr1 : chr2; Chromosome chrY = chr1.getIndex() < chr2.getIndex() ? chr2 : chr1; superAdapter.unsafeUpdateHiCChromosomes(chrX, chrY); setNormalizationDisplayState(superAdapter.getHiC()); updateThumbnail(superAdapter.getHiC()); } public void setSelectedChromosomesNoRefresh(Chromosome xChrom, Chromosome yChrom, Context xContext, Context yContext) { chrBox1.setSelectedIndex(yChrom.getIndex()); chrBox2.setSelectedIndex(xChrom.getIndex()); rulerPanelX.setContext(xContext, HiCRulerPanel.Orientation.HORIZONTAL); rulerPanelY.setContext(yContext, HiCRulerPanel.Orientation.VERTICAL); chromosomePanelX.setContext(xContext, HiCChromosomeFigPanel.Orientation.HORIZONTAL); chromosomePanelY.setContext(yContext, HiCChromosomeFigPanel.Orientation.VERTICAL); resolutionSlider.setEnabled(!ChromosomeHandler.isAllByAll(xChrom)); } /** * Chromosome "0" is whole genome * * @param handler for list of chromosomes */ void setChromosomes(ChromosomeHandler handler) { heatmapPanel.setChromosomeBoundaries(handler.getChromosomeBoundaries()); chrBox1.setModel(new DefaultComboBoxModel<>(handler.getChromosomeArray())); chrBox2.setModel(new DefaultComboBoxModel<>(handler.getChromosomeArray())); } private boolean isInterChromosomal() { Chromosome chr1 = (Chromosome) chrBox1.getSelectedItem(); Chromosome chr2 = (Chromosome) chrBox2.getSelectedItem(); return chr1.getIndex() != chr2.getIndex(); } /** * Note that both versions of isWholeGenome are needed otherwise we get * a bug when partial states have changed */ private boolean isWholeGenome() { Chromosome chr1 = (Chromosome) chrBox1.getSelectedItem(); Chromosome chr2 = (Chromosome) chrBox2.getSelectedItem(); return ChromosomeHandler.isAllByAll(chr1) || ChromosomeHandler.isAllByAll(chr2); } private boolean ifControlIsLoaded() { return controlIsLoaded; } private boolean isWholeGenome(HiC hic) { Chromosome chr1 = hic.getXContext().getChromosome(); Chromosome chr2 = hic.getYContext().getChromosome(); return ChromosomeHandler.isAllByAll(chr1) || ChromosomeHandler.isAllByAll(chr2); } public void setNormalizationDisplayState(HiC hic) { // Test for new dataset ("All"), or change in chromosome if (isWholeGenome()) { // for now only allow observed hic.setDisplayOption(MatrixType.OBSERVED); displayOptionComboBox.setSelectedIndex(0); observedNormalizationComboBox.setSelectedIndex(0); controlNormalizationComboBox.setSelectedIndex(0); } else if (isInterChromosomal()) { if (MatrixType.isOnlyIntrachromosomalType(hic.getDisplayOption())) { hic.setDisplayOption(MatrixType.OBSERVED); displayOptionComboBox.setSelectedIndex(0); } } observedNormalizationComboBox.setEnabled(!isWholeGenome(hic)); controlNormalizationComboBox.setEnabled(!isWholeGenome() && ifControlIsLoaded()); displayOptionComboBox.setEnabled(true); } public void repaintTrackPanels() { trackPanelX.repaint(); trackPanelY.repaint(); } public void repaintGridRulerPanels() { rulerPanelX.repaint(); rulerPanelY.repaint(); } public String getTrackPanelPrintouts(int x, int y) { String trackToolTip = ""; try { String text = trackPanelX.tooltipText(x, y, false); if (text != null) trackToolTip += "" + text + ""; text = trackPanelY.tooltipText(x, y, false); if (text != null) trackToolTip += "" + text + ""; } catch (Exception ignored) { } return trackToolTip; } public void updateThumbnail(HiC hic) { if (ignoreUpdateThumbnail) return; //new Exception().printStackTrace(); if (hic.getMatrix() != null) { // MatrixZoomData zd0 = initialZoom == null ? hic.getMatrix().getFirstZoomData(hic.getZoom().getUnit()) : // hic.getMatrix().getZoomData(initialZoom); MatrixZoomData zd0 = hic.getMatrix().getFirstZoomData(hic.getZoom().getUnit()); MatrixZoomData zdControl = null; if (hic.getControlMatrix() != null) { zdControl = hic.getControlMatrix().getFirstZoomData(hic.getZoom().getUnit()); } try { Image thumbnail = heatmapPanel.getThumbnailImage(zd0, zdControl, thumbnailPanel.getWidth(), thumbnailPanel.getHeight(), hic.getDisplayOption(), hic.getObsNormalizationType(), hic.getControlNormalizationType()); if (thumbnail != null) { thumbnailPanel.setImage(thumbnail); thumbnailPanel.repaint(); } } catch (Exception ignored) { thumbnailPanel.setImage(null); thumbnailPanel.repaint(); } } else { thumbnailPanel.setImage(null); } } public static void invertAssemblyMatCheck() { HiCGlobals.isAssemblyMatCheck = !HiCGlobals.isAssemblyMatCheck; } private void chrBox1ActionPerformed(ActionEvent e) { if (chrBox1.getSelectedIndex() == 0) { chrBox2.setSelectedIndex(0); } else if (HiCGlobals.isAssemblyMatCheck && chrBox1.getSelectedIndex() == (chrBox1.getItemCount() - 1)) { chrBox2.setSelectedIndex(chrBox1.getItemCount() - 1); } } private void chrBox2ActionPerformed(ActionEvent e) { if (chrBox2.getSelectedIndex() == 0) { chrBox1.setSelectedIndex(0); } else if (HiCGlobals.isAssemblyMatCheck && chrBox2.getSelectedIndex() == (chrBox1.getItemCount() - 1)) { chrBox1.setSelectedIndex(chrBox1.getItemCount() - 1); } } public boolean setResolutionSliderVisible(boolean state, SuperAdapter superAdapter) { // Test for new dataset ("All"), or change in chromosome boolean makeResVisible = state && !isWholeGenome(); resolutionSlider.setEnabled(makeResVisible); if (makeResVisible) { resolutionSlider.setForeground(Color.BLUE); } else { resolutionSlider.setForeground(Color.BLACK); } return true; // why are we calling this? why is this a boolean method? //return superAdapter.safeDisplayOptionComboBoxActionPerformed(); } public void updateTrackPanel(boolean hasTracks) { trackLabelPanel.updateLabels(); if (hasTracks) { if (!trackPanelX.isVisible()) { trackPanelX.setVisible(true); trackLabelPanel.setVisible(true); } if (!trackPanelY.isVisible()) { trackPanelY.setVisible(true); } } else { if (trackPanelX.isVisible()) { trackPanelX.setVisible(false); trackLabelPanel.setVisible(false); } if (trackPanelY.isVisible()) { trackPanelY.setVisible(false); } } trackPanelX.invalidate(); trackLabelPanel.invalidate(); trackPanelY.invalidate(); } public void setShowChromosomeFig(boolean showFigure) { if (showFigure) { if (!bottomChromosomeFigPanel.isVisible()) { bottomChromosomeFigPanel.setVisible(true); } if (!chromosomePanelY.isVisible()) { chromosomePanelY.setVisible(true); } if (!chrSidePanel.isVisible()) { chrSidePanel.setVisible(true); } if (!chrSidePanel3.isVisible()) { chrSidePanel3.setVisible(true); } } else { if (bottomChromosomeFigPanel.isVisible()) { bottomChromosomeFigPanel.setVisible(false); } if (chromosomePanelY.isVisible()) { chromosomePanelY.setVisible(false); } if (chrSidePanel.isVisible()) { chrSidePanel.setVisible(false); } if (chrSidePanel3.isVisible()) { chrSidePanel3.setVisible(false); } } HiCRulerPanel.setShowChromosomeFigure(showFigure); chromosomePanelY.invalidate(); bottomChromosomeFigPanel.invalidate(); chrSidePanel.invalidate(); chrSidePanel3.invalidate(); } public boolean getShowGridLines() { return heatmapPanel == null || heatmapPanel.getShowGridLines(); } public void setShowGridLines(boolean status) { if (heatmapPanel != null) { heatmapPanel.setShowGridLines(status); } } public String getToolTip() { return mouseHoverTextPanel.getText(); } public void setDisplayBox(int indx) { displayOptionComboBox.setSelectedIndex(indx); } public void setNormalizationEnabledForReload() { //observedNormalizationComboBox.setEnabled(true); observedNormalizationComboBox.setEnabled(!isWholeGenome()); controlNormalizationComboBox.setEnabled(!isWholeGenome() && ifControlIsLoaded()); } public void setPositionChrLeft(String newPositionDate) { goPanel.setPositionChrLeft(newPositionDate); } public void setPositionChrTop(String newPositionDate) { goPanel.setPositionChrTop(newPositionDate); } public void setEnableForAllElements(SuperAdapter superAdapter, boolean status) { chrBox1.setEnabled(status); chrBox2.setEnabled(status); refreshButton.setEnabled(status); colorRangePanel.setElementsVisible(status, superAdapter); if (setResolutionSliderVisible(status, superAdapter)) { // TODO succeeded } else { // TODO failed } goPanel.setEnabled(status); annotationsPanelToggleButton.setEnabled(status); miniAnnotationsLayerPanel.setEnabled(status); menuBar.setEnableForAllElements(status); } public String getColorRangeValues() { return colorRangePanel.getColorRangeValues(); } public double getColorRangeScaleFactor() { return colorRangePanel.getColorRangeScaleFactor(); } public void updateRatioColorSlider(HiC hic, double maxColor, double upColor) { colorRangePanel.updateRatioColorSlider(hic, maxColor, upColor); } public void updateColorSlider(HiC hic, double lowColor, double upColor, double maxColor) { colorRangePanel.updateColorSlider(hic, lowColor, upColor, maxColor); } public void setEnabledForNormalization(boolean isControl, String[] normalizationOptions, boolean versionStatus) { if (isControl) { controlIsLoaded = true; if (normalizationOptions != null && normalizationOptions.length == 1) { controlNormalizationComboBox.setEnabled(false); } else { controlNormalizationComboBox.setModel(new DefaultComboBoxModel<>(normalizationOptions)); controlNormalizationComboBox.setSelectedIndex(0); controlNormalizationComboBox.setEnabled(versionStatus && !isWholeGenome() && ifControlIsLoaded()); } } else { if (normalizationOptions.length == 1) { observedNormalizationComboBox.setEnabled(false); } else { observedNormalizationComboBox.setModel(new DefaultComboBoxModel<>(normalizationOptions)); observedNormalizationComboBox.setSelectedIndex(0); observedNormalizationComboBox.setEnabled(versionStatus && !isWholeGenome()); } } } public JComboBox getDisplayOptionComboBox() { return displayOptionComboBox; } public void resetResolutionSlider(HiC.Unit unit) { resolutionSlider.unit = unit != null ? unit : HiC.Unit.BP; resolutionSlider.reset(); } public void setSelectedDisplayOption(boolean isControl, boolean isControlAlreadyLoaded) { MatrixType[] options = MatrixType.getOptions(isControl || isControlAlreadyLoaded); MatrixType originalMatrixType; try { originalMatrixType = (MatrixType) displayOptionComboBox.getSelectedItem(); } catch (Exception e) { originalMatrixType = null; } displayOptionComboBox.setModel(new DefaultComboBoxModel<>(options)); if (originalMatrixType != null) { int indx = 0; for (int i = 0; i < displayOptionComboBox.getItemCount(); i++) { if (originalMatrixType.equals(displayOptionComboBox.getItemAt(i))) { indx = i; break; } } displayOptionComboBox.setSelectedIndex(indx); } else { displayOptionComboBox.setSelectedIndex(0); } } public JEditorPane getMouseHoverTextPanel() { return mouseHoverTextPanel; } public ResolutionControl getResolutionSlider() { return resolutionSlider; } public JColorRangePanel getColorRangePanel() { return colorRangePanel; } public boolean isTooltipAllowedToUpdate() { return tooltipAllowedToUpdate; } public void toggleToolTipUpdates(boolean tooltipAllowedToUpdated) { this.tooltipAllowedToUpdate = tooltipAllowedToUpdated; } public JComboBox getObservedNormalizationComboBox() { return observedNormalizationComboBox; } public JComboBox getControlNormalizationComboBox() { return controlNormalizationComboBox; } public HiCRulerPanel getRulerPanelY() { return rulerPanelY; } public HiCRulerPanel getRulerPanelX() { return rulerPanelX; } public HiCChromosomeFigPanel getChromosomeFigPanelY() { return chromosomePanelY; } public HiCChromosomeFigPanel getChromosomeFigPanelX() { return chromosomePanelX; } public void setAnnotationsPanelToggleButtonSelected(boolean status) { annotationsPanelToggleButton.setSelected(status); menuBar.setAnnotationPanelMenuItemSelected(status); } public void updateMiniAnnotationsLayerPanel(SuperAdapter superAdapter) { miniAnnotationsLayerPanel.updateRows(superAdapter); rightSidePanel.revalidate(); rightSidePanel.repaint(); } public boolean unsavedEditsExist() { return menuBar.unsavedEditsExist(); } public void addRecentMapMenuEntry(String title, boolean status) { menuBar.addRecentMapMenuEntry(title, status); } public void updatePrevStateNameFromImport(String path) { menuBar.updatePrevStateNameFromImport(path); } } ================================================ FILE: src/juicebox/gui/PseudoCountEditor.java ================================================ /* * The MIT License (MIT) * * Copyright (c) 2011-2021 Broad Institute, Aiden Lab, Rice University, Baylor College of Medicine * * Permission is hereby granted, free of charge, to any person obtaining a copy * of this software and associated documentation files (the "Software"), to deal * in the Software without restriction, including without limitation the rights * to use, copy, modify, merge, publish, distribute, sublicense, and/or sell * copies of the Software, and to permit persons to whom the Software is * furnished to do so, subject to the following conditions: * * The above copyright notice and this permission notice shall be included in * all copies or substantial portions of the Software. * * THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR * IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, * FITNESS FOR A PARTICULAR PURPOSE AND NON-INFRINGEMENT. IN NO EVENT SHALL THE * AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER * LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, * OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN * THE SOFTWARE. */ package juicebox.gui; import juicebox.mapcolorui.HeatmapRenderer; import javax.swing.*; import javax.swing.border.Border; import java.awt.*; import java.awt.event.ActionEvent; import java.awt.event.ActionListener; public class PseudoCountEditor extends JDialog { private static final long serialVersionUID = 9000026; public PseudoCountEditor(final SuperAdapter superAdapter) { super(superAdapter.getMainWindow()); Container contentPane = getContentPane(); contentPane.setLayout(new BorderLayout()); Border padding = BorderFactory.createEmptyBorder(20, 20, 5, 20); setModal(true); JLabel labelPseudocount = new JLabel("Pseudocount"); // todo error if called when pearson not loaded yet final JTextField textPseudocount = new JTextField("" + HeatmapRenderer.PSEUDO_COUNT); JPanel box = new JPanel(); box.setLayout(new GridLayout(0, 2)); box.add(labelPseudocount); box.add(textPseudocount); JButton updateButton = new JButton("Update Values"); updateButton.addActionListener(new ActionListener() { @Override public void actionPerformed(ActionEvent e) { HeatmapRenderer.PSEUDO_COUNT = Float.parseFloat(textPseudocount.getText()); superAdapter.refresh(); PseudoCountEditor.this.dispose(); } }); JButton resetButton = new JButton("Reset Values"); resetButton.addActionListener(new ActionListener() { @Override public void actionPerformed(ActionEvent e) { HeatmapRenderer.PSEUDO_COUNT = 1f; superAdapter.refresh(); PseudoCountEditor.this.dispose(); } }); JPanel buttonPanel = new JPanel(); buttonPanel.setBorder(padding); buttonPanel.setLayout(new GridLayout(0, 2)); buttonPanel.add(updateButton); buttonPanel.add(resetButton); contentPane.add(box, BorderLayout.CENTER); contentPane.add(buttonPanel, BorderLayout.PAGE_END); box.setBorder(padding); pack(); setLocationRelativeTo(getOwner()); setVisible(true); } } ================================================ FILE: src/juicebox/gui/SuperAdapter.java ================================================ /* * The MIT License (MIT) * * Copyright (c) 2011-2021 Broad Institute, Aiden Lab, Rice University, Baylor College of Medicine * * Permission is hereby granted, free of charge, to any person obtaining a copy * of this software and associated documentation files (the "Software"), to deal * in the Software without restriction, including without limitation the rights * to use, copy, modify, merge, publish, distribute, sublicense, and/or sell * copies of the Software, and to permit persons to whom the Software is * furnished to do so, subject to the following conditions: * * The above copyright notice and this permission notice shall be included in * all copies or substantial portions of the Software. * * THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR * IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, * FITNESS FOR A PARTICULAR PURPOSE AND NON-INFRINGEMENT. IN NO EVENT SHALL THE * AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER * LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, * OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN * THE SOFTWARE. */ package juicebox.gui; import juicebox.HiC; import juicebox.HiCGlobals; import juicebox.MainWindow; import juicebox.assembly.AssemblyStateTracker; import juicebox.data.*; import juicebox.data.anchor.MotifAnchorTools; import juicebox.data.basics.Chromosome; import juicebox.mapcolorui.HeatmapPanel; import juicebox.mapcolorui.PearsonColorScale; import juicebox.mapcolorui.PearsonColorScaleEditor; import juicebox.state.ImportStateFileDialog; import juicebox.state.LoadStateFromXMLFile; import juicebox.state.Slideshow; import juicebox.state.XMLFileHandling; import juicebox.tools.utils.norm.CustomNormVectorFileHandler; import juicebox.track.LoadAction; import juicebox.track.LoadEncodeAction; import juicebox.track.feature.*; import juicebox.windowui.*; import juicebox.windowui.layers.LayersPanel; import juicebox.windowui.layers.UnsavedAnnotationWarning; import org.broad.igv.ui.util.FileDialogUtils; import org.broad.igv.ui.util.MessageUtils; import javax.swing.*; import javax.swing.border.LineBorder; import java.awt.*; import java.awt.event.ActionEvent; import java.awt.event.ActionListener; import java.awt.geom.Point2D; import java.io.File; import java.io.FilenameFilter; import java.io.IOException; import java.util.ArrayList; import java.util.Collections; import java.util.List; import java.util.Properties; /** * Created by muhammadsaadshamim on 8/4/15. */ public class SuperAdapter { private static final List previousTempSelectedGroup = new ArrayList<>(); public static String currentlyLoadedMainFiles = ""; public static String currentlyLoadedControlFiles = ""; public static boolean assemblyModeCurrentlyActive = false; private static String datasetTitle = ""; private static String controlTitle; private final List annotationLayerHandlers = new ArrayList<>(); private MainWindow mainWindow; private HiC hic; private MainViewPanel mainViewPanel; private HiCZoom initialZoom; private AnnotationLayerHandler activeLayer; private AssemblyStateTracker assemblyStateTracker; private PearsonColorScale pearsonColorScale; private LayersPanel layersPanel; private boolean layerPanelIsVisible = false; public static String getDatasetTitle() { return datasetTitle; } public static void setDatasetTitle(String newDatasetTitle) { datasetTitle = newDatasetTitle; } public static void showMessageDialog(String message) { JOptionPane.showMessageDialog(MainWindow.getInstance(), message); } public static int showConfirmDialog(String message) { return JOptionPane.showConfirmDialog( MainWindow.getInstance(), message, "Confirm bundling", JOptionPane.YES_NO_OPTION); } public void setAdapters(MainWindow mainWindow, HiC hic, MainViewPanel mainViewPanel) { this.mainWindow = mainWindow; this.hic = hic; this.mainViewPanel = mainViewPanel; } public boolean unsavedEditsExist() { return mainViewPanel.unsavedEditsExist(); } public void addRecentMapMenuEntry(String title, boolean status) { mainViewPanel.addRecentMapMenuEntry(title, status); } // public Slideshow getSlideshow() { return new Slideshow(mainWindow,this); } public void showDataSetMetrics(boolean isControl) { if (hic.getDataset() == null) { JOptionPane.showMessageDialog(mainWindow, "File must be loaded to show info", "Error", JOptionPane.ERROR_MESSAGE); } else { try { String title = mainWindow.getTitle() + " QC Stats"; if (isControl) title += " (control)"; new QCDialog(mainWindow, hic, title, isControl); } catch (Exception e) { // TODO - test on hic file with no stats file specified e.printStackTrace(); JOptionPane.showMessageDialog(mainWindow, "Unable to launch QC Statistics", "Error", JOptionPane.ERROR_MESSAGE); } } } public void exportDataLauncher() { if (hic.getDataset() == null) { JOptionPane.showMessageDialog(mainWindow, "File must be loaded to show info", "Error", JOptionPane.ERROR_MESSAGE); } else { new DumpDialog(mainWindow, hic); } } public void setEnableForAllElements(boolean status) { mainViewPanel.setEnableForAllElements(this, status); for (AnnotationLayerHandler handler : annotationLayerHandlers) { handler.setImportAnnotationsEnabled(status); } } public void resetControlMap() { hic.setControlDataset(null); mainViewPanel.setSelectedDisplayOption(false, false); currentlyLoadedControlFiles = null; controlTitle = null; updateTitle(); } public void toggleAdvancedViews() { MatrixType.toggleAdvancedViews(); mainViewPanel.setSelectedDisplayOption(false, hic.isControlLoaded()); } public void launchSlideShow() { new Slideshow(mainWindow, this); } public void launchImportState(File fileForExport) { new ImportStateFileDialog(fileForExport, mainWindow); } public void launchLoadStateFromXML(String mapPath) { LoadStateFromXMLFile.reloadSelectedState(this, mapPath); } public void launchPearsonColorScaleEditor() { if (pearsonColorScale != null) new PearsonColorScaleEditor(this, pearsonColorScale); } public void launchSetPseudoCountEditor() { new PseudoCountEditor(this); } public void restoreLocation(String loc) { hic.restoreLocation(loc); } public LoadEncodeAction getEncodeAction() { if (layersPanel == null) { layersPanel = new LayersPanel(this); setLayersPanelVisible(false); } return layersPanel.getEncodeAction(); } public LoadAction getTrackLoadAction() { return layersPanel.getTrackLoadAction(); } public void updatePrevStateNameFromImport(String path) { mainViewPanel.updatePrevStateNameFromImport(path); } public void loadFromListActionPerformed(boolean control) { UnsavedAnnotationWarning unsaved = new UnsavedAnnotationWarning(this); if (unsaved.checkAndDelete(datasetTitle.length() > 0)) { HiCFileLoader.loadFromListActionPerformed(this, control); } } public void launchExportPDF() { new SaveImageDialog(null, hic, mainWindow, mainViewPanel.getHiCPanel(), ".pdf"); } public void launchExportSVG() { new SaveImageDialog(null, hic, mainWindow, mainViewPanel.getHiCPanel(), ".svg"); } public void loadFromRecentActionPerformed(String url, String title, boolean control) { UnsavedAnnotationWarning unsaved = new UnsavedAnnotationWarning(this); if (unsaved.checkAndDelete(datasetTitle.length() > 0)) { HiCFileLoader.loadFromRecentActionPerformed(this, url, title, control); } } public int clearCustomAnnotationDialog() { return JOptionPane.showConfirmDialog( mainWindow, "Are you sure you want to clear this layer's annotations?", "Confirm", JOptionPane.YES_NO_OPTION); } public int deleteCustomAnnotationDialog(String layerName) { return JOptionPane.showConfirmDialog( mainWindow, "Are you sure you want to delete this layer (" + layerName + ")?", "Confirm", JOptionPane.YES_NO_OPTION); } public void repaint() { mainWindow.revalidate(); mainWindow.repaint(); if (layersPanel != null) layersPanel.repaint(); } public void safeLoadFromURLActionPerformed(final Runnable refresh1DLayers) { Runnable runnable = new Runnable() { public void run() { if (hic.getDataset() == null) { JOptionPane.showMessageDialog(mainWindow, "HiC file must be loaded to load tracks", "Error", JOptionPane.ERROR_MESSAGE); return; } String url = JOptionPane.showInputDialog("Enter URL: "); if (url != null && url.length() > 0) { if (HiCFileTools.isDropboxURL(url)) { url = HiCFileTools.cleanUpDropboxURL(url); } url = url.trim(); hic.unsafeLoadTrack(url); } refresh1DLayers.run(); } }; mainWindow.executeLongRunningTask(runnable, "Load from url"); } public String getLocationDescription() { return hic.getLocationDescription(); } public String getDescription(String item) { return JOptionPane.showInputDialog(mainWindow, "Enter description for saved " + item + ":", hic.getDefaultLocationDescription()); } public void addNewStateToXML(String stateDescription) { XMLFileHandling.addNewStateToXML(stateDescription, this); } public void setNormalizationDisplayState() { mainViewPanel.setNormalizationDisplayState(hic); } public void centerMap(int xBP, int yBP) { hic.center(xBP, yBP); } public void moveMapBy(int dxBP, int dyBP) { hic.moveBy(dxBP, dyBP); } public boolean shouldVisibleWindowBeRendered() { return hic != null && hic.getXContext() != null; } public double getHiCScaleFactor() { return hic.getScaleFactor(); } public Point2D.Double getHiCOrigin() { return new Point2D.Double(hic.getXContext().getBinOrigin(), hic.getYContext().getBinOrigin()); } public Point2D.Double getHiCScale(int width, int height) { // TODO - why does this sometimes return null? try { return new Point2D.Double((double) hic.getZd().getXGridAxis().getBinCount() / width, (double) hic.getZd().getYGridAxis().getBinCount() / height); } catch (Exception e) { return null; // TODO is there a good default to return? } } public Point getHeatMapPanelDimensions() { return new Point(mainViewPanel.getHeatmapPanel().getWidth(), mainViewPanel.getHeatmapPanel().getHeight()); } public void initializeMainView(Container contentPane, Dimension screenSize, int taskBarHeight) { mainViewPanel.initializeMainView(this, contentPane, screenSize, taskBarHeight); } private void unsafeSetInitialZoom() { //For now, in case of Pearson - set initial to 500KB resolution. if (hic.isInPearsonsMode()) { initialZoom = hic.getMatrix().getFirstPearsonZoomData(HiC.Unit.BP).getZoom(); } else if (ChromosomeHandler.isAllByAll(hic.getXContext().getChromosome())) { mainViewPanel.getResolutionSlider().setEnabled(false); initialZoom = hic.getMatrix().getFirstZoomData().getZoom(); } else { mainViewPanel.getResolutionSlider().setEnabled(true); // todo this is throwing null pointer exceptions initialZoom = hic.getMatrix().getFirstZoomData().getZoom(); // If this is the initial load hic.currentZoom will be null if (hic.getZoom() != null) { HiC.Unit currentUnit = hic.getZoom().getUnit(); List zooms = (currentUnit == HiC.Unit.BP ? hic.getDataset().getBpZooms() : hic.getDataset().getFragZooms()); // Find right zoom level int pixels = mainViewPanel.getHeatmapPanel().getMinimumDimension(); long len; if (currentUnit == HiC.Unit.BP) { len = (Math.max(hic.getXContext().getChrLength(), hic.getYContext().getChrLength())); } else { len = Math.max(hic.getDataset().getFragmentCounts().get(hic.getXContext().getChromosome().getName()), hic.getDataset().getFragmentCounts().get(hic.getYContext().getChromosome().getName())); } int maxNBins = pixels; long bp_bin = len / maxNBins; initialZoom = zooms.get(zooms.size() - 1); for (int z = 1; z < zooms.size(); z++) { if (zooms.get(z).getBinSize() < bp_bin) { initialZoom = zooms.get(z - 1); break; } } } } hic.unsafeActuallySetZoomAndLocation(hic.getXContext().getChromosome().toString(), hic.getYContext().getChromosome().toString(), initialZoom, 0, 0, -1, true, HiC.ZoomCallType.INITIAL, true, isResolutionLocked() ? 1 : 0, true); } public void refresh() { mainViewPanel.getHeatmapPanel().clearTileCache(); mainViewPanel.updateThumbnail(hic); repaint(); } public void unsafeClearAllMatrixZoomCache() { //not sure if this is a right place for this hic.clearAllMatrixZoomDataCache(); } private void refreshMainOnly() { mainViewPanel.getHeatmapPanel().clearTileCache(); repaint(); } private static boolean genomesAreCompatible(Dataset dataset1, Dataset dataset2) { if (dataset1.getGenomeId().equalsIgnoreCase(dataset2.getGenomeId())) { return true; } String[] g1 = dataset1.getGenomeId().split("/"); String[] g2 = dataset2.getGenomeId().split("/"); if (g1[g1.length - 1].equalsIgnoreCase(g2[g2.length - 1])) { return true; } //todo can go chromosome by chromosome and check names/sizes System.err.println("Genome IDs do not match:\n" + dataset1.getGenomeId().toLowerCase() + " vs " + dataset2.getGenomeId().toLowerCase()); return false; } private boolean unsafeLoad(final List files, final boolean control, boolean restore) throws IOException { StringBuilder newFilesToBeLoaded = new StringBuilder(); boolean allFilesAreHiC = true; for (String file : files) { if (newFilesToBeLoaded.length() > 1) { newFilesToBeLoaded.append("##"); } newFilesToBeLoaded.append(file); allFilesAreHiC &= file.endsWith(".hic"); } if ((!control) && newFilesToBeLoaded.toString().equals(currentlyLoadedMainFiles)) { if (!restore) { JOptionPane.showMessageDialog(mainWindow, "File(s) already loaded"); } return false; } if (control && newFilesToBeLoaded.toString().equals(currentlyLoadedControlFiles)) { if (!restore) { JOptionPane.showMessageDialog(mainWindow, "File(s) already loaded"); } return false; } if (allFilesAreHiC) { mainViewPanel.setIgnoreUpdateThumbnail(true); //heatmapPanel.setBorder(LineBorder.createBlackLineBorder()); //thumbnailPanel.setBorder(LineBorder.createBlackLineBorder()); mainViewPanel.getMouseHoverTextPanel().setBorder(LineBorder.createGrayLineBorder()); DatasetReader reader = DatasetReaderFactory.getReader(files); if (reader == null) return false; Dataset dataset = reader.read(); if (reader.getVersion() < HiCGlobals.minVersion) { JOptionPane.showMessageDialog(mainWindow, "This version of \"hic\" format is no longer supported"); return false; } if (control && !genomesAreCompatible(dataset, hic.getDataset())) { JOptionPane.showMessageDialog(mainWindow, "Cannot load maps with different genomes"); return false; } if (control && dataset.getVersion() != hic.getDataset().getVersion() && (dataset.getVersion() < 7 || hic.getDataset().getVersion() < 7)) { JOptionPane.showMessageDialog(mainWindow, "Cannot load control with .hic files less than version 7"); return false; } if (assemblyModeCurrentlyActive) { if (!exitAssemblyMode()) { return false; //if user does not exit assembly mode then do not load new map } } if (!control && hic.getDataset() != null && !dataset.getGenomeId().equals(hic.getDataset().getGenomeId())) { resetControlMap(); } if (control) { hic.setControlDataset(dataset); mainViewPanel.setEnabledForNormalization(true, hic.getNormalizationOptions(true), dataset.getVersion() >= HiCGlobals.minVersion); } else { hic.reset(); hic.setDataset(dataset); hic.setChromosomeHandler(dataset.getChromosomeHandler()); mainViewPanel.setChromosomes(hic.getChromosomeHandler()); mainViewPanel.setEnabledForNormalization(false, hic.getNormalizationOptions(false), dataset.getVersion() >= HiCGlobals.minVersion); hic.resetContexts(); updateTrackPanel(); mainViewPanel.getMenuBar().getRecentLocationMenu().setEnabled(true); mainWindow.getContentPane().invalidate(); mainWindow.repaint(); mainViewPanel.resetResolutionSlider(hic.getDefaultUnit()); mainViewPanel.unsafeRefreshChromosomes(SuperAdapter.this); } mainViewPanel.setSelectedDisplayOption(control, hic.isControlLoaded()); setEnableForAllElements(true); if (control) { currentlyLoadedControlFiles = newFilesToBeLoaded.toString(); } else { currentlyLoadedMainFiles = newFilesToBeLoaded.toString(); } mainViewPanel.getMenuBar().updateMainMapHasBeenLoaded(true); if (control) { mainViewPanel.getMenuBar().updateControlMapHasBeenLoaded(true); } mainViewPanel.setIgnoreUpdateThumbnail(false); } else { JOptionPane.showMessageDialog(mainWindow, "Please choose a .hic file to load"); } return true; } public void safeLoad(final List files, final boolean control, final String title) { addRecentMapMenuEntry(title.trim() + RecentMenu.delimiter + files.get(0), true); Runnable runnable = new Runnable() { public void run() { boolean isRestorenMode = false; unsafeLoadWithTitleFix(files, control, title, isRestorenMode); } }; mainWindow.executeLongRunningTask(runnable, "MainWindow safe load"); } public void unsafeLoadWithTitleFix(List files, boolean control, String title, boolean restore) { String resetTitle = datasetTitle; if (control) resetTitle = controlTitle; getHeatmapPanel().disableAssemblyEditing(); resetAnnotationLayers(); HiCGlobals.hicMapScale = 1; // refresh(); ActionListener l = mainViewPanel.getDisplayOptionComboBox().getActionListeners()[0]; try { mainViewPanel.getDisplayOptionComboBox().removeActionListener(l); if (unsafeLoad(files, control, restore)) { //mainViewPanel.updateThumbnail(hic); refresh(); updateTitle(control, title); } } catch (IOException e) { // TODO somehow still have trouble reloading the previous file System.err.println("Error loading hic file " + e.getLocalizedMessage()); JOptionPane.showMessageDialog(mainWindow, "Error loading .hic file", "Error", JOptionPane.ERROR_MESSAGE); mainViewPanel.updateThumbnail(hic); updateTitle(control, resetTitle); } finally { mainViewPanel.getDisplayOptionComboBox().addActionListener(l); } } public KeyEventDispatcher getNewHiCKeyDispatcher() { return new HiCKeyDispatcher(this, hic, mainViewPanel.getDisplayOptionComboBox()); } public LoadDialog launchLoadFileDialog(Properties properties) { return new LoadDialog(mainWindow, properties, this); } void safeRefreshButtonActionPerformed() { Runnable runnable = new Runnable() { @Override public void run() { mainViewPanel.unsafeRefreshChromosomes(SuperAdapter.this); } }; mainWindow.executeLongRunningTask(runnable, "Refresh Button"); } public boolean safeDisplayOptionComboBoxActionPerformed() { final boolean[] retVal = new boolean[1]; Runnable runnable = new Runnable() { public void run() { retVal[0] = unsafeDisplayOptionComboBoxActionPerformed(); } }; mainWindow.executeLongRunningTask(runnable, "DisplayOptionsComboBox"); return retVal[0]; } void safeNormalizationComboBoxActionPerformed(final ActionEvent e, final boolean isForControl) { Runnable runnable = new Runnable() { public void run() { unsafeNormalizationComboBoxActionPerformed(isForControl); } }; mainWindow.executeLongRunningTask(runnable, "Normalization ComboBox"); } public boolean unsafeDisplayOptionComboBoxActionPerformed() { MatrixType option = (MatrixType) (mainViewPanel.getDisplayOptionComboBox().getSelectedItem()); if (hic.isWholeGenome() && !MatrixType.isValidGenomeWideOption(option)) { JOptionPane.showMessageDialog(mainWindow, option + " matrix is not available for whole-genome view."); mainViewPanel.getDisplayOptionComboBox().setSelectedItem(hic.getDisplayOption()); return false; } mainViewPanel.getColorRangePanel().handleNewFileLoading(option); if (MatrixType.isVSTypeDisplay(option)) { if (hic.getMatrix().isNotIntra()) { JOptionPane.showMessageDialog(mainWindow, "Observed VS Control is not available for inter-chr views."); mainViewPanel.getDisplayOptionComboBox().setSelectedItem(hic.getDisplayOption()); return false; } } if (MatrixType.isPearsonType(option)) { if (hic.getMatrix().isNotIntra()) { JOptionPane.showMessageDialog(mainWindow, "Pearson's matrix is not available for inter-chr views."); mainViewPanel.getDisplayOptionComboBox().setSelectedItem(hic.getDisplayOption()); return false; } else { try { if (hic.isPearsonsNotAvailableForFile(false)) { JOptionPane.showMessageDialog(mainWindow, "Pearson's matrix is not available at this resolution"); mainViewPanel.getDisplayOptionComboBox().setSelectedItem(hic.getDisplayOption()); return false; } if (MatrixType.isControlPearsonType(option) && hic.isPearsonsNotAvailableForFile(true)) { JOptionPane.showMessageDialog(mainWindow, "Control's Pearson matrix is not available at this resolution"); mainViewPanel.getDisplayOptionComboBox().setSelectedItem(hic.getDisplayOption()); return false; } } catch (Exception ex) { JOptionPane.showMessageDialog(mainWindow, "Pearson's matrix is not available at this region"); mainViewPanel.getDisplayOptionComboBox().setSelectedItem(hic.getDisplayOption()); return false; } } } hic.setDisplayOption(option); refresh(); // necessary to invalidate minimap when changing view return true; } /** * TODO deprecate * * @return hic */ public HiC getHiC() { return hic; } /** * TODO deprecate * * @return mainwindow */ public MainWindow getMainWindow() { return mainWindow; } public LayersPanel getLayersPanel() { return layersPanel; } public MainMenuBar getMainMenuBar() { return mainViewPanel.getMenuBar(); } public void revalidate() { mainWindow.revalidate(); if (layersPanel != null) layersPanel.revalidate(); } public void updateMainViewPanelToolTipText(String text) { mainViewPanel.updateToolTipText(text); } public void setPositionChrTop(String positionChrTop) { mainViewPanel.setPositionChrTop(positionChrTop); } public void setPositionChrLeft(String positionChrLeft) { mainViewPanel.setPositionChrLeft(positionChrLeft); } public String getToolTip() { return mainViewPanel.getToolTip(); } public void repaintTrackPanels() { mainViewPanel.repaintTrackPanels(); } public void repaintGridRulerPanels() { mainViewPanel.repaintGridRulerPanels(); } // only hic should call this public boolean isResolutionLocked() { return mainViewPanel.isResolutionLocked(); } public void updateThumbnail() { mainViewPanel.updateThumbnail(hic); } public void updateZoom(HiCZoom newZoom) { mainViewPanel.updateZoom(newZoom); } public void updateAndResetZoom(HiCZoom newZoom) { mainViewPanel.updateAndResetZoom(newZoom); } public void launchFileLoadingError(String urlString) { JOptionPane.showMessageDialog(mainWindow, "Error while trying to load " + urlString, "Error", JOptionPane.ERROR_MESSAGE); } private void updateTitle(boolean control, String title) { if (title != null && title.length() > 0) { if (control) controlTitle = title; else datasetTitle = title; updateTitle(); } } private void updateTitle() { String newTitle = datasetTitle; String fileVersions = ""; try { fileVersions += hic.getDataset().getVersion() + ""; } catch (Exception ignored) { } if (controlTitle != null && controlTitle.length() > 0) { newTitle += " (control=" + controlTitle + ")"; try { fileVersions += "/" + hic.getControlDataset().getVersion(); } catch (Exception ignored) { } } mainWindow.setTitle(HiCGlobals.juiceboxTitle + "<" + fileVersions + ">: " + newTitle); } public void launchGenericMessageDialog(String message, String error, int errorMessage) { JOptionPane.showMessageDialog(mainWindow, message, error, errorMessage); } public HeatmapPanel getHeatmapPanel() { return mainViewPanel.getHeatmapPanel(); } public void updateTrackPanel() { mainViewPanel.updateTrackPanel(hic.getLoadedTracks().size() > 0); } private void unsafeNormalizationComboBoxActionPerformed(boolean isForControl) { if (isForControl) { String value = (String) mainViewPanel.getControlNormalizationComboBox().getSelectedItem(); hic.setControlNormalizationType(value); } else { String value = (String) mainViewPanel.getObservedNormalizationComboBox().getSelectedItem(); hic.setObsNormalizationType(value); } refreshMainOnly(); } public MainViewPanel getMainViewPanel() { return mainViewPanel; } public boolean isTooltipAllowedToUpdated() { return mainViewPanel.isTooltipAllowedToUpdate(); } public void toggleToolTipUpdates(boolean b) { mainViewPanel.toggleToolTipUpdates(b); } public void executeLongRunningTask(Runnable runnable, String s) { mainWindow.executeLongRunningTask(runnable, s); } public void updateRatioColorSlider(int max, double val) { mainViewPanel.updateRatioColorSlider(hic, max, val); } public void updateColorSlider(double low, double high) { mainViewPanel.updateColorSlider(hic, low, high, high * 2); } public void unsafeSetSelectedChromosomes(Chromosome xC, Chromosome yC) { mainViewPanel.unsafeSetSelectedChromosomes(this, xC, yC); } public void setSelectedChromosomesNoRefresh(Chromosome chrX, Chromosome chrY) { mainViewPanel.setSelectedChromosomesNoRefresh(chrX, chrY, hic.getXContext(), hic.getYContext()); initialZoom = null; } public void unsafeUpdateHiCChromosomes(Chromosome chrX, Chromosome chrY) { hic.setSelectedChromosomes(chrX, chrY); mainViewPanel.getRulerPanelX().setContext(hic.getXContext(), HiCRulerPanel.Orientation.HORIZONTAL); mainViewPanel.getRulerPanelY().setContext(hic.getYContext(), HiCRulerPanel.Orientation.VERTICAL); mainViewPanel.getChromosomeFigPanelX().setContext(hic.getXContext(), HiCChromosomeFigPanel.Orientation.HORIZONTAL); mainViewPanel.getChromosomeFigPanelY().setContext(hic.getYContext(), HiCChromosomeFigPanel.Orientation.VERTICAL); unsafeSetInitialZoom(); } public void setShowChromosomeFig(boolean status) { mainViewPanel.setShowChromosomeFig(status); } public boolean getShowGridLines() { return mainViewPanel.getShowGridLines(); } public void setShowGridLines(boolean status) { mainViewPanel.setShowGridLines(status); } public AnnotationLayerHandler getActiveLayerHandler() { return activeLayer; } public void setActiveLayerHandler(AnnotationLayerHandler activeLayer) { this.activeLayer = activeLayer; for (AnnotationLayerHandler layer : annotationLayerHandlers) { layer.setActiveLayerButtonStatus(false); } activeLayer.setActiveLayerButtonStatus(true); } public List getAllLayers() { return annotationLayerHandlers; } // mhoeger - Used for contig layer, currently returns the first element public List getAssemblyLayerHandlers() { List handlers = new ArrayList<>(); for (AnnotationLayerHandler annotationLayerHandler : annotationLayerHandlers) { if (annotationLayerHandler.getAnnotationLayerType() == AnnotationLayer.LayerType.SCAFFOLD || annotationLayerHandler.getAnnotationLayerType() == AnnotationLayer.LayerType.SUPERSCAFFOLD || annotationLayerHandler.getAnnotationLayerType() == AnnotationLayer.LayerType.EDIT) { handlers.add(annotationLayerHandler); } } if (handlers.size() == 0) { handlers.add(annotationLayerHandlers.get(0)); } return handlers; } private AnnotationLayerHandler getAssemblyLayerHandler(AnnotationLayer.LayerType layerType) { for (AnnotationLayerHandler annotationLayerHandler : getAssemblyLayerHandlers()) { if (annotationLayerHandler.getAnnotationLayerType() == layerType) { return annotationLayerHandler; } } return null; } public AnnotationLayerHandler getMainLayer() { return getAssemblyLayerHandler(AnnotationLayer.LayerType.SCAFFOLD); } public AnnotationLayerHandler getGroupLayer() { return getAssemblyLayerHandler(AnnotationLayer.LayerType.SUPERSCAFFOLD); } public AnnotationLayerHandler getEditLayer() { return getAssemblyLayerHandler(AnnotationLayer.LayerType.EDIT); } public void exitActionPerformed() { UnsavedAnnotationWarning unsaved = new UnsavedAnnotationWarning(this); if (unsaved.checkAndDelete(true)) { mainWindow.exitActionPerformed(); } } /** * @param temp file, otherwise just pass null * @return active AnnotationLayerHandler */ public AnnotationLayerHandler createNewLayer(File temp) { if (temp != null) { activeLayer = new AnnotationLayerHandler(Feature2DParser.loadFeatures( temp.getAbsolutePath(), hic.getChromosomeHandler(), true, null, false)); } else { activeLayer = new AnnotationLayerHandler(); } annotationLayerHandlers.add(activeLayer); setActiveLayerHandler(activeLayer); // call this anyways because other layers need to fix button settings return activeLayer; } public void updateLayerDeleteStatus() { boolean isDeleteAllowed = annotationLayerHandlers.size() > 1; for (AnnotationLayerHandler handler : annotationLayerHandlers) { handler.setDeleteLayerButtonStatus(isDeleteAllowed); } } public int removeLayer(AnnotationLayerHandler handler) { int returnCode = -1; if (annotationLayerHandlers != null && annotationLayerHandlers.size() > 1) { // must have at least 1 layer returnCode = annotationLayerHandlers.size() - 1 - annotationLayerHandlers.indexOf(handler); annotationLayerHandlers.remove(handler); if (handler == activeLayer) { // need to set a new active layer; let's use first one as default setActiveLayerHandler(annotationLayerHandlers.get(0)); } } updateLayerDeleteStatus(); return returnCode; } private void resetAnnotationLayers() { annotationLayerHandlers.clear(); // currently must have at least 1 layer getActiveLayerHandler().getAnnotationLayer().resetCounter(); createNewLayer(null); updateMiniAnnotationsLayerPanel(); updateMainLayersPanel(); } public int moveDownIndex(AnnotationLayerHandler handler) { int currIndex = annotationLayerHandlers.indexOf(handler); int n = annotationLayerHandlers.size(); if (currIndex > 0) { Collections.swap(annotationLayerHandlers, currIndex, currIndex - 1); return n - currIndex; } return n - 1 - currIndex; } public int moveUpIndex(AnnotationLayerHandler handler) { int currIndex = annotationLayerHandlers.indexOf(handler); int n = annotationLayerHandlers.size(); if (currIndex < n - 1) { Collections.swap(annotationLayerHandlers, currIndex, currIndex + 1); return n - 2 - currIndex; } return n - 1 - currIndex; } public void setPearsonColorScale(PearsonColorScale pearsonColorScale) { this.pearsonColorScale = pearsonColorScale; } public String getTrackPanelPrintouts(int x, int y) { return mainViewPanel.getTrackPanelPrintouts(x, y); } public void setLayersPanelVisible(boolean status) { this.layerPanelIsVisible = status; if (layersPanel == null) { if (status) layersPanel = new LayersPanel(this); } layersPanel.setVisible(status); setLayersPanelGUIControllersSelected(status); } public void intializeLayersPanel() { layersPanel = new LayersPanel(this); } public void setLayersPanelGUIControllersSelected(boolean status) { mainViewPanel.setAnnotationsPanelToggleButtonSelected(status); } public void togglePanelVisible() { setLayersPanelVisible(!layerPanelIsVisible); } public AssemblyStateTracker getAssemblyStateTracker() { return assemblyStateTracker; } public void setAssemblyStateTracker(AssemblyStateTracker assemblyStateTracker) { this.assemblyStateTracker = assemblyStateTracker; } public void createCustomChromosomesFromBED() { FilenameFilter bedFilter = new FilenameFilter() { public boolean accept(File dir, String name) { return name.toLowerCase().endsWith(".bed"); } }; File[] files = FileDialogUtils.chooseMultiple("Choose .bed file(s)", LoadDialog.LAST_LOADED_HIC_FILE_PATH, bedFilter); if (files != null && files.length > 0) { LoadDialog.LAST_LOADED_HIC_FILE_PATH = files[0]; int minSize = MotifAnchorTools.getMinSizeForExpansionFromGUI(); for (File f : files) { Chromosome custom = hic.getChromosomeHandler().generateCustomChromosomeFromBED(f, minSize); updateChrHandlerAndMVP(custom); } } } public void createAssemblyChromosome() { Chromosome assembly = hic.getChromosomeHandler().generateAssemblyChromosome(); updateChrHandlerAndMVP(assembly); } public void createCustomChromosomeMap(Feature2DList featureList, String chrName) { Chromosome custom = hic.getChromosomeHandler().addCustomChromosome(featureList, chrName); updateChrHandlerAndMVP(custom); } private void updateChrHandlerAndMVP(Chromosome custom) { hic.setChromosomeHandler(hic.getChromosomeHandler()); mainViewPanel.getChrBox1().addItem(custom); mainViewPanel.getChrBox2().addItem(custom); } public void updateMiniAnnotationsLayerPanel() { try { getMainViewPanel().updateMiniAnnotationsLayerPanel(this); } catch (Exception ignored) { } } public void updateMainLayersPanel() { try { getLayersPanel().updateLayers2DPanel(this); } catch (Exception ignored) { } } public void updatePreviousTempSelectedGroups(Feature2D tempSelectedGroup) { previousTempSelectedGroup.add(tempSelectedGroup); } public void safeClearAllMZDCache() { Runnable runnable = new Runnable() { public void run() { unsafeClearAllMatrixZoomCache(); //split clear current zoom and put the rest in background? Seems to taking a lot of time refresh(); } }; executeLongRunningTask(runnable, "Assembly clear MZD cache"); } public boolean exitAssemblyMode() { MainMenuBar.exitAssemblyMode(); int dialogButton = JOptionPane.YES_NO_OPTION; int dialogResult = JOptionPane.showConfirmDialog(mainWindow, "This action will discard all unsaved assembly changes. Continue?", "Continue", dialogButton); if (dialogResult == JOptionPane.NO_OPTION) { return false; } else { if (layersPanel != null) { layersPanel.createNewLayerAndAddItToPanels(this, null); } if (getAssemblyLayerHandlers() != null) { for (AnnotationLayerHandler annotationLayerHandler : getAssemblyLayerHandlers()) removeLayer(annotationLayerHandler); if (layersPanel != null) { layersPanel.updateBothLayersPanels(this); } assemblyModeCurrentlyActive = false; safeClearAllMZDCache(); repaint(); } resetAnnotationLayers(); return true; } } public void safeLaunchImportNormalizations(boolean isControl) { final File[] files = FileDialogUtils.chooseMultiple("Choose custom normalization file(s)", LoadDialog.LAST_LOADED_HIC_FILE_PATH, null); Runnable runnable = new Runnable() { public void run() { if (files != null && files.length > 0) { LoadDialog.LAST_LOADED_HIC_FILE_PATH = files[0]; CustomNormVectorFileHandler.unsafeHandleUpdatingOfNormalizations(SuperAdapter.this, files, isControl, 1); boolean versionStatus = hic.getDataset().getVersion() >= HiCGlobals.minVersion; if (isControl) { versionStatus = hic.getControlDataset().getVersion() >= HiCGlobals.minVersion; } mainViewPanel.setEnabledForNormalization(isControl, hic.getNormalizationOptions(isControl), versionStatus); repaint(); } } }; mainWindow.executeLongRunningTask(runnable, "safe add custom norms"); } public void createGenomewideChromosomeFromChromDotSizes() { Chromosome custom = hic.getChromosomeHandler().addGenomeWideChromosome(); updateChrHandlerAndMVP(custom); } public static int getNewResolutionGUI() { int newResolution = -1; String newSize = MessageUtils.showInputDialog("Specify a new resolution", ""); try { newResolution = Integer.parseInt(newSize); } catch (Exception e) { if (HiCGlobals.guiIsCurrentlyActive) { SuperAdapter.showMessageDialog("Invalid resolution given (not integer): " + newSize); } else { MessageUtils.showMessage("Invalid resolution given (not integer): " + newSize); } } return newResolution; } public void safeLaunchCreateNewResolution() { int newResolution = getNewResolutionGUI(); if (newResolution > 0) { hic.createNewDynamicResolutions(newResolution); refresh(); getMainViewPanel().getResolutionSlider().reset(); } } public void clearEditsAndUpdateLayers() { getEditLayer().clearAnnotations(); if (getActiveLayerHandler() != getMainLayer()) { setActiveLayerHandler(getMainLayer()); getLayersPanel().updateBothLayersPanels(this); } } } ================================================ FILE: src/juicebox/mapcolorui/BoundingBoxRenderer.java ================================================ /* * The MIT License (MIT) * * Copyright (c) 2011-2021 Broad Institute, Aiden Lab, Rice University, Baylor College of Medicine * * Permission is hereby granted, free of charge, to any person obtaining a copy * of this software and associated documentation files (the "Software"), to deal * in the Software without restriction, including without limitation the rights * to use, copy, modify, merge, publish, distribute, sublicense, and/or sell * copies of the Software, and to permit persons to whom the Software is * furnished to do so, subject to the following conditions: * * The above copyright notice and this permission notice shall be included in * all copies or substantial portions of the Software. * * THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR * IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, * FITNESS FOR A PARTICULAR PURPOSE AND NON-INFRINGEMENT. IN NO EVENT SHALL THE * AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER * LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, * OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN * THE SOFTWARE. */ package juicebox.mapcolorui; import juicebox.HiCGlobals; import juicebox.data.ChromosomeHandler; import juicebox.data.CustomMatrixZoomData; import juicebox.data.MatrixZoomData; import java.awt.*; import java.util.List; public class BoundingBoxRenderer { private final HeatmapPanel parent; private long[] chromosomeBoundaries; public BoundingBoxRenderer(HeatmapPanel heatmapPanel) { parent = heatmapPanel; } public void drawAllByAllGrid(Graphics2D g, MatrixZoomData zd, boolean showGridLines, double binOriginX, double binOriginY, double scaleFactor) { if (HiCGlobals.isDarkulaModeEnabled) { g.setColor(Color.LIGHT_GRAY); } else { g.setColor(Color.DARK_GRAY); } long maxDimension = chromosomeBoundaries[chromosomeBoundaries.length - 1]; int maxHeight = getGridLineHeightLimit(zd, maxDimension, scaleFactor); int maxWidth = getGridLineWidthLimit(zd, maxDimension, scaleFactor); g.drawLine(0, 0, 0, maxHeight); g.drawLine(0, 0, maxWidth, 0); g.drawLine(maxWidth, 0, maxWidth, maxHeight); g.drawLine(0, maxHeight, maxWidth, maxHeight); // Draw grid lines only if option is selected if (showGridLines) { for (long bound : chromosomeBoundaries) { // vertical lines int xBin = zd.getXGridAxis().getBinNumberForGenomicPosition(bound); int x = (int) ((xBin - binOriginX) * scaleFactor); g.drawLine(x, 0, x, maxHeight); // horizontal lines int yBin = zd.getYGridAxis().getBinNumberForGenomicPosition(bound); int y = (int) ((yBin - binOriginY) * scaleFactor); g.drawLine(0, y, maxWidth, y); } } //Cover gray background for the empty parts of the matrix: if (HiCGlobals.isDarkulaModeEnabled) { g.setColor(Color.darkGray); } else { g.setColor(Color.white); } int pHeight = parent.getHeight(); int pWidth = parent.getWidth(); g.fillRect(maxHeight, 0, pHeight, pWidth); g.fillRect(0, maxWidth, pHeight, pWidth); g.fillRect(maxHeight, maxWidth, pHeight, pWidth); } private int getGridLineWidthLimit(MatrixZoomData zd, long maxPosition, double scaleFactor) { if (parent.getWidth() < 50 || scaleFactor < 1e-10) { return 0; } int xBin = zd.getXGridAxis().getBinNumberForGenomicPosition(maxPosition); return (int) (xBin * scaleFactor); } private int getGridLineHeightLimit(MatrixZoomData zd, long maxPosition, double scaleFactor) { if (parent.getHeight() < 50 || scaleFactor < 1e-10) { return 0; } int yBin = zd.getYGridAxis().getBinNumberForGenomicPosition(maxPosition); return (int) (yBin * scaleFactor); } public void setChromosomeBoundaries(long[] chromosomeBoundaries) { this.chromosomeBoundaries = chromosomeBoundaries; } public void drawRegularGrid(Graphics2D g, MatrixZoomData zd, boolean showGridLines, ChromosomeHandler handler, double binOriginX, double binOriginY, double scaleFactor) { if (showGridLines) { if (HiCGlobals.isDarkulaModeEnabled) { g.setColor(Color.LIGHT_GRAY); } else { g.setColor(Color.DARK_GRAY); } if (handler != null && zd != null) { if (handler.isCustomChromosome(zd.getChr1())) { if (zd instanceof CustomMatrixZoomData) { java.util.List xBins = ((CustomMatrixZoomData) zd).getBoundariesOfCustomChromosomeX(); //int maxSize = xBins.get(xBins.size() - 1); int maxSize = (int) ((zd.getYGridAxis().getBinCount() - binOriginY) * scaleFactor); for (long xBin : xBins) { int x = (int) ((xBin - binOriginX) * scaleFactor); g.drawLine(x, 0, x, maxSize); } } } if (handler.isCustomChromosome(zd.getChr2())) { if (zd instanceof CustomMatrixZoomData) { List yBins = ((CustomMatrixZoomData) zd).getBoundariesOfCustomChromosomeY(); //int maxSize = yBins.get(yBins.size() - 1); int maxSize = (int) ((zd.getXGridAxis().getBinCount() - binOriginX) * scaleFactor); for (long yBin : yBins) { int y = (int) ((yBin - binOriginY) * scaleFactor); g.drawLine(0, y, maxSize, y); } } } } } } } ================================================ FILE: src/juicebox/mapcolorui/ColorRangeDialog.java ================================================ /* * The MIT License (MIT) * * Copyright (c) 2011-2021 Broad Institute, Aiden Lab, Rice University, Baylor College of Medicine * * Permission is hereby granted, free of charge, to any person obtaining a copy * of this software and associated documentation files (the "Software"), to deal * in the Software without restriction, including without limitation the rights * to use, copy, modify, merge, publish, distribute, sublicense, and/or sell * copies of the Software, and to permit persons to whom the Software is * furnished to do so, subject to the following conditions: * * The above copyright notice and this permission notice shall be included in * all copies or substantial portions of the Software. * * THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR * IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, * FITNESS FOR A PARTICULAR PURPOSE AND NON-INFRINGEMENT. IN NO EVENT SHALL THE * AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER * LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, * OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN * THE SOFTWARE. */ package juicebox.mapcolorui; import juicebox.gui.SuperAdapter; import juicebox.windowui.MatrixType; import javax.swing.*; import javax.swing.border.EmptyBorder; import java.awt.*; import java.awt.event.ActionEvent; import java.awt.event.ActionListener; import java.awt.event.FocusEvent; import java.awt.event.FocusListener; import java.text.DecimalFormat; import java.text.ParseException; /** * @author Jim Robinson */ class ColorRangeDialog extends JDialog { private static final long serialVersionUID = 9000027; private final DecimalFormat df2; private final JTextField minimumField = new JTextField(); private final JTextField maximumField = new JTextField(); private final JTextField lowerField = new JTextField(); private final JTextField upperField = new JTextField(); private final JLabel minTextLabel = new JLabel("Minimum:"); private final JLabel lowerValTextLabel = new JLabel("Lower value:"); private final JLabel maxTextLabel = new JLabel("Maximum:"); private final JLabel higherValTextLabel = new JLabel("Higher value:"); public ColorRangeDialog(SuperAdapter superAdapter, JColorRangePanel colorRangePanel, RangeSlider colorSlider, double colorRangeFactor, MatrixType option) { super(superAdapter.getMainWindow()); boolean isOEColorScaleType = MatrixType.isOEColorScaleType(option); initComponents(superAdapter, colorRangePanel, isOEColorScaleType); df2 = new DecimalFormat("####.###"); minimumField.setText(df2.format(colorSlider.getMinimum() / colorRangeFactor)); maximumField.setText(df2.format(colorSlider.getMaximum() / colorRangeFactor)); lowerField.setText(df2.format(colorSlider.getLowerValue() / colorRangeFactor)); upperField.setText(df2.format(colorSlider.getUpperValue() / colorRangeFactor)); maximumField.requestFocusInWindow(); } private void initComponents(final SuperAdapter superAdapter, final JColorRangePanel colorRangePanel, final boolean isOEColorScaleType) { JPanel dialogPane = new JPanel(); dialogPane.setBorder(new EmptyBorder(12, 12, 12, 12)); dialogPane.setLayout(new BorderLayout()); JPanel titlePanel = new JPanel(); titlePanel.setLayout(new FlowLayout(FlowLayout.LEFT, 5, 25)); dialogPane.add(titlePanel, BorderLayout.NORTH); JLabel titleLabel = new JLabel("Set color slider control range"); if (isOEColorScaleType) { titleLabel.setText("Set log-scaled color slider control range"); } titlePanel.add(titleLabel); JPanel contentPanel = new JPanel(); contentPanel.setLayout(new BoxLayout(contentPanel, BoxLayout.Y_AXIS)); Container contentPane = getContentPane(); contentPane.setLayout(new BorderLayout()); JPanel minInfoEntryPanel = new JPanel(); minInfoEntryPanel.setLayout(new FlowLayout(FlowLayout.LEFT)); minInfoEntryPanel.add(minTextLabel); setDimension(minimumField); minInfoEntryPanel.add(minimumField); minInfoEntryPanel.add(lowerValTextLabel); setDimension(lowerField); minInfoEntryPanel.add(lowerField); if (isOEColorScaleType) { minimumField.setEnabled(false); } contentPanel.add(minInfoEntryPanel); JPanel maxInfoEntryPanel = new JPanel(new FlowLayout(FlowLayout.LEADING)); maxInfoEntryPanel.add(maxTextLabel); setDimension(maximumField); maxInfoEntryPanel.add(maximumField); maximumField.addFocusListener(new FocusListener() { @Override public void focusGained(FocusEvent focusEvent) { //To change body of implemented methods use File | Settings | File Templates. } @Override public void focusLost(FocusEvent focusEvent) { if (isOEColorScaleType) { double max; try { max = df2.parse(maximumField.getText()).doubleValue(); } catch (ParseException error) { return; } minimumField.setText(df2.format(-max)); } } }); maxInfoEntryPanel.add(higherValTextLabel); setDimension(upperField); maxInfoEntryPanel.add(upperField); upperField.addFocusListener(new FocusListener() { @Override public void focusGained(FocusEvent focusEvent) { //To change body of implemented methods use File | Settings | File Templates. } @Override public void focusLost(FocusEvent focusEvent) { if (isOEColorScaleType) { double max; try { max = df2.parse(upperField.getText()).doubleValue(); } catch (ParseException error) { return; } lowerField.setText(df2.format(-max)); } } }); contentPanel.add(maxInfoEntryPanel); dialogPane.add(contentPanel, BorderLayout.CENTER); JPanel buttonBar = new JPanel(new GridBagLayout()); buttonBar.setBorder(new EmptyBorder(12, 0, 0, 0)); ((GridBagLayout) buttonBar.getLayout()).columnWidths = new int[]{0, 85, 80}; ((GridBagLayout) buttonBar.getLayout()).columnWeights = new double[]{1.0, 0.0, 0.0}; //---- okButton ---- JButton okButton = new JButton("OK"); okButton.addActionListener(new ActionListener() { @Override public void actionPerformed(ActionEvent e) { okButtonActionPerformed(e, superAdapter, colorRangePanel, isOEColorScaleType); } }); buttonBar.add(okButton, new GridBagConstraints(1, 0, 1, 1, 0.0, 0.0, GridBagConstraints.CENTER, GridBagConstraints.BOTH, new Insets(0, 0, 0, 5), 0, 0)); JButton cancelButton = new JButton("Cancel"); cancelButton.addActionListener(new ActionListener() { @Override public void actionPerformed(ActionEvent e) { colorRangePanel.setColorRangeSliderVisible(true, superAdapter); if (!superAdapter.getMainViewPanel().setResolutionSliderVisible(true, superAdapter)) { System.err.println("Something went wrong"); } setVisible(false); } }); buttonBar.add(cancelButton, new GridBagConstraints(2, 0, 1, 1, 0.0, 0.0, GridBagConstraints.CENTER, GridBagConstraints.BOTH, new Insets(0, 0, 0, 0), 0, 0)); dialogPane.add(buttonBar, BorderLayout.SOUTH); contentPane.add(dialogPane, BorderLayout.CENTER); pack(); setLocationRelativeTo(getOwner()); } private void setDimension(JTextField field) { field.setMaximumSize(new Dimension(100, 20)); field.setMinimumSize(new Dimension(100, 20)); field.setPreferredSize(new Dimension(100, 20)); } private void okButtonActionPerformed(ActionEvent e, SuperAdapter superAdapter, JColorRangePanel colorRangePanel, boolean isOEColorScaleType) { double max = 0, min = 0; double lower = 0, upper = 0; try { if (isOEColorScaleType) { max = df2.parse(maximumField.getText()).doubleValue(); //upper = df2.parse(upperField.getText()).doubleValue(); } max = df2.parse(maximumField.getText()).doubleValue(); min = df2.parse(minimumField.getText()).doubleValue(); upper = df2.parse(upperField.getText()).doubleValue(); lower = df2.parse(lowerField.getText()).doubleValue(); } catch (ParseException error) { JOptionPane.showMessageDialog(this, "Must enter a number", "Error", JOptionPane.ERROR_MESSAGE); return; } if (max <= min || lower < min || upper <= min || upper <= lower || max <= lower || max < upper) { JOptionPane.showMessageDialog(this, "Values not appropriate", "Error", JOptionPane.ERROR_MESSAGE); return; } int iMax = (int) max; int iLower = (int) lower; int iUpper = (int) upper; if (isOEColorScaleType) { colorRangePanel.updateRatioColorSlider(superAdapter.getHiC(), iMax, iUpper); } else { colorRangePanel.updateColorSlider(superAdapter.getHiC(), iLower, iUpper, iMax); } colorRangePanel.setColorRangeSliderVisible(true, superAdapter); if (!superAdapter.getMainViewPanel().setResolutionSliderVisible(true, superAdapter)) { System.err.println("Error encountered 12134"); } setVisible(false); } } ================================================ FILE: src/juicebox/mapcolorui/ColorScaleHandler.java ================================================ /* * The MIT License (MIT) * * Copyright (c) 2011-2021 Broad Institute, Aiden Lab, Rice University, Baylor College of Medicine * * Permission is hereby granted, free of charge, to any person obtaining a copy * of this software and associated documentation files (the "Software"), to deal * in the Software without restriction, including without limitation the rights * to use, copy, modify, merge, publish, distribute, sublicense, and/or sell * copies of the Software, and to permit persons to whom the Software is * furnished to do so, subject to the following conditions: * * The above copyright notice and this permission notice shall be included in * all copies or substantial portions of the Software. * * THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR * IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, * FITNESS FOR A PARTICULAR PURPOSE AND NON-INFRINGEMENT. IN NO EVENT SHALL THE * AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER * LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, * OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN * THE SOFTWARE. */ package juicebox.mapcolorui; import juicebox.HiCGlobals; import juicebox.data.Block; import juicebox.data.ContactRecord; import juicebox.gui.SuperAdapter; import juicebox.matrix.BasicMatrix; import juicebox.windowui.MatrixType; import org.apache.commons.math3.stat.descriptive.DescriptiveStatistics; import org.broad.igv.renderer.ColorScale; import org.broad.igv.renderer.ContinuousColorScale; import java.awt.*; import java.util.HashMap; import java.util.List; import java.util.Map; public class ColorScaleHandler { private final PearsonColorScale pearsonColorScale = new PearsonColorScale(); private final Map observedColorScaleMap = new HashMap<>(); private final Map ratioColorScaleMap = new HashMap<>(); public static Color HIC_MAP_COLOR = Color.RED; public PearsonColorScale getPearsonColorScale() { return pearsonColorScale; } public void reset() { observedColorScaleMap.clear(); ratioColorScaleMap.clear(); } public Color getDenseMatrixColor(String key, float score, PearsonColorScale pearsonColorScale, ColorScale genericColorScale) { Color color; if (Float.isNaN(score) || Float.isInfinite(score)) { color = Color.gray; } else { if (pearsonColorScale != null) { color = score == 0 ? Color.black : pearsonColorScale.getColor(key, score); } else { color = genericColorScale.getColor(score); } } return color; } public void setNewDisplayRange(MatrixType displayOption, double min, double max, String key) { if (MatrixType.isOEColorScaleType(displayOption)) { OEColorScale oeColorScale = ratioColorScaleMap.get(key); if (oeColorScale == null) { oeColorScale = new OEColorScale(displayOption); ratioColorScaleMap.put(key, oeColorScale); } oeColorScale.setThreshold(max); } else { ContinuousColorScale observedColorScale = observedColorScaleMap.get(key); if (observedColorScale == null) { if (HiCGlobals.isDarkulaModeEnabled) { observedColorScale = new ContinuousColorScale(min, max, Color.black, HIC_MAP_COLOR); } else { observedColorScale = new ContinuousColorScale(min, max, Color.white, HIC_MAP_COLOR); } observedColorScaleMap.put(key, observedColorScale); } observedColorScale.setNegEnd(min); observedColorScale.setPosEnd(max); } } public ColorScale getColorScale(String key, MatrixType displayOption, boolean isWholeGenome, List blocks, List ctrlBlocks, float max) { if (blocks.isEmpty()) { return getColorScale(key, displayOption, isWholeGenome, ctrlBlocks, max); } else { return getColorScale(key, displayOption, isWholeGenome, blocks, max); } } public ColorScale getColorScale(String key, MatrixType displayOption, boolean wholeGenome, List blocks, float givenMax) { if (MatrixType.isOEColorScaleType(displayOption)) { OEColorScale oeColorScale = ratioColorScaleMap.get(key); if (oeColorScale == null) { oeColorScale = new OEColorScale(displayOption); ratioColorScaleMap.put(key, oeColorScale); } return oeColorScale; } else { //todo: why is the key flicking between resolutions when rendering a switch from "whole genome" to chromosome view? ContinuousColorScale observedColorScale = observedColorScaleMap.get(key); if (observedColorScale == null) { double percentile = wholeGenome ? 99 : 95; float max = givenMax; if (blocks != null) { max = computePercentile(blocks, percentile); } //observedColorScale = new ContinuousColorScale(0, max, Color.white, Color.red); if (HiCGlobals.isDarkulaModeEnabled) { observedColorScale = new ContinuousColorScale(0, max, Color.black, HIC_MAP_COLOR); } else { observedColorScale = new ContinuousColorScale(0, max, Color.white, HIC_MAP_COLOR); } observedColorScaleMap.put(key, observedColorScale); //mainWindow.updateColorSlider(0, 2 * max, max); } return observedColorScale; } } public void updateColorSliderFromColorScale(SuperAdapter superAdapter, MatrixType displayOption, String key) { if (MatrixType.isOEColorScaleType(displayOption)) { OEColorScale oeColorScale = ratioColorScaleMap.get(key); if (oeColorScale == null) { oeColorScale = new OEColorScale(displayOption); ratioColorScaleMap.put(key, oeColorScale); } superAdapter.updateRatioColorSlider((int) oeColorScale.getMax(), oeColorScale.getThreshold()); } else { ContinuousColorScale observedColorScale = observedColorScaleMap.get(key); if ((observedColorScale != null)) { superAdapter.updateColorSlider(observedColorScale.getMinimum(), observedColorScale.getMaximum()); } } } public float computePercentile(List blocks, double p) { DescriptiveStatistics stats = new DescriptiveStatistics(); if (blocks != null) { for (Block b : blocks) { for (int i = 0; i < b.getContactRecords().size(); i += 10) { ContactRecord rec = b.getContactRecords().get(i); if (rec.getBinX() != rec.getBinY()) { // Filter diagonal stats.addValue(rec.getCounts()); } } } } return stats.getN() == 0 ? 1 : (float) stats.getPercentile(p); } public float computePercentile(BasicMatrix bm, double p) { DescriptiveStatistics stats = new DescriptiveStatistics(); for (int i = 0; i < bm.getRowDimension(); i++) { for (int j = i + 1; j < bm.getColumnDimension(); j++) { stats.addValue(bm.getEntry(i, j)); } } return stats.getN() == 0 ? 1 : (float) stats.getPercentile( p); } public float computePercentile(BasicMatrix bm1, BasicMatrix bm2, double percentile) { return computePercentile(bm1, percentile) + computePercentile(bm2, percentile); } } ================================================ FILE: src/juicebox/mapcolorui/CursorRenderer.java ================================================ /* * The MIT License (MIT) * * Copyright (c) 2011-2021 Broad Institute, Aiden Lab, Rice University, Baylor College of Medicine * * Permission is hereby granted, free of charge, to any person obtaining a copy * of this software and associated documentation files (the "Software"), to deal * in the Software without restriction, including without limitation the rights * to use, copy, modify, merge, publish, distribute, sublicense, and/or sell * copies of the Software, and to permit persons to whom the Software is * furnished to do so, subject to the following conditions: * * The above copyright notice and this permission notice shall be included in * all copies or substantial portions of the Software. * * THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR * IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, * FITNESS FOR A PARTICULAR PURPOSE AND NON-INFRINGEMENT. IN NO EVENT SHALL THE * AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER * LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, * OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN * THE SOFTWARE. */ package juicebox.mapcolorui; import java.awt.*; public class CursorRenderer { private final HeatmapPanel parent; public CursorRenderer(HeatmapPanel heatmapPanel) { this.parent = heatmapPanel; } public void drawCursors(Graphics2D g, Point cursorPoint, Point diagonalCursorPoint, double binOriginX, double binOriginY, double scaleFactor, Color colorForRuler, double bRight, double bBottom) { if (cursorPoint != null) { g.setColor(colorForRuler); g.drawLine(cursorPoint.x, 0, cursorPoint.x, parent.getHeight()); g.drawLine(0, cursorPoint.y, parent.getWidth(), cursorPoint.y); } else if (diagonalCursorPoint != null) { g.setColor(colorForRuler); // quadrant 4 signs in plotting equal to quadrant 1 flipped across x in cartesian plane // y = -x + b // y + x = b int b = diagonalCursorPoint.x + diagonalCursorPoint.y; // at x = 0, y = b unless y exceeds height int pHeight = parent.getHeight(); int pWidth = parent.getWidth(); int leftEdgeY = Math.min(b, pHeight); int leftEdgeX = b - leftEdgeY; // at y = 0, x = b unless x exceeds width int rightEdgeX = Math.min(b, pWidth); int rightEdgeY = b - rightEdgeX; g.drawLine(leftEdgeX, leftEdgeY, rightEdgeX, rightEdgeY); // now we need to draw the perpendicular // line which intersects this at the mouse // m = -1, neg reciprocal is 1 // y2 = x2 + b2 // y2 - x2 = b2 int b2 = diagonalCursorPoint.y - diagonalCursorPoint.x; // at x2 = 0, y2 = b2 unless y less than 0 int leftEdgeY2 = Math.max(b2, 0); int leftEdgeX2 = leftEdgeY2 - b2; // at x2 = width, y2 = width+b2 unless x exceeds height int rightEdgeY2 = Math.min(pWidth + b2, pHeight); int rightEdgeX2 = rightEdgeY2 - b2; g.drawLine(leftEdgeX2, leftEdgeY2, rightEdgeX2, rightEdgeY2); // find a point on the diagonal (binx = biny) double binXYOrigin = Math.max(binOriginX, binOriginY); // ensure diagonal is in view if (binXYOrigin < bRight && binXYOrigin < bBottom) { int xDiag = (int) ((binXYOrigin - binOriginX) * scaleFactor); int yDiag = (int) ((binXYOrigin - binOriginY) * scaleFactor); // see if new point is above the line y2 = x2 + b2 // y' less than due to flipped topography int vertDisplacement = yDiag - (xDiag + b2); // displacement takes care of directionality of diagonal // being above/below is the second line we drew int b3 = b2 + (2 * vertDisplacement); // at x2 = 0, y2 = b2 unless y less than 0 int leftEdgeY3 = Math.max(b3, 0); int leftEdgeX3 = leftEdgeY3 - b3; // at x2 = width, y2 = width+b2 unless x exceeds height int rightEdgeY3 = Math.min(pWidth + b3, pHeight); int rightEdgeX3 = rightEdgeY3 - b3; g.drawLine(leftEdgeX3, leftEdgeY3, rightEdgeX3, rightEdgeY3); } } } } ================================================ FILE: src/juicebox/mapcolorui/Feature2DHandler.java ================================================ /* * The MIT License (MIT) * * Copyright (c) 2011-2020 Broad Institute, Aiden Lab, Rice University, Baylor College of Medicine * * Permission is hereby granted, free of charge, to any person obtaining a copy * of this software and associated documentation files (the "Software"), to deal * in the Software without restriction, including without limitation the rights * to use, copy, modify, merge, publish, distribute, sublicense, and/or sell * copies of the Software, and to permit persons to whom the Software is * furnished to do so, subject to the following conditions: * * The above copyright notice and this permission notice shall be included in * all copies or substantial portions of the Software. * * THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR * IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, * FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE * AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER * LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, * OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN * THE SOFTWARE. */ package juicebox.mapcolorui; import gnu.trove.procedure.TIntProcedure; import juicebox.data.ChromosomeHandler; import juicebox.data.MatrixZoomData; import juicebox.data.basics.Chromosome; import juicebox.gui.SuperAdapter; import juicebox.track.HiCGridAxis; import juicebox.track.feature.*; import net.sf.jsi.SpatialIndex; import net.sf.jsi.rtree.RTree; import java.awt.*; import java.util.ArrayList; import java.util.HashMap; import java.util.List; import java.util.Map; /** * Handles 2D features such as domains and peaks * Created by muhammadsaadshamim on 8/6/15. */ public class Feature2DHandler { //private static final float MAX_DIST_NEIGHBOR = 1000f; private static final int offsetPX = 4; public static int numberOfLoopsToFind = 1000; private final Map featureRtrees = new HashMap<>(); protected Feature2DList loopList; private boolean isTranslucentPlottingEnabled = false; private boolean sparseFeaturePlottingEnabled = false, isEnlargedPlottingEnabled = false; private boolean layerVisible = true; private String path = null; public Feature2DHandler() { loopList = new Feature2DList(); clearLists(); } public Feature2DHandler(Feature2DList inputList) { this(); setLoopList(inputList); } public Rectangle getRectangleFromFeature(HiCGridAxis xAxis, HiCGridAxis yAxis, Feature2D feature, double binOriginX, double binOriginY, double scaleFactor) { int binStart1 = xAxis.getBinNumberForGenomicPosition(feature.getStart1()); int binEnd1 = xAxis.getBinNumberForGenomicPosition(feature.getEnd1()); int binStart2 = yAxis.getBinNumberForGenomicPosition(feature.getStart2()); int binEnd2 = yAxis.getBinNumberForGenomicPosition(feature.getEnd2()); // option to draw larger rectangles for ease of viewing int offset = 0, offsetDoubled = 0; if (isEnlargedPlottingEnabled) { offset = offsetPX; offsetDoubled = offsetPX + offsetPX; } int x = (int) ((binStart1 - binOriginX) * scaleFactor) - offset; int y = (int) ((binStart2 - binOriginY) * scaleFactor) - offset; int w = (int) Math.max(1, scaleFactor * (binEnd1 - binStart1)) + offsetDoubled; int h = (int) Math.max(1, scaleFactor * (binEnd2 - binStart2)) + offsetDoubled; return new Rectangle(x, y, w, h); } public List convertFeaturesToFeaturePairs(AnnotationLayerHandler handler, List features, MatrixZoomData zd, double binOriginX, double binOriginY, double scale) { final List featurePairs = new ArrayList<>(); final HiCGridAxis xAxis = zd.getXGridAxis(); final HiCGridAxis yAxis = zd.getYGridAxis(); for (Feature2D feature : features) { featurePairs.add(new Feature2DGuiContainer( getRectangleFromFeature(xAxis, yAxis, feature, binOriginX, binOriginY, scale), feature, handler)); } return featurePairs; } protected void clearLists() { loopList = new Feature2DList(); layerVisible = true; featureRtrees.clear(); } public boolean getLayerVisibility() { return layerVisible; } public void setLayerVisibility(boolean showLoops) { this.layerVisible = showLoops; } protected void remakeRTree() { featureRtrees.clear(); loopList.processLists(new FeatureFunction() { @Override public void process(String key, List features) { SpatialIndex si = new RTree(); si.init(null); for (int i = 0; i < features.size(); i++) { Feature2D feature = features.get(i); si.add(new net.sf.jsi.Rectangle((float) feature.getStart1(), (float) feature.getStart2(), (float) feature.getEnd1(), (float) feature.getEnd2()), i); } featureRtrees.put(key, si); } }); //} } public resultContainer setLoopList(String path, ChromosomeHandler chromosomeHandler) { int numFeaturesAdded = 0; ArrayList attributes = null; Color color = null; if (this.path == null) { this.path = path; Feature2DList newList = Feature2DParser.loadFeatures(path, chromosomeHandler, true, null, false); numFeaturesAdded += newList.getNumTotalFeatures(); color = newList.extractSingleFeature().getColor(); attributes = newList.extractSingleFeature().getAttributeKeys(); loopList = newList; Map defaultAttributes = new HashMap<>(); //creates defaultAttributes map for (String attribute : attributes) { defaultAttributes.put(attribute, null); } loopList.setDefaultAttributes(defaultAttributes); } //loopLists.get(path).setVisible(true); remakeRTree(); return new resultContainer(numFeaturesAdded, color, attributes); } public void createNewMergedLoopLists(List lists) { for (Feature2DList list : lists) { if (list.getNumTotalFeatures() > 0) { addToLoopList(list, false); } } remakeRTree(); } public void setLoopList(Feature2DList feature2DList) { loopList = feature2DList; remakeRTree(); } private void addToLoopList(Feature2DList feature2DList, boolean remakeTree) { loopList.add(feature2DList); if (remakeTree) { remakeRTree(); } } public Feature2DList getAllVisibleLoops() { Feature2DList visibleLoopList = new Feature2DList(); if (layerVisible) { visibleLoopList = loopList; } return visibleLoopList; } public List getNearbyFeatures(MatrixZoomData zd, int chrIdx1, int chrIdx2, int x, int y, int n, final double binOriginX, final double binOriginY, final double scale) { final List foundFeatures = new ArrayList<>(); final String key = Feature2DList.getKey(chrIdx1, chrIdx2); final HiCGridAxis xAxis = zd.getXGridAxis(); final HiCGridAxis yAxis = zd.getYGridAxis(); if (featureRtrees.containsKey(key) && layerVisible) { if (sparseFeaturePlottingEnabled) { try { featureRtrees.get(key).nearestN( getGenomicPointFromXYCoordinate(x, y, xAxis, yAxis, binOriginX, binOriginY, scale), // the point for which we want to find nearby rectangles new TIntProcedure() { // a procedure whose execute() method will be called with the results public boolean execute(int i) { Feature2D feature = loopList.get(key).get(i); Rectangle rect = getRectangleFromFeature(xAxis, yAxis, feature, binOriginX, binOriginY, scale); if (!SuperAdapter.assemblyModeCurrentlyActive || (rect.getWidth() > 1 && rect.getHeight() > 1)) { foundFeatures.add(feature); } return true; // return true here to continue receiving results } }, n, // the number of nearby rectangles to find Float.MAX_VALUE // Don't bother searching further than this. MAX_VALUE means search everything ); } catch (Exception e) { System.err.println("Error encountered getting nearby features" + e.getLocalizedMessage()); } } else { for (Feature2D feature : loopList.get(key)) { Rectangle rect = getRectangleFromFeature(xAxis, yAxis, feature, binOriginX, binOriginY, scale); if (!SuperAdapter.assemblyModeCurrentlyActive || (rect.getWidth() > 1 && rect.getHeight() > 1)) { foundFeatures.add(feature); } } } } return foundFeatures; } public List getIntersectingFeatures(int chrIdx1, int chrIdx2, net.sf.jsi.Rectangle selectionWindow, boolean ignoreVisibility) { final List foundFeatures = new ArrayList<>(); final String key = Feature2DList.getKey(chrIdx1, chrIdx2); if (layerVisible || ignoreVisibility) { if (featureRtrees.containsKey(key)) { try { featureRtrees.get(key).intersects( selectionWindow, new TIntProcedure() { // a procedure whose execute() method will be called with the results public boolean execute(int i) { Feature2D feature = loopList.get(key).get(i); foundFeatures.add(feature); return true; // return true here to continue receiving results } }); } catch (Exception e) { System.err.println("Error encountered getting intersecting features" + e.getLocalizedMessage()); } } else { System.err.println("returning all; didn't find " + key + " intersecting"); List features = loopList.get(key); if (features != null) foundFeatures.addAll(features); } } return foundFeatures; } public List getContainedFeatures(int chrIdx1, int chrIdx2, net.sf.jsi.Rectangle currentWindow) { final List foundFeatures = new ArrayList<>(); final String key = Feature2DList.getKey(chrIdx1, chrIdx2); if (featureRtrees.containsKey(key)) { featureRtrees.get(key).contains( currentWindow, // the window in which we want to find all rectangles new TIntProcedure() { // a procedure whose execute() method will be called with the results public boolean execute(int i) { Feature2D feature = loopList.get(key).get(i); //System.out.println(feature.getChr1() + "\t" + feature.getStart1() + "\t" + feature.getStart2()); foundFeatures.add(feature); return true; // return true here to continue receiving results } } ); } else { System.err.println("returning all; key " + key + " not found contained"); List features = loopList.get(key); if (features != null) foundFeatures.addAll(features); } return foundFeatures; } private net.sf.jsi.Point getGenomicPointFromXYCoordinate(double x, double y, HiCGridAxis xAxis, HiCGridAxis yAxis, double binOriginX, double binOriginY, double scale) { float x2 = (float) (((x / scale) + binOriginX) * xAxis.getBinSize()); float y2 = (float) (((y / scale) + binOriginY) * yAxis.getBinSize()); return new net.sf.jsi.Point(x2, y2); } public void setSparsePlottingEnabled(boolean status) { sparseFeaturePlottingEnabled = status; } public boolean getIsSparsePlottingEnabled() { return sparseFeaturePlottingEnabled; } public boolean getIsTransparent() { return isTranslucentPlottingEnabled; } public void setIsTransparent(boolean status) { isTranslucentPlottingEnabled = status; } public boolean getIsEnlarged() { return isEnlargedPlottingEnabled; } public void setIsEnlarged(boolean status) { isEnlargedPlottingEnabled = status; } public void setColorOfAllAnnotations(Color color) { loopList.setColor(color); } public Feature2DList getFeatureList() { return loopList; } public List getContainedFeatures(Chromosome chrom, int rectULX, int rectULY, int rectLRX, int rectLRY, int resolution) { net.sf.jsi.Rectangle currentWindow = new net.sf.jsi.Rectangle( rectULX * resolution, rectULY * resolution, rectLRX * resolution, rectLRY * resolution); return getContainedFeatures(chrom.getIndex(), chrom.getIndex(), currentWindow); } public class resultContainer { public final int n; public final Color color; final ArrayList attributes; resultContainer(int n, Color color, ArrayList attributes) { this.n = n; this.color = color; this.attributes = attributes; } } } ================================================ FILE: src/juicebox/mapcolorui/FeatureRenderer.java ================================================ /* * The MIT License (MIT) * * Copyright (c) 2011-2021 Broad Institute, Aiden Lab, Rice University, Baylor College of Medicine * * Permission is hereby granted, free of charge, to any person obtaining a copy * of this software and associated documentation files (the "Software"), to deal * in the Software without restriction, including without limitation the rights * to use, copy, modify, merge, publish, distribute, sublicense, and/or sell * copies of the Software, and to permit persons to whom the Software is * furnished to do so, subject to the following conditions: * * The above copyright notice and this permission notice shall be included in * all copies or substantial portions of the Software. * * THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR * IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, * FITNESS FOR A PARTICULAR PURPOSE AND NON-INFRINGEMENT. IN NO EVENT SHALL THE * AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER * LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, * OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN * THE SOFTWARE. */ package juicebox.mapcolorui; import juicebox.data.HiCFileTools; import juicebox.data.MatrixZoomData; import juicebox.track.HiCGridAxis; import juicebox.track.feature.AnnotationLayerHandler; import juicebox.track.feature.Feature2D; import java.awt.*; import java.util.List; /** * Created by muhammadsaadshamim on 6/4/15. */ public class FeatureRenderer { public static final Color HIGHLIGHT_COLOR = Color.BLACK; public static void render(Graphics2D g2, AnnotationLayerHandler annotationHandler, List loops, MatrixZoomData zd, double binOriginX, double binOriginY, double scaleFactor, List highlightedFeatures, boolean showFeatureHighlight, int maxWidth, int maxHeight) { if (annotationHandler.getLineStyle() == LineStyle.DASHED) { Stroke dashed = new BasicStroke(1, BasicStroke.CAP_BUTT, BasicStroke.JOIN_BEVEL, 0, new float[]{1}, 0); g2.setStroke(dashed); } Feature2DHandler feature2DHandler = annotationHandler.getFeatureHandler(); PlottingOption enablePlottingOption = annotationHandler.getPlottingStyle(); // Note: we're assuming feature.chr1 == zd.chr1, and that chr1 is on x-axis HiCGridAxis xAxis = zd.getXGridAxis(); HiCGridAxis yAxis = zd.getYGridAxis(); if (loops != null) { for (Feature2D feature : loops) { if (!feature.isOnDiagonal()) { if (feature.isInLowerLeft()) { if (enablePlottingOption == PlottingOption.ONLY_UPPER_RIGHT) { continue; } } else if (feature.isInUpperRight()) { if (enablePlottingOption == PlottingOption.ONLY_LOWER_LEFT) { continue; } } } if (feature2DHandler.getIsTransparent()) { g2.setColor(feature.getTranslucentColor()); } else { g2.setColor(feature.getColor()); } Rectangle rect = feature2DHandler.getRectangleFromFeature(xAxis, yAxis, feature, binOriginX, binOriginY, scaleFactor); int x = (int) rect.getX(); int y = (int) rect.getY(); int w = (int) rect.getWidth(); int h = (int) rect.getHeight(); if (feature.isOnDiagonal()) { // contact domains if (enablePlottingOption == PlottingOption.ONLY_LOWER_LEFT) { plotInLowerLeft(g2, x, y, w, h); } else if (enablePlottingOption == PlottingOption.ONLY_UPPER_RIGHT) { plotInUpperRight(g2, x, y, w, h); } else if (enablePlottingOption == PlottingOption.EVERYTHING) { plotSimple(g2, x, y, w, h); } } else { plotSimple(g2, x, y, w, h); } } } if (highlightedFeatures != null && highlightedFeatures.size() != 0 && showFeatureHighlight) { g2.setColor(highlightedFeatures.get(0).getColor()); for (Feature2D highlightedFeature : highlightedFeatures) { int binStart1 = xAxis.getBinNumberForGenomicPosition(highlightedFeature.getStart1()); int binEnd1 = xAxis.getBinNumberForGenomicPosition(highlightedFeature.getEnd1()); int binStart2 = yAxis.getBinNumberForGenomicPosition(highlightedFeature.getStart2()); int binEnd2 = yAxis.getBinNumberForGenomicPosition(highlightedFeature.getEnd2()); g2.setColor(HIGHLIGHT_COLOR); if (HiCFileTools.equivalentChromosome(highlightedFeature.getChr1(), zd.getChr1())) { int x = (int) ((binStart1 - binOriginX) * scaleFactor); int h = (int) Math.max(1, scaleFactor * (binEnd1 - binStart1)); g2.drawLine(x, 0, x, maxHeight); g2.drawLine(x + h, 0, x + h, maxHeight); } if (HiCFileTools.equivalentChromosome(highlightedFeature.getChr2(), zd.getChr2())) { int y = (int) ((binStart2 - binOriginY) * scaleFactor); int w = (int) Math.max(1, scaleFactor * (binEnd2 - binStart2)); g2.drawLine(0, y, maxWidth, y); g2.drawLine(0, y + w, maxWidth, y + w); } } } } private static void plotSimple(Graphics2D g2, int x, int y, int w, int h) { g2.drawRect(x, y, w, h); if (w > 5) { g2.drawRect(x + 1, y + 1, w - 2, h - 2); } else { g2.drawRect(x - 1, y - 1, w + 2, h + 2); } } private static void plotInUpperRight(Graphics2D g2, int x, int y, int w, int h) { g2.drawLine(x, y, x + w, y); g2.drawLine(x + w, y, x + w, y + h); if (w > 5) { g2.drawLine(x + 1, y + 1, x + w + 1, y + 1); g2.drawLine(x + w + 1, y + 1, x + w + 1, y + h - 1); } } private static void plotInLowerLeft(Graphics2D g2, int x, int y, int w, int h) { g2.drawLine(x, y, x, y + h); g2.drawLine(x, y + h, x + w, y + h); if (w > 5) { g2.drawLine(x + 1, y + 1, x + 1, y + h + 1); g2.drawLine(x + 1, y + h + 1, x + w + 1, y + h + 1); } } public static PlottingOption getNextState(PlottingOption state) { if (state == PlottingOption.ONLY_LOWER_LEFT) { return FeatureRenderer.PlottingOption.ONLY_UPPER_RIGHT; } else if (state == PlottingOption.ONLY_UPPER_RIGHT) { return FeatureRenderer.PlottingOption.EVERYTHING; } else if (state == PlottingOption.EVERYTHING) { return FeatureRenderer.PlottingOption.ONLY_LOWER_LEFT; } return FeatureRenderer.PlottingOption.EVERYTHING; } public enum PlottingOption {ONLY_LOWER_LEFT, ONLY_UPPER_RIGHT, EVERYTHING} public enum LineStyle {DASHED, SOLID} } ================================================ FILE: src/juicebox/mapcolorui/GeneralTileManager.java ================================================ /* * The MIT License (MIT) * * Copyright (c) 2011-2021 Broad Institute, Aiden Lab, Rice University, Baylor College of Medicine * * Permission is hereby granted, free of charge, to any person obtaining a copy * of this software and associated documentation files (the "Software"), to deal * in the Software without restriction, including without limitation the rights * to use, copy, modify, merge, publish, distribute, sublicense, and/or sell * copies of the Software, and to permit persons to whom the Software is * furnished to do so, subject to the following conditions: * * The above copyright notice and this permission notice shall be included in * all copies or substantial portions of the Software. * * THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR * IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, * FITNESS FOR A PARTICULAR PURPOSE AND NON-INFRINGEMENT. IN NO EVENT SHALL THE * AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER * LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, * OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN * THE SOFTWARE. */ package juicebox.mapcolorui; import juicebox.HiC; import juicebox.HiCGlobals; import juicebox.data.MatrixZoomData; import juicebox.gui.SuperAdapter; import juicebox.windowui.MatrixType; import juicebox.windowui.NormalizationType; import javax.swing.*; import java.awt.*; public class GeneralTileManager { private static final int imageTileWidth = 500; private final HiCMapTileManager mapTileManager; public GeneralTileManager(ColorScaleHandler colorScaleHandler) { mapTileManager = new HiCMapTileManager(colorScaleHandler); } public boolean renderHiCTiles(HeatmapRenderer renderer, double binOriginX, double binOriginY, double bRight, double bBottom, MatrixZoomData zd, MatrixZoomData controlZd, double scaleFactor, Rectangle bounds, HiC hic, JComponent parent, SuperAdapter superAdapter) { boolean allTilesNull = true; MatrixType displayOption = hic.getDisplayOption(); NormalizationType observedNormalizationType = hic.getObsNormalizationType(); NormalizationType controlNormalizationType = hic.getControlNormalizationType(); // tile numbers int tLeft = (int) (binOriginX / imageTileWidth); int tRight = (int) Math.ceil(bRight / imageTileWidth); int tTop = (int) (binOriginY / imageTileWidth); int tBottom = (int) Math.ceil(bBottom / imageTileWidth); for (int tileRow = tTop; tileRow <= tBottom; tileRow++) { for (int tileColumn = tLeft; tileColumn <= tRight; tileColumn++) { ImageTile tile = null; try { tile = mapTileManager.getImageTile(zd, controlZd, tileRow, tileColumn, displayOption, observedNormalizationType, controlNormalizationType, hic, parent); } catch (Exception e) { System.err.println(e.getMessage()); } if (tile != null) { allTilesNull = false; int imageWidth = tile.image.getWidth(null); int imageHeight = tile.image.getHeight(null); int xSrc0 = 0; int xSrc1 = imageWidth; int ySrc0 = 0; int ySrc1 = imageHeight; int xDest0 = (int) ((tile.bLeft - binOriginX) * scaleFactor); int xDest1 = (int) ((tile.bLeft + imageWidth - binOriginX) * scaleFactor); int yDest0 = (int) ((tile.bTop - binOriginY) * scaleFactor); int yDest1 = (int) ((tile.bTop + imageHeight - binOriginY) * scaleFactor); // Trim off edges that are out of view -- take care if you attempt to simplify or rearrange this, // its easy to introduce alias and round-off errors due to the int casts. I suggest leaving it alone. final int screenRight = bounds.x + bounds.width; final int screenBottom = bounds.y + bounds.height; if (xDest0 < 0) { int leftExcess = (int) (-xDest0 / scaleFactor); xSrc0 += leftExcess; xDest0 = (int) ((tile.bLeft - binOriginX + leftExcess) * scaleFactor); } if (xDest1 > screenRight) { int rightExcess = (int) ((xDest1 - screenRight) / scaleFactor); xSrc1 -= rightExcess; xDest1 = (int) ((tile.bLeft + imageWidth - binOriginX - rightExcess) * scaleFactor); } if (yDest0 < 0) { int topExcess = (int) (-yDest0 / scaleFactor); ySrc0 += topExcess; yDest0 = (int) ((tile.bTop - binOriginY + topExcess) * scaleFactor); } if (yDest1 > screenBottom) { int bottomExcess = (int) ((yDest1 - screenBottom) / scaleFactor); ySrc1 -= bottomExcess; yDest1 = (int) ((tile.bTop + imageHeight - binOriginY - bottomExcess) * scaleFactor); } try { if (xDest0 < xDest1 && yDest0 < yDest1 && xSrc0 < xSrc1 && ySrc0 < ySrc1) { // basically ensure that we're not trying to plot empty space // also for some reason we have negative indices sometimes?? renderer.drawImage(tile.image, xDest0, yDest0, xDest1, yDest1, xSrc0, ySrc0, xSrc1, ySrc1); } } catch (Exception e) { // handling for svg export try { if (HiCGlobals.printVerboseComments) { System.out.println("svg plotting for\n" + xDest0 + "_" + yDest0 + "_" + xDest1 + "_" + yDest1 + "_" + xSrc0 + "_" + ySrc0 + "_" + xSrc1 + "_" + ySrc1); } bypassTileAndDirectlyDrawOnGraphics(renderer, zd, tileRow, tileColumn, displayOption, observedNormalizationType, controlNormalizationType, xDest0, yDest0, xDest1, yDest1, xSrc0, ySrc0, xSrc1, ySrc1, hic); //processedExportRegions.add(newKey); } catch (Exception e2) { System.err.println("SVG export did not work"); } } if (HiCGlobals.displayTiles) { renderer.drawRect(xDest0, yDest0, (xDest1 - xDest0), (yDest1 - yDest0)); } } } } //In case of change to map settings, get map color limits and update slider: //TODO: || might not catch all changed at once, if more then one parameter changed... if (hic.testZoomChanged() || hic.testDisplayOptionChanged() || hic.testNormalizationTypeChanged()) { //In case render is called as a result of zoom change event, check if //We need to update slider with map range: String cacheKey = HeatmapRenderer.getColorScaleCacheKey(zd, displayOption, observedNormalizationType, controlNormalizationType); mapTileManager.updateColorSliderFromColorScale(superAdapter, displayOption, cacheKey); //debrisFeatureSize = (int) (debrisFeatureSize * scaleFactor); } return allTilesNull; } private void bypassTileAndDirectlyDrawOnGraphics(HeatmapRenderer renderer, MatrixZoomData zd, int tileRow, int tileColumn, MatrixType displayOption, NormalizationType observedNormalizationType, NormalizationType controlNormalizationType, int xDest0, int yDest0, int xDest1, int yDest1, int xSrc0, int ySrc0, int xSrc1, int ySrc1, HiC hic) { // Image size can be smaller than tile width when zoomed out, or near the edges. long maxBinCountX = zd.getXGridAxis().getBinCount(); long maxBinCountY = zd.getYGridAxis().getBinCount(); if (maxBinCountX < 0 || maxBinCountY < 0) return; final int bx0 = tileColumn * imageTileWidth; final int by0 = tileRow * imageTileWidth; // set new origins renderer.translate(xDest0, yDest0); // scale drawing appropriately double widthDest = xDest1 - xDest0; double heightDest = yDest1 - yDest0; int widthSrc = xSrc1 - xSrc0; int heightSrc = ySrc1 - ySrc0; double horizontalScaling = widthDest / widthSrc; double verticalScaling = heightDest / heightSrc; renderer.scale(horizontalScaling, verticalScaling); final int bx0Offset = bx0 + xSrc0; final int by0Offset = by0 + ySrc0; renderer.render(bx0Offset, by0Offset, widthSrc, heightSrc, zd, hic.getControlZd(), displayOption, observedNormalizationType, controlNormalizationType, hic.getExpectedValues(), hic.getExpectedControlValues(), false); renderer.scale(1, 1); renderer.translate(0, 0); } public void clearTileCache() { mapTileManager.clearTileCache(); } static class ImageTile { final int bLeft; final int bTop; final Image image; ImageTile(Image image, int bLeft, int py0) { this.bLeft = bLeft; this.bTop = py0; this.image = image; } } } ================================================ FILE: src/juicebox/mapcolorui/HeatmapClickListener.java ================================================ /* * The MIT License (MIT) * * Copyright (c) 2011-2021 Broad Institute, Aiden Lab, Rice University, Baylor College of Medicine * * Permission is hereby granted, free of charge, to any person obtaining a copy * of this software and associated documentation files (the "Software"), to deal * in the Software without restriction, including without limitation the rights * to use, copy, modify, merge, publish, distribute, sublicense, and/or sell * copies of the Software, and to permit persons to whom the Software is * furnished to do so, subject to the following conditions: * * The above copyright notice and this permission notice shall be included in * all copies or substantial portions of the Software. * * THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR * IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, * FITNESS FOR A PARTICULAR PURPOSE AND NON-INFRINGEMENT. IN NO EVENT SHALL THE * AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER * LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, * OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN * THE SOFTWARE. */ package juicebox.mapcolorui; import juicebox.HiC; import juicebox.HiCGlobals; import juicebox.MainWindow; import juicebox.assembly.AssemblyOperationExecutor; import juicebox.data.basics.Chromosome; import juicebox.gui.SuperAdapter; import juicebox.track.feature.Feature2D; import juicebox.track.feature.Feature2DGuiContainer; import juicebox.windowui.HiCZoom; import javax.swing.*; import java.awt.*; import java.awt.event.ActionEvent; import java.awt.event.ActionListener; import java.awt.event.MouseAdapter; import java.awt.event.MouseEvent; import java.util.List; /** * Created by muhammadsaadshamim on 8/9/17. */ class HeatmapClickListener extends MouseAdapter implements ActionListener { private static final int clickDelay = 400; private final HeatmapPanel heatmapPanel; private final Timer clickTimer; private MouseEvent lastMouseEvent; private Feature2DGuiContainer currentUpstreamFeature = null; private Feature2DGuiContainer currentDownstreamFeature = null; HeatmapClickListener(HeatmapPanel heatmapPanel) { clickTimer = new Timer(clickDelay, this); this.heatmapPanel = heatmapPanel; } @Override public void actionPerformed(ActionEvent e) { clickTimer.stop(); singleClick(lastMouseEvent); } @Override public void mouseClicked(MouseEvent e) { if (heatmapPanel.getHiC() == null) return; safeMouseClicked(e); } private void unsafeMouseClickSubActionA(final MouseEvent eF) { HiC hic = heatmapPanel.getHiC(); long[] chromosomeBoundaries = heatmapPanel.getChromosomeBoundaries(); double binX = hic.getXContext().getBinOrigin() + (eF.getX() / hic.getScaleFactor()); double binY = hic.getYContext().getBinOrigin() + (eF.getY() / hic.getScaleFactor()); Chromosome xChrom = null; Chromosome yChrom = null; try { long xGenome = hic.getZd().getXGridAxis().getGenomicMid(binX); long yGenome = hic.getZd().getYGridAxis().getGenomicMid(binY); for (int i = 0; i < chromosomeBoundaries.length; i++) { if (xChrom == null && chromosomeBoundaries[i] > xGenome) { xChrom = hic.getChromosomeHandler().getChromosomeFromIndex(i + 1); } if (yChrom == null && chromosomeBoundaries[i] > yGenome) { yChrom = hic.getChromosomeHandler().getChromosomeFromIndex(i + 1); } } } catch (Exception ex) { // do nothing, leave chromosomes null } if (xChrom != null && yChrom != null) { heatmapPanel.unsafeSetSelectedChromosomes(xChrom, yChrom); } else { System.err.println("null chromosome " + xChrom + " - " + yChrom); } //Only if zoom is changed All->Chr: heatmapPanel.updateThumbnail(); } private void unsafeMouseClickSubActionB(double centerBinX, double centerBinY, HiCZoom newZoom) { HiC hic = heatmapPanel.getHiC(); try { final String chrXName = hic.getXContext().getChromosome().toString(); final String chrYName = hic.getYContext().getChromosome().toString(); final long xGenome = hic.getZd().getXGridAxis().getGenomicMid(centerBinX); final long yGenome = hic.getZd().getYGridAxis().getGenomicMid(centerBinY); hic.unsafeActuallySetZoomAndLocation(chrXName, chrYName, newZoom, xGenome, yGenome, -1, false, HiC.ZoomCallType.STANDARD, true, hic.isResolutionLocked() ? 1 : 0, true); } catch (Exception e) { e.printStackTrace(); } } private void safeMouseClicked(final MouseEvent eF) { HiC hic = heatmapPanel.getHiC(); if (!eF.isPopupTrigger() && eF.getButton() == MouseEvent.BUTTON1 && !eF.isControlDown()) { try { hic.getZd(); } catch (Exception e) { return; } if (eF.getClickCount() > 0) { lastMouseEvent = eF; if (clickTimer.isRunning()) { clickTimer.stop(); doubleClick(lastMouseEvent); } else { clickTimer.restart(); heatmapPanel.setPromptedAssemblyActionOnClick(heatmapPanel.getCurrentPromptedAssemblyAction()); currentUpstreamFeature = heatmapPanel.getCurrentUpstreamFeature(); currentDownstreamFeature = heatmapPanel.getCurrentDownstreamFeature(); } } } } private void singleClick(final MouseEvent lastMouseEvent) { HiC hic = heatmapPanel.getHiC(); MainWindow mainWindow = heatmapPanel.getMainWindow(); SuperAdapter superAdapter = heatmapPanel.getSuperAdapter(); if (hic.isWholeGenome()) { Runnable runnable = new Runnable() { public void run() { unsafeMouseClickSubActionA(lastMouseEvent); } }; mainWindow.executeLongRunningTask(runnable, "Mouse Click Set Chr"); } else { if (!lastMouseEvent.isShiftDown()) { List selectedFeatures = heatmapPanel.getSelectedFeatures(); HeatmapMouseHandler.PromptedAssemblyAction action = heatmapPanel.getPromptedAssemblyActionOnClick(); if (action == HeatmapMouseHandler.PromptedAssemblyAction.REGROUP) { AssemblyOperationExecutor.toggleGroup(superAdapter, currentUpstreamFeature.getFeature2D(), currentDownstreamFeature.getFeature2D()); heatmapPanel.repaint(); try { Robot bot = new Robot(); bot.mouseMove(MouseInfo.getPointerInfo().getLocation().x, MouseInfo.getPointerInfo().getLocation().y); } catch (AWTException e) { e.printStackTrace(); } } else if (action == HeatmapMouseHandler.PromptedAssemblyAction.PASTEBOTTOM) { heatmapPanel.moveSelectionToEnd(); // TODO fix this so that highlight moves with translated selection heatmapPanel.repaint(); // moveSelectionToEnd already handles removeSelection } else if (action == HeatmapMouseHandler.PromptedAssemblyAction.PASTETOP) { AssemblyOperationExecutor.moveSelection(superAdapter, selectedFeatures, null); removeAndRepaint(); // TODO fix this so that highlight moves with translated selection } else if (action == HeatmapMouseHandler.PromptedAssemblyAction.PASTE) { AssemblyOperationExecutor.moveSelection(superAdapter, selectedFeatures, currentUpstreamFeature.getFeature2D()); removeAndRepaint(); // TODO fix this so that highlight moves with translated selection } else if (action == HeatmapMouseHandler.PromptedAssemblyAction.INVERT) { AssemblyOperationExecutor.invertSelection(superAdapter, selectedFeatures); removeAndRepaint(); // TODO fix this so that highlight moves with translated selection } } } if (HiCGlobals.printVerboseComments) { try { superAdapter.getAssemblyStateTracker().getAssemblyHandler().toString(); } catch (Exception e) { System.err.println("Unable to print assembly state"); } } } private void removeAndRepaint() { heatmapPanel.removeSelection(); // TODO fix this so that highlight moves with translated selection heatmapPanel.repaint(); } private void doubleClick(MouseEvent lastMouseEvent) { HiC hic = heatmapPanel.getHiC(); MainWindow mainWindow = heatmapPanel.getMainWindow(); // Double click, zoom and center on click location try { // in all-by-all mimic single click if (hic.isWholeGenome()) { singleClick(lastMouseEvent); return; } final HiCZoom currentZoom = hic.getZd().getZoom(); final HiCZoom nextPotentialZoom = hic.getDataset().getNextZoom(currentZoom, !lastMouseEvent.isAltDown()); final HiCZoom newZoom = hic.isResolutionLocked() || hic.isPearsonEdgeCaseEncountered(nextPotentialZoom) ? currentZoom : nextPotentialZoom; // If newZoom == currentZoom adjust scale factor (no change in resolution) final double centerBinX = hic.getXContext().getBinOrigin() + (lastMouseEvent.getX() / hic.getScaleFactor()); final double centerBinY = hic.getYContext().getBinOrigin() + (lastMouseEvent.getY() / hic.getScaleFactor()); // perform superzoom / normal zoom / reverse-superzoom if (newZoom.equals(currentZoom)) { double mult = lastMouseEvent.isAltDown() ? 0.5 : 2.0; // if newScaleFactor > 1.0, performs superzoom // if newScaleFactor = 1.0, performs normal zoom // if newScaleFactor < 1.0, performs reverse superzoom double newScaleFactor = Math.max(0.0, hic.getScaleFactor() * mult); String chrXName = hic.getXContext().getChromosome().getName(); String chrYName = hic.getYContext().getChromosome().getName(); int genomeX = Math.max(0, (int) (centerBinX) * newZoom.getBinSize()); int genomeY = Math.max(0, (int) (centerBinY) * newZoom.getBinSize()); hic.unsafeActuallySetZoomAndLocation(chrXName, chrYName, newZoom, genomeX, genomeY, newScaleFactor, true, HiC.ZoomCallType.STANDARD, true, hic.isResolutionLocked() ? 1 : 0, true); } else { Runnable runnable = new Runnable() { public void run() { unsafeMouseClickSubActionB(centerBinX, centerBinY, newZoom); } }; mainWindow.executeLongRunningTask(runnable, "Mouse Click Zoom"); } } catch (Exception e) { e.printStackTrace(); } } } ================================================ FILE: src/juicebox/mapcolorui/HeatmapMouseHandler.java ================================================ /* * The MIT License (MIT) * * Copyright (c) 2011-2022 Broad Institute, Aiden Lab, Rice University, Baylor College of Medicine * * Permission is hereby granted, free of charge, to any person obtaining a copy * of this software and associated documentation files (the "Software"), to deal * in the Software without restriction, including without limitation the rights * to use, copy, modify, merge, publish, distribute, sublicense, and/or sell * copies of the Software, and to permit persons to whom the Software is * furnished to do so, subject to the following conditions: * * The above copyright notice and this permission notice shall be included in * all copies or substantial portions of the Software. * * THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR * IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, * FITNESS FOR A PARTICULAR PURPOSE AND NON-INFRINGEMENT. IN NO EVENT SHALL THE * AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER * LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, * OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN * THE SOFTWARE. */ package juicebox.mapcolorui; import com.jidesoft.swing.JidePopupMenu; import juicebox.HiC; import juicebox.HiCGlobals; import juicebox.MainWindow; import juicebox.assembly.AssemblyOperationExecutor; import juicebox.assembly.AssemblyScaffoldHandler; import juicebox.assembly.Scaffold; import juicebox.data.ChromosomeHandler; import juicebox.data.ExpectedValueFunction; import juicebox.data.Matrix; import juicebox.data.MatrixZoomData; import juicebox.data.basics.Chromosome; import juicebox.gui.SuperAdapter; import juicebox.track.HiCFragmentAxis; import juicebox.track.HiCGridAxis; import juicebox.track.feature.AnnotationLayer; import juicebox.track.feature.AnnotationLayerHandler; import juicebox.track.feature.Feature2D; import juicebox.track.feature.Feature2DGuiContainer; import juicebox.windowui.EditFeatureAttributesDialog; import juicebox.windowui.MatrixType; import org.broad.igv.util.Pair; import javax.swing.*; import java.awt.*; import java.awt.datatransfer.Clipboard; import java.awt.datatransfer.StringSelection; import java.awt.event.*; import java.text.NumberFormat; import java.util.ArrayList; import java.util.Collections; import java.util.List; import static java.awt.Toolkit.getDefaultToolkit; public class HeatmapMouseHandler extends MouseAdapter { public static final int clickDelay = 500; private static final int clickLong = 400; private final List highlightedFeatures = new ArrayList<>(); private final List selectedSuperscaffolds = new ArrayList<>(); private final NumberFormat formatter = NumberFormat.getInstance(); private final int RESIZE_SNAP = 5; private final HiC hic; private final SuperAdapter superAdapter; private final HeatmapPanel parent; private final List selectedFeatures = new ArrayList<>(); private final List allFeaturePairs = new ArrayList<>(); private final List allMainFeaturePairs = new ArrayList<>(); private final List allEditFeaturePairs = new ArrayList<>(); DragMode dragMode = DragMode.NONE; double startTime, endTime; private Robot heatmapMouseBot; private PromptedAssemblyAction currentPromptedAssemblyAction = PromptedAssemblyAction.NONE; private PromptedAssemblyAction promptedAssemblyActionOnClick = PromptedAssemblyAction.NONE; private Pair, Feature2D> preAdjustLoop = null; private boolean featureOptionMenuEnabled = false; private boolean firstAnnotation; private AdjustAnnotation adjustAnnotation = AdjustAnnotation.NONE; private Point lastMousePoint; private Point lastPressedMousePoint; private boolean straightEdgeEnabled = false, diagonalEdgeEnabled = false; private int debrisFeatureSize = RESIZE_SNAP; private Rectangle zoomRectangle; private Rectangle annotateRectangle; private Feature2DGuiContainer currentFeature = null; private boolean changedSize = false; private Feature2DGuiContainer currentUpstreamFeature = null; private Feature2DGuiContainer currentDownstreamFeature = null; private boolean showFeatureHighlight = true; private boolean activelyEditingAssembly = false; private Feature2D debrisFeature = null; private Feature2D tempSelectedGroup = null; public HeatmapMouseHandler(HiC hic, SuperAdapter superAdapter, HeatmapPanel parent) { this.hic = hic; this.superAdapter = superAdapter; this.parent = parent; this.firstAnnotation = true; try { heatmapMouseBot = new Robot(); } catch (AWTException ignored) { } } public List getHighlightedFeature() { return highlightedFeatures; } public void eraseHighlightedFeatures() { highlightedFeatures.clear(); hic.setHighlightedFeatures(new ArrayList<>()); } public void clearSelectedFeatures() { selectedSuperscaffolds.clear(); updateSelectedFeatures(false); selectedFeatures.clear(); } public boolean getIsActivelyEditingAssembly() { return activelyEditingAssembly; } public void clearFeaturePairs() { allFeaturePairs.clear(); if (activelyEditingAssembly) { allMainFeaturePairs.clear(); allEditFeaturePairs.clear(); } } public boolean getShouldShowHighlight() { return showFeatureHighlight; } public void setActivelyEditingAssembly(boolean bool) { activelyEditingAssembly = bool; } private JidePopupMenu getPopupMenu(final int xMousePos, final int yMousePos) { JidePopupMenu menu = new JidePopupMenu(); if (SuperAdapter.assemblyModeCurrentlyActive) { getAssemblyPopupMenu(xMousePos, yMousePos, menu); menu.addSeparator(); } final JMenuItem miUndoZoom = new JMenuItem("Undo Zoom"); miUndoZoom.addActionListener(new ActionListener() { @Override public void actionPerformed(ActionEvent e) { hic.setCursorPoint(new Point(xMousePos, yMousePos)); hic.undoZoomAction(); } }); miUndoZoom.setEnabled(hic.getZoomActionTracker().validateUndoZoom()); menu.add(miUndoZoom); final JMenuItem miRedoZoom = new JMenuItem("Redo Zoom"); miRedoZoom.addActionListener(new ActionListener() { @Override public void actionPerformed(ActionEvent e) { hic.setCursorPoint(new Point(xMousePos, yMousePos)); hic.redoZoomAction(); } }); miRedoZoom.setEnabled(hic.getZoomActionTracker().validateRedoZoom()); menu.add(miRedoZoom); // add Jump to Diagonal menu items addJumpToDiagonalMenuItems(menu, xMousePos, yMousePos); final JCheckBoxMenuItem mi = new JCheckBoxMenuItem("Enable straight edge"); mi.setSelected(straightEdgeEnabled); mi.addActionListener(new ActionListener() { @Override public void actionPerformed(ActionEvent e) { if (mi.isSelected()) { straightEdgeEnabled = true; diagonalEdgeEnabled = false; parent.setCursor(Cursor.getPredefinedCursor(Cursor.CROSSHAIR_CURSOR)); } else { straightEdgeEnabled = false; hic.setCursorPoint(null); parent.setCursor(Cursor.getDefaultCursor()); parent.repaint(); superAdapter.repaintTrackPanels(); } } }); menu.add(mi); final JCheckBoxMenuItem miv2 = new JCheckBoxMenuItem("Enable diagonal edge"); miv2.setSelected(diagonalEdgeEnabled); miv2.addActionListener(new ActionListener() { @Override public void actionPerformed(ActionEvent e) { if (miv2.isSelected()) { straightEdgeEnabled = false; diagonalEdgeEnabled = true; parent.setCursor(Cursor.getPredefinedCursor(Cursor.CROSSHAIR_CURSOR)); } else { diagonalEdgeEnabled = false; hic.setDiagonalCursorPoint(null); parent.setCursor(Cursor.getDefaultCursor()); parent.repaint(); superAdapter.repaintTrackPanels(); } } }); menu.add(miv2); // internally, single sync = what we previously called sync final JMenuItem mi3 = new JMenuItem("Broadcast Single Sync"); mi3.addActionListener(new ActionListener() { @Override public void actionPerformed(ActionEvent e) { hic.broadcastLocation(); } }); // internally, continuous sync = what we used to call linked final JCheckBoxMenuItem mi4 = new JCheckBoxMenuItem("Broadcast Continuous Sync"); mi4.addActionListener(new ActionListener() { @Override public void actionPerformed(ActionEvent e) { final boolean isLinked = mi4.isSelected(); if (isLinked) { HiCGlobals.wasLinkedBeforeMousePress = false; hic.broadcastLocation(); } hic.setLinkedMode(isLinked); } }); final JCheckBoxMenuItem mi5 = new JCheckBoxMenuItem("Freeze hover text"); mi5.setSelected(!superAdapter.isTooltipAllowedToUpdated()); mi5.addActionListener(new ActionListener() { @Override public void actionPerformed(ActionEvent e) { superAdapter.toggleToolTipUpdates(!superAdapter.isTooltipAllowedToUpdated()); } }); final JMenuItem mi6 = new JMenuItem("Copy hover text to clipboard"); mi6.addActionListener(new ActionListener() { @Override public void actionPerformed(ActionEvent e) { StringSelection stringSelection = new StringSelection(superAdapter.getToolTip()); Clipboard clpbrd = getDefaultToolkit().getSystemClipboard(); clpbrd.setContents(stringSelection, null); } }); final JMenuItem mi7 = new JMenuItem("Copy top position to clipboard"); mi7.addActionListener(new ActionListener() { @Override public void actionPerformed(ActionEvent e) { StringSelection stringSelection = new StringSelection(hic.getXPosition()); superAdapter.setPositionChrTop(hic.getXPosition().concat(":").concat(String.valueOf(hic.getXContext().getZoom().getBinSize()))); superAdapter.setPositionChrLeft(hic.getYPosition().concat(":").concat(String.valueOf(hic.getYContext().getZoom().getBinSize()))); Clipboard clpbrd = getDefaultToolkit().getSystemClipboard(); clpbrd.setContents(stringSelection, null); } }); // TODO - can we remove this second option and just have a copy position to clipboard? Is this used? final JMenuItem mi8 = new JMenuItem("Copy left position to clipboard"); mi8.addActionListener(new ActionListener() { @Override public void actionPerformed(ActionEvent e) { StringSelection stringSelection = new StringSelection(hic.getYPosition()); superAdapter.setPositionChrTop(hic.getXPosition().concat(":").concat(String.valueOf(hic.getXContext().getZoom().getBinSize()))); superAdapter.setPositionChrLeft(hic.getYPosition().concat(":").concat(String.valueOf(hic.getYContext().getZoom().getBinSize()))); Clipboard clpbrd = getDefaultToolkit().getSystemClipboard(); clpbrd.setContents(stringSelection, null); } }); final JCheckBoxMenuItem mi85Highlight = new JCheckBoxMenuItem("Highlight"); mi85Highlight.addActionListener(new ActionListener() { @Override public void actionPerformed(ActionEvent e) { //highlightedFeatures.clear(); addHighlightedFeature(currentFeature.getFeature2D()); } }); final JCheckBoxMenuItem mi86Toggle = new JCheckBoxMenuItem("Toggle Highlight Visibility"); mi86Toggle.addActionListener(new ActionListener() { @Override public void actionPerformed(ActionEvent e) { featureOptionMenuEnabled = false; showFeatureHighlight = !showFeatureHighlight; hic.setShowFeatureHighlight(showFeatureHighlight); parent.repaint(); } }); final JMenuItem mi87Remove = new JMenuItem("Remove Highlight"); mi87Remove.addActionListener(new ActionListener() { @Override public void actionPerformed(ActionEvent e) { parent.removeHighlightedFeature(); } }); final JMenuItem mi9_c = new JMenuItem("Export data centered on pixel"); mi9_c.addActionListener(new ActionListener() { @Override public void actionPerformed(ActionEvent e) { try { hic.exportDataCenteredAboutRegion(xMousePos, yMousePos); } catch (Exception ee) { ee.printStackTrace(); } } }); final JCheckBoxMenuItem mi9_h = new JCheckBoxMenuItem("Generate Horizontal 1D Track"); mi9_h.addActionListener(new ActionListener() { @Override public void actionPerformed(ActionEvent e) { hic.generateTrackFromLocation(yMousePos, true); } }); final JCheckBoxMenuItem mi9_v = new JCheckBoxMenuItem("Generate Vertical 1D Track"); mi9_v.addActionListener(new ActionListener() { @Override public void actionPerformed(ActionEvent e) { hic.generateTrackFromLocation(xMousePos, false); } }); final JMenuItem mi10_1 = new JMenuItem("Change Color"); mi10_1.addActionListener(new ActionListener() { @Override public void actionPerformed(ActionEvent e) { featureOptionMenuEnabled = false; Pair featureCopy = new Pair<>(currentFeature.getRectangle(), currentFeature.getFeature2D()); parent.launchColorSelectionMenu(featureCopy); } }); final JMenuItem mi10_2 = new JMenuItem("Change Attributes"); mi10_2.addActionListener(new ActionListener() { @Override public void actionPerformed(ActionEvent e) { featureOptionMenuEnabled = false; new EditFeatureAttributesDialog(parent.getMainWindow(), currentFeature.getFeature2D(), superAdapter.getActiveLayerHandler().getAnnotationLayer()); } }); final JMenuItem mi10_3 = new JMenuItem("Delete"); mi10_3.addActionListener(new ActionListener() { @Override public void actionPerformed(ActionEvent e) { featureOptionMenuEnabled = false; Feature2D feature = currentFeature.getFeature2D(); int chr1Idx = hic.getXContext().getChromosome().getIndex(); int chr2Idx = hic.getYContext().getChromosome().getIndex(); try { superAdapter.getActiveLayerHandler().removeFromList(hic.getZd(), chr1Idx, chr2Idx, 0, 0, Feature2DHandler.numberOfLoopsToFind, hic.getXContext().getBinOrigin(), hic.getYContext().getBinOrigin(), hic.getScaleFactor(), feature); } catch (Exception ee) { System.err.println("Could not remove custom annotation"); } superAdapter.refresh(); } }); final JMenu configureFeatureMenu = new JMenu("Configure feature"); configureFeatureMenu.add(mi10_1); configureFeatureMenu.add(mi10_2); configureFeatureMenu.add(mi10_3); if (hic != null) { // menu.add(mi2); menu.add(mi3); mi4.setSelected(hic.isLinkedMode()); menu.add(mi4); menu.add(mi5); menu.add(mi6); menu.add(mi7); menu.add(mi8); if (!ChromosomeHandler.isAllByAll(hic.getXContext().getChromosome()) && MatrixType.isObservedOrControl(hic.getDisplayOption())) { menu.addSeparator(); menu.add(mi9_h); menu.add(mi9_v); menu.add(mi9_c); } boolean menuSeparatorNotAdded = true; if (highlightedFeatures.size() > 0) { menu.addSeparator(); menuSeparatorNotAdded = false; mi86Toggle.setSelected(showFeatureHighlight); menu.add(mi86Toggle); } if (currentFeature != null) {//mouseIsOverFeature featureOptionMenuEnabled = true; if (menuSeparatorNotAdded) { menu.addSeparator(); } if (highlightedFeatures.size() > 0) { if (!highlightedFeatures.contains(currentFeature.getFeature2D())) { configureFeatureMenu.add(mi85Highlight); menu.add(mi87Remove); } else { configureFeatureMenu.add(mi87Remove); } } else { configureFeatureMenu.add(mi85Highlight); } menu.add(configureFeatureMenu); } else if (highlightedFeatures.size() > 0) { menu.add(mi87Remove); } } return menu; } public Feature2D getDebrisFeature() { return debrisFeature; } public Feature2D getTempSelectedGroup() { return tempSelectedGroup; } public void setTempSelectedGroup(Feature2D feature2D) { tempSelectedGroup = feature2D; } public List getSelectedFeatures() { return selectedFeatures; } private void addHighlightedFeatures(List feature2DList) { highlightedFeatures.addAll(feature2DList); featureOptionMenuEnabled = false; showFeatureHighlight = true; hic.setShowFeatureHighlight(showFeatureHighlight); hic.setHighlightedFeatures(highlightedFeatures); superAdapter.repaintTrackPanels(); parent.repaint(); } private void updateSelectedFeatures(boolean status) { for (Feature2D feature2D : selectedFeatures) { feature2D.setSetIsSelectedColorUpdate(status); } } public void resetCurrentPromptedAssemblyAction() { currentPromptedAssemblyAction = HeatmapMouseHandler.PromptedAssemblyAction.NONE; } private String getFloatString(float value) { String valueString; if (Float.isNaN(value)) { valueString = "NaN"; } else if (value < 0.001) { valueString = String.valueOf(value); } else { valueString = formatter.format(value); } return valueString; } private double getExpectedValue(int c1, int c2, int binX, int binY, MatrixZoomData zd, ExpectedValueFunction df) { double ev = 0; if (c1 == c2) { if (df != null) { int distance = Math.abs(binX - binY); ev = df.getExpectedValue(c1, distance); } } else { ev = zd.getAverageCount(); } return ev; } private void executeSplitMenuAction() { AssemblyOperationExecutor.splitContig(selectedFeatures.get(0), debrisFeature, superAdapter, hic, true); HiCGlobals.splitModeEnabled = false; Chromosome chrX = superAdapter.getHiC().getXContext().getChromosome(); Chromosome chrY = superAdapter.getHiC().getYContext().getChromosome(); superAdapter.getEditLayer().filterTempSelectedGroup(chrX.getIndex(), chrY.getIndex()); superAdapter.getEditLayer().clearAnnotations(); superAdapter.setActiveLayerHandler(superAdapter.getMainLayer()); debrisFeature = null; //moveDebrisToEnd(); parent.removeSelection(); reset(); } /* public Feature2D generateDebrisFeature(int xMousePos, int yMousePos) { final double scaleFactor = hic.getScaleFactor(); double binOriginX = hic.getXContext().getBinOrigin(); double binOriginY = hic.getYContext().getBinOrigin(); Rectangle annotateRectangle = new Rectangle(xMousePos, (int) (yMousePos + (binOriginX - binOriginY) * scaleFactor), RESIZE_SNAP, RESIZE_SNAP); superAdapter.getEditLayer().updateSelectionRegion(annotateRectangle); return superAdapter.getEditLayer().generateFeature(hic); } public void toggleActivelyEditingAssembly() { this.activelyEditingAssembly = !this.activelyEditingAssembly; } //private enum AdjustAnnotation {LEFT, RIGHT, NONE} */ public void setFeatureOptionMenuEnabled(boolean bool) { featureOptionMenuEnabled = bool; } public PromptedAssemblyAction getCurrentPromptedAssemblyAction() { return this.currentPromptedAssemblyAction; } public PromptedAssemblyAction getPromptedAssemblyActionOnClick() { return this.promptedAssemblyActionOnClick; } public void setPromptedAssemblyActionOnClick(PromptedAssemblyAction promptedAssemblyAction) { this.promptedAssemblyActionOnClick = promptedAssemblyAction; } @Override public void mouseEntered(MouseEvent e) { setProperCursor(); } public void reset() { debrisFeatureSize = RESIZE_SNAP; } private void setProperCursor() { if (straightEdgeEnabled || diagonalEdgeEnabled) { parent.setCursor(Cursor.getPredefinedCursor(Cursor.CROSSHAIR_CURSOR)); } else { parent.setCursor(Cursor.getDefaultCursor()); } } private void addHighlightedFeature(Feature2D feature2D) { highlightedFeatures.add(feature2D); featureOptionMenuEnabled = false; showFeatureHighlight = true; hic.setShowFeatureHighlight(showFeatureHighlight); hic.setHighlightedFeatures(highlightedFeatures); superAdapter.repaintTrackPanels(); parent.repaint(); } public void renderMouseAnnotations(Graphics2D g2) { if (zoomRectangle != null) { g2.draw(zoomRectangle); } if (annotateRectangle != null) { g2.draw(annotateRectangle); } } public void addAllFeatures(AnnotationLayerHandler handler, List loops, MatrixZoomData zd, double binOriginX, double binOriginY, double scaleFactor, boolean activelyEditingAssembly) { allFeaturePairs.addAll(handler.convertToFeaturePairs(handler, loops, zd, binOriginX, binOriginY, scaleFactor)); if (activelyEditingAssembly) { if (handler == superAdapter.getMainLayer()) { allMainFeaturePairs.addAll(superAdapter.getMainLayer().convertToFeaturePairs(handler, loops, zd, binOriginX, binOriginY, scaleFactor)); } else if (handler == superAdapter.getEditLayer() && !selectedFeatures.isEmpty()) { allEditFeaturePairs.addAll(superAdapter.getEditLayer().convertToFeaturePairs(handler, loops, zd, binOriginX, binOriginY, scaleFactor)); } } } @Override public void mouseExited(MouseEvent e) { hic.setCursorPoint(null); if (straightEdgeEnabled || diagonalEdgeEnabled) { superAdapter.repaintTrackPanels(); } } @Override public void mousePressed(final MouseEvent e) { startTime = System.nanoTime(); featureOptionMenuEnabled = false; if (hic.isWholeGenome()) { if (e.isPopupTrigger()) { getPopupMenu(e.getX(), e.getY()).show(parent, e.getX(), e.getY()); } return; } // Priority is right click if (e.isPopupTrigger()) { getPopupMenu(e.getX(), e.getY()).show(parent, e.getX(), e.getY()); } else { // turn off continuous sync for dragging if (hic.isLinkedMode()) { HiCGlobals.wasLinkedBeforeMousePress = true; hic.setLinkedMode(false); } // Alt down for zoom if (e.isAltDown()) { dragMode = DragMode.ZOOM; // Shift down for custom annotations } else if (e.isShiftDown() && (activelyEditingAssembly || superAdapter.getActiveLayerHandler().getAnnotationLayerType() != AnnotationLayer.LayerType.SCAFFOLD)) { if (!activelyEditingAssembly) { if (superAdapter.unsavedEditsExist() && firstAnnotation) { firstAnnotation = false; String text = "There are unsaved hand annotations from your previous session! \n" + "Go to 'Annotations > Hand Annotations > Load Last' to restore."; System.err.println(text); JOptionPane.showMessageDialog(superAdapter.getMainWindow(), text); } //superAdapter.getActiveLayerHandler().updateSelectionPoint(e.getX(), e.getY()); superAdapter.getActiveLayerHandler().doPeak(); } dragMode = DragMode.ANNOTATE; //superAdapter.getActiveLayer().updateSelectionPoint(e.getX(), e.getY()); superAdapter.getActiveLayerHandler().doPeak(); parent.setCursor(Cursor.getPredefinedCursor(Cursor.CROSSHAIR_CURSOR)); // Corners for resize annotation try { List newSelectedFeatures = superAdapter.getMainLayer().getSelectedFeatures(hic, e.getX(), e.getY()); if (!selectedFeatures.get(0).equals(newSelectedFeatures.get(0))) { HiCGlobals.splitModeEnabled = false; superAdapter.setActiveLayerHandler(superAdapter.getMainLayer()); superAdapter.getLayersPanel().updateBothLayersPanels(superAdapter); superAdapter.getEditLayer().clearAnnotations(); } if (selectedFeatures.size() == 1 && selectedFeatures.get(0).equals(newSelectedFeatures.get(0))) { HiCGlobals.splitModeEnabled = true; } } catch (Exception ignored) { } } else if (adjustAnnotation != AdjustAnnotation.NONE) { dragMode = DragMode.RESIZE; Feature2D loop; if (activelyEditingAssembly && currentPromptedAssemblyAction == PromptedAssemblyAction.ADJUST) { loop = superAdapter.getEditLayer().getFeatureHandler().getFeatureList().get(1, 1).get(0); } else { loop = currentFeature.getFeature2D(); } // Resizing upper left corner, keep end points stationary if (adjustAnnotation == AdjustAnnotation.LEFT) { superAdapter.getActiveLayerHandler().setStationaryEnd(loop.getEnd1(), loop.getEnd2()); // Resizing lower right corner, keep start points stationary } else { superAdapter.getActiveLayerHandler().setStationaryStart(loop.getStart1(), loop.getStart2()); } try { HiCGridAxis xAxis = hic.getZd().getXGridAxis(); HiCGridAxis yAxis = hic.getZd().getYGridAxis(); final double scaleFactor = hic.getScaleFactor(); double binOriginX = hic.getXContext().getBinOrigin(); double binOriginY = hic.getYContext().getBinOrigin(); // hic.getFeature2DHandler() annotateRectangle = superAdapter.getActiveLayerHandler().getFeatureHandler().getRectangleFromFeature( xAxis, yAxis, loop, binOriginX, binOriginY, scaleFactor); int chr1Idx = hic.getXContext().getChromosome().getIndex(); int chr2Idx = hic.getYContext().getChromosome().getIndex(); preAdjustLoop = new Pair<>(new Pair<>(chr1Idx, chr2Idx), loop); } catch (Exception ex) { ex.printStackTrace(); } } else if (!e.isShiftDown() && currentPromptedAssemblyAction == PromptedAssemblyAction.CUT) { Feature2D debrisFeature = generateDebrisFeature(e, debrisFeatureSize); setDebrisFeauture(debrisFeature); int chr1Idx = hic.getXContext().getChromosome().getIndex(); int chr2Idx = hic.getYContext().getChromosome().getIndex(); if (debrisFeature != null) { superAdapter.getEditLayer().getAnnotationLayer().getFeatureHandler().getFeatureList().checkAndRemoveFeature(chr1Idx, chr2Idx, debrisFeature); } superAdapter.getEditLayer().getAnnotationLayer().add(chr1Idx, chr2Idx, debrisFeature); HiCGlobals.splitModeEnabled = true; superAdapter.setActiveLayerHandler(superAdapter.getEditLayer()); restoreDefaultVariables(); parent.repaint(); } else { dragMode = DragMode.PAN; parent.setCursor(MainWindow.fistCursor); } lastMousePoint = e.getPoint(); lastPressedMousePoint = e.getPoint(); } } @Override public void mouseReleased(final MouseEvent e) { endTime = System.nanoTime(); if (e.isPopupTrigger()) { getPopupMenu(e.getX(), e.getY()).show(parent, e.getX(), e.getY()); dragMode = DragMode.NONE; lastMousePoint = null; zoomRectangle = null; annotateRectangle = null; setProperCursor(); // After popup, priority is assembly mode, highlighting those features. } /*else if (HiCGlobals.splitModeEnabled && activelyEditingAssembly) { if (dragMode == DragMode.ANNOTATE) { Feature2D feature2D = superAdapter.getActiveLayerHandler().generateFeature(hic); //TODO can modify split to wait for user to accept split if (feature2D == null) { int x = (int) lastMousePoint.getX(); int y = (int) lastMousePoint.getY(); Rectangle annotateRectangle = new Rectangle(x, y, 1, 1); superAdapter.getActiveLayerHandler().updateSelectionRegion(annotateRectangle); feature2D = superAdapter.getActiveLayerHandler().generateFeature(hic); //TODO can modify split to wait for user to accept split } AnnotationLayerHandler editLayerHandler = superAdapter.getEditLayer(); debrisFeature = feature2D; // editLayerHandler.getAnnotationLayer().add(Hic.); int chr1Idx = hic.getXContext().getChromosomeFromName().getIndex(); int chr2Idx = hic.getYContext().getChromosomeFromName().getIndex(); // executeSplitMenuAction(selectedFeatures.get(0),debrisFeature); editLayerHandler.getAnnotationLayer().add(chr1Idx, chr2Idx, debrisFeature); restoreDefaultVariables(); } }*/ else { // turn on continuous sync after dragging if (HiCGlobals.wasLinkedBeforeMousePress) { HiCGlobals.wasLinkedBeforeMousePress = false; hic.setLinkedMode(true); if (lastPressedMousePoint != null) { double deltaX = e.getX() - lastPressedMousePoint.getX(); double deltaY = e.getY() - lastPressedMousePoint.getY(); if (Math.abs(deltaX) > 0 && Math.abs(deltaY) > 0) { hic.broadcastLocation(); } } else { hic.broadcastLocation(); } } if (e.isShiftDown() && HiCGlobals.phasing) { //superscaffold selection handling in the phasing case Feature2DGuiContainer newSelectedSuperscaffold = getMouseHoverSuperscaffold(e.getX(), e.getY()); if (newSelectedSuperscaffold == null) { parent.removeSelection(); } else { int tentativeSuperscaffoldId = Integer.parseInt(newSelectedSuperscaffold.getFeature2D().getAttribute("Superscaffold #")) - 1; int altTentativeSuperscaffoldId; if (tentativeSuperscaffoldId % 2 == 0) { altTentativeSuperscaffoldId = tentativeSuperscaffoldId + 1; } else { altTentativeSuperscaffoldId = tentativeSuperscaffoldId - 1; } if (selectedSuperscaffolds.contains(tentativeSuperscaffoldId)) { selectedSuperscaffolds.remove(Integer.valueOf(tentativeSuperscaffoldId)); highlightedFeatures.remove(newSelectedSuperscaffold.getFeature2D()); } else if (selectedSuperscaffolds.contains(altTentativeSuperscaffoldId)) { return; } else { selectedSuperscaffolds.add(tentativeSuperscaffoldId); highlightedFeatures.add(newSelectedSuperscaffold.getFeature2D()); } addHighlightedFeatures(highlightedFeatures); superAdapter.getMainViewPanel().toggleToolTipUpdates(Boolean.TRUE); superAdapter.updateMainViewPanelToolTipText(toolTipText(e.getX(), e.getY())); superAdapter.getMainViewPanel().toggleToolTipUpdates(highlightedFeatures.isEmpty()); currentPromptedAssemblyAction = PromptedAssemblyAction.NONE; restoreDefaultVariables(); } return; } if (activelyEditingAssembly && HiCGlobals.splitModeEnabled && currentPromptedAssemblyAction == PromptedAssemblyAction.CUT) { // disable long click: it seems that no one is using it anyway. But let's keep it commented around for now.. // holdTime = (endTime - startTime) / Math.pow(10, 6); //Short click: execute split, long click: expert mode leave annotation be for editing purposes // if (holdTime <= clickDelay) { debrisFeature = generateDebrisFeature(e, debrisFeatureSize); executeSplitMenuAction(); // } currentPromptedAssemblyAction = PromptedAssemblyAction.NONE; } if (activelyEditingAssembly && (dragMode == DragMode.ANNOTATE || currentPromptedAssemblyAction == PromptedAssemblyAction.ADJUST)) { // New annotation is added (not single click) and new feature from custom annotation updateSelectedFeatures(false); highlightedFeatures.clear(); List newSelectedFeatures = superAdapter.getMainLayer().getSelectedFeatures(hic, e.getX(), e.getY()); // selects superscaffold if ((newSelectedFeatures == null || newSelectedFeatures.size() == 0) && selectedFeatures.size() == 0) { Feature2DGuiContainer newSelectedSuperscaffold = getMouseHoverSuperscaffold(e.getX(), e.getY()); if (newSelectedSuperscaffold != null) { final List curScaffolds = superAdapter.getAssemblyStateTracker().getAssemblyHandler().getListOfSuperscaffolds().get( Integer.parseInt(newSelectedSuperscaffold.getFeature2D().getAttribute("Superscaffold #")) - 1); newSelectedFeatures.clear(); for (int scaffold : curScaffolds) { Feature2D curScaffold = superAdapter.getAssemblyStateTracker().getAssemblyHandler().getListOfScaffolds().get(Math.abs(scaffold) - 1).getCurrentFeature2D(); newSelectedFeatures.add(curScaffold); } } } Collections.sort(newSelectedFeatures); // Damage rectangle is not precise, adjust boundaries... try { if (currentPromptedAssemblyAction == PromptedAssemblyAction.ADJUST) { if (adjustAnnotation == AdjustAnnotation.LEFT) { while (!selectedFeatures.contains(newSelectedFeatures.get(newSelectedFeatures.size() - 1)) && !newSelectedFeatures.isEmpty()) { newSelectedFeatures.remove(newSelectedFeatures.size() - 1); } } else { while (!selectedFeatures.contains(newSelectedFeatures.get(0)) && !newSelectedFeatures.isEmpty()) { newSelectedFeatures.remove(0); } } } } catch (Exception e1) { parent.removeSelection(); } if (HiCGlobals.translationInProgress) { translationInProgressMouseReleased(newSelectedFeatures); } else { if (selectedFeatures.equals(newSelectedFeatures) && currentPromptedAssemblyAction != PromptedAssemblyAction.ADJUST) { parent.removeSelection(); } else { selectedFeatures.clear(); selectedFeatures.addAll(newSelectedFeatures); } } updateSelectedFeatures(true); Chromosome chrX = superAdapter.getHiC().getXContext().getChromosome(); Chromosome chrY = superAdapter.getHiC().getYContext().getChromosome(); superAdapter.getEditLayer().filterTempSelectedGroup(chrX.getIndex(), chrY.getIndex()); parent.repaint(); if (!selectedFeatures.isEmpty()) { if (superAdapter.getMainLayer().getLayerVisibility()) { tempSelectedGroup = superAdapter.getEditLayer().addTempSelectedGroup(selectedFeatures, hic); addHighlightedFeature(tempSelectedGroup); } } else { parent.removeHighlightedFeature(); } //getAssemblyPopupMenu(e.getX(), e.getY()).show(parent, e.getX(), e.getY()); superAdapter.getMainViewPanel().toggleToolTipUpdates(true); superAdapter.updateMainViewPanelToolTipText(toolTipText(e.getX(), e.getY())); superAdapter.getMainViewPanel().toggleToolTipUpdates(selectedFeatures.isEmpty()); currentPromptedAssemblyAction = PromptedAssemblyAction.NONE; restoreDefaultVariables(); } else if ((dragMode == DragMode.ZOOM || dragMode == DragMode.SELECT) && zoomRectangle != null) { Runnable runnable = new Runnable() { @Override public void run() { unsafeDragging(); } }; superAdapter.executeLongRunningTask(runnable, "Mouse Drag"); } else if (dragMode == DragMode.ANNOTATE) { // New annotation is added (not single click) and new feature from custom annotation superAdapter.getActiveLayerHandler().addFeature(hic); restoreDefaultVariables(); } else if (dragMode == DragMode.RESIZE) { // New annotation is added (not single click) and new feature from custom annotation int idx1 = preAdjustLoop.getFirst().getFirst(); int idx2 = preAdjustLoop.getFirst().getSecond(); Feature2D secondLoop = preAdjustLoop.getSecond(); // Add a new loop if it was resized (prevents deletion on single click) try { final double scaleFactor = hic.getScaleFactor(); final int screenWidth = parent.getBounds().width; final int screenHeight = parent.getBounds().height; int centerX = (int) (screenWidth / scaleFactor) / 2; int centerY = (int) (screenHeight / scaleFactor) / 2; if (superAdapter.getActiveLayerHandler().hasLoop(hic.getZd(), idx1, idx2, centerX, centerY, Feature2DHandler.numberOfLoopsToFind, hic.getXContext().getBinOrigin(), hic.getYContext().getBinOrigin(), hic.getScaleFactor(), secondLoop) && changedSize) { Feature2D oldFeature2D = secondLoop.deepCopy(); superAdapter.getActiveLayerHandler().removeFromList(hic.getZd(), idx1, idx2, centerX, centerY, Feature2DHandler.numberOfLoopsToFind, hic.getXContext().getBinOrigin(), hic.getYContext().getBinOrigin(), hic.getScaleFactor(), secondLoop); Feature2D tempFeature2D = superAdapter.getActiveLayerHandler().addFeature(hic); superAdapter.getActiveLayerHandler().setLastItem(idx1, idx2, secondLoop); for (String newKey : oldFeature2D.getAttributeKeys()) { tempFeature2D.setAttribute(newKey, oldFeature2D.getAttribute(newKey)); } //remove preadjust loop from list if (activelyEditingAssembly && HiCGlobals.splitModeEnabled) { debrisFeature = tempFeature2D; } } } catch (Exception ee) { System.err.println("Unable to remove pre-resized loop"); } restoreDefaultVariables(); } else { setProperCursor(); } } } // works for only one selected contig private void translationInProgressMouseReleased(List newSelectedFeatures) { if (!selectedFeatures.isEmpty()) { Feature2D featureDestination = newSelectedFeatures.get(0); AssemblyOperationExecutor.moveSelection(superAdapter, selectedFeatures, featureDestination); parent.repaint(); } if (newSelectedFeatures != null) { selectedFeatures.addAll(newSelectedFeatures); } HiCGlobals.translationInProgress = false; parent.removeSelection(); //TODO fix this so that highlight moves with translated selection } Feature2D generateDebrisFeature(final MouseEvent eF, int debrisFeatureSize) { final double scaleFactor = hic.getScaleFactor(); double binOriginX = hic.getXContext().getBinOrigin(); double binOriginY = hic.getYContext().getBinOrigin(); Point mousePoint = eF.getPoint(); double x = mousePoint.getX(); double y = mousePoint.getY(); int rightCorner = (int) Math.max(x, y + (binOriginY - binOriginX) * scaleFactor); Rectangle annotateRectangle = new Rectangle(rightCorner - debrisFeatureSize, (int) (rightCorner - debrisFeatureSize - (binOriginY - binOriginX) * scaleFactor), debrisFeatureSize, debrisFeatureSize); superAdapter.getEditLayer().updateSelectionRegion(annotateRectangle); debrisFeature = superAdapter.getEditLayer().generateFeature(hic); return debrisFeature; } private void restoreDefaultVariables() { dragMode = DragMode.NONE; adjustAnnotation = AdjustAnnotation.NONE; annotateRectangle = null; lastMousePoint = null; zoomRectangle = null; preAdjustLoop = null; hic.setCursorPoint(null); changedSize = false; parent.setCursor(Cursor.getDefaultCursor()); parent.repaint(); superAdapter.repaintTrackPanels(); } private void unsafeDragging() { final double scaleFactor1 = hic.getScaleFactor(); double binX = hic.getXContext().getBinOrigin() + (zoomRectangle.x / scaleFactor1); double binY = hic.getYContext().getBinOrigin() + (zoomRectangle.y / scaleFactor1); double wBins = (int) (zoomRectangle.width / scaleFactor1); double hBins = (int) (zoomRectangle.height / scaleFactor1); try { final MatrixZoomData currentZD = hic.getZd(); long xBP0 = currentZD.getXGridAxis().getGenomicStart(binX); long yBP0 = currentZD.getYGridAxis().getGenomicEnd(binY); double newXBinSize = wBins * currentZD.getBinSize() / parent.getWidth(); double newYBinSize = hBins * currentZD.getBinSize() / parent.getHeight(); double newBinSize = Math.max(newXBinSize, newYBinSize); hic.zoomToDrawnBox(xBP0, yBP0, newBinSize); } catch (Exception e) { e.printStackTrace(); } dragMode = DragMode.NONE; lastMousePoint = null; zoomRectangle = null; setProperCursor(); } @Override final public void mouseDragged(final MouseEvent e) { Rectangle lastRectangle, damageRect; int x, y; double x_d, y_d; try { hic.getZd(); } catch (Exception ex) { return; } if (hic.isWholeGenome()) { return; } if (lastMousePoint == null) { lastMousePoint = e.getPoint(); return; } int deltaX = e.getX() - lastMousePoint.x; int deltaY = e.getY() - lastMousePoint.y; double deltaX_d = e.getX() - lastMousePoint.x; double deltaY_d = e.getY() - lastMousePoint.y; if (dragMode == DragMode.ZOOM) { lastRectangle = zoomRectangle; if (deltaX == 0 || deltaY == 0) { return; } // Constrain aspect ratio of zoom rectangle to that of panel double aspectRatio = (double) parent.getWidth() / parent.getHeight(); if (deltaX * aspectRatio > deltaY) { deltaY = (int) (deltaX / aspectRatio); } else { deltaX = (int) (deltaY * aspectRatio); } x = deltaX > 0 ? lastMousePoint.x : lastMousePoint.x + deltaX; y = deltaY > 0 ? lastMousePoint.y : lastMousePoint.y + deltaY; zoomRectangle = new Rectangle(x, y, Math.abs(deltaX), Math.abs(deltaY)); damageRect = lastRectangle == null ? zoomRectangle : zoomRectangle.union(lastRectangle); damageRect.x--; damageRect.y--; damageRect.width += 2; damageRect.height += 2; parent.paintImmediately(damageRect); } else if (dragMode == DragMode.ANNOTATE) { lastRectangle = annotateRectangle; if (deltaX_d == 0 || deltaY_d == 0) { return; } x = deltaX > 0 ? lastMousePoint.x : lastMousePoint.x + deltaX; y = deltaY > 0 ? lastMousePoint.y : lastMousePoint.y + deltaY; annotateRectangle = new Rectangle(x, y, Math.abs(deltaX), Math.abs(deltaY)); damageRect = lastRectangle == null ? annotateRectangle : annotateRectangle.union(lastRectangle); superAdapter.getActiveLayerHandler().updateSelectionRegion(damageRect); damageRect.x--; damageRect.y--; damageRect.width += 2; damageRect.height += 2; parent.paintImmediately(damageRect); } else if (dragMode == DragMode.RESIZE) { if (deltaX_d == 0 || deltaY_d == 0) { return; } lastRectangle = annotateRectangle; double rectX; double rectY; // Resizing upper left corner if (adjustAnnotation == AdjustAnnotation.LEFT) { rectX = annotateRectangle.getX() + annotateRectangle.getWidth(); rectY = annotateRectangle.getY() + annotateRectangle.getHeight(); // Resizing lower right corner } else { rectX = annotateRectangle.getX(); rectY = annotateRectangle.getY(); } deltaX_d = e.getX() - rectX; deltaY_d = e.getY() - rectY; x_d = deltaX_d > 0 ? rectX : rectX + deltaX_d; y_d = deltaY_d > 0 ? rectY : rectY + deltaY_d; annotateRectangle = new Rectangle((int) x_d, (int) y_d, (int) Math.abs(deltaX_d), (int) Math.abs(deltaY_d)); damageRect = lastRectangle == null ? annotateRectangle : annotateRectangle.union(lastRectangle); damageRect.width += 1; damageRect.height += 1; parent.paintImmediately(damageRect); superAdapter.getActiveLayerHandler().updateSelectionRegion(damageRect); changedSize = true; } else { lastMousePoint = e.getPoint(); // Always save the last Point double deltaXBins = -deltaX / hic.getScaleFactor(); double deltaYBins = -deltaY / hic.getScaleFactor(); hic.moveBy(deltaXBins, deltaYBins); } } @Override public void mouseMoved(MouseEvent e) { try { hic.getZd(); } catch (Exception ex) { return; } if (hic.getXContext() != null) { adjustAnnotation = AdjustAnnotation.NONE; currentPromptedAssemblyAction = PromptedAssemblyAction.NONE; // Update tool tip text if (!featureOptionMenuEnabled) { superAdapter.updateMainViewPanelToolTipText(toolTipText(e.getX(), e.getY())); } // Set check if hovering over feature corner // Following was commented out since it was causing flickering of the cursor on windows machines, don't know if was necessary // parent.setCursor(Cursor.getDefaultCursor()); int minDist = 20; if (currentFeature != null) { boolean resizeable = (currentFeature.getAnnotationLayerHandler().getAnnotationLayerType() != AnnotationLayer.LayerType.SCAFFOLD) && (currentFeature.getAnnotationLayerHandler().getAnnotationLayerType() != AnnotationLayer.LayerType.SUPERSCAFFOLD); // if (activelyEditingAssembly) { // resizeable = (resizeable && HiCGlobals.splitModeEnabled); // } if (resizeable) { Rectangle loop = currentFeature.getRectangle(); Point mousePoint = e.getPoint(); // Mouse near top left corner if ((Math.abs(loop.getMinX() - mousePoint.getX()) <= minDist && Math.abs(loop.getMinY() - mousePoint.getY()) <= minDist)) { adjustAnnotation = AdjustAnnotation.LEFT; parent.setCursor(Cursor.getPredefinedCursor(Cursor.NW_RESIZE_CURSOR)); // Mouse near bottom right corner } else if (Math.abs(loop.getMaxX() - mousePoint.getX()) <= minDist && Math.abs(loop.getMaxY() - mousePoint.getY()) <= minDist) { adjustAnnotation = AdjustAnnotation.RIGHT; parent.setCursor(Cursor.getPredefinedCursor(Cursor.SE_RESIZE_CURSOR)); } } } if (activelyEditingAssembly && !allMainFeaturePairs.isEmpty() && !e.isShiftDown()) { final double scaleFactor = hic.getScaleFactor(); double binOriginX = hic.getXContext().getBinOrigin(); double binOriginY = hic.getYContext().getBinOrigin(); Point mousePoint = e.getPoint(); double x = mousePoint.getX(); double y = mousePoint.getY(); // this is a good place to handle inserts to top and bottom as it should be done even if individual // features at the beginning of the assembly are not visible // find the x and y in relation to the displayed screen int topLeftCornerX = (int) ((0 - binOriginX) * scaleFactor); int topLeftCornerY = (int) ((0 - binOriginY) * scaleFactor); List listOfScaffolds = superAdapter.getAssemblyStateTracker().getAssemblyHandler().getListOfAggregateScaffolds(); long lastGenomicBin = 0; try { lastGenomicBin = listOfScaffolds.get(listOfScaffolds.size() - 1).getCurrentFeature2D().getEnd2() / hic.getZd().getBinSize(); } catch (NullPointerException e1) { e1.printStackTrace(); } int bottomRightCornerX = (int) ((lastGenomicBin - binOriginX) * scaleFactor); int bottomRightCornerY = (int) ((lastGenomicBin - binOriginY) * scaleFactor); if (!selectedFeatures.isEmpty() && !HiCGlobals.phasing) { if (mousePoint.getX() - topLeftCornerX >= 0 && mousePoint.getX() - topLeftCornerX <= minDist && mousePoint.getY() - topLeftCornerY >= 0 && mousePoint.getY() - topLeftCornerY <= minDist) { parent.setCursor(MainWindow.pasteNWCursor); currentPromptedAssemblyAction = PromptedAssemblyAction.PASTETOP; } if (bottomRightCornerX - mousePoint.getX() >= 0 && bottomRightCornerX - mousePoint.getX() <= minDist && bottomRightCornerY - mousePoint.getY() >= 0 && bottomRightCornerY - mousePoint.getY() <= minDist) { parent.setCursor(MainWindow.pasteSECursor); currentPromptedAssemblyAction = PromptedAssemblyAction.PASTEBOTTOM; } } currentUpstreamFeature = null; currentDownstreamFeature = null; for (Feature2DGuiContainer asmFragment : allMainFeaturePairs) { if (asmFragment.getRectangle().contains(x, x + (binOriginX - binOriginY) * scaleFactor)) { currentUpstreamFeature = asmFragment; } if (asmFragment.getRectangle().contains(y + (binOriginY - binOriginX) * scaleFactor, y)) { currentDownstreamFeature = asmFragment; } } if (currentUpstreamFeature != null && currentDownstreamFeature != null) { if (currentUpstreamFeature.getFeature2D().getStart1() > currentDownstreamFeature.getFeature2D().getStart1()) { Feature2DGuiContainer temp = currentUpstreamFeature; currentUpstreamFeature = currentDownstreamFeature; currentDownstreamFeature = temp; } // inserting from highlight: keeping for future development // if (!selectedFeatures.isEmpty()) { // // // upstream feature is the same // if (currentUpstreamFeature.getFeature2D().getStart1() >= selectedFeatures.get(0).getStart1() && // currentUpstreamFeature.getFeature2D().getEnd1() <= // selectedFeatures.get(selectedFeatures.size() - 1).getEnd1()) { // // int topYright = currentUpstreamFeature.getRectangle().y; // int bottomYright = // currentUpstreamFeature.getRectangle().y + (int) currentUpstreamFeature.getRectangle().getHeight(); // int leftXbottom = currentUpstreamFeature.getRectangle().x; // int rightXbottom = // currentUpstreamFeature.getRectangle().x + (int) currentUpstreamFeature.getRectangle().getWidth(); // // if (mousePoint.getY() >= topYright && mousePoint.getY() <= bottomYright) { // // if ((mousePoint.getX() >= currentDownstreamFeature.getRectangle().getMinX() && // mousePoint.getX() <= currentDownstreamFeature.getRectangle().getMinX() + minDist)) { // // // if the start doesn't match the end of the previous one, there's a gap, do not insert // if (currentDownstreamFeature.getFeature2D().getStart1() == // allMainFeaturePairs.get(idxUp - 1).getFeature2D().getEnd1()) { // parent.setCursor(MainWindow.pasteSWCursor); // currentUpstreamFeature = allMainFeaturePairs.get(idxUp - 1); // currentPromptedAssemblyAction = PromptedAssemblyAction.PASTE; // } // } // } // // if (mousePoint.getX() >= leftXbottom && mousePoint.getX() <= rightXbottom) { // // -y axis // if ((mousePoint.getY() >= currentDownstreamFeature.getRectangle().getMinY() && // mousePoint.getY() <= currentDownstreamFeature.getRectangle().getMinY() + minDist)) { // if (currentDownstreamFeature.getFeature2D().getStart1() == // allMainFeaturePairs.get(idxDown - 1).getFeature2D().getEnd1()) { // parent.setCursor(MainWindow.pasteNECursor); // currentUpstreamFeature = allMainFeaturePairs.get(idxDown - 1); // currentPromptedAssemblyAction = PromptedAssemblyAction.PASTE; // } // } // } // } // // // downstream feature the same // if ((currentDownstreamFeature.getFeature2D().getStart1() >= selectedFeatures.get(0).getStart1() && // currentDownstreamFeature.getFeature2D().getEnd1() <= // selectedFeatures.get(selectedFeatures.size() - 1).getEnd1()) // ) { // int topYleft = currentDownstreamFeature.getRectangle().y; // int bottomYleft = // currentDownstreamFeature.getRectangle().y + // (int) currentDownstreamFeature.getRectangle().getHeight(); // int leftXtop = currentDownstreamFeature.getRectangle().x; // int rightXtop = // currentDownstreamFeature.getRectangle().x + // (int) currentDownstreamFeature.getRectangle().getWidth(); // // // y axis // if (mousePoint.getX() >= leftXtop && mousePoint.getX() <= rightXtop) { // if ((mousePoint.getY() >= currentUpstreamFeature.getRectangle().getMaxY() - minDist && // mousePoint.getY() <= currentUpstreamFeature.getRectangle().getMaxY())) { // parent.setCursor(MainWindow.pasteSWCursor); // currentPromptedAssemblyAction = PromptedAssemblyAction.PASTE; // } // } // // -x axis // else if (mousePoint.getY() >= topYleft && mousePoint.getY() <= bottomYleft) { // if ((mousePoint.getX() >= currentUpstreamFeature.getRectangle().getMaxX() - minDist && // mousePoint.getX() <= (currentUpstreamFeature.getRectangle().getMaxX()))) { // parent.setCursor(MainWindow.pasteNECursor); // currentPromptedAssemblyAction = PromptedAssemblyAction.PASTE; // } // } // } // } if (!HiCGlobals.splitModeEnabled && (currentUpstreamFeature.getFeature2D().getEnd1() == currentDownstreamFeature.getFeature2D().getStart1()) || (currentDownstreamFeature == null && currentUpstreamFeature == null)) { if ((mousePoint.getX() - currentUpstreamFeature.getRectangle().getMaxX() >= 0) && (mousePoint.getX() - currentUpstreamFeature.getRectangle().getMaxX() <= minDist) && (currentUpstreamFeature.getRectangle().getMaxY() - mousePoint.getY() >= 0) && (currentUpstreamFeature.getRectangle().getMaxY() - mousePoint.getY() <= minDist)) { if (selectedFeatures == null || selectedFeatures.isEmpty()) { parent.setCursor(MainWindow.groupSWCursor); currentPromptedAssemblyAction = PromptedAssemblyAction.REGROUP; } else if (!(currentUpstreamFeature.getFeature2D().getEnd1() >= selectedFeatures.get(0).getStart1() && currentUpstreamFeature.getFeature2D().getEnd1() <= selectedFeatures.get(selectedFeatures.size() - 1).getEnd1())) { parent.setCursor(MainWindow.pasteSWCursor); currentPromptedAssemblyAction = PromptedAssemblyAction.PASTE; } } else if ((currentUpstreamFeature.getRectangle().getMaxX() - mousePoint.getX() >= 0) && (currentUpstreamFeature.getRectangle().getMaxX() - mousePoint.getX() <= minDist) && (mousePoint.getY() - currentUpstreamFeature.getRectangle().getMaxY() >= 0) && (mousePoint.getY() - currentUpstreamFeature.getRectangle().getMaxY() <= minDist)) { if (selectedFeatures.isEmpty()) { parent.setCursor(MainWindow.groupNECursor); currentPromptedAssemblyAction = PromptedAssemblyAction.REGROUP; } else if (!(currentUpstreamFeature.getFeature2D().getEnd1() >= selectedFeatures.get(0).getStart1() && currentUpstreamFeature.getFeature2D().getEnd1() <= selectedFeatures.get(selectedFeatures.size() - 1).getEnd1())) { parent.setCursor(MainWindow.pasteNECursor); currentPromptedAssemblyAction = PromptedAssemblyAction.PASTE; } } } } if (!HiCGlobals.splitModeEnabled && !selectedFeatures.isEmpty()) { for (Feature2DGuiContainer asmFragment : allEditFeaturePairs) { if (asmFragment.getFeature2D().equals(tempSelectedGroup) && !asmFragment.getFeature2D().equals(debrisFeature)) { if (Math.abs(asmFragment.getRectangle().getMaxX() - mousePoint.getX()) < minDist && Math.abs(asmFragment.getRectangle().getMinY() - mousePoint.getY()) < minDist) { parent.setCursor(MainWindow.invertSWCursor); if (debrisFeature != null) { int chr1Idx = hic.getXContext().getChromosome().getIndex(); int chr2Idx = hic.getYContext().getChromosome().getIndex(); superAdapter.getEditLayer().getAnnotationLayer().getFeatureHandler().getFeatureList().checkAndRemoveFeature(chr1Idx, chr2Idx, debrisFeature); } currentPromptedAssemblyAction = PromptedAssemblyAction.INVERT; } else if (Math.abs(asmFragment.getRectangle().getMinX() - mousePoint.getX()) < minDist && Math.abs(asmFragment.getRectangle().getMaxY() - mousePoint.getY()) < minDist) { parent.setCursor(MainWindow.invertNECursor); if (debrisFeature != null) { int chr1Idx = hic.getXContext().getChromosome().getIndex(); int chr2Idx = hic.getYContext().getChromosome().getIndex(); superAdapter.getEditLayer().getAnnotationLayer().getFeatureHandler().getFeatureList().checkAndRemoveFeature(chr1Idx, chr2Idx, debrisFeature); } currentPromptedAssemblyAction = PromptedAssemblyAction.INVERT; } else if (selectedFeatures.size() == 1 && Math.abs(x - (y + (binOriginY - binOriginX) * scaleFactor)) < minDist && Math.abs(y - (x + (binOriginX - binOriginY) * scaleFactor)) < minDist && x - asmFragment.getRectangle().getMinX() > debrisFeatureSize + RESIZE_SNAP + scaleFactor && asmFragment.getRectangle().getMaxX() - x > RESIZE_SNAP + scaleFactor && y - asmFragment.getRectangle().getMinY() > debrisFeatureSize + RESIZE_SNAP + scaleFactor && asmFragment.getRectangle().getMaxY() - y > RESIZE_SNAP + scaleFactor) { parent.setCursor(MainWindow.scissorCursor); currentPromptedAssemblyAction = PromptedAssemblyAction.CUT; int chr1Idx = hic.getXContext().getChromosome().getIndex(); int chr2Idx = hic.getYContext().getChromosome().getIndex(); if (debrisFeature != null) { superAdapter.getEditLayer().getAnnotationLayer().getFeatureHandler().getFeatureList().checkAndRemoveFeature(chr1Idx, chr2Idx, debrisFeature); } generateDebrisFeature(e, debrisFeatureSize); superAdapter.getEditLayer().getAnnotationLayer().add(chr1Idx, chr2Idx, debrisFeature); } else if (Math.abs(x - asmFragment.getRectangle().getMinX()) <= RESIZE_SNAP && Math.abs(y - asmFragment.getRectangle().getMinY()) <= RESIZE_SNAP && y + x < asmFragment.getRectangle().getMaxX() + asmFragment.getRectangle().getMinY()) { parent.setCursor(Cursor.getPredefinedCursor(Cursor.NW_RESIZE_CURSOR)); currentPromptedAssemblyAction = PromptedAssemblyAction.ADJUST; adjustAnnotation = AdjustAnnotation.LEFT; } else if (Math.abs(asmFragment.getRectangle().getMaxX() - x) <= RESIZE_SNAP && Math.abs(asmFragment.getRectangle().getMaxY() - y) <= RESIZE_SNAP && y + x > asmFragment.getRectangle().getMaxX() + asmFragment.getRectangle().getMinY()) { parent.setCursor(Cursor.getPredefinedCursor(Cursor.SE_RESIZE_CURSOR)); currentPromptedAssemblyAction = PromptedAssemblyAction.ADJUST; adjustAnnotation = AdjustAnnotation.RIGHT; } else if (debrisFeature != null) { int chr1Idx = hic.getXContext().getChromosome().getIndex(); int chr2Idx = hic.getYContext().getChromosome().getIndex(); superAdapter.getEditLayer().getAnnotationLayer().getFeatureHandler().getFeatureList().checkAndRemoveFeature(chr1Idx, chr2Idx, debrisFeature); } } } } } if (hic.isWholeGenome()) { synchronized (this) { hic.setGWCursorPoint(e.getPoint()); superAdapter.repaintGridRulerPanels(); } } else { hic.setGWCursorPoint(null); } if (straightEdgeEnabled || e.isShiftDown()) { synchronized (this) { hic.setCursorPoint(e.getPoint()); superAdapter.repaintTrackPanels(); } } else if (diagonalEdgeEnabled) { synchronized (this) { hic.setDiagonalCursorPoint(e.getPoint()); superAdapter.repaintTrackPanels(); } } else if (adjustAnnotation == AdjustAnnotation.NONE && currentPromptedAssemblyAction == PromptedAssemblyAction.NONE) { hic.setCursorPoint(null); parent.setCursor(Cursor.getDefaultCursor()); } parent.repaint(); } } @Override public void mouseWheelMoved(MouseWheelEvent e) { try { if (currentPromptedAssemblyAction == PromptedAssemblyAction.CUT) { final double scaleFactor = hic.getScaleFactor(); //double binOriginX = hic.getXContext().getBinOrigin(); //double binOriginY = hic.getYContext().getBinOrigin(); Point mousePoint = e.getPoint(); double x = mousePoint.getX(); double y = mousePoint.getY(); int rightCorner = (int) Math.max(x, y); debrisFeatureSize = debrisFeatureSize - e.getUnitsToScroll(); if (rightCorner - debrisFeatureSize < currentFeature.getRectangle().getMinX() + RESIZE_SNAP) { debrisFeatureSize = rightCorner - (int) currentFeature.getRectangle().getMinX() - RESIZE_SNAP - 1; } if (debrisFeatureSize <= scaleFactor) { debrisFeatureSize = (int) Math.max(scaleFactor, 1); } int chr1Idx = hic.getXContext().getChromosome().getIndex(); int chr2Idx = hic.getYContext().getChromosome().getIndex(); if (debrisFeature != null) { superAdapter.getEditLayer().getAnnotationLayer().getFeatureHandler().getFeatureList().checkAndRemoveFeature(chr1Idx, chr2Idx, debrisFeature); } generateDebrisFeature(e, debrisFeatureSize); superAdapter.getEditLayer().getAnnotationLayer().add(chr1Idx, chr2Idx, debrisFeature); parent.repaint(); return; } int scroll = (int) Math.round(e.getPreciseWheelRotation()); hic.moveBy(scroll, scroll); superAdapter.updateMainViewPanelToolTipText(toolTipText(e.getX(), e.getY())); } catch (Exception e2) { parent.repaint(); } } private Point calculateSelectionPoint(int unscaledX, int unscaledY) { final MatrixZoomData zd; try { zd = hic.getZd(); } catch (Exception err) { return null; } final HiCGridAxis xAxis = zd.getXGridAxis(); final HiCGridAxis yAxis = zd.getYGridAxis(); final double binOriginX = hic.getXContext().getBinOrigin(); final double binOriginY = hic.getYContext().getBinOrigin(); final double scale = hic.getScaleFactor(); float x = (float) (((unscaledX / scale) + binOriginX) * xAxis.getBinSize()); float y = (float) (((unscaledY / scale) + binOriginY) * yAxis.getBinSize()); return new Point((int) x, (int) y); } private void setDebrisFeauture(Feature2D debrisFeature) { this.debrisFeature = debrisFeature; } private Feature2DGuiContainer getMouseHoverSuperscaffold(int x, int y) { final Point mousePoint = calculateSelectionPoint(x, y); if (activelyEditingAssembly) { for (Feature2DGuiContainer loop : allFeaturePairs) { if (loop.getFeature2D().getFeatureType() == Feature2D.FeatureType.SUPERSCAFFOLD) { if (loop.getFeature2D().containsPoint(mousePoint)) { return loop; } } } } return null; } private String toolTipText(int x, int y) { // Update popup text final MatrixZoomData zd; HiCGridAxis xGridAxis, yGridAxis; try { zd = hic.getZd(); xGridAxis = zd.getXGridAxis(); yGridAxis = zd.getYGridAxis(); } catch (Exception e) { return ""; } int binX = (int) (hic.getXContext().getBinOrigin() + x / hic.getScaleFactor()); int binY = (int) (hic.getYContext().getBinOrigin() + y / hic.getScaleFactor()); long xGenomeStart = xGridAxis.getGenomicStart(binX) + 1; // Conversion from in internal "0" -> 1 base coordinates long yGenomeStart = yGridAxis.getGenomicStart(binY) + 1; long xGenomeEnd = xGridAxis.getGenomicEnd(binX); long yGenomeEnd = yGridAxis.getGenomicEnd(binY); if (hic.isWholeGenome()) { final long[] chromosomeBoundaries = parent.getChromosomeBoundaries(); Chromosome xChrom = getChromFromBoundaries(chromosomeBoundaries, xGenomeStart); Chromosome yChrom = getChromFromBoundaries(chromosomeBoundaries, yGenomeStart); if (xChrom != null && yChrom != null) { long leftBoundaryX = xChrom.getIndex() == 1 ? 0 : chromosomeBoundaries[xChrom.getIndex() - 2]; long leftBoundaryY = yChrom.getIndex() == 1 ? 0 : chromosomeBoundaries[yChrom.getIndex() - 2]; long xChromPos = (xGenomeStart - leftBoundaryX) * 1000; long yChromPos = (yGenomeStart - leftBoundaryY) * 1000; String txt = ""; txt += ""; txt += xChrom.getName(); txt += ":"; txt += String.valueOf(xChromPos); txt += "
"; txt += yChrom.getName(); txt += ":"; txt += String.valueOf(yChromPos); txt += ""; if (xChrom.getName().toLowerCase().contains("chr")) { hic.setXPosition(xChrom.getName() + ":" + xChromPos); } else { hic.setXPosition("chr" + xChrom.getName() + ":" + xChromPos); } if (yChrom.getName().toLowerCase().contains("chr")) { hic.setYPosition(yChrom.getName() + ":" + yChromPos); } else { hic.setYPosition("chr" + yChrom.getName() + ":" + yChromPos); } return txt; } } else { //Update Position in hic. Used for clipboard copy: if (hic.getXContext().getChromosome().getName().toLowerCase().contains("chr")) { hic.setXPosition(hic.getXContext().getChromosome().getName() + ":" + formatter.format(xGenomeStart) + "-" + formatter.format(xGenomeEnd)); } else { hic.setXPosition("chr" + hic.getXContext().getChromosome().getName() + ":" + formatter.format(xGenomeStart) + "-" + formatter.format(xGenomeEnd)); } if (hic.getYContext().getChromosome().getName().toLowerCase().contains("chr")) { hic.setYPosition(hic.getYContext().getChromosome().getName() + ":" + formatter.format(yGenomeStart) + "-" + formatter.format(yGenomeEnd)); } else { hic.setYPosition("chr" + hic.getYContext().getChromosome().getName() + ":" + formatter.format(yGenomeStart) + "-" + formatter.format(yGenomeEnd)); } //int binX = (int) ((mainWindow.xContext.getOrigin() + e.getX() * mainWindow.xContext.getScale()) / getBinWidth()); //int binY = (int) ((mainWindow.yContext.getOrigin() + e.getY() * mainWindow.yContext.getScale()) / getBinWidth()); StringBuilder txt = new StringBuilder(); txt.append(""); txt.append(hic.getXContext().getChromosome().getName()); txt.append(":"); txt.append(formatter.format(Math.round((xGenomeStart - 1) * HiCGlobals.hicMapScale + 1))); txt.append("-"); txt.append(formatter.format(Math.round(xGenomeEnd) * HiCGlobals.hicMapScale)); if (xGridAxis instanceof HiCFragmentAxis) { String fragNumbers; int binSize = zd.getZoom().getBinSize(); if (binSize == 1) { fragNumbers = formatter.format(binX); } else { int leftFragment = binX * binSize; int rightFragment = ((binX + 1) * binSize) - 1; fragNumbers = formatter.format(leftFragment) + "-" + formatter.format(rightFragment); } txt.append(" ("); txt.append(fragNumbers); txt.append(" len="); txt.append(formatter.format(xGenomeEnd - xGenomeStart)); txt.append(")"); } txt.append("
"); txt.append(hic.getYContext().getChromosome().getName()); txt.append(":"); txt.append(formatter.format(Math.round((yGenomeStart - 1) * HiCGlobals.hicMapScale + 1))); txt.append("-"); txt.append(formatter.format(Math.round(yGenomeEnd * HiCGlobals.hicMapScale))); if (yGridAxis instanceof HiCFragmentAxis) { String fragNumbers; int binSize = zd.getZoom().getBinSize(); if (binSize == 1) { fragNumbers = formatter.format(binY); } else { int leftFragment = binY * binSize; int rightFragment = ((binY + 1) * binSize) - 1; fragNumbers = formatter.format(leftFragment) + "-" + formatter.format(rightFragment); } txt.append(" ("); txt.append(fragNumbers); txt.append(" len="); txt.append(formatter.format(yGenomeEnd - yGenomeStart)); txt.append(")"); } txt.append(""); if (hic.isInPearsonsMode()) { float value = zd.getPearsonValue(binX, binY, hic.getObsNormalizationType()); if (!Float.isNaN(value)) { txt.append("
"); txt.append("value = "); txt.append(value); txt.append(""); } } else { float value = hic.getNormalizedObservedValue(binX, binY); if (!Float.isNaN(value)) { txt.append("
"); txt.append("observed value (O) = "); txt.append(getFloatString(value)); txt.append(""); } int c1 = hic.getXContext().getChromosome().getIndex(); int c2 = hic.getYContext().getChromosome().getIndex(); double ev = getExpectedValue(c1, c2, binX, binY, zd, hic.getExpectedValues()); String evString = ev < 0.001 || Double.isNaN(ev) ? String.valueOf(ev) : formatter.format(ev); txt.append("
expected value (E) = ").append(evString).append(""); if (ev > 0 && !Float.isNaN(value)) { txt.append("
O/E = "); txt.append(formatter.format(value / ev)).append(""); } else { txt.append("
O/E = NaN"); } MatrixZoomData controlZD = hic.getControlZd(); if (controlZD != null) { float controlValue = hic.getNormalizedControlValue(binX, binY); txt.append("

"); txt.append("control value (C) = "); txt.append(getFloatString(controlValue)); txt.append(""); double evCtrl = getExpectedValue(c1, c2, binX, binY, controlZD, hic.getExpectedControlValues()); String evStringCtrl = evCtrl < 0.001 || Double.isNaN(evCtrl) ? String.valueOf(evCtrl) : formatter.format(evCtrl); txt.append("
expected control value (EC) = ").append(evStringCtrl).append(""); if (evCtrl > 0 && !Float.isNaN(controlValue)) { txt.append("
C/EC = "); txt.append(formatter.format(controlValue / evCtrl)).append(""); txt.append("

(O/E)/(C/EC) = "); txt.append(formatter.format((value / ev) / (controlValue / evCtrl))).append(""); } else { txt.append("
C/EC = NaN"); } double obsAvg = zd.getAverageCount(); double obsValue = (value / obsAvg); txt.append("

"); txt.append("average observed value (AVG) = ").append(getFloatString((float) obsAvg)); txt.append("
O' = O/AVG = ").append(getFloatString((float) obsValue)); txt.append(""); double ctrlAvg = controlZD.getAverageCount(); double ctlValue = (float) (controlValue / ctrlAvg); txt.append("
"); txt.append("average control value (AVGC) = ").append(getFloatString((float) ctrlAvg)); txt.append("
C' = C/AVGC = ").append(getFloatString((float) ctlValue)); txt.append(""); if (value > 0 && controlValue > 0) { double ratio = obsValue / ctlValue; txt.append("
"); txt.append("O'/C' = ").append(getFloatString((float) ratio)); txt.append(""); double diff = (obsValue - ctlValue) * (obsAvg / 2. + ctrlAvg / 2.); txt.append("
"); txt.append("(O'-C')*(AVG/2 + AVGC/2) = "); txt.append(getFloatString((float) diff)); txt.append(""); } } txt.append(superAdapter.getTrackPanelPrintouts(x, y)); } Point currMouse = new Point(x, y); double minDistance = Double.POSITIVE_INFINITY; //mouseIsOverFeature = false; currentFeature = null; if (activelyEditingAssembly) { // current feature is populated only from all main feature pairs, contains does not work for (Feature2DGuiContainer loop : allMainFeaturePairs) { if (loop.getRectangle().contains(x, y)) { currentFeature = loop; } } if (!selectedFeatures.isEmpty()) { Collections.sort(selectedFeatures); appendWithSpan(txt, selectedFeatures); } else { StringBuilder txt0 = new StringBuilder(); for (Feature2DGuiContainer loop : allFeaturePairs) { if (loop.getRectangle().contains(x, y)) { // TODO - why is this code duplicated in this file? txt0.append("

"); txt0.append(loop.getFeature2D().tooltipText()); txt0.append(""); } } txt.insert(0, txt0); } } else { int numLayers = superAdapter.getAllLayers().size(); int globalPriority = numLayers; for (Feature2DGuiContainer loop : allFeaturePairs) { if (loop.getRectangle().contains(x, y)) { // TODO - why is this code duplicated in this file? txt.append("

"); txt.append(loop.getFeature2D().tooltipText()); txt.append(""); int layerNum = superAdapter.getAllLayers().indexOf(loop.getAnnotationLayerHandler()); int loopPriority = numLayers - layerNum; double distance = currMouse.distance(loop.getRectangle().getX(), loop.getRectangle().getY()); if (distance < minDistance && loopPriority <= globalPriority) { minDistance = distance; currentFeature = loop; globalPriority = loopPriority; } //mouseIsOverFeature = true; } } } txt.append("
"); txt.append(""); return txt.toString(); } return null; } private void appendWithSpan(StringBuilder txt, List selectedFeatures) { int numFeatures = selectedFeatures.size(); for (int i = 0; i < Math.min(numFeatures, 3); i++) { appendSectionWithSpan(txt, selectedFeatures.get(i).tooltipText()); } if (numFeatures == 3) { appendSectionWithSpan(txt, selectedFeatures.get(2).tooltipText()); } else if (numFeatures > 3) { appendSectionWithSpan(txt, "..."); appendSectionWithSpan(txt, selectedFeatures.get(numFeatures - 1).tooltipText()); } } private void appendSectionWithSpan(StringBuilder txt, String content) { txt.append("

"); txt.append(content); txt.append(""); } private Chromosome getChromFromBoundaries(long[] chromosomeBoundaries, long genomeStart) { Chromosome chrom = null; for (int i = 0; i < chromosomeBoundaries.length; i++) { if (chromosomeBoundaries[i] > genomeStart) { chrom = hic.getChromosomeHandler().getChromosomeFromIndex(i + 1); break; } } return chrom; } private void addJumpToDiagonalMenuItems(JidePopupMenu menu, int xMousePos, int yMousePos) { final double preJumpBinOriginX = hic.getXContext().getBinOrigin(); final double preJumpBinOriginY = hic.getYContext().getBinOrigin(); // xMousePos and yMousePos coordinates are relative to the heatmap panel and not the screen final int clickedBinX = (int) (preJumpBinOriginX + xMousePos / hic.getScaleFactor()); final int clickedBinY = (int) (preJumpBinOriginY + yMousePos / hic.getScaleFactor()); // these coordinates are relative to the screen and not the heatmap panel final int defaultPointerDestinationX = (int) (parent.getLocationOnScreen().getX() + xMousePos); final int defaultPointerDestinationY = (int) (parent.getLocationOnScreen().getY() + yMousePos); // get maximum number of bins on the X and Y axes Matrix matrix = hic.getMatrix(); MatrixZoomData matrixZoomData = matrix.getZoomData(hic.getZoom()); final long binCountX = matrixZoomData.getXGridAxis().getBinCount(); final long binCountY = matrixZoomData.getYGridAxis().getBinCount(); if (clickedBinX > clickedBinY) { final JMenuItem jumpToDiagonalLeft = new JMenuItem('\u25C0' + " Jump To Diagonal"); jumpToDiagonalLeft.setSelected(straightEdgeEnabled); jumpToDiagonalLeft.addActionListener(new ActionListener() { @Override public void actionPerformed(ActionEvent e) { double postJumpBinOriginX = preJumpBinOriginX - (clickedBinX - clickedBinY); hic.moveBy(clickedBinY - clickedBinX, 0); if (postJumpBinOriginX < 0) { heatmapMouseBot.mouseMove((int) (defaultPointerDestinationX + postJumpBinOriginX * hic.getScaleFactor()), defaultPointerDestinationY); return; } heatmapMouseBot.mouseMove(defaultPointerDestinationX, defaultPointerDestinationY); } }); menu.add(jumpToDiagonalLeft); final JMenuItem jumpToDiagonalDown = new JMenuItem('\u25BC' + " Jump To Diagonal"); jumpToDiagonalDown.setSelected(straightEdgeEnabled); jumpToDiagonalDown.addActionListener(new ActionListener() { @Override public void actionPerformed(ActionEvent e) { double postJumpBinOriginY = preJumpBinOriginY + (clickedBinX - clickedBinY); hic.moveBy(0, clickedBinX - clickedBinY); if (postJumpBinOriginY + parent.getHeight() / hic.getScaleFactor() > binCountY) { heatmapMouseBot.mouseMove(defaultPointerDestinationX, (int) (defaultPointerDestinationY + (postJumpBinOriginY + parent.getHeight() / hic.getScaleFactor() - binCountY))); return; } heatmapMouseBot.mouseMove(defaultPointerDestinationX, defaultPointerDestinationY); } }); menu.add(jumpToDiagonalDown); } else if (clickedBinX < clickedBinY) { final JMenuItem jumpToDiagonalUp = new JMenuItem('\u25B2' + " Jump To Diagonal"); jumpToDiagonalUp.setSelected(straightEdgeEnabled); jumpToDiagonalUp.addActionListener(new ActionListener() { @Override public void actionPerformed(ActionEvent e) { double postJumpBinOriginY = preJumpBinOriginY - (clickedBinY - clickedBinX); hic.moveBy(0, clickedBinX - clickedBinY); if (postJumpBinOriginY < 0) { heatmapMouseBot.mouseMove(defaultPointerDestinationX, (int) (defaultPointerDestinationY + postJumpBinOriginY * hic.getScaleFactor())); return; } heatmapMouseBot.mouseMove(defaultPointerDestinationX, defaultPointerDestinationY); } }); menu.add(jumpToDiagonalUp); final JMenuItem jumpToDiagonalRight = new JMenuItem('\u25B6' + " Jump To Diagonal"); jumpToDiagonalRight.setSelected(straightEdgeEnabled); jumpToDiagonalRight.addActionListener(new ActionListener() { @Override public void actionPerformed(ActionEvent e) { double postJumpBinOriginX = preJumpBinOriginX + (clickedBinY - clickedBinX); hic.moveBy(clickedBinY - clickedBinX, 0); if (postJumpBinOriginX + parent.getWidth() / hic.getScaleFactor() > binCountX) { heatmapMouseBot.mouseMove((int) (defaultPointerDestinationX + (postJumpBinOriginX + parent.getWidth() / hic.getScaleFactor() - binCountX)), defaultPointerDestinationY); return; } heatmapMouseBot.mouseMove(defaultPointerDestinationX, defaultPointerDestinationY); } }); menu.add(jumpToDiagonalRight); } } private JidePopupMenu getAssemblyPopupMenu(final int xMousePos, final int yMousePos, JidePopupMenu menu) { if (HiCGlobals.phasing) { final JMenuItem phaseMergeItems = new JMenuItem("Merge phased blocks"); phaseMergeItems.setEnabled(selectedSuperscaffolds.size() > 1); phaseMergeItems.addActionListener(new ActionListener() { @Override public void actionPerformed(ActionEvent e) { AssemblyOperationExecutor.phaseMerge(superAdapter, selectedSuperscaffolds); // Cleanup parent.removeSelection(); } }); menu.add(phaseMergeItems); } else { final JMenuItem miMoveToTop = new JMenuItem("Move to top"); miMoveToTop.setEnabled(!selectedFeatures.isEmpty()); miMoveToTop.addActionListener(new ActionListener() { @Override public void actionPerformed(ActionEvent e) { AssemblyOperationExecutor.moveSelection(superAdapter, selectedFeatures, null); parent.removeSelection(); } }); menu.add(miMoveToTop); final JMenuItem miMoveToDebris = new JMenuItem("Move to debris"); miMoveToDebris.setEnabled(!selectedFeatures.isEmpty()); miMoveToDebris.addActionListener(new ActionListener() { @Override public void actionPerformed(ActionEvent e) { parent.moveSelectionToEnd(); } }); menu.add(miMoveToDebris); final JMenuItem miMoveToDebrisAndDisperse = new JMenuItem("Move to debris and add boundaries"); miMoveToDebrisAndDisperse.setEnabled(selectedFeatures != null && !selectedFeatures.isEmpty()); miMoveToDebrisAndDisperse.addActionListener(new ActionListener() { @Override public void actionPerformed(ActionEvent e) { moveSelectionToEndAndDisperse(); } }); menu.add(miMoveToDebrisAndDisperse); final JMenuItem groupItems = new JMenuItem("Remove chr boundaries"); groupItems.setEnabled(selectedFeatures.size() > 1); groupItems.addActionListener(new ActionListener() { @Override public void actionPerformed(ActionEvent e) { AssemblyOperationExecutor.multiMerge(superAdapter, selectedFeatures); // Cleanup parent.removeSelection(); } }); menu.add(groupItems); final JMenuItem splitItems = new JMenuItem("Add chr boundaries"); splitItems.setEnabled(!selectedFeatures.isEmpty()); splitItems.addActionListener(new ActionListener() { @Override public void actionPerformed(ActionEvent e) { AssemblyOperationExecutor.multiSplit(superAdapter, selectedFeatures); // Cleanup parent.removeSelection(); } }); menu.add(splitItems); } final JMenuItem miUndo = new JMenuItem("Undo"); miUndo.addActionListener(new ActionListener() { @Override public void actionPerformed(ActionEvent e) { superAdapter.getAssemblyStateTracker().undo(); parent.removeSelection(); superAdapter.refresh(); } }); miUndo.setEnabled(superAdapter.getAssemblyStateTracker().checkUndo()); menu.add(miUndo); final JMenuItem miRedo = new JMenuItem("Redo"); miRedo.addActionListener(new ActionListener() { @Override public void actionPerformed(ActionEvent e) { superAdapter.getAssemblyStateTracker().redo(); parent.removeSelection(); superAdapter.refresh(); } }); miRedo.setEnabled(superAdapter.getAssemblyStateTracker().checkRedo()); menu.add(miRedo); return menu; } void moveSelectionToEndAndDisperse() { AssemblyScaffoldHandler assemblyHandler = superAdapter.getAssemblyStateTracker().getAssemblyHandler(); final List lastLine = assemblyHandler.getListOfSuperscaffolds().get(assemblyHandler.getListOfSuperscaffolds().size() - 1); int lastId = Math.abs(lastLine.get(lastLine.size() - 1)) - 1; AssemblyOperationExecutor.moveAndDisperseSelection(superAdapter, selectedFeatures, assemblyHandler.getListOfScaffolds().get(lastId).getCurrentFeature2D()); parent.removeSelection(); } public Feature2DGuiContainer getCurrentUpstreamFeature() { return this.currentUpstreamFeature; } public Feature2DGuiContainer getCurrentDownstreamFeature() { return this.currentDownstreamFeature; } public enum PromptedAssemblyAction {REGROUP, PASTE, INVERT, CUT, ADJUST, NONE, PASTETOP, PASTEBOTTOM} private enum DragMode {ZOOM, ANNOTATE, RESIZE, PAN, SELECT, NONE} private enum AdjustAnnotation {LEFT, RIGHT, NONE} // @Override // public String getToolTipText(MouseEvent e) { // return toolTipText(e.getX(), e.getY()); // // } } ================================================ FILE: src/juicebox/mapcolorui/HeatmapPanel.java ================================================ /* * The MIT License (MIT) * * Copyright (c) 2011-2021 Broad Institute, Aiden Lab, Rice University, Baylor College of Medicine * * Permission is hereby granted, free of charge, to any person obtaining a copy * of this software and associated documentation files (the "Software"), to deal * in the Software without restriction, including without limitation the rights * to use, copy, modify, merge, publish, distribute, sublicense, and/or sell * copies of the Software, and to permit persons to whom the Software is * furnished to do so, subject to the following conditions: * * The above copyright notice and this permission notice shall be included in * all copies or substantial portions of the Software. * * THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR * IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, * FITNESS FOR A PARTICULAR PURPOSE AND NON-INFRINGEMENT. IN NO EVENT SHALL THE * AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER * LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, * OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN * THE SOFTWARE. */ package juicebox.mapcolorui; import juicebox.HiC; import juicebox.HiCGlobals; import juicebox.MainWindow; import juicebox.assembly.AssemblyHeatmapHandler; import juicebox.assembly.AssemblyOperationExecutor; import juicebox.assembly.AssemblyScaffoldHandler; import juicebox.data.ChromosomeHandler; import juicebox.data.MatrixZoomData; import juicebox.data.basics.Chromosome; import juicebox.gui.SuperAdapter; import juicebox.track.feature.AnnotationLayerHandler; import juicebox.track.feature.Feature2D; import juicebox.track.feature.Feature2DGuiContainer; import juicebox.windowui.MatrixType; import juicebox.windowui.NormalizationType; import org.broad.igv.renderer.GraphicUtils; import org.broad.igv.ui.FontManager; import org.broad.igv.util.Pair; import javax.swing.*; import java.awt.*; import java.awt.image.BufferedImage; import java.util.ArrayList; import java.util.List; public class HeatmapPanel extends JComponent { //public static final int clickDelay1 = (Integer) Toolkit.getDefaultToolkit().getDesktopProperty("awt.multiClickInterval"); private static final long serialVersionUID = 9000028; private final MainWindow mainWindow; private final HiC hic; private final SuperAdapter superAdapter; private final ColorScaleHandler colorScaleHandler = new ColorScaleHandler(); private final GeneralTileManager tileManager = new GeneralTileManager(colorScaleHandler); private final HeatmapMouseHandler mouseHandler; private boolean showGridLines = true; private final HeatmapClickListener clickListener; private long[] chromosomeBoundaries; private final BoundingBoxRenderer boundingBoxRenderer = new BoundingBoxRenderer(this); public HeatmapPanel(SuperAdapter superAdapter) { this.mainWindow = superAdapter.getMainWindow(); this.superAdapter = superAdapter; this.hic = superAdapter.getHiC(); superAdapter.setPearsonColorScale(colorScaleHandler.getPearsonColorScale()); mouseHandler = new HeatmapMouseHandler(hic, superAdapter, this); clickListener = new HeatmapClickListener(this); addMouseMotionListener(mouseHandler); addMouseListener(mouseHandler); addMouseListener(clickListener); addMouseWheelListener(mouseHandler); } public long[] getChromosomeBoundaries() { return this.chromosomeBoundaries; } public void setChromosomeBoundaries(long[] chromosomeBoundaries) { this.chromosomeBoundaries = chromosomeBoundaries; boundingBoxRenderer.setChromosomeBoundaries(chromosomeBoundaries); } public int getMinimumDimension() { return Math.min(getWidth(), getHeight()); } @Override protected void paintComponent(Graphics g1) { Graphics2D g = (Graphics2D) g1; g.setRenderingHint(RenderingHints.KEY_ANTIALIASING, RenderingHints.VALUE_ANTIALIAS_ON); Rectangle clipBounds = g.getClipBounds(); g.clearRect(clipBounds.x, clipBounds.y, clipBounds.width, clipBounds.height); if (HiCGlobals.isDarkulaModeEnabled) { g.setColor(Color.darkGray); g.fillRect(clipBounds.x, clipBounds.y, clipBounds.width, clipBounds.height); } // Are we ready to draw? final MatrixZoomData zd; try { zd = hic.getZd(); } catch (Exception ex) { return; } MatrixZoomData controlZd = null; try { controlZd = hic.getControlZd(); } catch (Exception ee) { ee.printStackTrace(); } if (hic.getXContext() == null) return; // todo pearsons if (hic.isInPearsonsMode()) { // Possibly force asynchronous computation of pearsons if (hic.isPearsonsNotAvailableForFile(false)) { JOptionPane.showMessageDialog(this, "Pearson's matrix is not available at this " + "resolution, use 500KB or lower resolution."); return; } if (hic.isInControlPearsonsMode() && hic.isPearsonsNotAvailableForFile(false)) { JOptionPane.showMessageDialog(this, "Pearson's matrix is not available at this " + "resolution, use 500KB or lower resolution."); return; } } // Same scale used for X & Y (square pixels) final double scaleFactor = hic.getScaleFactor(); final int screenWidth = getBounds().width; final int screenHeight = getBounds().height; double binOriginX = hic.getXContext().getBinOrigin(); double bRight = binOriginX + (screenWidth / scaleFactor); double binOriginY = hic.getYContext().getBinOrigin(); double bBottom = binOriginY + (screenHeight / scaleFactor); HeatmapRenderer renderer = new HeatmapRenderer(g, colorScaleHandler); boolean allTilesNull = tileManager.renderHiCTiles(renderer, binOriginX, binOriginY, bRight, bBottom, zd, controlZd, scaleFactor, this.getBounds(), hic, this, superAdapter); boolean isWholeGenome = ChromosomeHandler.isWholeGenomeView(hic.getXContext(), hic.getYContext()); Color color0 = g.getColor(); if (isWholeGenome) { boundingBoxRenderer.drawAllByAllGrid(g, zd, showGridLines, binOriginX, binOriginY, scaleFactor); } else { boundingBoxRenderer.drawRegularGrid(g, zd, showGridLines, hic.getChromosomeHandler(), binOriginX, binOriginY, scaleFactor); } CursorRenderer cursorRenderer = new CursorRenderer(this); cursorRenderer.drawCursors(g, hic.getCursorPoint(), hic.getDiagonalCursorPoint(), binOriginX, binOriginY, scaleFactor, hic.getColorForRuler(), bRight, bBottom); g.setColor(color0); if (allTilesNull) { g.setFont(FontManager.getFont(12)); GraphicUtils.drawCenteredText("Normalization vectors not available at this resolution. Try a different normalization.", clipBounds, g); } else { // Render loops int centerX = (int) ((screenWidth / scaleFactor) / 2); int centerY = (int) ((screenHeight / scaleFactor) / 2); Graphics2D g2 = (Graphics2D) g.create(); mouseHandler.clearFeaturePairs(); final boolean activelyEditingAssembly = mouseHandler.getIsActivelyEditingAssembly(); List handlers; if (activelyEditingAssembly) { // Only look at assembly layers if we're in assembly mode handlers = superAdapter.getAssemblyLayerHandlers(); } else { handlers = superAdapter.getAllLayers(); } for (AnnotationLayerHandler handler : handlers) { List loops = handler.getNearbyFeatures(zd, zd.getChr1Idx(), zd.getChr2Idx(), centerX, centerY, Feature2DHandler.numberOfLoopsToFind, binOriginX, binOriginY, scaleFactor); List cLoopsReflected = new ArrayList<>(); for (Feature2D feature2D : loops) { if (zd.getChr1Idx() == zd.getChr2Idx() && !feature2D.isOnDiagonal()) { cLoopsReflected.add(feature2D.reflectionAcrossDiagonal()); } } loops.addAll(cLoopsReflected); mouseHandler.addAllFeatures(handler, loops, zd, binOriginX, binOriginY, scaleFactor, activelyEditingAssembly); final List highlightedFeatures = mouseHandler.getHighlightedFeature(); final boolean showFeatureHighlight = mouseHandler.getShouldShowHighlight(); FeatureRenderer.render(g2, handler, loops, zd, binOriginX, binOriginY, scaleFactor, highlightedFeatures, showFeatureHighlight, this.getWidth(), this.getHeight()); } mouseHandler.renderMouseAnnotations(g2); g2.dispose(); } } public Image getThumbnailImage(MatrixZoomData zd0, MatrixZoomData ctrl0, int tw, int th, MatrixType displayOption, NormalizationType observedNormalizationType, NormalizationType controlNormalizationType) { if (MatrixType.isPearsonType(displayOption) && hic.isPearsonsNotAvailableForFile(false)) { JOptionPane.showMessageDialog(this, "Pearson's matrix is not available at this resolution"); return null; } int maxBinCountX = (int) zd0.getXGridAxis().getBinCount(); int maxBinCountY = (int) zd0.getYGridAxis().getBinCount(); int wh = Math.max(maxBinCountX, maxBinCountY); // todo assumption for thumbnail //if (wh > 1000) wh=1000; // this can happen with single resolution hic files - breaks thumbnail localization BufferedImage image = (BufferedImage) createImage(wh, wh); Graphics2D g = image.createGraphics(); if (HiCGlobals.isDarkulaModeEnabled) { g.setColor(Color.darkGray); g.fillRect(0, 0, wh, wh); } HeatmapRenderer renderer = new HeatmapRenderer(g, colorScaleHandler); boolean success = renderer.render(0, 0, maxBinCountX, maxBinCountY, zd0, ctrl0, displayOption, observedNormalizationType, controlNormalizationType, hic.getExpectedValues(), hic.getExpectedControlValues(), false); if (!success) return null; return image.getScaledInstance(tw, th, Image.SCALE_REPLICATE); } public boolean getShowGridLines() { return showGridLines; } public void setShowGridLines(boolean showGridLines) { this.showGridLines = showGridLines; } public HiC getHiC() { return this.hic; } public MainWindow getMainWindow() { return this.mainWindow; } public SuperAdapter getSuperAdapter() { return this.superAdapter; } public void unsafeSetSelectedChromosomes(Chromosome xChrom, Chromosome yChrom) { superAdapter.unsafeSetSelectedChromosomes(xChrom, yChrom); } public void updateThumbnail() { superAdapter.updateThumbnail(); } public void clearTileCache() { tileManager.clearTileCache(); } public void launchColorSelectionMenu(Pair selectedFeaturePair) { JColorChooser colorChooser = new JColorChooser(selectedFeaturePair.getSecond().getColor()); JDialog dialog = JColorChooser.createDialog(new JPanel(null), "feature Color Selection", true, colorChooser, null, null); dialog.setVisible(true); Color c = colorChooser.getColor(); if (c != null) { selectedFeaturePair.getSecond().setColor(c); } } public void enableAssemblyEditing() { SuperAdapter.assemblyModeCurrentlyActive = true; mouseHandler.setActivelyEditingAssembly(true); AssemblyHeatmapHandler.setSuperAdapter(superAdapter); } public void disableAssemblyEditing() { mouseHandler.clearSelectedFeatures(); superAdapter.getMainViewPanel().toggleToolTipUpdates(true); mouseHandler.setActivelyEditingAssembly(false); HiCGlobals.splitModeEnabled = false; SuperAdapter.assemblyModeCurrentlyActive = false; } public void removeHighlightedFeature() { mouseHandler.setFeatureOptionMenuEnabled(false); mouseHandler.eraseHighlightedFeatures(); superAdapter.repaintTrackPanels(); repaint(); } public void removeSelection() { mouseHandler.clearSelectedFeatures(); superAdapter.updatePreviousTempSelectedGroups(mouseHandler.getTempSelectedGroup()); mouseHandler.setTempSelectedGroup(null); superAdapter.clearEditsAndUpdateLayers(); HiCGlobals.splitModeEnabled = false; superAdapter.getMainViewPanel().toggleToolTipUpdates(true); removeHighlightedFeature(); Chromosome chrX = superAdapter.getHiC().getXContext().getChromosome(); Chromosome chrY = superAdapter.getHiC().getYContext().getChromosome(); superAdapter.getEditLayer().filterTempSelectedGroup(chrX.getIndex(), chrY.getIndex()); final Feature2D debrisFeature = mouseHandler.getDebrisFeature(); if (debrisFeature != null) { superAdapter.getEditLayer().getAnnotationLayer().getFeatureHandler().getFeatureList().checkAndRemoveFeature( chrX.getIndex(), chrY.getIndex(), debrisFeature); } mouseHandler.resetCurrentPromptedAssemblyAction(); mouseHandler.reset(); repaint(); } public void moveSelectionToEnd() { AssemblyScaffoldHandler assemblyHandler = superAdapter.getAssemblyStateTracker().getAssemblyHandler(); final List lastLine = assemblyHandler.getListOfSuperscaffolds().get(assemblyHandler.getListOfSuperscaffolds().size() - 1); int lastId = Math.abs(lastLine.get(lastLine.size() - 1)) - 1; AssemblyOperationExecutor.moveSelection(superAdapter, getSelectedFeatures(), assemblyHandler.getListOfScaffolds().get(lastId).getCurrentFeature2D()); removeSelection(); } public void reset() { colorScaleHandler.reset(); clearTileCache(); } public void setNewDisplayRange(MatrixType displayOption, double min, double max, String key) { colorScaleHandler.setNewDisplayRange(displayOption, min, max, key); clearTileCache(); repaint(); } public HeatmapMouseHandler.PromptedAssemblyAction getCurrentPromptedAssemblyAction() { return mouseHandler.getCurrentPromptedAssemblyAction(); } public HeatmapMouseHandler.PromptedAssemblyAction getPromptedAssemblyActionOnClick() { return mouseHandler.getPromptedAssemblyActionOnClick(); } public void setPromptedAssemblyActionOnClick(HeatmapMouseHandler.PromptedAssemblyAction promptedAssemblyAction) { mouseHandler.setPromptedAssemblyActionOnClick(promptedAssemblyAction); } public List getSelectedFeatures() { return mouseHandler.getSelectedFeatures(); } public Feature2DGuiContainer getCurrentUpstreamFeature() { return mouseHandler.getCurrentUpstreamFeature(); } public Feature2DGuiContainer getCurrentDownstreamFeature() { return mouseHandler.getCurrentDownstreamFeature(); } } ================================================ FILE: src/juicebox/mapcolorui/HeatmapRenderer.java ================================================ /* * The MIT License (MIT) * * Copyright (c) 2011-2021 Broad Institute, Aiden Lab, Rice University, Baylor College of Medicine * * Permission is hereby granted, free of charge, to any person obtaining a copy * of this software and associated documentation files (the "Software"), to deal * in the Software without restriction, including without limitation the rights * to use, copy, modify, merge, publish, distribute, sublicense, and/or sell * copies of the Software, and to permit persons to whom the Software is * furnished to do so, subject to the following conditions: * * The above copyright notice and this permission notice shall be included in * all copies or substantial portions of the Software. * * THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR * IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, * FITNESS FOR A PARTICULAR PURPOSE AND NON-INFRINGEMENT. IN NO EVENT SHALL THE * AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER * LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, * OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN * THE SOFTWARE. */ package juicebox.mapcolorui; import juicebox.HiCGlobals; import juicebox.data.Block; import juicebox.data.ContactRecord; import juicebox.data.ExpectedValueFunction; import juicebox.data.MatrixZoomData; import juicebox.gui.SuperAdapter; import juicebox.matrix.BasicMatrix; import juicebox.windowui.MatrixType; import juicebox.windowui.NormalizationType; import org.broad.igv.renderer.ColorScale; import java.awt.*; import java.util.List; import java.util.*; /** * @author jrobinso * @since Aug 11, 2010 */ public class HeatmapRenderer { public static float PSEUDO_COUNT = 1f; protected static final int PIXEL_WIDTH = 1, PIXEL_HEIGHT = 1; private final ColorScaleHandler colorScaleHandler; private final Graphics2D g; public HeatmapRenderer(Graphics2D g, ColorScaleHandler colorScaleHandler) { this.g = g; this.colorScaleHandler = colorScaleHandler; } public static String getColorScaleCacheKey(MatrixZoomData zd, MatrixType displayOption, NormalizationType obsNorm, NormalizationType ctrlNorm) { return zd.getColorScaleKey(displayOption, obsNorm, ctrlNorm); } @SuppressWarnings("SuspiciousNameCombination") public boolean render(int originX, int originY, int width, int height, final MatrixZoomData zd, final MatrixZoomData controlZD, final MatrixType displayOption, final NormalizationType observedNormalizationType, final NormalizationType controlNormalizationType, final ExpectedValueFunction df, final ExpectedValueFunction controlDF, boolean isImportant) { if (g != null) { g.setRenderingHint(RenderingHints.KEY_COLOR_RENDERING, RenderingHints.VALUE_COLOR_RENDER_SPEED); g.setRenderingHint(RenderingHints.KEY_RENDERING, RenderingHints.VALUE_RENDER_SPEED); } int chr1 = zd.getChr1Idx(); int chr2 = zd.getChr2Idx(); int x = originX; int y = originY; boolean isWholeGenome = chr1 == 0 && chr2 == 0; boolean sameChr = (chr1 == chr2); if (sameChr) { // transpose if necessary; convention is to use upper diagonal if (x > y) { //noinspection SuspiciousNameCombination x = originY; y = originX; int tmp = width; width = height; height = tmp; } } int maxX = x + width - 1; int maxY = y + height - 1; String key = zd.getColorScaleKey(displayOption, observedNormalizationType, controlNormalizationType); String controlKey = zd.getColorScaleKey(displayOption, observedNormalizationType, controlNormalizationType); float pseudoCountObs = PSEUDO_COUNT; float pseudoCountCtrl = PSEUDO_COUNT; if (displayOption == MatrixType.NORM2) { renderNorm2(zd, isWholeGenome, observedNormalizationType, key, displayOption, originX, originY, width, height); } else if (displayOption == MatrixType.NORM2CTRL) { renderNorm2(controlZD, isWholeGenome, controlNormalizationType, controlKey, displayOption, originX, originY, width, height); } else if (displayOption == MatrixType.NORM2OBSVSCTRL) { if (controlDF == null) { System.err.println("Control DF is NULL"); return false; } renderNorm2VS(zd, controlZD, isWholeGenome, observedNormalizationType, controlNormalizationType, key, displayOption, originX, originY, width, height); } else if (displayOption == MatrixType.PEARSON) { renderPearson(zd, df, key, originX, originY, width, height); } else if (displayOption == MatrixType.PEARSONCTRL) { if (controlDF == null) { System.err.println("Control DF is NULL"); return false; } renderPearson(controlZD, controlDF, controlKey, originX, originY, width, height); } else if (displayOption == MatrixType.PEARSONVS) { if (controlDF == null) { System.err.println("Control DF is NULL"); return false; } renderPearsonVS(zd, controlZD, df, controlDF, key, originX, originY, width, height); } else if (displayOption == MatrixType.CONTROL) { List ctrlBlocks = getTheBlocks(controlZD, x, y, maxX, maxY, controlNormalizationType, isImportant); if (controlZD == null || ctrlBlocks == null) return false; ColorScale cs = colorScaleHandler.getColorScale(controlKey, displayOption, isWholeGenome, ctrlBlocks, 1f); renderSimpleMap(ctrlBlocks, cs, width, height, sameChr, originX, originY); } else if (displayOption == MatrixType.LOGC) { List ctrlBlocks = getTheBlocks(controlZD, x, y, maxX, maxY, controlNormalizationType, isImportant); if (controlZD == null || ctrlBlocks == null) return false; ColorScale cs = colorScaleHandler.getColorScale(controlKey, displayOption, isWholeGenome, ctrlBlocks, 1f); renderSimpleLogMap(ctrlBlocks, cs, width, height, sameChr, originX, originY); } else if (displayOption == MatrixType.OECTRLV2 || displayOption == MatrixType.OECTRL) { List ctrlBlocks = getTheBlocks(controlZD, x, y, maxX, maxY, controlNormalizationType, isImportant); if (controlZD == null || ctrlBlocks == null) return false; ColorScale cs = colorScaleHandler.getColorScale(controlKey, displayOption, isWholeGenome, ctrlBlocks, 1f); renderObservedOverExpectedMap(chr1, ctrlBlocks, controlDF, controlZD, cs, sameChr, originX, originY, width, height, 0); } else if (displayOption == MatrixType.OECTRLP1V2 || displayOption == MatrixType.OECTRLP1) { List ctrlBlocks = getTheBlocks(controlZD, x, y, maxX, maxY, controlNormalizationType, isImportant); if (controlZD == null || ctrlBlocks == null) return false; ColorScale cs = colorScaleHandler.getColorScale(controlKey, displayOption, isWholeGenome, ctrlBlocks, 1f); renderObservedOverExpectedMap(chr1, ctrlBlocks, controlDF, controlZD, cs, sameChr, originX, originY, width, height, pseudoCountCtrl); } else if (displayOption == MatrixType.LOGCEO) { List ctrlBlocks = getTheBlocks(controlZD, x, y, maxX, maxY, controlNormalizationType, isImportant); if (controlZD == null || ctrlBlocks == null) return false; ColorScale cs = colorScaleHandler.getColorScale(controlKey, displayOption, isWholeGenome, ctrlBlocks, 1f); renderLogObservedBaseExpectedMap(chr1, ctrlBlocks, controlDF, controlZD, cs, sameChr, originX, originY, width, height); } else if (displayOption == MatrixType.LOGEOVS || displayOption == MatrixType.OCMEVS || displayOption == MatrixType.VS || displayOption == MatrixType.LOGVS || displayOption == MatrixType.OEVSV2 || displayOption == MatrixType.OEVS || displayOption == MatrixType.OEVSP1V2 || displayOption == MatrixType.OEVSP1 || displayOption == MatrixType.OERATIOV2 || displayOption == MatrixType.OERATIO || displayOption == MatrixType.OERATIOP1V2 || displayOption == MatrixType.OERATIOP1) { List blocks = getTheBlocks(zd, x, y, maxX, maxY, observedNormalizationType, isImportant); List ctrlBlocks = getTheBlocks(controlZD, x, y, maxX, maxY, controlNormalizationType, isImportant); if (blocks == null || ctrlBlocks == null) return false; if (blocks.isEmpty() && ctrlBlocks.isEmpty()) return false; ColorScale cs = colorScaleHandler.getColorScale(key, displayOption, isWholeGenome, blocks, ctrlBlocks, 1f); if (displayOption == MatrixType.LOGEOVS) { renderLogObsOverExpVSMap(chr1, blocks, ctrlBlocks, df, controlDF, zd, controlZD, cs, sameChr, originX, originY, width, height); } else if (displayOption == MatrixType.OCMEVS) { // renderLogObsMinusExpVSMap(chr1, blocks, ctrlBlocks, df, controlDF, zd, controlZD, cs, sameChr, originX, originY, width, height); } else if (displayOption == MatrixType.VS) { renderSimpleVSMap(blocks, ctrlBlocks, zd, controlZD, originX, originY, width, height, cs, sameChr); } else if (displayOption == MatrixType.LOGVS) { renderSimpleLogVSMap(blocks, ctrlBlocks, zd, controlZD, originX, originY, width, height, cs, sameChr); } else if (displayOption == MatrixType.OEVSP1V2 || displayOption == MatrixType.OEVSP1) { renderObservedOverExpectedVSMap(chr1, blocks, ctrlBlocks, df, controlDF, zd, controlZD, cs, sameChr, originX, originY, width, height, pseudoCountObs, pseudoCountCtrl); } else if (displayOption == MatrixType.OEVSV2 || displayOption == MatrixType.OEVS) { renderObservedOverExpectedVSMap(chr1, blocks, ctrlBlocks, df, controlDF, zd, controlZD, cs, sameChr, originX, originY, width, height, 0, 0); } else if (displayOption == MatrixType.OERATIOV2 || displayOption == MatrixType.OERATIO) { if (controlZD == null) return false; if (sameChr && (df == null || controlDF == null)) return false; renderOERatioMap(blocks, ctrlBlocks, zd, controlZD, df, controlDF, originX, originY, width, height, 0, 0, cs, sameChr, controlNormalizationType, chr1); } else if (displayOption == MatrixType.OERATIOP1V2 || displayOption == MatrixType.OERATIOP1) { if (controlZD == null) return false; if (sameChr && (df == null || controlDF == null)) return false; renderOERatioMap(blocks, ctrlBlocks, zd, controlZD, df, controlDF, originX, originY, width, height, pseudoCountObs, pseudoCountCtrl, cs, sameChr, controlNormalizationType, chr1); } } else if (displayOption == MatrixType.EXPECTED) { List blocks = getTheBlocks(zd, x, y, maxX, maxY, observedNormalizationType, isImportant); if (blocks == null) return false; ColorScale cs = colorScaleHandler.getColorScale(key, displayOption, isWholeGenome, blocks, 1f); renderExpectedMap(zd, df, sameChr, cs, originX, originY, width, height, chr1); } else if (displayOption == MatrixType.OEV2 || displayOption == MatrixType.OE) { List blocks = getTheBlocks(zd, x, y, maxX, maxY, observedNormalizationType, isImportant); if (blocks == null) return false; ColorScale cs = colorScaleHandler.getColorScale(key, displayOption, isWholeGenome, blocks, 1f); renderObservedOverExpectedMap(chr1, blocks, df, zd, cs, sameChr, originX, originY, width, height, 0); } else if (displayOption == MatrixType.OEP1V2 || displayOption == MatrixType.OEP1) { List blocks = getTheBlocks(zd, x, y, maxX, maxY, observedNormalizationType, isImportant); if (blocks == null) return false; ColorScale cs = colorScaleHandler.getColorScale(key, displayOption, isWholeGenome, blocks, 1f); renderObservedOverExpectedMap(chr1, blocks, df, zd, cs, sameChr, originX, originY, width, height, pseudoCountObs); } else if (displayOption == MatrixType.LOGEO) { List blocks = getTheBlocks(zd, x, y, maxX, maxY, observedNormalizationType, isImportant); if (blocks == null) return false; ColorScale cs = colorScaleHandler.getColorScale(key, displayOption, isWholeGenome, blocks, 1f); renderLogObservedBaseExpectedMap(chr1, blocks, df, zd, cs, sameChr, originX, originY, width, height); } else if (displayOption == MatrixType.EXPLOGEO) { List blocks = getTheBlocks(zd, x, y, maxX, maxY, observedNormalizationType, isImportant); if (blocks == null) return false; ColorScale cs = colorScaleHandler.getColorScale(key, displayOption, isWholeGenome, blocks, 1f); renderNewBaseEMap(chr1, blocks, df, zd, cs, sameChr, originX, originY, width, height); } else if (displayOption == MatrixType.EXPLOGCEO) { List ctrlBlocks = getTheBlocks(controlZD, x, y, maxX, maxY, controlNormalizationType, isImportant); if (ctrlBlocks == null || controlZD == null) return false; ColorScale cs = colorScaleHandler.getColorScale(key, displayOption, isWholeGenome, ctrlBlocks, 1f); renderNewBaseEMap(chr1, ctrlBlocks, controlDF, controlZD, cs, sameChr, originX, originY, width, height); } else if (displayOption == MatrixType.LOGEORATIOV2 || displayOption == MatrixType.LOGEORATIO) { List blocks = getTheBlocks(zd, x, y, maxX, maxY, observedNormalizationType, isImportant); List ctrlBlocks = getTheBlocks(controlZD, x, y, maxX, maxY, controlNormalizationType, isImportant); if (blocks == null || ctrlBlocks == null || controlZD == null) return false; if (sameChr && (df == null || controlDF == null)) return false; ColorScale cs = colorScaleHandler.getColorScale(key, displayOption, isWholeGenome, blocks, 1f); renderLogRatioWithExpMap(blocks, ctrlBlocks, zd, controlZD, chr1, df, controlDF, originX, originY, width, height, cs, sameChr, controlNormalizationType); } else if (displayOption == MatrixType.OERATIOMINUS) { List blocks = getTheBlocks(zd, x, y, maxX, maxY, observedNormalizationType, isImportant); List ctrlBlocks = getTheBlocks(controlZD, x, y, maxX, maxY, controlNormalizationType, isImportant); if (blocks == null || ctrlBlocks == null || controlZD == null) return false; if (sameChr && (df == null || controlDF == null)) return false; ColorScale cs = colorScaleHandler.getColorScale(key, displayOption, isWholeGenome, blocks, 1f); renderOERatioMinus(blocks, ctrlBlocks, zd, controlZD, df, controlDF, chr1, 0, 0, originX, originY, width, height, cs, sameChr, controlNormalizationType); } else if (displayOption == MatrixType.OERATIOMINUSP1) { List blocks = getTheBlocks(zd, x, y, maxX, maxY, observedNormalizationType, isImportant); List ctrlBlocks = getTheBlocks(controlZD, x, y, maxX, maxY, controlNormalizationType, isImportant); if (blocks == null || ctrlBlocks == null || controlZD == null) return false; if (sameChr && (df == null || controlDF == null)) return false; ColorScale cs = colorScaleHandler.getColorScale(key, displayOption, isWholeGenome, blocks, 1f); renderOERatioMinus(blocks, ctrlBlocks, zd, controlZD, df, controlDF, chr1, pseudoCountObs, pseudoCountCtrl, originX, originY, width, height, cs, sameChr, controlNormalizationType); } else if (displayOption == MatrixType.RATIOV2 || displayOption == MatrixType.RATIO) { List blocks = getTheBlocks(zd, x, y, maxX, maxY, observedNormalizationType, isImportant); List ctrlBlocks = getTheBlocks(controlZD, x, y, maxX, maxY, controlNormalizationType, isImportant); if (blocks == null || ctrlBlocks == null || controlZD == null) return false; ColorScale cs = colorScaleHandler.getColorScale(key, displayOption, isWholeGenome, blocks, 1f); renderRatioWithAvgMap(blocks, ctrlBlocks, zd, controlZD, 0, 0, originX, originY, width, height, cs, sameChr, controlNormalizationType); } else if (displayOption == MatrixType.RATIOP1V2 || displayOption == MatrixType.RATIOP1) { List blocks = getTheBlocks(zd, x, y, maxX, maxY, observedNormalizationType, isImportant); List ctrlBlocks = getTheBlocks(controlZD, x, y, maxX, maxY, controlNormalizationType, isImportant); if (blocks == null || ctrlBlocks == null || controlZD == null) return false; ColorScale cs = colorScaleHandler.getColorScale(key, displayOption, isWholeGenome, blocks, 1f); renderRatioWithAvgMap(blocks, ctrlBlocks, zd, controlZD, pseudoCountObs, pseudoCountCtrl, originX, originY, width, height, cs, sameChr, controlNormalizationType); } else if (displayOption == MatrixType.LOGRATIOV2 || displayOption == MatrixType.LOGRATIO) { List blocks = getTheBlocks(zd, x, y, maxX, maxY, observedNormalizationType, isImportant); List ctrlBlocks = getTheBlocks(controlZD, x, y, maxX, maxY, controlNormalizationType, isImportant); if (blocks == null || ctrlBlocks == null || controlZD == null) return false; ColorScale cs = colorScaleHandler.getColorScale(key, displayOption, isWholeGenome, blocks, 1f); renderLogRatioWithAvgMap(blocks, ctrlBlocks, zd, controlZD, originX, originY, width, height, cs, sameChr, controlNormalizationType); } else if (displayOption == MatrixType.RATIO0V2 || displayOption == MatrixType.RATIO0) { List blocks = getTheBlocks(zd, x, y, maxX, maxY, observedNormalizationType, isImportant); List ctrlBlocks = getTheBlocks(controlZD, x, y, maxX, maxY, controlNormalizationType, isImportant); if (blocks == null || ctrlBlocks == null || controlZD == null) return false; if (sameChr && (df == null || controlDF == null)) return false; ColorScale cs = colorScaleHandler.getColorScale(key, displayOption, isWholeGenome, blocks, 1f); renderRatioWithExpMap(blocks, ctrlBlocks, zd, controlZD, chr1, df, controlDF, 0, 0, originX, originY, width, height, cs, sameChr, controlNormalizationType); } else if (displayOption == MatrixType.RATIO0P1V2 || displayOption == MatrixType.RATIO0P1) { List blocks = getTheBlocks(zd, x, y, maxX, maxY, observedNormalizationType, isImportant); List ctrlBlocks = getTheBlocks(controlZD, x, y, maxX, maxY, controlNormalizationType, isImportant); if (blocks == null || ctrlBlocks == null || controlZD == null) return false; if (sameChr && (df == null || controlDF == null)) return false; ColorScale cs = colorScaleHandler.getColorScale(key, displayOption, isWholeGenome, blocks, 1f); renderRatioWithExpMap(blocks, ctrlBlocks, zd, controlZD, chr1, df, controlDF, pseudoCountObs, pseudoCountCtrl, originX, originY, width, height, cs, sameChr, controlNormalizationType); } else if (displayOption == MatrixType.DIFF) { List blocks = getTheBlocks(zd, x, y, maxX, maxY, observedNormalizationType, isImportant); List ctrlBlocks = getTheBlocks(controlZD, x, y, maxX, maxY, controlNormalizationType, isImportant); if (blocks == null || ctrlBlocks == null || controlZD == null) return false; ColorScale cs = colorScaleHandler.getColorScale(key, displayOption, isWholeGenome, blocks, 1f); renderDiffMap(blocks, ctrlBlocks, zd, controlZD, originX, originY, width, height, cs, sameChr, controlNormalizationType); } else if (displayOption == MatrixType.LOG) { List blocks = getTheBlocks(zd, x, y, maxX, maxY, observedNormalizationType, isImportant); if (blocks == null) return false; ColorScale cs = colorScaleHandler.getColorScale(key, displayOption, isWholeGenome, blocks, 1f); renderSimpleLogMap(blocks, cs, width, height, sameChr, originX, originY); } else if (displayOption == MatrixType.OBSERVED) { List blocks = getTheBlocks(zd, x, y, maxX, maxY, observedNormalizationType, isImportant); if (blocks == null) return false; ColorScale cs = colorScaleHandler.getColorScale(key, displayOption, isWholeGenome, blocks, 1f); renderSimpleMap(blocks, cs, width, height, sameChr, originX, originY); } else { System.err.println("Invalid display option: " + displayOption); return false; } return true; } private void renderLogRatioWithExpMap(List blocks, List ctrlBlocks, MatrixZoomData zd, MatrixZoomData controlZD, int chr1, ExpectedValueFunction df, ExpectedValueFunction controlDF, int originX, int originY, int width, int height, ColorScale cs, boolean sameChr, NormalizationType controlNormalizationType) { Map controlBlocks = convertBlockListToMap(ctrlBlocks, controlZD); float averageCount = (float) zd.getAverageCount(); float ctrlAverageCount = controlZD == null ? 1 : (float) controlZD.getAverageCount(); if (sameChr) { for (Block b : blocks) { Collection recs = b.getContactRecords(); if (recs != null) { Map controlRecords = linkRecords(zd, controlNormalizationType, controlBlocks, b); for (ContactRecord rec : recs) { ContactRecord ctrlRecord = controlRecords.get(rec.getKey(controlNormalizationType)); if (ctrlRecord != null) { float num = rec.getCounts(); float den = ctrlRecord.getCounts(); float obsExpected = getExpectedValue(df, chr1, rec); float ctrlExpected = getExpectedValue(controlDF, chr1, rec); if (logPainting(cs, num, den, obsExpected, ctrlExpected)) continue; intraPainting(originX, originY, width, height, rec); } } } } } else { for (Block b : blocks) { Collection recs = b.getContactRecords(); if (recs != null) { Map controlRecords = linkRecords(zd, controlNormalizationType, controlBlocks, b); float obsExpected = (averageCount > 0 ? averageCount : 1); float ctrlExpected = (ctrlAverageCount > 0 ? ctrlAverageCount : 1); for (ContactRecord rec : recs) { ContactRecord ctrlRecord = controlRecords.get(rec.getKey(controlNormalizationType)); if (ctrlRecord != null) { float num = rec.getCounts(); float den = ctrlRecord.getCounts(); if (logPainting(cs, num, den, obsExpected, ctrlExpected)) continue; aboveDiagonalPainting(originX, originY, width, height, rec); } } } } } } private Map convertBlockListToMap(List ctrlBlocks, MatrixZoomData controlZD) { Map controlBlocks = new HashMap<>(); for (Block b : ctrlBlocks) { controlBlocks.put(controlZD.getNormLessBlockKey(b), b); } return controlBlocks; } private void renderLogRatioWithAvgMap(List blocks, List ctrlBlocks, MatrixZoomData zd, MatrixZoomData controlZD, int originX, int originY, int width, int height, ColorScale cs, boolean sameChr, NormalizationType controlNormalizationType) { float averageCount = (float) zd.getAverageCount(); float ctrlAverageCount = controlZD == null ? 1 : (float) controlZD.getAverageCount(); Map controlBlocks = convertBlockListToMap(ctrlBlocks, controlZD); for (Block b : blocks) { Collection recs = b.getContactRecords(); Map controlRecords = linkRecords(zd, controlNormalizationType, controlBlocks, b); if (recs != null) { for (ContactRecord rec : recs) { ContactRecord ctrlRecord = controlRecords.get(rec.getKey(controlNormalizationType)); if (ctrlRecord != null) { float num = (float) Math.log(rec.getCounts() / averageCount + 1); float den = (float) Math.log(ctrlRecord.getCounts() / ctrlAverageCount + 1); ratioPainting(originX, originY, width, height, cs, sameChr, rec, num, den); } } } } } private void renderDiffMap(List blocks, List ctrlBlocks, MatrixZoomData zd, MatrixZoomData controlZD, int originX, int originY, int width, int height, ColorScale cs, boolean sameChr, NormalizationType controlNormalizationType) { float averageCount = (float) zd.getAverageCount(); float ctrlAverageCount = controlZD == null ? 1 : (float) controlZD.getAverageCount(); float averageAcrossMapAndControl = (averageCount / 2f + ctrlAverageCount / 2f); Map controlBlocks = convertBlockListToMap(ctrlBlocks, controlZD); for (Block b : blocks) { Collection recs = b.getContactRecords(); Map controlRecords = linkRecords(zd, controlNormalizationType, controlBlocks, b); if (recs != null) { for (ContactRecord rec : recs) { ContactRecord ctrlRecord = controlRecords.get(rec.getKey(controlNormalizationType)); if (ctrlRecord != null) { float num = rec.getCounts() / averageCount; float den = ctrlRecord.getCounts() / ctrlAverageCount; float score = (num - den) * averageAcrossMapAndControl; if (Float.isNaN(score) || Float.isInfinite(score)) continue; setColor(cs.getColor(score)); intraPainting2(originX, originY, width, height, sameChr, rec); } } } } } private void renderRatioWithExpMap(List blocks, List ctrlBlocks, MatrixZoomData zd, MatrixZoomData controlZD, int chr1, ExpectedValueFunction df, ExpectedValueFunction controlDF, float pseudoCountObs, float pseudoCountCtrl, int originX, int originY, int width, int height, ColorScale cs, boolean sameChr, NormalizationType controlNormalizationType) { Map controlBlocks = convertBlockListToMap(ctrlBlocks, controlZD); for (Block b : blocks) { Collection recs = b.getContactRecords(); Map controlRecords = linkRecords(zd, controlNormalizationType, controlBlocks, b); if (recs != null) { for (ContactRecord rec : recs) { ContactRecord ctrlRecord = controlRecords.get(rec.getKey(controlNormalizationType)); if (ctrlRecord != null) { float num = ((rec.getCounts() + pseudoCountObs) / (getExpectedValue(df, chr1, 0, 0) + pseudoCountObs)); float den = ((ctrlRecord.getCounts() + pseudoCountCtrl) / (getExpectedValue(controlDF, chr1, 0, 0) + pseudoCountCtrl)); ratioPainting(originX, originY, width, height, cs, sameChr, rec, num, den); } } } } } private void renderRatioWithAvgMap(List blocks, List ctrlBlocks, MatrixZoomData zd, MatrixZoomData controlZD, float pseudoCountObs, float pseudoCountCtrl, int originX, int originY, int width, int height, ColorScale cs, boolean sameChr, NormalizationType controlNormalizationType) { float averageCount = (float) zd.getAverageCount(); float ctrlAverageCount = controlZD == null ? 1 : (float) controlZD.getAverageCount(); Map controlBlocks = convertBlockListToMap(ctrlBlocks, controlZD); for (Block b : blocks) { Collection recs = b.getContactRecords(); Map controlRecords = linkRecords(zd, controlNormalizationType, controlBlocks, b); if (recs != null) { for (ContactRecord rec : recs) { ContactRecord ctrlRecord = controlRecords.get(rec.getKey(controlNormalizationType)); if (ctrlRecord != null) { float num = (rec.getCounts() + pseudoCountObs) / (averageCount + pseudoCountObs); float den = (ctrlRecord.getCounts() + pseudoCountCtrl) / (ctrlAverageCount + pseudoCountCtrl); ratioPainting(originX, originY, width, height, cs, sameChr, rec, num, den); } } } } } private void renderOERatioMinus(List blocks, List ctrlBlocks, MatrixZoomData zd, MatrixZoomData controlZD, ExpectedValueFunction df, ExpectedValueFunction controlDF, int chr1, float pseudoCountObs, float pseudoCountCtrl, int originX, int originY, int width, int height, ColorScale cs, boolean sameChr, NormalizationType controlNormalizationType) { Map controlBlocks = convertBlockListToMap(ctrlBlocks, controlZD); float averageCount = (float) zd.getAverageCount(); float ctrlAverageCount = controlZD == null ? 1 : (float) controlZD.getAverageCount(); if (sameChr) { for (Block b : blocks) { Collection recs = b.getContactRecords(); if (recs != null) { Map controlRecords = linkRecords(zd, controlNormalizationType, controlBlocks, b); for (ContactRecord rec : recs) { ContactRecord ctrlRecord = controlRecords.get(rec.getKey(controlNormalizationType)); if (ctrlRecord != null) { float num = rec.getCounts() + pseudoCountObs; float den = ctrlRecord.getCounts() + pseudoCountCtrl; float obsExpected = getExpectedValue(df, chr1, rec) + pseudoCountObs; float ctrlExpected = getExpectedValue(controlDF, chr1, rec) + pseudoCountCtrl; float score = (num / obsExpected) - (den / ctrlExpected); if (Float.isNaN(score) || Float.isInfinite(score)) continue; setColor(cs.getColor(score)); intraPainting(originX, originY, width, height, rec); } } } } } else { for (Block b : blocks) { Collection recs = b.getContactRecords(); if (recs != null) { Map controlRecords = linkRecords(zd, controlNormalizationType, controlBlocks, b); float obsExpected = (averageCount > 0 ? averageCount : 1); float ctrlExpected = (ctrlAverageCount > 0 ? ctrlAverageCount : 1); obsExpected += pseudoCountObs; ctrlExpected += pseudoCountCtrl; for (ContactRecord rec : recs) { ContactRecord ctrlRecord = controlRecords.get(rec.getKey(controlNormalizationType)); if (ctrlRecord != null) { float num = rec.getCounts() + pseudoCountObs; float den = ctrlRecord.getCounts() + pseudoCountCtrl; float score = (num / obsExpected) - (den / ctrlExpected); if (Float.isNaN(score) || Float.isInfinite(score)) continue; setColor(cs.getColor(score)); aboveDiagonalPainting(originX, originY, width, height, rec); } } } } } } private Map linkRecords(MatrixZoomData zd, NormalizationType controlNormalizationType, Map controlBlocks, Block b) { Map controlRecords = new HashMap<>(); Block cb = controlBlocks.get(zd.getNormLessBlockKey(b)); if (cb != null) { for (ContactRecord ctrlRec : cb.getContactRecords()) { controlRecords.put(ctrlRec.getKey(controlNormalizationType), ctrlRec); } } return controlRecords; } private void renderOERatioMap(List blocks, List ctrlBlocks, MatrixZoomData zd, MatrixZoomData controlZD, ExpectedValueFunction df, ExpectedValueFunction controlDF, int originX, int originY, int width, int height, float pseudoCountObs, float pseudoCountCtrl, ColorScale cs, boolean sameChr, NormalizationType controlNormalizationType, int chr1) { Map controlBlocks = convertBlockListToMap(ctrlBlocks, controlZD); if (sameChr) { for (Block b : blocks) { Collection recs = b.getContactRecords(); if (recs != null) { Map controlRecords = linkRecords(zd, controlNormalizationType, controlBlocks, b); for (ContactRecord rec : recs) { ContactRecord ctrlRecord = controlRecords.get(rec.getKey(controlNormalizationType)); if (ctrlRecord != null) { float num = rec.getCounts() + pseudoCountObs; float den = ctrlRecord.getCounts() + pseudoCountCtrl; float obsExpected = getExpectedValue(df, chr1, rec) + pseudoCountObs; float ctrlExpected = getExpectedValue(controlDF, chr1, rec) + pseudoCountCtrl; float score = (num / obsExpected) / (den / ctrlExpected); if (Float.isNaN(score) || Float.isInfinite(score)) continue; setColor(cs.getColor(score)); intraPainting(originX, originY, width, height, rec); } } } } } else { float averageCount = (float) zd.getAverageCount(); float ctrlAverageCount = controlZD == null ? 1 : (float) controlZD.getAverageCount(); float obsExpected = (averageCount > 0 ? averageCount : 1); float ctrlExpected = (ctrlAverageCount > 0 ? ctrlAverageCount : 1); obsExpected += pseudoCountObs; ctrlExpected += pseudoCountCtrl; for (Block b : blocks) { Collection recs = b.getContactRecords(); if (recs != null) { Map controlRecords = linkRecords(zd, controlNormalizationType, controlBlocks, b); for (ContactRecord rec : recs) { ContactRecord ctrlRecord = controlRecords.get(rec.getKey(controlNormalizationType)); if (ctrlRecord != null) { float num = rec.getCounts() + pseudoCountObs; float den = ctrlRecord.getCounts() + pseudoCountCtrl; float score = (num / obsExpected) / (den / ctrlExpected); if (Float.isNaN(score) || Float.isInfinite(score)) continue; setColor(cs.getColor(score)); aboveDiagonalPainting(originX, originY, width, height, rec); } } } } } } private void renderNewBaseEMap(int chr1, List blocks, ExpectedValueFunction df, MatrixZoomData zd, ColorScale cs, boolean sameChr, int originX, int originY, int width, int height) { if (sameChr) { if (df != null) { for (Block b : blocks) { Collection recs = b.getContactRecords(); if (recs != null) { for (ContactRecord rec : recs) { float expected = getExpectedValue(df, chr1, rec); float score = (float) Math.exp((Math.log(rec.getCounts() + 1) / Math.log(expected + 1))); if (Float.isNaN(score) || Float.isInfinite(score)) continue; setColor(cs.getColor(score)); intraPainting(originX, originY, width, height, rec); } } } } } else { float averageCount = (float) zd.getAverageCount(); float expected = (averageCount > 0 ? averageCount : 1); for (Block b : blocks) { Collection recs = b.getContactRecords(); if (recs != null) { for (ContactRecord rec : recs) { float score = (float) Math.exp((Math.log(rec.getCounts() + 1) / Math.log(expected + 1))); if (Float.isNaN(score) || Float.isInfinite(score)) continue; setColor(cs.getColor(score)); interPainting(originX, originY, width, height, rec); } } } } } private void renderExpectedMap(MatrixZoomData zd, ExpectedValueFunction df, boolean sameChr, ColorScale cs, int originX, int originY, int width, int height, int chr1) { if (sameChr) { if (df != null) { for (int px = 0; px <= width; px++) { for (int py = 0; py <= height; py++) { int binX = px + originX; int binY = py + originY; float expected = getExpectedValue(df, chr1, binX, binY); setColor(cs.getColor(expected)); directPixelPainting(px, py); } } } } else { float averageCount = (float) zd.getAverageCount(); float expected = (averageCount > 0 ? averageCount : 1); setColor(cs.getColor(expected)); for (int px = 0; px <= width; px++) { for (int py = 0; py <= height; py++) { directPixelPainting(px, py); } } } } private void renderLogObsMinusExpVSMap(int chr1, List blocks, List ctrlBlocks, ExpectedValueFunction df, ExpectedValueFunction controlDF, MatrixZoomData zd, MatrixZoomData controlZD, ColorScale cs, boolean sameChr, int originX, int originY, int width, int height) { if (zd != null && df != null) { for (Block b : blocks) { Collection recs = b.getContactRecords(); if (recs != null) { for (ContactRecord rec : recs) { float score = rec.getCounts(); if (Float.isNaN(score) || Float.isInfinite(score)) continue; float expected = getExpectedValue(df, chr1, rec); score = rec.getCounts() - expected; setColor(cs.getColor(score)); aboveDiagonalPainting(originX, originY, width, height, rec); } } } } if (sameChr && controlZD != null && controlDF != null) { for (Block b : ctrlBlocks) { Collection recs = b.getContactRecords(); if (recs != null) { for (ContactRecord rec : recs) { float score = rec.getCounts(); if (Float.isNaN(score) || Float.isInfinite(score)) continue; int binX = rec.getBinX(); int binY = rec.getBinY(); if (binX != binY) { float expected = getExpectedValue(controlDF, chr1, rec); score = rec.getCounts() - expected; setColor(cs.getColor(score)); belowDiagonalPainting(originX, originY, width, height, rec); } } } } } } private void renderLogObsOverExpVSMap(int chr1, List blocks, List ctrlBlocks, ExpectedValueFunction df, ExpectedValueFunction controlDF, MatrixZoomData zd, MatrixZoomData controlZD, ColorScale cs, boolean sameChr, int originX, int originY, int width, int height) { if (zd != null && df != null) { for (Block b : blocks) { Collection recs = b.getContactRecords(); if (recs != null) { for (ContactRecord rec : recs) { float expected = getExpectedValue(df, chr1, rec); float score = (float) (Math.log(rec.getCounts() + 1) / Math.log(expected + 1)); if (Float.isNaN(score) || Float.isInfinite(score)) continue; setColor(cs.getColor(score)); aboveDiagonalPainting(originX, originY, width, height, rec); } } } } if (sameChr && controlZD != null && controlDF != null) { for (Block b : ctrlBlocks) { Collection recs = b.getContactRecords(); if (recs != null) { for (ContactRecord rec : recs) { int binX = rec.getBinX(); int binY = rec.getBinY(); if (binX != binY) { float expected = getExpectedValue(controlDF, chr1, rec); float score = (float) (Math.log(rec.getCounts() + 1) / Math.log(expected + 1)); if (Float.isNaN(score) || Float.isInfinite(score)) continue; setColor(cs.getColor(score)); belowDiagonalPainting(originX, originY, width, height, rec); } } } } } } private void renderSimpleLogVSMap(List blocks, List ctrlBlocks, MatrixZoomData zd, MatrixZoomData controlZD, int originX, int originY, int width, int height, ColorScale cs, boolean sameChr) { float averageCount = (float) zd.getAverageCount(); float ctrlAverageCount = (float) controlZD.getAverageCount(); float averageAcrossMapAndControl = (averageCount + ctrlAverageCount) / 2; if (blocks != null) { for (Block b : blocks) { Collection recs = b.getContactRecords(); if (recs != null) { for (ContactRecord rec : recs) { float score = (float) Math.log(averageAcrossMapAndControl * (rec.getCounts() / averageCount) + 1); if (Float.isNaN(score) || Float.isInfinite(score)) continue; setColor(cs.getColor(score)); aboveDiagonalPainting(originX, originY, width, height, rec); } } } } if (sameChr && ctrlBlocks != null) { for (Block b : ctrlBlocks) { Collection recs = b.getContactRecords(); if (recs != null) { for (ContactRecord rec : recs) { float score = (float) Math.log(averageAcrossMapAndControl * (rec.getCounts() / ctrlAverageCount) + 1); if (Float.isNaN(score) || Float.isInfinite(score)) continue; setColor(cs.getColor(score)); belowDiagonalPainting(originX, originY, width, height, rec); } } } } } private void renderSimpleVSMap(List blocks, List ctrlBlocks, MatrixZoomData zd, MatrixZoomData controlZD, int originX, int originY, int width, int height, ColorScale cs, boolean sameChr) { float averageCount = (float) zd.getAverageCount(); float ctrlAverageCount = (float) controlZD.getAverageCount(); float averageAcrossMapAndControl = (averageCount + ctrlAverageCount) / 2; if (blocks != null) { for (Block b : blocks) { Collection recs = b.getContactRecords(); if (recs != null) { for (ContactRecord rec : recs) { float score = rec.getCounts(); if (Float.isNaN(score) || Float.isInfinite(score)) continue; score = (score / averageCount) * averageAcrossMapAndControl; setColor(cs.getColor(score)); aboveDiagonalPainting(originX, originY, width, height, rec); } } } } if (sameChr && ctrlBlocks != null) { for (Block b : ctrlBlocks) { Collection recs = b.getContactRecords(); if (recs != null) { for (ContactRecord rec : recs) { float score = rec.getCounts(); if (Float.isNaN(score) || Float.isInfinite(score)) continue; score = (score / ctrlAverageCount) * averageAcrossMapAndControl; setColor(cs.getColor(score)); belowDiagonalPainting(originX, originY, width, height, rec); } } } } } private void renderLogObservedBaseExpectedMap(int chromosome, List blocks, ExpectedValueFunction df, MatrixZoomData zd, ColorScale cs, boolean sameChr, int originX, int originY, int width, int height) { if (sameChr) { if (df != null) { for (Block b : blocks) { Collection recs = b.getContactRecords(); if (recs != null) { for (ContactRecord rec : recs) { float expected = getExpectedValue(df, chromosome, rec); float score = (float) (Math.log(rec.getCounts() + 1) / Math.log(expected + 1)); if (Float.isNaN(score) || Float.isInfinite(score)) continue; setColor(cs.getColor(score)); intraPainting(originX, originY, width, height, rec); } } } } } else { float averageCount = (float) zd.getAverageCount(); float expected = (averageCount > 0 ? averageCount : 1); for (Block b : blocks) { Collection recs = b.getContactRecords(); if (recs != null) { for (ContactRecord rec : recs) { float score = (float) (Math.log(rec.getCounts() + 1) / Math.log(expected + 1)); if (Float.isNaN(score) || Float.isInfinite(score)) continue; setColor(cs.getColor(score)); interPainting(originX, originY, width, height, rec); } } } } } private void renderObservedOverExpectedVSMap(int chromosome, List blocks, List ctrlBlocks, ExpectedValueFunction df, ExpectedValueFunction controlDF, MatrixZoomData zd, MatrixZoomData controlZD, ColorScale cs, boolean sameChr, int originX, int originY, int width, int height, float pseudoCountObs, float pseudoCountCtrl) { if (zd != null && blocks != null && df != null) { for (Block b : blocks) { Collection recs = b.getContactRecords(); if (recs != null) { for (ContactRecord rec : recs) { float score = rec.getCounts(); if (Float.isNaN(score) || Float.isInfinite(score)) continue; float expected = getExpectedValue(df, chromosome, rec); score = (rec.getCounts() + pseudoCountObs) / (expected + pseudoCountObs); setColor(cs.getColor(score)); aboveDiagonalPainting(originX, originY, width, height, rec); } } } } if (sameChr && controlZD != null && ctrlBlocks != null && controlDF != null) { for (Block b : ctrlBlocks) { Collection recs = b.getContactRecords(); if (recs != null) { for (ContactRecord rec : recs) { float score = rec.getCounts(); if (Float.isNaN(score) || Float.isInfinite(score)) continue; int binX = rec.getBinX(); int binY = rec.getBinY(); if (binX != binY) { float expected = getExpectedValue(controlDF, chromosome, rec); score = (rec.getCounts() + pseudoCountCtrl) / (expected + pseudoCountCtrl); setColor(cs.getColor(score)); belowDiagonalPainting(originX, originY, width, height, rec); } } } } } } private float getExpectedValue(ExpectedValueFunction df, int chromosome, ContactRecord record) { return getExpectedValue(df, chromosome, record.getBinX(), record.getBinY()); } private float getExpectedValue(ExpectedValueFunction df, int chromosome, int binX, int binY) { int dist = Math.abs(binX - binY); return (float) df.getExpectedValue(chromosome, dist); } private void renderObservedOverExpectedMap(int chromosome, List blocks, ExpectedValueFunction df, MatrixZoomData zd, ColorScale cs, boolean sameChr, int originX, int originY, int width, int height, float pseudoCount) { if (sameChr) { if (df != null) { for (Block b : blocks) { Collection recs = b.getContactRecords(); if (recs != null) { for (ContactRecord rec : recs) { float expected = getExpectedValue(df, chromosome, rec); float score = (rec.getCounts() + pseudoCount) / (expected + pseudoCount); if (Float.isNaN(score) || Float.isInfinite(score)) continue; setColor(cs.getColor(score)); intraPainting(originX, originY, width, height, rec); } } } } } else { float averageCount = (float) zd.getAverageCount(); float expected = (averageCount > 0 ? averageCount : 1); for (Block b : blocks) { Collection recs = b.getContactRecords(); if (recs != null) { for (ContactRecord rec : recs) { float score = (rec.getCounts() + pseudoCount) / (expected + pseudoCount); if (Float.isNaN(score) || Float.isInfinite(score)) continue; setColor(cs.getColor(score)); interPainting(originX, originY, width, height, rec); } } } } } private void renderSimpleMap(List blocks, ColorScale cs, int width, int height, boolean sameChr, int originX, int originY) { for (Block b : blocks) { Collection recs = b.getContactRecords(); if (recs != null) { for (ContactRecord rec : recs) { float score = rec.getCounts(); simplePainting(cs, width, height, sameChr, originX, originY, rec, score); } } } } private void renderSimpleLogMap(List blocks, ColorScale cs, int width, int height, boolean sameChr, int originX, int originY) { for (Block b : blocks) { Collection recs = b.getContactRecords(); if (recs != null) { for (ContactRecord rec : recs) { float score = (float) Math.log(1 + rec.getCounts()); simplePainting(cs, width, height, sameChr, originX, originY, rec, score); } } } } private void renderPearsonVS(MatrixZoomData zd, MatrixZoomData controlZD, ExpectedValueFunction df, ExpectedValueFunction controlDF, String key, int originX, int originY, int width, int height) { BasicMatrix bm1 = zd.getPearsons(df); BasicMatrix bm2 = controlZD.getPearsons(controlDF); PearsonColorScale pearsonColorScale = colorScaleHandler.getPearsonColorScale(); if (pearsonColorScale.doesNotContainKey(key)) { float min = Math.min(bm1.getLowerValue(), bm2.getLowerValue()); float max = Math.max(bm1.getUpperValue(), bm2.getUpperValue()); pearsonColorScale.setMinMax(key, min, max); } renderDenseMatrix(bm1, bm2, originX, originY, width, height, pearsonColorScale, key, null); } private void renderPearson(MatrixZoomData zd, ExpectedValueFunction df, String key, int originX, int originY, int width, int height) { BasicMatrix bm = zd.getPearsons(df); PearsonColorScale pearsonColorScale = colorScaleHandler.getPearsonColorScale(); if (pearsonColorScale.doesNotContainKey(key)) { pearsonColorScale.setMinMax(key, bm.getLowerValue(), bm.getUpperValue()); } renderDenseMatrix(bm, null, originX, originY, width, height, pearsonColorScale, key, null); } private void renderNorm2VS(MatrixZoomData zd, MatrixZoomData controlZD, boolean isWholeGenome, NormalizationType observedNormalizationType, NormalizationType controlNormalizationType, String key, MatrixType displayOption, int originX, int originY, int width, int height) { BasicMatrix bm1 = zd.getNormSquared(observedNormalizationType); BasicMatrix bm2 = controlZD.getNormSquared(controlNormalizationType); double percentile = isWholeGenome ? 99 : 95; float max = colorScaleHandler.computePercentile(bm1, bm2, percentile); ColorScale cs = colorScaleHandler.getColorScale(key, displayOption, isWholeGenome, null, max); renderDenseMatrix(bm1, bm2, originX, originY, width, height, null, key, cs); } private void renderNorm2(MatrixZoomData zd, boolean isWholeGenome, NormalizationType normType, String key, MatrixType displayOption, int originX, int originY, int width, int height) { BasicMatrix bm = zd.getNormSquared(normType); double percentile = isWholeGenome ? 99 : 95; float max = colorScaleHandler.computePercentile(bm, percentile); ColorScale cs = colorScaleHandler.getColorScale(key, displayOption, isWholeGenome, null, max); renderDenseMatrix(bm, null, originX, originY, width, height, null, key, cs); } private List getTheBlocks(MatrixZoomData zd, int x, int y, int maxX, int maxY, NormalizationType normType, boolean isImportant) { if (zd != null) { try { return zd.getNormalizedBlocksOverlapping(x, y, maxX, maxY, normType, isImportant, false); } catch (Exception ee) { if (HiCGlobals.printVerboseComments) ee.printStackTrace(); } } return new ArrayList<>(); } /** * Render a dense matrix. Used for Pearson correlation. The bitmap is drawn at 1 data point * per pixel, scaling happens elsewhere. * * @param bm1 Matrix to render * @param bm2 Matrix to render * @param originX origin in pixels * @param originY origin in pixels * @param colorScale color scale to apply * @param key id for view */ private void renderDenseMatrix(BasicMatrix bm1, BasicMatrix bm2, int originX, int originY, int width, int height, PearsonColorScale colorScale, String key, ColorScale cs) { int endX = Math.min(originX + width, bm1.getColumnDimension()); int endY = Math.min(originY + height, bm1.getRowDimension()); // TODO -- need to check bounds before drawing for (int row = originY; row < endY; row++) { for (int col = originX; col < endX; col++) { float score = bm1.getEntry(row, col); Color color = colorScaleHandler.getDenseMatrixColor(key, score, colorScale, cs); setColor(color); directDensePainting(originX, originY, col, row); // Assuming same chromosome if (col != row) { if (bm2 != null) { float controlScore = bm2.getEntry(row, col); Color controlColor = colorScaleHandler.getDenseMatrixColor(key, controlScore, colorScale, cs); setColor(controlColor); } directDensePainting(originX, originY, row, col); } } } } public void updateColorSliderFromColorScale(SuperAdapter superAdapter, MatrixType displayOption, String cacheKey) { colorScaleHandler.updateColorSliderFromColorScale(superAdapter, displayOption, cacheKey); } private void interPainting(int originX, int originY, int width, int height, ContactRecord rec) { aboveDiagonalPainting(originX, originY, width, height, rec); } private void simplePainting(ColorScale cs, int width, int height, boolean sameChr, int originX, int originY, ContactRecord rec, float score) { if (Float.isNaN(score) || Float.isInfinite(score)) return; setColor(cs.getColor(score)); aboveDiagonalPainting(originX, originY, width, height, rec); if (sameChr) belowDiagonalPainting(originX, originY, width, height, rec); } private boolean logPainting(ColorScale cs, float num, float den, float obsExpected, float ctrlExpected) { float score = (float) ((Math.log(num + 1) / Math.log(obsExpected + 1)) / (Math.log(den + 1) / Math.log(ctrlExpected + 1))); if (Float.isNaN(score) || Float.isInfinite(score)) return true; setColor(cs.getColor(score)); return false; } private void ratioPainting(int originX, int originY, int width, int height, ColorScale cs, boolean sameChr, ContactRecord rec, float num, float den) { float score = num / den; if (Float.isNaN(score) || Float.isInfinite(score)) return; setColor(cs.getColor(score)); intraPainting2(originX, originY, width, height, sameChr, rec); } private void intraPainting2(int originX, int originY, int width, int height, boolean sameChr, ContactRecord rec) { aboveDiagonalPainting(originX, originY, width, height, rec); if (sameChr) belowDiagonalPainting(originX, originY, width, height, rec); } private void intraPainting(int originX, int originY, int width, int height, ContactRecord rec) { aboveDiagonalPainting(originX, originY, width, height, rec); belowDiagonalPainting(originX, originY, width, height, rec); } @SuppressWarnings("SuspiciousNameCombination") private void belowDiagonalPainting(int originX, int originY, int width, int height, ContactRecord rec) { int binX = rec.getBinX(); int binY = rec.getBinY(); if (binX != binY) { actualDiagonalPainting(originX, originY, width, height, binY, binX); } } //justPainting(originX, originY, width, height, rec); private void aboveDiagonalPainting(int originX, int originY, int width, int height, ContactRecord rec) { actualDiagonalPainting(originX, originY, width, height, rec.getBinX(), rec.getBinY()); } private void actualDiagonalPainting(int originX, int originY, int width, int height, int binX, int binY) { int px = binX - originX; int py = binY - originY; if (px > -1 && py > -1 && px <= width && py <= height) { directPixelPainting(px, py); } } private void directDensePainting(int originX, int originY, int binX, int binY) { int px = binX - originX; int py = binY - originY; directPixelPainting(px, py); } protected void setColor(Color color) { g.setColor(color); } protected void directPixelPainting(int px, int py) { g.fillRect(px, py, PIXEL_WIDTH, PIXEL_HEIGHT); } public void translate(int x, int y) { g.translate(x, y); } public void scale(double sx, double sy) { g.scale(sx, sy); } public void drawImage(Image image, int xDest0, int yDest0, int xDest1, int yDest1, int xSrc0, int ySrc0, int xSrc1, int ySrc1) { g.drawImage(image, xDest0, yDest0, xDest1, yDest1, xSrc0, ySrc0, xSrc1, ySrc1, null); } public void drawRect(int x, int y, int width, int height) { g.drawRect(x, y, width, height); } } ================================================ FILE: src/juicebox/mapcolorui/HiCMapTileManager.java ================================================ /* * The MIT License (MIT) * * Copyright (c) 2011-2021 Broad Institute, Aiden Lab, Rice University, Baylor College of Medicine * * Permission is hereby granted, free of charge, to any person obtaining a copy * of this software and associated documentation files (the "Software"), to deal * in the Software without restriction, including without limitation the rights * to use, copy, modify, merge, publish, distribute, sublicense, and/or sell * copies of the Software, and to permit persons to whom the Software is * furnished to do so, subject to the following conditions: * * The above copyright notice and this permission notice shall be included in * all copies or substantial portions of the Software. * * THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR * IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, * FITNESS FOR A PARTICULAR PURPOSE AND NON-INFRINGEMENT. IN NO EVENT SHALL THE * AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER * LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, * OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN * THE SOFTWARE. */ package juicebox.mapcolorui; import juicebox.HiC; import juicebox.HiCGlobals; import juicebox.data.ExpectedValueFunction; import juicebox.data.MatrixZoomData; import juicebox.gui.SuperAdapter; import juicebox.windowui.MatrixType; import juicebox.windowui.NormalizationType; import org.broad.igv.util.ObjectCache; import javax.swing.*; import java.awt.*; import java.awt.image.BufferedImage; public class HiCMapTileManager { private static final int imageTileWidth = 500; private final ObjectCache tileCache = new ObjectCache<>(30); private final ColorScaleHandler colorScaleHandler; public HiCMapTileManager(ColorScaleHandler colorScaleHandler) { this.colorScaleHandler = colorScaleHandler; } public void clearTileCache() { tileCache.clear(); } public GeneralTileManager.ImageTile getImageTile(MatrixZoomData zd, MatrixZoomData controlZd, int tileRow, int tileColumn, MatrixType displayOption, NormalizationType obsNormalizationType, NormalizationType ctrlNormalizationType, HiC hic, JComponent parent) { String key = zd.getTileKey(tileRow, tileColumn, displayOption); GeneralTileManager.ImageTile tile = tileCache.get(key); if (tile == null) { // Image size can be smaller than tile width when zoomed out, or near the edges. long maxBinCountX = zd.getXGridAxis().getBinCount(); long maxBinCountY = zd.getYGridAxis().getBinCount(); if (maxBinCountX < 0 || maxBinCountY < 0) return null; int imageWidth = maxBinCountX < imageTileWidth ? (int) maxBinCountX : imageTileWidth; int imageHeight = maxBinCountY < imageTileWidth ? (int) maxBinCountY : imageTileWidth; final int bx0 = tileColumn * imageTileWidth; final int by0 = tileRow * imageTileWidth; Image image = renderDataWithCPU(parent, bx0, by0, imageWidth, imageHeight, zd, controlZd, displayOption, obsNormalizationType, ctrlNormalizationType, hic.getExpectedValues(), hic.getExpectedControlValues()); // if (scaleFactor > 0.999 && scaleFactor < 1.001) { tile = new GeneralTileManager.ImageTile(image, bx0, by0); tileCache.put(key, tile); } return tile; } private BufferedImage renderDataWithCPU(JComponent parent, int bx0, int by0, int imageWidth, int imageHeight, MatrixZoomData zd, MatrixZoomData controlZd, MatrixType displayOption, NormalizationType obsNormalizationType, NormalizationType ctrlNormalizationType, ExpectedValueFunction expectedValues, ExpectedValueFunction expectedControlValues) { BufferedImage image = (BufferedImage) parent.createImage(imageWidth, imageHeight); Graphics2D g2D = (Graphics2D) image.getGraphics(); if (HiCGlobals.isDarkulaModeEnabled) { g2D.setColor(Color.darkGray); g2D.fillRect(0, 0, imageWidth, imageHeight); } HeatmapRenderer renderer = new HeatmapRenderer(g2D, colorScaleHandler); if (!renderer.render(bx0, by0, imageWidth, imageHeight, zd, controlZd, displayOption, obsNormalizationType, ctrlNormalizationType, expectedValues, expectedControlValues, true)) { return null; } return image; } public void updateColorSliderFromColorScale(SuperAdapter superAdapter, MatrixType displayOption, String cacheKey) { colorScaleHandler.updateColorSliderFromColorScale(superAdapter, displayOption, cacheKey); } } ================================================ FILE: src/juicebox/mapcolorui/JColorRangePanel.java ================================================ /* * The MIT License (MIT) * * Copyright (c) 2011-2021 Broad Institute, Aiden Lab, Rice University, Baylor College of Medicine * * Permission is hereby granted, free of charge, to any person obtaining a copy * of this software and associated documentation files (the "Software"), to deal * in the Software without restriction, including without limitation the rights * to use, copy, modify, merge, publish, distribute, sublicense, and/or sell * copies of the Software, and to permit persons to whom the Software is * furnished to do so, subject to the following conditions: * * The above copyright notice and this permission notice shall be included in * all copies or substantial portions of the Software. * * THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR * IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, * FITNESS FOR A PARTICULAR PURPOSE AND NON-INFRINGEMENT. IN NO EVENT SHALL THE * AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER * LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, * OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN * THE SOFTWARE. */ package juicebox.mapcolorui; import com.jidesoft.swing.JideButton; import juicebox.HiC; import juicebox.HiCGlobals; import juicebox.gui.SuperAdapter; import juicebox.windowui.MatrixType; import org.broad.igv.ui.FontManager; import javax.swing.*; import javax.swing.border.LineBorder; import javax.swing.event.ChangeEvent; import javax.swing.event.ChangeListener; import java.awt.*; import java.awt.event.ActionEvent; import java.awt.event.ActionListener; import java.awt.event.MouseAdapter; import java.awt.event.MouseEvent; import java.awt.font.TextAttribute; import java.util.Hashtable; import java.util.Map; /** * Created by muhammadsaadshamim on 8/3/15. */ public class JColorRangePanel extends JPanel { private static final long serialVersionUID = 9000029; private static RangeSlider colorRangeSlider; private static JLabel colorRangeLabel; private static JButton plusButton, minusButton; private double colorRangeScaleFactor = 1; private final HeatmapPanel heatmapPanel; public JColorRangePanel(final SuperAdapter superAdapter, final HeatmapPanel heatmapPanel) { super(); setLayout(new BorderLayout()); JPanel sliderPanel = new JPanel(); sliderPanel.setLayout(new BoxLayout(sliderPanel, BoxLayout.X_AXIS)); this.heatmapPanel = heatmapPanel; colorRangeSlider = new RangeSlider(); colorRangeSlider.addMouseListener(new MouseAdapter() { @Override public void mouseEntered(MouseEvent mouseEvent) { super.mouseEntered(mouseEvent); colorRangeSliderUpdateToolTip(superAdapter.getHiC().getDisplayOption()); } }); colorRangeSlider.setEnabled(false); colorRangeSlider.setDisplayToBlank(true); //---- colorRangeLabel ---- colorRangeLabel = new JLabel("Color Range"); colorRangeLabel.addMouseListener(new MouseAdapter() { private Font original; @SuppressWarnings({"unchecked", "rawtypes"}) @Override public void mouseEntered(MouseEvent e) { if (colorRangeSlider.isEnabled()) { original = e.getComponent().getFont(); Map attributes = original.getAttributes(); attributes.put(TextAttribute.UNDERLINE, TextAttribute.UNDERLINE_ON); e.getComponent().setFont(original.deriveFont(attributes)); } } @Override public void mouseExited(MouseEvent e) { //if (colorRangeSlider.isEnabled()) e.getComponent().setFont(original); } }); colorRangeLabel.setHorizontalAlignment(SwingConstants.CENTER); colorRangeLabel.setToolTipText("Range of color scale in counts per mega-base squared."); colorRangeLabel.setHorizontalTextPosition(SwingConstants.CENTER); colorRangeLabel.addMouseListener(new MouseAdapter() { @Override public void mousePressed(MouseEvent e) { if (e.isPopupTrigger() && colorRangeSlider.isEnabled()) { processClick(); } } @Override public void mouseClicked(MouseEvent e) { //No double click here... if (e.getClickCount() == 1 && colorRangeSlider.isEnabled()) { processClick(); } } private void processClick() { ColorRangeDialog rangeDialog = new ColorRangeDialog(superAdapter, JColorRangePanel.this, colorRangeSlider, colorRangeScaleFactor, superAdapter.getHiC().getDisplayOption()); setColorRangeSliderVisible(false, superAdapter); if (!superAdapter.getMainViewPanel().setResolutionSliderVisible(false, superAdapter)) { System.err.println("error 2984"); } rangeDialog.setVisible(true); } }); JPanel colorLabelPanel = new JPanel(new BorderLayout()); colorLabelPanel.setBackground(HiCGlobals.backgroundColor); //set color to gray colorLabelPanel.add(colorRangeLabel, BorderLayout.CENTER); add(colorLabelPanel, BorderLayout.PAGE_START); //---- colorRangeSlider ---- colorRangeSlider.setPaintTicks(false); colorRangeSlider.setPaintLabels(false); colorRangeSlider.setMaximumSize(new Dimension(32767, 52)); colorRangeSlider.setPreferredSize(new Dimension(200, 52)); colorRangeSlider.setMinimumSize(new Dimension(36, 52)); colorRangeSlider.addChangeListener(new ChangeListener() { public void stateChanged(ChangeEvent e) { double min = colorRangeSlider.getLowerValue() / colorRangeScaleFactor; double max = colorRangeSlider.getUpperValue() / colorRangeScaleFactor; HiC hic = superAdapter.getHiC(); String key = ""; try { if (hic != null && hic.getZd() != null && hic.getDisplayOption() != null) { key = HeatmapRenderer.getColorScaleCacheKey(hic.getZd(), hic.getDisplayOption(), hic.getObsNormalizationType(), hic.getControlNormalizationType()); } } catch (Exception e2) { if (HiCGlobals.printVerboseComments) { e2.printStackTrace(); } } heatmapPanel.setNewDisplayRange(hic.getDisplayOption(), min, max, key); colorRangeSliderUpdateToolTip(hic.getDisplayOption()); } }); sliderPanel.add(colorRangeSlider); JPanel plusMinusPanel = new JPanel(); plusMinusPanel.setLayout(new BoxLayout(plusMinusPanel, BoxLayout.Y_AXIS)); plusButton = new JideButton(); plusButton.setIcon(new ImageIcon(getClass().getResource("/images/zoom-plus.png"))); plusButton.addActionListener(new ActionListener() { @Override public void actionPerformed(ActionEvent e) { HiC hic = superAdapter.getHiC(); double newMax = (colorRangeSlider.getMaximum() / colorRangeScaleFactor) * 2; double newHigh = colorRangeSlider.getUpperValue() / colorRangeScaleFactor; double newLow = colorRangeSlider.getLowerValue() / colorRangeScaleFactor; if (MatrixType.isOEColorScaleType(hic.getDisplayOption())) { updateRatioColorSlider(hic, newMax, newHigh); } else { updateColorSlider(hic, newLow, newHigh, newMax); } } }); minusButton = new JideButton(); minusButton.setIcon(new ImageIcon(getClass().getResource("/images/zoom-minus.png"))); minusButton.addActionListener(new ActionListener() { @Override public void actionPerformed(ActionEvent e) { //Set limit to maximum range: HiC hic = superAdapter.getHiC(); double newMax = (colorRangeSlider.getMaximum() / colorRangeScaleFactor) / 2; double newHigh = Math.min(newMax, colorRangeSlider.getUpperValue() / colorRangeScaleFactor); double newLow = Math.min(newMax - 1, colorRangeSlider.getLowerValue() / colorRangeScaleFactor); if (MatrixType.isOEColorScaleType(hic.getDisplayOption())) { updateRatioColorSlider(hic, newMax, newHigh); } else { updateColorSlider(hic, newLow, newHigh, newMax); } } }); colorRangeSlider.setUpperValue(1200); colorRangeSlider.setDisplayToBlank(true); plusMinusPanel.add(plusButton); plusMinusPanel.add(minusButton); plusButton.setEnabled(false); minusButton.setEnabled(false); sliderPanel.add(plusMinusPanel); add(sliderPanel, BorderLayout.PAGE_END); setBorder(LineBorder.createGrayLineBorder()); setMinimumSize(new Dimension(96, 70)); setPreferredSize(new Dimension(202, 70)); setMaximumSize(new Dimension(32769, 70)); } public boolean setColorRangeSliderVisible(boolean state, SuperAdapter superAdapter) { plusButton.setEnabled(state); minusButton.setEnabled(state); colorRangeSlider.setEnabled(state); if (state) { colorRangeLabel.setForeground(Color.BLUE); } else { colorRangeLabel.setForeground(Color.BLACK); } return true; //why are we calling this? why is this method a boolean method at all? //return superAdapter.safeDisplayOptionComboBoxActionPerformed(); } public void updateColorSlider(HiC hic, double lower, double upper, double max) { if (max < 1) { max = 5; } // map going into zero state? if (upper == 0) { upper = 1; } if (upper == lower) { lower = upper - 1; } // We need to scale min and max to integers for the slider to work. Scale such that there are // 100 divisions between max and 0 colorRangeScaleFactor = 100.0 / max; colorRangeSlider.setPaintTicks(true); colorRangeSlider.setPaintLabels(true); int iMax = (int) (colorRangeScaleFactor * max); int lValue = (int) (colorRangeScaleFactor * lower); int uValue = (int) (colorRangeScaleFactor * upper); colorRangeSlider.setMinimum(0); colorRangeSlider.setMaximum(iMax); colorRangeSlider.setLowerValue(lValue); colorRangeSlider.setUpperValue(uValue); Hashtable labelTable = new Hashtable<>(); Font f = FontManager.getFont(8); final JLabel minTickLabel = new JLabel(String.valueOf(0)); minTickLabel.setFont(f); final JLabel maxTickLabel = new JLabel(String.valueOf((int) max)); maxTickLabel.setFont(f); final JLabel LoTickLabel = new JLabel(String.valueOf((int) lower)); LoTickLabel.setFont(f); final JLabel UpTickLabel = new JLabel(String.valueOf((int) upper)); UpTickLabel.setFont(f); labelTable.put(0, minTickLabel); labelTable.put(iMax, maxTickLabel); labelTable.put(lValue, LoTickLabel); labelTable.put(uValue, UpTickLabel); colorRangeSlider.setLabelTable(labelTable); String key = HeatmapRenderer.getColorScaleCacheKey(hic.getZd(), hic.getDisplayOption(), hic.getObsNormalizationType(), hic.getControlNormalizationType()); heatmapPanel.setNewDisplayRange(hic.getDisplayOption(), lower, upper, key); colorRangeSliderUpdateToolTip(hic.getDisplayOption()); } public void updateRatioColorSlider(HiC hic, double max, double val) { // We need to scale min and max to integers for the slider to work. Scale such that there are // 100 divisions between max and 0 if (max < 1) { max = 5; } // map going into zero state? if (val == 0) { val = 1; } colorRangeScaleFactor = 100.0 / (2 * max); colorRangeSlider.setPaintTicks(true); colorRangeSlider.setPaintLabels(true); int iMin = (int) (colorRangeScaleFactor * -max); int iMax = (int) (colorRangeScaleFactor * max); int lValue = (int) (colorRangeScaleFactor * -val); int uValue = (int) (colorRangeScaleFactor * val); colorRangeSlider.setMinimum(iMin); colorRangeSlider.setMaximum(iMax); colorRangeSlider.setLowerValue(lValue); colorRangeSlider.setUpperValue(uValue); Hashtable labelTable = new Hashtable<>(); Font f = FontManager.getFont(8); final JLabel minTickLabel = new JLabel(String.valueOf((int) -max)); minTickLabel.setFont(f); final JLabel maxTickLabel = new JLabel(String.valueOf((int) max)); maxTickLabel.setFont(f); final JLabel LoTickLabel = new JLabel(String.valueOf((int) -val)); LoTickLabel.setFont(f); final JLabel UpTickLabel = new JLabel(String.valueOf((int) val)); UpTickLabel.setFont(f); labelTable.put(iMin, minTickLabel); labelTable.put(iMax, maxTickLabel); labelTable.put(lValue, LoTickLabel); labelTable.put(uValue, UpTickLabel); colorRangeSlider.setLabelTable(labelTable); String key = HeatmapRenderer.getColorScaleCacheKey(hic.getZd(), hic.getDisplayOption(), hic.getObsNormalizationType(), hic.getControlNormalizationType()); heatmapPanel.setNewDisplayRange(hic.getDisplayOption(), -val, val, key); colorRangeSliderUpdateToolTip(hic.getDisplayOption()); } public String getColorRangeValues() { int iMin = colorRangeSlider.getMinimum(); int lowValue = colorRangeSlider.getLowerValue(); int upValue = colorRangeSlider.getUpperValue(); int iMax = colorRangeSlider.getMaximum(); return iMin + "$$" + lowValue + "$$" + upValue + "$$" + iMax;// + "$$" + dScaleFactor; } public double getColorRangeScaleFactor() { return colorRangeScaleFactor; } private void colorRangeSliderUpdateToolTip(MatrixType displayOption) { int iMin = colorRangeSlider.getMinimum(); int lValue = colorRangeSlider.getLowerValue(); int uValue = colorRangeSlider.getUpperValue(); int iMax = colorRangeSlider.getMaximum(); colorRangeSlider.setToolTipText("Range: " + (int) (iMin / colorRangeScaleFactor) + " " + (int) (iMax / colorRangeScaleFactor) + "
Showing: " + (int) (lValue / colorRangeScaleFactor) + " - " + (int) (uValue / colorRangeScaleFactor) + ""); Font f = FontManager.getFont(8); Hashtable labelTable = new Hashtable<>(); if (MatrixType.isOEColorScaleType(displayOption)) { colorRangeSlider.setToolTipText("Log Enrichment Values"); } else { colorRangeSlider.setToolTipText("Observed Counts"); } final JLabel minTickLabel = new JLabel(String.valueOf((int) (iMin / colorRangeScaleFactor))); minTickLabel.setFont(f); final JLabel LoTickLabel = new JLabel(String.valueOf((int) (lValue / colorRangeScaleFactor))); LoTickLabel.setFont(f); final JLabel UpTickLabel = new JLabel(String.valueOf((int) (uValue / colorRangeScaleFactor))); UpTickLabel.setFont(f); final JLabel maxTickLabel = new JLabel(String.valueOf((int) (iMax / colorRangeScaleFactor))); maxTickLabel.setFont(f); labelTable.put(iMin, minTickLabel); labelTable.put(lValue, LoTickLabel); labelTable.put(uValue, UpTickLabel); labelTable.put(iMax, maxTickLabel); colorRangeSlider.setLabelTable(labelTable); } public void setElementsVisible(boolean val, SuperAdapter superAdapter) { setColorRangeSliderVisible(val, superAdapter); colorRangeSlider.setDisplayToBlank(!val); plusButton.setEnabled(val); minusButton.setEnabled(val); } public void handleNewFileLoading(MatrixType option) { boolean isColorScaleType = MatrixType.isColorScaleType(option); colorRangeSlider.setEnabled(isColorScaleType); colorRangeSlider.setDisplayToOE(MatrixType.isOEColorScaleType(option)); plusButton.setEnabled(isColorScaleType); minusButton.setEnabled(isColorScaleType); } } ================================================ FILE: src/juicebox/mapcolorui/OEColorScale.java ================================================ /* * The MIT License (MIT) * * Copyright (c) 2011-2021 Broad Institute, Aiden Lab, Rice University, Baylor College of Medicine * * Permission is hereby granted, free of charge, to any person obtaining a copy * of this software and associated documentation files (the "Software"), to deal * in the Software without restriction, including without limitation the rights * to use, copy, modify, merge, publish, distribute, sublicense, and/or sell * copies of the Software, and to permit persons to whom the Software is * furnished to do so, subject to the following conditions: * * The above copyright notice and this permission notice shall be included in * all copies or substantial portions of the Software. * * THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR * IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, * FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE * AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER * LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, * OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN * THE SOFTWARE. */ package juicebox.mapcolorui; import juicebox.HiCGlobals; import juicebox.windowui.MatrixType; import org.broad.igv.renderer.ColorScale; import java.awt.*; /** * @author jrobinso * Date: 11/11/12 * Time: 11:32 PM */ class OEColorScale implements ColorScale { public static final int defaultMaxOEVal = 5; private final MatrixType type; private double threshold; public OEColorScale(MatrixType type) { super(); this.type = type; resetThreshold(); } private void resetThreshold() { if(type == MatrixType.DIFF) { threshold = defaultMaxOEVal; } else { threshold = Math.log(defaultMaxOEVal); } } public Color getColor(float score) { double newValue; if (MatrixType.isSubtactType(type)) { newValue = score; } else if (HiCGlobals.HACK_COLORSCALE_LINEAR) { if (score < 1) { newValue = 1 - (1 / score); } else { newValue = score - 1; } } else { newValue = Math.log(score); } int R, G, B; if (newValue > 0) { R = 255; newValue = Math.min(newValue, threshold); G = (int) (255 * (threshold - newValue) / threshold); B = (int) (255 * (threshold - newValue) / threshold); } else { newValue = -newValue; newValue = Math.min(newValue, threshold); B = 255; R = (int) (255 * (threshold - newValue) / threshold); G = (int) (255 * (threshold - newValue) / threshold); } if (HiCGlobals.HACK_COLORSCALE) { newValue = score; if (newValue > (threshold / 2)) { R = 255; newValue = Math.min(newValue, threshold); G = (int) (255 * (threshold - newValue) / (threshold / 2)); B = (int) (255 * (threshold - newValue) / (threshold / 2)); } else { newValue = Math.max(newValue, 0); B = 255; R = (int) (255 * (0 + newValue) / (threshold / 2)); G = (int) (255 * (0 + newValue) / (threshold / 2)); } } return new Color(R, G, B); } public Color getColor(String symbol) { return null; //To change body of implemented methods use File | Settings | File Templates. } public Color getNoDataColor() { return null; //To change body of implemented methods use File | Settings | File Templates. } public String asString() { return null; //To change body of implemented methods use File | Settings | File Templates. } public boolean isDefault() { return false; //To change body of implemented methods use File | Settings | File Templates. } public double getMax() { if (MatrixType.isSubtactType(type) || HiCGlobals.HACK_COLORSCALE || HiCGlobals.HACK_COLORSCALE_LINEAR) { return 2 * threshold; } else { return 2 * Math.exp(threshold); } } public float getThreshold() { if (MatrixType.isSubtactType(type) || HiCGlobals.HACK_COLORSCALE || HiCGlobals.HACK_COLORSCALE_LINEAR) { return (float) threshold; } else { return (float) Math.exp(threshold); } } public void setThreshold(double max) { if (MatrixType.isSubtactType(type) || HiCGlobals.HACK_COLORSCALE || HiCGlobals.HACK_COLORSCALE_LINEAR) { threshold = max; } else { threshold = Math.log(max); } } } ================================================ FILE: src/juicebox/mapcolorui/PearsonColorScale.java ================================================ /* * The MIT License (MIT) * * Copyright (c) 2011-2021 Broad Institute, Aiden Lab, Rice University, Baylor College of Medicine * * Permission is hereby granted, free of charge, to any person obtaining a copy * of this software and associated documentation files (the "Software"), to deal * in the Software without restriction, including without limitation the rights * to use, copy, modify, merge, publish, distribute, sublicense, and/or sell * copies of the Software, and to permit persons to whom the Software is * furnished to do so, subject to the following conditions: * * The above copyright notice and this permission notice shall be included in * all copies or substantial portions of the Software. * * THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR * IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, * FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE * AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER * LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, * OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN * THE SOFTWARE. */ package juicebox.mapcolorui; import java.awt.*; import java.util.HashMap; import java.util.Map; /** * @author Neva Cherniavsky * @since 3/22/12 */ public class PearsonColorScale { private final Map posMinMap = new HashMap<>(); private final Map posMaxMap = new HashMap<>(); private final Map negMinMap = new HashMap<>(); private final Map negMaxMap = new HashMap<>(); public PearsonColorScale() { } public float getPosMax(String key) { return posMaxMap.get(key); } public float getPosMin(String key) { return posMinMap.get(key); } public float getNegMax(String key) { return negMaxMap.get(key); } public float getNegMin(String key) { return negMinMap.get(key); } public void setMinMax(String key, float min, float max) { setMinMax(key, min, 0, 0, max); } public void setMinMax(String key, float negMin, float negMax, float posMin, float posMax) { negMinMap.put(key, negMin); negMaxMap.put(key, negMax); posMaxMap.put(key, posMax); posMinMap.put(key, posMin); } public Color getColor(String key, float score) { if (score > 0) { float min = getPosMin(key), max = getPosMax(key); score = (score - min) / (max - min); if (score > 0) { int R = (int) (255 * Math.min(score, 1)); int G = 0; int B = 0; return new Color(R, G, B); } } else if (score < 0) { float min = getNegMin(key), max = getNegMax(key); score = (score - max) / (min - max); if (score > 0) { //if (score < 0) score = -score; // this shouldn't happen but seems to be happening. int R = 0; int G = 0; int B = (int) (255 * Math.min(score, 1)); return new Color(R, G, B); } } return Color.black; } public Color getColor(String symbol) { return null; //To change body of implemented methods use File | Settings | File Templates. } public Color getNoDataColor() { return null; //To change body of implemented methods use File | Settings | File Templates. } public String asString() { return null; //To change body of implemented methods use File | Settings | File Templates. } public boolean isDefault() { return false; //To change body of implemented methods use File | Settings | File Templates. } public boolean doesNotContainKey(String key) { return !negMinMap.containsKey(key) || !posMaxMap.containsKey(key); } public void resetValues(String key) { negMinMap.remove(key); negMaxMap.remove(key); posMinMap.remove(key); posMaxMap.remove(key); } } ================================================ FILE: src/juicebox/mapcolorui/PearsonColorScaleEditor.java ================================================ /* * The MIT License (MIT) * * Copyright (c) 2011-2021 Broad Institute, Aiden Lab, Rice University, Baylor College of Medicine * * Permission is hereby granted, free of charge, to any person obtaining a copy * of this software and associated documentation files (the "Software"), to deal * in the Software without restriction, including without limitation the rights * to use, copy, modify, merge, publish, distribute, sublicense, and/or sell * copies of the Software, and to permit persons to whom the Software is * furnished to do so, subject to the following conditions: * * The above copyright notice and this permission notice shall be included in * all copies or substantial portions of the Software. * * THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR * IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, * FITNESS FOR A PARTICULAR PURPOSE AND NON-INFRINGEMENT. IN NO EVENT SHALL THE * AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER * LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, * OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN * THE SOFTWARE. */ package juicebox.mapcolorui; import juicebox.HiCGlobals; import juicebox.gui.SuperAdapter; import javax.swing.*; import javax.swing.border.Border; import java.awt.*; import java.awt.event.ActionEvent; import java.awt.event.ActionListener; /** * Created by muhammadsaadshamim on 1/25/17. */ public class PearsonColorScaleEditor extends JDialog { private static final long serialVersionUID = 9000030; public PearsonColorScaleEditor(final SuperAdapter superAdapter, final PearsonColorScale pearsonColorScale) { super(superAdapter.getMainWindow()); Container contentPane = getContentPane(); contentPane.setLayout(new BorderLayout()); Border padding = BorderFactory.createEmptyBorder(20, 20, 5, 20); setModal(true); final String key = superAdapter.getHiC().getColorScaleKey(); JLabel labelPosMax = new JLabel("Positive Max"); JLabel labelPosMin = new JLabel("Positive Min"); JLabel labelNegMax = new JLabel("Negative Max"); JLabel labelNegMin = new JLabel("Negative Min"); // todo error if called when pearson not loaded yet final JTextField textPosMax = new JTextField("" + pearsonColorScale.getPosMax(key)); final JTextField textPosMin = new JTextField("" + pearsonColorScale.getPosMin(key)); final JTextField textNegMax = new JTextField("" + pearsonColorScale.getNegMax(key)); final JTextField textNegMin = new JTextField("" + pearsonColorScale.getNegMin(key)); JPanel box = new JPanel(); box.setLayout(new GridLayout(0, 2)); box.add(labelPosMax); box.add(textPosMax); box.add(labelPosMin); box.add(textPosMin); box.add(labelNegMax); box.add(textNegMax); box.add(labelNegMin); box.add(textNegMin); JButton updateButton = new JButton("Update Values"); updateButton.addActionListener(new ActionListener() { @Override public void actionPerformed(ActionEvent e) { Color mainBackgroundColor = HiCGlobals.isDarkulaModeEnabled ? Color.DARK_GRAY : Color.WHITE; textPosMax.setBackground(mainBackgroundColor); textPosMin.setBackground(mainBackgroundColor); textNegMax.setBackground(mainBackgroundColor); textNegMin.setBackground(mainBackgroundColor); float maxA = Float.parseFloat(textPosMax.getText()); float minA = Float.parseFloat(textPosMin.getText()); float maxB = Float.parseFloat(textNegMax.getText()); float minB = Float.parseFloat(textNegMin.getText()); if (minA < 0) { textPosMin.setBackground(Color.RED); } else if (minA >= maxA) { textPosMax.setBackground(Color.RED); textPosMin.setBackground(Color.RED); } else if (maxB > 0) { textNegMax.setBackground(Color.RED); } else if (minB >= maxB) { textNegMax.setBackground(Color.RED); textNegMin.setBackground(Color.RED); } else { pearsonColorScale.setMinMax(key, minB, maxB, minA, maxA); superAdapter.refresh(); } } }); JButton resetButton = new JButton("Reset Values"); resetButton.addActionListener(new ActionListener() { @Override public void actionPerformed(ActionEvent e) { pearsonColorScale.resetValues(key); superAdapter.refresh(); PearsonColorScaleEditor.this.dispose(); } }); JPanel buttonPanel = new JPanel(); buttonPanel.setBorder(padding); buttonPanel.setLayout(new GridLayout(0, 2)); buttonPanel.add(updateButton); buttonPanel.add(resetButton); contentPane.add(box, BorderLayout.CENTER); contentPane.add(buttonPanel, BorderLayout.PAGE_END); box.setBorder(padding); pack(); setLocationRelativeTo(getOwner()); setVisible(true); } } ================================================ FILE: src/juicebox/mapcolorui/RangeSlider.java ================================================ /* * The MIT License (MIT) * * Copyright (c) 2011-2021 Broad Institute, Aiden Lab, Rice University, Baylor College of Medicine * * Permission is hereby granted, free of charge, to any person obtaining a copy * of this software and associated documentation files (the "Software"), to deal * in the Software without restriction, including without limitation the rights * to use, copy, modify, merge, publish, distribute, sublicense, and/or sell * copies of the Software, and to permit persons to whom the Software is * furnished to do so, subject to the following conditions: * * The above copyright notice and this permission notice shall be included in * all copies or substantial portions of the Software. * * THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR * IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, * FITNESS FOR A PARTICULAR PURPOSE AND NON-INFRINGEMENT. IN NO EVENT SHALL THE * AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER * LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, * OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN * THE SOFTWARE. */ package juicebox.mapcolorui; import javax.swing.*; /** * An extension of JSlider to select a range of values using two thumb controls. * The thumb controls are used to select the lower and upper value of a range * with predetermined minimum and maximum values. *

*

Note that RangeSlider makes use of the default BoundedRangeModel, which * supports an inner range defined by a value and an extent. The upper value * returned by RangeSlider is simply the lower value plus the extent.

* * @author Ernest Yu, Jim Robinson, Muhammad S Shamim */ class RangeSlider extends JSlider { private static final long serialVersionUID = 9000031; private RangeSliderUI rangeSliderUI; /** * Constructs a RangeSlider with default minimum and maximum values of 0 * and 100. */ public RangeSlider() { initSlider(); } /** * Initializes the slider by setting default properties. */ private void initSlider() { setOrientation(HORIZONTAL); } /** * Overrides the superclass method to install the UI delegate to draw two * thumbs. */ @Override public void updateUI() { rangeSliderUI = new RangeSliderUI(this); setUI(rangeSliderUI); // Update UI for slider labels. This must be called after updating the // UI of the slider. Refer to JSlider.updateUI(). updateLabelUIs(); } public int getLowerValue() { return getValue(); } public void setLowerValue(int value) { setValue(value); } /** * Sets the lower value in the range. */ @Override public void setValue(int value) { int oldValue = getValue(); if (oldValue == value) { return; } // Compute new value and extent to maintain upper value. int oldExtent = getExtent(); int newValue = Math.min(Math.max(getMinimum(), value), oldValue + oldExtent); int newExtent = oldExtent + oldValue - newValue; // Set new value and extent, and fire a single change event. getModel().setRangeProperties(newValue, newExtent, getMinimum(), getMaximum(), getValueIsAdjusting()); } /** * Returns the upper value in the range. */ public int getUpperValue() { return getValue() + getExtent(); } /** * Sets the upper value in the range. */ public void setUpperValue(int value) { // Compute new extent. int lowerValue = getValue(); int newExtent = Math.min(Math.max(0, value - lowerValue), getMaximum() - lowerValue); // Set extent to set upper value. setExtent(newExtent); } public void setDisplayToOE(boolean colorIsOE) { rangeSliderUI.setDisplayToOE(colorIsOE); } public void setDisplayToBlank(boolean colorIsBlank) { rangeSliderUI.setDisplayToBlank(colorIsBlank); } } ================================================ FILE: src/juicebox/mapcolorui/RangeSliderUI.java ================================================ /* * The MIT License (MIT) * * Copyright (c) 2011-2021 Broad Institute, Aiden Lab, Rice University, Baylor College of Medicine * * Permission is hereby granted, free of charge, to any person obtaining a copy * of this software and associated documentation files (the "Software"), to deal * in the Software without restriction, including without limitation the rights * to use, copy, modify, merge, publish, distribute, sublicense, and/or sell * copies of the Software, and to permit persons to whom the Software is * furnished to do so, subject to the following conditions: * * The above copyright notice and this permission notice shall be included in * all copies or substantial portions of the Software. * * THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR * IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, * FITNESS FOR A PARTICULAR PURPOSE AND NON-INFRINGEMENT. IN NO EVENT SHALL THE * AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER * LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, * OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN * THE SOFTWARE. */ package juicebox.mapcolorui; import juicebox.HiCGlobals; import javax.swing.*; import javax.swing.event.ChangeEvent; import javax.swing.event.ChangeListener; import javax.swing.plaf.basic.BasicSliderUI; import java.awt.*; import java.awt.event.MouseEvent; /** * UI delegate for the RangeSlider component. RangeSliderUI paints two thumbs, * one for the lower value and one for the upper value. * * @author Ernest Yu, Muhammad S Shamim */ class RangeSliderUI extends BasicSliderUI { private final Color rangeColorBlank = Color.gray; private final Color[] gradientColorsBlank = {Color.gray, Color.gray}; private final float[] fractionsBlank = {0.0f, 1.0f}; private final Color rangeColor = Color.RED; //private final Color[] gradientColors = {Color.WHITE, HICGlobals.HIC_MAP_COLOR}; private final float[] fractions = {0.0f, 1.0f}; private final Color[] gradientColorsOE = HiCGlobals.isDarkulaModeEnabled ? new Color[]{Color.BLUE, Color.BLACK, Color.RED} : new Color[]{Color.BLUE, Color.WHITE, Color.RED}; private final float[] fractionsOE = {0.0f, 0.5f, 1.0f}; private boolean colorIsOE = false; private boolean colorIsBlank = false; private final Object key = new Object(); /** * Location and size of thumb for upper value. */ private Rectangle upperThumbRect; /** * Indicator that determines whether upper thumb is selected. */ private boolean upperThumbSelected; /** * Indicator that determines whether lower thumb is being dragged. */ private transient boolean lowerDragging; /** * Indicator that determines whether upper thumb is being dragged. */ private transient boolean upperDragging; /** * Constructs a RangeSliderUI for the specified slider component. * * @param b RangeSlider */ public RangeSliderUI(RangeSlider b) { super(b); } /** * Installs this UI delegate on the specified component. */ @Override public void installUI(JComponent c) { upperThumbRect = new Rectangle(); super.installUI(c); } /** * Creates a listener to handle track events in the specified slider. */ @Override protected TrackListener createTrackListener(JSlider slider) { return new RangeTrackListener(); } /** * Creates a listener to handle change events in the specified slider. */ @Override protected ChangeListener createChangeListener(JSlider slider) { return new ChangeHandler(); } /** * Updates the dimensions for both thumbs. */ @Override protected void calculateThumbSize() { // Call superclass method for lower thumb size. super.calculateThumbSize(); // Set upper thumb size. upperThumbRect.setSize(thumbRect.width, thumbRect.height); } /** * Updates the locations for both thumbs. */ @Override protected void calculateThumbLocation() { // Call superclass method for lower thumb location. super.calculateThumbLocation(); // Adjust upper value to snap to ticks if necessary. if (slider.getSnapToTicks()) { int upperValue = slider.getValue() + slider.getExtent(); int snappedValue = upperValue; int majorTickSpacing = slider.getMajorTickSpacing(); int minorTickSpacing = slider.getMinorTickSpacing(); int tickSpacing = 0; if (minorTickSpacing > 0) { tickSpacing = minorTickSpacing; } else if (majorTickSpacing > 0) { tickSpacing = majorTickSpacing; } if (tickSpacing != 0) { // If it's not on a tick, change the value if ((upperValue - slider.getMinimum()) % tickSpacing != 0) { float temp = (float) (upperValue - slider.getMinimum()) / (float) tickSpacing; int whichTick = Math.round(temp); snappedValue = slider.getMinimum() + (whichTick * tickSpacing); } if (snappedValue != upperValue) { slider.setExtent(snappedValue - slider.getValue()); } } } // Calculate upper thumb location. The thumb is centered over its // value on the track. if (slider.getOrientation() == JSlider.HORIZONTAL) { int upperPosition = xPositionForValue(slider.getValue() + slider.getExtent()); upperThumbRect.x = upperPosition - (upperThumbRect.width / 2); upperThumbRect.y = trackRect.y; } else { int upperPosition = yPositionForValue(slider.getValue() + slider.getExtent()); upperThumbRect.x = trackRect.x; upperThumbRect.y = upperPosition - (upperThumbRect.height / 2); } } /** * Returns the size of a thumb. */ @Override protected Dimension getThumbSize() { return new Dimension(12, 12); } /** * Paints the slider. The selected thumb is always painted on top of the * other thumb. */ @Override public void paint(Graphics g, JComponent c) { super.paint(g, c); Rectangle clipRect = g.getClipBounds(); if (upperThumbSelected) { // Paint lower thumb first, then upper thumb. if (clipRect.intersects(thumbRect)) { paintLowerThumb(g); } if (clipRect.intersects(upperThumbRect)) { paintUpperThumb(g); } } else { // Paint upper thumb first, then lower thumb. if (clipRect.intersects(upperThumbRect)) { paintUpperThumb(g); } if (clipRect.intersects(thumbRect)) { paintLowerThumb(g); } } } /** * Paints the track. */ @Override public void paintTrack(Graphics g) { // Draw track. super.paintTrack(g); Rectangle trackBounds = trackRect; if (slider.getOrientation() == JSlider.HORIZONTAL) { // Save color Color oldColor = g.getColor(); // parameters for recolored track int subTrackWidth = upperThumbRect.x - thumbRect.x; int leftArrowX = thumbRect.x; int rightArrowX = leftArrowX + subTrackWidth; int leftArrowY = trackRect.y + trackRect.height / 4; int redTrackWidth = trackRect.x + trackRect.width - rightArrowX; Rectangle subRect = new Rectangle(leftArrowX, leftArrowY, subTrackWidth, trackRect.height / 2); Rectangle leftSide = new Rectangle(trackRect.x, leftArrowY, leftArrowX - trackRect.x, subRect.height); Rectangle rightSide = new Rectangle(rightArrowX, leftArrowY, redTrackWidth, subRect.height); Point startP = new Point(subRect.x, subRect.y); Point endP = new Point(subRect.x + subRect.width, subRect.y + subRect.height); if (colorIsBlank) { LinearGradientPaint gradient = new LinearGradientPaint(startP, endP, fractionsBlank, gradientColorsBlank); drawSubTrackRectangles((Graphics2D) g, gradient, subRect, Color.gray, leftSide, Color.gray, rightSide); oldColor = rangeColorBlank; } else if (colorIsOE) { LinearGradientPaint gradient = new LinearGradientPaint(startP, endP, fractionsOE, gradientColorsOE); drawSubTrackRectangles((Graphics2D) g, gradient, subRect, Color.BLUE, leftSide, Color.RED, rightSide); } else { Color backgroundColor = HiCGlobals.isDarkulaModeEnabled ? Color.BLACK : Color.WHITE; LinearGradientPaint gradient = new LinearGradientPaint(startP, endP, fractions, new Color[]{backgroundColor, ColorScaleHandler.HIC_MAP_COLOR}); drawSubTrackRectangles((Graphics2D) g, gradient, subRect, backgroundColor, leftSide, ColorScaleHandler.HIC_MAP_COLOR, rightSide); } g.setColor(oldColor); } else { // Determine position of selected range by moving from the middle // of one thumb to the other. int lowerY = thumbRect.x + (thumbRect.width / 2); int upperY = upperThumbRect.x + (upperThumbRect.width / 2); // Determine track position. int cx = (trackBounds.width / 2) - 2; // Save color and shift position. Color oldColor = g.getColor(); g.translate(trackBounds.x + cx, trackBounds.y); // TODO - this should eventually be changed to accommodate vertical gradients (see the horizontal gradients code above) // Draw selected range. g.setColor(rangeColor); for (int x = 0; x <= 3; x++) { g.drawLine(x, lowerY - trackBounds.y, x, upperY - trackBounds.y); } // Restore position and color. g.translate(-(trackBounds.x + cx), -trackBounds.y); g.setColor(oldColor); } } private void drawSubTrackRectangles(Graphics2D g, LinearGradientPaint gradientColor, Rectangle gradientRect, Paint leftColor, Rectangle leftRect, Paint rightColor, Rectangle rightRect) { g.setPaint(gradientColor); g.fill(gradientRect); g.setPaint(leftColor); g.fill(leftRect); g.setPaint(rightColor); g.fill(rightRect); } /** * Overrides superclass method to do nothing. Thumb painting is handled * within the paint() method. */ @Override public void paintThumb(Graphics g) { // Do nothing. } /** * Paints the thumb for the lower value using the specified graphics object. */ private void paintLowerThumb(Graphics g) { //Rectangle knobBounds = thumbRect; super.paintThumb(g); } /** * Paints the thumb for the upper value using the specified graphics object. */ private void paintUpperThumb(Graphics g) { Rectangle tmp = thumbRect; thumbRect = upperThumbRect; super.paintThumb(g); thumbRect = tmp; } /** * Sets the location of the upper thumb, and repaints the slider. This is * called when the upper thumb is dragged to repaint the slider. The * setThumbLocation() method performs the same task for the * lower thumb. */ private void setUpperThumbLocation(int x, int y) { Rectangle upperUnionRect = new Rectangle(); upperUnionRect.setBounds(upperThumbRect); upperThumbRect.setLocation(x, y); SwingUtilities.computeUnion(upperThumbRect.x, upperThumbRect.y, upperThumbRect.width, upperThumbRect.height, upperUnionRect); slider.repaint(upperUnionRect.x, upperUnionRect.y, upperUnionRect.width, upperUnionRect.height); } /** * Moves the selected thumb in the specified direction by a block preview. * This method is called when the user presses the Page Up or Down keys. */ public void scrollByBlock(int direction) { synchronized (key) { int blockIncrement = (slider.getMaximum() - slider.getMinimum()) / 10; if (blockIncrement <= 0 && slider.getMaximum() > slider.getMinimum()) { blockIncrement = 1; } int delta = blockIncrement * ((direction > 0) ? POSITIVE_SCROLL : NEGATIVE_SCROLL); if (upperThumbSelected) { int oldValue = ((RangeSlider) slider).getUpperValue(); ((RangeSlider) slider).setUpperValue(oldValue + delta); } else { int oldValue = slider.getValue(); slider.setValue(oldValue + delta); } } } /** * Moves the selected thumb in the specified direction by a unit preview. * This method is called when the user presses one of the arrow keys. */ public void scrollByUnit(int direction) { synchronized (key) { int delta = ((direction > 0) ? POSITIVE_SCROLL : NEGATIVE_SCROLL); if (upperThumbSelected) { int oldValue = ((RangeSlider) slider).getUpperValue(); ((RangeSlider) slider).setUpperValue(oldValue + delta); } else { int oldValue = slider.getValue(); slider.setValue(oldValue + delta); } } } public void setDisplayToOE(boolean isOE) { this.colorIsOE = isOE; } public void setDisplayToBlank(boolean isBlank) { this.colorIsBlank = isBlank; } /** * Listener to handle model change events. This calculates the thumb * locations and repaints the slider if the value change is not caused by * dragging a thumb. */ private class ChangeHandler implements ChangeListener { public void stateChanged(ChangeEvent arg0) { if (!lowerDragging && !upperDragging) { calculateThumbLocation(); slider.repaint(); } } } /** * Listener to handle mouse movements in the slider track. */ class RangeTrackListener extends TrackListener { @Override public void mousePressed(MouseEvent e) { if (!slider.isEnabled()) { return; } currentMouseX = e.getX(); currentMouseY = e.getY(); if (slider.isRequestFocusEnabled()) { slider.requestFocus(); } // Determine which thumb is pressed. If the upper thumb is // selected (last one dragged), then check its position first; // otherwise check the position of the lower thumb first. boolean lowerPressed = false; boolean upperPressed = false; if (upperThumbSelected) { if (upperThumbRect.contains(currentMouseX, currentMouseY)) { upperPressed = true; } else if (thumbRect.contains(currentMouseX, currentMouseY)) { lowerPressed = true; } } else { if (thumbRect.contains(currentMouseX, currentMouseY)) { lowerPressed = true; } else if (upperThumbRect.contains(currentMouseX, currentMouseY)) { upperPressed = true; } } // Handle lower thumb pressed. if (lowerPressed && !colorIsOE) { int orientation = slider.getOrientation(); if (orientation == SwingConstants.VERTICAL) { offset = currentMouseY - thumbRect.y; } else if (orientation == SwingConstants.HORIZONTAL) { offset = currentMouseX - thumbRect.x; } upperThumbSelected = false; lowerDragging = true; return; } lowerDragging = false; // Handle upper thumb pressed. if (upperPressed) { int orientation = slider.getOrientation(); if (orientation == SwingConstants.VERTICAL) { offset = currentMouseY - upperThumbRect.y; } else if (orientation == SwingConstants.HORIZONTAL) { offset = currentMouseX - upperThumbRect.x; } upperThumbSelected = true; upperDragging = true; return; } upperDragging = false; } @Override public void mouseReleased(MouseEvent e) { if (!slider.isEnabled()) { return; } slider.setValueIsAdjusting(false); lowerDragging = false; upperDragging = false; //super.mouseReleased(e); } @Override public void mouseDragged(MouseEvent e) { if (!slider.isEnabled()) { return; } currentMouseX = e.getX(); currentMouseY = e.getY(); if (lowerDragging && !colorIsOE) { slider.setValueIsAdjusting(true); moveLowerThumb(); } else if (upperDragging) { slider.setValueIsAdjusting(true); moveUpperThumb(); } } @Override public boolean shouldScroll(int direction) { return false; } /** * Moves the location of the lower thumb, and sets its corresponding * value in the slider. */ private void moveLowerThumb() { int thumbMiddle; int orientation = slider.getOrientation(); if (orientation == SwingConstants.VERTICAL) { int halfThumbHeight = thumbRect.height / 2; int thumbTop = currentMouseY - offset; int trackTop = trackRect.y; int trackBottom = trackRect.y + (trackRect.height - 1); int vMax = yPositionForValue(slider.getValue() + slider.getExtent()); // Apply bounds to thumb position. if (drawInverted()) { trackBottom = vMax; } else { trackTop = vMax; } thumbTop = Math.max(thumbTop, trackTop - halfThumbHeight); thumbTop = Math.min(thumbTop, trackBottom - halfThumbHeight); setThumbLocation(thumbRect.x, thumbTop); // Update slider value. thumbMiddle = thumbTop + halfThumbHeight; slider.setValue(valueForYPosition(thumbMiddle)); } else if (orientation == SwingConstants.HORIZONTAL) { int halfThumbWidth = thumbRect.width / 2; int thumbLeft = currentMouseX - offset; int trackLeft = trackRect.x; int trackRight = trackRect.x + (trackRect.width - 1); int hMax = xPositionForValue(slider.getValue() + slider.getExtent()); thumbLeft = Math.max(thumbLeft, trackLeft - halfThumbWidth); thumbLeft = Math.min(thumbLeft, trackRight - halfThumbWidth); // Apply bounds to thumb position. if (drawInverted()) { thumbLeft = Math.max(thumbLeft, hMax); } else { thumbLeft = Math.min(thumbLeft, hMax); } if (colorIsOE) { int midpoint = (trackRight - trackLeft) / 2 + trackLeft; thumbLeft = Math.min(thumbLeft, midpoint - halfThumbWidth); } setThumbLocation(thumbLeft, thumbRect.y); // Update slider value. thumbMiddle = thumbLeft + halfThumbWidth; slider.setValue(valueForXPosition(thumbMiddle)); if (colorIsOE) { int val = ((RangeSlider) slider).getLowerValue(); if (val == 0) { ((RangeSlider) slider).setLowerValue(-1); ((RangeSlider) slider).setUpperValue(1); } else { ((RangeSlider) slider).setUpperValue(-val); } } } } /** * Moves the location of the upper thumb, and sets its corresponding * value in the slider. */ private void moveUpperThumb() { int thumbMiddle; int orientation = slider.getOrientation(); if (orientation == SwingConstants.VERTICAL) { int halfThumbHeight = thumbRect.height / 2; int thumbTop = currentMouseY - offset; int trackTop = trackRect.y; int trackBottom = trackRect.y + (trackRect.height - 1); int vMin = yPositionForValue(slider.getValue()); // Apply bounds to thumb position. if (drawInverted()) { trackTop = vMin; } else { trackBottom = vMin; } thumbTop = Math.max(thumbTop, trackTop - halfThumbHeight); thumbTop = Math.min(thumbTop, trackBottom - halfThumbHeight); setUpperThumbLocation(thumbRect.x, thumbTop); // Update slider extent. thumbMiddle = thumbTop + halfThumbHeight; slider.setExtent(valueForYPosition(thumbMiddle) - slider.getValue()); } else if (orientation == SwingConstants.HORIZONTAL) { int halfThumbWidth = thumbRect.width / 2; int thumbLeft = currentMouseX - offset; int trackLeft = trackRect.x; int trackRight = trackRect.x + (trackRect.width - 1); int hMin = xPositionForValue(slider.getValue()); // Apply bounds to thumb position. if (drawInverted()) { trackRight = hMin; } else { trackLeft = hMin; } thumbLeft = Math.max(thumbLeft, trackLeft - halfThumbWidth); thumbLeft = Math.min(thumbLeft, trackRight - halfThumbWidth); if (colorIsOE) { int midpoint = (trackRight - trackLeft) / 2 + trackLeft; thumbLeft = Math.max(thumbLeft, midpoint - halfThumbWidth); } setUpperThumbLocation(thumbLeft, thumbRect.y); // Update slider extent. thumbMiddle = thumbLeft + halfThumbWidth; slider.setExtent(valueForXPosition(thumbMiddle) - slider.getValue()); if (colorIsOE) { int val = ((RangeSlider) slider).getUpperValue(); if (val == 0) { val = 1; ((RangeSlider) slider).setUpperValue(val); } ((RangeSlider) slider).setLowerValue(-val); } } } } } ================================================ FILE: src/juicebox/mapcolorui/ResolutionControl.java ================================================ /* * The MIT License (MIT) * * Copyright (c) 2011-2021 Broad Institute, Aiden Lab, Rice University, Baylor College of Medicine * * Permission is hereby granted, free of charge, to any person obtaining a copy * of this software and associated documentation files (the "Software"), to deal * in the Software without restriction, including without limitation the rights * to use, copy, modify, merge, publish, distribute, sublicense, and/or sell * copies of the Software, and to permit persons to whom the Software is * furnished to do so, subject to the following conditions: * * The above copyright notice and this permission notice shall be included in * all copies or substantial portions of the Software. * * THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR * IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, * FITNESS FOR A PARTICULAR PURPOSE AND NON-INFRINGEMENT. IN NO EVENT SHALL THE * AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER * LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, * OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN * THE SOFTWARE. */ package juicebox.mapcolorui; import com.jidesoft.swing.JideButton; import juicebox.HiC; import juicebox.HiCGlobals; import juicebox.data.MatrixZoomData; import juicebox.gui.SuperAdapter; import juicebox.windowui.HiCZoom; import org.broad.igv.ui.FontManager; import javax.swing.*; import javax.swing.border.LineBorder; import javax.swing.event.ChangeEvent; import javax.swing.event.ChangeListener; import java.awt.*; import java.awt.event.ActionEvent; import java.awt.event.ActionListener; import java.awt.event.MouseAdapter; import java.awt.event.MouseEvent; import java.awt.font.TextAttribute; import java.util.Dictionary; import java.util.Hashtable; import java.util.List; import java.util.Map; import java.util.concurrent.ConcurrentHashMap; public class ResolutionControl extends JPanel { private static final long serialVersionUID = 9000032; private final ImageIcon lockOpenIcon; private final ImageIcon lockIcon; private final HiC hic; private final HeatmapPanel heatmapPanel; private final JideButton lockButton; private final JLabel resolutionLabel; private final Map idxZoomMap = new ConcurrentHashMap<>(); private final Map bpLabelMap; private final HiCZoom pearsonZoom = new HiCZoom(HiC.Unit.BP, 500000); public HiC.Unit unit = HiC.Unit.BP; private boolean resolutionLocked = false; private final JSlider resolutionSlider; private int lastValue = 0; { // todo @nchernia shouldn't this use hic.getDataset().getBpZooms() ? bpLabelMap = new Hashtable<>(); bpLabelMap.put(2500000, "2.5 MB"); bpLabelMap.put(1000000, "1 MB"); bpLabelMap.put(500000, "500 KB"); bpLabelMap.put(250000, "250 KB"); bpLabelMap.put(100000, "100 KB"); bpLabelMap.put(50000, "50 KB"); bpLabelMap.put(25000, "25 KB"); bpLabelMap.put(10000, "10 KB"); bpLabelMap.put(5000, "5 KB"); bpLabelMap.put(1000, "1 KB"); } public ResolutionControl(final SuperAdapter superAdapter) { this.hic = superAdapter.getHiC(); this.heatmapPanel = superAdapter.getHeatmapPanel(); this.setBorder(LineBorder.createGrayLineBorder()); this.setLayout(new BorderLayout()); resolutionLabel = new JLabel(getUnitLabel()); resolutionLabel.setHorizontalAlignment(SwingConstants.CENTER); resolutionLabel.setBackground(HiCGlobals.backgroundColor); JPanel resolutionLabelPanel = new JPanel(); resolutionLabelPanel.setBackground(HiCGlobals.backgroundColor); resolutionLabelPanel.setLayout(new BorderLayout()); resolutionLabelPanel.add(resolutionLabel, BorderLayout.CENTER); // TODO not working // supposed to underline "resolution text" but why? is this an important gui issue? resolutionLabelPanel.addMouseListener(new MouseAdapter() { private Font original; @SuppressWarnings({"unchecked", "rawtypes"}) @Override public void mouseEntered(MouseEvent e) { original = e.getComponent().getFont(); if (resolutionSlider.isEnabled()) { original = e.getComponent().getFont(); Map attributes = original.getAttributes(); attributes.put(TextAttribute.UNDERLINE, TextAttribute.UNDERLINE_ON); e.getComponent().setFont(original.deriveFont(attributes)); } } @Override public void mouseExited(MouseEvent e) { e.getComponent().setFont(original); } }); resolutionLabelPanel.addMouseListener(new MouseAdapter() { @Override public void mousePressed(MouseEvent e) { if (e.isPopupTrigger() && resolutionSlider.isEnabled() && hic != null && hic.getDataset() != null) { if (hic.getDataset().hasFrags()) { processClick(); } } } @Override public void mouseClicked(MouseEvent e) { //No double click here... if (e.getClickCount() == 1 && resolutionSlider.isEnabled() && hic != null && hic.getDataset() != null) { if (hic.getDataset().hasFrags()) { processClick(); } } } private void processClick() { unit = (unit == HiC.Unit.FRAG ? HiC.Unit.BP : HiC.Unit.FRAG); resolutionLabel.setText(getUnitLabel()); Runnable runnable = new Runnable() { public void run() { reset(); superAdapter.refresh(); // necessary to correct BP/FRAG switching all red box } }; superAdapter.executeLongRunningTask(runnable, "Resolution switched"); } }); this.add(resolutionLabelPanel, BorderLayout.PAGE_START); JPanel resolutionButtonPanel = new JPanel(); resolutionButtonPanel.setLayout(new BoxLayout(resolutionButtonPanel, BoxLayout.X_AXIS)); //---- resolutionSlider ---- JPanel sliderPanel = new JPanel(); sliderPanel.setLayout(new BoxLayout(sliderPanel, BoxLayout.X_AXIS)); resolutionSlider = new JSlider(); sliderPanel.add(resolutionSlider); lockButton = new JideButton(); lockIcon = new ImageIcon(getClass().getResource("/images/lock.png")); lockOpenIcon = new ImageIcon(getClass().getResource("/images/lock_open.png")); resolutionLocked = false; lockButton.setIcon(lockOpenIcon); lockButton.addActionListener(new ActionListener() { @Override public void actionPerformed(ActionEvent e) { toggleLockButton(); } }); sliderPanel.add(lockButton); resolutionButtonPanel.add(sliderPanel); this.add(resolutionButtonPanel, BorderLayout.CENTER); // Setting the zoom should always be done by calling resolutionSlider.setValue() so work isn't done twice. resolutionSlider.addChangeListener(new ChangeListener() { // Change zoom level while staying centered on current location. // Centering is relative to the bounds of the data, which might not be the bounds of the window public void stateChanged(ChangeEvent e) { final MatrixZoomData zd; try { zd = hic.getZd(); } catch (Exception ex) { return; } if (hic == null || hic.getMatrix() == null || zd == null || resolutionSlider.getValueIsAdjusting()) return; final ChangeEvent eF = e; Runnable runnable = new Runnable() { public void run() { unsafeStateChanged(eF, zd); } }; superAdapter.executeLongRunningTask(runnable, "Resolution slider change"); } private void unsafeStateChanged(ChangeEvent e, MatrixZoomData zd) { int idx = resolutionSlider.getValue(); final HiCZoom zoom = idxZoomMap.get(idx); if (zoom == null) return; if (zoom.getBinSize() == hic.getXContext().getZoom().getBinSize() && zoom.getUnit() == hic.getXContext().getZoom().getUnit()) return; if (hic.isInPearsonsMode() && hic.isPearsonsNotAvailableAtSpecificZoom(false, zoom)) { JOptionPane.showMessageDialog(getParent(), "Pearson's matrix is not available at this resolution"); setZoom(pearsonZoom); return; } if (hic.getXContext() != null) { double scaledXWidth = heatmapPanel.getWidth() / hic.getScaleFactor(); double scaledYHeight = heatmapPanel.getHeight() / hic.getScaleFactor(); double centerBinX = hic.getXContext().getBinOrigin() + scaledXWidth / 2; double centerBinY = hic.getYContext().getBinOrigin() + scaledYHeight / 2; long xGenome = zd.getXGridAxis().getGenomicMid(centerBinX); long yGenome = zd.getYGridAxis().getGenomicMid(centerBinY); // this to center zooming when there is lots of whitespace in the margins try { if (scaledXWidth > hic.getZd().getXGridAxis().getBinCount()) { xGenome = hic.getXContext().getChrLength() / 2; } } catch (Exception ignored) { } try { if (scaledYHeight > hic.getZd().getYGridAxis().getBinCount()) { yGenome = hic.getYContext().getChrLength() / 2; } } catch (Exception ignored) { } final String chrXName = hic.getXContext().getChromosome().toString(); final String chrYName = hic.getYContext().getChromosome().toString(); if (zd == null) { hic.unsafeActuallySetZoomAndLocation(chrXName, chrYName, zoom, 0, 0, -1, true, HiC.ZoomCallType.STANDARD, true, isResolutionLocked() ? 1 : 0, true); } else { if (hic.unsafeActuallySetZoomAndLocation(chrXName, chrYName, zoom, xGenome, yGenome, -1, true, HiC.ZoomCallType.STANDARD, true, isResolutionLocked() ? 1 : 0, true)) { lastValue = resolutionSlider.getValue(); } else { resolutionSlider.setValue(lastValue); } } } } }); setEnabled(false); } private String getUnitLabel() { return unit == HiC.Unit.FRAG ? "Resolution (Frag)" : "Resolution (BP)"; } public void setEnabled(boolean enabled) { resolutionSlider.setEnabled(enabled); lockButton.setEnabled(enabled); } /** * Called when a new dataset is loaded, or when units are switched bp<->frag */ public void reset() { if (hic == null || hic.getDataset() == null) return; if (heatmapPanel != null) heatmapPanel.reset(); int currentIdx = resolutionSlider.getValue(); List binSizes = unit == HiC.Unit.BP ? hic.getDataset().getBpZooms() : hic.getDataset().getFragZooms(); idxZoomMap.clear(); for (int i = 0; i < binSizes.size(); i++) { HiCZoom zoom = binSizes.get(i); idxZoomMap.put(i, zoom); } int maxIdx = binSizes.size() - 1; resolutionSlider.setMaximum(maxIdx); resolutionSlider.setMajorTickSpacing(1); resolutionSlider.setPaintTicks(true); resolutionSlider.setSnapToTicks(true); resolutionSlider.setPaintLabels(true); resolutionSlider.setMinorTickSpacing(1); // Create labels Dictionary resolutionLabels = new Hashtable<>(); Font f = FontManager.getFont(8); int skip = maxIdx > 6 ? 2 : 1; // Skip every other if more than 6 levels for (int i = 0; i <= maxIdx; i++) { if (i % skip == 0) { String label = sizeToLabel(binSizes.get(i).getBinSize()); final JLabel tickLabel = new JLabel(label); tickLabel.setFont(f); resolutionLabels.put(i, tickLabel); } HiCZoom zoom = binSizes.get(i); idxZoomMap.put(i, zoom); } resolutionSlider.setLabelTable(resolutionLabels); // Really we should find the closest matching resolution int newIdx = Math.min(currentIdx, maxIdx); HiCZoom newZoom = idxZoomMap.get(newIdx); setZoom(newZoom); } private String sizeToLabel(int binSize) { if (unit == HiC.Unit.FRAG) { return binSize + " f"; } // TODO delete the bpLabelMap? We dont need a hard-coded map if the labels change based on hicMapScale // if (bpLabelMap.containsKey(binSize)) { // return bpLabelMap.get(binSize); // } String label; int adjustedBinSize = (int) (binSize * HiCGlobals.hicMapScale); if (adjustedBinSize >= 1000000) { label = ((double) adjustedBinSize / 1000000) + " MB"; } else if (adjustedBinSize >= 1000) { label = ((double) adjustedBinSize / 1000) + " KB"; } else { label = adjustedBinSize + " BP"; } return removeTrailingZeros(label); } private String removeTrailingZeros(String label) { return label.split(" ")[0].replaceAll("\\.(0)+$", "") + " " + label.split(" ")[1]; } public void setZoom(HiCZoom newZoom) { if (unit != newZoom.getUnit()) { unit = newZoom.getUnit(); reset(); } resolutionLabel.setText(getUnitLabel()); resolutionLabel.setForeground(Color.BLUE); for (Map.Entry entry : idxZoomMap.entrySet()) { if (entry.getValue().equals(newZoom)) { resolutionSlider.setValue(entry.getKey()); } } } private void toggleLockButton() { setResolutionLocked(!resolutionLocked); updateLockButton(); } private void updateLockButton() { lockButton.setIcon(resolutionLocked ? lockIcon : lockOpenIcon); } public boolean isResolutionLocked() { return resolutionLocked; } public void setResolutionLocked(boolean resolutionLocked) { this.resolutionLocked = resolutionLocked; updateLockButton(); } } ================================================ FILE: src/juicebox/mapcolorui/ThumbnailPanel.java ================================================ /* * The MIT License (MIT) * * Copyright (c) 2011-2021 Broad Institute, Aiden Lab, Rice University, Baylor College of Medicine * * Permission is hereby granted, free of charge, to any person obtaining a copy * of this software and associated documentation files (the "Software"), to deal * in the Software without restriction, including without limitation the rights * to use, copy, modify, merge, publish, distribute, sublicense, and/or sell * copies of the Software, and to permit persons to whom the Software is * furnished to do so, subject to the following conditions: * * The above copyright notice and this permission notice shall be included in * all copies or substantial portions of the Software. * * THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR * IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, * FITNESS FOR A PARTICULAR PURPOSE AND NON-INFRINGEMENT. IN NO EVENT SHALL THE * AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER * LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, * OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN * THE SOFTWARE. */ package juicebox.mapcolorui; import juicebox.MainWindow; import juicebox.gui.SuperAdapter; import javax.swing.*; import java.awt.*; import java.awt.event.MouseAdapter; import java.awt.event.MouseEvent; import java.awt.event.MouseMotionAdapter; import java.awt.geom.*; /** * @author jrobinso * @since Aug 2, 2010 */ public class ThumbnailPanel extends JComponent { private static final long serialVersionUID = 9000033; private static final AlphaComposite ALPHA_COMP = AlphaComposite.getInstance(AlphaComposite.SRC_OVER, 0.75f); private final SuperAdapter superAdapter; private Image image; private Point lastPoint = null; private Rectangle innerRectangle; public ThumbnailPanel(final SuperAdapter superAdapter) { this.superAdapter = superAdapter; addMouseListener(new MouseAdapter() { @Override public void mouseClicked(MouseEvent mouseEvent) { if (mouseEvent.getClickCount() >= 1) { try { Point2D.Double scale = superAdapter.getHiCScale(ThumbnailPanel.this.getWidth(), ThumbnailPanel.this.getHeight()); int xBP = (int) (mouseEvent.getX() * scale.getX()); int yBP = (int) (mouseEvent.getY() * scale.getY()); superAdapter.centerMap(xBP, yBP); } catch (Exception e) { System.err.println("Error when thumbnail clicked"); } } } @Override public void mousePressed(MouseEvent mouseEvent) { if (innerRectangle != null && innerRectangle.contains(mouseEvent.getPoint())) { lastPoint = mouseEvent.getPoint(); setCursor(MainWindow.fistCursor); } } @Override public void mouseReleased(MouseEvent mouseEvent) { lastPoint = null; setCursor(Cursor.getDefaultCursor()); } }); addMouseMotionListener(new MouseMotionAdapter() { @Override public void mouseDragged(MouseEvent mouseEvent) { if (lastPoint != null) { Point2D.Double scale = superAdapter.getHiCScale(ThumbnailPanel.this.getWidth(), ThumbnailPanel.this.getHeight()); int dxBP = ((int) ((mouseEvent.getX() - lastPoint.x) * scale.getX())); int dyBP = ((int) ((mouseEvent.getY() - lastPoint.y) * scale.getY())); superAdapter.moveMapBy(dxBP, dyBP); lastPoint = mouseEvent.getPoint(); } } }); } public void setImage(Image image) { this.image = image; } public String getName() { return null; } public void setName(String nm) { } @Override protected void paintComponent(Graphics g) { ((Graphics2D) g).setRenderingHint(RenderingHints.KEY_ANTIALIASING, RenderingHints.VALUE_ANTIALIAS_ON); if (image != null) { g.drawImage(image, 0, 0, null); try { renderVisibleWindow((Graphics2D) g); } catch (Exception ignored) { } } } private void renderVisibleWindow(Graphics2D g) { if (superAdapter.shouldVisibleWindowBeRendered()) { Rectangle outerRectangle = new Rectangle(0, 0, getBounds().width, getBounds().height); Point2D.Double scale = superAdapter.getHiCScale(getWidth(), getHeight()); double scaleFactor = superAdapter.getHiCScaleFactor(); Point2D.Double origin = superAdapter.getHiCOrigin(); Point windowDim = superAdapter.getHeatMapPanelDimensions(); int x = (int) (origin.x / scale.getX()); int y = (int) (origin.y / scale.getY()); double wBins = windowDim.getX() / scaleFactor; int w = (int) (wBins / scale.getX()); double yBins = windowDim.getY() / scaleFactor; int h = (int) (yBins / scale.getY()); if (w < 4) { int delta = 4 - w; x -= delta / 2; w = 4; } if (h < 4) { int delta = 4 - h; y -= delta / 2; h = 4; } innerRectangle = new Rectangle(x, y, w, h); Shape shape = new SquareDonut(outerRectangle, innerRectangle); g.setColor(Color.gray); g.setComposite(ALPHA_COMP); g.fill(shape); g.draw(innerRectangle); } } private static class SquareDonut implements Shape { private final Area area; SquareDonut(Rectangle outerRectangle, Rectangle innerRectangle) { this.area = new Area(outerRectangle); area.subtract(new Area(innerRectangle)); } public Rectangle getBounds() { return area.getBounds(); } public Rectangle2D getBounds2D() { return area.getBounds2D(); } public boolean contains(double v, double v1) { return area.contains(v, v1); } public boolean contains(Point2D point2D) { return area.contains(point2D); } public boolean intersects(double v, double v1, double v2, double v3) { return area.intersects(v, v1, v2, v3); } public boolean intersects(Rectangle2D rectangle2D) { return area.intersects(rectangle2D); } public boolean contains(double v, double v1, double v2, double v3) { return area.contains(v, v1, v2, v3); } public boolean contains(Rectangle2D rectangle2D) { return area.contains(rectangle2D); } public PathIterator getPathIterator(AffineTransform affineTransform) { return area.getPathIterator(affineTransform); } public PathIterator getPathIterator(AffineTransform affineTransform, double v) { return area.getPathIterator(affineTransform, v); } } } ================================================ FILE: src/juicebox/matrix/BasicMatrix.java ================================================ /* * The MIT License (MIT) * * Copyright (c) 2011-2020 Broad Institute, Aiden Lab, Rice University, Baylor College of Medicine * * Permission is hereby granted, free of charge, to any person obtaining a copy * of this software and associated documentation files (the "Software"), to deal * in the Software without restriction, including without limitation the rights * to use, copy, modify, merge, publish, distribute, sublicense, and/or sell * copies of the Software, and to permit persons to whom the Software is * furnished to do so, subject to the following conditions: * * The above copyright notice and this permission notice shall be included in * all copies or substantial portions of the Software. * * THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR * IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, * FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE * AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER * LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, * OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN * THE SOFTWARE. */ package juicebox.matrix; /** * @author jrobinso * Date: 7/13/12 * Time: 1:05 PM */ public interface BasicMatrix { float getEntry(int row, int col); int getRowDimension(); int getColumnDimension(); float getLowerValue(); float getUpperValue(); void setEntry(int i, int j, float corr); } ================================================ FILE: src/juicebox/matrix/DiskResidentBlockMatrix.java ================================================ /* * The MIT License (MIT) * * Copyright (c) 2011-2020 Broad Institute, Aiden Lab, Rice University, Baylor College of Medicine * * Permission is hereby granted, free of charge, to any person obtaining a copy * of this software and associated documentation files (the "Software"), to deal * in the Software without restriction, including without limitation the rights * to use, copy, modify, merge, publish, distribute, sublicense, and/or sell * copies of the Software, and to permit persons to whom the Software is * furnished to do so, subject to the following conditions: * * The above copyright notice and this permission notice shall be included in * all copies or substantial portions of the Software. * * THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR * IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, * FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE * AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER * LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, * OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN * THE SOFTWARE. */ package juicebox.matrix; import htsjdk.samtools.seekablestream.SeekableStream; import htsjdk.samtools.seekablestream.SeekableStreamFactory; import htsjdk.tribble.util.LittleEndianInputStream; import org.broad.igv.util.ObjectCache; import org.broad.igv.util.ParsingUtils; import java.io.BufferedInputStream; import java.io.ByteArrayInputStream; import java.io.IOException; import java.io.InputStream; /** * Matrix class backed by a file layed out in "block" format. *

* File format: * Field Type Description * Magic number Integer Value should be 6515048, which when read as a zero delimited string is “hic”. * Version Integer The version number, currently = 1 * Genome String The genome ID (e.g. “hg19”) * Chromosome 1 String Name of first chromosome * Chromosome 2 String Name of second chromosome * Bin size Integer The bin size in base-pairs * Lower bounds for scale Float 5th percentile suggested * Upper bounds for scale Float 95th percentile suggested * Number of rows Integer Number of rows in the matrix. Rows correspond to chromosome 1. * Number of columns Integer * Block size Integer * * @author jrobinso * Date: 8/8/12 * Time: 8:42 AM */ public class DiskResidentBlockMatrix implements BasicMatrix { private final String path; private final ObjectCache blockDataCache = new ObjectCache<>(200); boolean isLoading = false; private String genome; private String chr1; private String chr2; private int binSize; private float lowerValue; private float upperValue; private int dim; private int blockSize; private int remSize; // Dimension of last block private int arrayStartPosition; private int nFullBlocks; public DiskResidentBlockMatrix(String path) throws IOException { this.path = path; init(); } public String getChr1() { return chr1; } @Override public float getEntry(int row, int col) { int blockRowIdx = row / blockSize; int blockColIdx = col / blockSize; String key = "row" + blockRowIdx + "_col" + blockColIdx; float[][] blockData = blockDataCache.get(key); if (blockData == null) { blockData = loadBlockData(blockRowIdx, blockColIdx); blockDataCache.put(key, blockData); } if (blockData == null) { return Float.NaN; } else { int rowRelative = row - blockRowIdx * blockSize; int colRelative = col - blockColIdx * blockSize; int totalRows = blockData.length; int totalCols = blockData[0].length; // TODO: note this should not happen, probably the bug in MatrixZoomData where there are too many columns. if (rowRelative < totalRows && colRelative < totalCols) return blockData[rowRelative][colRelative]; else return Float.NaN; } } private synchronized float[][] loadBlockData(int blockRowIdx, int blockColIdx) { String key = "row" + blockRowIdx + "_col" + blockColIdx; float[][] blockData = blockDataCache.get(key); if (blockData != null) return blockData; // In case this was calculated in another thread SeekableStream is = null; try { is = SeekableStreamFactory.getInstance().getStreamFor(path); int pointsPerBlockRow = blockSize * dim; // Applies to all but the last row int rowDim = blockRowIdx < nFullBlocks ? blockSize : remSize; int colDim = blockColIdx < nFullBlocks ? blockSize : remSize; int l1 = blockRowIdx * pointsPerBlockRow; int l2 = blockColIdx * blockSize * rowDim; long startFilePosition = arrayStartPosition + (l1 + l2) * 4L; int nDataPoints = rowDim * colDim; int nBytes = nDataPoints * 4; byte[] byteArray = new byte[nBytes]; is.seek(startFilePosition); is.readFully(byteArray); ByteArrayInputStream bis = new ByteArrayInputStream(byteArray); LittleEndianInputStream les = new LittleEndianInputStream(bis); blockData = new float[rowDim][colDim]; for (int r = 0; r < rowDim; r++) { for (int c = 0; c < colDim; c++) { float f = les.readFloat(); blockData[r][c] = f; } } blockDataCache.put(key, blockData); return blockData; } catch (IOException e) { System.err.println("Error reading block data: " + blockRowIdx + "-" + blockColIdx + " " + e.getLocalizedMessage()); return null; } finally { if (is != null) try { is.close(); } catch (IOException e) { e.printStackTrace(); //To change body of catch statement use File | Settings | File Templates. } } } @Override public int getRowDimension() { return dim; //To change body of implemented methods use File | Settings | File Templates. } @Override public int getColumnDimension() { return dim; //To change body of implemented methods use File | Settings | File Templates. } public float getLowerValue() { return lowerValue; } public float getUpperValue() { return upperValue; } @Override public void setEntry(int i, int j, float corr) { } private void init() throws IOException { // Peak at file to determine version BufferedInputStream bis = null; try { InputStream is = ParsingUtils.openInputStream(path); bis = new BufferedInputStream(is); LittleEndianInputStream les = new LittleEndianInputStream(bis); int bytePosition = 0; int magic = les.readInt(); // <= 6515048 bytePosition += 4; //if (magic != 6515048) <= ERROR // Version number int version = les.readInt(); bytePosition += 4; genome = les.readString(); bytePosition += genome.length() + 1; chr1 = les.readString(); bytePosition += chr1.length() + 1; chr2 = les.readString(); bytePosition += chr2.length() + 1; binSize = les.readInt(); bytePosition += 4; lowerValue = les.readFloat(); bytePosition += 4; upperValue = les.readFloat(); bytePosition += 4; int nRows = les.readInt(); // # rows, assuming square matrix bytePosition += 4; int nCols = les.readInt(); bytePosition += 4; if (nRows == nCols) { dim = nRows; } else { throw new RuntimeException("Non-square matrices not supported"); } blockSize = les.readInt(); bytePosition += 4; nFullBlocks = dim / blockSize; remSize = dim - nFullBlocks * blockSize; this.arrayStartPosition = bytePosition; } finally { if (bis != null) bis.close(); } } } ================================================ FILE: src/juicebox/matrix/InMemoryMatrix.java ================================================ /* * The MIT License (MIT) * * Copyright (c) 2011-2020 Broad Institute, Aiden Lab, Rice University, Baylor College of Medicine * * Permission is hereby granted, free of charge, to any person obtaining a copy * of this software and associated documentation files (the "Software"), to deal * in the Software without restriction, including without limitation the rights * to use, copy, modify, merge, publish, distribute, sublicense, and/or sell * copies of the Software, and to permit persons to whom the Software is * furnished to do so, subject to the following conditions: * * The above copyright notice and this permission notice shall be included in * all copies or substantial portions of the Software. * * THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR * IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, * FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE * AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER * LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, * OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN * THE SOFTWARE. */ package juicebox.matrix; import org.apache.commons.math.stat.StatUtils; import org.apache.commons.math3.stat.descriptive.DescriptiveStatistics; import org.broad.igv.util.collections.DoubleArrayList; import java.util.Arrays; /** * Assumptions -- matrix is square * * @author jrobinso * Date: 7/13/12 * Time: 1:48 PM */ public class InMemoryMatrix implements BasicMatrix { private final int dim; private final float[] data; private float lowerValue = Float.NaN; private float upperValue = Float.NaN; public InMemoryMatrix(int dim) { this.dim = dim; this.data = new float[dim * dim]; } public InMemoryMatrix(int dim, float[] data) { this.data = data; this.dim = dim; } public void fill(float value) { Arrays.fill(data, value); // Invalidate bounds lowerValue = Float.NaN; upperValue = Float.NaN; } @Override public float getEntry(int row, int col) { int idx = row * dim + col; return idx < data.length ? data[idx] : Float.NaN; } public void setEntry(int row, int col, float value) { int idx = row * dim + col; data[idx] = value; // Invalidate bounds lowerValue = Float.NaN; upperValue = Float.NaN; } @Override public int getRowDimension() { return dim; } @Override public int getColumnDimension() { return dim; } @Override public float getLowerValue() { if (Float.isNaN(lowerValue)) { computeBounds(); } return lowerValue; } @Override public float getUpperValue() { if (Float.isNaN(upperValue)) { computeBounds(); } return upperValue; } private void computeBounds() { DescriptiveStatistics stats = new DescriptiveStatistics(); for (float datum : data) { if (!Float.isNaN(datum)) stats.addValue(datum); } lowerValue = (float) stats.getPercentile(5); upperValue = (float) stats.getPercentile(95); } } ================================================ FILE: src/juicebox/matrix/RealMatrixWrapper.java ================================================ /* * The MIT License (MIT) * * Copyright (c) 2011-2021 Broad Institute, Aiden Lab, Rice University, Baylor College of Medicine * * Permission is hereby granted, free of charge, to any person obtaining a copy * of this software and associated documentation files (the "Software"), to deal * in the Software without restriction, including without limitation the rights * to use, copy, modify, merge, publish, distribute, sublicense, and/or sell * copies of the Software, and to permit persons to whom the Software is * furnished to do so, subject to the following conditions: * * The above copyright notice and this permission notice shall be included in * all copies or substantial portions of the Software. * * THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR * IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, * FITNESS FOR A PARTICULAR PURPOSE AND NON-INFRINGEMENT. IN NO EVENT SHALL THE * AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER * LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, * OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN * THE SOFTWARE. */ package juicebox.matrix; import org.apache.commons.math3.linear.RealMatrix; import org.apache.commons.math3.stat.descriptive.DescriptiveStatistics; /** * Wrpas a apache commons RealMatrix. We don't expose the apache class so we can use other implementations. * * @author jrobinso * Date: 7/13/12 * Time: 1:02 PM */ public class RealMatrixWrapper implements BasicMatrix { private final RealMatrix matrix; private float lowerValue = -1; private float upperValue = 1; public RealMatrixWrapper(RealMatrix matrix) { this.matrix = matrix; computePercentiles(); } @Override public float getEntry(int row, int col) { return (float) matrix.getEntry(row, col); } @Override public int getRowDimension() { return matrix.getRowDimension(); } @Override public int getColumnDimension() { return matrix.getColumnDimension(); } @Override public float getLowerValue() { return lowerValue; } @Override public float getUpperValue() { return upperValue; } @Override public void setEntry(int i, int j, float corr) { } private void computePercentiles() { // Statistics, other attributes DescriptiveStatistics flattenedDataStats = new DescriptiveStatistics(); double min = 1; double max = -1; for (int i = 0; i < matrix.getRowDimension(); i++) { for (int j = 0; j < matrix.getColumnDimension(); j++) { double value = matrix.getEntry(i, j); if (!Double.isNaN(value) && value != 1) { min = Math.min(value, min); max = Math.max(value, max); flattenedDataStats.addValue(value); } } } // Stats lowerValue = (float) flattenedDataStats.getPercentile(5); upperValue = (float) flattenedDataStats.getPercentile(95); } public RealMatrix getMatrix() { return matrix; } } ================================================ FILE: src/juicebox/matrix/SparseSymmetricMatrix.java ================================================ /* * The MIT License (MIT) * * Copyright (c) 2011-2020 Broad Institute, Aiden Lab, Rice University, Baylor College of Medicine * * Permission is hereby granted, free of charge, to any person obtaining a copy * of this software and associated documentation files (the "Software"), to deal * in the Software without restriction, including without limitation the rights * to use, copy, modify, merge, publish, distribute, sublicense, and/or sell * copies of the Software, and to permit persons to whom the Software is * furnished to do so, subject to the following conditions: * * The above copyright notice and this permission notice shall be included in * all copies or substantial portions of the Software. * * THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR * IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, * FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE * AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER * LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, * OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN * THE SOFTWARE. */ package juicebox.matrix; import juicebox.data.ContactRecord; import org.broad.igv.util.collections.FloatArrayList; import org.broad.igv.util.collections.IntArrayList; import java.util.Arrays; import java.util.List; /** * Represents a sparse, symmetric matrix in the sense that value(x,y) == value(y,x). It is an error to * add an x,y value twice, or to add both x,y and y,x, although this is not checked. The class is designed * for minimum memory footprint and good performance for vector multiplication, it is not a general purpose * matrix class. It is not private only so it can be unit tested *

* TODO - able to do Pearson's and gradient? */ public class SparseSymmetricMatrix implements BasicMatrix { private final int numValsEstimate; private final IntArrayList rows1; private final IntArrayList cols1; private final FloatArrayList values1; private IntArrayList rows2 = null; private IntArrayList cols2 = null; private FloatArrayList values2 = null; public SparseSymmetricMatrix(int numValsEstimate) { this.numValsEstimate = numValsEstimate; rows1 = new IntArrayList(numValsEstimate); cols1 = new IntArrayList(numValsEstimate); values1 = new FloatArrayList(numValsEstimate); } public void populateMatrix(List list, int[] offset) { for (ContactRecord cr : list) { int x = cr.getBinX(); int y = cr.getBinY(); float value = cr.getCounts(); if (offset[x] != -1 && offset[y] != -1) { setEntry(offset[x], offset[y], value); } } } public double[] multiply(double[] vector) { double[] result = new double[vector.length]; Arrays.fill(result, 0); int[] rowArray1 = rows1.toArray(); int[] colArray1 = cols1.toArray(); float[] valueArray1 = values1.toArray(); int n = rowArray1.length; for (int i = 0; i < n; i++) { int row = rowArray1[i]; int col = colArray1[i]; float value = valueArray1[i]; result[row] += vector[col] * value; if (row != col) { result[col] += vector[row] * value; } } if (rows2 != null) { int[] rowArray2 = rows2.toArray(); int[] colArray2 = cols2.toArray(); float[] valueArray2 = values2.toArray(); int n2 = rowArray2.length; for (int j = 0; j < n2; j++) { int row = rowArray2[j]; int col = colArray2[j]; float value = valueArray2[j]; result[row] += vector[col] * value; if (row != col) { result[col] += vector[row] * value; } } } return result; } @Override public float getEntry(int row, int col) { notImplementedDontCall(); return 0; } /** * functions not implemented as they will reduce certain optimizations / add to runtime */ private void notImplementedDontCall() { System.err.println("called unimplemented function - terminate"); System.exit(9); } @Override public int getRowDimension() { notImplementedDontCall(); return 0; } @Override public int getColumnDimension() { notImplementedDontCall(); return 0; } @Override public float getLowerValue() { notImplementedDontCall(); return 0; } @Override public float getUpperValue() { notImplementedDontCall(); return 0; } @Override public void setEntry(int row, int col, float val) { if (!Float.isNaN(val)) { if (rows2 == null) { try { rows1.add(row); cols1.add(col); values1.add(val); } catch (NegativeArraySizeException error) { rows2 = new IntArrayList(numValsEstimate); cols2 = new IntArrayList(numValsEstimate); values2 = new FloatArrayList(numValsEstimate); rows2.add(row); cols2.add(col); values2.add(val); } } else { rows2.add(row); cols2.add(col); values2.add(val); } } } /* public void print() { print(new PrintWriter(System.out)); } private void print(PrintWriter pw) { for (int i = 0; i < totSize; i++) { float[] row = getRow(i); for (int j = 0; j < totSize; j++) { pw.print(row[j] + " "); } pw.println(); } pw.close(); } */ /* private float[] getRow(int rowNum) { float[] result = new float[totSize]; int size = rows1.size(); for (int i = 0; i < size; i++) { if (rows1.get(i) == rowNum) result[cols1.get(i)] = values1.get(i); } if (rows2 != null) { size = rows2.size(); for (int i = 0; i < size; i++) { if (rows2.get(i) == rowNum) result[cols2.get(i)] = values2.get(i); } } return result; } */ } ================================================ FILE: src/juicebox/matrix/SparseVector.java ================================================ /* * The MIT License (MIT) * * Copyright (c) 2011-2020 Broad Institute, Aiden Lab, Rice University, Baylor College of Medicine * * Permission is hereby granted, free of charge, to any person obtaining a copy * of this software and associated documentation files (the "Software"), to deal * in the Software without restriction, including without limitation the rights * to use, copy, modify, merge, publish, distribute, sublicense, and/or sell * copies of the Software, and to permit persons to whom the Software is * furnished to do so, subject to the following conditions: * * The above copyright notice and this permission notice shall be included in * all copies or substantial portions of the Software. * * THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR * IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, * FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE * AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER * LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, * OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN * THE SOFTWARE. */ package juicebox.matrix; import java.util.Collection; import java.util.HashMap; /** * Simple representation of a sparse vector. C */ class SparseVector { private final int length; private final HashMap values; public SparseVector(int length) { this.length = length; values = new HashMap<>(); } public void set(Integer i, Double v) { if (i >= length) { throw new IndexOutOfBoundsException("Index " + i + " is >= length " + length); } values.put(i, v); } public int getLength() { return length; } public Double get(Integer idx) { return values.getOrDefault(idx, 0.0); } public Collection getIndeces() { return values.keySet(); } /** * Computes the mean of occupied elements * * @return */ public Double getMean() { if (values.size() == 0) return Double.NaN; double sum = 0; for (Double v : values.values()) { sum += v; } return sum / values.size(); } } ================================================ FILE: src/juicebox/matrix/SymmetricMatrix.java ================================================ /* * The MIT License (MIT) * * Copyright (c) 2011-2020 Broad Institute, Aiden Lab, Rice University, Baylor College of Medicine * * Permission is hereby granted, free of charge, to any person obtaining a copy * of this software and associated documentation files (the "Software"), to deal * in the Software without restriction, including without limitation the rights * to use, copy, modify, merge, publish, distribute, sublicense, and/or sell * copies of the Software, and to permit persons to whom the Software is * furnished to do so, subject to the following conditions: * * The above copyright notice and this permission notice shall be included in * all copies or substantial portions of the Software. * * THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR * IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, * FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE * AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER * LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, * OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN * THE SOFTWARE. */ package juicebox.matrix; import org.apache.commons.math.stat.StatUtils; import org.apache.commons.math3.stat.descriptive.DescriptiveStatistics; import org.broad.igv.util.collections.DoubleArrayList; import java.util.Arrays; import java.util.HashSet; import java.util.Set; /** * @author jrobinso * Date: 2/28/14 * Time: 5:49 PM */ public class SymmetricMatrix implements BasicMatrix { private final int dim; private final float[] data; private final Set nullColumns; private float lowerValue = Float.NaN; private float upperValue = Float.NaN; public SymmetricMatrix(int dim) { this.dim = dim; int size = (dim * dim - dim) / 2 + dim; data = new float[size]; nullColumns = new HashSet<>(); } public void nullColumn(int i) { nullColumns.add(i); } public Set getNullColumns() { return nullColumns; } public void fill(float value) { Arrays.fill(data, value); } public void setEntry(int i, int j, float value) { data[getIdx(i, j)] = value; } private int getIdx(int i, int j) { return (i < j) ? i * dim - (i - 1) * i / 2 + j - i : j * dim - (j - 1) * j / 2 + i - j; } public float getColumnMean(int j) { float sum = 0; int count = 0; for (int i = 0; i < dim; i++) { float value = getEntry(i, j); if (!Float.isNaN(value)) { sum += value; count++; } } return count == 0 ? Float.NaN : sum / count; } public float getRowMean(int i) { float sum = 0; int count = 0; for (int j = 0; j < dim; j++) { float value = getEntry(i, j); if (!Float.isNaN(value)) { sum += value; count++; } } return count == 0 ? Float.NaN : sum / count; } @Override public float getEntry(int i, int j) { int idx = getIdx(i, j); return idx < data.length ? data[idx] : Float.NaN; } @Override public int getRowDimension() { return dim; } @Override public int getColumnDimension() { return dim; } @Override public float getLowerValue() { if (Float.isNaN(lowerValue)) { computePercentiles(); } return lowerValue; } @Override public float getUpperValue() { if (Float.isNaN(upperValue)) { computePercentiles(); } return upperValue; } private void computePercentiles() { // Statistics, other attributes DescriptiveStatistics flattenedDataStats = new DescriptiveStatistics(); for (float value : data) { if (!Float.isNaN(value) && value != 1) { flattenedDataStats.addValue(value); } } // Stats lowerValue = (float) flattenedDataStats.getPercentile(5); upperValue = (float) flattenedDataStats.getPercentile(95); } } ================================================ FILE: src/juicebox/state/ImportStateFileDialog.java ================================================ /* * The MIT License (MIT) * * Copyright (c) 2011-2021 Broad Institute, Aiden Lab, Rice University, Baylor College of Medicine * * Permission is hereby granted, free of charge, to any person obtaining a copy * of this software and associated documentation files (the "Software"), to deal * in the Software without restriction, including without limitation the rights * to use, copy, modify, merge, publish, distribute, sublicense, and/or sell * copies of the Software, and to permit persons to whom the Software is * furnished to do so, subject to the following conditions: * * The above copyright notice and this permission notice shall be included in * all copies or substantial portions of the Software. * * THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR * IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, * FITNESS FOR A PARTICULAR PURPOSE AND NON-INFRINGEMENT. IN NO EVENT SHALL THE * AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER * LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, * OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN * THE SOFTWARE. */ package juicebox.state; import juicebox.MainWindow; import org.xml.sax.ErrorHandler; import org.xml.sax.InputSource; import org.xml.sax.SAXParseException; import javax.swing.*; import javax.swing.filechooser.FileNameExtensionFilter; import javax.xml.parsers.DocumentBuilder; import javax.xml.parsers.DocumentBuilderFactory; import java.io.File; import java.io.FileInputStream; import java.io.FileOutputStream; import java.io.IOException; import java.nio.channels.FileChannel; /** * Created by Zulkifl on 7/23/2015. */ public class ImportStateFileDialog extends JFileChooser { private static final long serialVersionUID = 9000019; private final File originalStates = new File("OriginalSavedStates.xml"); public ImportStateFileDialog(File currentStates, MainWindow mainWindow) { super(); loadFile(currentStates, mainWindow); } private static void copyFile(File sourceFile, File destFile) throws IOException { if (!destFile.exists()) { destFile.createNewFile(); } FileChannel source = null; FileChannel destination = null; try { source = new FileInputStream(sourceFile).getChannel(); destination = new FileOutputStream(destFile).getChannel(); destination.transferFrom(source, 0, source.size()); } finally { if (source != null) { source.close(); } if (destination != null) { destination.close(); } } } private void loadFile(File currentFile, MainWindow mainWindow) { FileNameExtensionFilter filter = new FileNameExtensionFilter( "XML Files", "xml", "XML"); setFileFilter(filter); int actionDialog = showOpenDialog(mainWindow); if (actionDialog == APPROVE_OPTION) { File importedFile = getSelectedFile(); String path = importedFile.getAbsolutePath(); mainWindow.updateNamesFromImport(path); try { DocumentBuilderFactory factory = DocumentBuilderFactory.newInstance(); factory.setValidating(false); factory.setNamespaceAware(true); DocumentBuilder builder = factory.newDocumentBuilder(); builder.setErrorHandler(new SimpleErrorHandler()); builder.parse(new InputSource(path)); copyFile(currentFile, originalStates); copyFile(importedFile, currentFile); JOptionPane.showMessageDialog(mainWindow, "Importing File:\n" + importedFile.getName(), "Opening", JOptionPane.INFORMATION_MESSAGE); JOptionPane.showMessageDialog(mainWindow, "Previous states have been saved under file:\n" + originalStates.getName(), "Creating Backup", JOptionPane.INFORMATION_MESSAGE); } catch (Exception e) { JOptionPane.showMessageDialog(mainWindow, "Error while importing file:\n" + e.getMessage(), "Error", JOptionPane.ERROR_MESSAGE); e.printStackTrace(); } System.out.println("Opening File: " + importedFile.getName()); } } private static class SimpleErrorHandler implements ErrorHandler { public void warning(SAXParseException e) { System.out.println(e.getMessage()); } public void error(SAXParseException e) { System.out.println(e.getMessage()); } public void fatalError(SAXParseException e) { System.out.println(e.getMessage()); } } } ================================================ FILE: src/juicebox/state/LoadStateFromXMLFile.java ================================================ /* * The MIT License (MIT) * * Copyright (c) 2011-2020 Broad Institute, Aiden Lab, Rice University, Baylor College of Medicine * * Permission is hereby granted, free of charge, to any person obtaining a copy * of this software and associated documentation files (the "Software"), to deal * in the Software without restriction, including without limitation the rights * to use, copy, modify, merge, publish, distribute, sublicense, and/or sell * copies of the Software, and to permit persons to whom the Software is * furnished to do so, subject to the following conditions: * * The above copyright notice and this permission notice shall be included in * all copies or substantial portions of the Software. * * THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR * IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, * FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE * AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER * LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, * OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN * THE SOFTWARE. */ package juicebox.state; import juicebox.HiC; import juicebox.gui.SuperAdapter; import juicebox.track.*; import juicebox.windowui.MatrixType; import org.broad.igv.renderer.DataRange; import javax.swing.*; import java.awt.*; import java.io.IOException; import java.util.Arrays; import java.util.List; /** * Created by Zulkifl on 6/10/2015. */ public class LoadStateFromXMLFile { public static void reloadSelectedState(SuperAdapter superAdapter, String mapPath) { superAdapter.getHiC().clearTracksForReloadState(); // TODO - should only remove necessary ones try { loadSavedStatePreliminaryStep(XMLFileParser.parseXML(mapPath), superAdapter, superAdapter.getHiC()); } catch (IOException e) { e.printStackTrace(); } superAdapter.refresh(); } private static void loadSavedStatePreliminaryStep(String[] infoForReload, SuperAdapter superAdapter, HiC hic) throws IOException { String result = "OK"; String[] initialInfo = new String[6]; //hicURL,, controlURL,xChr,yChr,unitSize double[] doubleInfo = new double[8]; //xOrigin, yOrigin, ScaleFactor, minColorVal, lowerColorVal, upperColorVal, maxColorVal, colorScaleFactor String[] trackURLsAndNamesAndConfigInfo = new String[3]; //System.out.println("Executing: " + Arrays.toString(infoForReload)); //TODO for reload if (infoForReload.length > 0) { //int fileSize = infoForReload.length; if (infoForReload.length > 15) { try { // TODO cleanup extraction of data initialInfo[0] = infoForReload[1]; //HiC Map Name initialInfo[1] = infoForReload[2]; //hicURL initialInfo[2] = infoForReload[3]; //controlURL initialInfo[3] = infoForReload[4]; //xChr initialInfo[4] = infoForReload[5]; //yChr initialInfo[5] = infoForReload[6]; //unitSize int binSize = Integer.parseInt(infoForReload[7]); //binSize doubleInfo[0] = Double.parseDouble(infoForReload[8]); //xOrigin doubleInfo[1] = Double.parseDouble(infoForReload[9]); //yOrigin doubleInfo[2] = Double.parseDouble(infoForReload[10]); //ScaleFactor MatrixType displayOption = MatrixType.valueOf(infoForReload[11].toUpperCase()); String normType = infoForReload[12].toUpperCase(); doubleInfo[3] = Double.parseDouble(infoForReload[13]); //minColorVal doubleInfo[4] = Double.parseDouble(infoForReload[14]); //lowerColorVal doubleInfo[5] = Double.parseDouble(infoForReload[15]); //upperColorVal doubleInfo[6] = Double.parseDouble(infoForReload[16]); //maxColorVal doubleInfo[7] = Double.parseDouble(infoForReload[17]); //colorScaleFactor trackURLsAndNamesAndConfigInfo[0] = (infoForReload[18]); //trackURLs trackURLsAndNamesAndConfigInfo[1] = (infoForReload[19]); //trackNames trackURLsAndNamesAndConfigInfo[2] = (infoForReload[20]); //trackConfigInfo //Increase XMLFileParser::infoForReload when adding more elements. safeLoadStateFromXML(superAdapter, hic, initialInfo, binSize, doubleInfo, displayOption, normType, trackURLsAndNamesAndConfigInfo); } catch (NumberFormatException nfe) { JOptionPane.showMessageDialog(superAdapter.getMainWindow(), "Error:\n" + nfe.getMessage(), "Error", JOptionPane.ERROR_MESSAGE); } } else { throw new IOException("Not enough parameters"); } } else { throw new IOException("Unknown command string"); } } private static void safeLoadStateFromXML(final SuperAdapter superAdapter, final HiC hic, final String[] initialInfo, final int binSize, final double[] doubleInfo, final MatrixType displaySelection, final String normSelection, final String[] tracks) { Runnable runnable = new Runnable() { public void run() { try { unsafeLoadStateFromXML(superAdapter, hic, initialInfo, binSize, doubleInfo, displaySelection, normSelection, tracks); } catch (Exception e) { e.printStackTrace(); } } }; superAdapter.executeLongRunningTask(runnable, "Loading a saved state from XML"); } private static void unsafeLoadStateFromXML(SuperAdapter superAdapter, HiC hic, String[] initialInfo, int binSize, double[] doubleInfo, MatrixType displaySelection, String normSelection, String[] tracks) { superAdapter.resetControlMap(); //TODO test String mapNames = initialInfo[0]; String mapURLs = initialInfo[1]; String controlURLs = initialInfo[2]; String chrXName = initialInfo[3]; String chrYName = initialInfo[4]; String unitName = initialInfo[5]; double xOrigin = doubleInfo[0]; double yOrigin = doubleInfo[1]; double scalefactor = doubleInfo[2]; double minColor = doubleInfo[3]; double lowColor = doubleInfo[4]; double upColor = doubleInfo[5]; double maxColor = doubleInfo[6]; double colorScaleFactor = doubleInfo[7]; // TODO only do this if not identical to current file String[] temp = mapNames.split("\\(control="); String mainMapNames = temp[0]; List urls = Arrays.asList(mapURLs.split("\\#\\#")); superAdapter.unsafeLoadWithTitleFix(urls, false, mainMapNames, true); if (!controlURLs.contains("null") && temp.length > 1) { String ctrlMapNames = temp[1].substring(0, temp[1].length() - 1); List ctrlURLs = Arrays.asList(controlURLs.split("\\#\\#")); superAdapter.unsafeLoadWithTitleFix(ctrlURLs, true, ctrlMapNames, true); } hic.unsafeSetLocation(chrXName, chrYName, unitName, binSize, xOrigin, yOrigin, scalefactor, HiC.ZoomCallType.DIRECT, true); superAdapter.getMainViewPanel().setDisplayBox(displaySelection.ordinal()); // todo should not be implemented with ordinals; implement with proper lookup // leaving unimplemented at this time //superAdapter.getMainViewPanel().setNormalizationBox(normSelection.ordinal()); superAdapter.getMainViewPanel().setNormalizationEnabledForReload(); //todo: Check that color scale value is not 0! superAdapter.getMainViewPanel().updateColorSlider(hic, lowColor / colorScaleFactor, upColor / colorScaleFactor, maxColor / colorScaleFactor); superAdapter.setEnableForAllElements(true); LoadEncodeAction loadEncodeAction = superAdapter.getEncodeAction(); LoadAction loadAction = superAdapter.getTrackLoadAction(); // TODO - do not erase previous tracks, rather check if some may already be loaded try { if (tracks.length > 0 && !tracks[1].contains("none")) { String[] trackURLs = tracks[0].split("\\,"); String[] trackNames = tracks[1].split("\\,"); for (int i = 0; i < trackURLs.length; i++) { String currentTrack = trackURLs[i].trim(); if (!currentTrack.isEmpty()) { if (currentTrack.equals("Eigenvector")) { loadAction.checkBoxesForReload(trackNames[i].trim()); hic.loadEigenvectorTrack(); } else if (currentTrack.toLowerCase().contains("coverage") || currentTrack.toLowerCase().contains("balanced") || currentTrack.equals("Loaded")) { loadAction.checkBoxesForReload(trackNames[i].trim()); hic.loadCoverageTrack(currentTrack); } else if (currentTrack.contains("peaks") || currentTrack.contains("blocks") || currentTrack.contains("superloop")) { hic.getResourceTree().checkTrackBoxesForReloadState(currentTrack.trim()); hic.loadLoopList(currentTrack); } else if (currentTrack.contains("goldenPath") || currentTrack.toLowerCase().contains("ensemble")) { hic.unsafeLoadTrack(currentTrack); loadEncodeAction.checkEncodeBoxes(trackNames[i].trim()); } else { hic.unsafeLoadTrack(currentTrack); loadAction.checkBoxesForReload(trackNames[i].trim()); } } } for (HiCTrack loadedTrack : hic.getLoadedTracks()) { for (int i = 0; i < trackNames.length; i++) { if (trackURLs[i].contains(loadedTrack.getName())) { loadedTrack.setName(trackNames[i].trim()); if (!tracks[2].contains("none") && tracks[2].contains(trackNames[i].trim())) { HiCDataSource source = new HiCCoverageDataSource(hic, hic.getObsNormalizationType(), false); HiCDataTrack hiCDataTrack = new HiCDataTrack(hic, loadedTrack.getLocator(), source); String[] configTrackInfo = tracks[2].split("\\*\\*"); for (String aConfigTrackInfo : configTrackInfo) { String[] configInfo = aConfigTrackInfo.split("\\,"); //todo check hiCDataTrack.setPosColor(new Color(Integer.parseInt(configInfo[1]))); hiCDataTrack.setNegColor(new Color(Integer.parseInt(configInfo[2]))); DataRange newDataRange = new DataRange(Float.parseFloat(configInfo[3]), Float.parseFloat(configInfo[4]));//min,max if (Boolean.parseBoolean(configInfo[5])) { newDataRange.setType(DataRange.Type.LOG); } else { newDataRange.setType(DataRange.Type.LINEAR); } hiCDataTrack.setDataRange(newDataRange); } } } } } } } catch (Exception e) { e.printStackTrace(); } superAdapter.updateTrackPanel(); } } ================================================ FILE: src/juicebox/state/SaveFileDialog.java ================================================ /* * The MIT License (MIT) * * Copyright (c) 2011-2021 Broad Institute, Aiden Lab, Rice University, Baylor College of Medicine * * Permission is hereby granted, free of charge, to any person obtaining a copy * of this software and associated documentation files (the "Software"), to deal * in the Software without restriction, including without limitation the rights * to use, copy, modify, merge, publish, distribute, sublicense, and/or sell * copies of the Software, and to permit persons to whom the Software is * furnished to do so, subject to the following conditions: * * The above copyright notice and this permission notice shall be included in * all copies or substantial portions of the Software. * * THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR * IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, * FITNESS FOR A PARTICULAR PURPOSE AND NON-INFRINGEMENT. IN NO EVENT SHALL THE * AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER * LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, * OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN * THE SOFTWARE. */ package juicebox.state; import juicebox.HiCGlobals; import juicebox.MainWindow; import javax.swing.*; import javax.swing.filechooser.FileNameExtensionFilter; import java.io.File; import java.io.FileInputStream; import java.io.FileOutputStream; import java.io.IOException; import java.nio.channels.FileChannel; import java.text.SimpleDateFormat; import java.util.Date; /** * Created by Zulkifl on 7/23/2015. */ public class SaveFileDialog extends JFileChooser { private static final long serialVersionUID = 9000017; public SaveFileDialog(File fileToSave) { super(); setCurrentDirectory(new File(System.getProperty("user.dir"))); String timeStamp = new SimpleDateFormat("yyyy.MM.dd-HH.mm").format(new Date()); setSelectedFile(new File(timeStamp + ".xml")); FileNameExtensionFilter filter = new FileNameExtensionFilter("XML Files", "xml", "XML"); setFileFilter(filter); if (HiCGlobals.guiIsCurrentlyActive) { int actionDialog = showSaveDialog(MainWindow.getInstance()); if (actionDialog == JFileChooser.APPROVE_OPTION) { File file = getSelectedFile(); if (!file.getPath().endsWith(".xml") && !file.getPath().endsWith(".XML")) { file = new File(file + ".xml"); } try { copyFile(fileToSave, file); } catch (IOException e) { e.printStackTrace(); } } } } private static void copyFile(File sourceFile, File destFile) throws IOException { if (!destFile.exists()) { destFile.createNewFile(); } FileChannel source = null; FileChannel destination = null; try { source = new FileInputStream(sourceFile).getChannel(); destination = new FileOutputStream(destFile).getChannel(); destination.transferFrom(source, 0, source.size()); } finally { if (source != null) { source.close(); } if (destination != null) { destination.close(); } } } } ================================================ FILE: src/juicebox/state/Slideshow.java ================================================ /* * The MIT License (MIT) * * Copyright (c) 2011-2021 Broad Institute, Aiden Lab, Rice University, Baylor College of Medicine * * Permission is hereby granted, free of charge, to any person obtaining a copy * of this software and associated documentation files (the "Software"), to deal * in the Software without restriction, including without limitation the rights * to use, copy, modify, merge, publish, distribute, sublicense, and/or sell * copies of the Software, and to permit persons to whom the Software is * furnished to do so, subject to the following conditions: * * The above copyright notice and this permission notice shall be included in * all copies or substantial portions of the Software. * * THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR * IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, * FITNESS FOR A PARTICULAR PURPOSE AND NON-INFRINGEMENT. IN NO EVENT SHALL THE * AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER * LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, * OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN * THE SOFTWARE. */ package juicebox.state; import juicebox.HiCGlobals; import juicebox.MainWindow; import juicebox.gui.SuperAdapter; import org.w3c.dom.Document; import org.w3c.dom.NodeList; import org.xml.sax.SAXException; import javax.swing.*; import javax.xml.parsers.DocumentBuilder; import javax.xml.parsers.DocumentBuilderFactory; import javax.xml.parsers.ParserConfigurationException; import java.awt.*; import java.awt.event.ActionEvent; import java.awt.event.ActionListener; import java.io.IOException; import java.util.ArrayList; /** * Created by Zulkifl on 7/31/2015. */ public class Slideshow extends JDialog { private static final long serialVersionUID = 9000018; private final static JFrame carouselFrame = new JFrame(); private final static JPanel nextPanel = new JPanel(new BorderLayout()); private final static JPanel prevPanel = new JPanel(new BorderLayout()); private final static JPanel labelPanel = new JPanel(new BorderLayout()); private final static JButton nextButton = new JButton("\u25BA"); private final static JButton prevButton = new JButton("\u25C4"); private static ArrayList slideNames = new ArrayList<>(); private final JLabel slideLabel; private int counter; private int currentSlideNum; public Slideshow(MainWindow mainWindow, final SuperAdapter superAdapter) { //super(mainWindow); super(); // TODO zgire - if panel needs to be independent of juicebox, then remove the line above (i.e. pass in mainwindow as parent) ArrayList files = new ArrayList<>(); setLayout(new FlowLayout()); setResizable(true); setVisible(true); setSize(400, 100); add(prevPanel); add(labelPanel); add(nextPanel); prevPanel.add(prevButton, BorderLayout.EAST); prevPanel.setVisible(true); slideLabel = new JLabel(); labelPanel.add(slideLabel, BorderLayout.CENTER); labelPanel.setVisible(true); nextPanel.add(nextButton, BorderLayout.WEST); nextPanel.setVisible(true); try { final ArrayList savedStatePaths = new ArrayList<>(); final ArrayList xChromosomesForReload = new ArrayList<>(); final ArrayList yChromosomesForReload = new ArrayList<>(); final ArrayList unitNamesForReload = new ArrayList<>(); Document dom; DocumentBuilderFactory dbf = DocumentBuilderFactory.newInstance(); DocumentBuilder db = null; db = dbf.newDocumentBuilder(); dom = db.parse(HiCGlobals.xmlSavedStatesFile.getAbsolutePath()); NodeList nodeList = dom.getElementsByTagName("STATE"); for (int i = 0; i < nodeList.getLength(); i++) { savedStatePaths.add(nodeList.item(i).getAttributes().getNamedItem("SelectedPath").getNodeValue()); NodeList childNodes = nodeList.item(i).getChildNodes(); for (int k = 0; k < childNodes.getLength(); k++) { if (childNodes.item(k).getNodeName().equals("MapURL")) { files.add(childNodes.item(k).getTextContent()); } if (childNodes.item(k).getNodeName().equals("XChromosome")) { xChromosomesForReload.add(childNodes.item(k).getTextContent()); } if (childNodes.item(k).getNodeName().equals("YChromosome")) { yChromosomesForReload.add(childNodes.item(k).getTextContent()); } if (childNodes.item(k).getNodeName().equals("UnitName")) { unitNamesForReload.add(childNodes.item(k).getTextContent()); } } } final int numSlides = savedStatePaths.size(); //for(int j=0; j= 0) { counter = ((counter - 1) + numSlides) % numSlides; slideLabel.setText(savedStatePaths.get(counter)); LoadStateFromXMLFile.reloadSelectedState(superAdapter, savedStatePaths.get(counter)); currentSlideNum = counter; } } }); nextButton.addActionListener(new ActionListener() { @Override public void actionPerformed(ActionEvent e) { //int counter = savedStatePaths.indexOf(slideLabel.getText()); if (counter < numSlides) { counter = (counter + 1) % numSlides; slideLabel.setText(savedStatePaths.get(counter)); LoadStateFromXMLFile.reloadSelectedState(superAdapter, savedStatePaths.get(counter)); currentSlideNum = counter; } } }); } catch (ParserConfigurationException | IOException | SAXException e) { e.printStackTrace(); } setLocationRelativeTo(getOwner()); } public int currentSlideNumber() { return currentSlideNum + 1; } public String currentSlideName(int count) { return slideNames.get(count); } } ================================================ FILE: src/juicebox/state/State.java ================================================ /* * The MIT License (MIT) * * Copyright (c) 2011-2020 Broad Institute, Aiden Lab, Rice University, Baylor College of Medicine * * Permission is hereby granted, free of charge, to any person obtaining a copy * of this software and associated documentation files (the "Software"), to deal * in the Software without restriction, including without limitation the rights * to use, copy, modify, merge, publish, distribute, sublicense, and/or sell * copies of the Software, and to permit persons to whom the Software is * furnished to do so, subject to the following conditions: * * The above copyright notice and this permission notice shall be included in * all copies or substantial portions of the Software. * * THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR * IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, * FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE * AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER * LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, * OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN * THE SOFTWARE. */ package juicebox.state; /** * Created by mshamim on 7/31/2015. */ class State { private static final String MAPPATH = "MapPath"; private static final String MAP = "Map"; private static final String MAPURL = "MapURL"; private static final String CONTROLURL = "ControlURL"; private static final String XCHR = "XChromosome"; private static final String YCHR = "YChromosome"; private static final String UNIT = "UnitName"; private static final String BINSIZE = "BinSize"; private static final String XORIGIN = "xOrigin"; private static final String YORIGIN = "yOrigin"; private static final String SCALE = "ScaleFactor"; private static final String DISPLAY = "DisplayOption"; private static final String NORM = "NormalizationType"; private static final String MINCOLOR = "MinColorVal"; private static final String LOWCOLOR = "LowerColorVal"; private static final String UPPERCOLOR = "UpperColorVal"; private static final String MAXCOLOR = "MaxColorVal"; private static final String COLORSCALE = "colrScaleVal"; private static final String TRACKURLS = "LoadedTrackURLS"; private static final String TRACKNAMES = "LoadedTrackNames"; private static final String CONFIGTRACKINFO = "ConfigTrackInfo"; /* TODO implement switch case on enum enum StateVar {}*/ public static final String[] stateVarNames = new String[]{MAPPATH, MAP, MAPURL, CONTROLURL, XCHR, YCHR, UNIT, BINSIZE, XORIGIN, YORIGIN, SCALE, DISPLAY, NORM, MINCOLOR, LOWCOLOR, UPPERCOLOR, MAXCOLOR, COLORSCALE, TRACKURLS, TRACKNAMES, CONFIGTRACKINFO}; } ================================================ FILE: src/juicebox/state/XMLFileHandling.java ================================================ /* * The MIT License (MIT) * * Copyright (c) 2011-2021 Broad Institute, Aiden Lab, Rice University, Baylor College of Medicine * * Permission is hereby granted, free of charge, to any person obtaining a copy * of this software and associated documentation files (the "Software"), to deal * in the Software without restriction, including without limitation the rights * to use, copy, modify, merge, publish, distribute, sublicense, and/or sell * copies of the Software, and to permit persons to whom the Software is * furnished to do so, subject to the following conditions: * * The above copyright notice and this permission notice shall be included in * all copies or substantial portions of the Software. * * THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR * IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, * FITNESS FOR A PARTICULAR PURPOSE AND NON-INFRINGEMENT. IN NO EVENT SHALL THE * AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER * LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, * OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN * THE SOFTWARE. */ package juicebox.state; import juicebox.Context; import juicebox.HiC; import juicebox.HiCGlobals; import juicebox.data.Dataset; import juicebox.gui.SuperAdapter; import juicebox.track.HiCCoverageDataSource; import juicebox.track.HiCDataSource; import juicebox.track.HiCDataTrack; import juicebox.track.HiCTrack; import juicebox.track.feature.AnnotationLayerHandler; import juicebox.track.feature.Feature2DList; import juicebox.windowui.HiCZoom; import java.util.ArrayList; import java.util.List; /** * Created by Zulkifl Gire on 7/10/2015. */ public class XMLFileHandling { public static void addNewStateToXML(String stateID, SuperAdapter superAdapter) { HiC hic = superAdapter.getHiC(); Context xContext = hic.getXContext(); Context yContext = hic.getYContext(); HiCZoom zoom = hic.getZoom(); Dataset dataset = hic.getDataset(); String xChr = xContext.getChromosome().getName(); String yChr = yContext.getChromosome().getName(); String colorVals = superAdapter.getMainViewPanel().getColorRangeValues(); double colorRangeScaleFactor = superAdapter.getMainViewPanel().getColorRangeScaleFactor(); List currentTracks = hic.getLoadedTracks(); StringBuilder currentTrack = new StringBuilder(); StringBuilder currentTrackName = new StringBuilder(); String configTrackInfo = "none"; String controlFiles = SuperAdapter.currentlyLoadedControlFiles; if (controlFiles == null || controlFiles.length() < 1 || controlFiles.isEmpty()) { controlFiles = "null"; } String mapNameAndURLs = superAdapter.getMainWindow().getTitle().replace(HiCGlobals.juiceboxTitle, "") + "@@" + SuperAdapter.currentlyLoadedMainFiles + "@@" + controlFiles; String textToWrite = stateID + "--currentState:$$" + mapNameAndURLs + "$$" + xChr + "$$" + yChr + "$$" + zoom.getUnit().toString() + "$$" + zoom.getBinSize() + "$$" + xContext.getBinOrigin() + "$$" + yContext.getBinOrigin() + "$$" + hic.getScaleFactor() + "$$" + hic.getDisplayOption().name() + "$$" + hic.getObsNormalizationType().getLabel() + "$$" + colorVals + "$$" + colorRangeScaleFactor; if (currentTracks != null && !currentTracks.isEmpty()) { for (HiCTrack track : currentTracks) { //System.out.println("trackLocator: "+track.getLocator()); for debugging //System.out.println("track name: " + track.getName()); currentTrack.append(track.getLocator()).append(", "); currentTrackName.append(track.getName()).append(", "); track.getLocator().getColor(); try { HiCDataSource source = new HiCCoverageDataSource(hic, hic.getObsNormalizationType(), false); HiCDataTrack hiCDataTrack = new HiCDataTrack(hic, track.getLocator(), source); configTrackInfo = track.getName() + "," + hiCDataTrack.getPosColor().getRGB() + "," + hiCDataTrack.getNegColor().getRGB() + "," + hiCDataTrack.getDataRange().getMinimum() + "," + hiCDataTrack.getDataRange().getMaximum() + "," + hiCDataTrack.getDataRange().isLog() + "**"; //Name, PosColor, AltColor, Min, Max, isLogScale } catch (Exception e) { // Expected for tracks that cannot be configured } } } else { currentTrack = new StringBuilder("none"); currentTrackName = new StringBuilder("none"); } textToWrite += "$$" + currentTrack + "$$" + currentTrackName + "$$" + configTrackInfo; // TODO this needs some major restructuring List visibleLoops = new ArrayList<>(); for (AnnotationLayerHandler handler : superAdapter.getAllLayers()) { visibleLoops.add(handler.getAllVisibleLoops()); } if (visibleLoops != null && !visibleLoops.isEmpty()) { try { textToWrite += "$$" + dataset.getPeaks().toString() + "$$" + dataset.getBlocks().toString() + "$$" + dataset.getSuperLoops().toString(); } catch (Exception ignored) { } } //("currentState,xChr,yChr,resolution,zoom level,xbin,ybin,scale factor,display selection, // normalization type,color range values, tracks") HiCGlobals.savedStatesList.add(textToWrite); XMLFileWriter.overwriteXMLFile(); } } ================================================ FILE: src/juicebox/state/XMLFileParser.java ================================================ /* * The MIT License (MIT) * * Copyright (c) 2011-2020 Broad Institute, Aiden Lab, Rice University, Baylor College of Medicine * * Permission is hereby granted, free of charge, to any person obtaining a copy * of this software and associated documentation files (the "Software"), to deal * in the Software without restriction, including without limitation the rights * to use, copy, modify, merge, publish, distribute, sublicense, and/or sell * copies of the Software, and to permit persons to whom the Software is * furnished to do so, subject to the following conditions: * * The above copyright notice and this permission notice shall be included in * all copies or substantial portions of the Software. * * THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR * IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, * FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE * AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER * LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, * OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN * THE SOFTWARE. */ package juicebox.state; import juicebox.HiCGlobals; import org.w3c.dom.Document; import org.w3c.dom.NodeList; import org.xml.sax.ErrorHandler; import org.xml.sax.InputSource; import org.xml.sax.SAXParseException; import javax.xml.parsers.DocumentBuilder; import javax.xml.parsers.DocumentBuilderFactory; /** * Created by Zulkifl on 7/20/2015. */ class XMLFileParser { public static String[] parseXML(String mapSelection) { String[] infoForReload = new String[21]; Document dom; DocumentBuilderFactory dbf = DocumentBuilderFactory.newInstance(); try { DocumentBuilder db = dbf.newDocumentBuilder(); dom = db.parse(HiCGlobals.xmlSavedStatesFile.getAbsolutePath()); //validate dbf.setValidating(false); dbf.setNamespaceAware(true); DocumentBuilder builder = dbf.newDocumentBuilder(); builder.setErrorHandler(new SimpleErrorHandler()); builder.parse(new InputSource(HiCGlobals.xmlSavedStatesFile.getAbsolutePath())); dom.getDocumentElement(); NodeList nodeList = dom.getElementsByTagName("STATE"); for (int i = 0; i < nodeList.getLength(); i++) { //System.out.println(nodeList.item(i).getAttributes().getNamedItem("SelectedPath").getNodeValue() +" mapPath: "+mapSelection); if (nodeList.item(i).getAttributes().getNamedItem("SelectedPath").getNodeValue().equals(mapSelection)) { NodeList childNodes = nodeList.item(i).getChildNodes(); // +=2 because need to skip 2nd line which describes 1st line (but everything is type text) for (int c = 1; c < childNodes.getLength(); c += 2) { String varName = childNodes.item(c).getNodeName(); String varText = childNodes.item(c).getTextContent(); for (int k = 0; k < State.stateVarNames.length; k++) { if (varName.equals(State.stateVarNames[k])) { infoForReload[k] = varText; break; } } } break; } } } catch (Exception e) { e.printStackTrace(); } return infoForReload; } private static class SimpleErrorHandler implements ErrorHandler { public void warning(SAXParseException e) { System.err.println(e.getMessage()); } public void error(SAXParseException e) { System.err.println(e.getMessage()); } public void fatalError(SAXParseException e) { System.err.println(e.getMessage()); } } } ================================================ FILE: src/juicebox/state/XMLFileWriter.java ================================================ /* * The MIT License (MIT) * * Copyright (c) 2011-2020 Broad Institute, Aiden Lab, Rice University, Baylor College of Medicine * * Permission is hereby granted, free of charge, to any person obtaining a copy * of this software and associated documentation files (the "Software"), to deal * in the Software without restriction, including without limitation the rights * to use, copy, modify, merge, publish, distribute, sublicense, and/or sell * copies of the Software, and to permit persons to whom the Software is * furnished to do so, subject to the following conditions: * * The above copyright notice and this permission notice shall be included in * all copies or substantial portions of the Software. * * THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR * IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, * FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE * AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER * LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, * OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN * THE SOFTWARE. */ package juicebox.state; import juicebox.HiCGlobals; import org.w3c.dom.DOMImplementation; import org.w3c.dom.Document; import org.w3c.dom.Element; import org.w3c.dom.Node; import javax.xml.parsers.DocumentBuilder; import javax.xml.parsers.DocumentBuilderFactory; import javax.xml.parsers.ParserConfigurationException; import javax.xml.transform.OutputKeys; import javax.xml.transform.Transformer; import javax.xml.transform.TransformerException; import javax.xml.transform.TransformerFactory; import javax.xml.transform.dom.DOMSource; import javax.xml.transform.stream.StreamResult; /** * Created by Zulkifl Gire on 7/15/2015. */ public class XMLFileWriter { private static StreamResult streamResult; private static Document xmlDoc; public static void overwriteXMLFile() { try { streamResult = new StreamResult(HiCGlobals.xmlSavedStatesFile); Element root = initXML(); for (String stateString : HiCGlobals.savedStatesList) { System.out.println(stateString); convert(stateString, root); } writeXML(); } catch (Exception e) { e.printStackTrace(); } } private static Element initXML() throws ParserConfigurationException { DocumentBuilderFactory factory = DocumentBuilderFactory.newInstance(); DocumentBuilder builder = factory.newDocumentBuilder(); DOMImplementation impl = builder.getDOMImplementation(); xmlDoc = impl.createDocument(null, "SavedMaps", null); return xmlDoc.getDocumentElement(); } private static void convert(String s, Element root) { String[] elements = s.split("\\$\\$"); String[] title = elements[0].split("--"); String[] mapName = elements[1].split("\\@\\@"); Element e0 = xmlDoc.createElement("STATE"); e0.setAttribute("SelectedPath", title[0]); for (int i = 0; i < State.stateVarNames.length; i++) { Element e = xmlDoc.createElement(State.stateVarNames[i]); Node n = xmlDoc.createTextNode("none"); if (i == 0) {//mappath or id n = xmlDoc.createTextNode(title[0]); //System.out.println(title[0]); } else if (i == 1) {//mapname n = xmlDoc.createTextNode(mapName[0]); //System.out.println(mapName[0]); } else if (i == 2) {//mapurl n = xmlDoc.createTextNode(mapName[1]); //System.out.println(mapName[1]); } else if (i == 3) {//controlURL if (mapName.length > 2 && !mapName[2].contains("null") && mapName[2].length() > 1) { n = xmlDoc.createTextNode(mapName[2]); //System.out.println(mapName[2]); } else { n = xmlDoc.createTextNode("null"); } } else if (i < 19 || elements.length > 18) { // elements.length checked in case no annotations n = xmlDoc.createTextNode(elements[i - 2]); //System.out.println(elements[i-2]); } e.appendChild(n); e0.appendChild(e); } root.appendChild(e0); } private static void writeXML() throws TransformerException { DOMSource domSource = new DOMSource(xmlDoc); TransformerFactory tf = TransformerFactory.newInstance(); Transformer transformer = tf.newTransformer(); transformer.setOutputProperty(OutputKeys.METHOD, "xml"); transformer.setOutputProperty(OutputKeys.ENCODING, "ISO-8859-1"); transformer.setOutputProperty("{http://xml.apache.org/xslt}indent-amount", "4"); transformer.setOutputProperty(OutputKeys.INDENT, "yes"); transformer.transform(domSource, streamResult); } } ================================================ FILE: src/juicebox/tools/HiCTools.java ================================================ /* * The MIT License (MIT) * * Copyright (c) 2011-2022 Broad Institute, Aiden Lab, Rice University, Baylor College of Medicine * * Permission is hereby granted, free of charge, to any person obtaining a copy * of this software and associated documentation files (the "Software"), to deal * in the Software without restriction, including without limitation the rights * to use, copy, modify, merge, publish, distribute, sublicense, and/or sell * copies of the Software, and to permit persons to whom the Software is * furnished to do so, subject to the following conditions: * * The above copyright notice and this permission notice shall be included in * all copies or substantial portions of the Software. * * THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR * IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, * FITNESS FOR A PARTICULAR PURPOSE AND NON-INFRINGEMENT. IN NO EVENT SHALL THE * AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER * LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, * OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN * THE SOFTWARE. */ package juicebox.tools; import jargs.gnu.CmdLineParser; import juicebox.HiCGlobals; import juicebox.tools.clt.CLTFactory; import juicebox.tools.clt.CommandLineParser; import juicebox.tools.clt.CommandLineParserForJuicer; import juicebox.tools.clt.JuiceboxCLT; import org.broad.igv.Globals; /** * Command line tool handling through factory model * * @author Muhammad Shamim * @since 1/20/2015 */ public class HiCTools { public static void main(String[] argv) throws CmdLineParser.UnknownOptionException, CmdLineParser.IllegalOptionValueException { Globals.setHeadless(true); if (argv.length == 0 || argv[0].equals("-h") || argv[0].equals("--help") || argv[0].equals("-V") || argv[0].equals("--version")) { CLTFactory.generalUsage(); System.exit(0); } String cmdName = argv[0].toLowerCase(); if (cmdName.equalsIgnoreCase("addnorm2")) { System.out.println("Using addnorm2"); hic.tools.HiCTools.main(argv); return; } CommandLineParser parser = new CommandLineParser(); if (CommandLineParserForJuicer.isJuicerCommand(cmdName)) { parser = new CommandLineParserForJuicer(); HiCGlobals.useCache = false; //TODO until memory leak cleared } boolean help; boolean version; parser.parse(argv); if (CommandLineParserForJuicer.isJuicerCommand(cmdName)) { HiCGlobals.isLegacyOutputPrintingEnabled = ((CommandLineParserForJuicer) parser).getLegacyOutputOption(); } else if (parser.getAllPearsonsOption()) { HiCGlobals.MAX_PEARSON_ZOOM = 1; } help = parser.getHelpOption(); version = parser.getVersionOption(); HiCGlobals.printVerboseComments = parser.getVerboseOption(); String[] args = parser.getRemainingArgs(); JuiceboxCLT instanceOfCLT; String cmd = ""; if (args.length == 0) { instanceOfCLT = null; } else { cmd = args[0]; instanceOfCLT = CLTFactory.getCLTCommand(cmd); } if (instanceOfCLT != null) { if (version) { System.out.println("Juicer tools version " + HiCGlobals.versionNum); } if (args.length == 1 || help) { instanceOfCLT.printUsageAndExit(); } instanceOfCLT.readArguments(args, parser); instanceOfCLT.run(); } else { throw new RuntimeException("Unknown command: " + cmd); } } } ================================================ FILE: src/juicebox/tools/chrom/sizes/ChromosomeSizes.java ================================================ /* * The MIT License (MIT) * * Copyright (c) 2011-2020 Broad Institute, Aiden Lab, Rice University, Baylor College of Medicine * * Permission is hereby granted, free of charge, to any person obtaining a copy * of this software and associated documentation files (the "Software"), to deal * in the Software without restriction, including without limitation the rights * to use, copy, modify, merge, publish, distribute, sublicense, and/or sell * copies of the Software, and to permit persons to whom the Software is * furnished to do so, subject to the following conditions: * * The above copyright notice and this permission notice shall be included in * all copies or substantial portions of the Software. * * THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR * IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, * FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE * AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER * LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, * OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN * THE SOFTWARE. */ package juicebox.tools.chrom.sizes; /** * Empty class for directing *.sizes file tracking */ public class ChromosomeSizes { } ================================================ FILE: src/juicebox/tools/chrom/sizes/EBV.chrom.sizes ================================================ NC_007605 171824 ================================================ FILE: src/juicebox/tools/chrom/sizes/GRCm38.chrom.sizes ================================================ chr1 195471971 chr2 182113224 chr3 160039680 chr4 156508116 chr5 151834684 chr6 149736546 chr7 145441459 chr8 129401213 chr9 124595110 chr10 130694993 chr11 122082543 chr12 120129022 chr13 120421639 chr14 124902244 chr15 104043685 chr16 98207768 chr17 94987271 chr18 90702639 chr19 61431566 chrM 16299 chrX 171031299 chrY 91744698 ================================================ FILE: src/juicebox/tools/chrom/sizes/Pf3D7.chrom.sizes ================================================ M76611 5967 Pf3D7_01_v3 640851 Pf3D7_02_v3 947102 Pf3D7_03_v3 1067971 Pf3D7_04_v3 1200490 Pf3D7_05_v3 1343557 Pf3D7_06_v3 1418242 Pf3D7_07_v3 1445207 Pf3D7_08_v3 1472805 Pf3D7_09_v3 1541735 Pf3D7_10_v3 1687656 Pf3D7_11_v3 2038340 Pf3D7_12_v3 2271494 Pf3D7_13_v3 2925236 Pf3D7_14_v3 3291937 ================================================ FILE: src/juicebox/tools/chrom/sizes/TAIR10.chrom.sizes ================================================ gi|240254421|ref|NC_003070.9| 30427671 gi|240254678|ref|NC_003071.7| 19698289 gi|240255695|ref|NC_003074.8| 23459830 gi|240256243|ref|NC_003075.7| 18585056 gi|240256493|ref|NC_003076.8| 26975502 gi|26556996|ref|NC_001284.2| 366924 gi|7525012|ref|NC_000932.1| 154479 ================================================ FILE: src/juicebox/tools/chrom/sizes/aedAeg1.chrom.sizes ================================================ supercont1.1 5856339 supercont1.2 5729030 supercont1.4 5177111 supercont1.3 5167134 supercont1.6 5075626 supercont1.5 5058281 supercont1.8 4905038 supercont1.7 4891900 supercont1.9 4759463 supercont1.11 4706946 supercont1.12 4526317 supercont1.10 4486241 supercont1.16 4402401 supercont1.13 4376253 supercont1.14 4341222 supercont1.15 4333154 supercont1.17 4314454 supercont1.18 4266046 supercont1.19 4221289 supercont1.20 4138018 supercont1.22 4100794 supercont1.24 4087421 supercont1.21 4040890 supercont1.23 3969038 supercont1.25 3904351 ================================================ FILE: src/juicebox/tools/chrom/sizes/anasPlat1.chrom.sizes ================================================ KB742833.1 5998093 KB742808.1 5763044 KB742479.1 5108439 KB742929.1 5090982 KB742471.1 4921412 KB742432.1 4403347 KB742629.1 4356576 KB742619.1 4198679 KB742441.1 4177285 KB743145.1 4130403 KB742931.1 4102838 KB742969.1 4012685 KB743197.1 4002947 KB742773.1 3977919 KB742733.1 3900964 KB742443.1 3766509 KB742490.1 3751842 KB743944.1 3697998 KB742887.1 3651307 KB742685.1 3651088 ================================================ FILE: src/juicebox/tools/chrom/sizes/assembly.chrom.sizes ================================================ assembly 2147000000 ================================================ FILE: src/juicebox/tools/chrom/sizes/b37.chrom.sizes ================================================ 1 249250621 2 243199373 3 198022430 4 191154276 5 180915260 6 171115067 7 159138663 8 146364022 9 141213431 10 135534747 11 135006516 12 133851895 13 115169878 14 107349540 15 102531392 16 90354753 17 81195210 18 78077248 19 59128983 20 63025520 21 48129895 22 51304566 X 155270560 Y 59373566 MT 16569 ================================================ FILE: src/juicebox/tools/chrom/sizes/bTaurus3.chrom.sizes ================================================ 1 158337067 2 137060424 3 121430405 4 120829699 5 121191424 6 119458736 7 112638659 8 113384836 9 105708250 10 104305016 11 107310763 12 91163125 13 84240350 14 84648390 15 85296676 16 81724687 17 75158596 18 66004023 19 64057457 20 72042655 21 71599096 22 61435874 23 52530062 24 62714930 25 42904170 26 51681464 27 45407902 28 46312546 29 51505224 X 148823899 ================================================ FILE: src/juicebox/tools/chrom/sizes/calJac3.chrom.sizes ================================================ CM000856.1 210400635 CM000857.1 204313951 CM000858.1 190850796 CM000859.1 171630274 CM000860.1 159171411 CM000861.1 158406734 CM000862.1 155834243 CM000863.1 128169293 CM000864.1 124281992 CM000865.1 132174527 CM000866.1 130397257 CM000867.1 121768101 CM000868.1 117903854 CM000869.1 108792865 CM000870.1 98464013 CM000871.1 96796970 CM000872.1 74750902 CM000873.1 47448759 CM000874.1 49578535 CM000875.1 44557958 CM000876.1 50472720 CM000877.1 49145316 CM000878.1 142054208 CM000879.1 2853901 ================================================ FILE: src/juicebox/tools/chrom/sizes/canFam3.chrom.sizes ================================================ chr1 122678785 chr2 85426708 chr3 91889043 chr4 88276631 chr5 88915250 chr6 77573801 chr7 80974532 chr8 74330416 chr9 61074082 chr10 69331447 chr11 74389097 chr12 72498081 chr13 63241923 chr14 60966679 chr15 64190966 chr16 59632846 chr17 64289059 chr18 55844845 chr19 53741614 chr20 58134056 chr21 50858623 chr22 61439934 chr23 52294480 chr24 47698779 chr25 51628933 chr26 38964690 chr27 45876710 chr28 41182112 chr29 41845238 chr30 40214260 chr31 39895921 chr32 38810281 chr33 31377067 chr34 42124431 chr35 26524999 chr36 30810995 chr37 30902991 chr38 23914537 chrX 123869143 ================================================ FILE: src/juicebox/tools/chrom/sizes/capHir1.chrom.sizes ================================================ CM001710.1 155011307 CM001711.1 135415751 CM001712.1 116796116 CM001713.1 115961478 CM001714.1 111055201 CM001715.1 114334461 CM001716.1 106547263 CM001717.1 111020524 CM001718.1 90293942 CM001719.1 99198151 CM001720.1 105305070 CM001721.1 82535142 CM001722.1 80625018 CM001723.1 92306894 CM001724.1 78986926 CM001725.1 77678508 CM001726.1 71877645 CM001727.1 61067880 CM001728.1 62130014 CM001729.1 71279863 CM001730.1 66773250 CM001731.1 57956300 CM001732.1 49403180 CM001733.1 61756751 CM001734.1 41496684 CM001735.1 50169583 CM001736.1 44118849 CM001737.1 43231948 CM001738.1 48376377 CM001739.1 121952644 ================================================ FILE: src/juicebox/tools/chrom/sizes/ce10.chrom.sizes ================================================ chrI 15072423 chrII 15279345 chrIII 13783700 chrIV 17493793 chrV 20924149 chrX 17718866 chrM 13794 ================================================ FILE: src/juicebox/tools/chrom/sizes/dMel.chrom.sizes ================================================ arm_2L 23011544 arm_2R 21146708 arm_3L 24543557 arm_3R 27905053 arm_4 1351858 arm_X 22422827 ================================================ FILE: src/juicebox/tools/chrom/sizes/dm3.chrom.sizes ================================================ chr2L 23011544 chr2LHet 368872 chr2R 21146708 chr2RHet 3288761 chr3L 24543557 chr3LHet 2555491 chr3R 27905053 chr3RHet 2517507 chr4 1351857 chrU 10049037 chrUextra 29004656 chrX 22422827 chrXHet 204112 chrYHet 347038 chrM 19517 ================================================ FILE: src/juicebox/tools/chrom/sizes/dm6.chrom.sizes ================================================ chr2L 23513712 chr2R 25286936 chr3L 28110227 chr3R 32079331 chr4 1348131 chrX 23542271 chrY 3667352 chrM 19524 ================================================ FILE: src/juicebox/tools/chrom/sizes/equCab2.chrom.sizes ================================================ chr1 185838109 chr2 120857687 chr3 119479920 chr4 108569075 chr5 99680356 chr6 84719076 chr7 98542428 chr8 94057673 chr9 83561422 chr10 83980604 chr11 61308211 chr12 33091231 chr13 42578167 chr14 93904894 chr15 91571448 chr16 87365405 chr17 80757907 chr18 82527541 chr19 59975221 chr20 64166202 chr21 57723302 chr22 49946797 chr23 55726280 chr24 46749900 chr25 39536964 chr26 41866177 chr27 39960074 chr28 46177339 chr29 33672925 chr30 30062385 chr31 24984650 chrX 124114077 chrM 16660 ================================================ FILE: src/juicebox/tools/chrom/sizes/felCat8.chrom.sizes ================================================ CM001378.2 240380223 CM001379.2 168638799 CM001380.2 140925898 CM001381.2 206538554 CM001382.2 152998503 CM001383.2 148068395 CM001384.2 142431058 CM001385.2 222198629 CM001386.2 159252932 CM001387.2 115468741 CM001388.2 88096124 CM001389.2 94101111 CM001390.2 94492513 CM001391.2 61081816 CM001392.2 61960243 CM001393.2 41224383 CM001394.2 70119229 CM001395.2 83953389 CM001396.2 127282370 ================================================ FILE: src/juicebox/tools/chrom/sizes/galGal4.chrom.sizes ================================================ chr1 195276750 chr2 148809762 chr3 110447801 chr4 90216835 chr5 59580361 chr6 34951654 chr7 36245040 chr8 28767244 chr9 23441680 chr10 19911089 chr11 19401079 chr12 19897011 chr13 17760035 chr14 15161805 chr15 12656803 chr16 535270 chr17 10454150 chr18 11219875 chr19 9983394 chr20 14302601 chr21 6802778 chr22 4081097 chr23 5723239 chr24 6323281 chr25 2191139 chr26 5329985 chr27 5209285 chr28 4742627 chr32 1028 chrW 1248174 chrZ 82363669 chrM 16776 ================================================ FILE: src/juicebox/tools/chrom/sizes/hg18.chrom.sizes ================================================ 1 247249719 2 242951149 3 199501827 4 191273063 5 180857866 6 170899992 7 158821424 8 146274826 9 140273252 10 135374737 11 134452384 12 132349534 13 114142980 14 106368585 15 100338915 16 88827254 17 78774742 18 76117153 19 63811651 20 62435964 21 46944323 22 49691432 X 154913754 Y 57772954 MT 16571 ================================================ FILE: src/juicebox/tools/chrom/sizes/hg19.chrom.sizes ================================================ 1 249250621 2 243199373 3 198022430 4 191154276 5 180915260 6 171115067 7 159138663 8 146364022 9 141213431 10 135534747 11 135006516 12 133851895 13 115169878 14 107349540 15 102531392 16 90354753 17 81195210 18 78077248 19 59128983 20 63025520 21 48129895 22 51304566 X 155270560 Y 59373566 MT 16569 ================================================ FILE: src/juicebox/tools/chrom/sizes/hg19_contig.chrom.sizes ================================================ 1 249250621 2 243199373 3 198022430 4 191154276 5 180915260 6 171115067 7 159138663 8 146364022 9 141213431 10 135534747 11 135006516 12 133851895 13 115169878 14 107349540 15 102531392 16 90354753 17 81195210 18 78077248 19 59128983 20 63025520 21 48129895 22 51304566 X 155270560 Y 59373566 MT 16569 GL000207.1 4262 GL000226.1 15008 GL000229.1 19913 GL000231.1 27386 GL000210.1 27682 GL000239.1 33824 GL000235.1 34474 GL000201.1 36148 GL000247.1 36422 GL000245.1 36651 GL000197.1 37175 GL000203.1 37498 GL000246.1 38154 GL000249.1 38502 GL000196.1 38914 GL000248.1 39786 GL000244.1 39929 GL000238.1 39939 GL000202.1 40103 GL000234.1 40531 GL000232.1 40652 GL000206.1 41001 GL000240.1 41933 GL000236.1 41934 GL000241.1 42152 GL000243.1 43341 GL000242.1 43523 GL000230.1 43691 GL000237.1 45867 GL000233.1 45941 GL000204.1 81310 GL000198.1 90085 GL000208.1 92689 GL000191.1 106433 GL000227.1 128374 GL000228.1 129120 GL000214.1 137718 GL000221.1 155397 GL000209.1 159169 GL000218.1 161147 GL000220.1 161802 GL000213.1 164239 GL000211.1 166566 GL000199.1 169874 GL000217.1 172149 GL000216.1 172294 GL000215.1 172545 GL000205.1 174588 GL000219.1 179198 GL000224.1 179693 GL000223.1 180455 GL000195.1 182896 GL000212.1 186858 GL000222.1 186861 GL000200.1 187035 GL000193.1 189789 GL000194.1 191469 GL000225.1 211173 GL000192.1 547496 NC_007605 171824 ================================================ FILE: src/juicebox/tools/chrom/sizes/hg38.chrom.sizes ================================================ chr1 248956422 chr2 242193529 chr3 198295559 chr4 190214555 chr5 181538259 chr6 170805979 chr7 159345973 chr8 145138636 chr9 138394717 chr10 133797422 chr11 135086622 chr12 133275309 chr13 114364328 chr14 107043718 chr15 101991189 chr16 90338345 chr17 83257441 chr18 80373285 chr19 58617616 chr20 64444167 chr21 46709983 chr22 50818468 chrX 156040895 chrY 57227415 chrM 16569 ================================================ FILE: src/juicebox/tools/chrom/sizes/loxAfr3.chrom.sizes ================================================ chr1 214701375 chr2 225582790 chr3 205080690 chr4 166642186 chr5 143278944 chr6 163261726 chr7 83540442 chr8 128409435 chr9 94531929 chr10 103745917 chr11 68864707 chr12 83603808 chr13 103893473 chr14 70853943 chr15 88640724 chr16 45784276 chr17 69133140 chr18 72444150 chr19 68937429 chr20 79033276 chr21 62548349 chr22 54904812 chr23 53701227 chr24 27123610 chr25 58263816 chr26 76958368 chr27 50221267 chrX 120050768 ================================================ FILE: src/juicebox/tools/chrom/sizes/macMul1.chrom.sizes ================================================ 1 228252215 2 189746636 3 196418989 4 167655696 5 182086969 6 178205221 7 169801366 8 147794981 9 133323859 10 94855758 11 134511895 12 106505843 13 138028943 14 133002572 15 110119387 16 78773432 17 94452569 18 73567989 19 64391591 20 88221753 X 153947521 MT 16564 ================================================ FILE: src/juicebox/tools/chrom/sizes/macMulBaylor.chrom.sizes ================================================ Contig0 180098346 Contig1 172710926 Contig2 108978359 Contig3 149211636 Contig4 190546021 Contig5 225580804 Contig6 133734168 Contig7 204782720 Contig8 125551809 Contig9 169647287 Contig10 53664290 Contig11 129959547 Contig12 74970154 Contig13 127942257 Contig14 111341137 Contig15 144305081 Contig16 70287280 Contig17 77213416 Contig18 92976557 Contig19 185820995 Contig20 95678607 ================================================ FILE: src/juicebox/tools/chrom/sizes/mm10.chrom.sizes ================================================ chr1 195471971 chr2 182113224 chr3 160039680 chr4 156508116 chr5 151834684 chr6 149736546 chr7 145441459 chr8 129401213 chr9 124595110 chr10 130694993 chr11 122082543 chr12 120129022 chr13 120421639 chr14 124902244 chr15 104043685 chr16 98207768 chr17 94987271 chr18 90702639 chr19 61431566 chrM 16299 chrX 171031299 chrY 91744698 ================================================ FILE: src/juicebox/tools/chrom/sizes/mm9.chrom.sizes ================================================ chr1 197195432 chr2 181748087 chr3 159599783 chr4 155630120 chr5 152537259 chr6 149517037 chr7 152524553 chr8 131738871 chr9 124076172 chr10 129993255 chr11 121843856 chr12 121257530 chr13 120284312 chr14 125194864 chr15 103494974 chr16 98319150 chr17 95272651 chr18 90772031 chr19 61342430 chrX 166650296 chrY 15902555 chrM 16300 ================================================ FILE: src/juicebox/tools/chrom/sizes/oryCun2.chrom.sizes ================================================ chr1 194850757 chr2 174332312 chr3 155691105 chr4 91394100 chr5 37992211 chr6 27502587 chr7 173684459 chr8 111795807 chr9 116251907 chr10 47997241 chr11 87554214 chr12 155355395 chr13 143360832 chr14 163896628 chr15 109054052 chr16 84478945 chr17 85008467 chr18 69800736 chr19 57279966 chr20 33191332 chr21 15578276 chrX 111700775 chrM 17246 ================================================ FILE: src/juicebox/tools/chrom/sizes/oryLat2.chrom.sizes ================================================ 1 39973033 2 31118443 3 36623554 4 34636364 5 33792114 6 26576615 7 29492121 8 25865442 9 33213694 10 27595823 11 29412213 12 30041894 13 33409148 14 33607196 15 30000224 16 30014384 17 31848461 18 29908082 19 23451325 20 24728221 21 31883787 22 28810691 23 24050845 24 24165179 MT 16714 ================================================ FILE: src/juicebox/tools/chrom/sizes/panTro4.chrom.sizes ================================================ CM000314.2 228333871 CM000315.2 113622374 CM000316.2 247518478 CM000317.2 202329955 CM000318.2 193495092 CM000319.2 182651097 CM000320.2 172623881 CM000321.3 161824586 CM000322.3 143986469 CM000323.2 137840987 CM000324.2 133524379 CM000325.2 133121534 CM000326.2 134246214 CM000327.2 115123233 CM000328.2 106544938 CM000329.2 99548318 CM000330.2 89983829 CM000331.2 82630442 CM000332.2 76611499 CM000333.2 63644993 CM000334.3 61729293 BA000046.3 32799110 CM000335.2 49737984 CM000336.2 156848144 DP000054.2 26342871 ================================================ FILE: src/juicebox/tools/chrom/sizes/ratNor5.chrom.sizes ================================================ 1 290094216 2 285068071 3 183740530 4 248343840 5 177180328 6 156897508 7 143501887 8 132457389 9 121549591 10 112200500 11 93518069 12 54450796 13 118718031 14 115151701 15 114627140 16 90051983 17 92503511 18 87229863 19 72914587 20 57791882 X 154597545 MT 16313 ================================================ FILE: src/juicebox/tools/chrom/sizes/ratNor6.chrom.sizes ================================================ NC_005100.4 282763074 NC_005101.4 266435125 NC_005102.4 177699992 NC_005103.4 184226339 NC_005104.4 173707219 NC_005105.4 147991367 NC_005106.4 145729302 NC_005107.4 133307652 NC_005108.4 122095297 NC_005109.4 112626471 NC_005110.4 90463843 NC_005111.4 52716770 NC_005112.4 114033958 NC_005113.4 115493446 NC_005114.4 111246239 NC_005115.4 90668790 NC_005116.4 90843779 NC_005117.4 88201929 NC_005118.4 62275575 NC_005119.4 56205956 NC_005120.4 159970021 NC_024475.1 3310458 NC_001665.2 16314 ================================================ FILE: src/juicebox/tools/chrom/sizes/sCerS288c.chrom.sizes ================================================ chrI 230218 chrII 813184 chrIII 316620 chrIV 1531933 chrIX 439888 chrV 576874 chrVI 270161 chrVII 1090940 chrVIII 562643 chrX 745751 chrXI 666816 chrXII 1078177 chrXIII 924431 chrXIV 784333 chrXV 1091291 chrXVI 948066 chrM 85780 ================================================ FILE: src/juicebox/tools/chrom/sizes/sacCer3.chrom.sizes ================================================ chrI 230218 chrII 813184 chrIII 316620 chrIV 1531933 chrIX 439888 chrV 576874 chrVI 270161 chrVII 1090940 chrVIII 562643 chrX 745751 chrXI 666816 chrXII 1078177 chrXIII 924431 chrXIV 784333 chrXV 1091291 chrXVI 948066 chrM 85780 ================================================ FILE: src/juicebox/tools/chrom/sizes/spretus.chrom.sizes ================================================ chr1 198846266 chr2 182815943 chr3 160222558 chr4 152946536 chr5 152823684 chr6 150978388 chr7 136257712 chr8 130317789 chr9 126249303 chr10 131945496 chr11 125065471 chr12 114123490 chr13 117181667 chr14 117542938 chr15 104786220 chr16 97876770 chr17 94415995 chr18 90668104 chr19 59623150 chrX 148322236 ================================================ FILE: src/juicebox/tools/chrom/sizes/susScr3.chrom.sizes ================================================ chr1 315321322 chr2 162569375 chr3 144787322 chr4 143465943 chr5 111506441 chr6 157765593 chr7 134764511 chr8 148491826 chr9 153670197 chr10 79102373 chr11 87690581 chr12 63588571 chr13 218635234 chr14 153851969 chr15 157681621 chr16 86898991 chr17 69701581 chr18 61220071 chrX 144288218 chrY 1637716 chrM 16614 ================================================ FILE: src/juicebox/tools/clt/AggregateProcessing.java ================================================ /* * The MIT License (MIT) * * Copyright (c) 2011-2021 Broad Institute, Aiden Lab, Rice University, Baylor College of Medicine * * Permission is hereby granted, free of charge, to any person obtaining a copy * of this software and associated documentation files (the "Software"), to deal * in the Software without restriction, including without limitation the rights * to use, copy, modify, merge, publish, distribute, sublicense, and/or sell * copies of the Software, and to permit persons to whom the Software is * furnished to do so, subject to the following conditions: * * The above copyright notice and this permission notice shall be included in * all copies or substantial portions of the Software. * * THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR * IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, * FITNESS FOR A PARTICULAR PURPOSE AND NON-INFRINGEMENT. IN NO EVENT SHALL THE * AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER * LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, * OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN * THE SOFTWARE. */ package juicebox.tools.clt; /** * Created for testing multiple CLTs at once * Basically scratch space */ class AggregateProcessing { public static void main(String[] argv) throws Exception { } } ================================================ FILE: src/juicebox/tools/clt/CLTFactory.java ================================================ /* * The MIT License (MIT) * * Copyright (c) 2011-2022 Broad Institute, Aiden Lab, Rice University, Baylor College of Medicine * * Permission is hereby granted, free of charge, to any person obtaining a copy * of this software and associated documentation files (the "Software"), to deal * in the Software without restriction, including without limitation the rights * to use, copy, modify, merge, publish, distribute, sublicense, and/or sell * copies of the Software, and to permit persons to whom the Software is * furnished to do so, subject to the following conditions: * * The above copyright notice and this permission notice shall be included in * all copies or substantial portions of the Software. * * THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR * IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, * FITNESS FOR A PARTICULAR PURPOSE AND NON-INFRINGEMENT. IN NO EVENT SHALL THE * AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER * LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, * OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN * THE SOFTWARE. */ package juicebox.tools.clt; import juicebox.HiCGlobals; import juicebox.tools.clt.juicer.*; import juicebox.tools.clt.old.*; import juicebox.tools.dev.APAvsDistance; import juicebox.tools.dev.CompareVectors; import juicebox.tools.dev.GeneFinder; import juicebox.tools.utils.Benchmark; /** * Factory for command line tools to call different functions * * @author Muhammad Shamim * @since 1/30/2015 */ public class CLTFactory { // Commenting some out because we're not going to release all these when we release CLT private final static String[] commandLineToolUsages = { // "addNorm", "addNorm [0 for no frag, 1 for no single frag]", // "bigWig", "bigWig [chr] [start base] [end base]", // "binToPairs", "binToPairs ", // "bpToFrag", "bpToFrag ", // "calcKR", "calcKR ", // "fragmentToBed","fragmentToBed ", // "pairsToBin", "pairsToBin ", // "db", "db [items]", Dump.getUsage(), PreProcessing.getBasicUsage(), AddNorm.getBasicUsage(), Pearsons.getBasicUsage(), Eigenvector.getUsage(), APA.getBasicUsage(), Arrowhead.getBasicUsage(), HiCCUPS.getBasicUsage(), HiCCUPSDiff.getBasicUsage(), ValidateFile.getUsage() }; public static void generalUsage() { System.out.println("Juicer Tools Version " + HiCGlobals.versionNum); System.out.println("Usage:"); for (String usage : commandLineToolUsages) { System.out.println("\t" + usage); } System.out.println("\t" + "-h, --help print help"); System.out.println("\t" + "-v, --verbose verbose mode"); System.out.println("\t" + "-V, --version print version"); System.out.println("Type juicer_tools for more detailed usage instructions"); } public static JuiceboxCLT getCLTCommand(String cmd) { cmd = cmd.toLowerCase(); if (cmd.equals("pre")) { return new PreProcessing(); } else if (cmd.equals("sum")) { return new Summation(); } else if (cmd.equals("dump")) { return new Dump(); } else if (cmd.equals("compare-vectors")) { return new CompareVectors(); } else if (cmd.equals("validate")) { return new ValidateFile(); } else if (cmd.equals("addnorm")) { return new AddNorm(); } else if (cmd.equals("apa")) { return new APA(); } else if (cmd.equals("compare")) { return new CompareLists(); } else if (cmd.equals("arrowhead")) { return new Arrowhead(); } else if (cmd.equals("bigwig")) { return new BigWig(); } else if (cmd.equals("bintopairs")) { return new BinToPairs(); //} else if (cmd.equals("booleanBalance".toLowerCase())) { // return new BooleanBalancing(); } else if (cmd.equals("bptofrag")) { return new BPToFragment(); } else if (cmd.equals("calckr")) { return new CalcKR(); } else if (cmd.equals("calcmatrixsum")) { return new CalcMatrixSum(); } else if (cmd.equals("fragmenttobed")) { return new FragmentToBed(); } else if (cmd.equals("hiccups")) { return new HiCCUPS(); } else if (cmd.equals("hiccups2")) { return new HiCCUPS2(); } else if (cmd.equals("hiccups-scores")) { return new HiCCUPSscores(); } else if (cmd.equals("localizer")) { return new Localizer(); } else if (cmd.equals("loop_domains")) { return new LoopDomains(); } else if (cmd.equals("motifs")) { return new MotifFinder(); } else if (cmd.equals("pairstobin")) { return new PairsToBin(); } else if (cmd.equals("db")) { return new SQLDatabase(); } else if (cmd.equals("hiccupsdiff")) { return new HiCCUPSDiff(); } else if (cmd.equals("ab_compdiff")) { return new ABCompartmentsDiff(); } else if (cmd.equals("genes")) { return new GeneFinder(); } else if (cmd.equals("benchmark")) { return new Benchmark(); } else if (cmd.equals("pearsons")) { return new Pearsons(); } else if (cmd.equals("eigenvector")) { return new Eigenvector(); } else if (cmd.contains("librarycomplexity")) { return new LibraryComplexity(cmd); } else if (cmd.equals("apa_vs_distance")) { //Todo check if okay return new APAvsDistance(); } else if (cmd.equals("statistics")) { return new Statistics(); } return null; } } ================================================ FILE: src/juicebox/tools/clt/CommandLineParser.java ================================================ /* * The MIT License (MIT) * * Copyright (c) 2011-2021 Broad Institute, Aiden Lab, Rice University, Baylor College of Medicine * * Permission is hereby granted, free of charge, to any person obtaining a copy * of this software and associated documentation files (the "Software"), to deal * in the Software without restriction, including without limitation the rights * to use, copy, modify, merge, publish, distribute, sublicense, and/or sell * copies of the Software, and to permit persons to whom the Software is * furnished to do so, subject to the following conditions: * * The above copyright notice and this permission notice shall be included in * all copies or substantial portions of the Software. * * THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR * IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, * FITNESS FOR A PARTICULAR PURPOSE AND NON-INFRINGEMENT. IN NO EVENT SHALL THE * AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER * LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, * OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN * THE SOFTWARE. */ package juicebox.tools.clt; import jargs.gnu.CmdLineParser; import juicebox.windowui.NormalizationHandler; import juicebox.windowui.NormalizationType; import java.util.*; /** * Command Line Parser for original (Pre/Dump) calls. Created by muhammadsaadshamim on 9/4/15. */ public class CommandLineParser extends CmdLineParser { // available // blou // used // d h x v n p k F V f t s g m q w c r z a y j i // universal protected final Option verboseOption = addBooleanOption('v', "verbose"); protected final Option helpOption = addBooleanOption('h', "help"); protected final Option versionOption = addBooleanOption('V', "version"); // boolean private final Option diagonalsOption = addBooleanOption('d', "diagonals"); private final Option removeCacheMemoryOption = addBooleanOption('x', "remove-memory-cache"); private final Option noNormOption = addBooleanOption('n', "no_normalization"); private final Option allPearsonsOption = addBooleanOption('p', "pearsons-all-resolutions"); private final Option noFragNormOption = addBooleanOption('F', "no_fragment-normalization"); private final Option randomizePositionOption = addBooleanOption("randomize_position"); private final Option throwIntraFragOption = addBooleanOption("skip-intra-frag"); private final Option useMinRAM = addBooleanOption("conserve-ram"); private final Option checkMemory = addBooleanOption("check-ram-usage"); private final Option fromHIC = addBooleanOption("from-hic"); // String private final Option fragmentOption = addStringOption('f', "restriction-fragment-site-file"); private final Option tmpDirOption = addStringOption('t', "tmpdir"); private final Option statsOption = addStringOption('s', "statistics"); private final Option graphOption = addStringOption('g', "graphs"); private final Option genomeIDOption = addStringOption('y', "genomeid"); private final Option expectedVectorOption = addStringOption('e', "expected-vector-file"); protected final Option normalizationTypeOption = addStringOption('k', "normalization"); private final Option mndIndexOption = addStringOption('i', "mndindex"); private final Option ligationOption = addStringOption("ligation"); private final Option shellOption = addStringOption("shell"); // ints private final Option blockCapacityOption = addIntegerOption("block-capacity"); private final Option countThresholdOption = addIntegerOption('m', "min-count"); private final Option mapqOption = addIntegerOption('q', "mapq"); private final Option genomeWideOption = addIntegerOption('w', "genomewide"); private final Option alignmentFilterOption = addIntegerOption('a', "alignment"); private final Option threadNumOption = addIntegerOption('j', "threads"); private final Option matrixThreadNumOption = addIntegerOption("mthreads"); private final Option v9DepthBaseOption = addIntegerOption("v9-depth-base"); // double private final Option subsampleOption = addDoubleOption("subsample"); // sets of strings private final Option multipleChromosomesOption = addStringOption('c', "chromosomes"); private final Option resolutionOption = addStringOption('r', "resolutions"); private final Option randomizePositionMapsOption = addStringOption("frag-site-maps"); //set of ints private final Option multipleMapQOption = addStringOption("mapqs"); //filter optrectionalion based on diity private final Option hicFileScalingOption = addDoubleOption('z', "scale"); private final Option randomSeedOption = addLongOption("random-seed"); public CommandLineParser() { } /** * boolean flags */ protected boolean optionToBoolean(Option option) { Object opt = getOptionValue(option); return opt != null && (Boolean) opt; } public boolean getHelpOption() { return optionToBoolean(helpOption);} public boolean getDiagonalsOption() { return optionToBoolean(diagonalsOption); } public boolean useCacheMemory() { return optionToBoolean(removeCacheMemoryOption); } public boolean getVerboseOption() { return optionToBoolean(verboseOption); } public boolean getNoNormOption() { return optionToBoolean(noNormOption); } public boolean getAllPearsonsOption() { return optionToBoolean(allPearsonsOption); } public boolean getNoFragNormOption() { return optionToBoolean(noFragNormOption); } public boolean getVersionOption() { return optionToBoolean(versionOption); } public boolean getRandomizePositionsOption() { return optionToBoolean(randomizePositionOption); } public boolean getThrowIntraFragOption() { return optionToBoolean(throwIntraFragOption); } public boolean getDontPutAllContactsIntoRAM() { return optionToBoolean(useMinRAM); } public boolean shouldCheckRAMUsage() { return optionToBoolean(checkMemory); } public boolean getFromHICOption() { return optionToBoolean(fromHIC); } /** * String flags */ protected String optionToString(Option option) { Object opt = getOptionValue(option); return opt == null ? null : opt.toString(); } public String getFragmentOption() { return optionToString(fragmentOption); } public String getStatsOption() { return optionToString(statsOption); } public String getGraphOption() { return optionToString(graphOption); } public String getGenomeOption() { return optionToString(genomeIDOption); } public String getTmpdirOption() { return optionToString(tmpDirOption); } public String getExpectedVectorOption() { return optionToString(expectedVectorOption); } public String getMndIndexOption() { return optionToString(mndIndexOption); } public String getLigationOption() { return optionToString(ligationOption); } public String getShellOption() { return optionToString(shellOption); } public Alignment getAlignmentOption() { int alignmentInt = optionToInt(alignmentFilterOption); if (alignmentInt == 0) { return null; } if (alignmentInt == 1) { return Alignment.INNER; } else if (alignmentInt == 2) { return Alignment.OUTER; } else if (alignmentInt == 3) { return Alignment.LL; } else if (alignmentInt == 4) { return Alignment.RR; } else if (alignmentInt == 5) { return Alignment.TANDEM; } else { throw new IllegalArgumentException(String.format("alignment option %d not supported", alignmentInt)); } } /** * int flags */ protected int optionToInt(Option option) { Object opt = getOptionValue(option); return opt == null ? 0 : ((Number) opt).intValue(); } public int getBlockCapacityOption() { return optionToInt(blockCapacityOption); } public int getCountThresholdOption() { return optionToInt(countThresholdOption); } public int getMapqThresholdOption() { return optionToInt(mapqOption); } public int getGenomeWideOption() { return optionToInt(genomeWideOption); } protected long optionToLong(Option option) { Object opt = getOptionValue(option); return opt == null ? 0 : ((Number) opt).longValue(); } public long getRandomPositionSeedOption() { return optionToLong(randomSeedOption); } public enum Alignment {INNER, OUTER, LL, RR, TANDEM} public int getNumThreads() { return optionToInt(threadNumOption); } public int getNumMatrixOperationThreads() { return optionToInt(matrixThreadNumOption); } public int getV9DepthBase() { return optionToInt(v9DepthBaseOption); } /** * double flags */ protected double optionToDouble(Option option) { Object opt = getOptionValue(option); return opt == null ? -1 : ((Number) opt).doubleValue(); } public double getScalingOption() { double opt = optionToDouble(hicFileScalingOption); if (opt > -1) return opt; return 1; } public double getSubsampleOption() { return optionToDouble(subsampleOption); } /** * String Set flags */ protected Set optionToStringSet(Option option) { Object opt = getOptionValue(option); return opt == null ? null : new HashSet<>(Arrays.asList(opt.toString().split(","))); } protected List optionToStringList(Option option) { Object opt = getOptionValue(option); return opt == null ? null : new ArrayList<>(Arrays.asList(opt.toString().split(","))); } public Set getChromosomeSetOption() { return optionToStringSet(multipleChromosomesOption); } public List getResolutionOption() { return optionToStringList(resolutionOption); } public Set getRandomizePositionMaps() {return optionToStringSet(randomizePositionMapsOption);} /** * Int Set flags */ protected List optionToIntList(Option option) { Object opt = getOptionValue(option); if(opt == null){ return null; } String[] temp = opt.toString().split(","); List options = new ArrayList<>(); for(String s : temp){ options.add(Integer.parseInt(s)); } return options; } public List getMultipleMapQOptions() {return optionToIntList(multipleMapQOption);} public List getAllNormalizationTypesOption() { NormalizationHandler normalizationHandler = new NormalizationHandler(); List normStrings = optionToStringList(normalizationTypeOption); if (normStrings == null || normStrings.size() < 1) { return normalizationHandler.getDefaultSetForHiCFileBuilding(); } List normalizationTypes = new ArrayList<>(); for (String normString : normStrings) { normalizationTypes.add(retrieveNormalization(normString, normalizationHandler)); } return normalizationTypes; } protected NormalizationType retrieveNormalization(String norm, NormalizationHandler normalizationHandler) { if (norm == null || norm.length() < 1) return null; try { return normalizationHandler.getNormTypeFromString(norm); } catch (IllegalArgumentException error) { System.err.println("Normalization must be one of \"NONE\", \"VC\", \"VC_SQRT\", \"KR\", \"GW_KR\", \"GW_VC\", \"INTER_KR\", or \"INTER_VC\"."); System.exit(7); } return null; } } ================================================ FILE: src/juicebox/tools/clt/CommandLineParserForJuicer.java ================================================ /* * The MIT License (MIT) * * Copyright (c) 2011-2021 Broad Institute, Aiden Lab, Rice University, Baylor College of Medicine * * Permission is hereby granted, free of charge, to any person obtaining a copy * of this software and associated documentation files (the "Software"), to deal * in the Software without restriction, including without limitation the rights * to use, copy, modify, merge, publish, distribute, sublicense, and/or sell * copies of the Software, and to permit persons to whom the Software is * furnished to do so, subject to the following conditions: * * The above copyright notice and this permission notice shall be included in * all copies or substantial portions of the Software. * * THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR * IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, * FITNESS FOR A PARTICULAR PURPOSE AND NON-INFRINGEMENT. IN NO EVENT SHALL THE * AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER * LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, * OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN * THE SOFTWARE. */ package juicebox.tools.clt; import juicebox.windowui.NormalizationHandler; import juicebox.windowui.NormalizationType; import java.util.List; /** * Command Line Parser for Juicer commands (hiccups, arrowhead, apa) * @author Muhammad Shamim */ public class CommandLineParserForJuicer extends CommandLineParser { // used flags // wmnxcrplafdptkqbvuhgjyzoe // available flags // s // General private final Option matrixSizeOption = addIntegerOption('m', "matrix-width"); private final Option multipleChromosomesOption = addStringOption('c', "chromosomes"); private final Option multipleResolutionsOption = addStringOption('r', "resolutions"); private final Option legacyOutputOption = addBooleanOption('g', "legacy"); // APA private final Option apaWindowOption = addIntegerOption('w', "window"); private final Option apaMinValOption = addDoubleOption('n', "min-dist"); private final Option apaMaxValOption = addDoubleOption('x', "max-dist"); private final Option multipleCornerRegionDimensionsOption = addStringOption('q', "corner-width"); private final Option includeInterChromosomalOption = addBooleanOption('e', "include-inter-chr"); private final Option apaSaveAllData = addBooleanOption('u', "save-all"); private final Option apaDontIncludePlots = addBooleanOption('o', "no-plots"); // HICCUPS private final Option fdrOption = addStringOption('f', "fdr-thresholds"); private final Option windowOption = addStringOption('i', "window-width"); private final Option peakOption = addStringOption('p', "peak-width"); private final Option clusterRadiusOption = addStringOption('d', "centroid-radii"); private final Option thresholdOption = addStringOption('t', "postprocessing-thresholds"); private final Option cpuVersionHiCCUPSOption = addBooleanOption('j', "cpu"); private final Option restrictSearchRegionsOption = addBooleanOption('y', "restrict"); //Localizer private final Option expandSize = addIntegerOption('e', "expand"); private final Option numPeaks = addIntegerOption("num-peaks"); private final Option relativeLocationOption = addStringOption('l', "location-type"); private final Option multipleAttributesOption = addStringOption('a', "attributes"); public CommandLineParserForJuicer() { } public static boolean isJuicerCommand(String cmd) { return cmd.equals("hiccups") || cmd.equals("hiccups2") || cmd.equals("hiccups-scores") || cmd.equals("apa") || cmd.equals("arrowhead") || cmd.equals("motifs") || cmd.equals("cluster") || cmd.equals("compare") || cmd.equals("loop_domains") || cmd.equals("localizer") || cmd.equals("hiccupsdiff") || cmd.equals("ab_compdiff") || cmd.equals("genes") || cmd.equals("apa_vs_distance"); } public boolean getLegacyOutputOption() { return optionToBoolean(legacyOutputOption); } public boolean getIncludeInterChromosomal() { return optionToBoolean(includeInterChromosomalOption); } public boolean getAPASaveAllData() { return optionToBoolean(apaSaveAllData); } public boolean getAPADontIncludePlots() { return optionToBoolean(apaDontIncludePlots); } /** * String flags */ public NormalizationType getNormalizationTypeOption(NormalizationHandler normalizationHandler) { return retrieveNormalization(optionToString(normalizationTypeOption), normalizationHandler); } public NormalizationType[] getBothNormalizationTypeOption(NormalizationHandler normHandler1, NormalizationHandler normHandler2) { NormalizationType[] normalizationTypes = new NormalizationType[2]; String normStrings = optionToString(normalizationTypeOption); if (normStrings != null) { String[] bothNorms = normStrings.split(","); if (bothNorms.length > 2 || bothNorms.length < 1) { System.err.println("Invalid norm syntax: " + normStrings); return null; } else if (bothNorms.length == 2) { normalizationTypes[0] = retrieveNormalization(bothNorms[0], normHandler1); normalizationTypes[1] = retrieveNormalization(bothNorms[1], normHandler2); } else if (bothNorms.length == 1) { normalizationTypes[0] = retrieveNormalization(bothNorms[0], normHandler1); normalizationTypes[1] = retrieveNormalization(bothNorms[0], normHandler2); } return normalizationTypes; } return null; } /** * int flags */ public int getAPAWindowSizeOption() { return optionToInt(apaWindowOption); } public int getMatrixSizeOption() { return optionToInt(matrixSizeOption); } public int getExpandSize() { return optionToInt(expandSize);} public int getNumPeaks() { return optionToInt(numPeaks);} /** * double flags */ public double getAPAMinVal() { return optionToDouble(apaMinValOption); } public double getAPAMaxVal() { return optionToDouble(apaMaxValOption); } /** * String Set flags */ List getChromosomeListOption() { return optionToStringList(multipleChromosomesOption); } // todo fix to return list of ints public List getMultipleResolutionOptions() { return optionToStringList(multipleResolutionsOption); } public List getAPACornerRegionDimensionOptions() { return optionToStringList(multipleCornerRegionDimensionsOption); } public List getFDROptions() { return optionToStringList(fdrOption); } public List getPeakOptions() { return optionToStringList(peakOption); } public List getWindowOptions() { return optionToStringList(windowOption); } public List getClusterRadiusOptions() { return optionToStringList(clusterRadiusOption); } public List getThresholdOptions() { return optionToStringList(thresholdOption); } public boolean getCPUVersionOfHiCCUPSOptions() { Object opt = getOptionValue(cpuVersionHiCCUPSOption); return opt != null; } public boolean restrictSearchRegionsOptions() { return optionToBoolean(restrictSearchRegionsOption); } } ================================================ FILE: src/juicebox/tools/clt/JuiceboxCLT.java ================================================ /* * The MIT License (MIT) * * Copyright (c) 2011-2021 Broad Institute, Aiden Lab, Rice University, Baylor College of Medicine * * Permission is hereby granted, free of charge, to any person obtaining a copy * of this software and associated documentation files (the "Software"), to deal * in the Software without restriction, including without limitation the rights * to use, copy, modify, merge, publish, distribute, sublicense, and/or sell * copies of the Software, and to permit persons to whom the Software is * furnished to do so, subject to the following conditions: * * The above copyright notice and this permission notice shall be included in * all copies or substantial portions of the Software. * * THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR * IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, * FITNESS FOR A PARTICULAR PURPOSE AND NON-INFRINGEMENT. IN NO EVENT SHALL THE * AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER * LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, * OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN * THE SOFTWARE. */ package juicebox.tools.clt; import juicebox.data.Dataset; import juicebox.data.HiCFileTools; import juicebox.data.iterator.IteratorContainer; import juicebox.windowui.NormalizationType; import java.util.Arrays; /** * All command line tools should extend from this class */ public abstract class JuiceboxCLT { private static String usage; protected Dataset dataset = null; protected NormalizationType norm = null; protected static int numCPUThreads = 1; protected static int numCPUThreadsForSecondTask = 1; protected boolean usingMultiThreadedVersion = false; protected JuiceboxCLT(String usage) { setUsage(usage); } public static String[] splitToList(String nextLine) { return nextLine.trim().split("\\s+"); } public abstract void readArguments(String[] args, CommandLineParser parser); public abstract void run(); private void setUsage(String newUsage) { usage = newUsage; } public void printUsageAndExit() { System.out.println("Usage: juicer_tools " + usage); System.exit(0); } public void printUsageAndExit(int exitcode) { System.out.println("Usage: juicer_tools " + usage); System.exit(exitcode); } protected void setDatasetAndNorm(String files, String normType, boolean allowPrinting) { dataset = HiCFileTools.extractDatasetForCLT(Arrays.asList(files.split("\\+")), allowPrinting); norm = dataset.getNormalizationHandler().getNormTypeFromString(normType); if (norm == null) { System.err.println("Normalization type " + norm + " unrecognized. Normalization type must be one of \n" + "\"NONE\", \"VC\", \"VC_SQRT\", \"KR\", \"GW_KR\"," + " \"GW_VC\", \"INTER_KR\", \"INTER_VC\", or a custom added normalization."); System.exit(16); } } public static int getAppropriateNumberOfThreads(int numThreads, int defaultNum) { if (numThreads > 0) { return numThreads; } else if (numThreads < 0) { return Math.abs(numThreads) * Runtime.getRuntime().availableProcessors(); } else { return defaultNum; } } protected void updateNumberOfCPUThreads(CommandLineParser parser, int numDefaultThreads) { int numThreads = parser.getNumThreads(); numCPUThreads = getAppropriateNumberOfThreads(numThreads, numDefaultThreads); System.out.println("Using " + numCPUThreads + " CPU thread(s) for primary task"); } protected void updateSecondaryNumberOfCPUThreads(CommandLineParser parser, int numDefaultThreads) { int numMThreads = parser.getNumMatrixOperationThreads(); numCPUThreadsForSecondTask = getAppropriateNumberOfThreads(numMThreads, numDefaultThreads); System.out.println("Using " + IteratorContainer.numCPUMatrixThreads + " CPU thread(s) for secondary task"); } } ================================================ FILE: src/juicebox/tools/clt/JuicerCLT.java ================================================ /* * The MIT License (MIT) * * Copyright (c) 2011-2021 Broad Institute, Aiden Lab, Rice University, Baylor College of Medicine * * Permission is hereby granted, free of charge, to any person obtaining a copy * of this software and associated documentation files (the "Software"), to deal * in the Software without restriction, including without limitation the rights * to use, copy, modify, merge, publish, distribute, sublicense, and/or sell * copies of the Software, and to permit persons to whom the Software is * furnished to do so, subject to the following conditions: * * The above copyright notice and this permission notice shall be included in * all copies or substantial portions of the Software. * * THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR * IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, * FITNESS FOR A PARTICULAR PURPOSE AND NON-INFRINGEMENT. IN NO EVENT SHALL THE * AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER * LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, * OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN * THE SOFTWARE. */ package juicebox.tools.clt; import juicebox.data.ChromosomeHandler; import juicebox.data.Dataset; import juicebox.data.Matrix; import juicebox.data.basics.Chromosome; import juicebox.windowui.HiCZoom; import juicebox.windowui.NormalizationHandler; import juicebox.windowui.NormalizationType; import java.util.ArrayList; import java.util.List; /** * Created by muhammadsaadshamim on 9/21/15. */ public abstract class JuicerCLT extends JuiceboxCLT { protected NormalizationType norm = NormalizationHandler.SCALE; protected List givenChromosomes = null; //TODO set to protected protected JuicerCLT(String usage) { super(usage); } protected int determineHowManyChromosomesWillActuallyRun(Dataset ds, ChromosomeHandler chromosomeHandler, HiCZoom zoom) { int maxProgressStatus = 0; for (Chromosome chr : chromosomeHandler.getChromosomeArrayWithoutAllByAll()) { Matrix matrix = ds.getMatrix(chr, chr); if (matrix == null) continue; if (matrix.getZoomData(zoom) == null) continue; maxProgressStatus++; } return maxProgressStatus; } @Override public void readArguments(String[] args, CommandLineParser parser) { CommandLineParserForJuicer juicerParser = (CommandLineParserForJuicer)parser; assessIfChromosomesHaveBeenSpecified(juicerParser); readJuicerArguments(args, juicerParser); } protected abstract void readJuicerArguments(String[] args, CommandLineParserForJuicer juicerParser); private void assessIfChromosomesHaveBeenSpecified(CommandLineParserForJuicer juicerParser) { List possibleChromosomes = juicerParser.getChromosomeListOption(); if (possibleChromosomes != null && possibleChromosomes.size() > 0) { givenChromosomes = new ArrayList<>(possibleChromosomes); } } } ================================================ FILE: src/juicebox/tools/clt/UnitTests.java ================================================ /* * The MIT License (MIT) * * Copyright (c) 2011-2021 Broad Institute, Aiden Lab, Rice University, Baylor College of Medicine * * Permission is hereby granted, free of charge, to any person obtaining a copy * of this software and associated documentation files (the "Software"), to deal * in the Software without restriction, including without limitation the rights * to use, copy, modify, merge, publish, distribute, sublicense, and/or sell * copies of the Software, and to permit persons to whom the Software is * furnished to do so, subject to the following conditions: * * The above copyright notice and this permission notice shall be included in * all copies or substantial portions of the Software. * * THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR * IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, * FITNESS FOR A PARTICULAR PURPOSE AND NON-INFRINGEMENT. IN NO EVENT SHALL THE * AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER * LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, * OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN * THE SOFTWARE. */ package juicebox.tools.clt; import juicebox.HiC; import juicebox.HiCGlobals; import juicebox.data.*; import juicebox.data.basics.Chromosome; import juicebox.matrix.BasicMatrix; import juicebox.tools.utils.common.MatrixTools; import juicebox.tools.utils.juicer.hiccups.HiCCUPSConfiguration; import juicebox.tools.utils.juicer.hiccups.HiCCUPSUtils; import juicebox.track.feature.Feature2DList; import juicebox.track.feature.Feature2DParser; import juicebox.windowui.HiCZoom; import juicebox.windowui.NormalizationHandler; import juicebox.windowui.NormalizationType; import java.io.File; import java.util.*; /** * Created by muhammadsaadshamim on 7/22/15. */ class UnitTests { public static void pearsonsAndEigenvector() { List files = new ArrayList<>(); files.add("/Users/mshamim/Desktop/hicfiles/gm12878_rh14_30.hic"); Dataset ds = HiCFileTools.extractDatasetForCLT(files, false); Chromosome chrom = ds.getChromosomeHandler().getChromosomeFromName("10"); Matrix matrix = ds.getMatrix(chrom, chrom); HiCGlobals.MAX_PEARSON_ZOOM = 50000; HiCZoom zoom = new HiCZoom(HiC.Unit.BP, 50000); MatrixZoomData zd = matrix.getZoomData(zoom); ExpectedValueFunction df = ds.getExpectedValues(zoom, NormalizationHandler.KR); HiCGlobals.guiIsCurrentlyActive = true; long time0 = System.nanoTime(); BasicMatrix bm1 = zd.getPearsons(df); long time1 = System.nanoTime(); System.out.println("Pearsons Time: " + (time1 - time0) * 1e-9); long Etime0 = System.nanoTime(); double[] eig = zd.computeEigenvector(df, 0); long Etime1 = System.nanoTime(); System.out.println("Eig Time: " + (Etime1 - Etime0) * 1e-9); MatrixTools.saveMatrixTextNumpy("/Users/mshamim/Desktop/research/pearson/c20.npy", toDenseMatrix(bm1)); MatrixTools.saveMatrixTextNumpy("/Users/mshamim/Desktop/research/pearson/E20.npy", eig); } private static float[][] toDenseMatrix(BasicMatrix bm1) { float[][] vals = new float[bm1.getRowDimension()][bm1.getColumnDimension()]; for (int i = 0; i < vals.length; i++) { for (int j = 0; j < vals[i].length; j++) { vals[i][j] = bm1.getEntry(i, j); } } return vals; } private static void testingMergerOfHiCCUPSPostprocessing() { HiCGlobals.printVerboseComments = true; // example with hard-coded links String folder = "/Users/muhammadsaadshamim/Desktop/T0_48/0/exp1/"; String baseLink = folder + "postprocessed_pixels_"; String link1 = baseLink + "5000"; String link2 = baseLink + "10000"; String link3 = baseLink + "25000"; String outputPath = folder + "new_merged_loops"; Map map = new HashMap<>(); map.put(5000, Feature2DParser.loadFeatures(link1, "hg19", true, null, false)); map.put(10000, Feature2DParser.loadFeatures(link2, "hg19", true, null, false)); map.put(25000, Feature2DParser.loadFeatures(link3, "hg19", true, null, false)); Feature2DList newMerger = HiCCUPSUtils.mergeAllResolutions(map); newMerger.exportFeatureList(new File(outputPath), false, Feature2DList.ListFormat.FINAL); folder = "/Users/muhammad/Desktop/local_hiccups_gm12878/results3/"; baseLink = folder + "enriched_pixels_"; link1 = baseLink + "5000.bedpe"; link2 = baseLink + "10000.bedpe"; link3 = baseLink + "25000.bedpe"; map = new HashMap<>(); map.put(5000, Feature2DParser.loadFeatures(link1, "hg19", true, null, false)); map.put(10000, Feature2DParser.loadFeatures(link2, "hg19", true, null, false)); map.put(25000, Feature2DParser.loadFeatures(link3, "hg19", true, null, false)); Dataset ds1 = HiCFileTools.extractDatasetForCLT(Arrays.asList("/Users/muhammad/Desktop/local_hic_files/gm12878_intra_nofrag_30.hic"), true); File outputDirectory = new File("/Users/muhammad/Desktop/local_hiccups_gm12878/results5"); File outputMergedGivenFile = new File(outputDirectory, HiCCUPSUtils.getMergedRequestedLoopsFileName()); HiCCUPSUtils.postProcess(map, ds1, ds1.getChromosomeHandler(), HiCCUPSConfiguration.getDefaultSetOfConfigsForUsers(), NormalizationHandler.KR, outputDirectory, false, outputMergedGivenFile, 1); } public static void testingHiCCUPSPostprocessing() { // example with hard-coded links String folder = "/Users/muhammadsaadshamim/Desktop/test_adam/"; File outputDirectory = new File(folder); Dataset ds = HiCFileTools.extractDatasetForCLT(Collections.singletonList(folder + "inter_30.hic"), true); File outputMergedFile = new File(outputDirectory, "merged_loops"); ChromosomeHandler chromosomeHandler = ds.getChromosomeHandler(); NormalizationType norm = NormalizationHandler.KR; List filteredConfigurations = new ArrayList<>(); filteredConfigurations.add(new HiCCUPSConfiguration(10000, 10, 2, 5, 20000)); filteredConfigurations.add(new HiCCUPSConfiguration(5000, 10, 4, 7, 20000)); String baseLink = folder + "enriched_pixels_"; String link1 = baseLink + "5000"; String link2 = baseLink + "10000"; Map loopLists = new HashMap<>(); loopLists.put(5000, Feature2DParser.loadFeatures(link1, chromosomeHandler, true, null, false)); loopLists.put(10000, Feature2DParser.loadFeatures(link2, chromosomeHandler, true, null, false)); HiCCUPSUtils.postProcess(loopLists, ds, chromosomeHandler, filteredConfigurations, norm, outputDirectory, false, outputMergedFile, 1); } /* public static void testCustomFastScaling() { ArrayList files = new ArrayList<>(); files.add("/Users/muhammad/Desktop/local_hic_files/gm12878_intra_nofrag_30.hic"); Dataset ds = HiCFileTools.extractDatasetForCLT(files, false); Chromosome chr1 = ds.getChromosomeHandler().getAutosomalChromosomesArray()[0]; MatrixZoomData zd = HiCFileTools.getMatrixZoomData(ds, chr1, chr1, 50000); int numEntries = (int)(chr1.getLength() / 50000) + 1; // assume for this test double[] targetVectorInitial = new double[numEntries]; Arrays.fill(targetVectorInitial, 1); HiCGlobals.printVerboseComments = true; BigContactRecordList listOfLists = new ArrayList<>(); listOfLists.addAll(zd.getContactRecordList()); double[] result = ZeroScale.scale(listOfLists, targetVectorInitial, zd.getKey()); System.out.println(Arrays.toString(result)); } public void runUnitTests() { // TODO tests for all matrix/array tools // TODO tests for all CLTs // TODO tests for other standalone parts of code /* MatrixTools.print(MatrixTools.reshapeFlatMatrix(new float[]{1, 2, 3, 1, 2, 3}, 3, 2)); RealMatrix rm = MatrixTools.cleanArray2DMatrix(2000); for(int i = 0; i < 20; i++){ for(int j = 0; j < 20; j++){ rm.setEntry(i,j,1); } } for(int i = 99; i < 120; i++){ for(int j = 99; j < 120; j++){ rm.setEntry(i,j,1); } } for(int i = 299; i < 400; i++){ for(int j = 299; j < 400; j++){ rm.setEntry(i,j,20000); } } for(int i = 349; i < 600; i++){ for(int j = 349; j < 600; j++){ rm.setEntry(i,j,5000); } } Random generator = new Random(); for(int i = 1399; i < 1600; i++){ for(int j = 1399; j < 1600; j++){ rm.setEntry(i,j,5000*generator.nextDouble()); } } BlockResults b = new BlockResults(rm, 1000, .4, new ArrowheadScoreList(), new ArrowheadScoreList()); b.offsetResultsIndex(1); for(HighScore h : b.getResults()) System.out.println(h); // super("arrowhead "); // http://adam.bcma.bcm.edu/hiseq/ */ /* String[] l1 = {"hiccups", "-r", "50000", "-c", "1", "-m", "100", "https://hicfiles.s3.amazonaws.com/hiseq/gm12878/in-situ/combined.hic", "/Users/muhammadsaadshamim/Desktop/j3/out1_100", "/Users/muhammadsaadshamim/Desktop/j3/out2_100"}; long time = System.currentTimeMillis(); HiCTools.main(l1); time = (System.currentTimeMillis() - time) / 1000; long mins = time/60; long secs = time%60; System.out.println("Total time " + mins + " min "+ secs + " sec"); /* String[] l1 = {"dump","observed", HiCFileTools.KR, "https://hicfiles.s3.amazonaws.com/hiseq/gm12878/in-situ/combined.hic", "1", "1", HiCFileTools.BP, "5000", "/Users/muhammadsaadshamim/Desktop/perseus/chr1.bin"}; String[] l4 = {"apa", "-r","50000", "-c","17,18", //"http://adam.bcma.bcm.edu/miseq/HIC1357.hic,http://adam.bcma.bcm.edu/miseq/HIC1357_30.hic,http://adam.bcma.bcm.edu/miseq/HIC1358.hic,http://adam.bcma.bcm.edu/miseq/HIC1358_30.hic,http://adam.bcma.bcm.edu/miseq/HIC1359.hic,http://adam.bcma.bcm.edu/miseq/HIC1359_30.hic,http://adam.bcma.bcm.edu/miseq/HIC1360.hic,http://adam.bcma.bcm.edu/miseq/HIC1360_30.hic,http://adam.bcma.bcm.edu/miseq/HIC1361.hic,http://adam.bcma.bcm.edu/miseq/HIC1361_30.hic,http://adam.bcma.bcm.edu/miseq/HIC1362.hic,http://adam.bcma.bcm.edu/miseq/HIC1362_30.hic,http://adam.bcma.bcm.edu/miseq/HIC1363.hic,http://adam.bcma.bcm.edu/miseq/HIC1363_30.hic", "https://hicfiles.s3.amazonaws.com/hiseq/gm12878/in-situ/combined.hic", "/Users/muhammadsaadshamim/Desktop/Elena_APA/all_loops.txt", "/Users/muhammadsaadshamim/Desktop/Elena_APA/newt"}; long time = System.currentTimeMillis(); HiCTools.main(l3); time = System.currentTimeMillis() - time; System.out.println("Total time (ms): "+time); */ /* * Example: this dumps data of each chromosome * for 5 single cell Hi-C experiments * at 5, 10, and 25 kb resolutions * * https://hicfiles.s3.amazonaws.com/hiseq/gm12878/in-situ/combined.hic */ /* String[] l1 = {"apa","-r","5000", "/Users/muhammadsaadshamim/Desktop/Leviathan/nagano/cell-1/inter.hic", "/Users/muhammadsaadshamim/Desktop/Leviathan/nagano/mouse_list.txt", "/Users/muhammadsaadshamim/Desktop/apaTest1"}; RealMatrix rm = new Array2DRowRealMatrix(new double[][] { {0.0605, 0.6280, 0.1672, 0.3395, 0.2691}, {0.3993, 0.2920, 0.1062, 0.9516, 0.4228}, {0.5269, 0.4317, 0.3724, 0.9203, 0.5479}, {0.4168, 0.0155, 0.1981, 0.0527, 0.9427}, {0.6569, 0.9841, 0.4897, 0.7379, 0.4177}}); rm = new Array2DRowRealMatrix(new double[][] { {1,0,0,0,0,0,0,0}, {0,1,0,0,0,0,0,0}, {0,2,0,0,0,0,0,0}, {0,0,1,0,0,0,0,0}, {0,0,0,1,0,0,1,0}, {0,0,0,0,1,0,0,0}, {3,0,0,1,0,0,0,0}, {1,1,1,0,0,0,0,0}}); String[] chrs = {"1","2","3","4","5","6","7","8","9","10","11","12","13","14","15","16","17","18","19","X"}; String[] kbs = {"5","10","25"}; for(String kb : kbs) { for (int i = 1; i < 6; i++) { for (String chr : chrs) { String[] line = {"dump", "observed", "NONE", "/Users/muhammadsaadshamim/Desktop/nagano/cell-" + i + "/inter.hic", "chr" + chr, "chr" + chr, HiCFileTools.BP, kb+"000", "/Users/muhammadsaadshamim/Desktop/nagano/apa_"+kb+"kb_" + i + "/counts/counts_" + chr + ".txt"}; HiCTools.main(line); } } } */ /* int[] is = {5}; for(int i : is) { for (String chr : chrs) { String[] line = {"dump", "observed", "NONE", "/Users/muhammadsaadshamim/Desktop/nagano/cell-" + i + "/inter.hic", "chr" + chr, "chr" + chr, HiCFileTools.BP, "5000", "/Users/muhammadsaadshamim/Desktop/nagano/apa_5kb_" + i + "/counts/counts_" + chr + ".txt"}; HiCTools.main(line); } } */ /* * For verifying file identity using python: * { * import filecmp * print filecmp.cmp('output1.hic', 'output2.hic') # byte by byte comparison of output files * } */ /* String[] l2 = {"addNorm", "/Users/muhammadsaadshamim/Desktop/testing/mouse.hic", "100000000"}; String[] l3 = {"binToPairs", "/Users/muhammadsaadshamim/Desktop/testing/mouse.hic", "/Users/muhammadsaadshamim/Desktop/testing/mousesc3.hic"}; String[] l4 = {"calcKR", "/Users/muhammadsaadshamim/Desktop/testing/mouse.hic"}; String[] l5 = {"dump", "observed", "NONE", "/Users/muhammadsaadshamim/Desktop/testing/mouse.hic", "chr2", "chr2", HiCFileTools.BP, "1000000", "/Users/muhammadsaadshamim/Desktop/testing/mousesc.txt"}; String[] l6 = {"pairsToBin", "/Users/muhammadsaadshamim/Desktop/testing/mouse.hic", "/Users/muhammadsaadshamim/Desktop/testing/mousesc2.hic", "mm10"}; String[] l7 = { "pre", "/Users/muhammadsaadshamim/Desktop/HIC156_smaller.txt", "/Users/muhammadsaadshamim/Desktop/HIC156_smaller", "hg19" }; */ /** * * testing dump * * HiCGlobals.printVerboseComments = true; String[] ajkhsd = {"dump", "observed", HiCFileTools.KR, "/Users/muhammadsaadshamim/Desktop/LocalFiles/rice_mbr19_30.hic", "19","19", HiCFileTools.BP, "5000", "/Users/muhammadsaadshamim/Desktop/test_dump/dump_5k_19_full_kr"}; //HiCTools.main(ajkhsd); ajkhsd = new String[]{"dump", "observed", HiCFileTools.KR, "/Users/muhammadsaadshamim/Desktop/LocalFiles/rice_mbr19_30.hic", "19","19", HiCFileTools.BP, "5000", "/Users/muhammadsaadshamim/Desktop/test_dump/dump_5k_19_full_kr"}; HiCTools.main(ajkhsd); ajkhsd = new String[]{"dump", "observed", HiCFileTools.KR, "/Users/muhammadsaadshamim/Desktop/LocalFiles/rice_mbr19_30.hic", "19:0:59128983","19:10000000:20000000", HiCFileTools.BP, "5000", "/Users/muhammadsaadshamim/Desktop/test_dump/dump_5k_19_sub1_kr"}; HiCTools.main(ajkhsd); ajkhsd = new String[]{"dump", "observed", HiCFileTools.KR, "/Users/muhammadsaadshamim/Desktop/LocalFiles/rice_mbr19_30.hic", "19","19:10000000:20000000", HiCFileTools.BP, "5000", "/Users/muhammadsaadshamim/Desktop/test_dump/dump_5k_19_sub1_kr_v2"}; HiCTools.main(ajkhsd); ajkhsd = new String[]{"dump", "observed", HiCFileTools.KR, "/Users/muhammadsaadshamim/Desktop/LocalFiles/rice_mbr19_30.hic", "19:10000000:20000000","19:0:59128983", HiCFileTools.BP, "5000", "/Users/muhammadsaadshamim/Desktop/test_dump/dump_5k_19_sub2_kr"}; HiCTools.main(ajkhsd); ajkhsd = new String[]{"dump", "observed", HiCFileTools.KR, "/Users/muhammadsaadshamim/Desktop/LocalFiles/rice_mbr19_30.hic", "19:10000000:20000000","19", HiCFileTools.BP, "5000", "/Users/muhammadsaadshamim/Desktop/test_dump/dump_5k_19_sub2_kr_v2"}; HiCTools.main(ajkhsd); ajkhsd = new String[]{"dump", "observed", HiCFileTools.KR, "/Users/muhammadsaadshamim/Desktop/LocalFiles/rice_mbr19_30.hic", "19:10000000:20000000","19:10000000:20000000", HiCFileTools.BP, "5000", "/Users/muhammadsaadshamim/Desktop/test_dump/dump_5k_19_sub3_kr"}; HiCTools.main(ajkhsd); * } */ } ================================================ FILE: src/juicebox/tools/clt/juicer/ABCompartmentsDiff.java ================================================ /* * The MIT License (MIT) * * Copyright (c) 2011-2020 Broad Institute, Aiden Lab, Rice University, Baylor College of Medicine * * Permission is hereby granted, free of charge, to any person obtaining a copy * of this software and associated documentation files (the "Software"), to deal * in the Software without restriction, including without limitation the rights * to use, copy, modify, merge, publish, distribute, sublicense, and/or sell * copies of the Software, and to permit persons to whom the Software is * furnished to do so, subject to the following conditions: * * The above copyright notice and this permission notice shall be included in * all copies or substantial portions of the Software. * * THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR * IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, * FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE * AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER * LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, * OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN * THE SOFTWARE. */ package juicebox.tools.clt.juicer; import juicebox.HiC; import juicebox.HiCGlobals; import juicebox.data.ChromosomeHandler; import juicebox.data.Dataset; import juicebox.data.HiCFileTools; import juicebox.data.basics.Chromosome; import juicebox.tools.clt.CommandLineParserForJuicer; import juicebox.tools.clt.JuicerCLT; import juicebox.tools.utils.common.ArrayTools; import juicebox.windowui.HiCZoom; import juicebox.windowui.NormalizationType; import java.io.File; import java.io.IOException; import java.io.PrintWriter; import java.util.Arrays; /** * Created by muhammadsaadshamim on 6/2/16. */ public class ABCompartmentsDiff extends JuicerCLT { private final HiCZoom highZoom = new HiCZoom(HiC.Unit.BP, 500000); private ChromosomeHandler chromosomeHandler; private Dataset ds1, ds2; private PrintWriter diffFileWriter, simFileWriter; public ABCompartmentsDiff() { super("ab_compdiff [-c chromosome(s)] "); } @Override protected void readJuicerArguments(String[] args, CommandLineParserForJuicer juicerParser) { if (args.length != 4) { printUsageAndExit(); } File outputDirectory = HiCFileTools.createValidDirectory(args[3]); File diffFile = new File(outputDirectory, "diff_AB_compartments.wig"); File simFile = new File(outputDirectory, "similar_AB_compartments.wig"); try { diffFileWriter = new PrintWriter(diffFile); simFileWriter = new PrintWriter(simFile); } catch (IOException e) { System.err.println("Unable to create files in output directory"); System.exit(1); } ds1 = HiCFileTools.extractDatasetForCLT(Arrays.asList(args[1].split("\\+")), true); ds2 = HiCFileTools.extractDatasetForCLT(Arrays.asList(args[2].split("\\+")), true); if (!(ds1.getGenomeId().equals(ds2.getGenomeId()))) { System.err.println("Hi-C maps must be from the same genome"); System.exit(2); } chromosomeHandler = ds1.getChromosomeHandler(); if (givenChromosomes != null) chromosomeHandler = HiCFileTools.stringToChromosomes(givenChromosomes, chromosomeHandler); NormalizationType preferredNorm = juicerParser.getNormalizationTypeOption(ds1.getNormalizationHandler()); if (preferredNorm != null) norm = preferredNorm; System.out.println("Running differential A/B compartments at resolution " + highZoom.getBinSize()); } @Override public void run() { double maxProgressStatus = determineHowManyChromosomesWillActuallyRun(ds1, chromosomeHandler, highZoom); int currentProgressStatus = 0; for (Chromosome chromosome : chromosomeHandler.getChromosomeArrayWithoutAllByAll()) { if (HiCGlobals.printVerboseComments) { System.out.println("\nProcessing " + chromosome.getName()); } double[] eigenvector1, eigenvector2; try { eigenvector1 = ds1.getEigenvector(chromosome, highZoom, 0, norm); eigenvector2 = ds2.getEigenvector(chromosome, highZoom, 0, norm); } catch (Exception e) { System.err.println("Unable to get eigenvector for " + chromosome); continue; } int n = eigenvector1.length, n2 = eigenvector2.length; if (n != n2) { System.err.println(chromosome + " eigenvector lengths do not match: L1=" + n + " L2=" + n2); n = Math.min(n, n2); System.err.println("Using length " + n); } // first determine orientation (sign) of control eigenvector relative to observed // eigenvectors can be multiplied by any scalar and remain an eigenvector of the matrix // default sign is arbitrary int scalarMultipleForControlEigenvector = 1; int numSimilarities = 0, numDifferences = 0; for (int i = 0; i < n; i++) { double a = eigenvector1[i]; double b = eigenvector2[i]; if ((a > 0 && b > 0) || (a < 0 && b < 0)) { numSimilarities++; } else if ((a > 0 && b < 0) || (a < 0 && b > 0)) { numDifferences++; } } if (numDifferences > numSimilarities) { // unlikely outcome unless vastly different species are being studied // ctrl_eigenvector probably should be multiplied by -1 scalarMultipleForControlEigenvector = -1; } if (HiCGlobals.printVerboseComments) { System.out.println("\nScalar " + scalarMultipleForControlEigenvector); } // Now actually find the differences double[] differencesA2B = new double[n]; double[] similaritiesA2B = new double[n]; for (int i = 0; i < n; i++) { double a = eigenvector1[i]; double b = scalarMultipleForControlEigenvector * eigenvector2[i]; if ((a > 0 && b > 0) || (a < 0 && b < 0)) { similaritiesA2B[i] = Math.copySign(a - b, a); } else if ((a > 0 && b < 0) || (a < 0 && b > 0)) { differencesA2B[i] = Math.copySign(a - b, a); } } ArrayTools.exportChr1DArrayToWigFormat(differencesA2B, diffFileWriter, chromosome.getName(), highZoom.getBinSize()); ArrayTools.exportChr1DArrayToWigFormat(similaritiesA2B, simFileWriter, chromosome.getName(), highZoom.getBinSize()); System.out.println(((int) Math.floor((100.0 * ++currentProgressStatus) / maxProgressStatus)) + "% "); } diffFileWriter.close(); simFileWriter.close(); System.out.println("Differential A/B Compartments Complete"); } } ================================================ FILE: src/juicebox/tools/clt/juicer/APA.java ================================================ /* * The MIT License (MIT) * * Copyright (c) 2011-2021 Broad Institute, Aiden Lab, Rice University, Baylor College of Medicine * * Permission is hereby granted, free of charge, to any person obtaining a copy * of this software and associated documentation files (the "Software"), to deal * in the Software without restriction, including without limitation the rights * to use, copy, modify, merge, publish, distribute, sublicense, and/or sell * copies of the Software, and to permit persons to whom the Software is * furnished to do so, subject to the following conditions: * * The above copyright notice and this permission notice shall be included in * all copies or substantial portions of the Software. * * THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR * IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, * FITNESS FOR A PARTICULAR PURPOSE AND NON-INFRINGEMENT. IN NO EVENT SHALL THE * AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER * LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, * OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN * THE SOFTWARE. */ package juicebox.tools.clt.juicer; import com.google.common.primitives.Ints; import juicebox.HiC; import juicebox.HiCGlobals; import juicebox.data.ChromosomeHandler; import juicebox.data.Dataset; import juicebox.data.HiCFileTools; import juicebox.data.MatrixZoomData; import juicebox.data.basics.Chromosome; import juicebox.tools.clt.CommandLineParserForJuicer; import juicebox.tools.clt.JuicerCLT; import juicebox.tools.utils.juicer.apa.APADataStack; import juicebox.tools.utils.juicer.apa.APARegionStatistics; import juicebox.tools.utils.juicer.apa.APAUtils; import juicebox.track.feature.Feature2D; import juicebox.track.feature.Feature2DList; import juicebox.track.feature.Feature2DParser; import juicebox.track.feature.FeatureFilter; import juicebox.windowui.HiCZoom; import juicebox.windowui.NormalizationType; import org.apache.commons.math.linear.RealMatrix; import java.io.File; import java.util.*; import java.util.concurrent.ConcurrentHashMap; import java.util.concurrent.ExecutorService; import java.util.concurrent.Executors; import java.util.concurrent.atomic.AtomicInteger; /** * Aggregate Peak Analysis developed by mhuntley *

* Implemented in Juicer by mshamim *

* --- * APA * --- * The "apa" command takes three required arguments and a number of optional * arguments. *

* apa [-n minval] [-x maxval] [-w window] [-r resolution(s)] [-c chromosome(s)] * [-k NONE/VC/VC_SQRT/KR] [SavePrefix] *

* The required arguments are: *

* : Address of HiC File(s) which should end with ".hic". This is the file you will * load into Juicebox. URLs or local addresses may be used. To sum multiple HiC Files together, * use the '+' symbol between the addresses (no whitespace between addresses) * : List of peaks in standard 2D feature format (chr1 x1 x2 chr2 y1 y2 color ...) * : Working directory where outputs will be saved *

* The optional arguments are: * -n minimum distance away from the diagonal. Used to filter peaks too close to the diagonal. * Units are in terms of the provided resolution. (e.g. -n 30 @ resolution 5kB will filter loops * within 30*(5000/sqrt(2)) units of the diagonal) * -x maximum distance away from the diagonal. Used to filter peaks too far from the diagonal. * Units are in terms of the provided resolution. (e.g. -n 30 @ resolution 5kB will filter loops * further than 30*(5000/sqrt(2)) units of the diagonal) * -r resolution for APA; multiple resolutions can be specified using commas (e.g. 5000,10000) * -c Chromosome(s) on which APA will be run. The number/letter for the chromosome can be * used with or without appending the "chr" string. Multiple chromosomes can be specified using * commas (e.g. 1,chr2,X,chrY) * -k Normalizations (case sensitive) that can be selected. Generally, * KR (Knight-Ruiz) balancing should be used when available. *

* Default settings of optional arguments: * -n 30 * -x (infinity) * -r 25000,10000 * -c (all_chromosomes) * -k KR *

* ------------ * APA Examples * ------------ *

* apa HIC006.hic all_loops.txt results1 * > This command will run APA on HIC006 using loops from the all_loops files * > and save them under the results1 folder. *

* apa https://hicfiles.s3.amazonaws.com/hiseq/gm12878/in-situ/combined.hic * all_loops.txt results1 * > This command will run APA on the GM12878 mega map using loops from the all_loops * > files and save them under the results1 folder. *

* apa -r 10000,5000 -c 17,18 HIC006.hic+HIC007.hic all_loops.txt results * > This command will run APA at 50 kB resolution on chromosomes 17 and 18 for the * > summed HiC maps (HIC006 and HIC007) using loops from the all_loops files * > and save them under the results folder */ public class APA extends JuicerCLT { private boolean saveAllData = false; private boolean dontIncludePlots = false; private String loopListPath; private File outputDirectory; private Dataset ds; //defaults // TODO right now these units are based on n*res/sqrt(2) // TODO the sqrt(2) scaling should be removed (i.e. handle scaling internally) private double minPeakDist = 30; // distance between two bins, can be changed in opts private double maxPeakDist = Double.POSITIVE_INFINITY; private int window = 10; private int[] resolutions = new int[]{25000, 10000, 5000}; private int[] regionWidths = new int[]{6, 6, 3}; private boolean includeInterChr = false; private final Object key = new Object(); /** * Usage for APA */ public APA() { super("apa [-n minval] [-x maxval] [-w window] [-r resolution(s)] [-c chromosomes]" + " [-k NONE/VC/VC_SQRT/KR] [-q corner_width] [--include-inter-chr] [--save-all]" + " "); HiCGlobals.useCache = false; } public static String getBasicUsage() { return "apa "; } public void initializeDirectly(String inputHiCFileName, String inputPeaksFile, String outputDirectoryPath, int[] resolutions,double minPeakDist, double maxPeakDist){ this.resolutions=resolutions; List summedHiCFiles = Arrays.asList(inputHiCFileName.split("\\+")); ds = HiCFileTools.extractDatasetForCLT(summedHiCFiles, true); this.loopListPath=inputPeaksFile; outputDirectory = HiCFileTools.createValidDirectory(outputDirectoryPath); this.minPeakDist=minPeakDist; this.maxPeakDist=maxPeakDist; } @Override protected void readJuicerArguments(String[] args, CommandLineParserForJuicer juicerParser) { if (args.length != 4) { printUsageAndExit(); } loopListPath = args[2]; outputDirectory = HiCFileTools.createValidDirectory(args[3]); List summedHiCFiles = Arrays.asList(args[1].split("\\+")); ds = HiCFileTools.extractDatasetForCLT(summedHiCFiles, true); NormalizationType preferredNorm = juicerParser.getNormalizationTypeOption(ds.getNormalizationHandler()); if (preferredNorm != null) norm = preferredNorm; double potentialMinPeakDist = juicerParser.getAPAMinVal(); if (potentialMinPeakDist > -1) minPeakDist = potentialMinPeakDist; double potentialMaxPeakDist = juicerParser.getAPAMaxVal(); if (potentialMaxPeakDist > -1) maxPeakDist = potentialMaxPeakDist; int potentialWindow = juicerParser.getAPAWindowSizeOption(); if (potentialWindow > 0) window = potentialWindow; includeInterChr = juicerParser.getIncludeInterChromosomal(); saveAllData = juicerParser.getAPASaveAllData(); dontIncludePlots = juicerParser.getAPADontIncludePlots(); List possibleRegionWidths = juicerParser.getAPACornerRegionDimensionOptions(); if (possibleRegionWidths != null) { List widths = new ArrayList<>(); for (String res : possibleRegionWidths) { widths.add(Integer.parseInt(res)); } regionWidths = Ints.toArray(widths); } List possibleResolutions = juicerParser.getMultipleResolutionOptions(); if (possibleResolutions != null) { List intResolutions = new ArrayList<>(); for (String res : possibleResolutions) { intResolutions.add(Integer.parseInt(res)); } resolutions = Ints.toArray(intResolutions); } updateNumberOfCPUThreads(juicerParser, 1); } @Override public void run() { runWithReturn(); } public APARegionStatistics runWithReturn() { APARegionStatistics result = null; //Calculate parameters that will need later int L = 2 * window + 1; for (final int resolution : HiCFileTools.filterResolutions(ds.getBpZooms(), resolutions)) { AtomicInteger[] gwPeakNumbers = {new AtomicInteger(0), new AtomicInteger(0), new AtomicInteger(0)}; //Arrays.fill(gwPeakNumbers, 0); // determine the region width corresponding to the resolution int currentRegionWidth = resolution == 5000 ? 3 : 6; try { if (regionWidths != null && regionWidths.length > 0) { for (int i = 0; i < resolutions.length; i++) { if (resolutions[i] == resolution) { currentRegionWidth = regionWidths[i]; } } } } catch (Exception e) { currentRegionWidth = resolution == 5000 ? 3 : 6; } final int finalCurrentRegionWidth = currentRegionWidth; System.out.println("Processing APA for resolution " + resolution); HiCZoom zoom = new HiCZoom(HiC.Unit.BP, resolution); ChromosomeHandler handler = ds.getChromosomeHandler(); if (givenChromosomes != null) handler = HiCFileTools.stringToChromosomes(givenChromosomes, handler); // Metrics resulting from apa filtering final Map filterMetrics = new HashMap<>(); //looplist is empty here why?? Feature2DList loopList = Feature2DParser.loadFeatures(loopListPath, handler, false, new FeatureFilter() { // Remove duplicates and filters by size // also save internal metrics for these measures @Override public List filter(String chr, List features) { List uniqueFeatures = new ArrayList<>(new HashSet<>(features)); List filteredUniqueFeatures = APAUtils.filterFeaturesBySize(uniqueFeatures, minPeakDist, maxPeakDist, resolution); filterMetrics.put(chr, new Integer[]{filteredUniqueFeatures.size(), uniqueFeatures.size(), features.size()}); return filteredUniqueFeatures; } }, false); if (loopList.getNumTotalFeatures() > 0) { double maxProgressStatus = handler.size(); final AtomicInteger currentProgressStatus = new AtomicInteger(0); Map chromosomePairs = new ConcurrentHashMap<>(); int pairCounter = 1; for (Chromosome chr1 : handler.getChromosomeArrayWithoutAllByAll()) { for (Chromosome chr2 : handler.getChromosomeArrayWithoutAllByAll()) { Chromosome[] chromosomePair = {chr1,chr2}; chromosomePairs.put(pairCounter, chromosomePair); pairCounter++; } } final int chromosomePairCounter = pairCounter; final AtomicInteger chromosomePair = new AtomicInteger(1); ExecutorService executor = Executors.newFixedThreadPool(numCPUThreads); APADataStack.initializeDataSaveFolder(outputDirectory,"" + resolution); for (int l = 0; l < numCPUThreads; l++) { Runnable worker = new Runnable() { @Override public void run() { int threadPair = chromosomePair.getAndIncrement(); while (threadPair < chromosomePairCounter) { Chromosome chr1 = chromosomePairs.get(threadPair)[0]; Chromosome chr2 = chromosomePairs.get(threadPair)[1]; if ((chr2.getIndex() > chr1.getIndex() && includeInterChr) || (chr2.getIndex() == chr1.getIndex())) { APADataStack apaDataStack = new APADataStack(L, outputDirectory, "" + resolution); MatrixZoomData zd; synchronized (key) { zd = HiCFileTools.getMatrixZoomData(ds, chr1, chr2, zoom); } if (zd == null) { threadPair = chromosomePair.getAndIncrement(); continue; } if (HiCGlobals.printVerboseComments) { System.out.println("CHR " + chr1.getName() + " " + chr1.getIndex() + " CHR " + chr2.getName() + " " + chr2.getIndex()); } List loops = loopList.get(chr1.getIndex(), chr2.getIndex()); if (loops == null || loops.size() == 0) { if (HiCGlobals.printVerboseComments) { System.out.println("CHR " + chr1.getName() + " CHR " + chr2.getName() + " - no loops, check loop filtering constraints"); } threadPair = chromosomePair.getAndIncrement(); continue; } Integer[] peakNumbers = filterMetrics.get(Feature2DList.getKey(chr1, chr2)); if (loops.size() != peakNumbers[0]) System.err.println("Error reading statistics from " + chr1 + chr2); for (int i = 0; i < peakNumbers.length; i++) { gwPeakNumbers[i].addAndGet(peakNumbers[i]); } for (Feature2D loop : loops) { try { RealMatrix newData; synchronized (key) { newData = APAUtils.extractLocalizedData(zd, loop, L, resolution, window, norm); } apaDataStack.addData(newData); //apaDataStack.addData(APAUtils.extractLocalizedData(zd, loop, L, resolution, window, norm)); } catch (Exception e) { System.err.println(e.getMessage()); System.err.println("Unable to find data for loop: " + loop); } } apaDataStack.updateGenomeWideData(); if (saveAllData) { apaDataStack.exportDataSet(chr1.getName() + 'v' + chr2.getName(), peakNumbers, finalCurrentRegionWidth, saveAllData, dontIncludePlots); } if (chr2.getIndex() == chr1.getIndex()) { System.out.print(((int) Math.floor((100.0 * currentProgressStatus.incrementAndGet()) / maxProgressStatus)) + "% "); } } threadPair = chromosomePair.getAndIncrement(); } } }; executor.execute(worker); } executor.shutdown(); // Wait until all threads finish while (!executor.isTerminated()) { } System.out.println("Exporting APA results..."); //save data as int array result= APADataStack.retrieveDataStatistics(currentRegionWidth); //should retrieve data Integer[] gwPeakNumbersArray = {gwPeakNumbers[0].get(),gwPeakNumbers[1].get(),gwPeakNumbers[2].get()}; APADataStack.exportGenomeWideData(gwPeakNumbersArray, currentRegionWidth, saveAllData, dontIncludePlots); APADataStack.clearAllData(); } else { System.err.println("Loop list is empty or incorrect path provided."); System.exit(3); } } System.out.println("APA complete"); return result; //if no data return null } } ================================================ FILE: src/juicebox/tools/clt/juicer/Arrowhead.java ================================================ /* * The MIT License (MIT) * * Copyright (c) 2011-2021 Broad Institute, Aiden Lab, Rice University, Baylor College of Medicine * * Permission is hereby granted, free of charge, to any person obtaining a copy * of this software and associated documentation files (the "Software"), to deal * in the Software without restriction, including without limitation the rights * to use, copy, modify, merge, publish, distribute, sublicense, and/or sell * copies of the Software, and to permit persons to whom the Software is * furnished to do so, subject to the following conditions: * * The above copyright notice and this permission notice shall be included in * all copies or substantial portions of the Software. * * THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR * IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, * FITNESS FOR A PARTICULAR PURPOSE AND NON-INFRINGEMENT. IN NO EVENT SHALL THE * AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER * LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, * OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN * THE SOFTWARE. */ package juicebox.tools.clt.juicer; import juicebox.HiC; import juicebox.HiCGlobals; import juicebox.data.*; import juicebox.data.basics.Chromosome; import juicebox.tools.clt.CommandLineParserForJuicer; import juicebox.tools.clt.JuicerCLT; import juicebox.tools.utils.juicer.arrowhead.ArrowheadScoreList; import juicebox.tools.utils.juicer.arrowhead.BlockBuster; import juicebox.tools.utils.juicer.hiccups.HiCCUPSUtils; import juicebox.track.feature.Feature2DList; import juicebox.track.feature.Feature2DParser; import juicebox.windowui.HiCZoom; import juicebox.windowui.NormalizationHandler; import juicebox.windowui.NormalizationType; import java.io.File; import java.util.Arrays; import java.util.List; import java.util.concurrent.ExecutorService; import java.util.concurrent.Executors; import java.util.concurrent.atomic.AtomicInteger; /** * Arrowhead *

* Developed by Miriam Huntley and Neva Durand * Implemented by Muhammad Shamim *

* ------- * Arrowhead * ------- *

* arrowhead [-c chromosome(s)] [-m matrix size] * [feature_list] [control_list] * * * The required arguments are: *

* One of the normalizations must be selected (case sensitive). Generally, KR (Knight-Ruiz) * balancing should be used. *

* : Address of HiC File(s) which should end with .hic. This is the file you will * load into Juicebox. URLs or local addresses may be used. To sum multiple HiC Files together, * use the '+' symbol between the addresses (no whitespace between addresses). *

* : Final list of all contact domains found by Arrowhead. Can be visualized directly in Juicebox * as a 2D annotation. *

* : Integer resolution for which Arrowhead will be run. Generally, 5kB (5000) or 10kB (10000) * resolution is used depending on the depth of sequencing in the hic file(s). *

* -- NOTE -- If you want to find scores for a feature and control list, both must be provided: *

* [feature_list]: Feature list of loops/domains for which block scores are to be calculated *

* [control_list]: Control list of loops/domains for which block scores are to be calculated *

*

* The optional arguments are: *

* -m Size of the sliding window along the diagonal in which contact domains will be found. Must be an even * number as (m/2) is used as the increment for the sliding window. (Default 2000) *

* -c Chromosome(s) on which Arrowhead will be run. The number/letter for the chromosome can be used with or * without appending the "chr" string. Multiple chromosomes can be specified using commas (e.g. 1,chr2,X,chrY) *

*

* ---------------- * Arrowhead Examples * ---------------- *

* arrowhead -m 2000 KR ch12-lx-b-lymphoblasts_mapq_30.hic contact_domains_list 10000 * This command will run Arrowhead on a mouse cell line HiC map and save all contact domains to the * contact_domains_list file. These are the settings used to generate the official contact domain list on the * ch12-lx-b-lymphoblast cell line. *

* arrowhead KR GM12878_mapq_30.hic contact_domains_list 5000 * This command will run Arrowhead on the GM12878 HiC map and save all contact domains to the contact_domains_list * file. These are the settings used to generate the official GM12878 contact domain list. */ public class Arrowhead extends JuicerCLT { private static int matrixSize = 2000; private File outputDirectory; private boolean configurationsSetByUser = false; private boolean controlAndListProvided = false; private String featureList, controlList; // must be passed via command line private int resolution = 10000; private Dataset ds; public Arrowhead() { super("arrowhead [-c chromosome(s)] [-m matrix size] [-r resolution] [-k normalization (NONE/VC/VC_SQRT/KR)] " + " [feature_list] [control_list]"); HiCGlobals.useCache = false; } public static String getBasicUsage() { return "arrowhead "; } @Override protected void readJuicerArguments(String[] args, CommandLineParserForJuicer juicerParser) { if (args.length != 3 && args.length != 5) { // 3 - standard, 5 - when list/control provided printUsageAndExit(); // this will exit } ds = HiCFileTools.extractDatasetForCLT(Arrays.asList(args[1].split("\\+")), true); outputDirectory = HiCFileTools.createValidDirectory(args[2]); NormalizationType preferredNorm = juicerParser.getNormalizationTypeOption(ds.getNormalizationHandler()); if (preferredNorm != null) norm = preferredNorm; List potentialResolution = juicerParser.getMultipleResolutionOptions(); if (potentialResolution != null && potentialResolution.size() > 0) { resolution = Integer.parseInt(potentialResolution.get(0)); configurationsSetByUser = true; } if (args.length == 5) { controlAndListProvided = true; featureList = args[3]; controlList = args[4]; } int specifiedMatrixSize = juicerParser.getMatrixSizeOption(); if (specifiedMatrixSize > 1) { matrixSize = specifiedMatrixSize; } updateNumberOfCPUThreads(juicerParser, 1); List t = juicerParser.getThresholdOptions(); if (t != null && t.size() == 6) { double[] thresholds = HiCCUPSUtils.extractDoubleValues(t, 6, Double.NaN); if (thresholds.length == 6) { if (!Double.isNaN(thresholds[0])) BlockBuster.varThreshold = thresholds[0]; if (!Double.isNaN(thresholds[1])) BlockBuster.highSignThreshold = thresholds[1]; if (!Double.isNaN(thresholds[2])) BlockBuster.maxLowSignThreshold = thresholds[2]; if (!Double.isNaN(thresholds[3])) BlockBuster.minLowSignThreshold = thresholds[3]; if (!Double.isNaN(thresholds[4])) BlockBuster.decrementLowSignThreshold = thresholds[4]; if (!Double.isNaN(thresholds[5])) BlockBuster.minBlockSize = (int) thresholds[5]; } } } @Override public void run() { try { final ExpectedValueFunction df = ds.getExpectedValues(new HiCZoom(HiC.Unit.BP, 2500000), NormalizationHandler.NONE); double firstExpected = df.getExpectedValuesNoNormalization().getFirstValue(); // expected value on diagonal // From empirical testing, if the expected value on diagonal at 2.5Mb is >= 100,000 // then the map had more than 300M contacts. if (firstExpected < 100000) { System.err.println("Warning: Hi-C map may be too sparse to find many domains via Arrowhead."); } // high quality (IMR90, GM12878) maps have different settings if (!configurationsSetByUser) { matrixSize = 2000; if (firstExpected > 250000) { resolution = 5000; System.out.println("Default settings for 5kb being used"); } else { resolution = 10000; System.out.println("Default settings for 10kb being used"); } } } catch (Exception e) { System.err.println("Unable to assess map sparsity; continuing with Arrowhead"); if (!configurationsSetByUser) { matrixSize = 2000; resolution = 10000; System.out.println("Default settings for 10kb being used"); } } ChromosomeHandler chromosomeHandler = ds.getChromosomeHandler(); final Feature2DList contactDomainsGenomeWide = new Feature2DList(); final Feature2DList contactDomainListScoresGenomeWide = new Feature2DList(); final Feature2DList contactDomainControlScoresGenomeWide = new Feature2DList(); final Feature2DList inputList = new Feature2DList(); final Feature2DList inputControl = new Feature2DList(); if (controlAndListProvided) { inputList.add(Feature2DParser.loadFeatures(featureList, chromosomeHandler, true, null, false)); inputControl.add(Feature2DParser.loadFeatures(controlList, chromosomeHandler, true, null, false)); } File outputBlockFile = new File(outputDirectory, resolution + "_blocks.bedpe"); File outputListFile = null; File outputControlFile = null; if (controlAndListProvided) { outputListFile = new File(outputDirectory, resolution + "_list_scores.bedpe"); outputControlFile = new File(outputDirectory, resolution + "_control_scores.bedpe"); } // chromosome filtering must be done after input/control created // because full set of chromosomes required to parse lists if (givenChromosomes != null) chromosomeHandler = HiCFileTools.stringToChromosomes(givenChromosomes, chromosomeHandler); final HiCZoom zoom = new HiCZoom(HiC.Unit.BP, resolution); final double maxProgressStatus = determineHowManyChromosomesWillActuallyRun(ds, chromosomeHandler, zoom); if (maxProgressStatus < 1) { System.err.println("No valid chromosome matrices at given resolution"); return; } final AtomicInteger currentProgressStatus = new AtomicInteger(0); System.out.println("max " + maxProgressStatus); ExecutorService executor = Executors.newFixedThreadPool(numCPUThreads); for (final Chromosome chr : chromosomeHandler.getChromosomeArrayWithoutAllByAll()) { Runnable worker = new Runnable() { @Override public void run() { MatrixZoomData zd = HiCFileTools.getMatrixZoomData(ds, chr, chr, zoom); if (zd != null) { ArrowheadScoreList list = new ArrowheadScoreList(inputList, chr, resolution); ArrowheadScoreList control = new ArrowheadScoreList(inputControl, chr, resolution); if (HiCGlobals.printVerboseComments) { System.out.println("\nProcessing " + chr.getName()); } // actual Arrowhead algorithm BlockBuster.run(chr, resolution, matrixSize, zd, norm, list, control, contactDomainsGenomeWide, contactDomainListScoresGenomeWide, contactDomainControlScoresGenomeWide); //todo should this be inside if? But the wouldn't increment for skipped chr;s? int currProg = currentProgressStatus.incrementAndGet(); System.out.println(((int) Math.floor((100.0 * currProg) / maxProgressStatus)) + "% "); } } }; executor.execute(worker); } executor.shutdown(); // Wait until all threads finish while (!executor.isTerminated()) { } // save the data on local machine contactDomainsGenomeWide.exportFeatureList(outputBlockFile, true, Feature2DList.ListFormat.ARROWHEAD); System.out.println(contactDomainsGenomeWide.getNumTotalFeatures() + " domains written to file: " + outputBlockFile.getAbsolutePath()); if (controlAndListProvided) { contactDomainListScoresGenomeWide.exportFeatureList(outputListFile, false, Feature2DList.ListFormat.NA); contactDomainControlScoresGenomeWide.exportFeatureList(outputControlFile, false, Feature2DList.ListFormat.NA); } System.out.println("Arrowhead complete"); } } ================================================ FILE: src/juicebox/tools/clt/juicer/CompareLists.java ================================================ /* * The MIT License (MIT) * * Copyright (c) 2011-2020 Broad Institute, Aiden Lab, Rice University, Baylor College of Medicine * * Permission is hereby granted, free of charge, to any person obtaining a copy * of this software and associated documentation files (the "Software"), to deal * in the Software without restriction, including without limitation the rights * to use, copy, modify, merge, publish, distribute, sublicense, and/or sell * copies of the Software, and to permit persons to whom the Software is * furnished to do so, subject to the following conditions: * * The above copyright notice and this permission notice shall be included in * all copies or substantial portions of the Software. * * THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR * IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, * FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE * AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER * LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, * OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN * THE SOFTWARE. */ package juicebox.tools.clt.juicer; import juicebox.HiCGlobals; import juicebox.data.ChromosomeHandler; import juicebox.data.HiCFileTools; import juicebox.data.anchor.MotifAnchorTools; import juicebox.tools.clt.CommandLineParserForJuicer; import juicebox.tools.clt.JuicerCLT; import juicebox.track.feature.*; import java.awt.*; import java.io.File; /** * Created by muhammadsaadshamim on 9/14/15. */ public class CompareLists extends JuicerCLT { public final static String PARENT_ATTRIBUTE = "parent_list"; public static final Color AAA = new Color(102, 0, 153); public static final Color BBB = new Color(255, 102, 0); /** * Arbitrary colors for comparison list **/ private static final Color AB = new Color(34, 139, 34); private static final Color AA = new Color(0, 255, 150); private static final Color BB = new Color(150, 255, 0); private int threshold = 10000, compareTypeID = 0; private String genomeID, inputFileA, inputFileB, outputPath = "comparison_list.bedpe"; public CompareLists() { super("compare [-m threshold] [-c chromosome(s)] [output_path]\n" + "comparetype: 0 - overlap/intersect within distance threshold\n" + " 1 - comparison with ctcf motifs\n" + " 2 - convergence calculation for list1 with ctcf motifs"); HiCGlobals.useCache = false; } @Override protected void readJuicerArguments(String[] args, CommandLineParserForJuicer juicerParser) { if (args.length != 5 && args.length != 6) { printUsageAndExit(); } compareTypeID = Integer.parseInt(args[1]); genomeID = args[2]; inputFileA = args[3]; inputFileB = args[4]; if (args.length == 6) { outputPath = args[5]; } else { if (inputFileB.endsWith(".txt")) { outputPath = inputFileB.substring(0, inputFileB.length() - 4) + "_comparison_results.bedpe"; } else if (inputFileB.endsWith(".bedpe")) { outputPath = inputFileB.substring(0, inputFileB.length() - 6) + "_comparison_results.bedpe"; } else { outputPath = inputFileB + "_comparison_results.bedpe"; } } int specifiedMatrixSize = juicerParser.getMatrixSizeOption(); if (specifiedMatrixSize >= 0) { threshold = specifiedMatrixSize; } } @Override public void run() { ChromosomeHandler handler = HiCFileTools.loadChromosomes(genomeID); if (givenChromosomes != null) handler = HiCFileTools.stringToChromosomes(givenChromosomes, handler); Feature2DList listA = null, listB = null; if (compareTypeID == 0) { listA = Feature2DParser.loadFeatures(inputFileA, handler, false, null, false); listB = Feature2DParser.loadFeatures(inputFileB, handler, false, null, false); } else if (compareTypeID == 1 || compareTypeID == 2) { Feature2DWithMotif.useSimpleOutput = true; listA = Feature2DParser.loadFeatures(inputFileA, handler, true, null, true); listB = Feature2DParser.loadFeatures(inputFileB, handler, true, null, true); } if (compareTypeID == 2) { generateHistogramMetrics(listB); } else { compareTwoLists(listA, listB, compareTypeID); } } private void generateHistogramMetrics(Feature2DList list) { final int[] metrics = MotifAnchorTools.calculateConvergenceHistogram(list); System.out.println("++ : " + metrics[0] + " +- : " + metrics[1] + " -+ : " + metrics[2] + " -- : " + metrics[3] + " not unique : " + metrics[4] + " not complete : " + metrics[5]); } private void compareTwoLists(Feature2DList listA, Feature2DList listB, int compareTypeID) { int sizeA = listA.getNumTotalFeatures(); int sizeB = listB.getNumTotalFeatures(); System.out.println("List Size: " + sizeA + "(A) " + sizeB + "(B)"); if (compareTypeID == 0) { Feature2D.tolerance = 0; } else if (compareTypeID == 1) { Feature2D.tolerance = threshold; } Feature2DWithMotif.lenientEqualityEnabled = false; Feature2DList exactMatches = Feature2DList.getIntersection(listA, listB); int numExactMatches = exactMatches.getNumTotalFeatures(); System.out.println("Number of exact matches: " + numExactMatches); Feature2D.tolerance = this.threshold; Feature2DWithMotif.lenientEqualityEnabled = true; //Feature2DList matchesWithinToleranceFromA = Feature2DList.getIntersection(listA, listB); //Feature2DList matchesWithinToleranceFromB = Feature2DList.getIntersection(listB, listA); if (compareTypeID == 0 || compareTypeID == 1) { Feature2D.tolerance = threshold; } Feature2DWithMotif.lenientEqualityEnabled = false; Feature2DList matchesWithinToleranceUniqueToA = Feature2DTools.subtract(listA, exactMatches); matchesWithinToleranceUniqueToA = Feature2DList.getIntersection(matchesWithinToleranceUniqueToA, listB); Feature2DList matchesWithinToleranceUniqueToB = Feature2DTools.subtract(listB, exactMatches); matchesWithinToleranceUniqueToB = Feature2DList.getIntersection(matchesWithinToleranceUniqueToB, listA); int numMatchesWithinTolA = matchesWithinToleranceUniqueToA.getNumTotalFeatures(); int numMatchesWithinTolB = matchesWithinToleranceUniqueToB.getNumTotalFeatures(); System.out.println("Number of matches within tolerance: " + numMatchesWithinTolA + "(A) " + numMatchesWithinTolB + "(B)"); Feature2DList uniqueToA = Feature2DTools.subtract(listA, exactMatches); uniqueToA = Feature2DTools.subtract(uniqueToA, matchesWithinToleranceUniqueToA); uniqueToA = Feature2DTools.subtract(uniqueToA, listB); Feature2DList uniqueToB = Feature2DTools.subtract(listB, exactMatches); uniqueToB = Feature2DTools.subtract(uniqueToB, matchesWithinToleranceUniqueToB); uniqueToB = Feature2DTools.subtract(uniqueToB, listA); int numUniqueToA = uniqueToA.getNumTotalFeatures(); int numUniqueToB = uniqueToB.getNumTotalFeatures(); System.out.println("Number of unique features: " + numUniqueToA + "(A) " + numUniqueToB + "(B)"); // set parent attribute exactMatches.addAttributeFieldToAll(PARENT_ATTRIBUTE, "Common"); matchesWithinToleranceUniqueToA.addAttributeFieldToAll(PARENT_ATTRIBUTE, "A"); matchesWithinToleranceUniqueToB.addAttributeFieldToAll(PARENT_ATTRIBUTE, "B"); uniqueToA.addAttributeFieldToAll(PARENT_ATTRIBUTE, "A*"); uniqueToB.addAttributeFieldToAll(PARENT_ATTRIBUTE, "B*"); // set colors exactMatches.setColor(AB); matchesWithinToleranceUniqueToA.setColor(AA); matchesWithinToleranceUniqueToB.setColor(BB); uniqueToA.setColor(AAA); uniqueToB.setColor(BBB); Feature2DList finalResults = new Feature2DList(exactMatches); finalResults.add(matchesWithinToleranceUniqueToA); finalResults.add(matchesWithinToleranceUniqueToB); finalResults.add(uniqueToA); finalResults.add(uniqueToB); uniqueToA.exportFeatureList(new File(outputPath + "_AAA.bedpe"), false, Feature2DList.ListFormat.NA); uniqueToB.exportFeatureList(new File(outputPath + "_BBB.bedpe"), false, Feature2DList.ListFormat.NA); finalResults.exportFeatureList(new File(outputPath), false, Feature2DList.ListFormat.NA); int percentMatch = (int) Math.round(100 * ((double) (sizeB - numUniqueToB)) / ((double) sizeB)); if (percentMatch > 95) { System.out.println("Test passed"); } else { System.out.println("Test failed - " + percentMatch + "% match with reference list"); } } } ================================================ FILE: src/juicebox/tools/clt/juicer/HiCCUPS.java ================================================ /* * The MIT License (MIT) * * Copyright (c) 2011-2021 Broad Institute, Aiden Lab, Rice University, Baylor College of Medicine * * Permission is hereby granted, free of charge, to any person obtaining a copy * of this software and associated documentation files (the "Software"), to deal * in the Software without restriction, including without limitation the rights * to use, copy, modify, merge, publish, distribute, sublicense, and/or sell * copies of the Software, and to permit persons to whom the Software is * furnished to do so, subject to the following conditions: * * The above copyright notice and this permission notice shall be included in * all copies or substantial portions of the Software. * * THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR * IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, * FITNESS FOR A PARTICULAR PURPOSE AND NON-INFRINGEMENT. IN NO EVENT SHALL THE * AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER * LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, * OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN * THE SOFTWARE. */ package juicebox.tools.clt.juicer; import com.google.common.primitives.Doubles; import com.google.common.primitives.Floats; import juicebox.HiC; import juicebox.HiCGlobals; import juicebox.data.ChromosomeHandler; import juicebox.data.Dataset; import juicebox.data.ExpectedValueFunction; import juicebox.data.HiCFileTools; import juicebox.data.basics.Chromosome; import juicebox.mapcolorui.Feature2DHandler; import juicebox.tools.clt.CommandLineParserForJuicer; import juicebox.tools.clt.JuicerCLT; import juicebox.tools.utils.common.ArrayTools; import juicebox.tools.utils.juicer.hiccups.*; import juicebox.track.feature.Feature2D; import juicebox.track.feature.Feature2DList; import juicebox.track.feature.Feature2DTools; import juicebox.windowui.HiCZoom; import juicebox.windowui.NormalizationHandler; import juicebox.windowui.NormalizationType; import java.awt.*; import java.io.File; import java.io.IOException; import java.io.PrintWriter; import java.math.RoundingMode; import java.text.DecimalFormat; import java.util.Arrays; import java.util.HashMap; import java.util.List; import java.util.Map; import java.util.concurrent.ExecutorService; import java.util.concurrent.Executors; import java.util.concurrent.atomic.AtomicInteger; /** * HiC Computational Unbiased Peak Search *

* Developed by Suhas Rao * Implemented by Muhammad Shamim *

* ------- * HiCCUPS * ------- *

* hiccups [-m matrixSize] [-c chromosome(s)] [-r resolution(s)] [-f fdr] [-p peak width] [-w window] * [-t thresholds] [-d centroid distances] *

* hiccups [-m matrixSize] [-c chromosome(s)] [-r resolution(s)] [-f fdr] [-p peak width] [-i window] * *

* The required arguments are: *

* : Address of HiC File(s) which should end with .hic. This is the file you will * load into Juicebox. URLs or local addresses may be used. To sum multiple HiC Files together, * use the '+' symbol between the addresses (no whitespace between addresses). *

* : Final list of all loops found by HiCCUPS. Can be visualized directly in Juicebox as a 2D annotation. * By default, various values critical to the HICCUPS algorithm are saved as attributes for each loop found. These can be * disabled using the suppress flag below. *

* -- OR -- If you do not want to run post processing and simply want the enriched pixels *

* : thresholds used in the HiCCUPS algorithm for the Bottom Left, Donut, Horizontal, and Vertical masks *

* : Final list of all enriched pixels found by HiCCUPS. Can be visualized directly in Juicebox as * 2D annotations. *

*

* The optional arguments are: *

* -m Maximum size of the submatrix within the chromosome passed on to GPU (Must be an even number greater than 40 * to prevent issues from running the CUDA kernel). The upper limit will depend on your GPU. Dedicated GPUs * should be able to use values such as 500, 1000, or 2048 without trouble. Integrated GPUs are unlikely to run * sizes larger than 90 or 100. Matrix size will not effect the result, merely the time it takes for hiccups. * Larger values (with a dedicated GPU) will run fastest. *

* -c Chromosome(s) on which HiCCUPS will be run. The number/letter for the chromosome can be used with or * without appending the "chr" string. Multiple chromosomes can be specified using commas (e.g. 1,chr2,X,chrY) *

* -r Resolution(s) for which HiCCUPS will be run. Multiple resolutions can be specified using commas * (e.g. 25000,10000,5000). Due ot the nature of DNA looping, it is unlikely that loops will be found at * lower resolutions (i.e. 50kB or 100kB) * IMPORTANT: if multiple resolutions are used, the flags below can be configured so that different parameters are * used for the different resolutions. *

* -f FDR values actually corresponding to max_q_val (i.e. for 1% FDR use 0.01, for 10%FDR use 0.1). Different * FDR values can be used for each resolution using commas. (e.g "-r 5000,10000 -f 0.1,0.15" would run HiCCUPS at * 10% FDR for resolution 5000 and 15% FDR for resolution 10000) *

* -p Peak width used for finding enriched pixels in HiCCUPS. Different peak widths can be used for each * resolution using commas. (e.g "-r 5000,10000 -p 4,2" would run at peak width 4 for resolution 5000 and * peak width 2 for resolution 10000) *

* -w Window width used for finding enriched pixels in HiCCUPS. Different window widths can be used for each * resolution using commas. (e.g "-r 5000,10000 -p 10,6" would run at window width 10 for resolution 5000 and * window width 6 for resolution 10000) *

* -t Thresholds for merging loop lists of different resolutions. Four values must be given, separated by * commas (e.g. 0.02,1.5,1.75,2). These thresholds (in order) represent: * > threshold allowed for sum of FDR values of horizontal, vertical donut mask, and bottom left regions * (an accepted loop must stay below this threshold) * > threshold ratio of observed value to expected horizontal/vertical value * (an accepted loop must exceed this threshold) * > threshold ratio of observed value to expected donut mask value * (an accepted loop must exceed this threshold) * > threshold ratio of observed value to expected bottom left value * (an accepted loop must exceed this threshold) *

* -d Distances used for merging centroids across different resolutions. Three values must be given, separated by * commas (e.g. 20000,20000,50000). These thresholds (in order) represent: * > distance (radius) around centroid used for merging at 5kB resolution (if present) * > distance (radius) around centroid used for merging at 10kB resolution (if present) * > distance (radius) around centroid used for merging at 25kB resolution (if present) * If a resolution (5kB, 10kB, or 25kB) is not available, that centroid distance will be ignored during the merger * step (but a distance value should still be passed as a parameter for that resolution e.g. 0) *

* ---------------- * HiCCUPS Examples * ---------------- *

* hiccups HIC006.hic all_hiccups_loops * > This command will run HiCCUPS on HIC006 and save all found loops to the all_hiccups_loops files *

* hiccups -m 500 -r 5000,10000 -f 0.1,0.1 -p 4,2 -w 7,5 -d 20000,20000,0 -c 22 HIC006.hic all_hiccups_loops * > This command will run HiCCUPS on chromosome 22 of HIC006 at 5kB and 10kB resolution using the following values: * >> 5kB: fdr 10%, peak width 4, window width 7, and centroid distance 20kB * >> 10kB: fdr 10%, peak width 2, window width 5, and centroid distance 20kB * > The resulting loop list will be merged and saved as all_hiccups_loops * > Note that these are values used for generating the GM12878 loop list */ public class HiCCUPS extends JuicerCLT { public static final int regionMargin = 20; public static final int krNeighborhood = 5; public static final Color defaultPeakColor = Color.cyan; public static final boolean shouldColorBeScaledByFDR = false; public static final String CPU_VERSION_WARNING = "WARNING - You are using the CPU version of HiCCUPS.\n" + "The GPU version of HiCCUPS is the official version and has been tested extensively.\n" + "The CPU version only searches for loops within 8MB (by default) of the diagonal and is still experimental."; private static final int totalMargin = 2 * regionMargin; public static final int w1 = 40; // TODO dimension should be variably set private static final int w2 = 10000; // TODO dimension should be variably set private static final boolean dataShouldBePostProcessed = true; public static double fdrsum = 0.02; public static double oeThreshold1 = 1.5; public static double oeThreshold2 = 1.75; public static double oeThreshold3 = 2; public static double oeThreshold4 = 0; private static int matrixSize = 512;// 540 original private static int regionWidth = matrixSize - totalMargin; private boolean configurationsSetByUser = false; private String featureListPath; private boolean listGiven = false; private ChromosomeHandler directlyInitializedChromosomeHandler = null; /* * Reasonable Commands * * fdr = 0.10 for all resolutions * peak width = 1 for 25kb, 2 for 10kb, 4 for 5kb * window = 3 for 25kb, 5 for 10kb, 7 for 5kb * * cluster radius is 20kb for 5kb and 10kb res and 50kb for 25kb res * fdrsumthreshold is 0.02 for all resolutions * oeThreshold1 = 1.5 for all res * oeThreshold2 = 1.75 for all res * oeThreshold3 = 2 for all res * * published GM12878 looplist was only generated with 5kb and 10kb resolutions * same with published IMR90 looplist * published CH12 looplist only generated with 10kb */ private File outputDirectory; private List configurations; private Dataset ds; private boolean useCPUVersionHiCCUPS = false, restrictSearchRegions = false; public HiCCUPS() { super("hiccups [-m matrixSize] [-k normalization (NONE/VC/VC_SQRT/KR)] " + "[-c chromosome(s)] [-r resolution(s)] [--restrict] " + "[-f fdr] [-p peak width] [-i window] [-t thresholds] [-d centroid distances] " + " [specified_loop_list]"); Feature2D.allowHiCCUPSOrdering = true; } public static String getBasicUsage() { return "hiccups "; } @Override protected void readJuicerArguments(String[] args, CommandLineParserForJuicer juicerParser) { if (args.length != 3 && args.length != 4) { printUsageAndExit(); } // TODO: add code here to check for CUDA/GPU installation. The below is not ideal. ds = HiCFileTools.extractDatasetForCLT(Arrays.asList(args[1].split("\\+")), true); outputDirectory = HiCFileTools.createValidDirectory(args[2]); if (args.length == 4) { listGiven = true; featureListPath = args[3]; } NormalizationType preferredNorm = juicerParser.getNormalizationTypeOption(ds.getNormalizationHandler()); if (preferredNorm != null) norm = preferredNorm; determineValidMatrixSize(juicerParser); determineValidConfigurations(juicerParser, ds.getBpZooms()); if (juicerParser.restrictSearchRegionsOptions()) { restrictSearchRegions = true; System.out.println("WARNING - You are restricting the regions the HiCCUPS will explore."); } if (juicerParser.getCPUVersionOfHiCCUPSOptions()) { useCPUVersionHiCCUPS = true; restrictSearchRegions = true; System.out.println(CPU_VERSION_WARNING); } updateNumberOfCPUThreads(juicerParser, 1); } /** * Used by hiccups diff to set the properties of hiccups directly without resorting to command line usage * * @param dataset * @param outputDirectoryPath * @param featureListPath * @param preferredNorm * @param matrixSize * @param providedCommonChromosomeHandler * @param configurations * @param thresholds */ public void initializeDirectly(Dataset dataset, String outputDirectoryPath, String featureListPath, NormalizationType preferredNorm, int matrixSize, ChromosomeHandler providedCommonChromosomeHandler, List configurations, double[] thresholds, boolean usingCPUVersion, boolean restrictSearchRegions) { this.ds = dataset; outputDirectory = HiCFileTools.createValidDirectory(outputDirectoryPath); if (featureListPath != null) { listGiven = true; this.featureListPath = featureListPath; } directlyInitializedChromosomeHandler = providedCommonChromosomeHandler; if (preferredNorm != null) norm = preferredNorm; // will just confirm matrix size is large enough determineValidMatrixSize(matrixSize); // configurations should have been passed in if (configurations != null && configurations.size() > 0) { configurationsSetByUser = true; this.configurations = configurations; } // fdr & oe thresholds directly sent in if (thresholds != null) setHiCCUPSFDROEThresholds(thresholds); this.restrictSearchRegions = restrictSearchRegions; if (usingCPUVersion) { useCPUVersionHiCCUPS = true; this.restrictSearchRegions = true; } } @Override public void run() { try { final ExpectedValueFunction df = ds.getExpectedValues(new HiCZoom(HiC.Unit.BP, 2500000), NormalizationHandler.NONE); double firstExpected = df.getExpectedValuesNoNormalization().getFirstValue(); // expected value on diagonal // From empirical testing, if the expected value on diagonal at 2.5Mb is >= 100,000 // then the map had more than 300M contacts. if (firstExpected < 100000) { System.err.println("Warning Hi-C map may be too sparse to find many loops via HiCCUPS."); } } catch (Exception e) { System.err.println("Unable to assess map sparsity; continuing with HiCCUPS"); } if (!configurationsSetByUser) { configurations = HiCCUPSConfiguration.getDefaultSetOfConfigsForUsers(); } ChromosomeHandler commonChromosomesHandler = ds.getChromosomeHandler(); if (directlyInitializedChromosomeHandler != null && directlyInitializedChromosomeHandler.size() > 0) { commonChromosomesHandler = directlyInitializedChromosomeHandler; } else if (givenChromosomes != null && givenChromosomes.size() > 0) { commonChromosomesHandler = HiCFileTools.stringToChromosomes(givenChromosomes, commonChromosomesHandler); } Map loopLists = new HashMap<>(); Map givenLoopLists = new HashMap<>(); File outputMergedFile = new File(outputDirectory, HiCCUPSUtils.getMergedLoopsFileName()); File outputMergedGivenFile = new File(outputDirectory, HiCCUPSUtils.getMergedRequestedLoopsFileName()); Feature2DHandler inputListFeature2DHandler = new Feature2DHandler(); if (listGiven) { inputListFeature2DHandler.setLoopList(featureListPath, commonChromosomesHandler); } for (HiCCUPSConfiguration conf : configurations) { System.out.println("Running HiCCUPS for resolution " + conf.getResolution()); Feature2DList enrichedPixels = runHiccupsProcessing(ds, conf, commonChromosomesHandler, inputListFeature2DHandler, givenLoopLists); if (enrichedPixels != null) { loopLists.put(conf.getResolution(), enrichedPixels); } } if (dataShouldBePostProcessed) { HiCCUPSUtils.postProcess(loopLists, ds, commonChromosomesHandler, configurations, norm, outputDirectory, false, outputMergedFile, 1); if (listGiven) { HiCCUPSUtils.postProcess(givenLoopLists, ds, commonChromosomesHandler, configurations, norm, outputDirectory, true, outputMergedGivenFile, 1); } } System.out.println("HiCCUPS complete"); // else the thresholds and raw pixels were already saved when hiccups was run } /** * Actual run of the HiCCUPS algorithm * * @param ds dataset from hic file * @param conf configuration of hiccups inputs * @param chromosomeHandler list of chromosomes to run hiccups on * @param givenLoopLists * @return list of enriched pixels */ private Feature2DList runHiccupsProcessing(Dataset ds, final HiCCUPSConfiguration conf, ChromosomeHandler chromosomeHandler, final Feature2DHandler inputListFeature2DHandler, Map givenLoopLists) { long begin_time = System.currentTimeMillis(); HiCZoom zoom = ds.getZoomForBPResolution(conf.getResolution()); if (zoom == null) { System.err.println("Data not available at " + conf.getResolution() + " resolution"); return null; } // open the print writer early so the file I/O capability is verified before running hiccups PrintWriter outputFDR = HiCFileTools.openWriter( new File(outputDirectory, HiCCUPSUtils.getFDRThresholdsFilename(conf.getResolution()))); final long[][] histBL = new long[w1][w2]; final long[][] histDonut = new long[w1][w2]; final long[][] histH = new long[w1][w2]; final long[][] histV = new long[w1][w2]; final float[][] fdrLogBL = new float[w1][w2]; final float[][] fdrLogDonut = new float[w1][w2]; final float[][] fdrLogH = new float[w1][w2]; final float[][] fdrLogV = new float[w1][w2]; final float[] thresholdBL = ArrayTools.newValueInitializedFloatArray(w1, (float) w2); final float[] thresholdDonut = ArrayTools.newValueInitializedFloatArray(w1, (float) w2); final float[] thresholdH = ArrayTools.newValueInitializedFloatArray(w1, (float) w2); final float[] thresholdV = ArrayTools.newValueInitializedFloatArray(w1, (float) w2); // to hold all enriched pixels found in second run final Feature2DList globalList = new Feature2DList(); final Feature2DList requestedList = new Feature2DList(); // two runs, 1st to build histograms, 2nd to identify loops final HiCCUPSRegionHandler regionHandler = new HiCCUPSRegionHandler(ds, chromosomeHandler, zoom, norm, conf, regionWidth, regionMargin, restrictSearchRegions); for (final int runNum : new int[]{0, 1}) { final AtomicInteger currentProgressStatus = new AtomicInteger(0); final AtomicInteger indexOfHiCCUPSRegion = new AtomicInteger(0); ExecutorService executor = Executors.newFixedThreadPool(numCPUThreads); for (int l = 0; l < numCPUThreads; l++) { Runnable worker = new Runnable() { @Override public void run() { runCoreCodeForHiCCUPS(conf, indexOfHiCCUPSRegion, currentProgressStatus, regionHandler, matrixSize, thresholdBL, thresholdDonut, thresholdH, thresholdV, norm, zoom, histBL, histDonut, histH, histV, runNum, fdrLogBL, fdrLogDonut, fdrLogH, fdrLogV, inputListFeature2DHandler, requestedList, globalList); } }; executor.execute(worker); } executor.shutdown(); // Wait until all threads finish while (!executor.isTerminated()) { } if (runNum == 0) { long thresh_time0 = System.currentTimeMillis(); long[][] rcsHistBL = ArrayTools.makeReverse2DCumulativeArray(histBL); long[][] rcsHistDonut = ArrayTools.makeReverse2DCumulativeArray(histDonut); long[][] rcsHistH = ArrayTools.makeReverse2DCumulativeArray(histH); long[][] rcsHistV = ArrayTools.makeReverse2DCumulativeArray(histV); for (int i = 0; i < w1; i++) { float[] unitPoissonPMF = Floats.toArray(Doubles.asList(ArrayTools.generatePoissonPMF(i, w2))); HiCCUPSUtils.calculateThresholdAndFDR(i, w2, conf.getFDRThreshold(), unitPoissonPMF, rcsHistBL, thresholdBL, fdrLogBL); HiCCUPSUtils.calculateThresholdAndFDR(i, w2, conf.getFDRThreshold(), unitPoissonPMF, rcsHistDonut, thresholdDonut, fdrLogDonut); HiCCUPSUtils.calculateThresholdAndFDR(i, w2, conf.getFDRThreshold(), unitPoissonPMF, rcsHistH, thresholdH, fdrLogH); HiCCUPSUtils.calculateThresholdAndFDR(i, w2, conf.getFDRThreshold(), unitPoissonPMF, rcsHistV, thresholdV, fdrLogV); } if (HiCGlobals.printVerboseComments) { long thresh_time1 = System.currentTimeMillis(); System.out.println("Time to calculate thresholds: " + (thresh_time1 - thresh_time0) + "ms"); } } } globalList.exportFeatureList(new File(outputDirectory, HiCCUPSUtils.getEnrichedPixelFileName(conf.getResolution())), true, Feature2DList.ListFormat.ENRICHED); if (listGiven) { requestedList.exportFeatureList(new File(outputDirectory, HiCCUPSUtils.getRequestedLoopsFileName(conf.getResolution())), true, Feature2DList.ListFormat.ENRICHED); givenLoopLists.put(conf.getResolution(), requestedList); } for (int i = 0; i < w1; i++) { outputFDR.println(i + "\t" + thresholdBL[i] + "\t" + thresholdDonut[i] + "\t" + thresholdH[i] + "\t" + thresholdV[i]); } outputFDR.close(); if (HiCGlobals.printVerboseComments) { long final_time = System.currentTimeMillis(); System.out.println("Total time: " + (final_time - begin_time)); } return globalList; } private void runCoreCodeForHiCCUPS(HiCCUPSConfiguration conf, AtomicInteger indexOfHiCCUPSRegion, AtomicInteger currentProgressStatus, HiCCUPSRegionHandler regionHandler, int matrixSize, float[] thresholdBL, float[] thresholdDonut, float[] thresholdH, float[] thresholdV, NormalizationType norm, HiCZoom zoom, long[][] histBL, long[][] histDonut, long[][] histH, long[][] histV, int runNum, float[][] fdrLogBL, float[][] fdrLogDonut, float[][] fdrLogH, float[][] fdrLogV, Feature2DHandler inputListFeature2DHandler, Feature2DList requestedList, Feature2DList globalList) { int indexOfRegionForThread = indexOfHiCCUPSRegion.getAndIncrement(); GPUController gpuController = buildGPUController(conf); while (indexOfRegionForThread < regionHandler.getSize()) { HiCCUPSRegionContainer regionContainer = regionHandler.getRegionFromIndex(indexOfRegionForThread); try { if (HiCGlobals.printVerboseComments) { System.out.println(); System.out.println("GPU Run Details"); System.out.println("Row bounds " + Arrays.toString(regionContainer.getRowBounds())); System.out.println("Col bounds " + Arrays.toString(regionContainer.getColumnBounds())); } int[] rowBounds = regionContainer.getRowBounds(); int[] columnBounds = regionContainer.getColumnBounds(); GPUOutputContainer gpuOutputs = gpuController.process(regionHandler, regionContainer, matrixSize, thresholdBL, thresholdDonut, thresholdH, thresholdV, norm, zoom); int diagonalCorrection = (rowBounds[4] - columnBounds[4]) + conf.getPeakWidth() + 2; if (runNum == 0) { gpuOutputs.cleanUpBinNans(); gpuOutputs.cleanUpBinDiagonal(diagonalCorrection); gpuOutputs.updateHistograms(histBL, histDonut, histH, histV, w1, w2); } else if (runNum == 1) { gpuOutputs.cleanUpPeakNaNs(); gpuOutputs.cleanUpPeakDiagonal(diagonalCorrection); Chromosome chromosome = regionContainer.getChromosome(); Feature2DList peaksList = gpuOutputs.extractPeaks(chromosome.getIndex(), chromosome.getName(), w1, w2, rowBounds[4], columnBounds[4], conf.getResolution()); Feature2DTools.calculateFDR(peaksList, fdrLogBL, fdrLogDonut, fdrLogH, fdrLogV); globalList.add(peaksList); if (listGiven) { float rowBound1GenomeCoords = ((float) rowBounds[4]) * conf.getResolution(); float columnBound1GenomeCoords = ((float) columnBounds[4]) * conf.getResolution(); float rowBound2GenomeCoords = ((float) rowBounds[5] - 1) * conf.getResolution(); float columnBound2GenomeCoords = ((float) columnBounds[5] - 1) * conf.getResolution(); // System.out.println(chromosome.getIndex() + "\t" + rowBound1GenomeCoords + "\t" + rowBound2GenomeCoords + "\t" + columnBound1GenomeCoords + "\t" + columnBound2GenomeCoords); net.sf.jsi.Rectangle currentWindow = new net.sf.jsi.Rectangle(rowBound1GenomeCoords, columnBound1GenomeCoords, rowBound2GenomeCoords, columnBound2GenomeCoords); List inputListFoundFeatures = inputListFeature2DHandler.getContainedFeatures(chromosome.getIndex(), chromosome.getIndex(), currentWindow); Feature2DList peaksRequestedList = gpuOutputs.extractPeaksListGiven(chromosome.getIndex(), chromosome.getName(), w1, w2, rowBounds[4], columnBounds[4], conf.getResolution(), inputListFoundFeatures); Feature2DTools.calculateFDR(peaksRequestedList, fdrLogBL, fdrLogDonut, fdrLogH, fdrLogV); requestedList.add(peaksRequestedList); } } int currProg = currentProgressStatus.incrementAndGet(); int resonableDivisor = Math.max(regionHandler.getSize() / 20, 1); if (HiCGlobals.printVerboseComments || currProg % resonableDivisor == 0) { DecimalFormat df = new DecimalFormat("#.####"); df.setRoundingMode(RoundingMode.FLOOR); System.out.println(df.format(Math.floor((100.0 * currProg) / regionHandler.getSize())) + "% "); } } catch (IOException e) { System.err.println("No data in map region"); } indexOfRegionForThread = indexOfHiCCUPSRegion.getAndIncrement(); } } private GPUController buildGPUController(HiCCUPSConfiguration conf) { try { return new GPUController(conf.getWindowWidth(), matrixSize, conf.getPeakWidth(), useCPUVersionHiCCUPS); } catch (Exception e) { e.printStackTrace(); System.err.println("GPU/CUDA Installation Not Detected"); System.err.println("Exiting HiCCUPS"); System.exit(26); return null; } } /** * @param juicerParser Parser to determine configurations * @param availableZooms */ private void determineValidConfigurations(CommandLineParserForJuicer juicerParser, List availableZooms) { configurations = HiCCUPSConfiguration.extractConfigurationsFromCommandLine(juicerParser, availableZooms, 1); if (configurations == null) { System.out.println("No valid configurations specified, using default settings"); configurationsSetByUser = false; } else { configurationsSetByUser = true; } try { List t = juicerParser.getThresholdOptions(); if (t != null && t.size() == 4) { double[] thresholds = HiCCUPSUtils.extractDoubleValues(t, 4, Double.NaN); setHiCCUPSFDROEThresholds(thresholds); } else if (t != null && t.size() == 5) { double[] thresholds = HiCCUPSUtils.extractDoubleValues(t, 5, Double.NaN); setHiCCUPSFDROEThresholds(thresholds); } else if (t != null && t.size() == 6) { double[] thresholds = HiCCUPSUtils.extractDoubleValues(t, 6, Double.NaN); setHiCCUPSFDROEThresholds(thresholds); } } catch (Exception e) { // do nothing - use default postprocessing thresholds } } private void determineValidMatrixSize(CommandLineParserForJuicer juicerParser) { determineValidMatrixSize(juicerParser.getMatrixSizeOption()); } private void determineValidMatrixSize(int specifiedMatrixSize) { if (specifiedMatrixSize > 2 * regionMargin) { matrixSize = specifiedMatrixSize; regionWidth = specifiedMatrixSize - totalMargin; } if (HiCGlobals.printVerboseComments) { System.out.println("Using Matrix Size " + matrixSize); } } private void setHiCCUPSFDROEThresholds(double[] thresholds) { if (thresholds != null && thresholds.length == 4) { if (!Double.isNaN(thresholds[0]) && thresholds[0] > 0) fdrsum = thresholds[0]; if (!Double.isNaN(thresholds[1]) && thresholds[1] > 0) oeThreshold1 = thresholds[1]; if (!Double.isNaN(thresholds[2]) && thresholds[2] > 0) oeThreshold2 = thresholds[2]; if (!Double.isNaN(thresholds[3]) && thresholds[3] > 0) oeThreshold3 = thresholds[3]; } } } ================================================ FILE: src/juicebox/tools/clt/juicer/HiCCUPS2.java ================================================ /* * The MIT License (MIT) * * Copyright (c) 2011-2020 Broad Institute, Aiden Lab * * Permission is hereby granted, free of charge, to any person obtaining a copy * of this software and associated documentation files (the "Software"), to deal * in the Software without restriction, including without limitation the rights * to use, copy, modify, merge, publish, distribute, sublicense, and/or sell * copies of the Software, and to permit persons to whom the Software is * furnished to do so, subject to the following conditions: * * The above copyright notice and this permission notice shall be included in * all copies or substantial portions of the Software. * * THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR * IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, * FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE * AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER * LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, * OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN * THE SOFTWARE. */ package juicebox.tools.clt.juicer; import com.google.common.primitives.Doubles; import com.google.common.primitives.Floats; import jcuda.CudaException; import jcuda.driver.CUcontext; import jcuda.driver.CUdevice; import jcuda.driver.CUresult; import juicebox.HiC; import juicebox.HiCGlobals; import juicebox.data.ChromosomeHandler; import juicebox.data.Dataset; import juicebox.data.ExpectedValueFunction; import juicebox.data.HiCFileTools; import juicebox.data.basics.Chromosome; import juicebox.data.basics.ListOfFloatArrays; import juicebox.mapcolorui.Feature2DHandler; import juicebox.tools.clt.CommandLineParserForJuicer; import juicebox.tools.clt.JuicerCLT; import juicebox.tools.utils.common.ArrayTools; import juicebox.tools.utils.juicer.hiccups.*; import juicebox.track.feature.Feature2D; import juicebox.track.feature.Feature2DList; import juicebox.track.feature.Feature2DTools; import juicebox.windowui.HiCZoom; import juicebox.windowui.NormalizationHandler; import juicebox.windowui.NormalizationType; import java.awt.*; import java.io.File; import java.io.IOException; import java.io.PrintWriter; import java.math.RoundingMode; import java.text.DecimalFormat; import java.util.*; import java.util.List; import java.util.concurrent.ExecutorService; import java.util.concurrent.Executors; import java.util.concurrent.atomic.AtomicInteger; import java.util.stream.LongStream; import static jcuda.driver.JCudaDriver.*; import static jcuda.driver.JCudaDriver.cuCtxCreate; /** * */ public class HiCCUPS2 extends JuicerCLT { public static final int regionMargin = 20; public static final int krNeighborhood = 5; public static final Color defaultPeakColor = Color.cyan; public static final boolean shouldColorBeScaledByFDR = false; public static final String CPU_VERSION_WARNING = "WARNING - You are using the CPU version of HiCCUPS.\n" + "The GPU version of HiCCUPS is the official version and has been tested extensively.\n" + "The CPU version only searches for loops within 8MB (by default) of the diagonal and is still experimental."; private static final int totalMargin = 2 * regionMargin; public static final int w1 = 50; // TODO dimension should be variably set private static final int w2 = 10000; // TODO dimension should be variably set private static final boolean dataShouldBePostProcessed = true; public static double fdrsum1 = 0.00001; public static double fdrsum2 = 0.00003; public static double oeThreshold1 = 1.5; public static double oeThreshold2 = 1.75; public static double oeThreshold3 = 2; public static double oeThreshold4 = 40; private static int matrixSize = 512;// 540 original private static int regionWidth = matrixSize - totalMargin; private boolean configurationsSetByUser = false; private String featureListPath; private boolean listGiven = false; private boolean checkMapDensityThreshold = true; private ChromosomeHandler directlyInitializedChromosomeHandler = null; /* * Reasonable Commands * * fdr = 0.10 for all resolutions * peak width = 1 for 25kb, 2 for 10kb, 4 for 5kb * window = 3 for 25kb, 5 for 10kb, 7 for 5kb * * cluster radius is 20kb for 5kb and 10kb res and 50kb for 25kb res * fdrsumthreshold is 0.02 for all resolutions * oeThreshold1 = 1.5 for all res * oeThreshold2 = 1.75 for all res * oeThreshold3 = 2 for all res * * published GM12878 looplist was only generated with 5kb and 10kb resolutions * same with published IMR90 looplist * published CH12 looplist only generated with 10kb */ private File outputDirectory; private List configurations; private Dataset ds; private boolean useCPUVersionHiCCUPS = false, restrictSearchRegions = true; public HiCCUPS2() { super("hiccups2 [-m matrixSize] [-k normalization (NONE/VC/VC_SQRT/KR)] [-c chromosome(s)] [-r resolution(s)] " + "[-f fdr] [-p peak width] [-i window] [-t thresholds] [-d centroid distances] [--ignore-sparsity]" + " [specified_loop_list]"); Feature2D.allowHiCCUPSOrdering = true; } public static String getBasicUsage() { return "hiccups2 "; } @Override protected void readJuicerArguments(String[] args, CommandLineParserForJuicer juicerParser) { if (args.length != 3 && args.length != 4) { printUsageAndExit(); } // TODO: add code here to check for CUDA/GPU installation. The below is not ideal. ds = HiCFileTools.extractDatasetForCLT(Arrays.asList(args[1].split("\\+")), true); outputDirectory = HiCFileTools.createValidDirectory(args[2]); if (args.length == 4) { listGiven = true; featureListPath = args[3]; } NormalizationType preferredNorm = juicerParser.getNormalizationTypeOption(ds.getNormalizationHandler()); if (preferredNorm != null) norm = preferredNorm; determineValidMatrixSize(juicerParser); determineValidConfigurations(juicerParser, ds.getBpZooms()); if (juicerParser.restrictSearchRegionsOptions()) { restrictSearchRegions = true; System.out.println("WARNING - You are restricting the regions the HiCCUPS will explore."); } if (juicerParser.getCPUVersionOfHiCCUPSOptions()) { useCPUVersionHiCCUPS = true; restrictSearchRegions = true; System.out.println(CPU_VERSION_WARNING); } updateNumberOfCPUThreads(juicerParser, 1); } /** * Used by hiccups diff to set the properties of hiccups directly without resorting to command line usage * * @param dataset * @param outputDirectoryPath * @param featureListPath * @param preferredNorm * @param matrixSize * @param providedCommonChromosomeHandler * @param configurations * @param thresholds */ public void initializeDirectly(Dataset dataset, String outputDirectoryPath, String featureListPath, NormalizationType preferredNorm, int matrixSize, ChromosomeHandler providedCommonChromosomeHandler, List configurations, double[] thresholds, boolean usingCPUVersion, boolean restrictSearchRegions) { this.ds = dataset; outputDirectory = HiCFileTools.createValidDirectory(outputDirectoryPath); if (featureListPath != null) { listGiven = true; this.featureListPath = featureListPath; } directlyInitializedChromosomeHandler = providedCommonChromosomeHandler; if (preferredNorm != null) norm = preferredNorm; // will just confirm matrix size is large enough determineValidMatrixSize(matrixSize); // configurations should have been passed in if (configurations != null && configurations.size() > 0) { configurationsSetByUser = true; this.configurations = configurations; } // fdr & oe thresholds directly sent in if (thresholds != null) setHiCCUPSFDROEThresholds(thresholds); // force hiccups to run checkMapDensityThreshold = false; this.restrictSearchRegions = restrictSearchRegions; if (usingCPUVersion) { useCPUVersionHiCCUPS = true; this.restrictSearchRegions = true; } } @Override public void run() { try { final ExpectedValueFunction df = ds.getExpectedValues(new HiCZoom(HiC.Unit.BP, 2500000), NormalizationHandler.NONE); double firstExpected = df.getExpectedValuesNoNormalization().getFirstValue(); // expected value on diagonal // From empirical testing, if the expected value on diagonal at 2.5Mb is >= 100,000 // then the map had more than 300M contacts. if (firstExpected < 100000) { System.err.println("Warning Hi-C map is too sparse to find many loops via HiCCUPS2."); } } catch (Exception e) { System.err.println("Unable to assess map sparsity; continuing with HiCCUPS2"); } if (!configurationsSetByUser) { configurations = HiCCUPSConfiguration.getHiCCUPS2DefaultSetOfConfigsForUsers(); } ChromosomeHandler commonChromosomesHandler = ds.getChromosomeHandler(); if (directlyInitializedChromosomeHandler != null && directlyInitializedChromosomeHandler.size() > 0) { commonChromosomesHandler = directlyInitializedChromosomeHandler; } else if (givenChromosomes != null && givenChromosomes.size() > 0) { commonChromosomesHandler = HiCFileTools.stringToChromosomes(givenChromosomes, commonChromosomesHandler); } Map loopLists = new HashMap<>(); Map givenLoopLists = new HashMap<>(); File outputMergedFile = new File(outputDirectory, HiCCUPSUtils.getMergedLoopsFileName()); File outputMergedGivenFile = new File(outputDirectory, HiCCUPSUtils.getMergedRequestedLoopsFileName()); Feature2DHandler inputListFeature2DHandler = new Feature2DHandler(); if (listGiven) { inputListFeature2DHandler.setLoopList(featureListPath, commonChromosomesHandler); } for (HiCCUPSConfiguration conf : configurations) { System.out.println("Running HiCCUPS2 for resolution " + conf.getResolution()); Feature2DList enrichedPixels = runHiccups2Processing(ds, conf, commonChromosomesHandler, inputListFeature2DHandler, givenLoopLists); if (enrichedPixels != null) { loopLists.put(conf.getResolution(), enrichedPixels); } } if (dataShouldBePostProcessed) { HiCCUPSUtils.postProcess(loopLists, ds, commonChromosomesHandler, configurations, norm, outputDirectory, false, outputMergedFile, 2); if (listGiven) { HiCCUPSUtils.postProcess(givenLoopLists, ds, commonChromosomesHandler, configurations, norm, outputDirectory, true, outputMergedGivenFile, 2); } } System.out.println("HiCCUPS2 complete"); // else the thresholds and raw pixels were already saved when hiccups was run } /** * Actual run of the HiCCUPS algorithm * * @param ds dataset from hic file * @param conf configuration of hiccups inputs * @param chromosomeHandler list of chromosomes to run hiccups on * @param givenLoopLists * @return list of enriched pixels */ private Feature2DList runHiccups2Processing(Dataset ds, final HiCCUPSConfiguration conf, ChromosomeHandler chromosomeHandler, final Feature2DHandler inputListFeature2DHandler, Map givenLoopLists) { long begin_time = System.currentTimeMillis(); HiCZoom zoom = ds.getZoomForBPResolution(conf.getResolution()); if (zoom == null) { System.err.println("Data not available at " + conf.getResolution() + " resolution"); return null; } // open the print writer early so the file I/O capability is verified before running hiccups PrintWriter outputFDR = HiCFileTools.openWriter( new File(outputDirectory, HiCCUPSUtils.getFDRThresholdsFilename(conf.getResolution()))); final long[][] histBL = new long[w1][2]; final long[][] histDonut = new long[w1][2]; final long[][] histH = new long[w1][2]; final long[][] histV = new long[w1][2]; final Map> pvalBL = new HashMap<>(); final Map> pvalDonut = new HashMap<>(); final Map> pvalH = new HashMap<>(); final Map> pvalV = new HashMap<>(); for (int i = 0; i < w1; i++) { pvalBL.put(i, new HashMap<>()); pvalDonut.put(i, new HashMap<>()); pvalH.put(i, new HashMap<>()); pvalV.put(i, new HashMap<>()); } final float[] thresholdBL = ArrayTools.newValueInitializedFloatArray(w1, (float) 0); final float[] thresholdDonut = ArrayTools.newValueInitializedFloatArray(w1, (float) 0); final float[] thresholdH = ArrayTools.newValueInitializedFloatArray(w1, (float) 0); final float[] thresholdV = ArrayTools.newValueInitializedFloatArray(w1, (float) 0); // to hold all enriched pixels found in second run final Feature2DList globalList = new Feature2DList(); final Feature2DList requestedList = new Feature2DList(); // two runs, 1st to build histograms, 2nd to identify loops final HiCCUPSRegionHandler regionHandler = new HiCCUPSRegionHandler(ds, chromosomeHandler, zoom, norm, conf, regionWidth, regionMargin, restrictSearchRegions); for (final int runNum : new int[]{0, 1, 2}) { final AtomicInteger currentProgressStatus = new AtomicInteger(0); final AtomicInteger indexOfHiCCUPSRegion = new AtomicInteger(0); ExecutorService executor = Executors.newFixedThreadPool(numCPUThreads); for (int l = 0; l < numCPUThreads; l++) { Runnable worker = new Runnable() { @Override public void run() { runCoreCodeForHiCCUPS2(conf, indexOfHiCCUPSRegion, currentProgressStatus, regionHandler, matrixSize, thresholdBL, thresholdDonut, thresholdH, thresholdV, norm, zoom, pvalBL, pvalDonut, pvalH, pvalV, histBL, histDonut, histH, histV, runNum, inputListFeature2DHandler, requestedList, globalList); } }; executor.execute(worker); } executor.shutdown(); // Wait until all threads finish while (!executor.isTerminated()) { } if (runNum == 1) { long thresh_time0 = System.currentTimeMillis(); executor = Executors.newFixedThreadPool(w1); for (int i = 0; i < w1; i++) { final int bin = i; Runnable worker = new Runnable() { @Override public void run() { if (pvalBL.get(bin) == null) { synchronized(thresholdBL) { thresholdBL[bin] = 0; } } else { float tempBLthresh = (float) ((HiCCUPSUtils.histogramPvals(pvalBL.get(bin), histBL[bin][0], histBL[bin][1]) * (1. / conf.getFDRThreshold())) / histBL[bin][0]); synchronized(thresholdBL) { thresholdBL[bin] = tempBLthresh; } synchronized(pvalBL) { pvalBL.remove(bin); } } if (pvalDonut.get(bin) == null) { synchronized(thresholdDonut) { thresholdDonut[bin] = 0; } } else { float tempDonutthresh = (float) ((HiCCUPSUtils.histogramPvals(pvalDonut.get(bin), histDonut[bin][0], histDonut[bin][1]) * (1. / conf.getFDRThreshold())) / histDonut[bin][0]); synchronized(thresholdDonut) { thresholdDonut[bin] = tempDonutthresh; } synchronized(pvalDonut) { pvalDonut.remove(bin); } } if (pvalH.get(bin) == null) { synchronized(thresholdH) { thresholdH[bin] = 0; } } else { float tempHthresh = (float) ((HiCCUPSUtils.histogramPvals(pvalH.get(bin), histH[bin][0], histH[bin][1]) * (1. / conf.getFDRThreshold())) / histH[bin][0]); synchronized(thresholdH) { thresholdH[bin] = tempHthresh; } synchronized(pvalH) { pvalH.remove(bin); } } if (pvalV.get(bin) == null) { synchronized(thresholdV) { thresholdV[bin] = 0; } } else { float tempVthresh = (float) ((HiCCUPSUtils.histogramPvals(pvalV.get(bin), histV[bin][0], histV[bin][1]) * (1. / conf.getFDRThreshold())) / histV[bin][0]); synchronized(thresholdV) { thresholdV[bin] = tempVthresh; } synchronized(pvalH) { pvalH.remove(bin); } } } }; executor.execute(worker); } executor.shutdown(); // Wait until all threads finish while (!executor.isTerminated()) { } if (HiCGlobals.printVerboseComments) { long thresh_time1 = System.currentTimeMillis(); System.out.println("Time to calculate thresholds: " + (thresh_time1 - thresh_time0) + "ms"); } } } globalList.exportFeatureList(new File(outputDirectory, HiCCUPSUtils.getEnrichedPixelFileName(conf.getResolution())), true, Feature2DList.ListFormat.ENRICHED); if (listGiven) { requestedList.exportFeatureList(new File(outputDirectory, HiCCUPSUtils.getRequestedLoopsFileName(conf.getResolution())), true, Feature2DList.ListFormat.ENRICHED); givenLoopLists.put(conf.getResolution(), requestedList); } for (int i = 0; i < w1; i++) { outputFDR.println(i + "\t" + thresholdBL[i] + "\t" + thresholdDonut[i] + "\t" + thresholdH[i] + "\t" + thresholdV[i] + "\t" + histBL[i] + "\t" + histDonut[i] + "\t" + histH[i] + "\t" + histV[i]); } outputFDR.close(); if (HiCGlobals.printVerboseComments) { long final_time = System.currentTimeMillis(); System.out.println("Total time: " + (final_time - begin_time)); } return globalList; } private void runCoreCodeForHiCCUPS2(HiCCUPSConfiguration conf, AtomicInteger indexOfHiCCUPSRegion, AtomicInteger currentProgressStatus, HiCCUPSRegionHandler regionHandler, int matrixSize, float[] thresholdBL, float[] thresholdDonut, float[] thresholdH, float[] thresholdV, NormalizationType norm, HiCZoom zoom, Map> pvalBL, Map> pvalDonut, Map> pvalH, Map> pvalV, long[][] histBL, long[][] histDonut, long[][] histH, long[][] histV, int runNum, Feature2DHandler inputListFeature2DHandler, Feature2DList requestedList, Feature2DList globalList) { int indexOfRegionForThread = indexOfHiCCUPSRegion.getAndIncrement(); GPUController2 gpuController = buildGPUController(conf); while (indexOfRegionForThread < regionHandler.getSize()) { HiCCUPSRegionContainer regionContainer = regionHandler.getRegionFromIndex(indexOfRegionForThread); try { if (HiCGlobals.printVerboseComments) { System.out.println(); System.out.println("GPU Run Details"); System.out.println("Row bounds " + Arrays.toString(regionContainer.getRowBounds())); System.out.println("Col bounds " + Arrays.toString(regionContainer.getColumnBounds())); } int[] rowBounds = regionContainer.getRowBounds(); int[] columnBounds = regionContainer.getColumnBounds(); GPUOutputContainer2 gpuOutputs = gpuController.process(regionHandler, regionContainer, matrixSize, thresholdBL, thresholdDonut, thresholdH, thresholdV, norm, zoom); int diagonalCorrection = (rowBounds[4] - columnBounds[4]) + conf.getPeakWidth() + 2; if (runNum == 0) { gpuOutputs.cleanUpBinNans(); gpuOutputs.cleanUpBinDiagonal(diagonalCorrection); synchronized (histBL) { gpuOutputs.updateHistograms(histBL, histDonut, histH, histV, w1); } } else if (runNum == 1) { gpuOutputs.cleanUpPvalNans(); synchronized(pvalBL) { gpuOutputs.updatePvalLists(pvalBL, pvalDonut, pvalH, pvalV, histBL, histDonut, histH, histV, w1, (1. / conf.getFDRThreshold())); } } else if (runNum == 2) { gpuOutputs.cleanUpPvalNans(); gpuOutputs.cleanUpPeakNaNs(); gpuOutputs.cleanUpPeakDiagonal(diagonalCorrection); Chromosome chromosome = regionContainer.getChromosome(); Feature2DList peaksList = gpuOutputs.extractPeaks(chromosome.getIndex(), chromosome.getName(), w1, w2, rowBounds[4], columnBounds[4], conf.getResolution()); globalList.add(peaksList); if (listGiven) { float rowBound1GenomeCoords = ((float) rowBounds[4]) * conf.getResolution(); float columnBound1GenomeCoords = ((float) columnBounds[4]) * conf.getResolution(); float rowBound2GenomeCoords = ((float) rowBounds[5] - 1) * conf.getResolution(); float columnBound2GenomeCoords = ((float) columnBounds[5] - 1) * conf.getResolution(); // System.out.println(chromosome.getIndex() + "\t" + rowBound1GenomeCoords + "\t" + rowBound2GenomeCoords + "\t" + columnBound1GenomeCoords + "\t" + columnBound2GenomeCoords); net.sf.jsi.Rectangle currentWindow = new net.sf.jsi.Rectangle(rowBound1GenomeCoords, columnBound1GenomeCoords, rowBound2GenomeCoords, columnBound2GenomeCoords); List inputListFoundFeatures = inputListFeature2DHandler.getContainedFeatures(chromosome.getIndex(), chromosome.getIndex(), currentWindow); Feature2DList peaksRequestedList = gpuOutputs.extractPeaksListGiven(chromosome.getIndex(), chromosome.getName(), w1, w2, rowBounds[4], columnBounds[4], conf.getResolution(), inputListFoundFeatures); requestedList.add(peaksRequestedList); } } int currProg = currentProgressStatus.incrementAndGet(); int resonableDivisor = Math.max(regionHandler.getSize() / 20, 1); if (HiCGlobals.printVerboseComments || currProg % resonableDivisor == 0) { DecimalFormat df = new DecimalFormat("#.####"); df.setRoundingMode(RoundingMode.FLOOR); System.out.println(df.format(Math.floor((100.0 * currProg) / regionHandler.getSize())) + "% "); } } catch (IOException e) { System.err.println("No data in map region"); } indexOfRegionForThread = indexOfHiCCUPSRegion.getAndIncrement(); } } private GPUController2 buildGPUController(HiCCUPSConfiguration conf) { try { return new GPUController2(conf.getWindowWidth(), conf.getResolution(), matrixSize, conf.getPeakWidth(), useCPUVersionHiCCUPS); } catch (Exception e) { e.printStackTrace(); System.err.println("GPU/CUDA Installation Not Detected"); System.err.println("Exiting HiCCUPS"); System.exit(26); return null; } } /** * @param juicerParser Parser to determine configurations * @param availableZooms */ private void determineValidConfigurations(CommandLineParserForJuicer juicerParser, List availableZooms) { configurations = HiCCUPSConfiguration.extractConfigurationsFromCommandLine(juicerParser, availableZooms, 2); if (configurations == null) { System.out.println("No valid configurations specified, using default settings"); configurationsSetByUser = false; } else { configurationsSetByUser = true; } try { List t = juicerParser.getThresholdOptions(); if (t != null && t.size() == 4) { double[] thresholds = HiCCUPSUtils.extractDoubleValues(t, 4, Double.NaN); setHiCCUPSFDROEThresholds(thresholds); } else if (t != null && t.size() == 5) { double[] thresholds = HiCCUPSUtils.extractDoubleValues(t, 5, Double.NaN); setHiCCUPSFDROEThresholds(thresholds); } else if (t != null && t.size() == 6) { double[] thresholds = HiCCUPSUtils.extractDoubleValues(t, 6, Double.NaN); setHiCCUPSFDROEThresholds(thresholds); } } catch (Exception e) { // do nothing - use default postprocessing thresholds } HiCCUPS2.fdrsum1 = fdrsum1; HiCCUPS2.fdrsum2 = fdrsum2; HiCCUPS2.oeThreshold1 = oeThreshold1; HiCCUPS2.oeThreshold2 = oeThreshold2; HiCCUPS2.oeThreshold3 = oeThreshold3; } private void determineValidMatrixSize(CommandLineParserForJuicer juicerParser) { determineValidMatrixSize(juicerParser.getMatrixSizeOption()); } private void determineValidMatrixSize(int specifiedMatrixSize) { if (specifiedMatrixSize > 2 * regionMargin) { matrixSize = specifiedMatrixSize; regionWidth = specifiedMatrixSize - totalMargin; } if (HiCGlobals.printVerboseComments) { System.out.println("Using Matrix Size " + matrixSize); } } private void setHiCCUPSFDROEThresholds(double[] thresholds) { if (thresholds != null && thresholds.length == 4) { if (!Double.isNaN(thresholds[0]) && thresholds[0] > 0) fdrsum1 = thresholds[0]; if (!Double.isNaN(thresholds[0]) && thresholds[0] > 0) fdrsum2 = thresholds[0]; if (!Double.isNaN(thresholds[1]) && thresholds[1] > 0) oeThreshold1 = thresholds[1]; if (!Double.isNaN(thresholds[2]) && thresholds[2] > 0) oeThreshold2 = thresholds[2]; if (!Double.isNaN(thresholds[3]) && thresholds[3] > 0) oeThreshold3 = thresholds[3]; } if (thresholds != null && thresholds.length == 5) { if (!Double.isNaN(thresholds[0]) && thresholds[0] > 0) fdrsum1 = thresholds[0]; if (!Double.isNaN(thresholds[1]) && thresholds[1] > 0) fdrsum2 = thresholds[1]; if (!Double.isNaN(thresholds[2]) && thresholds[2] > 0) oeThreshold1 = thresholds[2]; if (!Double.isNaN(thresholds[3]) && thresholds[3] > 0) oeThreshold2 = thresholds[3]; if (!Double.isNaN(thresholds[4]) && thresholds[4] > 0) oeThreshold3 = thresholds[4]; } if (thresholds != null && thresholds.length == 6) { if (!Double.isNaN(thresholds[0]) && thresholds[0] > 0) fdrsum1 = thresholds[0]; if (!Double.isNaN(thresholds[1]) && thresholds[1] > 0) fdrsum2 = thresholds[1]; if (!Double.isNaN(thresholds[2]) && thresholds[2] > 0) oeThreshold1 = thresholds[2]; if (!Double.isNaN(thresholds[3]) && thresholds[3] > 0) oeThreshold2 = thresholds[3]; if (!Double.isNaN(thresholds[4]) && thresholds[4] > 0) oeThreshold3 = thresholds[4]; if (!Double.isNaN(thresholds[5]) && thresholds[5] > 0) oeThreshold3 = thresholds[5]; } } } ================================================ FILE: src/juicebox/tools/clt/juicer/HiCCUPSDiff.java ================================================ /* * The MIT License (MIT) * * Copyright (c) 2011-2021 Broad Institute, Aiden Lab, Rice University, Baylor College of Medicine * * Permission is hereby granted, free of charge, to any person obtaining a copy * of this software and associated documentation files (the "Software"), to deal * in the Software without restriction, including without limitation the rights * to use, copy, modify, merge, publish, distribute, sublicense, and/or sell * copies of the Software, and to permit persons to whom the Software is * furnished to do so, subject to the following conditions: * * The above copyright notice and this permission notice shall be included in * all copies or substantial portions of the Software. * * THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR * IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, * FITNESS FOR A PARTICULAR PURPOSE AND NON-INFRINGEMENT. IN NO EVENT SHALL THE * AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER * LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, * OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN * THE SOFTWARE. */ package juicebox.tools.clt.juicer; import juicebox.data.ChromosomeHandler; import juicebox.data.Dataset; import juicebox.data.HiCFileTools; import juicebox.tools.clt.CommandLineParserForJuicer; import juicebox.tools.clt.JuicerCLT; import juicebox.tools.utils.juicer.hiccups.HiCCUPSConfiguration; import juicebox.tools.utils.juicer.hiccups.HiCCUPSUtils; import juicebox.track.feature.Feature2DList; import juicebox.track.feature.Feature2DParser; import juicebox.track.feature.Feature2DTools; import juicebox.windowui.HiCZoom; import juicebox.windowui.NormalizationHandler; import juicebox.windowui.NormalizationType; import java.io.File; import java.util.ArrayList; import java.util.Arrays; import java.util.List; /** * HiCCUPS Diff *

* Developed by Suhas Rao, ported by Suhas Rao + Neva Durand *

* ------- * Takes as input two Hi-C maps and their associated loop calls
* Outputs two differential loop lists: loops that are in the first but not in the second * and loops that are in the second but not in the first
* Other parameters are used for the two HiCCUPS calls on the alternate loop lists * @see juicebox.tools.clt.juicer.HiCCUPS * hiccupsdiff [-m matrixSize] [-k normalization (NONE/VC/VC_SQRT/KR)] [-c chromosome(s)] [-r resolution(s)] * [-f fdr] [-p peak width] [-i window] [-t thresholds] [-d centroid distances] * * firstLoopList is the loop list generated by running HiCCUPS on firstHicFile * secondLoopList is the loop list generated by running HiCCUPS on secondHicFile */ public class HiCCUPSDiff extends JuicerCLT { private final float maxEnrich = 1.3f; private HiCCUPS hiccups1 = null; private HiCCUPS hiccups2 = null; private Feature2DList looplist1; private Feature2DList looplist2; private File outputDirectory; private ChromosomeHandler commonChromosomesHandler; private List configs; private NormalizationType norm1 = NormalizationHandler.KR, norm2 = NormalizationHandler.KR; public HiCCUPSDiff() { // what variables should they be able to send in? // need to add maxEnrich super("hiccupsdiff [-m matrixSize] [-k normalization (NONE/VC/VC_SQRT/KR)] [-c chromosome(s)] " + "[-f fdr] [-p peak width] [-i window] [-t thresholds] [-d centroid distances] " + " "); } public static String getBasicUsage() { return "hiccupsdiff "; } @Override protected void readJuicerArguments(String[] args, CommandLineParserForJuicer juicerParser) { if (args.length != 6) { printUsageAndExit(); } outputDirectory = HiCFileTools.createValidDirectory(args[5]); Dataset ds1 = HiCFileTools.extractDatasetForCLT(Arrays.asList(args[1].split("\\+")), true); Dataset ds2 = HiCFileTools.extractDatasetForCLT(Arrays.asList(args[2].split("\\+")), true); if (!(ds1.getGenomeId().equals(ds2.getGenomeId()))) { System.err.println("Hi-C maps must be from the same genome"); System.exit(27); } // intersecting for the edge case where one of the hic files may not be using all chromosomes // e.g. the mbr_19 files for testing commonChromosomesHandler = HiCFileTools.getChromosomeSetIntersection(ds1.getChromosomeHandler(), ds2.getChromosomeHandler()); if (givenChromosomes != null && givenChromosomes.size() > 0) commonChromosomesHandler = HiCFileTools.stringToChromosomes(givenChromosomes, commonChromosomesHandler); List availableZooms = new ArrayList<>(HiCFileTools.getZoomSetIntersection( ds1.getBpZooms(), ds1.getBpZooms())); looplist1 = Feature2DParser.loadFeatures(args[3], commonChromosomesHandler, true, null, false); looplist2 = Feature2DParser.loadFeatures(args[4], commonChromosomesHandler, true, null, false); configs = HiCCUPSConfiguration.extractConfigurationsFromCommandLine(juicerParser, availableZooms, 1); if (configs == null) { configs = new ArrayList<>(); if (Feature2DTools.isResolutionPresent(looplist1, 5000) && Feature2DTools.isResolutionPresent(looplist2, 5000)) { configs.add(HiCCUPSConfiguration.getDefaultConfigFor5K()); } if (Feature2DTools.isResolutionPresent(looplist1, 10000) && Feature2DTools.isResolutionPresent(looplist2, 10000)) { configs.add(HiCCUPSConfiguration.getDefaultConfigFor10K()); } if (Feature2DTools.isResolutionPresent(looplist1, 25000) && Feature2DTools.isResolutionPresent(looplist2, 25000)) { configs.add(HiCCUPSConfiguration.getDefaultConfigFor25K()); } if (configs.size() == 0) { System.err.println("The loop lists have no resolutions in common."); System.exit(28); } } System.out.println("Running differential HiCCUPs with resolutions:"); for (HiCCUPSConfiguration config : configs) { System.out.println(config); } boolean processed = true; for (HiCCUPSConfiguration config : configs) { String fname = outputDirectory + File.separator + "file1" + File.separator + "requested_list_" + config.getResolution() + ".bedpe"; if (!new File(fname).exists()) processed = false; fname = outputDirectory + File.separator + "file2" + File.separator + "requested_list_" + config.getResolution() + ".bedpe"; if (!new File(fname).exists()) processed = false; } boolean restrictSearchRegions = false; if (juicerParser.restrictSearchRegionsOptions()) { restrictSearchRegions = true; System.out.println("WARNING - You are restricting the regions the HiCCUPS will explore."); } if (processed) { System.out.println("Using already created differential lists in " + outputDirectory + File.separator + "file1 and " + outputDirectory + File.separator + "file2"); } else { NormalizationType[] preferredNorms = juicerParser.getBothNormalizationTypeOption(ds1.getNormalizationHandler(), ds2.getNormalizationHandler()); if (preferredNorms != null && preferredNorms.length == 2) { norm1 = preferredNorms[0]; norm2 = preferredNorms[1]; } int matrixSize = juicerParser.getMatrixSizeOption(); if (matrixSize <= 0) matrixSize = 1024; boolean usingCPUVersion = false; if (juicerParser.getCPUVersionOfHiCCUPSOptions()) { usingCPUVersion = true; System.out.println(HiCCUPS.CPU_VERSION_WARNING); } double[] thresholds = null; List t = juicerParser.getThresholdOptions(); if (t != null && t.size() == 4) { thresholds = HiCCUPSUtils.extractDoubleValues(t, 4, Double.NaN); } updateNumberOfCPUThreads(juicerParser, 1); System.out.println("Running HiCCUPS with alternate loop lists"); hiccups1 = new HiCCUPS(); hiccups2 = new HiCCUPS(); hiccups1.initializeDirectly(ds1, outputDirectory + File.separator + "file1", args[4], norm1, matrixSize, commonChromosomesHandler, configs, thresholds, usingCPUVersion, restrictSearchRegions); hiccups2.initializeDirectly(ds2, outputDirectory + File.separator + "file2", args[3], norm2, matrixSize, commonChromosomesHandler, configs, thresholds, usingCPUVersion, restrictSearchRegions); } } @Override public void run() { if (hiccups1 != null && hiccups2 != null) { hiccups1.run(); hiccups2.run(); } // for every feature in second loop list, see if there's a reasonably close one in first list (and vice versa) Feature2DList conservedLoopList2 = Feature2DTools.extractReproducibleCentroids(looplist1, looplist2, 50000, 0.2); Feature2DList conservedLoopList1 = Feature2DTools.extractReproducibleCentroids(looplist2, looplist1, 50000, 0.2); // get the differences - loops that appear only in the respective loop list Feature2DList diff1 = Feature2DTools.compareLists(conservedLoopList1, looplist1, false); Feature2DList diff2 = Feature2DTools.compareLists(conservedLoopList2, looplist2, false); // load all the loops resulting from running HiCCUPs on the first HiC file with the second loop list (and vice versa) // then filter by max enrichment: observed < maxEnrich*expected BL & donut & V & H Feature2DList results1 = HiCCUPSUtils.filterOutFeaturelistByEnrichment(configs, outputDirectory + File.separator + "file1", maxEnrich, commonChromosomesHandler); Feature2DList results2 = HiCCUPSUtils.filterOutFeaturelistByEnrichment(configs, outputDirectory + File.separator + "file2", maxEnrich, commonChromosomesHandler); // differential loop list 1 is loops that appeared in list1 that are not enriched in Hi-C file 2 Feature2DList differentialList1 = Feature2DList.getIntersection(diff1, results2); // differential loop list 2 is loops that appeared in list2 that are not enriched in Hi-C file 1 Feature2DList differentialList2 = Feature2DList.getIntersection(diff2, results1); differentialList1.exportFeatureList(new File(outputDirectory, "differential_loops1.bedpe"), true, Feature2DList.ListFormat.FINAL); differentialList2.exportFeatureList(new File(outputDirectory, "differential_loops2.bedpe"), true, Feature2DList.ListFormat.FINAL); } } ================================================ FILE: src/juicebox/tools/clt/juicer/HiCCUPSRegionHandler.java ================================================ /* * The MIT License (MIT) * * Copyright (c) 2011-2020 Broad Institute, Aiden Lab, Rice University, Baylor College of Medicine * * Permission is hereby granted, free of charge, to any person obtaining a copy * of this software and associated documentation files (the "Software"), to deal * in the Software without restriction, including without limitation the rights * to use, copy, modify, merge, publish, distribute, sublicense, and/or sell * copies of the Software, and to permit persons to whom the Software is * furnished to do so, subject to the following conditions: * * The above copyright notice and this permission notice shall be included in * all copies or substantial portions of the Software. * * THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR * IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, * FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE * AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER * LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, * OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN * THE SOFTWARE. */ package juicebox.tools.clt.juicer; import juicebox.HiCGlobals; import juicebox.data.*; import juicebox.data.basics.Chromosome; import juicebox.tools.utils.juicer.hiccups.HiCCUPSConfiguration; import juicebox.tools.utils.juicer.hiccups.HiCCUPSRegionContainer; import juicebox.windowui.HiCZoom; import juicebox.windowui.NormalizationHandler; import juicebox.windowui.NormalizationType; import org.broad.igv.util.Pair; import java.util.ArrayList; import java.util.HashMap; import java.util.List; import java.util.Map; public class HiCCUPSRegionHandler { final List allRegionContainers = new ArrayList<>(); final Map, MatrixZoomData> zoomDataMap = new HashMap<>(); final Map, double[]> normVectorMap = new HashMap<>(); final Map, double[]> expectedVectorMap = new HashMap<>(); public HiCCUPSRegionHandler(Dataset ds, ChromosomeHandler chromosomeHandler, HiCZoom zoom, NormalizationType norm, HiCCUPSConfiguration conf, int regionWidth, int regionMargin, boolean restrictSearchRegions) { for (final Chromosome chromosome : chromosomeHandler.getChromosomeArrayWithoutAllByAll()) { // skip these matrices Matrix matrix = ds.getMatrix(chromosome, chromosome); if (matrix == null) continue; // get matrix data access long start_time = System.currentTimeMillis(); final MatrixZoomData zd = matrix.getZoomData(zoom); Pair pairKey = new Pair<>(chromosome.getIndex(), zoom); zoomDataMap.put(pairKey, zd); //NormalizationType preferredNormalization = HiCFileTools.determinePreferredNormalization(ds); NormalizationVector normVector = ds.getNormalizationVector(chromosome.getIndex(), zoom, norm); if (normVector != null || norm.equals(NormalizationHandler.NONE)) { if (!norm.equals(NormalizationHandler.NONE)) { final double[] normalizationVector = normVector.getData().getValues().get(0); normVectorMap.put(pairKey, normalizationVector); } final double[] expectedVector = HiCFileTools.extractChromosomeExpectedVector(ds, chromosome.getIndex(), zoom, norm).getValues().get(0); expectedVectorMap.put(pairKey, expectedVector); // need overall bounds for the chromosome int chrMatrixWidth = (int) Math.ceil((double) chromosome.getLength() / conf.getResolution()); if (norm.equals(NormalizationHandler.NONE)) { final double[] normalizationVector = new double[chrMatrixWidth]; for (int i=0;i 8000000) { continue; } final int[] columnBounds = calculateRegionBounds(j, regionWidth, chrMatrixWidth, regionMargin); if (HiCGlobals.printVerboseComments) { System.out.print("."); } if (columnBounds[4] < chrMatrixWidth - regionMargin) { allRegionContainers.add(new HiCCUPSRegionContainer(chromosome, rowBounds, columnBounds)); } } } } } else { System.err.println("Data not available for " + chromosome + " at " + conf.getResolution() + " resolution"); } } } private int[] calculateRegionBounds(int index, int regionWidth, int chrMatrixWidth, int regionMargin) { int bound1R = Math.min(regionMargin + (index * regionWidth), chrMatrixWidth - regionMargin); int bound1 = bound1R - regionMargin; int bound2R = Math.min(bound1R + regionWidth, chrMatrixWidth - regionMargin); int bound2 = bound2R + regionMargin; int diff1 = bound1R - bound1; int diff2 = bound2 - bound2R; return new int[]{bound1, bound2, diff1, diff2, bound1R, bound2R}; } public int getSize() { return allRegionContainers.size(); } public synchronized HiCCUPSRegionContainer getRegionFromIndex(int indexOfRegionForThread) { return allRegionContainers.get(indexOfRegionForThread); } public MatrixZoomData getZoomData(HiCCUPSRegionContainer regionContainer, HiCZoom zoom) { return zoomDataMap.get(new Pair<>(regionContainer.getChromosome().getIndex(), zoom)); } public double[] getNormalizationVector(HiCCUPSRegionContainer regionContainer, HiCZoom zoom) { return normVectorMap.get(new Pair<>(regionContainer.getChromosome().getIndex(), zoom)); } public double[] getExpectedVector(HiCCUPSRegionContainer regionContainer, HiCZoom zoom) { return expectedVectorMap.get(new Pair<>(regionContainer.getChromosome().getIndex(), zoom)); } } ================================================ FILE: src/juicebox/tools/clt/juicer/HiCCUPSscores.java ================================================ /* * The MIT License (MIT) * * Copyright (c) 2011-2020 Broad Institute, Aiden Lab * * Permission is hereby granted, free of charge, to any person obtaining a copy * of this software and associated documentation files (the "Software"), to deal * in the Software without restriction, including without limitation the rights * to use, copy, modify, merge, publish, distribute, sublicense, and/or sell * copies of the Software, and to permit persons to whom the Software is * furnished to do so, subject to the following conditions: * * The above copyright notice and this permission notice shall be included in * all copies or substantial portions of the Software. * * THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR * IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, * FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE * AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER * LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, * OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN * THE SOFTWARE. */ package juicebox.tools.clt.juicer; import juicebox.HiC; import juicebox.HiCGlobals; import juicebox.data.ChromosomeHandler; import juicebox.data.Dataset; import juicebox.data.ExpectedValueFunction; import juicebox.data.HiCFileTools; import juicebox.data.basics.Chromosome; import juicebox.mapcolorui.Feature2DHandler; import juicebox.tools.clt.CommandLineParserForJuicer; import juicebox.tools.clt.JuicerCLT; import juicebox.tools.utils.common.ArrayTools; import juicebox.tools.utils.juicer.hiccups.*; import juicebox.track.feature.Feature2D; import juicebox.track.feature.Feature2DList; import juicebox.windowui.HiCZoom; import juicebox.windowui.NormalizationHandler; import juicebox.windowui.NormalizationType; import java.awt.*; import java.io.File; import java.io.IOException; import java.io.PrintWriter; import java.math.RoundingMode; import java.text.DecimalFormat; import java.util.Arrays; import java.util.HashMap; import java.util.List; import java.util.Map; import java.util.concurrent.ExecutorService; import java.util.concurrent.Executors; import java.util.concurrent.atomic.AtomicInteger; /** * */ public class HiCCUPSscores extends JuicerCLT { public static final int regionMargin = 20; public static final int krNeighborhood = 5; public static final Color defaultPeakColor = Color.cyan; public static final boolean shouldColorBeScaledByFDR = false; public static final String CPU_VERSION_WARNING = "WARNING - You are using the CPU version of HiCCUPS.\n" + "The GPU version of HiCCUPS is the official version and has been tested extensively.\n" + "The CPU version only searches for loops within 8MB (by default) of the diagonal and is still experimental."; private static final int totalMargin = 2 * regionMargin; public static final int w1 = 50; // TODO dimension should be variably set private static final int w2 = 10000; // TODO dimension should be variably set private static final boolean dataShouldBePostProcessed = true; public static double fdrsum1 = 0.00001; public static double fdrsum2 = 0.00003; public static double oeThreshold1 = 1.5; public static double oeThreshold2 = 1.75; public static double oeThreshold3 = 2; public static double oeThreshold4 = 40; private static int matrixSize = 512;// 540 original private static int regionWidth = matrixSize - totalMargin; private boolean configurationsSetByUser = false; private String featureListPath; private boolean listGiven = false; private boolean checkMapDensityThreshold = true; private ChromosomeHandler directlyInitializedChromosomeHandler = null; /* * Reasonable Commands * * fdr = 0.10 for all resolutions * peak width = 1 for 25kb, 2 for 10kb, 4 for 5kb * window = 3 for 25kb, 5 for 10kb, 7 for 5kb * * cluster radius is 20kb for 5kb and 10kb res and 50kb for 25kb res * fdrsumthreshold is 0.02 for all resolutions * oeThreshold1 = 1.5 for all res * oeThreshold2 = 1.75 for all res * oeThreshold3 = 2 for all res * * published GM12878 looplist was only generated with 5kb and 10kb resolutions * same with published IMR90 looplist * published CH12 looplist only generated with 10kb */ private File outputDirectory; private List configurations; private Dataset ds; private boolean useCPUVersionHiCCUPS = false, restrictSearchRegions = true; public HiCCUPSscores() { super("hiccups-scores [-m matrixSize] [-k normalization (NONE/VC/VC_SQRT/KR)] [-c chromosome(s)] [-r resolution(s)] " + "[-p peak width] [-i window]" + " "); Feature2D.allowHiCCUPSOrdering = true; } public static String getBasicUsage() { return "hiccups2 "; } @Override protected void readJuicerArguments(String[] args, CommandLineParserForJuicer juicerParser) { if (args.length != 4) { printUsageAndExit(); } // TODO: add code here to check for CUDA/GPU installation. The below is not ideal. ds = HiCFileTools.extractDatasetForCLT(Arrays.asList(args[1].split("\\+")), true); outputDirectory = HiCFileTools.createValidDirectory(args[2]); listGiven = true; featureListPath = args[3]; NormalizationType preferredNorm = juicerParser.getNormalizationTypeOption(ds.getNormalizationHandler()); if (preferredNorm != null) norm = preferredNorm; determineValidMatrixSize(juicerParser); determineValidConfigurations(juicerParser, ds.getBpZooms()); if (juicerParser.restrictSearchRegionsOptions()) { restrictSearchRegions = true; System.out.println("WARNING - You are restricting the regions the HiCCUPS will explore."); } if (juicerParser.getCPUVersionOfHiCCUPSOptions()) { useCPUVersionHiCCUPS = true; restrictSearchRegions = true; System.out.println(CPU_VERSION_WARNING); } updateNumberOfCPUThreads(juicerParser, 1); } /** * Used by hiccups diff to set the properties of hiccups directly without resorting to command line usage * * @param dataset * @param outputDirectoryPath * @param featureListPath * @param preferredNorm * @param matrixSize * @param providedCommonChromosomeHandler * @param configurations * @param thresholds */ public void initializeDirectly(Dataset dataset, String outputDirectoryPath, String featureListPath, NormalizationType preferredNorm, int matrixSize, ChromosomeHandler providedCommonChromosomeHandler, List configurations, double[] thresholds, boolean usingCPUVersion, boolean restrictSearchRegions) { this.ds = dataset; outputDirectory = HiCFileTools.createValidDirectory(outputDirectoryPath); if (featureListPath != null) { listGiven = true; this.featureListPath = featureListPath; } directlyInitializedChromosomeHandler = providedCommonChromosomeHandler; if (preferredNorm != null) norm = preferredNorm; // will just confirm matrix size is large enough determineValidMatrixSize(matrixSize); // configurations should have been passed in if (configurations != null && configurations.size() > 0) { configurationsSetByUser = true; this.configurations = configurations; } // fdr & oe thresholds directly sent in if (thresholds != null) setHiCCUPSFDROEThresholds(thresholds); // force hiccups to run checkMapDensityThreshold = false; this.restrictSearchRegions = restrictSearchRegions; if (usingCPUVersion) { useCPUVersionHiCCUPS = true; this.restrictSearchRegions = true; } } @Override public void run() { try { final ExpectedValueFunction df = ds.getExpectedValues(new HiCZoom(HiC.Unit.BP, 2500000), NormalizationHandler.NONE); double firstExpected = df.getExpectedValuesNoNormalization().getFirstValue(); // expected value on diagonal // From empirical testing, if the expected value on diagonal at 2.5Mb is >= 100,000 // then the map had more than 300M contacts. if (firstExpected < 100000) { System.err.println("Warning Hi-C map is too sparse to find many loops via HiCCUPS2."); } } catch (Exception e) { System.err.println("Unable to assess map sparsity; continuing with HiCCUPS2"); } if (!configurationsSetByUser) { configurations = HiCCUPSConfiguration.getHiCCUPS2DefaultSetOfConfigsForUsers(); } ChromosomeHandler commonChromosomesHandler = ds.getChromosomeHandler(); if (directlyInitializedChromosomeHandler != null && directlyInitializedChromosomeHandler.size() > 0) { commonChromosomesHandler = directlyInitializedChromosomeHandler; } else if (givenChromosomes != null && givenChromosomes.size() > 0) { commonChromosomesHandler = HiCFileTools.stringToChromosomes(givenChromosomes, commonChromosomesHandler); } Map givenLoopLists = new HashMap<>(); File outputMergedGivenFile = new File(outputDirectory, HiCCUPSUtils.getMergedRequestedLoopsFileName()); Feature2DHandler inputListFeature2DHandler = new Feature2DHandler(); inputListFeature2DHandler.setLoopList(featureListPath, commonChromosomesHandler); for (HiCCUPSConfiguration conf : configurations) { System.out.println("Running HiCCUPS2 for resolution " + conf.getResolution()); runHiccupsScoresProcessing(ds, conf, commonChromosomesHandler, inputListFeature2DHandler, givenLoopLists); } if (dataShouldBePostProcessed) { HiCCUPSUtils.postProcess(givenLoopLists, ds, commonChromosomesHandler, configurations, norm, outputDirectory, true, outputMergedGivenFile, 2); } System.out.println("HiCCUPS2 complete"); // else the thresholds and raw pixels were already saved when hiccups was run } /** * Actual run of the HiCCUPS algorithm * * @param ds dataset from hic file * @param conf configuration of hiccups inputs * @param chromosomeHandler list of chromosomes to run hiccups on * @param givenLoopLists * @return list of enriched pixels */ private void runHiccupsScoresProcessing(Dataset ds, final HiCCUPSConfiguration conf, ChromosomeHandler chromosomeHandler, final Feature2DHandler inputListFeature2DHandler, Map givenLoopLists) { long begin_time = System.currentTimeMillis(); HiCZoom zoom = ds.getZoomForBPResolution(conf.getResolution()); if (zoom == null) { System.err.println("Data not available at " + conf.getResolution() + " resolution"); return; } final float[] thresholdBL = ArrayTools.newValueInitializedFloatArray(w1, (float) 0); final float[] thresholdDonut = ArrayTools.newValueInitializedFloatArray(w1, (float) 0); final float[] thresholdH = ArrayTools.newValueInitializedFloatArray(w1, (float) 0); final float[] thresholdV = ArrayTools.newValueInitializedFloatArray(w1, (float) 0); // to hold all enriched pixels found in second run final Feature2DList requestedList = new Feature2DList(); // two runs, 1st to build histograms, 2nd to identify loops final HiCCUPSRegionHandler regionHandler = new HiCCUPSRegionHandler(ds, chromosomeHandler, zoom, norm, conf, regionWidth, regionMargin, restrictSearchRegions); final AtomicInteger currentProgressStatus = new AtomicInteger(0); final AtomicInteger indexOfHiCCUPSRegion = new AtomicInteger(0); ExecutorService executor = Executors.newFixedThreadPool(numCPUThreads); for (int l = 0; l < numCPUThreads; l++) { Runnable worker = new Runnable() { @Override public void run() { runCoreCodeForHiCCUPS2(conf, indexOfHiCCUPSRegion, currentProgressStatus, regionHandler, matrixSize, thresholdBL, thresholdDonut, thresholdH, thresholdV, norm, zoom, inputListFeature2DHandler, requestedList); } }; executor.execute(worker); } executor.shutdown(); // Wait until all threads finish while (!executor.isTerminated()) { } requestedList.exportFeatureList(new File(outputDirectory, HiCCUPSUtils.getRequestedLoopsFileName(conf.getResolution())), true, Feature2DList.ListFormat.ENRICHED); givenLoopLists.put(conf.getResolution(), requestedList); if (HiCGlobals.printVerboseComments) { long final_time = System.currentTimeMillis(); System.out.println("Total time: " + (final_time - begin_time)); } } private void runCoreCodeForHiCCUPS2(HiCCUPSConfiguration conf, AtomicInteger indexOfHiCCUPSRegion, AtomicInteger currentProgressStatus, HiCCUPSRegionHandler regionHandler, int matrixSize, float[] thresholdBL, float[] thresholdDonut, float[] thresholdH, float[] thresholdV, NormalizationType norm, HiCZoom zoom, Feature2DHandler inputListFeature2DHandler, Feature2DList requestedList) { int indexOfRegionForThread = indexOfHiCCUPSRegion.getAndIncrement(); GPUController2 gpuController = buildGPUController(conf); while (indexOfRegionForThread < regionHandler.getSize()) { HiCCUPSRegionContainer regionContainer = regionHandler.getRegionFromIndex(indexOfRegionForThread); try { if (HiCGlobals.printVerboseComments) { System.out.println(); System.out.println("GPU Run Details"); System.out.println("Row bounds " + Arrays.toString(regionContainer.getRowBounds())); System.out.println("Col bounds " + Arrays.toString(regionContainer.getColumnBounds())); } int[] rowBounds = regionContainer.getRowBounds(); int[] columnBounds = regionContainer.getColumnBounds(); Chromosome chromosome = regionContainer.getChromosome(); float rowBound1GenomeCoords = ((float) rowBounds[4]) * conf.getResolution(); float columnBound1GenomeCoords = ((float) columnBounds[4]) * conf.getResolution(); float rowBound2GenomeCoords = ((float) rowBounds[5] - 1) * conf.getResolution(); float columnBound2GenomeCoords = ((float) columnBounds[5] - 1) * conf.getResolution(); // System.out.println(chromosome.getIndex() + "\t" + rowBound1GenomeCoords + "\t" + rowBound2GenomeCoords + "\t" + columnBound1GenomeCoords + "\t" + columnBound2GenomeCoords); net.sf.jsi.Rectangle currentWindow = new net.sf.jsi.Rectangle(rowBound1GenomeCoords, columnBound1GenomeCoords, rowBound2GenomeCoords, columnBound2GenomeCoords); List inputListFoundFeatures = inputListFeature2DHandler.getContainedFeatures(chromosome.getIndex(), chromosome.getIndex(), currentWindow); if (inputListFoundFeatures.size()>0) { GPUOutputContainer2 gpuOutputs = gpuController.process(regionHandler, regionContainer, matrixSize, thresholdBL, thresholdDonut, thresholdH, thresholdV, norm, zoom); int diagonalCorrection = (rowBounds[4] - columnBounds[4]) + conf.getPeakWidth() + 2; gpuOutputs.cleanUpPvalNans(); gpuOutputs.cleanUpPeakNaNs(); gpuOutputs.cleanUpPeakDiagonal(diagonalCorrection); Feature2DList peaksRequestedList = gpuOutputs.extractPeaksListGiven(chromosome.getIndex(), chromosome.getName(), w1, w2, rowBounds[4], columnBounds[4], conf.getResolution(), inputListFoundFeatures); requestedList.add(peaksRequestedList); } int currProg = currentProgressStatus.incrementAndGet(); int resonableDivisor = Math.max(regionHandler.getSize() / 20, 1); if (HiCGlobals.printVerboseComments || currProg % resonableDivisor == 0) { DecimalFormat df = new DecimalFormat("#.####"); df.setRoundingMode(RoundingMode.FLOOR); System.out.println(df.format(Math.floor((100.0 * currProg) / regionHandler.getSize())) + "% "); } } catch (IOException e) { System.err.println("No data in map region"); } indexOfRegionForThread = indexOfHiCCUPSRegion.getAndIncrement(); } } private GPUController2 buildGPUController(HiCCUPSConfiguration conf) { try { return new GPUController2(conf.getWindowWidth(), conf.getResolution(), matrixSize, conf.getPeakWidth(), useCPUVersionHiCCUPS); } catch (Exception e) { e.printStackTrace(); System.err.println("GPU/CUDA Installation Not Detected"); System.err.println("Exiting HiCCUPS"); System.exit(26); return null; } } /** * @param juicerParser Parser to determine configurations * @param availableZooms */ private void determineValidConfigurations(CommandLineParserForJuicer juicerParser, List availableZooms) { configurations = HiCCUPSConfiguration.extractConfigurationsFromCommandLine(juicerParser, availableZooms, 2); if (configurations == null) { System.out.println("No valid configurations specified, using default settings"); configurationsSetByUser = false; } else { configurationsSetByUser = true; } try { List t = juicerParser.getThresholdOptions(); if (t != null && t.size() == 4) { double[] thresholds = HiCCUPSUtils.extractDoubleValues(t, 4, Double.NaN); setHiCCUPSFDROEThresholds(thresholds); } else if (t != null && t.size() == 5) { double[] thresholds = HiCCUPSUtils.extractDoubleValues(t, 5, Double.NaN); setHiCCUPSFDROEThresholds(thresholds); } else if (t != null && t.size() == 6) { double[] thresholds = HiCCUPSUtils.extractDoubleValues(t, 6, Double.NaN); setHiCCUPSFDROEThresholds(thresholds); } } catch (Exception e) { // do nothing - use default postprocessing thresholds } HiCCUPSscores.fdrsum1 = fdrsum1; HiCCUPSscores.fdrsum2 = fdrsum2; HiCCUPSscores.oeThreshold1 = oeThreshold1; HiCCUPSscores.oeThreshold2 = oeThreshold2; HiCCUPSscores.oeThreshold3 = oeThreshold3; } private void determineValidMatrixSize(CommandLineParserForJuicer juicerParser) { determineValidMatrixSize(juicerParser.getMatrixSizeOption()); } private void determineValidMatrixSize(int specifiedMatrixSize) { if (specifiedMatrixSize > 2 * regionMargin) { matrixSize = specifiedMatrixSize; regionWidth = specifiedMatrixSize - totalMargin; } if (HiCGlobals.printVerboseComments) { System.out.println("Using Matrix Size " + matrixSize); } } private void setHiCCUPSFDROEThresholds(double[] thresholds) { if (thresholds != null && thresholds.length == 4) { if (!Double.isNaN(thresholds[0]) && thresholds[0] > 0) fdrsum1 = thresholds[0]; if (!Double.isNaN(thresholds[0]) && thresholds[0] > 0) fdrsum2 = thresholds[0]; if (!Double.isNaN(thresholds[1]) && thresholds[1] > 0) oeThreshold1 = thresholds[1]; if (!Double.isNaN(thresholds[2]) && thresholds[2] > 0) oeThreshold2 = thresholds[2]; if (!Double.isNaN(thresholds[3]) && thresholds[3] > 0) oeThreshold3 = thresholds[3]; } if (thresholds != null && thresholds.length == 5) { if (!Double.isNaN(thresholds[0]) && thresholds[0] > 0) fdrsum1 = thresholds[0]; if (!Double.isNaN(thresholds[1]) && thresholds[1] > 0) fdrsum2 = thresholds[1]; if (!Double.isNaN(thresholds[2]) && thresholds[2] > 0) oeThreshold1 = thresholds[2]; if (!Double.isNaN(thresholds[3]) && thresholds[3] > 0) oeThreshold2 = thresholds[3]; if (!Double.isNaN(thresholds[4]) && thresholds[4] > 0) oeThreshold3 = thresholds[4]; } if (thresholds != null && thresholds.length == 6) { if (!Double.isNaN(thresholds[0]) && thresholds[0] > 0) fdrsum1 = thresholds[0]; if (!Double.isNaN(thresholds[1]) && thresholds[1] > 0) fdrsum2 = thresholds[1]; if (!Double.isNaN(thresholds[2]) && thresholds[2] > 0) oeThreshold1 = thresholds[2]; if (!Double.isNaN(thresholds[3]) && thresholds[3] > 0) oeThreshold2 = thresholds[3]; if (!Double.isNaN(thresholds[4]) && thresholds[4] > 0) oeThreshold3 = thresholds[4]; if (!Double.isNaN(thresholds[5]) && thresholds[5] > 0) oeThreshold3 = thresholds[5]; } } } ================================================ FILE: src/juicebox/tools/clt/juicer/Localizer.java ================================================ /* * The MIT License (MIT) * * Copyright (c) 2011-2020 Broad Institute, Aiden Lab * * Permission is hereby granted, free of charge, to any person obtaining a copy * of this software and associated documentation files (the "Software"), to deal * in the Software without restriction, including without limitation the rights * to use, copy, modify, merge, publish, distribute, sublicense, and/or sell * copies of the Software, and to permit persons to whom the Software is * furnished to do so, subject to the following conditions: * * The above copyright notice and this permission notice shall be included in * all copies or substantial portions of the Software. * * THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR * IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, * FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE * AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER * LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, * OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN * THE SOFTWARE. */ package juicebox.tools.clt.juicer; import com.google.common.primitives.Ints; import juicebox.HiC; import juicebox.HiCGlobals; import juicebox.data.ChromosomeHandler; import juicebox.data.Dataset; import juicebox.data.HiCFileTools; import juicebox.data.MatrixZoomData; import juicebox.data.anchor.GenericLocus; import juicebox.data.anchor.GenericLocusTools; import juicebox.data.anchor.MotifAnchorTools; import juicebox.data.basics.Chromosome; import juicebox.data.feature.GenomeWideList; import juicebox.tools.clt.CommandLineParserForJuicer; import juicebox.tools.clt.JuicerCLT; import juicebox.tools.utils.juicer.apa.APARegionStatistics; import juicebox.tools.utils.juicer.localizer.LocalizerUtils; import juicebox.track.feature.Feature2D; import juicebox.track.feature.Feature2DList; import juicebox.track.feature.Feature2DParser; import juicebox.track.feature.FeatureFilter; import juicebox.windowui.HiCZoom; import juicebox.windowui.NormalizationHandler; import juicebox.windowui.NormalizationType; import org.apache.commons.math.linear.RealMatrix; import java.io.File; import java.math.RoundingMode; import java.text.DecimalFormat; import java.time.Instant; import java.util.*; import java.util.concurrent.ConcurrentHashMap; import java.util.concurrent.ExecutorService; import java.util.concurrent.Executors; import java.util.concurrent.atomic.AtomicInteger; /** */ public class Localizer extends JuicerCLT { private String loopListPath; private File outputDirectory; private Dataset ds; private List summedHiCFiles; //defaults // TODO right now these units are based on n*res/sqrt(2) // TODO the sqrt(2) scaling should be removed (i.e. handle scaling internally) private int window = 1; private int expandSize = 2500; private int numLocalizedPeaks = 1; private int[] resolutions = new int[]{100}; private int[] regionWidths = new int[]{window}; private boolean includeInterChr = false; private Feature2DList finalLoopList = new Feature2DList(); private Feature2DList finalPrimaryLoopList = new Feature2DList(); private GenomeWideList highResAnchorList = new GenomeWideList<>(); private GenomeWideList highResAnchorPrimaryList = new GenomeWideList<>(); private GenomeWideList upstreamAnchorList = new GenomeWideList<>(); private GenomeWideList upstreamAnchorPrimaryList = new GenomeWideList<>(); private GenomeWideList downstreamAnchorList = new GenomeWideList<>(); private GenomeWideList downstreamAnchorPrimaryList = new GenomeWideList<>(); /** * Usage for APA */ public Localizer() { super("localizer [-n minval] [-x maxval] [-w window] [-r resolution(s)] [-c chromosomes]" + " [-k NONE/VC/VC_SQRT/KR] [-q corner_width] [-e include_inter_chr] [-u save_all_data]" + " "); HiCGlobals.useCache = false; } public static String getBasicUsage() { return "localizer "; } public void initializeDirectly(String inputHiCFileName, String inputPeaksFile, String outputDirectoryPath, int[] resolutions){ this.resolutions=resolutions; List summedHiCFiles = Arrays.asList(inputHiCFileName.split("\\+")); ds = HiCFileTools.extractDatasetForCLT(summedHiCFiles, true); this.loopListPath=inputPeaksFile; outputDirectory = HiCFileTools.createValidDirectory(outputDirectoryPath); //ds = HiCFileTools.extractDatasetForCLT(Arrays.asList(inputHiCFileName.split("\\+")), true); // outputDirectory = HiCFileTools.createValidDirectory(outputDirectoryPath); } @Override protected void readJuicerArguments(String[] args, CommandLineParserForJuicer juicerParser) { if (args.length != 4) { printUsageAndExit(); } loopListPath = args[2]; outputDirectory = HiCFileTools.createValidDirectory(args[3]); summedHiCFiles = Arrays.asList(args[1].split("\\+")); ds = HiCFileTools.extractDatasetForCLT(summedHiCFiles, true); NormalizationType preferredNorm = juicerParser.getNormalizationTypeOption(ds.getNormalizationHandler()); if (preferredNorm != null) norm = preferredNorm; int potentialWindow = juicerParser.getAPAWindowSizeOption(); if (potentialWindow > 0) window = potentialWindow; includeInterChr = juicerParser.getIncludeInterChromosomal(); List possibleRegionWidths = juicerParser.getAPACornerRegionDimensionOptions(); if (possibleRegionWidths != null) { List widths = new ArrayList<>(); for (String res : possibleRegionWidths) { widths.add(Integer.parseInt(res)); } regionWidths = Ints.toArray(widths); } List possibleResolutions = juicerParser.getMultipleResolutionOptions(); if (possibleResolutions != null) { List intResolutions = new ArrayList<>(); for (String res : possibleResolutions) { intResolutions.add(Integer.parseInt(res)); } resolutions = Ints.toArray(intResolutions); } numCPUThreads = juicerParser.getNumThreads(); expandSize = juicerParser.getExpandSize(); if (expandSize <= 0) { expandSize = 2500; } numLocalizedPeaks = juicerParser.getNumPeaks(); if (numLocalizedPeaks <= 0) { numLocalizedPeaks = 1; } } @Override public void run() { //Calculate parameters that will need later for (final int resolution : HiCFileTools.filterResolutions(ds.getBpZooms(), resolutions)) { AtomicInteger[] gwPeakNumbers = {new AtomicInteger(0), new AtomicInteger(0), new AtomicInteger(0)}; System.out.println("Processing Localizer for resolution " + resolution + " with window " + window); HiCZoom zoom = new HiCZoom(HiC.Unit.BP, resolution); ChromosomeHandler handler = ds.getChromosomeHandler(); if (givenChromosomes != null) handler = HiCFileTools.stringToChromosomes(givenChromosomes, handler); //Load loop list for localizer Feature2DList loopList = Feature2DParser.loadFeatures(loopListPath, handler, true, new FeatureFilter() { // Remove duplicates and filters by size // also save internal metrics for these measures @Override public List filter(String chr, List features) { List uniqueFeatures = new ArrayList<>(new HashSet<>(features)); return uniqueFeatures; } }, false); if (loopList.getNumTotalFeatures() > 0) { // output coarse anchors a la Rao & Huntley et al Cell 2014 GenomeWideList featureAnchors = GenericLocusTools.extractAnchorsFromIntrachromosomalFeatures(loopList, false, handler, expandSize); GenericLocusTools.updateOriginalFeatures(featureAnchors, "coarse"); featureAnchors.simpleExport(new File(outputDirectory, "coarseLoopAnchors_"+expandSize+".bed")); double maxProgressStatus = handler.size(); final AtomicInteger currentProgressStatus = new AtomicInteger(0); Map chromosomePairs = new ConcurrentHashMap<>(); int pairCounter = 1; for (Chromosome chr1 : handler.getChromosomeArrayWithoutAllByAll()) { for (Chromosome chr2 : handler.getChromosomeArrayWithoutAllByAll()) { Chromosome[] chromosomePair = {chr1,chr2}; chromosomePairs.put(pairCounter, chromosomePair); pairCounter++; } } final int chromosomePairCounter = pairCounter; // loop over chromosome pairs for (int i = 1; i < chromosomePairCounter; i++) { Chromosome chr1 = chromosomePairs.get(i)[0]; Chromosome chr2 = chromosomePairs.get(i)[1]; if ((chr2.getIndex() > chr1.getIndex() && includeInterChr) || (chr2.getIndex() == chr1.getIndex())) { System.out.println("processing: "+chr1.getName() + " " + chr2.getName()); //load zoom data MatrixZoomData zd; zd = HiCFileTools.getMatrixZoomData(ds, chr1, chr2, zoom); if (zd == null) { continue; } if (HiCGlobals.printVerboseComments) { System.out.println("CHR " + chr1.getName() + " " + chr1.getIndex() + " CHR " + chr2.getName() + " " + chr2.getIndex()); } //load loops for given chromosome pair List loops = loopList.get(chr1.getIndex(), chr2.getIndex()); if (loops == null || loops.size() == 0) { if (HiCGlobals.printVerboseComments) { System.out.println("CHR " + chr1.getName() + " CHR " + chr2.getName() + " - no loops, check loop filtering constraints"); } continue; } //multithread loop processing, 100 loops per thread int numOfLoopChunks = (loops.size() / 100) + 1; int numOfLoops = loops.size(); final AtomicInteger loopChunk = new AtomicInteger(0); ExecutorService executor = Executors.newFixedThreadPool(numCPUThreads); for (int l = 0; l < numCPUThreads; l++) { final int threadNum = l; Runnable worker = new Runnable() { @Override public void run() { int threadChunk = loopChunk.getAndIncrement(); while (threadChunk < numOfLoopChunks) { Instant A = Instant.now(); // loop over loops in threadchunk, process one loop at a time for (int loopIndex = threadChunk * 100; loopIndex < Math.min(numOfLoops, (threadChunk + 1) * 100); loopIndex++) { Feature2D loop = loops.get(loopIndex); int newWindow = window; try { // set radius to search for localization, uses radius attribute from HiCCUPS, otherwise uses defaults int radius = 0; if (loop.containsAttributeKey("radius")) { radius = (int) Float.parseFloat(loop.getAttribute("radius")) / resolution; } if (radius <= 0) { radius = (int) (loop.getEnd1() - loop.getStart1()) / resolution; } else if (radius <= 2000 / resolution) { radius = 2000 / resolution; } // load raw data and relevant portions of norm vector RealMatrix newData; List> normParts; newData = LocalizerUtils.extractLocalizedData(zd, loop, ((radius+newWindow) * 2) + 1, resolution, radius + newWindow, NormalizationHandler.NONE); synchronized(ds) { normParts = LocalizerUtils.extractNormParts(ds, zd, loop, resolution, radius + newWindow, norm); } // find localization List> localizedPeaks = LocalizerUtils.localMax(newData, normParts.get(0), normParts.get(1), newWindow, numLocalizedPeaks, 0.05, outputDirectory); //code for expanding smoothing window in case localization not found //int counter = 1; //while (localizedPeaks.get(0).size() == 0 && counter < 2) { // newWindow = window * (int) Math.pow(2,counter); // newData = LocalizerUtils.extractLocalizedData(zd, loop, ((radius+newWindow) * 2) + 1, resolution, radius + newWindow, NormalizationHandler.NONE); // synchronized(ds) { // normParts = LocalizerUtils.extractNormParts(ds, zd, loop, resolution, radius + newWindow, norm); // } // localizedPeaks = LocalizerUtils.localMax(newData, normParts.get(0), normParts.get(1), newWindow, numLocalizedPeaks, 0.05, outputDirectory); // counter++; //} // if localization not found, fill in localizer fields with NA if (localizedPeaks.get(0).size() == 0) { Feature2D newLoop = loop.deepCopy(); newLoop.addStringAttribute("localX", "" + "NA"); newLoop.addStringAttribute("localY", "" + "NA"); newLoop.addStringAttribute("localPval", "" + "NA"); newLoop.addStringAttribute("localObserved", "" + "NA"); newLoop.addStringAttribute("localPeakID", "" + "NA"); newLoop.addStringAttribute("localPeakZ", "" + "NA"); newLoop.addStringAttribute("highRes_start_1", "" + "NA"); newLoop.addStringAttribute("highRes_end_1", "" + "NA"); newLoop.addStringAttribute("highRes_start_2", "" + "NA"); newLoop.addStringAttribute("highRes_end_2", "" + "NA"); newLoop.addStringAttribute("upstream_start_1", "" + "NA"); newLoop.addStringAttribute("upstream_end_1", "" + "NA"); newLoop.addStringAttribute("downstream_start_2", "" + "NA"); newLoop.addStringAttribute("downstream_end_2", "" + "NA"); Feature2D newPrimaryLoop = newLoop.deepCopy(); synchronized (finalPrimaryLoopList) { finalPrimaryLoopList.add(chr1.getIndex(), chr2.getIndex(), newPrimaryLoop); } // if number of requested localized peaks is greater than 1, create a separate list given potential multiple entries if (numLocalizedPeaks > 1) { synchronized (finalLoopList) { finalLoopList.add(chr1.getIndex(), chr2.getIndex(), newLoop); } } } // create features for localized peaks for (int peak = 0; peak < localizedPeaks.get(0).size(); peak++) { Feature2D newLoop = loop.deepCopy(); long localPeakX = newLoop.getMidPt1() / resolution - radius - newWindow + localizedPeaks.get(0).get(peak).intValue(); long localPeakY = newLoop.getMidPt2() / resolution - radius - newWindow + localizedPeaks.get(1).get(peak).intValue(); double localPeakP = localizedPeaks.get(2).get(peak); double localPeakO = localizedPeaks.get(3).get(peak); double localPeakZ = localizedPeaks.get(4).get(peak); newLoop.addStringAttribute("localX", "" + (localPeakX * resolution)); newLoop.addStringAttribute("localY", "" + (localPeakY * resolution)); newLoop.addStringAttribute("localPval", "" + localPeakP); newLoop.addStringAttribute("localObserved", "" + localPeakO); newLoop.addStringAttribute("localPeakZ", "" + localPeakZ); newLoop.addStringAttribute("localPeakID", "" + peak); Feature2D newPrimaryLoop = newLoop.deepCopy(); List originalFeatures = new ArrayList<>(); originalFeatures.add(newLoop); List originalPrimaryFeatures = new ArrayList<>(); originalPrimaryFeatures.add(newPrimaryLoop); List emptyList = new ArrayList<>(); if (peak == 0) { GenericLocus primaryAnchor1 = new GenericLocus(newPrimaryLoop.getChr1(), (long) (localPeakX-newWindow-0.5)*resolution, (long) (localPeakX+newWindow+0.5)*resolution, originalPrimaryFeatures, emptyList); GenericLocus primaryAnchor2 = new GenericLocus(newPrimaryLoop.getChr2(), (long) (localPeakY-newWindow-0.5)*resolution, (long) (localPeakY+newWindow+0.5)*resolution, emptyList, originalPrimaryFeatures); synchronized (finalPrimaryLoopList) { finalPrimaryLoopList.add(chr1.getIndex(), chr2.getIndex(), newPrimaryLoop); } synchronized (highResAnchorPrimaryList) { highResAnchorPrimaryList.addFeature(newLoop.getChr1(), primaryAnchor1); highResAnchorPrimaryList.addFeature(newLoop.getChr2(), primaryAnchor2); } synchronized (upstreamAnchorPrimaryList) { upstreamAnchorPrimaryList.addFeature(newLoop.getChr1(), primaryAnchor1); } synchronized (downstreamAnchorPrimaryList) { downstreamAnchorPrimaryList.addFeature(newLoop.getChr2(), primaryAnchor2); } } if (numLocalizedPeaks>1) { GenericLocus anchor1 = new GenericLocus(newLoop.getChr1(), (long) (localPeakX-newWindow-0.5)*resolution, (long) (localPeakX+newWindow+0.5)*resolution, originalFeatures, emptyList); GenericLocus anchor2 = new GenericLocus(newLoop.getChr2(), (long) (localPeakY-newWindow-0.5)*resolution, (long) (localPeakY+newWindow+0.5)*resolution, emptyList, originalFeatures); synchronized (finalLoopList) { finalLoopList.add(chr1.getIndex(), chr2.getIndex(), newLoop); } synchronized (highResAnchorList) { highResAnchorList.addFeature(newLoop.getChr1(), anchor1); highResAnchorList.addFeature(newLoop.getChr2(), anchor2); } synchronized (upstreamAnchorList) { upstreamAnchorList.addFeature(newLoop.getChr1(), anchor1); } synchronized (downstreamAnchorList) { downstreamAnchorList.addFeature(newLoop.getChr2(), anchor2); } } } } catch (Exception e) { System.err.println(e); e.printStackTrace(); System.err.println("Unable to find data for loop: " + loop); } } int reasonableDivisor = Math.max(numOfLoopChunks / 20, 1); //if (HiCGlobals.printVerboseComments || threadChunk % reasonableDivisor == 0) { // DecimalFormat df = new DecimalFormat("#.####"); // df.setRoundingMode(RoundingMode.FLOOR); // System.out.println(df.format(Math.floor((100.0 * threadChunk) / numOfLoopChunks)) + "% "); //} threadChunk = loopChunk.getAndIncrement(); } } }; executor.execute(worker); } executor.shutdown(); // Wait until all threads finish while (!executor.isTerminated()) { } } } System.out.println("Exporting localizer results..."); // output primary list GenericLocusTools.callMergeAnchors(highResAnchorPrimaryList); GenericLocusTools.updateOriginalFeatures(highResAnchorPrimaryList, "highRes"); GenericLocusTools.callMergeAnchors(upstreamAnchorPrimaryList); GenericLocusTools.updateOriginalFeatures(upstreamAnchorPrimaryList, "upstream"); GenericLocusTools.callMergeAnchors(downstreamAnchorPrimaryList); GenericLocusTools.updateOriginalFeatures(downstreamAnchorPrimaryList, "downstream"); highResAnchorPrimaryList.simpleExport(new File(outputDirectory, "highRes_primary_loopAnchors.bed")); upstreamAnchorPrimaryList.simpleExport(new File(outputDirectory, "upstream_primary_loopAnchors.bed")); downstreamAnchorPrimaryList.simpleExport(new File(outputDirectory, "downstream_primary_loopAnchors.bed")); finalPrimaryLoopList.exportFeatureList(new File(outputDirectory, "localizedList_primary_"+resolution+".bedpe"), true, Feature2DList.ListFormat.LOCALIZED); // output secondary list if number of requested localized peaks > 1 if (numLocalizedPeaks > 1) { GenericLocusTools.callMergeAnchors(highResAnchorList); GenericLocusTools.updateOriginalFeatures(highResAnchorList, "highRes"); GenericLocusTools.callMergeAnchors(upstreamAnchorList); GenericLocusTools.updateOriginalFeatures(upstreamAnchorList, "upstream"); GenericLocusTools.callMergeAnchors(downstreamAnchorList); GenericLocusTools.updateOriginalFeatures(downstreamAnchorList, "downstream"); highResAnchorList.simpleExport(new File(outputDirectory, "highRes_loopAnchors.bed")); finalLoopList.exportFeatureList(new File(outputDirectory, "localizedList_" + resolution + ".bedpe"), true, Feature2DList.ListFormat.LOCALIZED); } } else { System.err.println("Loop list is empty or incorrect path provided."); System.exit(3); } } System.out.println("Localizer complete"); //if no data return null } } ================================================ FILE: src/juicebox/tools/clt/juicer/LoopDomains.java ================================================ /* * The MIT License (MIT) * * Copyright (c) 2011-2020 Broad Institute, Aiden Lab, Rice University, Baylor College of Medicine * * Permission is hereby granted, free of charge, to any person obtaining a copy * of this software and associated documentation files (the "Software"), to deal * in the Software without restriction, including without limitation the rights * to use, copy, modify, merge, publish, distribute, sublicense, and/or sell * copies of the Software, and to permit persons to whom the Software is * furnished to do so, subject to the following conditions: * * The above copyright notice and this permission notice shall be included in * all copies or substantial portions of the Software. * * THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR * IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, * FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE * AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER * LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, * OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN * THE SOFTWARE. */ package juicebox.tools.clt.juicer; import juicebox.HiCGlobals; import juicebox.data.ChromosomeHandler; import juicebox.data.HiCFileTools; import juicebox.tools.clt.CommandLineParserForJuicer; import juicebox.tools.clt.JuicerCLT; import juicebox.track.feature.*; import java.awt.*; import java.io.File; import java.util.ArrayList; import java.util.Collections; import java.util.List; /** * Created by muhammadsaadshamim on 12/29/15. */ public class LoopDomains extends JuicerCLT { private static final Color C_LOOP = new Color(34, 149, 34); private static final Color C_CONTACT = new Color(0, 105, 0); private static final Color C_LONE = new Color(102, 0, 153); /** * For every domain boundary, find the overlapping loop anchors. * this is just an intersection of domain boundary and loop anchor tracks, * but you'll need to give the domain boundaries a bit of width since there * are offsets and the exact boundary positions returned by arrowhead aren't * entirely reliable. There should be one or two loop anchors associated * with a domain boundary (two is the case where there are loops in * both directions) *

* For every loop anchor at a domain boundary, find the motifs required to * disrupt the loop. this is (almost) returned by the motif finder * (if we had completed the enhancements). but in the case of a unique motif or * inferred motif, that should be returned; otherwise, the collection of motifs * should be returned. this gives the set of motifs required to disrupt the domain boundary. **/ private int threshold = 25000; private String genomeID, loopListPath, domainListPath; private File outputFile = new File("loop_domains_list.bedpe"); /* * Assumes that the loop list provided already has associated motifs */ public LoopDomains() { super("loop_domains [-m threshold] [-c chromosome(s)] " + " [output_path]"); HiCGlobals.useCache = false; } @Override protected void readJuicerArguments(String[] args, CommandLineParserForJuicer juicerParser) { if (args.length != 4 && args.length != 5) { printUsageAndExit(); } genomeID = args[1]; loopListPath = args[2]; domainListPath = args[3]; if (args.length == 5) { String outputPath = args[4]; outputFile = new File(outputPath); if (!outputFile.exists()) { try { outputFile.createNewFile(); } catch (Exception e) { System.err.println("Couldn't create output file " + outputPath); System.exit(43); } } } int specifiedMatrixSize = juicerParser.getMatrixSizeOption(); if (specifiedMatrixSize > 0) { threshold = specifiedMatrixSize; } } @Override public void run() { ChromosomeHandler chromosomeHandler = HiCFileTools.loadChromosomes(genomeID); if (givenChromosomes != null) { chromosomeHandler = HiCFileTools.stringToChromosomes(givenChromosomes, chromosomeHandler); } // need to keep motifs for loop list final Feature2DList loopList = Feature2DParser.loadFeatures(loopListPath, chromosomeHandler, true, null, true); // domains have to use the extended with motif class, but they'll just have null values for that Feature2DList domainList = Feature2DParser.loadFeatures(domainListPath, chromosomeHandler, false, null, true); loopList.clearAllAttributes(); domainList.clearAllAttributes(); // only motifs are preserved due to usage of feature2DWithMotif class (the last boolean // parameter in feature load line) // not necessary as size of feature makes it pretty obvious... loopList.addAttributeFieldToAll("Type", "Loop"); domainList.addAttributeFieldToAll("Type", "Domain"); final Feature2DList loopDomainList = new Feature2DList(); domainList.processLists(new FeatureFunction() { @Override public void process(String chr, List feature2DList) { List domains = new ArrayList<>(feature2DList); List loops = new ArrayList<>(); if (loopList.containsKey(chr)) { loops.addAll(loopList.get(chr)); } Collections.sort(domains); Collections.sort(loops); for (Feature2D domain : domains) { boolean domainHasNoLoops = true; for (Feature2D loop : loops) { // since we've sorted, avoid assessing loops too far away if (Feature2DTools.loopIsUpstreamOfDomain(loop, domain, threshold)) { continue; } if (Feature2DTools.loopIsDownstreamOfDomain(loop, domain, threshold)) { break;// since list is sorted, all valid options should have been considered } if (Feature2DTools.domainContainsLoopWithinExpandedTolerance(loop, domain, threshold)) { // inside larger box if (!Feature2DTools.domainContainsLoopWithinExpandedTolerance(loop, domain, -threshold)) { // not inside smaller box, i.e. along boundary domainHasNoLoops = false; loop.setColor(C_LOOP); loopDomainList.addByKey(chr, loop); } } } if (domainHasNoLoops) { domain.setColor(C_LONE); } else { domain.setColor(C_CONTACT); } loopDomainList.addByKey(chr, domain); } } }); loopDomainList.exportFeatureList(outputFile, false, Feature2DList.ListFormat.NA); } } ================================================ FILE: src/juicebox/tools/clt/juicer/MotifFinder.java ================================================ /* * The MIT License (MIT) * * Copyright (c) 2011-2020 Broad Institute, Aiden Lab, Rice University, Baylor College of Medicine * * Permission is hereby granted, free of charge, to any person obtaining a copy * of this software and associated documentation files (the "Software"), to deal * in the Software without restriction, including without limitation the rights * to use, copy, modify, merge, publish, distribute, sublicense, and/or sell * copies of the Software, and to permit persons to whom the Software is * furnished to do so, subject to the following conditions: * * The above copyright notice and this permission notice shall be included in * all copies or substantial portions of the Software. * * THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR * IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, * FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE * AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER * LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, * OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN * THE SOFTWARE. */ package juicebox.tools.clt.juicer; import juicebox.data.ChromosomeHandler; import juicebox.data.HiCFileTools; import juicebox.data.anchor.*; import juicebox.data.feature.GenomeWideList; import juicebox.tools.clt.CommandLineParserForJuicer; import juicebox.tools.clt.JuicerCLT; import juicebox.track.feature.Feature2DList; import juicebox.track.feature.Feature2DParser; import java.io.File; import java.io.IOException; import java.util.ArrayList; import java.util.List; /** * Created by muhammadsaadshamim on 9/4/15. */ public class MotifFinder extends JuicerCLT { private final List tierOneFiles = new ArrayList<>(); private final List tierTwoFiles = new ArrayList<>(); private final List tierThreeFiles = new ArrayList<>(); private String outputPath; private String loopListPath; private String genomeID; private List proteinsForUniqueMotifPaths, proteinsForInferredMotifPaths; private String globalMotifListPath; private GenomeWideList genomeWideAnchorsList = new GenomeWideList<>(); public MotifFinder() { super("motifs [custom_global_motif_list]"); MotifAnchor.uniquenessShouldSupercedeConvergentRule = true; } private static GenomeWideList getIntersectionOfBEDFiles(ChromosomeHandler handler, List bedFiles) { GenomeWideList proteins = GenericLocusParser.loadFromBEDFile(handler, bedFiles.get(0)); for (int i = 1; i < bedFiles.size(); i++) { GenomeWideList nextProteinList = GenericLocusParser.loadFromBEDFile(handler, bedFiles.get(i)); MotifAnchorTools.intersectLists(proteins, nextProteinList, false); } return proteins; } @Override protected void readJuicerArguments(String[] args, CommandLineParserForJuicer juicerParser) { if (args.length != 4 && args.length != 5) { this.printUsageAndExit(); } int i = 1; genomeID = args[i++]; String bedFileDirPath = args[i++]; loopListPath = args[i++]; if (args.length == 5) { globalMotifListPath = args[i++]; } if (loopListPath.endsWith(".txt")) { outputPath = loopListPath.substring(0, loopListPath.length() - 4) + "_with_motifs.bedpe"; } else if (loopListPath.endsWith(".bedpe")) { outputPath = loopListPath.substring(0, loopListPath.length() - 6) + "_with_motifs.bedpe"; } else { outputPath = loopListPath + "_with_motifs.bedpe"; } try { retrieveAllBEDFiles(bedFileDirPath); } catch (Exception e) { System.err.println("Unable to locate BED files"); System.err.println("All BED files should include the '.bed' extension"); System.err.println("BED files for locating unique motifs should be located in " + bedFileDirPath + "/unique/*.bed"); System.err.println("BED files for locating inferred motifs should be located in " + bedFileDirPath + "/inferred/*.bed"); System.exit(54); } // TODO add specific chromosome option (i.e. use givenChromosomes) } @Override public void run() { ChromosomeHandler handler = HiCFileTools.loadChromosomes(genomeID); Feature2DList features = Feature2DParser.loadFeatures(loopListPath, handler, true, null, true); findUniqueMotifs(handler, features); findInferredMotifs(handler, features); features.exportFeatureList(new File(outputPath), false, Feature2DList.ListFormat.NA); System.out.println("Motif Finder complete"); } private void findInferredMotifs(ChromosomeHandler handler, Feature2DList features) { /* 1. identify all peak loci that overlap multiple CTCF peaks in the track CTCF_collapsed.narrowpeak. 2. split peak loci from step 1 by whether they are upstream peak loci or downstream peak loci. 3. For upstream peak loci, find the best motif match in each of the overlapping CTCF peaks from step 1. If there is only 1 overlapping CTCF peak with a best match motif that is a forward motif, retain that motif as the inferred motif for the peak locus. 4. For downstream peak loci, find the best motif match in each of the overlapping CTCF peaks from step 1. If there is only 1 overlapping CTCF peak with a best match motif that is a reverse motif, retain that motif as the inferred motif for the peak locus. Previously on Motif Finder: fourth step: the 1-d peak tracks provided in (iii) are intersected. fifth step: the 1-d peak track from step 4 are intersected with the genomewide motif list (best motif match) and split into a forward motif track and a reverse motif track. sixth step: upstream peak loci that did not have a unique motif are intersected with the forward motif track from step 5, and for each peak locus if the peak locus has only one forward motif, that is an inferred mapping (these motifs are outputted as 'i'). downstream peak loci that did not have a unique motif are intersected with the reverse motif track from step 5, and for each peak locus if the peak locus has only one reverse motif, that is an inferred mapping (these motifs are outputted as 'i'). Peak loci that form loops in both directions are ignored. */ GenomeWideList inferredProteins = getIntersectionOfBEDFiles(handler, proteinsForInferredMotifPaths); GenomeWideList featureAnchors = MotifAnchorTools.extractAnchorsFromIntrachromosomalFeatures(features, true, handler,15000); GenomeWideList globalAnchors = retrieveFreshMotifs(); GenomeWideList upStreamAnchors = MotifAnchorTools.extractDirectionalAnchors(featureAnchors, true); MotifAnchorTools.retainProteinsInLocus(inferredProteins, upStreamAnchors, false, true); MotifAnchorTools.retainBestMotifsInLocus(globalAnchors, inferredProteins); MotifAnchorTools.updateOriginalFeatures(globalAnchors, false, 1); // reset inferredProteins = getIntersectionOfBEDFiles(handler, proteinsForInferredMotifPaths); globalAnchors = retrieveFreshMotifs(); GenomeWideList downStreamAnchors = MotifAnchorTools.extractDirectionalAnchors(featureAnchors, false); MotifAnchorTools.retainProteinsInLocus(inferredProteins, downStreamAnchors, false, true); MotifAnchorTools.retainBestMotifsInLocus(globalAnchors, inferredProteins); MotifAnchorTools.updateOriginalFeatures(globalAnchors, false, 1); MotifAnchorTools.updateOriginalFeatures(globalAnchors, false, -1); } private void setUpThreeTieredFiltration() { for (String filename : proteinsForUniqueMotifPaths) { String nameLC = filename.toLowerCase(); if (nameLC.contains("ctcf") || nameLC.startsWith("1")) { tierOneFiles.add(filename); } else if (nameLC.contains("rad21") || nameLC.startsWith("2")) { tierTwoFiles.add(filename); } else { // smc3, and anything else tierThreeFiles.add(filename); } } } private GenomeWideList getThreeTierFilteredProteinTrack(ChromosomeHandler handler, GenomeWideList baseList) { if (tierOneFiles.size() > 0) { GenomeWideList tierOneProteins = getIntersectionOfBEDFiles(handler, tierOneFiles); MotifAnchorTools.retainProteinsInLocus(tierOneProteins, baseList, true, true); if (tierTwoFiles.size() > 0) { GenomeWideList tierTwoProteins = getIntersectionOfBEDFiles(handler, tierTwoFiles); if (tierTwoProteins.size() > 0) { MotifAnchorTools.preservativeIntersectLists(tierOneProteins, tierTwoProteins, false); } } if (tierThreeFiles.size() > 0) { GenomeWideList tierThreeProteins = getIntersectionOfBEDFiles(handler, tierThreeFiles); if (tierThreeProteins.size() > 0) { MotifAnchorTools.preservativeIntersectLists(tierOneProteins, tierThreeProteins, false); } } return tierOneProteins; } else { // no files System.err.println("No CTCF files provided"); System.exit(55); } return null; } private void findUniqueMotifs(ChromosomeHandler handler, Feature2DList features) { /* 1. take in loop list 2. convert to anchor list by splitting out each anchor of each loop, removing duplicates, merging adjacent anchors, and expanding anchors to 15kb if they are less than 15kb ---> (should be 12,903 peak loci using GEO GM12878 loop list) 3. intersecting peak loci with CTCF track, retaining CTCF sites that are unique in a peak locus ---> (should be 8,011 CTCF sites using CTCF_collasped.narrowpeak track and 12,903 peak loci from step 2) 4 (optional). intersecting unique CTCF sites with RAD21 sites and retaining sites that overlap a RAD21---> (should be 7,727 sites left using 8,011 from above and RAD21_collapsed.narrowPeak track) 5. (optional). intersection unique CTCF+RAD21 sites with SMC3 sites and retaining sites that overlap an SMC3. ---> (should be 7,599 sites left using 7,727 sites from above and SMC3 track) 6. intersecting list from latest step of {3,4,5} with motif list and retaining best (positive match score) motifs in each of the sites from latest step of {3,4,5} (Throw out sites that do not have a positive match score; if a huge number of sites are getting filtered here, we may want to increase the p-val threshold parameter on FIMO). */ setUpThreeTieredFiltration(); GenomeWideList featureAnchors = MotifAnchorTools.extractAnchorsFromIntrachromosomalFeatures(features, false, handler, 15000); GenomeWideList threeTierFilteredProteins = getThreeTierFilteredProteinTrack(handler, featureAnchors); GenomeWideList globalAnchors = retrieveFreshMotifs(); //MotifAnchorTools.intersectLists(threeTierFilteredProteins,globalAnchors, true); MotifAnchorTools.retainBestMotifsInLocus(globalAnchors, threeTierFilteredProteins); MotifAnchorTools.updateOriginalFeatures(globalAnchors, true, 0); } private GenomeWideList retrieveFreshMotifs() { if (genomeWideAnchorsList.size() < 10) { GenomeWideList anchors; if (globalMotifListPath == null || globalMotifListPath.length() < 1) { anchors = MotifAnchorParser.loadMotifsFromGenomeID(genomeID, null); } else { if (globalMotifListPath.contains("http")) { // url anchors = MotifAnchorParser.loadMotifsFromURL(globalMotifListPath, genomeID, null); } else { // local file anchors = MotifAnchorParser.loadMotifsFromLocalFile(globalMotifListPath, genomeID, null); } } genomeWideAnchorsList = new GenomeWideList<>(anchors); return anchors; } else { return new GenomeWideList<>(genomeWideAnchorsList); } } private void retrieveAllBEDFiles(String path) throws IOException { File bedFileDir = new File(path); if (bedFileDir.exists()) { String uniqueBEDFilesPath = path + "/unique"; String inferredBEDFilesPath = path + "/inferred"; // if the '/' was already included if (path.endsWith("/")) { uniqueBEDFilesPath = path + "unique"; inferredBEDFilesPath = path + "inferred"; } proteinsForUniqueMotifPaths = retrieveBEDFilesByExtensionInFolder(uniqueBEDFilesPath, "Unique"); proteinsForInferredMotifPaths = retrieveBEDFilesByExtensionInFolder(inferredBEDFilesPath, "Inferred"); } else { throw new IOException("BED files directory not valid"); } } private List retrieveBEDFilesByExtensionInFolder(String directoryPath, String description) throws IOException { List bedFiles = new ArrayList<>(); File folder = new File(directoryPath); File[] listOfFiles = folder.listFiles(); for (File file : listOfFiles) { if (file.isFile()) { String path = file.getAbsolutePath(); if (path.endsWith(".bed")) { bedFiles.add(path); } } } if (bedFiles.size() < 1) { throw new IOException(description + " BED files not found"); } return bedFiles; } } ================================================ FILE: src/juicebox/tools/clt/old/AddNorm.java ================================================ /* * The MIT License (MIT) * * Copyright (c) 2011-2021 Broad Institute, Aiden Lab, Rice University, Baylor College of Medicine * * Permission is hereby granted, free of charge, to any person obtaining a copy * of this software and associated documentation files (the "Software"), to deal * in the Software without restriction, including without limitation the rights * to use, copy, modify, merge, publish, distribute, sublicense, and/or sell * copies of the Software, and to permit persons to whom the Software is * furnished to do so, subject to the following conditions: * * The above copyright notice and this permission notice shall be included in * all copies or substantial portions of the Software. * * THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR * IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, * FITNESS FOR A PARTICULAR PURPOSE AND NON-INFRINGEMENT. IN NO EVENT SHALL THE * AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER * LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, * OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN * THE SOFTWARE. */ package juicebox.tools.clt.old; import juicebox.HiCGlobals; import juicebox.data.iterator.IteratorContainer; import juicebox.tools.clt.CommandLineParser; import juicebox.tools.clt.JuiceboxCLT; import juicebox.tools.utils.norm.CustomNormVectorFileHandler; import juicebox.tools.utils.norm.NormalizationVectorUpdater; import juicebox.windowui.NormalizationHandler; import juicebox.windowui.NormalizationType; import java.io.IOException; import java.util.ArrayList; import java.util.HashMap; import java.util.List; import java.util.Map; public class AddNorm extends JuiceboxCLT { private boolean noFragNorm = false; private String inputVectorFile = null; private int genomeWideResolution = -100; private String file; private final List normalizationTypes = new ArrayList<>(); private Map resolutionsToBuildTo; public AddNorm() { super(getBasicUsage() + "\n" + " : -d use intra chromosome (diagonal) [false]\n" + " : -F don't calculate normalization for fragment-delimited maps [false]\n" + " : -w calculate genome-wide resolution on all resolutions >= input resolution [not set]\n" + " Above options ignored if input_vector_file present\n" + " : -k normalizations to include\n" + " : -r resolutions for respective normalizations to build to\n" + " : -j number of CPU threads to use\n" + " : --conserve-ram will minimize RAM usage\n" + " : --check-ram-usage will check ram requirements prior to running" ); } public static String getBasicUsage() { return "addNorm [input_vector_file]"; } public static Map defaultHashMapForResToBuildTo(List normalizationTypes) { HashMap map = new HashMap<>(); for (NormalizationType norm : normalizationTypes) { map.put(norm, NormalizationHandler.getIdealResolutionLimit(norm)); } return map; } public static void launch(String outputFile, List normalizationTypes, int genomeWide, boolean noFragNorm, int numCPUThreads, Map resolutionsToBuildTo) throws IOException { HiCGlobals.useCache = false; NormalizationVectorUpdater updater = new NormalizationVectorUpdater(); updater.updateHicFile(outputFile, normalizationTypes, resolutionsToBuildTo, genomeWide, noFragNorm); } @Override public void readArguments(String[] args, CommandLineParser parser) { if (parser.getHelpOption()) { printUsageAndExit(); } if (args.length == 3) { inputVectorFile = args[2]; } else if (args.length != 2) { printUsageAndExit(); } noFragNorm = parser.getNoFragNormOption(); HiCGlobals.USE_ITERATOR_NOT_ALL_IN_RAM = parser.getDontPutAllContactsIntoRAM(); HiCGlobals.CHECK_RAM_USAGE = parser.shouldCheckRAMUsage(); updateNumberOfCPUThreads(parser, 10); IteratorContainer.numCPUMatrixThreads = numCPUThreads; usingMultiThreadedVersion = numCPUThreads > 1; genomeWideResolution = parser.getGenomeWideOption(); normalizationTypes.addAll(parser.getAllNormalizationTypesOption()); resolutionsToBuildTo = defaultHashMapForResToBuildTo(normalizationTypes); List resolutions = parser.getResolutionOption(); if (resolutions != null && resolutions.size() > 0) { if (resolutions.size() != normalizationTypes.size()) { System.err.println("Error: Number of resolutions and normalizations need to be the same"); System.exit(0); } for (int k = 0; k < resolutions.size(); k++) { NormalizationType normType = normalizationTypes.get(k); try { int resVal = Integer.parseInt(resolutions.get(k)); resolutionsToBuildTo.put(normType, resVal); } catch (Exception e) { resolutionsToBuildTo.put(normType, NormalizationHandler.getIdealResolutionLimit(normType)); } } } file = args[1]; } @Override public void run() { HiCGlobals.allowDynamicBlockIndex = false; try { if (inputVectorFile != null) { CustomNormVectorFileHandler.updateHicFile(file, inputVectorFile, numCPUThreads); } else { launch(file, normalizationTypes, genomeWideResolution, noFragNorm, numCPUThreads, resolutionsToBuildTo); } } catch (Exception e) { e.printStackTrace(); } } } ================================================ FILE: src/juicebox/tools/clt/old/BPToFragment.java ================================================ /* * The MIT License (MIT) * * Copyright (c) 2011-2020 Broad Institute, Aiden Lab, Rice University, Baylor College of Medicine * * Permission is hereby granted, free of charge, to any person obtaining a copy * of this software and associated documentation files (the "Software"), to deal * in the Software without restriction, including without limitation the rights * to use, copy, modify, merge, publish, distribute, sublicense, and/or sell * copies of the Software, and to permit persons to whom the Software is * furnished to do so, subject to the following conditions: * * The above copyright notice and this permission notice shall be included in * all copies or substantial portions of the Software. * * THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR * IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, * FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE * AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER * LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, * OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN * THE SOFTWARE. */ package juicebox.tools.clt.old; import htsjdk.samtools.util.Locatable; import juicebox.HiCGlobals; import juicebox.tools.clt.CommandLineParser; import juicebox.tools.clt.JuiceboxCLT; import juicebox.tools.utils.original.FragmentCalculation; import org.broad.igv.util.ParsingUtils; import java.io.*; import java.util.HashMap; import java.util.Map; import java.util.regex.Pattern; public class BPToFragment extends JuiceboxCLT { private String fragFile, inputBedFile, outputFile; public BPToFragment() { super("bpToFrag "); } private static void bpToFrag(String fragmentFile, String inputFile, String outputDir) throws IOException { BufferedReader fragmentReader = null; Pattern pattern = Pattern.compile("\\s"); Map fragmentMap = new HashMap<>(); // Map of chr -> site positions try { fragmentReader = new BufferedReader(new FileReader(fragmentFile), HiCGlobals.bufferSize); String nextLine; while ((nextLine = fragmentReader.readLine()) != null) { //String[] tokens = pattern.split(nextLine); String[] tokens = splitToList(nextLine); // A hack, could use IGV's genome alias definitions String chr = getChrAlias(tokens[0]); int[] sites = new int[tokens.length]; sites[0] = 0; // Convenient convention for (int i = 1; i < tokens.length; i++) { sites[i] = Integer.parseInt(tokens[i]) - 1; } fragmentMap.put(chr, sites); } } finally { assert fragmentReader != null; fragmentReader.close(); } // inputFile contains a list of files or URLs. BufferedReader reader = null; try { File dir = new File(outputDir); if (!dir.exists() || !dir.isDirectory()) { System.out.println("Output directory does not exist, or is not directory"); System.exit(6); } reader = new BufferedReader(new FileReader(inputFile), HiCGlobals.bufferSize); String nextLine; while ((nextLine = reader.readLine()) != null) { String path = nextLine.trim(); int lastSlashIdx = path.lastIndexOf("/"); if (lastSlashIdx < 0) lastSlashIdx = path.lastIndexOf("\\"); // Windows convention String fn = lastSlashIdx < 0 ? path : path.substring(lastSlashIdx); File outputFile = new File(dir, fn + ".sites"); annotateWithSites(fragmentMap, path, outputFile); } } finally { if (reader != null) reader.close(); } } /** * Find fragments that overlap the input bed file. Its assumed the bed file is sorted by start position, otherwise * an exception is thrown. If a fragment overlaps 2 or more bed featuers it is only outputted once. * * @param fragmentMap * @param bedFile * @param outputBedFile * @throws java.io.IOException */ private static void annotateWithSites(Map fragmentMap, String bedFile, File outputBedFile) throws IOException { BufferedReader bedReader = null; PrintWriter bedWriter = null; try { //bedReader = ParsingUtils.openBufferedReader(bedFile); bedReader = new BufferedReader(new InputStreamReader(ParsingUtils.openInputStream(bedFile)), HiCGlobals.bufferSize); bedWriter = new PrintWriter(new BufferedWriter(new FileWriter(outputBedFile))); String nextLine; while ((nextLine = bedReader.readLine()) != null) { if (nextLine.startsWith("track") || nextLine.startsWith("browser") || nextLine.startsWith("#")) continue; BedLikeFeature feature = new BedLikeFeature(nextLine); //String[] tokens = Globals.whitespacePattern.split(nextLine); String[] tokens = splitToList(nextLine); String chr = tokens[0]; int start = Integer.parseInt(tokens[1]); int end = Integer.parseInt(tokens[2]); int[] sites = fragmentMap.get(feature.getContig()); if (sites == null) continue; int firstSite = FragmentCalculation.binarySearch(sites, feature.getStart()); int lastSite = FragmentCalculation.binarySearch(sites, feature.getEnd()); bedWriter.print(chr + "\t" + start + "\t" + end + "\t" + firstSite + "\t" + lastSite); for (int i = 3; i < tokens.length; i++) { bedWriter.print("\t" + tokens.length); } bedWriter.println(); } } finally { if (bedReader != null) bedReader.close(); if (bedWriter != null) bedWriter.close(); } } private static String getChrAlias(String token) { if (token.equals("MT")) { return "chrM"; } else if (!token.startsWith("chr")) { return "chr" + token; } else { return token; } } @Override public void readArguments(String[] args, CommandLineParser parser) { //setUsage("juicebox bpToFrag "); if (args.length != 4) { printUsageAndExit(); } fragFile = args[1]; inputBedFile = args[2]; outputFile = args[3]; } @Override public void run() { try { bpToFrag(fragFile, inputBedFile, outputFile); } catch (Exception e) { e.printStackTrace(); } } private static class BedLikeFeature implements Locatable { final String chr; final String line; int start; int end; String name; BedLikeFeature(String line) { this.line = line; //String[] tokens = Globals.whitespacePattern.split(line); String[] tokens = splitToList(line); this.chr = tokens[0]; this.start = Integer.parseInt(tokens[1]); this.end = Integer.parseInt(tokens[2]); if (tokens.length > 3) { this.name = name; // TODO - is this supposed to be this.name = tokens[x]? otherwise a redundant line } } public int getStart() { return start; } public void setStart(int start) { this.start = start; } public int getEnd() { return end; } public void setEnd(int end) { this.end = end; } public float getScore() { return 0; } @Override public String getContig() { return chr; } } } ================================================ FILE: src/juicebox/tools/clt/old/BigWig.java ================================================ /* * The MIT License (MIT) * * Copyright (c) 2011-2021 Broad Institute, Aiden Lab, Rice University, Baylor College of Medicine * * Permission is hereby granted, free of charge, to any person obtaining a copy * of this software and associated documentation files (the "Software"), to deal * in the Software without restriction, including without limitation the rights * to use, copy, modify, merge, publish, distribute, sublicense, and/or sell * copies of the Software, and to permit persons to whom the Software is * furnished to do so, subject to the following conditions: * * The above copyright notice and this permission notice shall be included in * all copies or substantial portions of the Software. * * THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR * IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, * FITNESS FOR A PARTICULAR PURPOSE AND NON-INFRINGEMENT. IN NO EVENT SHALL THE * AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER * LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, * OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN * THE SOFTWARE. */ package juicebox.tools.clt.old; import juicebox.tools.clt.CommandLineParser; import juicebox.tools.clt.JuiceboxCLT; import juicebox.tools.utils.original.BigWigUtils; public class BigWig extends JuiceboxCLT { private int version = -1; private int start = -1, end = -1, windowSize = -1; private String chr, path; public BigWig() { super("bigWig [chr] [start base] [end base]"); } @Override public void readArguments(String[] args, CommandLineParser parser) { //setUsage("juicebox bigWig [chr] [start base] [end base]"); if (!(args.length == 3 || args.length == 4 || args.length == 6)) { printUsageAndExit(); } path = args[1]; windowSize = Integer.parseInt(args[2]); if (args.length == 3) { version = 0; } else { chr = args[3]; if (args.length == 4) { version = 1; } else { start = Integer.parseInt(args[4]) - 1; // Convert to "zero" based coords end = Integer.parseInt(args[5]); version = 2; } } } @Override public void run() { try { if (version == 0) { BigWigUtils.computeBins(path, windowSize); } else if (version == 1) { BigWigUtils.computeBins(path, chr, 0, Integer.MAX_VALUE, windowSize); } else if (version == 2) { BigWigUtils.computeBins(path, chr, start, end, windowSize); } else { System.err.println("Invalid Option Setup"); printUsageAndExit(); } } catch (Exception e) { e.printStackTrace(); } } } ================================================ FILE: src/juicebox/tools/clt/old/BinToPairs.java ================================================ /* * The MIT License (MIT) * * Copyright (c) 2011-2021 Broad Institute, Aiden Lab, Rice University, Baylor College of Medicine * * Permission is hereby granted, free of charge, to any person obtaining a copy * of this software and associated documentation files (the "Software"), to deal * in the Software without restriction, including without limitation the rights * to use, copy, modify, merge, publish, distribute, sublicense, and/or sell * copies of the Software, and to permit persons to whom the Software is * furnished to do so, subject to the following conditions: * * The above copyright notice and this permission notice shall be included in * all copies or substantial portions of the Software. * * THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR * IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, * FITNESS FOR A PARTICULAR PURPOSE AND NON-INFRINGEMENT. IN NO EVENT SHALL THE * AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER * LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, * OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN * THE SOFTWARE. */ package juicebox.tools.clt.old; import juicebox.tools.clt.CommandLineParser; import juicebox.tools.clt.JuiceboxCLT; import juicebox.tools.utils.original.mnditerator.AsciiToBinConverter; public class BinToPairs extends JuiceboxCLT { private String ifile, ofile; public BinToPairs() { super("binToPairs "); } @Override public void readArguments(String[] args, CommandLineParser parser) { if (args.length != 3) { printUsageAndExit(); } ifile = args[1]; ofile = args[2]; } @Override public void run() { try { AsciiToBinConverter.convertBack(ifile, ofile); } catch (Exception e) { e.printStackTrace(); } } } ================================================ FILE: src/juicebox/tools/clt/old/CalcKR.java ================================================ /* * The MIT License (MIT) * * Copyright (c) 2011-2021 Broad Institute, Aiden Lab, Rice University, Baylor College of Medicine * * Permission is hereby granted, free of charge, to any person obtaining a copy * of this software and associated documentation files (the "Software"), to deal * in the Software without restriction, including without limitation the rights * to use, copy, modify, merge, publish, distribute, sublicense, and/or sell * copies of the Software, and to permit persons to whom the Software is * furnished to do so, subject to the following conditions: * * The above copyright notice and this permission notice shall be included in * all copies or substantial portions of the Software. * * THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR * IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, * FITNESS FOR A PARTICULAR PURPOSE AND NON-INFRINGEMENT. IN NO EVENT SHALL THE * AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER * LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, * OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN * THE SOFTWARE. */ package juicebox.tools.clt.old; import juicebox.data.ContactRecord; import juicebox.data.iterator.IteratorContainer; import juicebox.data.iterator.ListIteratorContainer; import juicebox.tools.clt.CommandLineParser; import juicebox.tools.clt.JuiceboxCLT; import juicebox.tools.utils.norm.NormalizationCalculations; import juicebox.windowui.NormalizationHandler; import org.broad.igv.Globals; import java.io.BufferedReader; import java.io.IOException; import java.util.ArrayList; import java.util.List; public class CalcKR extends JuiceboxCLT { private String infile = null; public CalcKR() { super("calcKR "); } @Override public void readArguments(String[] args, CommandLineParser parser) { //setUsage("juicebox calcKR "); if (!(args.length == 2)) { printUsageAndExit(); } infile = args[1]; } public static void calcKR(String path) throws IOException { BufferedReader reader = org.broad.igv.util.ParsingUtils.openBufferedReader(path); String nextLine; int lineCount = 0; int maxBin = 0; List readList = new ArrayList<>(); while ((nextLine = reader.readLine()) != null) { lineCount++; String[] tokens = Globals.singleTabMultiSpacePattern.split(nextLine); int nTokens = tokens.length; if (nTokens != 3) { System.err.println("Number of columns incorrect at line" + lineCount + ": " + nextLine); System.exit(62); } int binX = Integer.parseInt(tokens[0]); int binY = Integer.parseInt(tokens[1]); int count = Integer.parseInt(tokens[2]); ContactRecord record = new ContactRecord(binX, binY, count); readList.add(record); if (binX > maxBin) maxBin = binX; if (binY > maxBin) maxBin = binY; } IteratorContainer ic = new ListIteratorContainer(readList, maxBin + 1); NormalizationCalculations nc = new NormalizationCalculations(ic); for (float[] array : nc.getNorm(NormalizationHandler.KR).getValues()) { for (double d : array) { System.out.println(d); } } } @Override public void run() { try { calcKR(infile); } catch (Exception e) { e.printStackTrace(); } } } ================================================ FILE: src/juicebox/tools/clt/old/CalcMatrixSum.java ================================================ /* * The MIT License (MIT) * * Copyright (c) 2011-2021 Broad Institute, Aiden Lab, Rice University, Baylor College of Medicine * * Permission is hereby granted, free of charge, to any person obtaining a copy * of this software and associated documentation files (the "Software"), to deal * in the Software without restriction, including without limitation the rights * to use, copy, modify, merge, publish, distribute, sublicense, and/or sell * copies of the Software, and to permit persons to whom the Software is * furnished to do so, subject to the following conditions: * * The above copyright notice and this permission notice shall be included in * all copies or substantial portions of the Software. * * THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR * IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, * FITNESS FOR A PARTICULAR PURPOSE AND NON-INFRINGEMENT. IN NO EVENT SHALL THE * AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER * LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, * OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN * THE SOFTWARE. */ package juicebox.tools.clt.old; import juicebox.data.*; import juicebox.data.basics.Chromosome; import juicebox.data.iterator.IteratorContainer; import juicebox.tools.clt.CommandLineParser; import juicebox.tools.clt.JuiceboxCLT; import juicebox.tools.utils.common.MatrixTools; import juicebox.tools.utils.norm.NormalizationCalculations; import juicebox.windowui.HiCZoom; import juicebox.windowui.NormalizationType; import java.io.File; import java.io.FileNotFoundException; import java.io.FileOutputStream; import java.io.PrintWriter; import java.util.*; import java.util.concurrent.ExecutorService; import java.util.concurrent.Executors; public class CalcMatrixSum extends JuiceboxCLT { private File outputSummaryFile, outputNpyFile, outputTxtFile; private ChromosomeHandler chromosomeHandler; private PrintWriter printWriter; public CalcMatrixSum() { super("calcMatrixSum "); } private static String getKeyWithNorm(Chromosome chromosome, HiCZoom zoom, NormalizationType normalizationType) { return chromosome.getName() + "_" + zoom.getKey() + "_" + normalizationType.getLabel(); } @Override public void readArguments(String[] args, CommandLineParser parser) { if (!(args.length == 4)) { printUsageAndExit(); } setDatasetAndNorm(args[2], args[1], false); File outputDirectory = HiCFileTools.createValidDirectory(args[3]); outputSummaryFile = new File(outputDirectory, "matrix_sums_summary.txt"); outputNpyFile = new File(outputDirectory, "matrix_sums_data.npy"); outputTxtFile = new File(outputDirectory, "matrix_sums_data.txt"); chromosomeHandler = dataset.getChromosomeHandler(); try { printWriter = new PrintWriter(new FileOutputStream(outputSummaryFile)); } catch (FileNotFoundException e) { e.printStackTrace(); System.exit(-5); } } @Override public void run() { int numCPUThreads = Runtime.getRuntime().availableProcessors(); ExecutorService executor = Executors.newFixedThreadPool(numCPUThreads); Map zoomToMatrixSumMap = new HashMap<>(); for (Chromosome chromosome : chromosomeHandler.getChromosomeArrayWithoutAllByAll()) { for (HiCZoom zoom : dataset.getBpZooms()) { Runnable worker = new Runnable() { @Override public void run() { NormalizationVector normalizationVector = dataset.getNormalizationVector(chromosome.getIndex(), zoom, norm); double[] actualVector; MatrixZoomData zd; try { actualVector = normalizationVector.getData().getValues().get(0); zd = HiCFileTools.getMatrixZoomData(dataset, chromosome, chromosome, zoom); } catch (Exception e) { System.err.println("No data for " + norm.getLabel() + " - " + chromosome + " at " + zoom); return; } if (zd == null) { System.err.println("Null MatrixZoomData"); return; } NormalizationCalculations calculations = new NormalizationCalculations(zd.getIteratorContainer()); Double[] matrixSum = getNormMatrixSumFactor(actualVector, zd.getIteratorContainer()); int numValidVectorEntries = calculations.getNumberOfValidEntriesInVector(actualVector); Double[] result = new Double[]{matrixSum[0], matrixSum[1], (double) numValidVectorEntries}; String key = getKeyWithNorm(chromosome, zoom, norm); synchronized (zoomToMatrixSumMap) { zoomToMatrixSumMap.put(key, result); } System.out.println("Finished: " + key); /* testCode(zoom, zd.getContactRecordList(), actualVector, 1. / matrixSum[0], numValidVectorEntries / matrixSum[0]); */ } }; executor.execute(worker); } } executor.shutdown(); while (!executor.isTerminated()) { } printWriter.println("Normalization Type: " + norm); List matrixFormat = new ArrayList<>(); for (Chromosome chromosome : chromosomeHandler.getChromosomeArrayWithoutAllByAll()) { printWriter.println("Chromsome: " + chromosome + " index: " + chromosome.getIndex()); for (HiCZoom zoom : dataset.getBpZooms()) { String key = getKeyWithNorm(chromosome, zoom, norm); if (zoomToMatrixSumMap.containsKey(key)) { printWriter.println("Zoom: " + zoom + " Normalized Matrix Sum: " + zoomToMatrixSumMap.get(key)[0] + " Original Matrix Sum: " + zoomToMatrixSumMap.get(key)[1] + " Number of Positive Entries in Vector: " + zoomToMatrixSumMap.get(key)[2]); matrixFormat.add(new double[]{ (double) chromosome.getIndex(), (double) zoom.getBinSize(), zoomToMatrixSumMap.get(key)[0], zoomToMatrixSumMap.get(key)[1], zoomToMatrixSumMap.get(key)[2] }); } } } printWriter.close(); double[][] matrixFormatArray = new double[matrixFormat.size()][5]; for (int i = 0; i < matrixFormat.size(); i++) { matrixFormatArray[i] = matrixFormat.get(i); } MatrixTools.saveMatrixTextV2(outputTxtFile.getAbsolutePath(), matrixFormatArray); MatrixTools.saveMatrixTextNumpy(outputNpyFile.getAbsolutePath(), matrixFormatArray); } public Double[] getNormMatrixSumFactor(double[] norm, IteratorContainer ic) { double matrix_sum = 0; double norm_sum = 0; Iterator iterator = ic.getNewContactRecordIterator(); while (iterator.hasNext()) { ContactRecord cr = iterator.next(); int x = cr.getBinX(); int y = cr.getBinY(); float value = cr.getCounts(); double valX = norm[x]; double valY = norm[y]; if (!Double.isNaN(valX) && !Double.isNaN(valY) && valX > 0 && valY > 0) { // want total sum of matrix, not just upper triangle if (x == y) { norm_sum += value / (valX * valY); matrix_sum += value; } else { norm_sum += 2 * value / (valX * valY); matrix_sum += 2 * value; } } } return new Double[]{norm_sum, matrix_sum}; } private void testCode(HiCZoom zoom, List contactRecordList, double[] actualVector, double scalar1, double scalar2) { if (zoom.getBinSize() > 100000) { System.out.println("No scaling"); System.out.println(Arrays.toString(MatrixTools.getRowSums(contactRecordList, 1, actualVector))); System.out.println("Scale by 1/sum"); System.out.println(Arrays.toString(MatrixTools.getRowSums(contactRecordList, scalar1, actualVector))); System.out.println("Scale by N/M"); System.out.println(Arrays.toString(MatrixTools.getRowSums(contactRecordList, scalar2, actualVector))); } } } ================================================ FILE: src/juicebox/tools/clt/old/Dump.java ================================================ /* * The MIT License (MIT) * * Copyright (c) 2011-2021 Broad Institute, Aiden Lab, Rice University, Baylor College of Medicine * * Permission is hereby granted, free of charge, to any person obtaining a copy * of this software and associated documentation files (the "Software"), to deal * in the Software without restriction, including without limitation the rights * to use, copy, modify, merge, publish, distribute, sublicense, and/or sell * copies of the Software, and to permit persons to whom the Software is * furnished to do so, subject to the following conditions: * * The above copyright notice and this permission notice shall be included in * all copies or substantial portions of the Software. * * THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR * IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, * FITNESS FOR A PARTICULAR PURPOSE AND NON-INFRINGEMENT. IN NO EVENT SHALL THE * AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER * LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, * OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN * THE SOFTWARE. */ package juicebox.tools.clt.old; import htsjdk.tribble.util.LittleEndianOutputStream; import juicebox.HiC; import juicebox.HiCGlobals; import juicebox.data.*; import juicebox.data.basics.Chromosome; import juicebox.data.basics.ListOfDoubleArrays; import juicebox.data.iterator.GWIteratorContainer; import juicebox.data.iterator.IteratorContainer; import juicebox.tools.clt.CommandLineParser; import juicebox.tools.clt.JuiceboxCLT; import juicebox.tools.utils.common.MatrixTools; import juicebox.tools.utils.norm.NormalizationCalculations; import juicebox.tools.utils.original.ExpectedValueCalculation; import juicebox.windowui.HiCZoom; import juicebox.windowui.MatrixType; import juicebox.windowui.NormalizationHandler; import org.broad.igv.util.ParsingUtils; import org.broad.igv.util.ResourceLocator; import java.io.*; import java.util.Arrays; import java.util.Iterator; public class Dump extends JuiceboxCLT { private static long[] regionIndices = new long[]{-1, -1, -1, -1}; private static boolean useRegionIndices = false; private HiC.Unit unit = null; private String chr1, chr2; private ChromosomeHandler chromosomeHandler; private int binSize = 0; private MatrixType matrixType = null; private PrintWriter pw = null; private LittleEndianOutputStream les = null; private HiCZoom zoom = null; private boolean includeIntra = false; private boolean dense = false; private String feature = null; private String ofile = null; public Dump() { super(getUsage()); } public static String getUsage(){ return "dump [:x1:x2] [:y1:y2] [outfile]\n" + "\tdump [outfile]\n" + "\tdump [outfile]"; } private void dumpGenomeWideData() { if (unit == HiC.Unit.FRAG) { System.err.println("All versus All currently not supported on fragment resolution"); System.exit(8); } // This is for internal purposes only - to print the All vs All matrix // This matrix should not in general be exposed since it is arbitrarily binned // If in the future we wish to expose, we should use a more reasonable flag. if (zoom.getBinSize() == 6197 || zoom.getBinSize() == 6191) { Chromosome chr = chromosomeHandler.getChromosomeFromName("All"); MatrixZoomData zd = HiCFileTools.getMatrixZoomData(dataset, chr, chr, zoom); if (zd == null) { System.err.println("No All vs. All matrix; be sure zoom is correct"); System.exit(1); } Iterator iterator = zd.getIteratorContainer().getNewContactRecordIterator(); while (iterator.hasNext()) { ContactRecord cr = iterator.next(); pw.println(cr.getBinX() + "\t" + cr.getBinY() + "\t" + cr.getCounts()); } pw.close(); return; } // Build a "whole-genome" matrix IteratorContainer ic = new GWIteratorContainer(dataset, chromosomeHandler, zoom, includeIntra); if (ic.getNumberOfContactRecords() < 1) { System.err.println("No reads found at " + zoom + ". Include intra is " + includeIntra); return; } NormalizationCalculations calculations = new NormalizationCalculations(ic); float[] vector = calculations.getNorm(norm).getValues().get(0); if (matrixType == MatrixType.NORM) { ExpectedValueCalculation evKR = new ExpectedValueCalculation(chromosomeHandler, binSize, null, NormalizationHandler.GW_KR); int addY = 0; // Loop through chromosomes for (Chromosome chr : chromosomeHandler.getChromosomeArrayWithoutAllByAll()) { final int chrIdx = chr.getIndex(); MatrixZoomData zd = HiCFileTools.getMatrixZoomData(dataset, chr, chr, zoom); if (zd == null) continue; Iterator iterator = zd.getIteratorContainer().getNewContactRecordIterator(); while (iterator.hasNext()) { ContactRecord cr = iterator.next(); int x = cr.getBinX(); int y = cr.getBinY(); final float counts = cr.getCounts(); if (vector[x + addY] > 0 && vector[y + addY] > 0 && !Double.isNaN(vector[x + addY]) && !Double.isNaN(vector[y + addY])) { double value = counts / (vector[x + addY] * vector[y + addY]); evKR.addDistance(chrIdx, x, y, value); } } addY += chr.getLength() / binSize + 1; } evKR.computeDensity(); ListOfDoubleArrays exp = evKR.getDensityAvg(); pw.println(binSize + "\t" + vector.length + "\t" + exp.getLength()); for (double aVector : vector) { pw.println(aVector); } for (double[] values : exp.getValues()) { for (double aVector : values) { pw.println(aVector); } } } else { // type == "observed" Iterator iterator = ic.getNewContactRecordIterator(); while (iterator.hasNext()) { ContactRecord cr = iterator.next(); int x = cr.getBinX(); int y = cr.getBinY(); float value = cr.getCounts(); if (vector[x] != 0 && vector[y] != 0 && !Double.isNaN(vector[x]) && !Double.isNaN(vector[y])) { value = (value / (vector[x] * vector[y])); } else { value = Float.NaN; } pw.println(x + "\t" + y + "\t" + value); } } pw.close(); } private void dumpGeneralVector() { Chromosome chromosome = chromosomeHandler.getChromosomeFromName(chr1); if (matrixType == MatrixType.NORM) { NormalizationVector nv = dataset.getNormalizationVector(chromosome.getIndex(), zoom, norm); if (nv == null) { System.err.println("Norm not available at " + zoom + " " + norm); System.exit(9); } int count = 0; long total = (chromosome.getLength() / zoom.getBinSize()) + 1; // print out vector for (double[] array : nv.getData().getValues()) { for (double element : array) { pw.println(element); count++; // Do not print out more entries than length of chromosome if (zoom.getUnit() == HiC.Unit.BP) { if (count >= total) break; } } } pw.close(); } else if (matrixType == MatrixType.EXPECTED) { final ExpectedValueFunction df = dataset.getExpectedValuesOrExit(zoom, norm, chromosome, true); ListOfDoubleArrays values; if (!ChromosomeHandler.isAllByAll(chromosome)) { values = df.getExpectedValuesWithNormalization(chromosome.getIndex()); } else { values = df.getExpectedValuesNoNormalization(); } if (ofile != null && ofile.endsWith(".npy")) { MatrixTools.saveMatrixTextNumpy(ofile, values.getValues().get(0)); // todo fix } else { for (double[] vals : values.getValues()) { for (double element : vals) { pw.println(element); } } pw.close(); } } } /** * Dumps the matrix. Does more argument checking, thus this should not be called outside of this class. * * @throws java.io.IOException In case of problems writing out matrix */ private void dumpMatrix() throws IOException { Chromosome chromosome1 = chromosomeHandler.getChromosomeFromName(chr1); Chromosome chromosome2 = chromosomeHandler.getChromosomeFromName(chr2); if (chromosome2.getIndex() < chromosome1.getIndex()) { regionIndices = new long[]{regionIndices[2], regionIndices[3], regionIndices[0], regionIndices[1]}; } MatrixZoomData zd = HiCFileTools.getMatrixZoomData(dataset, chromosome1, chromosome2, zoom); if (zd == null) { System.err.println("No reads in " + chr1 + " " + chr2); System.err.println("Unknown resolution: " + zoom); System.err.println("This data set has the following bin sizes (in bp): "); for (int zoomIdx = 0; zoomIdx < dataset.getNumberZooms(HiC.Unit.BP); zoomIdx++) { System.err.print(dataset.getZoom(HiC.Unit.BP, zoomIdx).getBinSize() + " "); } System.err.println("\nand the following bin sizes (in frag): "); for (int zoomIdx = 0; zoomIdx < dataset.getNumberZooms(HiC.Unit.FRAG); zoomIdx++) { System.err.print(dataset.getZoom(HiC.Unit.FRAG, zoomIdx).getBinSize() + " "); } System.exit(13); } ExpectedValueFunction df = null; if (MatrixType.isExpectedValueType(matrixType)) { df = dataset.getExpectedValuesOrExit(zd.getZoom(), norm, chromosome1, true); } zd.dump(pw, les, norm, matrixType, useRegionIndices, regionIndices, df, dense); } private void dumpFeature() throws IOException { ResourceLocator locator; if (feature.equals("loops")) { locator = dataset.getPeaks(); } else locator = dataset.getBlocks(); if (locator == null) { System.err.println("Sorry, " + feature + " is not available for this dataset"); System.exit(0); } BufferedReader br = new BufferedReader(new InputStreamReader(ParsingUtils.openInputStream(locator.getPath())), HiCGlobals.bufferSize); String nextLine; // header while ((nextLine = br.readLine()) != null) { pw.println(nextLine); } pw.close(); } @Override public void readArguments(String[] args, CommandLineParser parser) { String ofile = null; if (args.length == 3 || args.length == 4) { if (!(args[1].equals("loops") || args[1].equals("domains"))) { printUsageAndExit(); } if (!args[2].endsWith("hic") || !args[2].startsWith("http")) { printUsageAndExit(); } dataset = HiCFileTools.extractDatasetForCLT(Arrays.asList(args[2].split("\\+")), false); feature = args[1]; if (args.length == 4) { ofile = args[3]; } } else { // -d in pre means diagonal, in dump means dense dense = parser.getDiagonalsOption(); // -n in pre means no norm, in dump means includeIntra for the whole genome includeIntra = parser.getNoNormOption(); if (args.length < 7) { printUsageAndExit(); } String mType = args[1].toLowerCase(); matrixType = MatrixType.enumValueFromString(mType); if (!(MatrixType.isDumpMatrixType(matrixType) || MatrixType.isDumpVectorType(matrixType))) { System.err.println("Matrix or vector must be one of \"observed\", \"oe\", \"norm\", or \"expected\"."); System.exit(15); } setDatasetAndNorm(args[3], args[2], false); chromosomeHandler = dataset.getChromosomeHandler(); // retrieve input chromosomes / regions chr1 = args[4]; if (MatrixType.isDumpMatrixType(matrixType)) { chr2 = args[5]; } else chr2 = chr1; extractChromosomeRegionIndices(); // at the end of this, chr1&2 will just be the chr key names if (chromosomeHandler.doesNotContainChromosome(chr1)) { System.err.println("Unknown chromosome: " + chr1); System.exit(18); } if (chromosomeHandler.doesNotContainChromosome(chr2)) { System.err.println("Unknown chromosome: " + chr2); System.exit(19); } try { if (MatrixType.isDumpMatrixType(matrixType)) { unit = HiC.valueOfUnit(args[6]); } else { unit = HiC.valueOfUnit(args[5]); } } catch (IllegalArgumentException error) { System.err.println("Unit must be in BP or FRAG."); System.exit(20); } String binSizeSt; if (MatrixType.isDumpMatrixType(matrixType)) { binSizeSt = args[7]; } else { binSizeSt = args[6]; } try { binSize = Integer.parseInt(binSizeSt); } catch (NumberFormatException e) { System.err.println("Integer expected for bin size. Found: " + binSizeSt + "."); System.exit(21); } zoom = new HiCZoom(unit, binSize); if (MatrixType.isDumpMatrixType(matrixType)) { if (args.length == 9) ofile = args[8]; } else { if (args.length == 8) ofile = args[7]; } } try { if (ofile != null && ofile.length() > 0) { if (ofile.endsWith(".bin")) { BufferedOutputStream bos = new BufferedOutputStream(new FileOutputStream(args[6])); les = new LittleEndianOutputStream(bos); } else if (ofile.endsWith(".npy")) { this.ofile = ofile; } else { pw = new PrintWriter(new FileOutputStream(ofile)); } } else { pw = new PrintWriter(System.out); } } catch (IOException error) { System.err.println("Unable to open " + ofile + " for writing."); System.exit(22); } } /** * Added for benchmark */ public void setQuery(String chr1, String chr2, int binSize) { this.chr1 = chr1; this.chr2 = chr2; this.binSize = binSize; extractChromosomeRegionIndices(); } public int[] getBpBinSizes() { int[] bpBinSizes = new int[dataset.getNumberZooms(HiC.Unit.BP)]; for (int zoomIdx = 0; zoomIdx < bpBinSizes.length; zoomIdx++) { bpBinSizes[zoomIdx] = dataset.getZoom(HiC.Unit.BP, zoomIdx).getBinSize(); } return bpBinSizes; } /** * Added so that subregions could be dumped without dumping the full chromosome */ private void extractChromosomeRegionIndices() { if (chr1.contains(":")) { String[] regionComponents = chr1.split(":"); if (regionComponents.length != 3) { System.err.println("Invalid number of indices for chr1: " + regionComponents.length + ", should be 3 --> chromosome_name:start_index:end_index"); printUsageAndExit(); } else { try { chr1 = regionComponents[0]; regionIndices[0] = Integer.parseInt(regionComponents[1]); regionIndices[1] = Integer.parseInt(regionComponents[2]); useRegionIndices = true; } catch (Exception e) { System.err.println("Invalid indices for chr1: " + chr1); printUsageAndExit(); } } } else { Chromosome chromosome1 = chromosomeHandler.getChromosomeFromName(chr1); if (chromosome1 == null) { System.err.println("Invalid chromosome " + chr1); System.exit(77); } regionIndices[0] = 0; regionIndices[1] = chromosome1.getLength(); } if (chr2.contains(":")) { String[] regionComponents = chr2.split(":"); if (regionComponents.length != 3) { System.err.println("Invalid number of indices for chr2 : " + regionComponents.length + ", should be 3 --> chromosome_name:start_index:end_index"); printUsageAndExit(); } else { try { chr2 = regionComponents[0]; regionIndices[2] = Integer.parseInt(regionComponents[1]); regionIndices[3] = Integer.parseInt(regionComponents[2]); useRegionIndices = true; } catch (Exception e) { System.err.println("Invalid indices for chr2: " + chr2); printUsageAndExit(); } } } else { Chromosome chromosome2 = chromosomeHandler.getChromosomeFromName(chr2); if (chromosome2 == null) { System.err.println("Invalid chromosome " + chr2); System.exit(78); } regionIndices[2] = 0; regionIndices[3] = chromosome2.getLength(); } } @Override public void run() { HiCGlobals.allowDynamicBlockIndex = false; try { if (feature != null) { dumpFeature(); } else if ((matrixType == MatrixType.OBSERVED || matrixType == MatrixType.NORM) && ChromosomeHandler.isAllByAll(chr1) && ChromosomeHandler.isAllByAll(chr2)) { dumpGenomeWideData(); } else if (MatrixType.isDumpMatrixType(matrixType)) { dumpMatrix(); } else if (MatrixType.isDumpVectorType(matrixType)) { dumpGeneralVector(); } } catch (Exception e) { System.err.println("Unable to dump"); e.printStackTrace(); } } public ChromosomeHandler getChromosomeHandler() { return chromosomeHandler; } } ================================================ FILE: src/juicebox/tools/clt/old/Eigenvector.java ================================================ /* * The MIT License (MIT) * * Copyright (c) 2011-2021 Broad Institute, Aiden Lab, Rice University, Baylor College of Medicine * * Permission is hereby granted, free of charge, to any person obtaining a copy * of this software and associated documentation files (the "Software"), to deal * in the Software without restriction, including without limitation the rights * to use, copy, modify, merge, publish, distribute, sublicense, and/or sell * copies of the Software, and to permit persons to whom the Software is * furnished to do so, subject to the following conditions: * * The above copyright notice and this permission notice shall be included in * all copies or substantial portions of the Software. * * THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR * IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, * FITNESS FOR A PARTICULAR PURPOSE AND NON-INFRINGEMENT. IN NO EVENT SHALL THE * AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER * LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, * OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN * THE SOFTWARE. */ package juicebox.tools.clt.old; import juicebox.HiC; import juicebox.HiCGlobals; import juicebox.data.ChromosomeHandler; import juicebox.data.ExpectedValueFunction; import juicebox.data.HiCFileTools; import juicebox.data.MatrixZoomData; import juicebox.data.basics.Chromosome; import juicebox.tools.clt.CommandLineParser; import juicebox.tools.clt.JuiceboxCLT; import juicebox.windowui.HiCZoom; import java.io.FileOutputStream; import java.io.IOException; import java.io.PrintWriter; /** * Class for calculating Eigenvector (separated out from Dump) * @author Neva Durand */ public class Eigenvector extends JuiceboxCLT { private HiC.Unit unit = null; private int binSize = 0; private Chromosome chromosome1; private PrintWriter pw; public Eigenvector() { super(getUsage() + "\n\t-p, --pearsons_all_resolutions: calculate eigenvector at all resolutions"); } public static String getUsage(){ return "eigenvector -p [outfile]"; } @Override public void readArguments(String[] args, CommandLineParser parser) { if (args.length != 7 && args.length != 6) { printUsageAndExit(); } setDatasetAndNorm(args[2], args[1], false); ChromosomeHandler chromosomeHandler = dataset.getChromosomeHandler(); if (chromosomeHandler.doesNotContainChromosome(args[3])) { System.err.println("Unknown chromosome: " + args[3]); System.exit(18); } chromosome1 = chromosomeHandler.getChromosomeFromName(args[3]); try { unit = HiC.valueOfUnit(args[4]); } catch (IllegalArgumentException error) { System.err.println("Unit must be in BP or FRAG."); System.exit(20); } String binSizeSt = args[5]; try { binSize = Integer.parseInt(binSizeSt); } catch (NumberFormatException e) { System.err.println("Integer expected for bin size. Found: " + binSizeSt + "."); System.exit(21); } if ((unit == HiC.Unit.BP && binSize < HiCGlobals.MAX_EIGENVECTOR_ZOOM) || (unit == HiC.Unit.FRAG && binSize < HiCGlobals.MAX_EIGENVECTOR_ZOOM / 1000)) { System.out.println("WARNING: Eigenvector calculation at high resolution can take a long time"); } if (args.length == 7) { try { pw = new PrintWriter(new FileOutputStream(args[6])); } catch (IOException error) { System.err.println("Cannot write to " + args[6]); error.printStackTrace(); System.exit(22); } } else pw = new PrintWriter(System.out); } @Override public void run() { HiCZoom zoom = new HiCZoom(unit, binSize); MatrixZoomData zd = HiCFileTools.getMatrixZoomData(dataset, chromosome1, chromosome1, zoom); if (zd == null) { System.err.println("No reads in " + chromosome1); System.err.println("Unknown resolution: " + zoom); System.err.println("This data set has the following bin sizes (in bp): "); for (int zoomIdx = 0; zoomIdx < dataset.getNumberZooms(HiC.Unit.BP); zoomIdx++) { System.err.print(dataset.getZoom(HiC.Unit.BP, zoomIdx).getBinSize() + " "); } System.err.println("\nand the following bin sizes (in frag): "); for (int zoomIdx = 0; zoomIdx < dataset.getNumberZooms(HiC.Unit.FRAG); zoomIdx++) { System.err.print(dataset.getZoom(HiC.Unit.FRAG, zoomIdx).getBinSize() + " "); } System.exit(13); } ExpectedValueFunction df = dataset.getExpectedValuesOrExit(zd.getZoom(), norm, chromosome1, true); double[] vector = dataset.getEigenvector(chromosome1, zoom, 0, norm); // mean center and print int count = 0; double total = 0; for (double element : vector) { if (!Double.isNaN(element)) { total += element; count++; } } double mean = total / count; // sum is now mean // print out vector for (double element : vector) { pw.println(element - mean); } pw.close(); } } ================================================ FILE: src/juicebox/tools/clt/old/FragmentToBed.java ================================================ /* * The MIT License (MIT) * * Copyright (c) 2011-2020 Broad Institute, Aiden Lab, Rice University, Baylor College of Medicine * * Permission is hereby granted, free of charge, to any person obtaining a copy * of this software and associated documentation files (the "Software"), to deal * in the Software without restriction, including without limitation the rights * to use, copy, modify, merge, publish, distribute, sublicense, and/or sell * copies of the Software, and to permit persons to whom the Software is * furnished to do so, subject to the following conditions: * * The above copyright notice and this permission notice shall be included in * all copies or substantial portions of the Software. * * THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR * IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, * FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE * AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER * LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, * OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN * THE SOFTWARE. */ package juicebox.tools.clt.old; import juicebox.HiCGlobals; import juicebox.tools.clt.CommandLineParser; import juicebox.tools.clt.JuiceboxCLT; import java.io.*; import java.util.regex.Pattern; public class FragmentToBed extends JuiceboxCLT { private String filename; public FragmentToBed() { super("fragmentToBed "); } /** * Convert a fragment site file to a "bed" file * * @param filename fragment site file * @throws java.io.IOException */ private static void fragToBed(String filename) throws IOException { BufferedReader reader = null; PrintWriter writer = null; try { File inputFile = new File(filename); reader = new BufferedReader(new FileReader(inputFile), HiCGlobals.bufferSize); writer = new PrintWriter(new BufferedWriter(new FileWriter(filename + ".bed"))); Pattern pattern = Pattern.compile("\\s"); String nextLine; while ((nextLine = reader.readLine()) != null) { //String[] tokens = pattern.split(nextLine); String[] tokens = splitToList(nextLine); String chr = tokens[0]; int fragNumber = 0; int beg = Integer.parseInt(tokens[1]) - 1; // 1 vs 0 based coords for (int i = 2; i < tokens.length; i++) { int end = Integer.parseInt(tokens[i]) - 1; writer.println(chr + "\t" + beg + "\t" + end + "\t" + fragNumber); beg = end; fragNumber++; } } } finally { if (reader != null) reader.close(); } } @Override public void readArguments(String[] args, CommandLineParser parser) { //setUsage("juicebox fragmentToBed "); if (args.length != 2) { printUsageAndExit(); } filename = args[1]; } @Override public void run() { try { fragToBed(filename); } catch (Exception e) { e.printStackTrace(); } } } ================================================ FILE: src/juicebox/tools/clt/old/LibraryComplexity.java ================================================ /* * The MIT License (MIT) * * Copyright (c) 2011-2021 Broad Institute, Aiden Lab, Rice University, Baylor College of Medicine * * Permission is hereby granted, free of charge, to any person obtaining a copy * of this software and associated documentation files (the "Software"), to deal * in the Software without restriction, including without limitation the rights * to use, copy, modify, merge, publish, distribute, sublicense, and/or sell * copies of the Software, and to permit persons to whom the Software is * furnished to do so, subject to the following conditions: * * The above copyright notice and this permission notice shall be included in * all copies or substantial portions of the Software. * * THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR * IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, * FITNESS FOR A PARTICULAR PURPOSE AND NON-INFRINGEMENT. IN NO EVENT SHALL THE * AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER * LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, * OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN * THE SOFTWARE. */ package juicebox.tools.clt.old; import juicebox.tools.clt.CommandLineParser; import juicebox.tools.clt.JuiceboxCLT; import java.io.BufferedReader; import java.io.File; import java.io.FileReader; import java.io.IOException; import java.text.NumberFormat; import java.text.ParseException; import java.util.Locale; import java.util.concurrent.*; import java.util.concurrent.atomic.AtomicBoolean; public class LibraryComplexity extends JuiceboxCLT { private String localWorkingDirectory; private long dupReadPairs = 0; private long uniqueReadPairs = 0; private long opticalDups = 0; private long totalReadPairs = 0; private String fileName = "inter.txt"; private final boolean filesAlreadyCounted; public LibraryComplexity(String command) { super(getUsage()); filesAlreadyCounted = command.contains("fast"); } private static String getUsage() { return "LibraryComplexity \n" + "FastLibraryComplexity \n" + "FastLibraryComplexity "; } /** * Estimates the size of a library based on the number of paired end molecules * observed and the number of unique pairs observed. *
* Based on the Lander-Waterman equation that states:
* C/X = 1 - exp( -N/X )
* where
* X = number of distinct molecules in library
* N = number of read pairs
* C = number of distinct fragments observed in read pairs
*/ public static long estimateLibrarySize(final long duplicateReadPairs, final long uniqueReadPairs) { long totalReadPairs = duplicateReadPairs + uniqueReadPairs; if (totalReadPairs > 0 && duplicateReadPairs > 0) { double m = 1.0, M = 100.0; if (uniqueReadPairs >= totalReadPairs || f(m * uniqueReadPairs, uniqueReadPairs, totalReadPairs) < 0) { throw new IllegalStateException("Invalid values for pairs and unique pairs: " + totalReadPairs + ", " + uniqueReadPairs); } while (f(M * uniqueReadPairs, uniqueReadPairs, totalReadPairs) >= 0) { m = M; M *= 10.0; } double r = (m + M) / 2.0; double u = f(r * uniqueReadPairs, uniqueReadPairs, totalReadPairs); int i = 0; while (u != 0 && i < 1000) { if (u > 0) m = r; else M = r; r = (m + M) / 2.0; u = f(r * uniqueReadPairs, uniqueReadPairs, totalReadPairs); i++; } if (i == 1000) { System.err.println("Iterated 1000 times, returning estimate"); } return (long) (uniqueReadPairs * (m + M) / 2.0); } else { return 0; } } /** * Method that is used in the computation of estimated library size. */ private static double f(double x, double c, double n) { return c / x - 1 + Math.exp(-n / x); } @Override public void readArguments(String[] args, CommandLineParser parser) { if (args.length != 2 && args.length != 3 && args.length != 4) { System.out.println(getUsage()); System.exit(0); } if (filesAlreadyCounted) { if (args.length == 4) { try { determineCountsFromInput(args); } catch (NumberFormatException error) { System.err.println("When called with three arguments, must be integers"); System.exit(1); } } else { try { determineCountsFromFile(args[1]); if (args.length == 3) fileName = args[2]; } catch (Exception error) { System.err.println(error.getLocalizedMessage()); System.exit(1); } } } else if (args.length == 3 || args.length == 2) { localWorkingDirectory = args[1]; if (args.length == 3) fileName = args[2]; } } private void determineCountsFromFile(String file) throws IOException { BufferedReader reader = new BufferedReader(new FileReader(file)); dupReadPairs = Long.parseLong(reader.readLine().trim()); uniqueReadPairs = Long.parseLong(reader.readLine().trim()); try { opticalDups = Long.parseLong(reader.readLine().trim()); } catch (Exception e) { opticalDups = 0L; } reader.close(); } private void determineCountsFromInput(String[] args) throws NumberFormatException { uniqueReadPairs = Long.parseLong(args[1]); dupReadPairs = Long.parseLong(args[2]); opticalDups = Long.parseLong(args[3]); } @Override public void run() { NumberFormat nf = NumberFormat.getInstance(Locale.US); if (!filesAlreadyCounted) { final AtomicBoolean somethingFailed = new AtomicBoolean(false); try { ExecutorService executor = Executors.newFixedThreadPool(3); Callable taskOptDups = () -> { File f = new File(localWorkingDirectory + "/opt_dups.txt"); if (f.exists()) { try { long opticalDupsT = 0L; BufferedReader reader = new BufferedReader(new FileReader(f)); while (reader.readLine() != null) opticalDupsT++; reader.close(); return opticalDupsT; } catch (Exception e) { somethingFailed.set(true); return 0L; } } else { return 0L; } }; Callable taskUniqueReads = () -> { File f = new File(localWorkingDirectory + "/merged_nodups.txt"); if (f.exists()) { try { long uniqueReadPairsT = 0L; BufferedReader reader = new BufferedReader(new FileReader(f)); while (reader.readLine() != null) uniqueReadPairsT++; reader.close(); return uniqueReadPairsT; } catch (Exception e) { somethingFailed.set(true); return 0L; } } else { return 0L; } }; Callable taskDupReadPairs = () -> { File f = new File(localWorkingDirectory + "/dups.txt"); if (f.exists()) { try { long readPairsT = 0; BufferedReader reader = new BufferedReader(new FileReader(localWorkingDirectory + "/dups.txt")); while (reader.readLine() != null) readPairsT++; reader.close(); return readPairsT; } catch (Exception e) { somethingFailed.set(true); return 0L; } } else { return 0L; } }; Future futureOptDups = executor.submit(taskOptDups); Future futureUniqueReads = executor.submit(taskUniqueReads); Future futureDupReadPairs = executor.submit(taskDupReadPairs); File f = new File(localWorkingDirectory + "/" + fileName); if (f.exists()) { BufferedReader reader = new BufferedReader(new FileReader(localWorkingDirectory + "/" + fileName)); String line = reader.readLine(); boolean done = false; while (line != null && !done) { if (line.contains("Sequenced Read")) { String[] parts = line.split(":"); try { totalReadPairs = nf.parse(parts[1].trim()).longValue(); } catch (ParseException ignored) { } done = true; } line = reader.readLine(); } reader.close(); } opticalDups = futureOptDups.get(); uniqueReadPairs = futureUniqueReads.get(); dupReadPairs = futureDupReadPairs.get(); executor.shutdown(); if (somethingFailed.get()) { System.err.println("Something failed in a thread"); System.exit(1); } } catch (IOException error) { System.err.println("Problem counting lines in merged_nodups and dups"); System.exit(1); } catch (InterruptedException e) { System.err.println("Threads interrupted exception"); System.exit(1); } catch (ExecutionException e) { System.err.println("Threads execution exception"); System.exit(1); } } NumberFormat decimalFormat = NumberFormat.getPercentInstance(); decimalFormat.setMinimumFractionDigits(2); decimalFormat.setMaximumFractionDigits(2); System.out.print("Unique Reads: " + NumberFormat.getInstance().format(uniqueReadPairs) + " "); if (totalReadPairs > 0) { System.out.println("(" + decimalFormat.format(uniqueReadPairs / (double) totalReadPairs) + ")"); } else { System.out.println(); } System.out.print("PCR Duplicates: " + nf.format(dupReadPairs) + " "); if (totalReadPairs > 0) { System.out.println("(" + decimalFormat.format(dupReadPairs / (double) totalReadPairs) + ")"); } else { System.out.println(); } System.out.print("Optical Duplicates: " + nf.format(opticalDups) + " "); if (totalReadPairs > 0) { System.out.println("(" + decimalFormat.format(opticalDups / (double) totalReadPairs) + ")"); } else { System.out.println(); } long result; try { result = estimateLibrarySize(dupReadPairs, uniqueReadPairs); } catch (NullPointerException e) { result = 0; } System.out.println("Library Complexity Estimate: " + nf.format(result)); } } ================================================ FILE: src/juicebox/tools/clt/old/PairsToBin.java ================================================ /* * The MIT License (MIT) * * Copyright (c) 2011-2021 Broad Institute, Aiden Lab, Rice University, Baylor College of Medicine * * Permission is hereby granted, free of charge, to any person obtaining a copy * of this software and associated documentation files (the "Software"), to deal * in the Software without restriction, including without limitation the rights * to use, copy, modify, merge, publish, distribute, sublicense, and/or sell * copies of the Software, and to permit persons to whom the Software is * furnished to do so, subject to the following conditions: * * The above copyright notice and this permission notice shall be included in * all copies or substantial portions of the Software. * * THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR * IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, * FITNESS FOR A PARTICULAR PURPOSE AND NON-INFRINGEMENT. IN NO EVENT SHALL THE * AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER * LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, * OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN * THE SOFTWARE. */ package juicebox.tools.clt.old; import juicebox.data.ChromosomeHandler; import juicebox.data.HiCFileTools; import juicebox.tools.clt.CommandLineParser; import juicebox.tools.clt.JuiceboxCLT; import juicebox.tools.utils.original.mnditerator.AsciiToBinConverter; public class PairsToBin extends JuiceboxCLT { private String ifile, ofile, genomeId; public PairsToBin() { super("pairsToBin "); } @Override public void readArguments(String[] args, CommandLineParser parser) { if (args.length != 4) { printUsageAndExit(); } ifile = args[1]; ofile = args[2]; genomeId = args[3]; } @Override public void run() { ChromosomeHandler chromosomeHandler = HiCFileTools.loadChromosomes(genomeId); try { AsciiToBinConverter.convert(ifile, ofile, chromosomeHandler); } catch (Exception e) { System.err.println("Unable to convert from ascii to bin"); e.printStackTrace(); } } } ================================================ FILE: src/juicebox/tools/clt/old/Pearsons.java ================================================ /* * The MIT License (MIT) * * Copyright (c) 2011-2021 Broad Institute, Aiden Lab, Rice University, Baylor College of Medicine * * Permission is hereby granted, free of charge, to any person obtaining a copy * of this software and associated documentation files (the "Software"), to deal * in the Software without restriction, including without limitation the rights * to use, copy, modify, merge, publish, distribute, sublicense, and/or sell * copies of the Software, and to permit persons to whom the Software is * furnished to do so, subject to the following conditions: * * The above copyright notice and this permission notice shall be included in * all copies or substantial portions of the Software. * * THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR * IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, * FITNESS FOR A PARTICULAR PURPOSE AND NON-INFRINGEMENT. IN NO EVENT SHALL THE * AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER * LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, * OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN * THE SOFTWARE. */ package juicebox.tools.clt.old; import htsjdk.tribble.util.LittleEndianInputStream; import htsjdk.tribble.util.LittleEndianOutputStream; import juicebox.HiC; import juicebox.HiCGlobals; import juicebox.data.ChromosomeHandler; import juicebox.data.ExpectedValueFunction; import juicebox.data.HiCFileTools; import juicebox.data.MatrixZoomData; import juicebox.data.basics.Chromosome; import juicebox.matrix.BasicMatrix; import juicebox.matrix.DiskResidentBlockMatrix; import juicebox.matrix.InMemoryMatrix; import juicebox.tools.clt.CommandLineParser; import juicebox.tools.clt.JuiceboxCLT; import juicebox.tools.dev.ParallelizedJuicerTools; import juicebox.tools.utils.dev.PearsonCorrelationMetric; import juicebox.windowui.HiCZoom; import org.broad.igv.util.ParsingUtils; import java.io.*; import java.util.BitSet; import java.util.concurrent.atomic.AtomicInteger; /** * Class for calculating Pearsons (separated out from Dump) * @author Neva Durand */ public class Pearsons extends JuiceboxCLT { private static final int BLOCK_TILE = 500; private String ofile = null; private HiC.Unit unit = null; private int binSize = 0; private Chromosome chromosome1; public Pearsons() { super(getBasicUsage() + "\n\t-p, --pearsons_all_resolutions: calculate Pearson's at all resolutions"); } public static String getBasicUsage(){ return "pearsons [-p] [outfile]"; } public static BasicMatrix readPearsons(String path) throws IOException { // Peak at file to determine version BufferedInputStream bis = null; int magic; try { InputStream is = ParsingUtils.openInputStream(path); bis = new BufferedInputStream(is); LittleEndianInputStream les = new LittleEndianInputStream(bis); magic = les.readInt(); if (magic != 6515048) { System.err.println("Problem reading Pearson's " + path); return null; } } finally { if (bis != null) bis.close(); } return new DiskResidentBlockMatrix(path); } /** * Return the mean of the given vector, ignoring NaNs * * @param vector Vector to calculate the mean on * @return The mean of the vector, not including NaNs. */ private static double getVectorMean(double[] vector) { double sum = 0; int count = 0; for (double aVector : vector) { if (!Double.isNaN(aVector)) { sum += aVector; count++; } } return count == 0 ? 0 : sum / count; } public static BasicMatrix computePearsons(double[][] matrix, int dim, BitSet bitSet) { // Subtract row means double[] rowMeans = new double[dim]; for (int i = 0; i < dim; i++) { if (bitSet.get(i)) { rowMeans[i] = getVectorMean(matrix[i]); } } for (int i = 0; i < dim; i++) { if (bitSet.get(i)) { for (int j = 0; j < dim; j++) { matrix[i][j] -= rowMeans[j]; } } } BasicMatrix pearsons = new InMemoryMatrix(dim); for (int i = 0; i < dim; i++) { if (bitSet.get(i)) { for (int j = i + 1; j < dim; j++) { if (bitSet.get(j)) { float corr = (float) PearsonCorrelationMetric.corr(matrix[i], matrix[j]); pearsons.setEntry(i, j, corr); pearsons.setEntry(j, i, corr); } else { pearsons.setEntry(i, j, Float.NaN); pearsons.setEntry(j, i, Float.NaN); } } } else { for (int j = i + 1; j < dim; j++) { pearsons.setEntry(i, j, Float.NaN); pearsons.setEntry(j, i, Float.NaN); } } } // Set diagonal to 1, set centromere to NaN for (int i = 0; i < dim; i++) { if (bitSet.get(i)) { pearsons.setEntry(i, i, 1.0f); } else { pearsons.setEntry(i, i, Float.NaN); } } return pearsons; } public static BasicMatrix computeParallelizedPearsons(double[][] matrix, int dim, BitSet bitSet) { // Subtract row means inPlaceParallelSubtractRowMeans(matrix, dim, bitSet); BasicMatrix pearsons = new InMemoryMatrix(dim); // Set diagonal to 1, set centromere to NaN AtomicInteger dCounter = new AtomicInteger(0); ParallelizedJuicerTools.launchParallelizedCode(() -> { int i = dCounter.getAndIncrement(); while (i < dim) { if (bitSet.get(i)) { for (int j = i + 1; j < dim; j++) { float corr; if (bitSet.get(j)) { corr = (float) PearsonCorrelationMetric.corr(matrix[i], matrix[j]); } else { corr = Float.NaN; } synchronized (pearsons) { pearsons.setEntry(i, j, corr); pearsons.setEntry(j, i, corr); } } } else { synchronized (pearsons) { for (int j = i + 1; j < dim; j++) { pearsons.setEntry(i, j, Float.NaN); pearsons.setEntry(j, i, Float.NaN); } } } i = dCounter.getAndIncrement(); } }); for (int i = 0; i < dim; i++) { if (bitSet.get(i)) { pearsons.setEntry(i, i, 1.0f); } else { pearsons.setEntry(i, i, Float.NaN); } } return pearsons; } private static void inPlaceParallelSubtractRowMeans(double[][] matrix, int dim, BitSet bitSet) { double[] rowMeans = new double[dim]; AtomicInteger index = new AtomicInteger(0); ParallelizedJuicerTools.launchParallelizedCode(() -> { int i = index.getAndIncrement(); while (i < dim) { if (bitSet.get(i)) { rowMeans[i] = getVectorMean(matrix[i]); } i = index.getAndIncrement(); } }); AtomicInteger index2 = new AtomicInteger(0); ParallelizedJuicerTools.launchParallelizedCode(() -> { int i = index2.getAndIncrement(); while (i < dim) { if (bitSet.get(i)) { for (int j = 0; j < dim; j++) { matrix[i][j] -= rowMeans[j]; } } i = index2.getAndIncrement(); } }); } @Override public void readArguments(String[] args, CommandLineParser parser) { if (args.length != 7 && args.length != 6) { printUsageAndExit(); } //HiCGlobals.MAX_PEARSON_ZOOM = 500000; setDatasetAndNorm(args[2], args[1], true); ChromosomeHandler chromosomeHandler = dataset.getChromosomeHandler(); if (chromosomeHandler.doesNotContainChromosome(args[3])) { System.err.println("Unknown chromosome: " + args[3]); System.exit(18); } chromosome1 = chromosomeHandler.getChromosomeFromName(args[3]); try { unit = HiC.valueOfUnit(args[4]); } catch (IllegalArgumentException error) { System.err.println("Unit must be in BP or FRAG."); System.exit(20); } String binSizeSt = args[5]; try { binSize = Integer.parseInt(binSizeSt); } catch (NumberFormatException e) { System.err.println("Integer expected for bin size. Found: " + binSizeSt + "."); System.exit(21); } if ((unit == HiC.Unit.BP && binSize < HiCGlobals.MAX_PEARSON_ZOOM) || (unit == HiC.Unit.FRAG && binSize < HiCGlobals.MAX_PEARSON_ZOOM / 1000)) { System.out.println("Pearson's and Eigenvector are not calculated for high resolution datasets"); System.out.println("To override this limitation, send in the \"-p\" flag."); System.exit(0); } if (args.length == 7) { ofile = args[6]; } } @Override public void run() { HiCZoom zoom = new HiCZoom(unit, binSize); MatrixZoomData zd = HiCFileTools.getMatrixZoomData(dataset, chromosome1, chromosome1, zoom); if (zd == null) { System.err.println("No reads in " + chromosome1); System.err.println("Unknown resolution: " + zoom); System.err.println("This data set has the following bin sizes (in bp): "); for (int zoomIdx = 0; zoomIdx < dataset.getNumberZooms(HiC.Unit.BP); zoomIdx++) { System.err.print(dataset.getZoom(HiC.Unit.BP, zoomIdx).getBinSize() + " "); } System.err.println("\nand the following bin sizes (in frag): "); for (int zoomIdx = 0; zoomIdx < dataset.getNumberZooms(HiC.Unit.FRAG); zoomIdx++) { System.err.print(dataset.getZoom(HiC.Unit.FRAG, zoomIdx).getBinSize() + " "); } System.exit(13); } ExpectedValueFunction df = dataset.getExpectedValuesOrExit(zd.getZoom(), norm, chromosome1, true); BasicMatrix pearsons = zd.getPearsons(df); if (pearsons == null) { System.err.println("Pearson's not available at zoom " + zoom + ". For high resolution, try again with -p"); System.exit(15); } LittleEndianOutputStream les = null; PrintWriter txtWriter = null; if (ofile != null) { try { if (ofile.endsWith(".bin")) { BufferedOutputStream bos = new BufferedOutputStream(new FileOutputStream(ofile)); les = new LittleEndianOutputStream(bos); } else { txtWriter = new PrintWriter(new FileOutputStream(ofile)); } } catch (IOException error) { System.err.println("Cannot write to " + ofile); error.printStackTrace(); System.exit(22); } } else { txtWriter = new PrintWriter(System.out); } if (les == null) { int dim = pearsons.getRowDimension(); for (int i = 0; i < dim; i++) { for (int j = 0; j < dim; j++) { float output = pearsons.getEntry(i, j); txtWriter.print(output + " "); } txtWriter.println(); } txtWriter.flush(); } else { try { int dim = pearsons.getRowDimension(); writeHeader(les, dim, pearsons.getLowerValue(), pearsons.getUpperValue()); int block_side = (int) Math.ceil((float) dim / (float) BLOCK_TILE); for (int i = 0; i < block_side; i++) { int block_row_start = i * BLOCK_TILE; int block_row_end = Math.min(block_row_start + BLOCK_TILE, dim); int row_len = block_row_end - block_row_start; for (int j = 0; j < block_side; j++) { int block_col_start = j * BLOCK_TILE; int block_col_end = Math.min(block_col_start + BLOCK_TILE, dim); int col_len = block_col_end - block_col_start; for (int ui = 0; ui < row_len; ui++) { for (int uj = 0; uj < col_len; uj++) { int now_i = ui + block_row_start; int now_j = uj + block_col_start; float output = pearsons.getEntry(now_i, now_j); les.writeFloat(output); } } } } les.close(); } catch (IOException error) { System.err.println("Problem when writing Pearson's"); error.printStackTrace(); System.exit(1); } } } private void writeHeader(LittleEndianOutputStream les, int dim, float lower, float upper) throws IOException { // Magic number - 4 bytes les.writeByte('h'); les.writeByte('i'); les.writeByte('c'); les.writeByte(0); // Version number les.writeInt(1); // Genome -- les.writeString(dataset.getGenomeId()); // Chromosomes les.writeString(chromosome1.getName()); les.writeString(chromosome1.getName()); // Resolution (bin size) les.writeInt(binSize); // Statistics, other attributes les.writeFloat(lower); // this is supposed to be lower quartile les.writeFloat(upper); // this is supposed to be upper quartile les.writeInt(dim); // # rows les.writeInt(dim); // # cols les.writeInt(BLOCK_TILE); } } ================================================ FILE: src/juicebox/tools/clt/old/PreProcessing.java ================================================ /* * The MIT License (MIT) * * Copyright (c) 2011-2022 Broad Institute, Aiden Lab, Rice University, Baylor College of Medicine * * Permission is hereby granted, free of charge, to any person obtaining a copy * of this software and associated documentation files (the "Software"), to deal * in the Software without restriction, including without limitation the rights * to use, copy, modify, merge, publish, distribute, sublicense, and/or sell * copies of the Software, and to permit persons to whom the Software is * furnished to do so, subject to the following conditions: * * The above copyright notice and this permission notice shall be included in * all copies or substantial portions of the Software. * * THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR * IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, * FITNESS FOR A PARTICULAR PURPOSE AND NON-INFRINGEMENT. IN NO EVENT SHALL THE * AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER * LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, * OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN * THE SOFTWARE. */ package juicebox.tools.clt.old; import juicebox.HiCGlobals; import juicebox.data.ChromosomeHandler; import juicebox.data.HiCFileTools; import juicebox.data.iterator.IteratorContainer; import juicebox.tools.clt.CommandLineParser; import juicebox.tools.clt.JuiceboxCLT; import juicebox.tools.utils.common.ShellCommandRunner; import juicebox.tools.utils.original.MultithreadedPreprocessor; import juicebox.tools.utils.original.MultithreadedPreprocessorHic; import juicebox.tools.utils.original.Preprocessor; import juicebox.windowui.NormalizationType; import java.io.File; import java.util.ArrayList; import java.util.List; import java.util.Map; public class PreProcessing extends JuiceboxCLT { public static String flags = " : -d only calculate intra chromosome (diagonal) [false]\n" + " : -f calculate fragment map\n" + " : -m only write cells with count above threshold m [0]\n" + " : -q filter by MAPQ score greater than or equal to q [not set]\n" + " : -c only calculate map on specific chromosome [not set]\n" + " : -r Only calculate specific resolutions [not set]\n" + " : -t Set a temporary directory for writing\n" + " : -s Add the text statistics file to the Hi-C file header\n" + " : -g Add the text graphs file to the Hi-C file header\n" + " : -n Don't normalize the matrices\n" + " : -z scale factor for hic file\n" + " : -a <1, 2, 3, 4, 5> filter based on inner, outer, left-left, right-right, tandem pairs respectively\n" + " : --randomize_position randomize positions between fragment sites\n" + " : --random_seed for seeding random number generator\n" + " : --frag_site_maps for randomization\n" + " : -k normalizations to include\n" + " : -j number of CPU threads to use\n" + " : --threads number of threads \n" + " : --mndindex to mnd chr block indices\n" + " : --conserve-ram will minimize RAM usage\n" + " : --check-ram-usage will check ram requirements prior to running\n" + " : --shell how to execute shell (sh, bash, zsh, etc); default: sh"; private String inputFile; private String outputFile; private Preprocessor preprocessor; private boolean noNorm = false; private boolean noFragNorm = false; private boolean fromHIC = false; private int genomeWide; private String shell = "sh"; private final List normalizationTypes = new ArrayList<>(); public PreProcessing() { super(getBasicUsage() + "\n" + flags); } public static String getBasicUsage() { return "pre [options] "; } @Override public void readArguments(String[] args, CommandLineParser parser) { String genomeId = ""; try { genomeId = args[3]; } catch (ArrayIndexOutOfBoundsException e) { System.err.println("No genome ID given"); printUsageAndExit(); } ChromosomeHandler chromHandler = HiCFileTools.loadChromosomes(genomeId); inputFile = args[1]; outputFile = args[2]; String tmpDir = parser.getTmpdirOption(); double hicFileScalingFactor = parser.getScalingOption(); updateNumberOfCPUThreads(parser, 1); updateSecondaryNumberOfCPUThreads(parser, 10); IteratorContainer.numCPUMatrixThreads = numCPUThreadsForSecondTask; fromHIC = parser.getFromHICOption(); if (fromHIC) { preprocessor = new MultithreadedPreprocessorHic(new File(outputFile), genomeId, chromHandler, hicFileScalingFactor, numCPUThreads); usingMultiThreadedVersion = true; } else { if (numCPUThreads < 2) { preprocessor = new Preprocessor(new File(outputFile), genomeId, chromHandler, hicFileScalingFactor); usingMultiThreadedVersion = false; } else { try { preprocessor = new MultithreadedPreprocessor(new File(outputFile), genomeId, chromHandler, hicFileScalingFactor, numCPUThreads, parser.getMndIndexOption()); usingMultiThreadedVersion = true; } catch (Exception e) { System.err.println(e.getLocalizedMessage() + "\nUsing single threaded preprocessor"); preprocessor = new Preprocessor(new File(outputFile), genomeId, chromHandler, hicFileScalingFactor); usingMultiThreadedVersion = false; } } } preprocessor.setFromHIC(fromHIC); preprocessor.setIncludedChromosomes(parser.getChromosomeSetOption()); preprocessor.setCountThreshold(parser.getCountThresholdOption()); preprocessor.setV9DepthBase(parser.getV9DepthBase()); preprocessor.setMapqThreshold(parser.getMapqThresholdOption()); preprocessor.setDiagonalsOnly(parser.getDiagonalsOption()); preprocessor.setFragmentFile(parser.getFragmentOption()); preprocessor.setExpectedVectorFile(parser.getExpectedVectorOption()); preprocessor.setTmpdir(tmpDir); preprocessor.setStatisticsFile(parser.getStatsOption()); preprocessor.setGraphFile(parser.getGraphOption()); preprocessor.setGenome(parser.getGenomeOption()); preprocessor.setResolutions(parser.getResolutionOption()); preprocessor.setAlignmentFilter(parser.getAlignmentOption()); preprocessor.setRandomizePosition(parser.getRandomizePositionsOption()); preprocessor.setPositionRandomizerSeed(parser.getRandomPositionSeedOption()); preprocessor.setRandomizeFragMaps(parser.getRandomizePositionMaps()); preprocessor.setThrowOutIntraFragOption(parser.getThrowIntraFragOption()); preprocessor.setSubsampler(parser.getSubsampleOption()); int blockCapacity = parser.getBlockCapacityOption(); if (blockCapacity > 10) { Preprocessor.BLOCK_CAPACITY = blockCapacity; } String customShell = parser.getShellOption(); if (customShell != null && customShell.length() > 0) { shell = customShell; } noNorm = parser.getNoNormOption(); genomeWide = parser.getGenomeWideOption(); noFragNorm = parser.getNoFragNormOption(); normalizationTypes.addAll(parser.getAllNormalizationTypesOption()); HiCGlobals.USE_ITERATOR_NOT_ALL_IN_RAM = parser.getDontPutAllContactsIntoRAM(); HiCGlobals.CHECK_RAM_USAGE = parser.shouldCheckRAMUsage(); } @Override public void run() { HiCGlobals.allowDynamicBlockIndex = false; try { long currentTime = System.currentTimeMillis(); if (usingMultiThreadedVersion) { preprocessor.preprocess(inputFile, null, null, null); ShellCommandRunner.runShellFile(shell, outputFile + MultithreadedPreprocessor.CAT_SCRIPT); } else { preprocessor.preprocess(inputFile, outputFile, outputFile, null); } if (HiCGlobals.printVerboseComments) { System.out.println("\nBinning contact matrices took: " + (System.currentTimeMillis() - currentTime) + " milliseconds"); } if (!noNorm) { Map resolutionsToBuildTo = AddNorm.defaultHashMapForResToBuildTo(normalizationTypes); AddNorm.launch(outputFile, normalizationTypes, genomeWide, noFragNorm, numCPUThreads, resolutionsToBuildTo); } else { System.out.println("Done creating .hic file. Normalization not calculated due to -n flag."); System.out.println("To run normalization, run: java -jar juicer_tools.jar addNorm "); } } catch (Exception e) { e.printStackTrace(); System.exit(56); } } } ================================================ FILE: src/juicebox/tools/clt/old/SQLDatabase.java ================================================ /* * The MIT License (MIT) * * Copyright (c) 2011-2020 Broad Institute, Aiden Lab, Rice University, Baylor College of Medicine * * Permission is hereby granted, free of charge, to any person obtaining a copy * of this software and associated documentation files (the "Software"), to deal * in the Software without restriction, including without limitation the rights * to use, copy, modify, merge, publish, distribute, sublicense, and/or sell * copies of the Software, and to permit persons to whom the Software is * furnished to do so, subject to the following conditions: * * The above copyright notice and this permission notice shall be included in * all copies or substantial portions of the Software. * * THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR * IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, * FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE * AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER * LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, * OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN * THE SOFTWARE. */ package juicebox.tools.clt.old; import juicebox.tools.clt.CommandLineParser; import juicebox.tools.clt.JuiceboxCLT; import juicebox.tools.utils.original.HiCDBUtils; import java.io.IOException; import java.sql.SQLException; public class SQLDatabase extends JuiceboxCLT { private String[] dbArgs; public SQLDatabase() { super("db [items]"); } @Override public void readArguments(String[] args, CommandLineParser parser) { //setUsage("juicebox db [items]"); dbArgs = new String[args.length - 1]; System.arraycopy(args, 1, dbArgs, 0, args.length - 1); } @Override public void run() { try { HiCDBUtils.main(dbArgs); } catch (SQLException e) { System.err.println("Sql exception: " + e.getMessage()); e.printStackTrace(); System.exit(61); } catch (IOException e) { e.printStackTrace(); } } } ================================================ FILE: src/juicebox/tools/clt/old/Statistics.java ================================================ /* * The MIT License (MIT) * * Copyright (c) 2011-2021 Broad Institute, Aiden Lab, Rice University, Baylor College of Medicine * * Permission is hereby granted, free of charge, to any person obtaining a copy * of this software and associated documentation files (the "Software"), to deal * in the Software without restriction, including without limitation the rights * to use, copy, modify, merge, publish, distribute, sublicense, and/or sell * copies of the Software, and to permit persons to whom the Software is * furnished to do so, subject to the following conditions: * * The above copyright notice and this permission notice shall be included in * all copies or substantial portions of the Software. * * THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR * IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, * FITNESS FOR A PARTICULAR PURPOSE AND NON-INFRINGEMENT. IN NO EVENT SHALL THE * AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER * LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, * OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN * THE SOFTWARE. */ package juicebox.tools.clt.old; import juicebox.data.ChromosomeHandler; import juicebox.data.HiCFileTools; import juicebox.tools.clt.CommandLineParser; import juicebox.tools.clt.JuiceboxCLT; import juicebox.tools.utils.original.Chunk; import juicebox.tools.utils.original.FragmentCalculation; import juicebox.tools.utils.original.MTIndexHandler; import juicebox.tools.utils.original.stats.LoneStatisticsWorker; import juicebox.tools.utils.original.stats.ParallelStatistics; import juicebox.tools.utils.original.stats.StatisticsContainer; import java.util.ArrayList; import java.util.HashMap; import java.util.List; import java.util.Map; import java.util.concurrent.ConcurrentHashMap; public class Statistics extends JuiceboxCLT { private String siteFile; private String ligationJunction = "none"; private String inFile; private String mndIndexFile; private ChromosomeHandler localHandler = null; private final List mndChunks = new ArrayList<>(); private final List statsFiles = new ArrayList<>(); private final List mapqThresholds = new ArrayList<>(); public Statistics() { super(getUsage()); } public static String getUsage() { return " Usage: statistics [--ligation NNNN] [--mapqs mapq1,maqp2] [--mndindex mndindex.txt] [--threads numthreads]\n " + " [stats_file_2] \n" + " --ligation: ligation junction\n" + " --mapqs: mapping quality threshold(s), do not consider reads < threshold\n" + " --mndindex: file of indices for merged nodups to read from\n" + " --threads: number of threads to be executed \n" + " : list of HindIII restriction sites, one line per chromosome\n" + " : output file containing total reads, for library complexity\n" + " : file in intermediate format to calculate statistics on, can be stream\n" + " : file to create chromosome handler\n" + " [stats file 2]: output file containing total reads for second mapping quality threshold\n"; } public void setMndIndex() { if (localHandler != null && mndIndexFile != null && mndIndexFile.length() > 1) { Map chromosomePairIndexes = new ConcurrentHashMap<>(); MTIndexHandler.populateChromosomePairIndexes(localHandler, chromosomePairIndexes, new HashMap<>(), new HashMap<>(), new HashMap<>()); Map> mndIndex = MTIndexHandler.readMndIndex(mndIndexFile, chromosomePairIndexes); for (List values : mndIndex.values()) { mndChunks.addAll(values); } } } private FragmentCalculation readSiteFile(String siteFile) { //read in restriction site file and store as multidimensional array q if (!siteFile.contains("none")) { //if restriction enzyme exists, find the RE distance// return FragmentCalculation.readFragments(siteFile, localHandler, "Stats"); } return null; } @Override public void readArguments(String[] args, CommandLineParser parser) { if (args.length != 6 && args.length != 5) { printUsageAndExit(); } //set required arguments to variables siteFile = args[1]; statsFiles.add(args[2]); if (args.length == 6) {// two map q values,input text files statsFiles.add(args[3]); inFile = args[4]; tryToReadLocalHandler(args[5]); } else {//only one mapq value inFile = args[3]; tryToReadLocalHandler(args[4]); } //check for flags, else use default values List mapQT = parser.getMultipleMapQOptions(); if (mapQT != null && (mapQT.size() == 1 || mapQT.size() == 2)) { //only one or two mapq values int mapqThreshold = mapQT.get(0) > 0 ? mapQT.get(0) : 1; mapqThresholds.add(mapqThreshold); if (statsFiles.size() == 2) { mapqThreshold = 30; if (mapQT.size() == 2) { mapqThreshold = mapQT.get(1) > 0 ? mapQT.get(1) : 30; } mapqThresholds.add(mapqThreshold); } } else { mapqThresholds.add(1); if (statsFiles.size() == 2) { mapqThresholds.add(30); } } String ligJunc = parser.getLigationOption(); if (ligJunc != null && ligJunc.length() > 1) { ligationJunction = ligJunc; } //multithreading flags updateNumberOfCPUThreads(parser, 1); mndIndexFile = parser.getMndIndexOption(); } private void tryToReadLocalHandler(String genomeID) { if (genomeID.equalsIgnoreCase("na") || genomeID.equalsIgnoreCase("null") || genomeID.equalsIgnoreCase("none")) { localHandler = null; } else { localHandler = HiCFileTools.loadChromosomes(genomeID); //genomeID } } @Override public void run() { setMndIndex(); FragmentCalculation fragmentCalculation = readSiteFile(siteFile); StatisticsContainer container; if (localHandler == null || mndChunks.size() < 2 || numCPUThreads == 1) { LoneStatisticsWorker runner = new LoneStatisticsWorker(siteFile, statsFiles, mapqThresholds, ligationJunction, inFile, fragmentCalculation); runner.infileStatistics(); container = runner.getResultsContainer(); } else { container = new StatisticsContainer(); ParallelStatistics pStats = new ParallelStatistics(numCPUThreads, container, mndChunks, siteFile, statsFiles, mapqThresholds, ligationJunction, inFile, localHandler, fragmentCalculation); pStats.launchThreads(); } container.calculateConvergence(statsFiles.size()); container.outputStatsFile(statsFiles); container.writeHistFile(statsFiles); } } ================================================ FILE: src/juicebox/tools/clt/old/Summation.java ================================================ /* * The MIT License (MIT) * * Copyright (c) 2011-2024 Broad Institute, Aiden Lab, Rice University, Baylor College of Medicine * * Permission is hereby granted, free of charge, to any person obtaining a copy * of this software and associated documentation files (the "Software"), to deal * in the Software without restriction, including without limitation the rights * to use, copy, modify, merge, publish, distribute, sublicense, and/or sell * copies of the Software, and to permit persons to whom the Software is * furnished to do so, subject to the following conditions: * * The above copyright notice and this permission notice shall be included in * all copies or substantial portions of the Software. * * THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR * IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, * FITNESS FOR A PARTICULAR PURPOSE AND NON-INFRINGEMENT. IN NO EVENT SHALL THE * AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER * LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, * OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN * THE SOFTWARE. */ package juicebox.tools.clt.old; import juicebox.HiCGlobals; import juicebox.data.ChromosomeHandler; import juicebox.data.Dataset; import juicebox.data.HiCFileTools; import juicebox.tools.clt.CommandLineParser; import juicebox.tools.clt.JuiceboxCLT; import juicebox.tools.utils.common.ShellCommandRunner; import juicebox.tools.utils.original.MultithreadedPreprocessor; import juicebox.tools.utils.original.MultithreadedPreprocessorHic; import juicebox.tools.utils.original.Preprocessor; import juicebox.windowui.HiCZoom; import java.io.File; import java.util.ArrayList; import java.util.List; public class Summation extends JuiceboxCLT { private String inputFile; private String outputFile; private MultithreadedPreprocessorHic preprocessor; private String shell = "sh"; public Summation() { super(getBasicUsage() + "\n" + PreProcessing.flags); } public static String getBasicUsage() { return "sum [options] ..."; } @Override public void readArguments(String[] args, CommandLineParser parser) { outputFile = args[1]; inputFile = getRemainingFiles(args); String[] genomeId = new String[1]; List resolutionStrings = new ArrayList<>(); populateParameters(args[2], genomeId, resolutionStrings, parser.getGenomeOption()); ChromosomeHandler chromHandler = HiCFileTools.loadChromosomes(genomeId[0]); String tmpDir = parser.getTmpdirOption(); double hicFileScalingFactor = parser.getScalingOption(); updateNumberOfCPUThreads(parser, 1); preprocessor = new MultithreadedPreprocessorHic(new File(outputFile), genomeId[0], chromHandler, hicFileScalingFactor, numCPUThreads); usingMultiThreadedVersion = true; preprocessor.setFromHIC(true); preprocessor.setGenome(genomeId[0]); List customResolutions = parser.getResolutionOption(); if (customResolutions != null && customResolutions.size() > 0) { preprocessor.setResolutions(customResolutions); } else { preprocessor.setResolutions(resolutionStrings); } preprocessor.setIncludedChromosomes(parser.getChromosomeSetOption()); preprocessor.setCountThreshold(parser.getCountThresholdOption()); preprocessor.setV9DepthBase(parser.getV9DepthBase()); preprocessor.setMapqThreshold(parser.getMapqThresholdOption()); preprocessor.setDiagonalsOnly(parser.getDiagonalsOption()); preprocessor.setFragmentFile(parser.getFragmentOption()); preprocessor.setExpectedVectorFile(parser.getExpectedVectorOption()); preprocessor.setTmpdir(tmpDir); preprocessor.setAlignmentFilter(parser.getAlignmentOption()); preprocessor.setRandomizePosition(parser.getRandomizePositionsOption()); preprocessor.setPositionRandomizerSeed(parser.getRandomPositionSeedOption()); preprocessor.setRandomizeFragMaps(parser.getRandomizePositionMaps()); preprocessor.setThrowOutIntraFragOption(parser.getThrowIntraFragOption()); preprocessor.setSubsampler(parser.getSubsampleOption()); int blockCapacity = parser.getBlockCapacityOption(); if (blockCapacity > 10) { Preprocessor.BLOCK_CAPACITY = blockCapacity; } String customShell = parser.getShellOption(); if (customShell != null && customShell.length() > 0) { shell = customShell; } } @Override public void run() { HiCGlobals.allowDynamicBlockIndex = false; try { long currentTime = System.currentTimeMillis(); preprocessor.preprocess(inputFile, null, null, null); ShellCommandRunner.runShellFile(shell, outputFile + MultithreadedPreprocessor.CAT_SCRIPT); if (HiCGlobals.printVerboseComments) { System.out.println("\nBinning contact matrices took: " + (System.currentTimeMillis() - currentTime) + " milliseconds"); } System.out.println("Done creating .hic file. Normalization not calculated due to -n flag."); System.out.println("To run normalization, run: java -jar juicer_tools.jar addNorm "); } catch (Exception e) { e.printStackTrace(); System.exit(56); } } private void populateParameters(String hicFile, String[] genomeId, List resolutionStrings, String genomeOptionIfAvailable) { List files = new ArrayList<>(); files.add(hicFile); Dataset ds = HiCFileTools.extractDatasetForCLT(files, false); genomeId[0] = cleanUpGenome(ds.getGenomeId()); if (genomeOptionIfAvailable != null && genomeOptionIfAvailable.length() > 1) { genomeId[0] = genomeOptionIfAvailable; } for (HiCZoom zoom : ds.getBpZooms()) { resolutionStrings.add("" + zoom.getBinSize()); } } private String cleanUpGenome(String genomeId) { String g2 = genomeId.toLowerCase(); if (g2.endsWith("hg19")) return "hg19"; if (g2.endsWith("hg38")) return "hg38"; if (g2.endsWith("mm9")) return "mm9"; if (g2.endsWith("mm10")) return "mm10"; return genomeId; } private String getRemainingFiles(String[] args) { StringBuilder result = new StringBuilder(args[2]); for (int i = 3; i < args.length; i++) { result.append("+").append(args[i]); } return result.toString(); } } ================================================ FILE: src/juicebox/tools/clt/old/ValidateFile.java ================================================ /* * The MIT License (MIT) * * Copyright (c) 2011-2020 Broad Institute, Aiden Lab, Rice University, Baylor College of Medicine * * Permission is hereby granted, free of charge, to any person obtaining a copy * of this software and associated documentation files (the "Software"), to deal * in the Software without restriction, including without limitation the rights * to use, copy, modify, merge, publish, distribute, sublicense, and/or sell * copies of the Software, and to permit persons to whom the Software is * furnished to do so, subject to the following conditions: * * The above copyright notice and this permission notice shall be included in * all copies or substantial portions of the Software. * * THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR * IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, * FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE * AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER * LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, * OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN * THE SOFTWARE. */ package juicebox.tools.clt.old; import juicebox.HiCGlobals; import juicebox.data.*; import juicebox.data.basics.Chromosome; import juicebox.tools.clt.CommandLineParser; import juicebox.tools.clt.JuiceboxCLT; import juicebox.windowui.HiCZoom; import juicebox.windowui.NormalizationType; import java.io.IOException; import java.util.Arrays; import java.util.List; /** * Created by muhammadsaadshamim on 6/2/16. */ public class ValidateFile extends JuiceboxCLT { private String filePath; public ValidateFile() { super(getUsage()); } public static String getUsage() { return "validate "; } @Override public void readArguments(String[] args, CommandLineParser parser) { if (args.length != 2) { printUsageAndExit(); } filePath = args[1]; } @Override public void run() { try { DatasetReader reader = HiCFileTools.extractDatasetReaderForCLT(Arrays.asList(filePath.split("\\+")), true); Dataset ds = reader.read(); HiCGlobals.verifySupportedHiCFileVersion(reader.getVersion()); assert ds.getGenomeId() != null; assert ds.getChromosomeHandler().size() > 0; List zooms = ds.getBpZooms(); List norms = ds.getNormalizationTypes(); for (NormalizationType type : norms) { System.out.println("File has normalization: " + type.getLabel()); System.out.println("Description: " + type.getDescription()); } for (HiCZoom zoom : zooms) { System.out.println("File has zoom: " + zoom); } Chromosome[] array = ds.getChromosomeHandler().getChromosomeArrayWithoutAllByAll(); for (Chromosome chr: array) { for (Chromosome chr2: array) { System.out.print("."); Matrix matrix = ds.getMatrix(chr, chr2); if (matrix == null) { System.err.println("Warning: no reads in " + chr.getName() + " " + chr2.getName()); } else { for (HiCZoom zoom: zooms) { MatrixZoomData zd = matrix.getZoomData(zoom); for (NormalizationType type: norms) { reader.readNormalizedBlock(0, zd, type); } } } } System.out.println(); } System.out.println("(-: Validation successful"); System.exit(0); throw new IOException("t"); } catch (IOException error) { System.err.println(":( Validation failed"); error.printStackTrace(); System.exit(1); } } } ================================================ FILE: src/juicebox/tools/dev/APAvsDistance.java ================================================ /* * The MIT License (MIT) * * Copyright (c) 2011-2020 Broad Institute, Aiden Lab, Rice University, Baylor College of Medicine * * Permission is hereby granted, free of charge, to any person obtaining a copy * of this software and associated documentation files (the "Software"), to deal * in the Software without restriction, including without limitation the rights * to use, copy, modify, merge, publish, distribute, sublicense, and/or sell * copies of the Software, and to permit persons to whom the Software is * furnished to do so, subject to the following conditions: * * The above copyright notice and this permission notice shall be included in * all copies or substantial portions of the Software. * * THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR * IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, * FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE * AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER * LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, * OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN * THE SOFTWARE. */ package juicebox.tools.dev; import com.google.common.primitives.Ints; import juicebox.HiCGlobals; import juicebox.data.HiCFileTools; import juicebox.tools.clt.CommandLineParserForJuicer; import juicebox.tools.clt.JuicerCLT; import juicebox.tools.clt.juicer.APA; import org.jfree.chart.ChartFactory; import org.jfree.chart.ChartUtilities; import org.jfree.chart.JFreeChart; import org.jfree.chart.plot.PlotOrientation; import org.jfree.data.xy.XYSeries; import org.jfree.data.xy.XYSeriesCollection; import java.io.File; import java.io.IOException; import java.io.PrintWriter; import java.util.ArrayList; import java.util.List; /** * Aggregated Peak Analysis vs Distance * Created by muhammadsaadshamim on 1/19/16. * Developed by Fanny Huang * Implemented by Nathan Musial *

* Except for superloops, we don't observe long-range loops. Why not? *

* The first possibility is that long-range loops do not form, either because: *

* a) there is some mechanism that creates a hard cap on the length of loops, * such as the processivity of the excom, or *

* b) given a convergent pair A/B separated by >2Mb, * there are too many competing ctcf motifs in between. *

* Alternatively, loops do form between pairs of convergent CTCF sites that are far apart, * but those loops are too weak for us to see in our maps. *

* A simple way to probe this is to do APA. Bin pairs of convergent loop anchors by 1d distance, * and then do APA on the pairs in each bin. You should get a strong apa score at 300kb. * what about 3mb? 30mb? */ public class APAvsDistance extends JuicerCLT { private String hicFilePaths; private String PeaksFile; private String SaveFolderPath; private File SaveFolder; //TODO add new flags for (exponent, numBins) //todo appears to have bugs / see commented code for processing flags //todo adjust binning algorithm so that there is enough features in each bucket for apa to run private int[] resolutions = new int[]{25000}; private int numBuckets=8; private double exponent=2; private double minPeakDist=0; private double maxPeakDist=30; public APAvsDistance() { super("APAvsDistance [-n minval] [-x maxval] [-w window] [-r resolution(s)] [-c chromosomes]" + " [-k NONE/VC/VC_SQRT/KR] [-q corner_width] [-e include_inter_chr] [-u save_all_data]" + " "); HiCGlobals.useCache = false; } public static String getBasicUsage() { return "apa_vs_distance "; } public void initializeDirectly(String inputHiCFileName, String inputPeaksFile, String outputDirectoryPath, int numBuckets, double exponent, double minPeakDist, double maxPeakDist) { this.hicFilePaths=inputHiCFileName; this.PeaksFile=inputPeaksFile; this.SaveFolderPath=outputDirectoryPath; this.numBuckets=numBuckets; this.exponent=exponent; this.minPeakDist=minPeakDist; this.maxPeakDist=maxPeakDist; } @Override protected void readJuicerArguments(String[] args, CommandLineParserForJuicer juicerParser) { if (args.length != 4) { printUsageAndExit(); } hicFilePaths = args[1]; PeaksFile = args[2]; SaveFolderPath=args[3]; SaveFolder = HiCFileTools.createValidDirectory(args[3]); /* NormalizationType preferredNorm = juicerParser.getNormalizationTypeOption(); if (preferredNorm != null) norm = preferredNorm; */ double potentialMinPeakDist = juicerParser.getAPAMinVal(); if (potentialMinPeakDist > -1) minPeakDist = potentialMinPeakDist; double potentialMaxPeakDist = juicerParser.getAPAMaxVal(); if (potentialMaxPeakDist > -1) maxPeakDist = potentialMaxPeakDist; /* int potentialWindow = juicerParser.getAPAWindowSizeOption(); if (potentialWindow > 0) window = potentialWindow; includeInterChr = juicerParser.getIncludeInterChromosomal(); saveAllData = juicerParser.getAPASaveAllData(); List possibleRegionWidths = juicerParser.getAPACornerRegionDimensionOptions(); if (possibleRegionWidths != null) { List widths = new ArrayList<>(); for (String res : possibleRegionWidths) { widths.add(Integer.parseInt(res)); } regionWidths = Ints.toArray(widths); } */ List possibleResolutions = juicerParser.getMultipleResolutionOptions(); if (possibleResolutions != null) { List intResolutions = new ArrayList<>(); for (String res : possibleResolutions) { intResolutions.add(Integer.parseInt(res)); } resolutions = Ints.toArray(intResolutions); } } private static void printResults(String[] windows, double[] results, String SaveFolderPath) { File outFolder = new File(SaveFolderPath + "/results.txt"); try { PrintWriter pw = new PrintWriter(outFolder); pw.println("PeaktoPeak Distance\tAPA Score"); for (int i = 0; i < results.length; i++) { pw.println(windows[i] + "\t" + results[i]); } pw.close(); } catch (IOException ex) { ex.printStackTrace(); } } private static void plotChart(String SaveFolderPath, XYSeries results) { File file = new File(SaveFolderPath + "/results.png"); final XYSeriesCollection dataset = new XYSeriesCollection(); dataset.addSeries(results); JFreeChart Chart = ChartFactory.createXYLineChart( "APA vs Distance", "Distance Bucket", "APA Score", dataset, PlotOrientation.VERTICAL, true, true, false); /* LogarithmicAxis logAxis= new LogarithmicAxis("Distance (log)"); XYPlot plot= Chart.getXYPlot(); plot.setDomainAxis(logAxis); XYLineAndShapeRenderer renderer = (XYLineAndShapeRenderer)plot.getRenderer(); renderer.setSeriesShapesVisible(0, true); ChartFrame frame = new ChartFrame("My Chart", Chart); frame.pack(); frame.setVisible(true); */ int width = 640; /* Width of the image */ int height = 480; /* Height of the image */ try { ChartUtilities.saveChartAsPNG(file, Chart, width, height); } catch (IOException ex) { ex.printStackTrace(); } } @Override public void run() { for (int resolution : resolutions) { SaveFolder = new File(SaveFolderPath + resolution); numBuckets = 8; exponent = 2; double[] results = new double[numBuckets]; String[] windows = new String[numBuckets]; XYSeries XYresults = new XYSeries("APA Result: " + resolution); for (int i = 0; i < numBuckets; i++) { APA apa = new APA(); apa.initializeDirectly(hicFilePaths, PeaksFile, SaveFolderPath + "/" + (int) minPeakDist + "-" + (int) maxPeakDist, new int[]{resolution}, minPeakDist, maxPeakDist); windows[i] = minPeakDist + "-" + maxPeakDist; System.out.println("Bucket:" + (i + 1) + " Window: " + windows[i]); //results[i]=i; //for testing binning algorithm results[i] = apa.runWithReturn().getPeak2LL(); // calls APA returns results of apa and gets LL score System.out.println(results[i]); XYresults.add(Math.log(maxPeakDist), results[i]); minPeakDist = maxPeakDist; maxPeakDist *= exponent; } plotChart(SaveFolderPath + resolution, XYresults); printResults(windows, results, SaveFolderPath + resolution); } } } ================================================ FILE: src/juicebox/tools/dev/ChromosomeCalculation.java ================================================ /* * The MIT License (MIT) * * Copyright (c) 2011-2021 Broad Institute, Aiden Lab, Rice University, Baylor College of Medicine * * Permission is hereby granted, free of charge, to any person obtaining a copy * of this software and associated documentation files (the "Software"), to deal * in the Software without restriction, including without limitation the rights * to use, copy, modify, merge, publish, distribute, sublicense, and/or sell * copies of the Software, and to permit persons to whom the Software is * furnished to do so, subject to the following conditions: * * The above copyright notice and this permission notice shall be included in * all copies or substantial portions of the Software. * * THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR * IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, * FITNESS FOR A PARTICULAR PURPOSE AND NON-INFRINGEMENT. IN NO EVENT SHALL THE * AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER * LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, * OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN * THE SOFTWARE. */ package juicebox.tools.dev; import juicebox.HiCGlobals; import juicebox.data.ContactRecord; import juicebox.data.Dataset; import juicebox.data.HiCFileTools; import juicebox.data.MatrixZoomData; import juicebox.data.basics.Chromosome; import juicebox.tools.utils.common.ArrayTools; import java.io.BufferedWriter; import java.io.File; import java.io.FileOutputStream; import java.io.OutputStreamWriter; import java.util.*; public class ChromosomeCalculation { public static void sum(int resolution, int slidingWindow, String filePath, String outputFolder) { ArrayList files = new ArrayList<>(); File outFolder = new File(outputFolder); if (!outFolder.exists()) { outFolder.mkdir(); } String colString = "column_sum_" + resolution + "_" + slidingWindow + ".bedgraph"; String diagString = "diagonal_val_" + resolution + "_" + slidingWindow + ".bedgraph"; File columnSumsFile = new File(outputFolder, colString); File diagValFile = new File(outputFolder, diagString); File slidingAvgColumnSumsFile = new File(outputFolder, "slide_avg_" + colString); File slidingAvgDiagValFile = new File(outputFolder, "slide_avg_" + diagString); File logEnrichColumnSumsFile = new File(outputFolder, "log_enrich_" + colString); File logEnrichDiagValFile = new File(outputFolder, "log_enrich_" + diagString); HiCGlobals.useCache = false; files.add(filePath); // replace with hic file paths Dataset ds = HiCFileTools.extractDatasetForCLT(files, false); // see this class and its functions Chromosome[] chromosomes = ds.getChromosomeHandler().getAutosomalChromosomesArray(); Map> chromosomeToColumnSumsMap = new HashMap<>(); Map> chromosomeToDiagonalValueMap = new HashMap<>(); for (int i = 0; i < chromosomes.length; i++) { Chromosome chromosome1 = chromosomes[i]; for (int j = i; j < chromosomes.length; j++) { Chromosome chromosome2 = chromosomes[j]; MatrixZoomData zd = HiCFileTools.getMatrixZoomData(ds, chromosome1, chromosome2, resolution); // 1,000,000 resolution if (zd == null) continue; // do the summing, iterate over contact records in matrixZoomData object sumColumn(zd, chromosomeToColumnSumsMap, chromosomeToDiagonalValueMap, chromosome1, chromosome2); } } writeDataToFile(chromosomeToColumnSumsMap, columnSumsFile, resolution); writeDataToFile(chromosomeToDiagonalValueMap, diagValFile, resolution); slidingAverageAcrossData(slidingWindow, chromosomeToColumnSumsMap); slidingAverageAcrossData(slidingWindow, chromosomeToDiagonalValueMap); writeDataToFile(chromosomeToColumnSumsMap, slidingAvgColumnSumsFile, resolution); writeDataToFile(chromosomeToDiagonalValueMap, slidingAvgDiagValFile, resolution); //calculateLogEnrichmentOfObservedOverExpected(chromosomeToColumnSumsMap); //calculateLogEnrichmentOfObservedOverExpected(chromosomeToDiagonalValueMap); //writeDataToFile(chromosomeToColumnSumsMap, logEnrichColumnSumsFile, resolution); //writeDataToFile(chromosomeToDiagonalValueMap, logEnrichDiagValFile, resolution); } public static void slidingAverageAcrossData(int slidingWindow, Map> dataMap) { for (Map dataMapForChromosome : dataMap.values()) { int maxIndex = Collections.max(dataMapForChromosome.keySet()); float[] values = new float[maxIndex + 1]; for (int idx : dataMapForChromosome.keySet()) { values[idx] = dataMapForChromosome.get(idx); } float[] newAvgAfterSliding = ArrayTools.runSlidingAverageOnArray(slidingWindow, values); for (int idx : dataMapForChromosome.keySet()) { if (values[idx] > 0) { dataMapForChromosome.put(idx, newAvgAfterSliding[idx]); } } } } private static void writeDataToFile(Map> dataHashMap, File outputFile, int resolution) { try { BufferedWriter bw = new BufferedWriter((new OutputStreamWriter((new FileOutputStream(outputFile))))); for (Chromosome key : dataHashMap.keySet()) { List indices = new ArrayList<>(dataHashMap.get(key).keySet()); Collections.sort(indices); for (int index : indices) { String s = key.getName() + "\t" + (index) * resolution + "\t" + (index + 1) * resolution + "\t" + dataHashMap.get(key).get(index); bw.write(s); bw.newLine(); } } bw.close(); } catch (Exception e) { e.printStackTrace(); } } private static void sumColumn(MatrixZoomData zd, Map> mapOfSums, Map> mapOfDiagValues, Chromosome chrI, Chromosome chrJ) { if (chrI.getIndex() == chrJ.getIndex()) { Map subMapOfSumsForChr = mapOfSums.getOrDefault(chrI, new HashMap<>()); Map subMapOfDiagForChr = mapOfDiagValues.getOrDefault(chrI, new HashMap<>()); Iterator iterator = zd.getIteratorContainer().getNewContactRecordIterator(); while (iterator.hasNext()) { ContactRecord contact = iterator.next(); float count = contact.getCounts(); int x = contact.getBinX(); int y = contact.getBinY(); if (x == y) { subMapOfSumsForChr.put(x, subMapOfSumsForChr.getOrDefault(x, 0f) + count); subMapOfDiagForChr.put(x, count); } else { subMapOfSumsForChr.put(x, subMapOfSumsForChr.getOrDefault(x, 0f) + count); subMapOfSumsForChr.put(y, subMapOfSumsForChr.getOrDefault(y, 0f) + count); } } mapOfSums.put(chrI, subMapOfSumsForChr); mapOfDiagValues.put(chrI, subMapOfDiagForChr); } else { Map subMap = mapOfSums.getOrDefault(chrI, new HashMap<>()); Map subMap2 = mapOfSums.getOrDefault(chrJ, new HashMap<>()); Iterator iterator = zd.getIteratorContainer().getNewContactRecordIterator(); while (iterator.hasNext()) { ContactRecord contact = iterator.next(); float count = contact.getCounts(); int x = contact.getBinX(); int y = contact.getBinY(); subMap.put(x, subMap.getOrDefault(x, 0f) + count); subMap2.put(y, subMap.getOrDefault(y, 0f) + count); } mapOfSums.put(chrI, subMap); mapOfSums.put(chrJ, subMap2); } } public static void calculateLogEnrichmentOfObservedOverExpected(Map> map) { float total = 0; int size = 0; for (Chromosome key : map.keySet()) { for (int subKey : map.get(key).keySet()) { float val = map.get(key).get(subKey); if (val > 1) { total += val; size += 1; } } } float currentAverage = total / size; System.out.println(currentAverage); for (Chromosome key : map.keySet()) { for (int subKey : map.get(key).keySet()) { float newVal = (float) Math.log(map.get(key).get(subKey) / currentAverage); map.get(key).put(subKey, newVal); } } } } ================================================ FILE: src/juicebox/tools/dev/CompareVectors.java ================================================ /* * The MIT License (MIT) * * Copyright (c) 2011-2020 Broad Institute, Aiden Lab, Rice University, Baylor College of Medicine * * Permission is hereby granted, free of charge, to any person obtaining a copy * of this software and associated documentation files (the "Software"), to deal * in the Software without restriction, including without limitation the rights * to use, copy, modify, merge, publish, distribute, sublicense, and/or sell * copies of the Software, and to permit persons to whom the Software is * furnished to do so, subject to the following conditions: * * The above copyright notice and this permission notice shall be included in * all copies or substantial portions of the Software. * * THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR * IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, * FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE * AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER * LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, * OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN * THE SOFTWARE. */ package juicebox.tools.dev; import juicebox.HiC; import juicebox.data.ChromosomeHandler; import juicebox.data.NormalizationVector; import juicebox.data.basics.Chromosome; import juicebox.tools.clt.CommandLineParser; import juicebox.tools.clt.JuiceboxCLT; import juicebox.tools.utils.common.MatrixTools; import juicebox.tools.utils.common.UNIXTools; import juicebox.windowui.HiCZoom; import juicebox.windowui.NormalizationType; import java.io.File; public class CompareVectors extends JuiceboxCLT { ChromosomeHandler chromosomeHandler; NormalizationType norm2; File outputFolder; HiCZoom zoom; public CompareVectors() { super(getUsage()); } private static String getUsage() { return "compare-vectors "; } @Override public void readArguments(String[] args, CommandLineParser parser) { if (args.length != 7 && args.length != 6) { printUsageAndExit(); } setDatasetAndNorm(args[3], args[1], false); norm2 = dataset.getNormalizationHandler().getNormTypeFromString(args[2]); chromosomeHandler = dataset.getChromosomeHandler(); try { zoom = new HiCZoom(HiC.Unit.BP, Integer.parseInt(args[4])); } catch (NumberFormatException e) { System.err.println("Integer expected for bin size. Found: " + args[4] + "."); System.exit(21); } outputFolder = new File(args[5]); UNIXTools.makeDir(outputFolder); } @Override public void run() { for (Chromosome chromosome : chromosomeHandler.getChromosomeArrayWithoutAllByAll()) { NormalizationVector nv1 = dataset.getNormalizationVector(chromosome.getIndex(), zoom, norm); NormalizationVector nv2 = dataset.getNormalizationVector(chromosome.getIndex(), zoom, norm2); if (nv2 == null) { System.err.println(norm2 + " not available for " + chromosome.getName()); } if (chromosome.getLength() / zoom.getBinSize() + 1 < Integer.MAX_VALUE) { int numElements = (int) (chromosome.getLength() / zoom.getBinSize()) + 1; double[][] result = new double[2][numElements]; fillInVector(result, nv1, 0, norm, chromosome); fillInVector(result, nv2, 1, norm2, chromosome); File rOut = new File(outputFolder, chromosome.getName() + "_" + norm.getLabel() + "_vs_" + norm2.getLabel() + ".npy"); MatrixTools.saveMatrixTextNumpy(rOut.getAbsolutePath(), result); } else { System.err.println("long vector support not currently available"); } } } private void fillInVector(double[][] array, NormalizationVector nv, int rowIdx, NormalizationType normalizationType, Chromosome chromosome) { if (nv == null) { System.err.println(normalizationType + " not available for " + chromosome.getName()); } else { System.arraycopy(nv.getData().getValues().get(0), 0, array[rowIdx], 0, array[rowIdx].length); } } } ================================================ FILE: src/juicebox/tools/dev/GeneFinder.java ================================================ /* * The MIT License (MIT) * * Copyright (c) 2011-2020 Broad Institute, Aiden Lab, Rice University, Baylor College of Medicine * * Permission is hereby granted, free of charge, to any person obtaining a copy * of this software and associated documentation files (the "Software"), to deal * in the Software without restriction, including without limitation the rights * to use, copy, modify, merge, publish, distribute, sublicense, and/or sell * copies of the Software, and to permit persons to whom the Software is * furnished to do so, subject to the following conditions: * * The above copyright notice and this permission notice shall be included in * all copies or substantial portions of the Software. * * THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR * IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, * FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE * AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER * LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, * OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN * THE SOFTWARE. */ package juicebox.tools.dev; import juicebox.data.ChromosomeHandler; import juicebox.data.HiCFileTools; import juicebox.data.anchor.*; import juicebox.data.feature.FeatureFunction; import juicebox.data.feature.GenomeWideList; import juicebox.tools.clt.CommandLineParserForJuicer; import juicebox.tools.clt.JuicerCLT; import juicebox.tools.utils.juicer.GeneTools; import juicebox.track.feature.Feature2D; import juicebox.track.feature.Feature2DList; import juicebox.track.feature.Feature2DParser; import java.io.BufferedWriter; import java.io.File; import java.io.FileWriter; import java.util.ArrayList; import java.util.HashSet; import java.util.List; import java.util.Set; /** * Created by muhammadsaadshamim on 8/3/16. */ public class GeneFinder extends JuicerCLT { private String genomeID, bedFilePath, loopListPath; private File outFile; public GeneFinder() { super("genes [output]"); } @Override protected void readJuicerArguments(String[] args, CommandLineParserForJuicer juicerParser) { if (args.length != 3 && args.length != 4 && args.length != 5) { printUsageAndExit(); } genomeID = args[1]; bedFilePath = args[2]; if (args.length >= 4) loopListPath = args[3]; String outputPath = "active_genes"; if (args.length == 5) { outputPath = args[4]; } outFile = new File(outputPath); } @Override public void run() { ChromosomeHandler handler = HiCFileTools.loadChromosomes(genomeID); try { GenomeWideList genes = GeneTools.parseGenome(genomeID, handler); System.out.println("Starting with " + genes.size() + " genes"); if (loopListPath != null) { final Feature2DList allLoops = Feature2DParser.loadFeatures(loopListPath, handler, false, null, false); GenomeWideList allAnchors = MotifAnchorTools.extractAnchorsFromIntrachromosomalFeatures(allLoops, false, handler, 15000 ); final Feature2DList filteredLoops = new Feature2DList(); if ((new File(bedFilePath)).exists()) { GenomeWideList proteins = GenericLocusParser.loadFromBEDFile(handler, bedFilePath); MotifAnchorTools.preservativeIntersectLists(allAnchors, proteins, false); allAnchors.processLists(new FeatureFunction() { @Override public void process(String chr, List anchors) { List restoredLoops = new ArrayList<>(); for (GenericLocus anchor : anchors) { restoredLoops.addAll(anchor.getOriginalFeatures1()); restoredLoops.addAll(anchor.getOriginalFeatures2()); } filteredLoops.addByKey(chr + "_" + chr, restoredLoops); } }); } else { System.err.println("No bed file provided, all loops being assessed."); filteredLoops.add(allLoops); } // note, this is NOT identical to all anchors after preservative intersect // because this restores both of the loops anchors even if one was eliminated // in the previous intersection as long as one of its anchors hit the protein GenomeWideList filteredAnchors = MotifAnchorTools.extractAnchorsFromIntrachromosomalFeatures(filteredLoops, false, handler, 15000); MotifAnchorTools.preservativeIntersectLists(genes, filteredAnchors, false); } else { if ((new File(bedFilePath)).exists()) { System.out.println("Just using bed file"); GenomeWideList proteins = GenericLocusParser.loadFromBEDFile(handler, bedFilePath); //MotifAnchorTools.mergeAndExpandSmallAnchors(proteins, 1000); MotifAnchorTools.preservativeIntersectLists(genes, proteins, false); } } final Set geneNames = new HashSet<>(); genes.processLists(new FeatureFunction() { @Override public void process(String chr, List featureList) { for (GenericLocus anchor : featureList) { geneNames.add(anchor.getName()); } } }); BufferedWriter writer = new BufferedWriter(new FileWriter(outFile)); StringBuilder sb = new StringBuilder(); for (String s : geneNames) { sb.append(s); sb.append("\n"); } writer.write(sb.toString()); writer.flush(); writer.close(); } catch (Exception e) { e.printStackTrace(); } } } ================================================ FILE: src/juicebox/tools/dev/HiCArtMNDWriter.java ================================================ /* * The MIT License (MIT) * * Copyright (c) 2011-2021 Broad Institute, Aiden Lab, Rice University, Baylor College of Medicine * * Permission is hereby granted, free of charge, to any person obtaining a copy * of this software and associated documentation files (the "Software"), to deal * in the Software without restriction, including without limitation the rights * to use, copy, modify, merge, publish, distribute, sublicense, and/or sell * copies of the Software, and to permit persons to whom the Software is * furnished to do so, subject to the following conditions: * * The above copyright notice and this permission notice shall be included in * all copies or substantial portions of the Software. * * THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR * IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, * FITNESS FOR A PARTICULAR PURPOSE AND NON-INFRINGEMENT. IN NO EVENT SHALL THE * AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER * LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, * OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN * THE SOFTWARE. */ package juicebox.tools.dev; import java.io.*; import java.util.*; class HiCArtMNDWriter { public static void main(String[] args) { writeMergedNoDupsFromTimeSeq(args[0], args[1]); } private static void writeMergedNoDupsFromTimeSeq(String seqPath, String newPath) { List listPositions = new ArrayList<>(); int distanceLimit = 0; try (BufferedReader br = new BufferedReader(new FileReader(seqPath))) { Set positions = new HashSet<>(); for (String line; (line = br.readLine()) != null; ) { String[] parts = line.split(","); Integer[] xy = new Integer[]{Integer.parseInt(parts[0]), Integer.parseInt(parts[1])}; listPositions.add(xy); positions.add(xy[0]); positions.add(xy[1]); } distanceLimit = (Collections.max(positions) - Collections.min(positions)) / 2; } catch (Exception ignored) { //ignored.printStackTrace(); } try { PrintWriter p0 = new PrintWriter(new FileWriter(newPath)); for (int i = 0; i < listPositions.size(); i++) { Integer[] pos_xy_1 = listPositions.get(i); for (int j = i; j < listPositions.size(); j++) { Integer[] pos_xy_2 = listPositions.get(j); double distance = Math.sqrt((pos_xy_1[0] - pos_xy_2[0]) ^ 2 + (pos_xy_1[1] - pos_xy_2[1]) ^ 2); if (distance < distanceLimit) { double value = 1. / Math.max(.5, distance); if (!Double.isNaN(value) && value > 0) { p0.println("0 art " + i + " 0 16 art " + j + " 1 " + value); } } } } p0.close(); } catch (IOException ignored) { //ignored.printStackTrace(); } } } ================================================ FILE: src/juicebox/tools/dev/IntraChromTriple.java ================================================ /* * The MIT License (MIT) * * Copyright (c) 2011-2020 Broad Institute, Aiden Lab, Rice University, Baylor College of Medicine * * Permission is hereby granted, free of charge, to any person obtaining a copy * of this software and associated documentation files (the "Software"), to deal * in the Software without restriction, including without limitation the rights * to use, copy, modify, merge, publish, distribute, sublicense, and/or sell * copies of the Software, and to permit persons to whom the Software is * furnished to do so, subject to the following conditions: * * The above copyright notice and this permission notice shall be included in * all copies or substantial portions of the Software. * * THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR * IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, * FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE * AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER * LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, * OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN * THE SOFTWARE. */ package juicebox.tools.dev; import juicebox.data.ChromosomeHandler; import juicebox.data.feature.Feature; import java.util.ArrayList; import java.util.Collections; import java.util.List; public class IntraChromTriple extends Feature implements Comparable { private final Integer x1, x2, x3, chrIndex; public IntraChromTriple(int chrIndex, int x1, int x2, int x3) { this.chrIndex = chrIndex; this.x1 = x1; this.x2 = x2; this.x3 = x3; } private IntraChromTriple(int chrIndex, List ints) { this.chrIndex = chrIndex; Collections.sort(ints); x1 = ints.get(0); x2 = ints.get(1); x3 = ints.get(2); } /** * assuming syntax * chr1 x1 chr2 x2 chr3 x3 */ public static IntraChromTriple parse(String line, ChromosomeHandler handler) { String[] parsedText = line.split("\\s+"); int chrIndex; if (parsedText[0].equalsIgnoreCase(parsedText[2]) && parsedText[2].equalsIgnoreCase(parsedText[4])) { chrIndex = handler.getChromosomeFromName(parsedText[0]).getIndex(); } else { return null; } Integer y1 = Integer.parseInt(parsedText[1]); Integer y2 = Integer.parseInt(parsedText[3]); Integer y3 = Integer.parseInt(parsedText[5]); if (Math.abs(y1 - y2) > 20 && Math.abs(y1 - y3) > 20 && Math.abs(y2 - y3) > 20) { List ints = new ArrayList<>(); ints.add(y1); ints.add(y2); ints.add(y3); return new IntraChromTriple(chrIndex, ints); } return null; } @Override public int compareTo(IntraChromTriple o) { int comparison = chrIndex.compareTo(o.chrIndex); if (comparison == 0) comparison = x1.compareTo(o.x1); if (comparison == 0) comparison = x2.compareTo(o.x2); if (comparison == 0) comparison = x3.compareTo(o.x3); return comparison; } @Override public String getKey() { return "" + chrIndex; } @Override public String toString() { return chrIndex + "\t" + x1 + "\t" + x2 + "\t" + x3; } @Override public Feature deepClone() { return new IntraChromTriple(chrIndex, x1, x2, x3); } public Integer getX1() { return x1; } public Integer getX2() { return x2; } public Integer getX3() { return x3; } public TripleCentroid toTripleCentroid() { return new TripleCentroid(chrIndex, x1, x2, x3); } } ================================================ FILE: src/juicebox/tools/dev/MapSelectionPanel.java ================================================ /* * The MIT License (MIT) * * Copyright (c) 2011-2021 Broad Institute, Aiden Lab, Rice University, Baylor College of Medicine * * Permission is hereby granted, free of charge, to any person obtaining a copy * of this software and associated documentation files (the "Software"), to deal * in the Software without restriction, including without limitation the rights * to use, copy, modify, merge, publish, distribute, sublicense, and/or sell * copies of the Software, and to permit persons to whom the Software is * furnished to do so, subject to the following conditions: * * The above copyright notice and this permission notice shall be included in * all copies or substantial portions of the Software. * * THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR * IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, * FITNESS FOR A PARTICULAR PURPOSE AND NON-INFRINGEMENT. IN NO EVENT SHALL THE * AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER * LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, * OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN * THE SOFTWARE. */ package juicebox.tools.dev; import juicebox.HiC; import juicebox.HiCGlobals; import juicebox.data.Dataset; import juicebox.gui.SuperAdapter; import javax.swing.*; import javax.swing.border.Border; import java.awt.*; import java.awt.event.ActionEvent; import java.awt.event.ActionListener; import java.util.ArrayList; import java.util.List; /** * Created by muhammadsaadshamim on 8/4/16. */ class MapSelectionPanel extends JPanel { private static final long serialVersionUID = 900003; private final List actionListeners = new ArrayList<>(); /** * @param reader * @param controlReader */ private MapSelectionPanel(SuperAdapter superAdapter, Dataset reader, Dataset controlReader) { super(new BorderLayout()); Border padding = BorderFactory.createEmptyBorder(20, 20, 5, 20); JTabbedPane tabbedPane = new JTabbedPane(); actionListeners.clear(); JPanel mainMaps = generateMapActivationPanel(superAdapter, reader, "Active Hi-C Maps:"); if (mainMaps != null) { mainMaps.setBorder(padding); tabbedPane.addTab("Main Map", null, mainMaps, "The main maps"); } JPanel controlMaps = generateMapActivationPanel(superAdapter, controlReader, "Active Control Hi-C Maps:"); if (controlMaps != null) { controlMaps.setBorder(padding); tabbedPane.addTab("Control Map", null, controlMaps, "The control maps"); } add(tabbedPane, BorderLayout.CENTER); } /** * @param superAdapter */ public static void launchMapSubsetGUI(SuperAdapter superAdapter) { HiC hic = superAdapter.getHiC(); Dataset reader = hic.getDataset(); Dataset controlReader = hic.getControlDataset(); if (reader != null) { JFrame frame = new JFrame("Map Selection Panel"); MapSelectionPanel newContentPane = new MapSelectionPanel(superAdapter, reader, controlReader); newContentPane.setOpaque(true); frame.setContentPane(newContentPane); frame.pack(); frame.setVisible(true); } } /** * @param superAdapter * @param reader * @param title * @return */ private JPanel generateMapActivationPanel(final SuperAdapter superAdapter, Dataset reader, String title) { final JButton showItButton = new JButton("Update View"); if (reader != null) { List checkBoxes = reader.getCheckBoxes(actionListeners); showItButton.addActionListener(new ActionListener() { public void actionPerformed(ActionEvent e) { for (ActionListener listener : actionListeners) { listener.actionPerformed(e); } // todo because cache keys currently don't account for map activation // actually don't need to do this, just do a clear cache whenever triggered HiCGlobals.useCache = false; superAdapter.refresh(); } }); return createPane(title, checkBoxes, showItButton); } return null; } /** * @param description * @param checkBoxes * @param showButton * @return */ private JPanel createPane(String description, List checkBoxes, JButton showButton) { JLabel label = new JLabel(description); JPanel box = new JPanel(); box.setLayout(new BoxLayout(box, BoxLayout.PAGE_AXIS)); for (JCheckBox checkBox : checkBoxes) { box.add(checkBox); } JScrollPane scrollPane = new JScrollPane(box, JScrollPane.VERTICAL_SCROLLBAR_AS_NEEDED, JScrollPane.HORIZONTAL_SCROLLBAR_NEVER); JPanel pane = new JPanel(new BorderLayout()); pane.add(label, BorderLayout.PAGE_START); pane.add(scrollPane, BorderLayout.CENTER); pane.add(showButton, BorderLayout.PAGE_END); return pane; } } ================================================ FILE: src/juicebox/tools/dev/ParallelizedJuicerTools.java ================================================ /* * The MIT License (MIT) * * Copyright (c) 2011-2020 Broad Institute, Aiden Lab, Rice University, Baylor College of Medicine * * Permission is hereby granted, free of charge, to any person obtaining a copy * of this software and associated documentation files (the "Software"), to deal * in the Software without restriction, including without limitation the rights * to use, copy, modify, merge, publish, distribute, sublicense, and/or sell * copies of the Software, and to permit persons to whom the Software is * furnished to do so, subject to the following conditions: * * The above copyright notice and this permission notice shall be included in * all copies or substantial portions of the Software. * * THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR * IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, * FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE * AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER * LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, * OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN * THE SOFTWARE. */ package juicebox.tools.dev; import java.util.concurrent.ExecutorService; import java.util.concurrent.Executors; public class ParallelizedJuicerTools { public static void launchParallelizedCode(Runnable runnable) { launchParallelizedCode(Runtime.getRuntime().availableProcessors(), runnable); } public static void launchParallelizedCode(int numCPUThreads, Runnable runnable) { ExecutorService executor = Executors.newFixedThreadPool(numCPUThreads); for (int l = 0; l < numCPUThreads; l++) { Runnable worker = new Runnable() { @Override public void run() { runnable.run(); } }; executor.execute(worker); } executor.shutdown(); // Wait until all threads finish while (!executor.isTerminated()) { } } } ================================================ FILE: src/juicebox/tools/dev/Private.java ================================================ /* * The MIT License (MIT) * * Copyright (c) 2011-2020 Broad Institute, Aiden Lab, Rice University, Baylor College of Medicine * * Permission is hereby granted, free of charge, to any person obtaining a copy * of this software and associated documentation files (the "Software"), to deal * in the Software without restriction, including without limitation the rights * to use, copy, modify, merge, publish, distribute, sublicense, and/or sell * copies of the Software, and to permit persons to whom the Software is * furnished to do so, subject to the following conditions: * * The above copyright notice and this permission notice shall be included in * all copies or substantial portions of the Software. * * THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR * IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, * FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE * AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER * LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, * OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN * THE SOFTWARE. */ package juicebox.tools.dev; import juicebox.gui.SuperAdapter; /** * Created by muhammadsaadshamim on 8/15/16. */ public class Private { public static boolean assessGenomeForRE(String genomeId) { return genomeId.equalsIgnoreCase("anasPlat1"); } public static boolean assessGenomeForRE2(String genomeId) { return genomeId.equalsIgnoreCase("hg19_contig"); } public static String reForDMEL(int sites) { if (sites == 185217) return "MseI"; return null; } public static boolean assessGenomeForRE3(String genomeId) { return genomeId.equalsIgnoreCase("galGal4"); } public static String reForHG18(int sites) { if (sites == 64338) return "HindIII"; return null; } public static String reForHG19(int sites) { if (sites == 22706) return "Acc65I"; if (sites == 4217) return "AgeI"; if (sites == 158473) return "BseYI"; if (sites == 74263) return "BspHI"; if (sites == 60834) return "BstUI2"; if (sites == 2284472) return "CpG"; if (sites == 139125) return "HinP1I"; if (sites == 160930) return "HpyCH4IV2"; if (sites == 1632) return "MluI"; if (sites == 1428208) return "MseI"; if (sites == 194423) return "MspI"; if (sites == 22347) return "NheI"; if (sites == 1072254) return "NlaIII"; if (sites == 1128) return "NruI"; if (sites == 2344) return "SaII"; if (sites == 1006921) return "StyD4I"; if (sites == 256163) return "StyI"; if (sites == 119506) return "TaqI2"; if (sites == 9958) return "XhoI"; if (sites == 31942) return "XmaI"; return null; } public static String reForMM9(int sites) { if (sites == 1157974) return "MseI"; if (sites == 933321) return "NlaIII"; return null; } public static boolean assessGenomeForRE4(String genomeId) { return genomeId.equalsIgnoreCase("susScr3"); } public static void launchMapSubsetGUI(SuperAdapter superAdapter) { MapSelectionPanel.launchMapSubsetGUI(superAdapter); } } ================================================ FILE: src/juicebox/tools/dev/RandomUtils.java ================================================ /* * The MIT License (MIT) * * Copyright (c) 2011-2020 Broad Institute, Aiden Lab, Rice University, Baylor College of Medicine * * Permission is hereby granted, free of charge, to any person obtaining a copy * of this software and associated documentation files (the "Software"), to deal * in the Software without restriction, including without limitation the rights * to use, copy, modify, merge, publish, distribute, sublicense, and/or sell * copies of the Software, and to permit persons to whom the Software is * furnished to do so, subject to the following conditions: * * The above copyright notice and this permission notice shall be included in * all copies or substantial portions of the Software. * * THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR * IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, * FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE * AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER * LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, * OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN * THE SOFTWARE. */ package juicebox.tools.dev; import juicebox.data.ChromosomeHandler; import juicebox.data.HiCFileTools; import juicebox.track.feature.Feature2D; import juicebox.track.feature.Feature2DList; import juicebox.track.feature.Feature2DParser; import java.io.File; import java.util.ArrayList; import java.util.List; class RandomUtils { /** * Usage *

* String[] inputFiles = new String[]{"/Users/muhammad/Desktop/loops/gm12878.bedpe", * "/Users/muhammad/Desktop/loops/hela.bedpe", * "/Users/muhammad/Desktop/loops/imr90.bedpe", * "/Users/muhammad/Desktop/loops/k562.bedpe", * "/Users/muhammad/Desktop/loops/nhek.bedpe", * "/Users/muhammad/Desktop/loops/hap1.bedpe", * "/Users/muhammad/Desktop/loops/hmec.bedpe", * "/Users/muhammad/Desktop/loops/huvec.bedpe"}; *

*

* RandomUtils.mergeLoopLists("hg19", inputFiles, new File("/Users/muhammad/Desktop/loops/merged.bedpe")); * * @param genomeID * @param fileNames * @param outputFile */ public static void intersectLoopLists(String genomeID, String[] fileNames, File outputFile) { ChromosomeHandler handler = HiCFileTools.loadChromosomes(genomeID); List lists = new ArrayList<>(); for (String fileName : fileNames) { lists.add(Feature2DParser.loadFeatures(fileName, handler, false, null, false)); } Feature2D.tolerance = 10000; Feature2DList exactMatches = Feature2DList.getIntersection(lists.get(0), lists.get(0)); for (Feature2DList list : lists) { exactMatches = Feature2DList.getIntersection(exactMatches, list); int numExactMatches = exactMatches.getNumTotalFeatures(); System.out.println("Number of exact matches: " + numExactMatches); } exactMatches.exportFeatureList(outputFile, true, Feature2DList.ListFormat.FINAL); } } ================================================ FILE: src/juicebox/tools/dev/TripleCentroid.java ================================================ /* * The MIT License (MIT) * * Copyright (c) 2011-2020 Broad Institute, Aiden Lab, Rice University, Baylor College of Medicine * * Permission is hereby granted, free of charge, to any person obtaining a copy * of this software and associated documentation files (the "Software"), to deal * in the Software without restriction, including without limitation the rights * to use, copy, modify, merge, publish, distribute, sublicense, and/or sell * copies of the Software, and to permit persons to whom the Software is * furnished to do so, subject to the following conditions: * * The above copyright notice and this permission notice shall be included in * all copies or substantial portions of the Software. * * THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR * IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, * FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE * AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER * LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, * OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN * THE SOFTWARE. */ package juicebox.tools.dev; import java.util.HashSet; import java.util.Set; public class TripleCentroid { private final Integer chrIndex; private final Set x1s = new HashSet<>(); private final Set x2s = new HashSet<>(); private final Set x3s = new HashSet<>(); private Integer x1; private Integer x2; private Integer x3; public TripleCentroid(Integer chrIndex, Integer x1, Integer x2, Integer x3) { this.chrIndex = chrIndex; this.x1 = x1; this.x2 = x2; this.x3 = x3; x1s.add(x1); x2s.add(x2); x3s.add(x3); } public void consumeDuplicate(IntraChromTriple triple) { x1s.add(triple.getX1()); x2s.add(triple.getX2()); x3s.add(triple.getX3()); x1 = average(x1s); x2 = average(x2s); x3 = average(x3s); } private Integer average(Set xs) { int accum = 0; for (int val : xs) { accum += val; } return accum / xs.size(); } public boolean hasOverlapWithTriple(IntraChromTriple triple, int tolerance) { return Math.abs(triple.getX1() - x1) < tolerance && Math.abs(triple.getX2() - x2) < tolerance && Math.abs(triple.getX3() - x3) < tolerance; } public IntraChromTriple toIntraChromTriple() { return new IntraChromTriple(chrIndex, x1, x2, x3); } } ================================================ FILE: src/juicebox/tools/dev/TriplesAPA.java ================================================ /* * The MIT License (MIT) * * Copyright (c) 2011-2021 Broad Institute, Aiden Lab, Rice University, Baylor College of Medicine * * Permission is hereby granted, free of charge, to any person obtaining a copy * of this software and associated documentation files (the "Software"), to deal * in the Software without restriction, including without limitation the rights * to use, copy, modify, merge, publish, distribute, sublicense, and/or sell * copies of the Software, and to permit persons to whom the Software is * furnished to do so, subject to the following conditions: * * The above copyright notice and this permission notice shall be included in * all copies or substantial portions of the Software. * * THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR * IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, * FITNESS FOR A PARTICULAR PURPOSE AND NON-INFRINGEMENT. IN NO EVENT SHALL THE * AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER * LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, * OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN * THE SOFTWARE. */ package juicebox.tools.dev; import juicebox.data.ChromosomeHandler; import juicebox.data.HiCFileTools; import juicebox.data.anchor.*; import juicebox.data.feature.FeatureFilter; import juicebox.data.feature.FeatureFunction; import juicebox.data.feature.GenomeWideList; import juicebox.tools.clt.CommandLineParserForJuicer; import juicebox.tools.clt.JuicerCLT; import java.io.BufferedReader; import java.io.FileReader; import java.util.*; public class TriplesAPA extends JuicerCLT { public TriplesAPA() { super("ignore_for_now"); } private static void removeAnchorsThatAreTooCloseTogether(GenomeWideList anchors, final int filterSize) { MotifAnchorTools.mergeAndExpandSmallAnchors(anchors, filterSize); anchors.filterLists(new FeatureFilter() { @Override public List filter(String chr, List featureList) { List newAnchors = new ArrayList<>(); for (GenericLocus anchor : featureList) { if (anchor.getWidth() == filterSize) { newAnchors.add(anchor); } } return newAnchors; } }); } private static GenomeWideList readInIntraChromTriple(ChromosomeHandler handler, String triplesPath) { GenomeWideList triples = new GenomeWideList<>(handler); try (BufferedReader br = new BufferedReader(new FileReader(triplesPath))) { for (String line; (line = br.readLine()) != null; ) { IntraChromTriple triple = IntraChromTriple.parse(line, handler); if (triple != null) { triples.addFeature(triple.getKey(), triple); } } } catch (Exception ignored) { //ignored.printStackTrace(); } return triples; } @Override protected void readJuicerArguments(String[] args, CommandLineParserForJuicer juicerParser) { } @Override public void run() { ChromosomeHandler handler = HiCFileTools.loadChromosomes("hg19"); GenomeWideList anchors = GenericLocusParser.loadFromBEDFile(handler, "/Users/muhammadsaadshamim/Desktop/goodell_2/GrandCanyons.bed"); //anchors = MotifAnchorParser.loadFromBEDFile(handler, "/Users/muhammadsaadshamim/Desktop/goodell_2/ComboSubClique.1.2.6.7.bed"); GenomeWideList triples = readInIntraChromTriple(handler, "/Users/muhammadsaadshamim/Desktop/goodell_2/dimension_3"); /* for(int tolerance = 0; tolerance <= 100; tolerance +=5) { GenomeWideList triples = readInIntraChromTriple(handler, "/Users/muhammadsaadshamim/Desktop/goodell_2/dimension_3"); dedupTriples(triples, tolerance); System.out.println(tolerance+"\t"+triples.size()); } */ int interval = 300000; int numIntervals = 7; int filterSize = interval * numIntervals; removeAnchorsThatAreTooCloseTogether(anchors, filterSize); int translation = 000000; int tolerance = 20; translateAnchors(anchors, translation); System.out.println("width " + filterSize); System.out.println("trans " + translation); System.out.println("num anchors " + anchors.size()); System.out.println("Pre dedup num triples " + triples.size()); dedupTriples(triples, tolerance); System.out.println("Tol " + tolerance); System.out.println("Post dedup num triples " + triples.size()); //threeDimHandling(triples, anchors, interval, numIntervals); threeDimSearching(triples, interval); } private void threeDimSearching(GenomeWideList triples, final int interval) { triples.processLists(new FeatureFunction() { @Override public void process(String chr, List tripleList) { final Map plot3D = new HashMap<>(); Collections.sort(tripleList); for (IntraChromTriple triple : tripleList) { int diff_1 = (triple.getX1()) / interval; int diff_2 = (triple.getX2()) / interval; int diff_3 = (triple.getX3()) / interval; if (Math.abs(diff_1 - diff_2) > 10 && Math.abs(diff_3 - diff_2) > 10 && Math.abs(diff_1 - diff_3) > 10) { String key = makeKey(diff_1, diff_2, diff_3); if (plot3D.containsKey(key)) { plot3D.put(key, plot3D.get(key) + 1); } else { plot3D.put(key, 1); } } } //System.out.println( chr+" - "+internalCount); if (!plot3D.isEmpty()) { int max = Collections.max(plot3D.values()); int min = Collections.min(plot3D.values()); int limit = Math.max((2 * max) / 3, min * 2); System.out.println(chr + " max/min/limit vals: " + max + "/" + min + "/" + limit); for (String key : plot3D.keySet()) { int val = plot3D.get(key); if (val > limit) { String[] indices = key.split("\t"); int y1 = Integer.parseInt(indices[0]) * interval; int y2 = Integer.parseInt(indices[1]) * interval; int y3 = Integer.parseInt(indices[2]) * interval; System.out.println(y1 + "," + y2 + "," + y3 + "\t" + val); } } } } }); } private void threeDimHandling(GenomeWideList triples, final GenomeWideList anchors, final int interval, int numInterval) { final int[] count = new int[1]; count[0] = 0; final Map plot3D = new HashMap<>(); final int midNumPoint = numInterval / 2; triples.processLists(new FeatureFunction() { @Override public void process(String chr, List tripleList) { List canyons = anchors.getFeatures(chr); Collections.sort(tripleList); Collections.sort(canyons); for (IntraChromTriple triple : tripleList) { int i0 = -1, j0 = -1, k0 = -1; for (int i = 0; i < canyons.size(); i++) { if (canyons.get(i).contains(triple.getX1())) { i0 = i; break; } } if (i0 > -1) { for (int j = i0 + 1; j < canyons.size(); j++) { if (canyons.get(j).contains(triple.getX2())) { j0 = j; break; } } if (j0 > -1) { for (int k = j0 + 1; k < canyons.size(); k++) { if (canyons.get(k).contains(triple.getX3())) { k0 = k; break; } } if (k0 > -1) { int diff_1 = (int) ((triple.getX1() - canyons.get(i0).getX1()) / interval - midNumPoint); int diff_2 = (int) ((triple.getX2() - canyons.get(j0).getX1()) / interval - midNumPoint); int diff_3 = (int) ((triple.getX3() - canyons.get(k0).getX1()) / interval - midNumPoint); String key = makeKey(diff_1, diff_2, diff_3); if (plot3D.containsKey(key)) { plot3D.put(key, plot3D.get(key) + 1); } else { plot3D.put(key, 1); } count[0]++; } } } } //System.out.println( chr+" - "+internalCount); } }); System.out.println("count " + count[0]); int max = Collections.max(plot3D.values()); System.out.println("max val " + max); for (String key : plot3D.keySet()) { System.out.println(key + "\t" + plot3D.get(key)); } } private String makeKey(int diff_1, int diff_2, int diff_3) { return "" + diff_1 + "\t" + diff_2 + "\t" + diff_3; } private void dedupTriples(GenomeWideList anchors, final int tolerance) { anchors.filterLists(new FeatureFilter() { @Override public List filter(String chr, List triplesList) { Collections.sort(triplesList); IntraChromTriple first = triplesList.get(0); TripleCentroid centroid = first.toTripleCentroid(); List uniqueTriples = new ArrayList<>(); for (IntraChromTriple triple : triplesList) { if (centroid.hasOverlapWithTriple(triple, tolerance)) { centroid.consumeDuplicate(triple); } else { uniqueTriples.add(centroid.toIntraChromTriple()); centroid = triple.toTripleCentroid(); } } uniqueTriples.add(centroid.toIntraChromTriple()); return uniqueTriples; } }); } private void translateAnchors(GenomeWideList anchors, final int translation) { if (translation != 0) { anchors.filterLists(new FeatureFilter() { @Override public List filter(String chr, List featureList) { List translated = new ArrayList<>(); for (GenericLocus anchor : featureList) { GenericLocus anchorT = new MotifAnchor(anchor.getChr(), anchor.getX1() + translation, anchor.getX2() + translation); if (anchorT.getX1() > 0) { translated.add(anchorT); } } return translated; } }); } } } ================================================ FILE: src/juicebox/tools/utils/Benchmark.java ================================================ /* * The MIT License (MIT) * * Copyright (c) 2011-2020 Broad Institute, Aiden Lab, Rice University, Baylor College of Medicine * * Permission is hereby granted, free of charge, to any person obtaining a copy * of this software and associated documentation files (the "Software"), to deal * in the Software without restriction, including without limitation the rights * to use, copy, modify, merge, publish, distribute, sublicense, and/or sell * copies of the Software, and to permit persons to whom the Software is * furnished to do so, subject to the following conditions: * * The above copyright notice and this permission notice shall be included in * all copies or substantial portions of the Software. * * THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR * IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, * FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE * AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER * LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, * OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN * THE SOFTWARE. */ package juicebox.tools.utils; import juicebox.data.ChromosomeHandler; import juicebox.data.basics.Chromosome; import juicebox.tools.clt.CommandLineParser; import juicebox.tools.clt.JuiceboxCLT; import juicebox.tools.clt.old.Dump; import org.broad.igv.Globals; import java.util.Random; /** * Created by Neva Durand on 8/4/16 for benchmark testing for DCIC. */ public class Benchmark extends JuiceboxCLT { private final int NUM_QUERIES = 1000; // Query 10,000 times at 256x256 and 2048x2048 private int QUERY_SIZE = 256; private Dump dump; public Benchmark() { super(getUsage()); } private static String getUsage() { return "benchmark "; } @Override public void readArguments(String[] argv, CommandLineParser parser) { Globals.setHeadless(true); if (argv.length != 3) { printUsageAndExit(); } dump = new Dump(); // dump will read in the index of the .hic file and output the observed matrix with no normalization // change "NONE" to "KR" or "VC" for different normalizations // change outputfile if needed // the other values are dummy and will be reset String[] args = {"dump", "observed", argv[2], argv[1], "X", "X", "BP", "1000000", "/Users/nchernia/Downloads/output2.txt"}; dump.readArguments(args, parser); } @Override public void run() { // will use to make sure we're not off the end of the chromosome ChromosomeHandler handler = dump.getChromosomeHandler(); Random random = new Random(); // chromosomes in this dataset, so we query them String[] chrs = new String[handler.size() - 1]; int ind=0; for (Chromosome chr : handler.getChromosomeArray()) { if (!chr.getName().equalsIgnoreCase("All")) chrs[ind++] = chr.getName(); } // BP bin sizes in this dataset int[] bpBinSizes = dump.getBpBinSizes(); long sum=0; for (int i=0; i -1; i--) { total += inputArray[i]; outputArray[i] = total; } return outputArray; } private static long[] makeReverseCumulativeArray(long[] inputArray) { long[] outputArray = new long[inputArray.length]; long total = 0; for (int i = inputArray.length - 1; i > -1; i--) { total += inputArray[i]; outputArray[i] = total; } return outputArray; } public static long[][] makeReverse2DCumulativeArray(long[][] data) { long[][] rcsData = new long[data.length][data[0].length]; for (int i = 0; i < data.length; i++) { rcsData[i] = ArrayTools.makeReverseCumulativeArray(data[i]); if (HiCGlobals.printVerboseComments && data[i][0] < 0) { System.out.println("poss source2: i " + i + " " + data[i][0]); } } return rcsData; } public static float[] newValueInitializedFloatArray(int n, float val) { float[] array = new float[n]; Arrays.fill(array, val); return array; } public static float[] scalarMultiplyArray(long scaleFactor, float[] array) { float[] scaledArray = newValueInitializedFloatArray(array.length, scaleFactor); for (int i = 0; i < array.length; i++) { scaledArray[i] *= array[i]; } return scaledArray; } /** * Assumes array passed in is <= length, otherwise indexOutOfBounds error will be thrown * * @param original * @param length * @param val * @return */ public static float[] padEndOfArray(float[] original, int length, float val) { float[] paddedArray = new float[length]; System.arraycopy(original, 0, paddedArray, 0, original.length); for (int i = original.length; i < length; i++) { paddedArray[i] = val; } return paddedArray; } public static int[] extractIntegers(List stringList) { int[] array = new int[stringList.size()]; int index = 0; for (String val : stringList) { array[index] = Integer.parseInt(val); index++; } return array; } public static float[] extractFloats(List stringList) { float[] array = new float[stringList.size()]; int index = 0; for (String val : stringList) { array[index] = Float.parseFloat(val); index++; } return array; } public static int[] preInitializeIntArray(int val, int n) { int[] array = new int[n]; for (int i = 0; i < n; i++) { array[i] = val; } return array; } public static float[] preInitializeFloatArray(float val, int n) { float[] array = new float[n]; for (int i = 0; i < n; i++) { array[i] = val; } return array; } public static float[] inverseArrayValues(float[] array) { float[] inverses = new float[array.length]; for (int i = 0; i < array.length; i++) { inverses[i] = 1f / array[i]; } return inverses; } public static double[] preInitializeDoubleArray(double val, int n) { double[] array = new double[n]; for (int i = 0; i < n; i++) { array[i] = val; } return array; } public static double[] extractDoubles(List stringList) { double[] array = new double[stringList.size()]; int index = 0; for (String val : stringList) { array[index] = Double.parseDouble(val); index++; } return array; } public static double[] inverseArrayValues(double[] array) { double[] inverses = new double[array.length]; for (int i = 0; i < array.length; i++) { inverses[i] = 1. / array[i]; } return inverses; } public static double[] flipArrayValues(double[] array) { double[] flipped = new double[array.length]; for (int i = 0; i < array.length; i++) { flipped[i] = -1 * array[i]; } return flipped; } /** * Print out a given vector in wig style format to the specified writer * @param vector * @param pw * @param name * @param res */ public static void exportChr1DArrayToWigFormat(double[] vector, PrintWriter pw, String name, int res) { pw.println("fixedStep chrom=chr" + name.replace("chr", "") + " start=1 step=" + res + " span=" + res); for(double val : vector){ pw.println(val); } } public static float[] runSlidingAverageOnArray(int radius, float[] values) { float[] newValues = new float[values.length]; for (int i = 0; i < values.length; i++) { float sum = 0; int numVals = 0; for (int j = Math.max(i - radius, 0); j < Math.min(i + radius, values.length); j++) { if (values[j] > 0) { sum += values[j]; numVals++; } } if (numVals == 0) { newValues[i] = 0; } else { newValues[i] = sum / numVals; } } return newValues; } } ================================================ FILE: src/juicebox/tools/utils/common/HiCFileUtils.java ================================================ /* * The MIT License (MIT) * * Copyright (c) 2011-2020 Broad Institute, Aiden Lab, Rice University, Baylor College of Medicine * * Permission is hereby granted, free of charge, to any person obtaining a copy * of this software and associated documentation files (the "Software"), to deal * in the Software without restriction, including without limitation the rights * to use, copy, modify, merge, publish, distribute, sublicense, and/or sell * copies of the Software, and to permit persons to whom the Software is * furnished to do so, subject to the following conditions: * * The above copyright notice and this permission notice shall be included in * all copies or substantial portions of the Software. * * THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR * IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, * FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE * AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER * LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, * OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN * THE SOFTWARE. */ package juicebox.tools.utils.common; import juicebox.HiC; import juicebox.data.*; import juicebox.data.basics.Chromosome; import juicebox.windowui.HiCZoom; import juicebox.windowui.NormalizationHandler; import juicebox.windowui.NormalizationType; import java.io.IOException; import java.util.Map; /** * Utility functions to dump various bits of a hic file to stdout or file(s) * * @author jrobinso * Date: 2/11/13 * Time: 2:01 PM */ class HiCFileUtils { private final Dataset dataset; private HiCFileUtils(String hicfile) throws IOException { DatasetReaderV2 reader = new DatasetReaderV2(hicfile); dataset = reader.read(); } public static void main(String[] args) throws IOException { HiCFileUtils utils = new HiCFileUtils(args[0]); utils.dumpNormalizationVectors(NormalizationHandler.KR, "1", HiC.Unit.BP, 250000); utils.dumpExpectedVectors(NormalizationHandler.KR, HiC.Unit.BP, 1000000); } private void dumpNormalizationVectors(NormalizationType normType, String chrName, HiC.Unit unit, int binSize) { Chromosome chromosome = findChromosome(chrName); HiCZoom zoom = new HiCZoom(unit, binSize); NormalizationVector nv = dataset.getNormalizationVector(chromosome.getIndex(), zoom, normType); String label = "Normalization vector: type = " + normType.getLabel() + " chr = " + chrName + " resolution = " + binSize + " " + unit; System.out.println(label); /* for(int i=0; i expValFunMap = dataset.getExpectedValueFunctionMap(); for (Map.Entry entry : expValFunMap.entrySet()) { ExpectedValueFunctionImpl ev = (ExpectedValueFunctionImpl) entry.getValue(); if (ev.getUnit().equals(unit) && ev.getBinSize() == binSize && ev.getNormalizationType().equals(normType)) { String label = ev.getNormalizationType() + "\t" + ev.getUnit() + "\t" + ev.getBinSize(); System.out.println("Norm factors: " + label); for (Map.Entry nf : ev.getNormFactors().entrySet()) { System.out.println(nf.getKey() + "\t" + nf.getValue()); } System.out.println("Expected values: " + label); /* for (int i = 0; i < values.length; i++) { System.out.println(values[i]); } */ for (double[] values : ev.getExpectedValuesNoNormalization().getValues()) { for (double datum : values) { System.out.println(datum); } } System.out.println("End expected values: " + label); System.out.println(); } } } private Chromosome findChromosome(String name) { for (Chromosome chr : dataset.getChromosomeHandler().getChromosomeArray()) { if (chr.getName().equalsIgnoreCase(name)) return chr; } return null; } } ================================================ FILE: src/juicebox/tools/utils/common/MatrixTools.java ================================================ /* * The MIT License (MIT) * * Copyright (c) 2011-2020 Broad Institute, Aiden Lab, Rice University, Baylor College of Medicine * * Permission is hereby granted, free of charge, to any person obtaining a copy * of this software and associated documentation files (the "Software"), to deal * in the Software without restriction, including without limitation the rights * to use, copy, modify, merge, publish, distribute, sublicense, and/or sell * copies of the Software, and to permit persons to whom the Software is * furnished to do so, subject to the following conditions: * * The above copyright notice and this permission notice shall be included in * all copies or substantial portions of the Software. * * THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR * IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, * FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE * AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER * LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, * OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN * THE SOFTWARE. */ package juicebox.tools.utils.common; import juicebox.data.ContactRecord; import juicebox.tools.utils.juicer.apa.APARegionStatistics; import org.apache.commons.math.linear.Array2DRowRealMatrix; import org.apache.commons.math.linear.RealMatrix; import org.apache.commons.math3.stat.descriptive.rank.Median; import org.jetbrains.bio.npy.NpyFile; import java.io.*; import java.nio.charset.StandardCharsets; import java.nio.file.Paths; import java.text.DecimalFormat; import java.util.ArrayList; import java.util.Arrays; import java.util.List; import java.util.Random; /** * Helper methods to handle matrix operations */ public class MatrixTools { /** * @return matrix initialized with 0s */ public static RealMatrix cleanArray2DMatrix(int n) { return cleanArray2DMatrix(n, n); } /** * @return matrix initialized with 0s */ public static RealMatrix cleanArray2DMatrix(int rows, int cols) { return presetValueMatrix(rows, cols, 0); } /** * @return matrix initialized with 1s */ public static RealMatrix ones(int n) { return ones(n, n); } /** * @return matrix initialized with 1s */ private static RealMatrix ones(int rows, int cols) { return presetValueMatrix(rows, cols, 1); } /** * @return matrix of size m x n initialized with a specified value */ private static RealMatrix presetValueMatrix(int numRows, int numCols, int val) { RealMatrix matrix = new Array2DRowRealMatrix(numRows, numCols); for (int r = 0; r < numRows; r++) for (int c = 0; c < numCols; c++) matrix.setEntry(r, c, val); return matrix; } /** * @return matrix randomly initialized with 1s and 0s */ public static RealMatrix randomUnitMatrix(int n) { return randomUnitMatrix(n, n); } /** * Generate a matrix with randomly initialized 1s and 0s * * @param rows number of rows * @param cols number of columns * @return randomized binary matrix */ private static RealMatrix randomUnitMatrix(int rows, int cols) { Random generator = new Random(); RealMatrix matrix = cleanArray2DMatrix(rows, cols); for (int r = 0; r < rows; r++) for (int c = 0; c < cols; c++) if (generator.nextBoolean()) matrix.setEntry(r, c, 1); return matrix; } /** * @return minimal positive entry in the matrix greater than 0 */ public static double minimumPositive(RealMatrix data) { return minimumPositive(data.getData()); } /** * @return minimal positive entry in the matrix greater than 0 */ private static double minimumPositive(double[][] data) { double minVal = Double.MAX_VALUE; for (double[] row : data) { for (double val : row) { if (val > 0 && val < minVal) minVal = val; } } if (minVal == Double.MAX_VALUE) minVal = 0; return minVal; } /** * @return mean of matrix */ public static double mean(RealMatrix matrix) { return APARegionStatistics.statistics(matrix.getData()).getMean(); } /** * Flatten a 2D double matrix into a double array * * @param matrix * @return 1D double array in row major order */ public static double[] flattenedRowMajorOrderMatrix(RealMatrix matrix) { int m = matrix.getRowDimension(); int n = matrix.getColumnDimension(); int numElements = m * n; double[] flattenedMatrix = new double[numElements]; int index = 0; for (int i = 0; i < m; i++) { System.arraycopy(matrix.getRow(i), 0, flattenedMatrix, index, n); index += n; } return flattenedMatrix; } public static double[] flattenedRowMajorOrderMatrix(double[][] matrix) { int m = matrix.length; int n = matrix[0].length; int numElements = m * n; double[] flattenedMatrix = new double[numElements]; int index = 0; for (double[] doubles : matrix) { System.arraycopy(doubles, 0, flattenedMatrix, index, n); index += n; } return flattenedMatrix; } public static float[] flattenedRowMajorOrderMatrix(float[][] matrix) { int m = matrix.length; int n = matrix[0].length; int numElements = m * n; float[] flattenedMatrix = new float[numElements]; int index = 0; for (float[] floats : matrix) { System.arraycopy(floats, 0, flattenedMatrix, index, n); index += n; } return flattenedMatrix; } public static int[] flattenedRowMajorOrderMatrix(int[][] matrix) { int m = matrix.length; int n = matrix[0].length; int numElements = m * n; int[] flattenedMatrix = new int[numElements]; int index = 0; for (int[] ints : matrix) { System.arraycopy(ints, 0, flattenedMatrix, index, n); index += n; } return flattenedMatrix; } /** * Write data from matrix out to specified file with each row on a separate line * * @param filename * @param realMatrix */ public static void saveMatrixText(String filename, RealMatrix realMatrix) { Writer writer = null; try { writer = new BufferedWriter(new OutputStreamWriter(new FileOutputStream(filename), StandardCharsets.UTF_8)); double[][] matrix = realMatrix.getData(); for (double[] row : matrix) { writer.write(Arrays.toString(row) + "\n"); } } catch (IOException ex) { ex.printStackTrace(); } finally { try { if (writer != null) writer.close(); } catch (Exception ex) { ex.printStackTrace(); } } } /** * Reshape array into square matrix * * @param flatMatrix * @param n * @return properly dimensioned matrix */ public static float[][] reshapeFlatMatrix(float[] flatMatrix, int n) { return reshapeFlatMatrix(flatMatrix, n, n); } /** * Reshape array into a matrix * * @param flatMatrix * @param numRows * @param numCols * @return properly dimensioned matrix */ private static float[][] reshapeFlatMatrix(float[] flatMatrix, int numRows, int numCols) { float[][] matrix = new float[numRows][numCols]; for (int i = 0; i < numRows; i++) { System.arraycopy(flatMatrix, i * numCols, matrix[i], 0, numCols); } return matrix; } /** * From Matrix M, extract out M[r1:r2,c1:c2] * r2, c2 not inclusive (~python numpy) * * @return extracted matrix region M[r1:r2,c1:c2] */ public static float[][] extractLocalMatrixRegion(float[][] matrix, int r1, int r2, int c1, int c2) { int numRows = r2 - r1; int numColumns = c2 - c1; float[][] extractedRegion = new float[numRows][numColumns]; for (int i = 0; i < numRows; i++) { System.arraycopy(matrix[r1 + i], c1, extractedRegion[i], 0, numColumns); } return extractedRegion; } /** * From Matrix M, extract out M[r1:r2,c1:c2] * r2, c2 not inclusive (~python numpy, not like Matlab) * * @return extracted matrix region M[r1:r2,c1:c2] */ public static RealMatrix extractLocalMatrixRegion(RealMatrix matrix, int r1, int r2, int c1, int c2) { int numRows = r2 - r1; int numColumns = c2 - c1; RealMatrix extractedRegion = cleanArray2DMatrix(numRows, numColumns); for (int i = 0; i < numRows; i++) { for (int j = 0; j < numColumns; j++) { extractedRegion.setEntry(i, j, matrix.getEntry(r1 + i, c1 + j)); } } return extractedRegion; } /** * Returns the values along the diagonal of the matrix * * @param matrix * @return diagonal */ public static RealMatrix extractDiagonal(RealMatrix matrix) { int n = Math.min(matrix.getColumnDimension(), matrix.getRowDimension()); RealMatrix diagonal = MatrixTools.cleanArray2DMatrix(n); for (int i = 0; i < n; i++) { diagonal.setEntry(i, i, matrix.getEntry(i, i)); } return diagonal; } /** * Returns the values along the diagonal of the matrix * * @param matrix * @return diagonal */ public static RealMatrix makeSymmetricMatrix(RealMatrix matrix) { RealMatrix symmetricMatrix = extractDiagonal(matrix); int n = symmetricMatrix.getRowDimension(); for (int i = 0; i < n; i++) { for (int j = i + 1; j < n; j++) { double val = matrix.getEntry(i, j); symmetricMatrix.setEntry(i, j, val); symmetricMatrix.setEntry(j, i, val); } } return symmetricMatrix; } /** * @return matrix flipped across the antidiagonal */ public static RealMatrix flipAcrossAntiDiagonal(RealMatrix matrix) { int n = Math.min(matrix.getColumnDimension(), matrix.getRowDimension()); RealMatrix antiDiagFlippedMatrix = cleanArray2DMatrix(n, n); int maxIndex = n - 1; for (int i = 0; i < n; i++) { for (int j = 0; j < n; j++) { antiDiagFlippedMatrix.setEntry(maxIndex - j, maxIndex - i, matrix.getEntry(i, j)); } } return antiDiagFlippedMatrix; } /** * @return matrix flipped Left-Right */ public static RealMatrix flipLeftRight(RealMatrix matrix) { int r = matrix.getRowDimension(), c = matrix.getColumnDimension(); RealMatrix leftRightFlippedMatrix = cleanArray2DMatrix(r, c); for (int i = 0; i < r; i++) { for (int j = 0; j < c; j++) { leftRightFlippedMatrix.setEntry(i, c - 1 - j, matrix.getEntry(i, j)); } } return leftRightFlippedMatrix; } /** * @return matrix flipped Top-Bottom */ public static RealMatrix flipTopBottom(RealMatrix matrix) { int r = matrix.getRowDimension(), c = matrix.getColumnDimension(); RealMatrix topBottomFlippedMatrix = cleanArray2DMatrix(r, c); for (int i = 0; i < r; i++) { for (int j = 0; j < c; j++) { topBottomFlippedMatrix.setEntry(r - 1 - i, j, matrix.getEntry(i, j)); } } return topBottomFlippedMatrix; } /** * @return Element-wise multiplication of matrices i.e. M.*N in Matlab */ public static RealMatrix elementBasedMultiplication(RealMatrix matrix1, RealMatrix matrix2) { // chooses minimal intersection of dimensions int r = Math.min(matrix1.getRowDimension(), matrix2.getRowDimension()); int c = Math.min(matrix1.getColumnDimension(), matrix2.getColumnDimension()); RealMatrix elementwiseMultipliedMatrix = cleanArray2DMatrix(r, c); for (int i = 0; i < r; i++) { for (int j = 0; j < c; j++) { elementwiseMultipliedMatrix.setEntry(i, j, matrix1.getEntry(i, j) * matrix2.getEntry(i, j)); } } return elementwiseMultipliedMatrix; } /** * @return Element-wise division of matrices i.e. M./N in Matlab */ public static RealMatrix elementBasedDivision(RealMatrix matrix1, RealMatrix matrix2) { // chooses minimal intersection of dimensions int r = Math.min(matrix1.getRowDimension(), matrix2.getRowDimension()); int c = Math.min(matrix1.getColumnDimension(), matrix2.getColumnDimension()); RealMatrix elementwiseDividedMatrix = cleanArray2DMatrix(r, c); for (int i = 0; i < r; i++) { for (int j = 0; j < c; j++) { elementwiseDividedMatrix.setEntry(i, j, matrix1.getEntry(i, j) / matrix2.getEntry(i, j)); } } return elementwiseDividedMatrix; } /** * Replace NaNs in given matrix with given value */ public static void setNaNs(RealMatrix matrix, int val) { for (int i = 0; i < matrix.getRowDimension(); i++) { for (int j = 0; j < matrix.getColumnDimension(); j++) { if (Double.isNaN(matrix.getEntry(i, j))) { matrix.setEntry(i, j, val); } } } } /** * Return sign of values in matrix: * val > 0 : 1 * val = 0 : 0 * val < 0 : -1 */ public static RealMatrix sign(RealMatrix matrix) { int r = matrix.getRowDimension(); int c = matrix.getColumnDimension(); RealMatrix signMatrix = cleanArray2DMatrix(r, c); for (int i = 0; i < r; i++) { for (int j = 0; j < c; j++) { double val = matrix.getEntry(i, j); if (val > 0) { signMatrix.setEntry(i, j, 1); } else if (val < 0) { signMatrix.setEntry(i, j, -1); } } } return signMatrix; } /** * Replace all of a given value in a matrix with a new value */ public static void replaceValue(RealMatrix matrix, int initialVal, int newVal) { for (int i = 0; i < matrix.getRowDimension(); i++) { for (int j = 0; j < matrix.getColumnDimension(); j++) { if (matrix.getEntry(i, j) == initialVal) { matrix.setEntry(i, j, newVal); } } } } /** * Normalize matrix by dividing by max element * * @return matrix * (1/max_element) */ public static RealMatrix normalizeByMax(RealMatrix matrix) { double max = calculateMax(matrix); return matrix.scalarMultiply(1 / max); } /** * @return max element in matrix */ public static double calculateMax(RealMatrix matrix) { double max = matrix.getEntry(0, 0); for (int i = 0; i < matrix.getRowDimension(); i++) { for (int j = 0; j < matrix.getColumnDimension(); j++) { double val = matrix.getEntry(i, j); if (max < val) { max = val; } } } return max; } /** * @return min element in matrix */ public static double calculateMin(RealMatrix matrix) { double min = matrix.getEntry(0, 0); for (int i = 0; i < matrix.getRowDimension(); i++) { for (int j = 0; j < matrix.getColumnDimension(); j++) { double val = matrix.getEntry(i, j); if (min > val) { min = val; } } } return min; } /** * print for matrix */ public static void print(RealMatrix matrix) { print(matrix.getData()); } /** * print for 2D array */ private static void print(double[][] data) { for (double[] row : data) { System.out.println(Arrays.toString(row)); } } /** * print for 2D array */ private static void print(float[][] data) { for (float[] row : data) { System.out.println(Arrays.toString(row)); } } /** * @return region within matrix specified by indices */ public static RealMatrix getSubMatrix(RealMatrix matrix, int[] indices) { return matrix.getSubMatrix(indices[0], indices[1], indices[2], indices[3]); } /** * Fill lower left triangle with values from upper right triangle * * @param matrix * @return */ public static RealMatrix fillLowerLeftTriangle(RealMatrix matrix) { for (int r = 0; r < matrix.getRowDimension(); r++) for (int c = 0; c < matrix.getColumnDimension(); c++) matrix.setEntry(c, r, matrix.getEntry(r, c)); return matrix; } public static void thresholdValues(RealMatrix matrix, int val) { for (int i = 0; i < matrix.getRowDimension(); i++) { for (int j = 0; j < matrix.getColumnDimension(); j++) { if (matrix.getEntry(i, j) > val) { matrix.setEntry(i, j, val); } } } } public static void thresholdValuesDouble(RealMatrix matrix, double lowVal, double highVal) { for (int i = 0; i < matrix.getRowDimension(); i++) { for (int j = 0; j < matrix.getColumnDimension(); j++) { if (matrix.getEntry(i, j) > highVal) { matrix.setEntry(i, j, highVal); } if (matrix.getEntry(i, j) < lowVal) { matrix.setEntry(i, j, lowVal); } } } } public static int[][] normalizeMatrixUsingColumnSum(int[][] matrix) { int[][] newMatrix = new int[matrix.length][matrix[0].length]; int[] columnSum = new int[matrix[0].length]; for (int[] row : matrix) { for (int i = 0; i < row.length; i++) { columnSum[i] += row[i]; } } for (int i = 0; i < matrix.length; i++) { for (int j = 0; j < matrix[i].length; j++) { newMatrix[i][j] = matrix[i][j] / columnSum[j]; } } return newMatrix; } public static int[][] normalizeMatrixUsingRowSum(int[][] matrix) { int[][] newMatrix = new int[matrix.length][matrix[0].length]; int[] rowSum = getRowSums(matrix); for (int i = 0; i < matrix.length; i++) { for (int j = 0; j < matrix[i].length; j++) { newMatrix[i][j] = matrix[i][j] / rowSum[i]; } } return newMatrix; } public static int[] getRowSums(int[][] matrix) { int[] rowSum = new int[matrix.length]; for (int i = 0; i < matrix.length; i++) { for (int val : matrix[i]) { rowSum[i] += val; } } return rowSum; } public static double[] getRowSums(double[][] matrix) { double[] rowSum = new double[matrix.length]; for (int i = 0; i < matrix.length; i++) { for (double val : matrix[i]) { rowSum[i] += val; } } return rowSum; } public static float[] getAbsValColSums(float[][] matrix) { float[] colSum = new float[matrix[0].length]; for (float[] floats : matrix) { for (int j = 0; j < floats.length; j++) { colSum[j] += Math.abs(floats[j]); } } return colSum; } public static int[] getAbsValColSums(int[][] matrix) { int[] colSum = new int[matrix[0].length]; for (int[] ints : matrix) { for (int j = 0; j < ints.length; j++) { colSum[j] += Math.abs(ints[j]); } } return colSum; } public static float[] getRowSums(float[][] matrix) { float[] rowSum = new float[matrix.length]; for (int i = 0; i < matrix.length; i++) { for (float val : matrix[i]) { rowSum[i] += val; } } return rowSum; } public static double[] getRowSums(List unNormedRecordList, double scalar, double[] normVector) { double[] rowSum = new double[normVector.length]; for (ContactRecord record : unNormedRecordList) { int x = record.getBinX(); int y = record.getBinY(); float counts = record.getCounts(); double normVal = counts * scalar / (normVector[x] * normVector[y]); rowSum[x] += normVal; if (x != y) { rowSum[y] += normVal; } } return rowSum; } public static void cleanUpNaNs(RealMatrix matrix) { for (int r = 0; r < matrix.getRowDimension(); r++) { for (int c = 0; c < matrix.getColumnDimension(); c++) { if (Double.isNaN(matrix.getEntry(r, c))) { matrix.setEntry(r, c, 0); } } } } public static void cleanUpNaNs(double[][] matrix) { for (int r = 0; r < matrix.length; r++) { for (int c = 0; c < matrix[r].length; c++) { if (Double.isNaN(matrix[r][c])) { matrix[r][c] = 0; } } } } public static void cleanUpNaNs(float[][] matrix) { for (int r = 0; r < matrix.length; r++) { for (int c = 0; c < matrix[r].length; c++) { if (Float.isNaN(matrix[r][c])) { matrix[r][c] = 0; } } } } public static double sum(double[][] data) { double sum = 0; for (double[] row : data) { for (double val : row) { sum += val; } } return sum; } public static double getAverage(RealMatrix data) { return getAverage(data.getData()); } private static double getAverage(double[][] data) { double average = 0; if (data.length > 0) { double total = 0; for (double[] vals : data) { for (double val : vals) { total += val; } } average = (total / data.length) / data[0].length; } return average; } public static void exportData(double[][] data, File file) { try { DecimalFormat df = new DecimalFormat("##.###"); final FileWriter fw = new FileWriter(file); for (double[] row : data) { for (double val : row) { if (Double.isNaN(val)) { fw.write("NaN, "); } else { fw.write(Double.valueOf(df.format(val)) + ", "); } } fw.write("0\n"); } fw.close(); } catch (Exception e) { System.err.println("Error exporting matrix"); e.printStackTrace(); System.exit(86); } } public static double[][] transpose(double[][] matrix) { int h0 = matrix.length; int w0 = matrix[0].length; double[][] transposedMatrix = new double[w0][h0]; for (int i = 0; i < h0; i++) { for (int j = 0; j < w0; j++) { transposedMatrix[j][i] = matrix[i][j]; } } return transposedMatrix; } public static float[][] transpose(float[][] matrix) { int h0 = matrix.length; int w0 = matrix[0].length; float[][] transposedMatrix = new float[w0][h0]; for (int i = 0; i < h0; i++) { for (int j = 0; j < w0; j++) { transposedMatrix[j][i] = matrix[i][j]; } } return transposedMatrix; } public static double[][] convertToDoubleMatrix(boolean[][] adjacencyMatrix) { double[][] matrix = new double[adjacencyMatrix.length][adjacencyMatrix[0].length]; for (int i = 0; i < adjacencyMatrix.length; i++) { for (int j = 0; j < adjacencyMatrix[0].length; j++) { if (adjacencyMatrix[i][j]) { matrix[i][j] = 1; } } } return matrix; } public static double[][] convertToDoubleMatrix(int[][] adjacencyMatrix) { double[][] matrix = new double[adjacencyMatrix.length][adjacencyMatrix[0].length]; for (int i = 0; i < adjacencyMatrix.length; i++) { for (int j = 0; j < adjacencyMatrix[0].length; j++) { matrix[i][j] = adjacencyMatrix[i][j]; } } return matrix; } public static float[][] convertToFloatMatrix(double[][] dataMatrix) { float[][] matrix = new float[dataMatrix.length][dataMatrix[0].length]; for (int i = 0; i < dataMatrix.length; i++) { for (int j = 0; j < dataMatrix[0].length; j++) { matrix[i][j] = (float) dataMatrix[i][j]; } } return matrix; } public static void copyFromAToBRegion(double[][] source, double[][] destination, int rowOffSet, int colOffSet) { for (int i = 0; i < source.length; i++) { System.arraycopy(source[i], 0, destination[i + rowOffSet], colOffSet, source[0].length); } } public static void copyFromAToBRegion(float[][] source, float[][] destination, int rowOffSet, int colOffSet) { for (int i = 0; i < source.length; i++) { System.arraycopy(source[i], 0, destination[i + rowOffSet], colOffSet, source[0].length); } } public static void saveMatrixTextV2(String filename, RealMatrix realMatrix) { saveMatrixTextV2(filename, realMatrix.getData()); } public static void saveMatrixTextV2(String filename, double[][] matrix) { Writer writer = null; try { writer = new BufferedWriter(new OutputStreamWriter(new FileOutputStream(filename), StandardCharsets.UTF_8)); for (double[] row : matrix) { String s = Arrays.toString(row);//.replaceAll().replaceAll("]","").trim(); s = s.replaceAll("\\[", "").replaceAll("\\]", "").trim(); writer.write(s + "\n"); } } catch (IOException ex) { ex.printStackTrace(); } finally { try { if (writer != null) writer.close(); } catch (Exception ex) { ex.printStackTrace(); } } } public static void saveMatrixTextV2(String filename, float[][] matrix) { Writer writer = null; try { writer = new BufferedWriter(new OutputStreamWriter(new FileOutputStream(filename), StandardCharsets.UTF_8)); for (float[] row : matrix) { String s = Arrays.toString(row);//.replaceAll().replaceAll("]","").trim(); s = s.replaceAll("\\[", "").replaceAll("\\]", "").trim(); writer.write(s + "\n"); } } catch (IOException ex) { ex.printStackTrace(); } finally { try { if (writer != null) writer.close(); } catch (Exception ex) { ex.printStackTrace(); } } } public static void saveMatrixTextV2(String filename, int[][] matrix) { Writer writer = null; try { writer = new BufferedWriter(new OutputStreamWriter(new FileOutputStream(filename), StandardCharsets.UTF_8)); for (int[] row : matrix) { String s = Arrays.toString(row);//.replaceAll().replaceAll("]","").trim(); s = s.replaceAll("\\[", "").replaceAll("\\]", "").trim(); writer.write(s + "\n"); } } catch (IOException ex) { ex.printStackTrace(); } finally { try { if (writer != null) writer.close(); } catch (Exception ex) { ex.printStackTrace(); } } } public static void saveMatrixTextNumpy(String filename, double[][] matrix) { int numRows = matrix.length; int numCols = matrix[0].length; double[] flattenedArray = MatrixTools.flattenedRowMajorOrderMatrix(matrix); NpyFile.write(Paths.get(filename), flattenedArray, new int[]{numRows, numCols}); } public static void saveMatrixTextNumpy(String filename, float[][] matrix) { int numRows = matrix.length; int numCols = matrix[0].length; float[] flattenedArray = MatrixTools.flattenedRowMajorOrderMatrix(matrix); NpyFile.write(Paths.get(filename), flattenedArray, new int[]{numRows, numCols}); } public static void saveMatrixTextNumpy(String filename, int[][] matrix) { int numRows = matrix.length; int numCols = matrix[0].length; int[] flattenedArray = MatrixTools.flattenedRowMajorOrderMatrix(matrix); NpyFile.write(Paths.get(filename), flattenedArray, new int[]{numRows, numCols}); } public static void saveMatrixTextNumpy(String filename, int[] matrix) { NpyFile.write(Paths.get(filename), matrix, new int[]{1, matrix.length}); } public static void saveMatrixTextNumpy(String filename, double[] matrix) { NpyFile.write(Paths.get(filename), matrix, new int[]{1, matrix.length}); } public static float[][] generateCompositeMatrixWithNansCleaned(RealMatrix matrixDiag1, RealMatrix matrixDiag2, RealMatrix matrix1vs2) { return generateCompositeMatrixWithNansCleaned( convertToFloatMatrix(matrixDiag1.getData()), convertToFloatMatrix(matrixDiag2.getData()), convertToFloatMatrix(matrix1vs2.getData())); } private static float[][] generateCompositeMatrixWithNansCleaned(float[][] matrixDiag1, float[][] matrixDiag2, float[][] matrix1vs2) { int newLength = matrixDiag1.length + matrixDiag2.length; float[][] compositeMatrix = new float[newLength][newLength]; copyFromAToBRegion(matrixDiag1, compositeMatrix, 0, 0); copyFromAToBRegion(matrixDiag2, compositeMatrix, matrixDiag1.length, matrixDiag1.length); for (int i = 0; i < matrix1vs2.length; i++) { for (int j = 0; j < matrix1vs2[0].length; j++) { compositeMatrix[i][matrixDiag1.length + j] = matrix1vs2[i][j]; compositeMatrix[matrixDiag1.length + j][i] = matrix1vs2[i][j]; } } MatrixTools.cleanUpNaNs(compositeMatrix); return compositeMatrix; } public static double[][] deepClone(double[][] data) { double[][] copy = new double[data.length][data[0].length]; for (int i = 0; i < data.length; i++) { System.arraycopy(data[i], 0, copy[i], 0, data[i].length); } return copy; } public static float[][] deepClone(float[][] data) { float[][] copy = new float[data.length][data[0].length]; for (int i = 0; i < data.length; i++) { System.arraycopy(data[i], 0, copy[i], 0, data[i].length); } return copy; } public static void labelRegionWithOnes(int[][] labelsMatrix, int rowLength, int numRows, int colLength, int numCols, int startRowOf1, int startColOf1) { for (int i = 0; i < Math.min(rowLength, numRows); i++) { for (int j = 0; j < Math.min(colLength, numCols); j++) { labelsMatrix[startRowOf1 + i][startColOf1 + j] = 1; } } } public static void labelEnrichedRegionWithOnes(int[][] labelsMatrix, double[][] data, int rowLength, int numRows, int colLength, int numCols, int startRowOf1, int startColOf1) { double total = 0; int numVals = 0; for (int i = 0; i < Math.min(rowLength, numRows); i++) { for (int j = 0; j < Math.min(colLength, numCols); j++) { total += data[startRowOf1 + i][startColOf1 + j]; numVals++; } } double average = total / numVals; for (int i = 0; i < Math.min(rowLength, numRows); i++) { for (int j = 0; j < Math.min(colLength, numCols); j++) { if (data[startRowOf1 + i][startColOf1 + j] > average) { labelsMatrix[startRowOf1 + i][startColOf1 + j] = 1; } } } } // column length assumed identical and kept the same public static double[][] stitchMultipleMatricesTogetherByRowDim(List data) { // todo currently assuming each one identical... int colNums = data.get(0)[0].length; int rowNums = 0; for (double[][] mtrx : data) { rowNums += mtrx.length; } double[][] aggregate = new double[rowNums][colNums]; int rowOffSet = 0; for (double[][] region : data) { MatrixTools.copyFromAToBRegion(region, aggregate, rowOffSet, 0); rowOffSet += region.length; } return aggregate; } public static double[][] takeDerivativeDownColumn(double[][] data) { double[][] derivative = new double[data.length][data[0].length - 1]; for (int i = 0; i < data.length; i++) { System.arraycopy(data[i], 0, derivative[i], 0, derivative[i].length); } for (int i = 0; i < derivative.length; i++) { for (int j = 0; j < derivative[i].length; j++) { derivative[i][j] -= data[i][j + 1]; } } return derivative; } public static double[][] smoothAndAppendDerivativeDownColumn(double[][] data, double[] convolution) { int numColumns = data[0].length; if (convolution != null && convolution.length > 1) { numColumns -= (convolution.length - 1); } double[][] appendedDerivative = new double[data.length][2 * numColumns - 1]; if (convolution != null && convolution.length > 1) { for (int i = 0; i < data.length; i++) { for (int j = 0; j < numColumns; j++) { for (int k = 0; k < convolution.length; k++) { appendedDerivative[i][j] += convolution[k] * data[i][j + k]; } } } } else { for (int i = 0; i < data.length; i++) { System.arraycopy(data[i], 0, appendedDerivative[i], 0, numColumns); } } for (int i = 0; i < data.length; i++) { for (int j = 0; j < numColumns - 1; j++) { appendedDerivative[i][numColumns + j] = appendedDerivative[i][j] - appendedDerivative[i][j + 1]; } } return appendedDerivative; } public static float[][] getNormalizedThresholdedAndAppendedDerivativeDownColumn(float[][] data, float maxVal, float scaleDerivFactor, float derivativeThreshold) { double[] averageVal = new double[data.length]; for (int i = 0; i < data.length; i++) { for (float val : data[i]) { averageVal[i] += val; } } for (int i = 0; i < data.length; i++) { averageVal[i] = averageVal[i] / data[i].length; } float[][] thresholdedData = new float[data.length][data[0].length]; for (int i = 0; i < data.length; i++) { for (int j = 0; j < data[i].length; j++) { thresholdedData[i][j] = (float) Math.min(maxVal, data[i][j] / averageVal[i]); } } return getMainAppendedDerivativeScaledPosDownColumn(thresholdedData, scaleDerivFactor, derivativeThreshold); } public static float[][] getNormalizedThresholdedByMedian(float[][] data, float maxVal) { double[] medianVal = new double[data.length]; for (int i = 0; i < data.length; i++) { medianVal[i] = getMedian(data[i]); } float[][] thresholdedData = new float[data.length][data[0].length]; for (int i = 0; i < data.length; i++) { for (int j = 0; j < data[i].length; j++) { thresholdedData[i][j] = (float) Math.min(maxVal, data[i][j] / medianVal[i]); } } return thresholdedData; } public static double getMedian(float[] values) { double[] array = new double[values.length]; for (int k = 0; k < values.length; k++) { array[k] = values[k]; } Median median = new Median(); return median.evaluate(array); } public static float[][] getMainAppendedDerivativeScaledPosDownColumn(float[][] data, float scaleDerivFactor, float threshold) { int numColumns = data[0].length; float[][] derivative = getRelevantDerivativeScaledPositive(data, scaleDerivFactor, threshold); float[][] appendedDerivative = new float[data.length][numColumns + derivative[0].length]; for (int i = 0; i < data.length; i++) { System.arraycopy(data[i], 0, appendedDerivative[i], 0, numColumns); } for (int i = 0; i < data.length; i++) { System.arraycopy(derivative[i], 0, appendedDerivative[i], numColumns, derivative[i].length); } return appendedDerivative; } public static float[][] getMainAppendedDerivativeDownColumnV2(float[][] data, float scaleDerivFactor, float threshold) { int numColumns = data[0].length; float[][] derivative = getRelevantDerivative(data, scaleDerivFactor, threshold); float[][] appendedDerivative = new float[data.length][numColumns + derivative[0].length]; for (int i = 0; i < data.length; i++) { System.arraycopy(data[i], 0, appendedDerivative[i], 0, numColumns); } for (int i = 0; i < data.length; i++) { for (int j = 0; j < data[i].length; j++) { appendedDerivative[i][j] = Math.min(.5f, Math.max(-.5f, appendedDerivative[i][j])); } } for (int i = 0; i < data.length; i++) { System.arraycopy(derivative[i], 0, appendedDerivative[i], numColumns, derivative[i].length); } return appendedDerivative; } public static float[][] getMainAppendedDerivativeDownColumn(float[][] data, float scaleDerivFactor, float threshold) { int numColumns = data[0].length; float[][] derivative = getRelevantDerivative(data, scaleDerivFactor, threshold); float[][] appendedDerivative = new float[data.length][numColumns + derivative[0].length]; for (int i = 0; i < data.length; i++) { System.arraycopy(data[i], 0, appendedDerivative[i], 0, numColumns); } for (int i = 0; i < data.length; i++) { System.arraycopy(derivative[i], 0, appendedDerivative[i], numColumns, derivative[i].length); } return appendedDerivative; } public static float[][] getRelevantDerivativeScaledPositive(float[][] data, float scaleDerivFactor, float threshold) { float[][] derivative = new float[data.length][data[0].length - 1]; for (int i = 0; i < data.length; i++) { for (int j = 0; j < data[0].length - 1; j++) { derivative[i][j] = data[i][j] - data[i][j + 1]; } } float[] columnSums = getAbsValColSums(derivative); List indicesToUse = new ArrayList<>(); for (int k = 0; k < columnSums.length; k++) { if (columnSums[k] > 0) { indicesToUse.add(k); } } float[][] importantDerivative = new float[data.length][indicesToUse.size()]; for (int i = 0; i < data.length; i++) { for (int k = 0; k < indicesToUse.size(); k++) { int indexToUse = indicesToUse.get(k); importantDerivative[i][k] = Math.min(threshold, Math.max(-threshold, derivative[i][indexToUse] * scaleDerivFactor)) + threshold; } } return importantDerivative; } public static float[][] getRelevantDerivative(float[][] data, float scaleDerivFactor, float threshold) { float[][] derivative = new float[data.length][data[0].length - 1]; for (int i = 0; i < data.length; i++) { for (int j = 0; j < data[0].length - 1; j++) { derivative[i][j] = data[i][j] - data[i][j + 1]; } } float[] columnSums = getAbsValColSums(derivative); List indicesToUse = new ArrayList<>(); for (int k = 0; k < columnSums.length; k++) { if (columnSums[k] > 0) { indicesToUse.add(k); } } float[][] importantDerivative = new float[data.length][indicesToUse.size()]; for (int i = 0; i < data.length; i++) { for (int k = 0; k < indicesToUse.size(); k++) { int indexToUse = indicesToUse.get(k); importantDerivative[i][k] = Math.min(threshold, Math.max(-threshold, derivative[i][indexToUse] * scaleDerivFactor)); } } return importantDerivative; } public static float[][] getRelevantDiscreteIntDerivativeScaledPositive(float[][] data, float scaleDerivFactor, float threshold) { int[][] derivative = new int[data.length][data[0].length - 1]; for (int i = 0; i < data.length; i++) { for (int j = 0; j < data[0].length - 1; j++) { float tempVal = (data[i][j] - data[i][j + 1]); tempVal = Math.min(threshold, Math.max(-threshold, tempVal * scaleDerivFactor)); derivative[i][j] = Math.round(tempVal); } } int[] columnSums = getAbsValColSums(derivative); List indicesToUse = new ArrayList<>(); for (int k = 0; k < columnSums.length; k++) { if (columnSums[k] > 0) { indicesToUse.add(k); } } float[][] importantDerivative = new float[data.length][indicesToUse.size()]; for (int i = 0; i < data.length; i++) { for (int k = 0; k < indicesToUse.size(); k++) { int indexToUse = indicesToUse.get(k); importantDerivative[i][k] = derivative[i][indexToUse] + threshold; } } return importantDerivative; } } ================================================ FILE: src/juicebox/tools/utils/common/ShellCommandRunner.java ================================================ /* * The MIT License (MIT) * * Copyright (c) 2011-2021 Broad Institute, Aiden Lab, Rice University, Baylor College of Medicine * * Permission is hereby granted, free of charge, to any person obtaining a copy * of this software and associated documentation files (the "Software"), to deal * in the Software without restriction, including without limitation the rights * to use, copy, modify, merge, publish, distribute, sublicense, and/or sell * copies of the Software, and to permit persons to whom the Software is * furnished to do so, subject to the following conditions: * * The above copyright notice and this permission notice shall be included in * all copies or substantial portions of the Software. * * THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR * IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, * FITNESS FOR A PARTICULAR PURPOSE AND NON-INFRINGEMENT. IN NO EVENT SHALL THE * AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER * LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, * OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN * THE SOFTWARE. */ package juicebox.tools.utils.common; import java.io.BufferedReader; import java.io.InputStreamReader; public class ShellCommandRunner { public static void runShellFile(String command, String filepath) { Process p; try { String[] cmd = {command, filepath}; p = Runtime.getRuntime().exec(cmd); p.waitFor(); BufferedReader reader = new BufferedReader(new InputStreamReader( p.getInputStream())); String line; while ((line = reader.readLine()) != null) { System.out.println(line); } } catch (Exception e) { System.err.println(e.getLocalizedMessage()); System.err.println("Unable to execute shell file: " + filepath); System.err.println("Run this file in your shell and then start from normalization"); System.exit(45); } } } ================================================ FILE: src/juicebox/tools/utils/common/StatPercentile.java ================================================ /* * The MIT License (MIT) * * Copyright (c) 2011-2020 Broad Institute, Aiden Lab, Rice University, Baylor College of Medicine * * Permission is hereby granted, free of charge, to any person obtaining a copy * of this software and associated documentation files (the "Software"), to deal * in the Software without restriction, including without limitation the rights * to use, copy, modify, merge, publish, distribute, sublicense, and/or sell * copies of the Software, and to permit persons to whom the Software is * furnished to do so, subject to the following conditions: * * The above copyright notice and this permission notice shall be included in * all copies or substantial portions of the Software. * * THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR * IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, * FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE * AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER * LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, * OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN * THE SOFTWARE. */ package juicebox.tools.utils.common; import java.util.Arrays; public class StatPercentile { private final double[] statsData; public StatPercentile(double[] data) { statsData = new double[data.length]; System.arraycopy(data, 0, statsData, 0, data.length); Arrays.sort(statsData); } // TODO actually could be much more optimized since same vals are queried // some binary search like technique etc public double evaluate(double val) { return internalEvaluate(val) * 100; } /** * @param val * @return percentile of given value as ranked relative to values in internal array */ private double internalEvaluate(double val) { for (int i = 0; i < statsData.length; i++) { if (statsData[i] >= val) { if (statsData[i] > val) { return Math.max(0.0, i / statsData.length); } else { double percentile = 0; int num = 0; for (int j = i; j < statsData.length; j++) { if (statsData[j] > val) { break; } percentile += ((double) i) / statsData.length; num++; } return percentile / num; } } } return 1.0; } } ================================================ FILE: src/juicebox/tools/utils/common/UNIXTools.java ================================================ /* * The MIT License (MIT) * * Copyright (c) 2011-2020 Broad Institute, Aiden Lab, Rice University, Baylor College of Medicine * * Permission is hereby granted, free of charge, to any person obtaining a copy * of this software and associated documentation files (the "Software"), to deal * in the Software without restriction, including without limitation the rights * to use, copy, modify, merge, publish, distribute, sublicense, and/or sell * copies of the Software, and to permit persons to whom the Software is * furnished to do so, subject to the following conditions: * * The above copyright notice and this permission notice shall be included in * all copies or substantial portions of the Software. * * THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR * IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, * FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE * AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER * LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, * OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN * THE SOFTWARE. */ package juicebox.tools.utils.common; import juicebox.HiCGlobals; import java.io.BufferedReader; import java.io.File; import java.io.InputStreamReader; import java.io.PrintWriter; import java.util.List; /** * Created by muhammadsaadshamim on 9/29/15. */ public class UNIXTools { public static String extractElement(String str, int i) { String[] strSplit = str.split("\t"); return strSplit[strSplit.length - i]; } public static String makeDir(String path) { File file = new File(path); if (!file.isDirectory()) { file.mkdir(); } return path; } public static File makeDir(File folder) { if (!folder.isDirectory()) { folder.mkdir(); } return folder; } public static void redirectOutput(List command, String outputFilePath) { String output = executeComplexCommand(command); File outputFile = new File(outputFilePath); try { outputFile.createNewFile(); PrintWriter writer = new PrintWriter(outputFile); writer.print(output); writer.close(); } catch (Exception e) { System.err.println("Unable to write command line output to file: " + outputFilePath); e.printStackTrace(); } } public static String executeSimpleCommand(String command) { StringBuilder output = new StringBuilder(); try { Process p = Runtime.getRuntime().exec(command); p.waitFor(); BufferedReader reader = new BufferedReader(new InputStreamReader(p.getInputStream()), HiCGlobals.bufferSize); String line; while ((line = reader.readLine()) != null) { output.append(line).append("\n"); } } catch (Exception e) { e.printStackTrace(); } return output.toString(); } private static String executeComplexCommand(List command) { StringBuilder output = new StringBuilder(); //System.out.println(System.getenv()); ProcessBuilder b = new ProcessBuilder(command); //Map env = b.environment(); //System.out.println(env); Process p; try { //p = Runtime.getRuntime().exec(command); p = b.redirectErrorStream(true).start(); if (HiCGlobals.printVerboseComments) { System.out.println("Command exec " + p.waitFor()); } else { p.waitFor(); } BufferedReader reader = new BufferedReader(new InputStreamReader(p.getInputStream()), HiCGlobals.bufferSize); String line; while ((line = reader.readLine()) != null) { output.append(line).append("\n"); } } catch (Exception e) { e.printStackTrace(); } return output.toString(); } } ================================================ FILE: src/juicebox/tools/utils/dev/AFAUtils.java ================================================ /* * The MIT License (MIT) * * Copyright (c) 2011-2020 Broad Institute, Aiden Lab, Rice University, Baylor College of Medicine * * Permission is hereby granted, free of charge, to any person obtaining a copy * of this software and associated documentation files (the "Software"), to deal * in the Software without restriction, including without limitation the rights * to use, copy, modify, merge, publish, distribute, sublicense, and/or sell * copies of the Software, and to permit persons to whom the Software is * furnished to do so, subject to the following conditions: * * The above copyright notice and this permission notice shall be included in * all copies or substantial portions of the Software. * * THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR * IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, * FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE * AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER * LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, * OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN * THE SOFTWARE. */ package juicebox.tools.utils.dev; import juicebox.data.HiCFileTools; import juicebox.data.MatrixZoomData; import juicebox.track.feature.Feature2D; import juicebox.windowui.NormalizationType; import org.apache.commons.math.linear.RealMatrix; import java.io.IOException; import java.util.ArrayList; import java.util.List; /** * Created by muhammadsaadshamim on 9/9/15. */ class AFAUtils { public static List filterFeaturesByAttribute(List features, String attribute) { List filteredFeatures = new ArrayList<>(); for (Feature2D feature : features) { if (feature.containsAttributeValue(attribute)) { filteredFeatures.add(feature); } } return filteredFeatures; } /* * loading filtered looplists categorized by attributes { Feature2DList featureList = Feature2DParser.loadFeatures(files[1], chromosomes, true, new FeatureFilter() { // Remove duplicates and filters by size // also save internal metrics for these measures @Override public List filter(String chr, List features) { List uniqueFeatures = new ArrayList(new HashSet(features)); List filteredUniqueFeatures; if (attribute.length() > 0) { filteredUniqueFeatures = AFAUtils.filterFeaturesByAttribute(uniqueFeatures, attribute); } else { System.out.println("No filtering by attribute"); filteredUniqueFeatures = uniqueFeatures; } filterMetrics.put(chr, new Integer[]{filteredUniqueFeatures.size(), uniqueFeatures.size(), features.size()}); return filteredUniqueFeatures; } }, false); } */ public static RealMatrix extractLocalizedData(MatrixZoomData zd, Feature2D feature, int L, int resolution, int window, NormalizationType norm, LocationType relativeLocation) throws IOException { long loopX, loopY; if (relativeLocation.equals(LocationType.TL)) { loopX = feature.getStart1(); loopY = feature.getStart2(); } else if (relativeLocation.equals(LocationType.BR)) { loopX = feature.getEnd1(); loopY = feature.getEnd2(); } else {//LocationType.CENTER loopX = feature.getMidPt1(); loopY = feature.getMidPt2(); } loopX /= resolution; loopY /= resolution; long binXStart = loopX - window; long binXEnd = loopX + (window + 1); long binYStart = loopY - window; long binYEnd = loopY + (window + 1); return HiCFileTools.extractLocalBoundedRegion(zd, binXStart, binXEnd, binYStart, binYEnd, L, L, norm, false); } } ================================================ FILE: src/juicebox/tools/utils/dev/LocalGenomeRegion.java ================================================ /* * The MIT License (MIT) * * Copyright (c) 2011-2020 Broad Institute, Aiden Lab, Rice University, Baylor College of Medicine * * Permission is hereby granted, free of charge, to any person obtaining a copy * of this software and associated documentation files (the "Software"), to deal * in the Software without restriction, including without limitation the rights * to use, copy, modify, merge, publish, distribute, sublicense, and/or sell * copies of the Software, and to permit persons to whom the Software is * furnished to do so, subject to the following conditions: * * The above copyright notice and this permission notice shall be included in * all copies or substantial portions of the Software. * * THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR * IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, * FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE * AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER * LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, * OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN * THE SOFTWARE. */ package juicebox.tools.utils.dev; import java.util.ArrayList; import java.util.Collections; import java.util.List; public class LocalGenomeRegion { private final int initialIndex; private List neighbors = new ArrayList<>(); private final int maxNumValsToStore; public LocalGenomeRegion(int initialIndex, int maxNumValsToStore) { this.initialIndex = initialIndex; this.maxNumValsToStore = maxNumValsToStore; } public synchronized void addNeighbor(int y, float counts) { neighbors.add(new Neighbor(y, counts)); if (neighbors.size() > maxNumValsToStore) { neighbors.sort(Collections.reverseOrder()); neighbors.remove(neighbors.size() - 1); } } public synchronized void filterDownValues(int numNeighborsAllowed) { neighbors.sort(Collections.reverseOrder()); if (neighbors.size() > numNeighborsAllowed) { float valueToKeep = neighbors.get(numNeighborsAllowed - 1).value; int willKeepUpTo = neighbors.size(); for (int k = numNeighborsAllowed; k < neighbors.size(); k++) { if (neighbors.get(k).value < valueToKeep) { willKeepUpTo = k; break; } } neighbors = neighbors.subList(0, willKeepUpTo); } } public synchronized boolean notConnectedWith(int index) { for (Neighbor neighbor : neighbors) { if (neighbor.index == index) { return false; } } return true; } public synchronized int getOutlierContacts(boolean isBadUpstream, int cliqueSize) { neighbors.sort(Collections.reverseOrder()); for (Neighbor neighbor : neighbors) { if (Math.abs(neighbor.index - initialIndex) > cliqueSize) { if (isBadUpstream) { if (neighbor.index < initialIndex) { return neighbor.index; } } else { // is bad downstream if (neighbor.index > initialIndex) { return neighbor.index; } } } } return -1; } @Override public String toString() { StringBuilder nei = new StringBuilder(); neighbors.sort(Collections.reverseOrder()); for (Neighbor neighbor : neighbors) { nei.append(neighbor.index).append("-").append(neighbor.value).append("__"); } return initialIndex + " - " + nei; } private class Neighbor implements Comparable { final Integer index; final Float value; Neighbor(int index, float value) { this.index = index; this.value = value; } @Override public int compareTo(Neighbor o) { int compareVal = value.compareTo(o.value); if (compareVal == 0) { return index.compareTo(o.index); } return compareVal; } } } ================================================ FILE: src/juicebox/tools/utils/dev/LocationType.java ================================================ /* * The MIT License (MIT) * * Copyright (c) 2011-2020 Broad Institute, Aiden Lab, Rice University, Baylor College of Medicine * * Permission is hereby granted, free of charge, to any person obtaining a copy * of this software and associated documentation files (the "Software"), to deal * in the Software without restriction, including without limitation the rights * to use, copy, modify, merge, publish, distribute, sublicense, and/or sell * copies of the Software, and to permit persons to whom the Software is * furnished to do so, subject to the following conditions: * * The above copyright notice and this permission notice shall be included in * all copies or substantial portions of the Software. * * THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR * IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, * FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE * AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER * LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, * OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN * THE SOFTWARE. */ package juicebox.tools.utils.dev; /** * Created by muhammadsaadshamim on 9/9/15. */ public enum LocationType { TL("TopLeft"), BR("BottomRight"), CENTER("Center"); private final String label; LocationType(String label) { this.label = label; } public static LocationType enumValueFromString(String text) { if (text != null) { for (LocationType region : LocationType.values()) { if (text.equalsIgnoreCase(region.label)) { return region; } } } return null; } public String getLabel() { return label; } } ================================================ FILE: src/juicebox/tools/utils/dev/PearsonCorrelationMetric.java ================================================ /* * The MIT License (MIT) * * Copyright (c) 2011-2021 Broad Institute, Aiden Lab, Rice University, Baylor College of Medicine * * Permission is hereby granted, free of charge, to any person obtaining a copy * of this software and associated documentation files (the "Software"), to deal * in the Software without restriction, including without limitation the rights * to use, copy, modify, merge, publish, distribute, sublicense, and/or sell * copies of the Software, and to permit persons to whom the Software is * furnished to do so, subject to the following conditions: * * The above copyright notice and this permission notice shall be included in * all copies or substantial portions of the Software. * * THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR * IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, * FITNESS FOR A PARTICULAR PURPOSE AND NON-INFRINGEMENT. IN NO EVENT SHALL THE * AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER * LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, * OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN * THE SOFTWARE. */ package juicebox.tools.utils.dev; public class PearsonCorrelationMetric { public static double corr(final double[] x, final double[] y) { double sumX = 0; double sumY = 0; for (int i = 0; i < x.length; i++) { sumX += x[i]; sumY += y[i]; } double muX = sumX / x.length; double muY = sumY / x.length; double dotProduct = 0.0; double normX = 0.0; double normY = 0.0; for (int i = 0; i < x.length; i++) { double nX = x[i] - muX; double nY = y[i] - muY; dotProduct += nX * nY; normX += nX * nX; normY += nY * nY; } return dotProduct / Math.sqrt(normX * normY); } } ================================================ FILE: src/juicebox/tools/utils/juicer/GeneTools.java ================================================ /* * The MIT License (MIT) * * Copyright (c) 2011-2020 Broad Institute, Aiden Lab, Rice University, Baylor College of Medicine * * Permission is hereby granted, free of charge, to any person obtaining a copy * of this software and associated documentation files (the "Software"), to deal * in the Software without restriction, including without limitation the rights * to use, copy, modify, merge, publish, distribute, sublicense, and/or sell * copies of the Software, and to permit persons to whom the Software is * furnished to do so, subject to the following conditions: * * The above copyright notice and this permission notice shall be included in * all copies or substantial portions of the Software. * * THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR * IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, * FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE * AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER * LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, * OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN * THE SOFTWARE. */ package juicebox.tools.utils.juicer; import juicebox.data.ChromosomeHandler; import juicebox.data.GeneLocation; import juicebox.data.anchor.GenericLocus; import juicebox.data.anchor.MotifAnchor; import juicebox.data.anchor.MotifAnchorParser; import juicebox.data.basics.Chromosome; import juicebox.data.feature.GenomeWideList; import java.io.BufferedReader; import java.io.FileNotFoundException; import java.io.FileReader; import java.io.IOException; import java.net.URL; import java.util.ArrayList; import java.util.HashMap; import java.util.List; import java.util.Map; /** * Created by muhammadsaadshamim on 8/3/16. */ public class GeneTools { public static BufferedReader getStreamToGeneFile(String genomeID) { String path = extractProperGeneFilePath(genomeID); try { return new BufferedReader(new FileReader(path)); } catch (FileNotFoundException e) { System.err.println("Unable to read from " + path); System.exit(56); } return null; } private static String extractProperGeneFilePath(String genomeID) { if (genomeID.equals("hg19") || genomeID.equals("hg38") || genomeID.equals("mm9") || genomeID.equals("mm10")) { String newURL = "http://hicfiles.s3.amazonaws.com/internal/" + genomeID + "_refGene.txt"; try { return MotifAnchorParser.downloadFromUrl(new URL(newURL), "genes"); } catch (IOException e) { System.err.println("Unable to download file from online; attempting to use direct file path"); } } else { try { return MotifAnchorParser.uncompressFromGzip(genomeID, "genes"); } catch (IOException e) { System.err.println("Unable to unzip file; attempting to use direct file path"); } } return genomeID; } public static Map getLocationMap(BufferedReader reader, ChromosomeHandler handler) throws IOException { Map geneLocationHashMap = new HashMap<>(); String nextLine; while ((nextLine = reader.readLine()) != null) { String[] values = nextLine.split("\\s+"); if (values.length == 4 || values.length == 16) { // 16 is refGene official format // transcript start; for 4 column format, just position-1 int txStart = (values.length == 4) ? Integer.parseInt(values[3].trim()) - 1 : Integer.parseInt(values[4].trim()); // transcript end; for 4 column format, just position+1 //int txEnd = (values.length==4) ? Integer.valueOf(values[3].trim())+1 : Integer.valueOf(values[5].trim()); String name = values[1].trim(); String name2 = (values.length==4) ? values[0].trim() : values[12].trim(); Chromosome chr = handler.getChromosomeFromName(values[2]); GeneLocation location = new GeneLocation(chr, txStart); geneLocationHashMap.put(name2.toLowerCase(), location); geneLocationHashMap.put(name.trim().toLowerCase(), location); } } return geneLocationHashMap; } public static GenomeWideList parseGenome(String genomeID, ChromosomeHandler handler) { BufferedReader reader = getStreamToGeneFile(genomeID); List allGenes = extractAllGenes(reader, handler); return new GenomeWideList<>(handler, allGenes); } private static List extractAllGenes(BufferedReader reader, ChromosomeHandler handler) { List genes = new ArrayList<>(); String nextLine; try { while ((nextLine = reader.readLine()) != null) { String[] values = nextLine.split("\\s+"); if (values.length == 4 || values.length == 16) { // 16 is refGene official format Chromosome chr = handler.getChromosomeFromName(values[2]); // refGene contains contigs as well, ignore these genes if (chr != null) { int chrIndex = chr.getIndex(); // transcript start; for 4 column format, just position-1 int txStart = (values.length == 4) ? Integer.parseInt(values[3].trim()) - 1 : Integer.parseInt(values[4].trim()); // transcript end; for 4 column format, just position+1 int txEnd = (values.length == 4) ? Integer.parseInt(values[3].trim()) + 1 : Integer.parseInt(values[5].trim()); String name = (values.length==4) ? values[1].trim() : values[12].trim(); MotifAnchor gene = new MotifAnchor(chr.getName(), txStart, txEnd, name); genes.add(gene); } } } } catch (Exception e) { System.err.println("Gene database not properly formatted"); System.exit(50); } if (genes.size() == 0) { System.err.println("Gene database not properly formatted"); System.exit(51); } return genes; } } ================================================ FILE: src/juicebox/tools/utils/juicer/apa/APADataStack.java ================================================ /* * The MIT License (MIT) * * Copyright (c) 2011-2021 Broad Institute, Aiden Lab, Rice University, Baylor College of Medicine * * Permission is hereby granted, free of charge, to any person obtaining a copy * of this software and associated documentation files (the "Software"), to deal * in the Software without restriction, including without limitation the rights * to use, copy, modify, merge, publish, distribute, sublicense, and/or sell * copies of the Software, and to permit persons to whom the Software is * furnished to do so, subject to the following conditions: * * The above copyright notice and this permission notice shall be included in * all copies or substantial portions of the Software. * * THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR * IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, * FITNESS FOR A PARTICULAR PURPOSE AND NON-INFRINGEMENT. IN NO EVENT SHALL THE * AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER * LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, * OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN * THE SOFTWARE. */ package juicebox.tools.utils.juicer.apa; import juicebox.HiCGlobals; import juicebox.data.HiCFileTools; import juicebox.tools.utils.common.MatrixTools; import org.apache.commons.math.linear.RealMatrix; import java.io.File; import java.text.SimpleDateFormat; import java.util.ArrayList; import java.util.Date; import java.util.List; /** * Created by muhammadsaadshamim on 5/1/15. */ public class APADataStack { // genome wide variables private static boolean genomeWideVariablesNotSet = true; private static RealMatrix gwAPAMatrix; private static RealMatrix gwNormedAPAMatrix; private static RealMatrix gwCenterNormedAPAMatrix; private static RealMatrix gwRankAPAMatrix; private static List gwEnhancement; private static final Object key = new Object(); // saving data variables private static int[] axesRange; private static File dataDirectory; // chr variables private final List enhancement; private RealMatrix APAMatrix; private RealMatrix normedAPAMatrix; private RealMatrix centerNormedAPAMatrix; private RealMatrix rankAPAMatrix; /** * class for saving data from chromosme wide run of APA, keeps static class to store genomide data * * @param n width of matrix * @param outputFolder location for saving data * @param customPrefix optional file/folder prefix */ public APADataStack(int n, File outputFolder, String customPrefix) { APAMatrix = MatrixTools.cleanArray2DMatrix(n, n); normedAPAMatrix = MatrixTools.cleanArray2DMatrix(n, n); centerNormedAPAMatrix = MatrixTools.cleanArray2DMatrix(n, n); rankAPAMatrix = MatrixTools.cleanArray2DMatrix(n, n); enhancement = new ArrayList<>(); initializeGenomeWideVariables(n); initializeDataSaveFolder(outputFolder, customPrefix); axesRange = new int[]{-n / 2, 1, -n / 2, 1}; } /** * Ensure that directory for saving exists * * @param outputFolderDirectory to directory * @param prefix of files to be saved */ public static void initializeDataSaveFolder(File outputFolderDirectory, String prefix) { if (prefix.length() < 1) {// no preference specified dataDirectory = new File(outputFolderDirectory, new SimpleDateFormat("yyyy.MM.dd.HH.mm").format(new Date())); } else { dataDirectory = new File(outputFolderDirectory, prefix); } dataDirectory = HiCFileTools.createValidDirectory(dataDirectory.getAbsolutePath()); } private static void initializeGenomeWideVariables(int n) { if (genomeWideVariablesNotSet) { gwAPAMatrix = MatrixTools.cleanArray2DMatrix(n, n); gwNormedAPAMatrix = MatrixTools.cleanArray2DMatrix(n, n); gwCenterNormedAPAMatrix = MatrixTools.cleanArray2DMatrix(n, n); gwRankAPAMatrix = MatrixTools.cleanArray2DMatrix(n, n); //gwCoverage = APAUtils.cleanArray2DMatrix(n, n); gwEnhancement = new ArrayList<>(); genomeWideVariablesNotSet = false; } } public static void exportGenomeWideData(Integer[] peakNumbers, int currentRegionWidth, boolean saveAllData, boolean dontIncludePlots) { double gwNPeaksUsedInv = 1. / peakNumbers[0]; gwNormedAPAMatrix = gwNormedAPAMatrix.scalarMultiply(gwNPeaksUsedInv); gwCenterNormedAPAMatrix = gwCenterNormedAPAMatrix.scalarMultiply(gwNPeaksUsedInv); gwRankAPAMatrix = gwRankAPAMatrix.scalarMultiply(gwNPeaksUsedInv); RealMatrix[] matrices = {gwAPAMatrix, gwNormedAPAMatrix, gwCenterNormedAPAMatrix, gwRankAPAMatrix}; String[] titles = {"APA", "normedAPA", "centerNormedAPA", "rankAPA"}; saveDataSet("gw", matrices, titles, gwEnhancement, peakNumbers, currentRegionWidth, saveAllData, dontIncludePlots); } public static APARegionStatistics retrieveDataStatistics(int currentRegionWidth){ return new APARegionStatistics(gwAPAMatrix, currentRegionWidth); } private static void saveDataSet(String prefix, RealMatrix[] apaMatrices, String[] apaDataTitles, List givenEnhancement, Integer[] peakNumbers, int currentRegionWidth, boolean saveAllData, boolean dontIncludePlots) { File subFolder = HiCFileTools.createValidDirectory(new File(dataDirectory, prefix).getAbsolutePath()); if (HiCGlobals.printVerboseComments) { System.out.println("Saving chr " + prefix + " data to " + subFolder); } for (int i = 0; i < apaMatrices.length; i++) { if (!saveAllData && i > 0) continue; String title = "N=" + peakNumbers[0] + " (filtered) " + peakNumbers[1] + " (unique) " + peakNumbers[2] + " (total)"; if (!dontIncludePlots) { APAPlotter.plot(apaMatrices[i], axesRange, new File(subFolder, apaDataTitles[i] + ".png"), title, currentRegionWidth, apaDataTitles[i].equals("APA")); } MatrixTools.saveMatrixText((new File(subFolder, apaDataTitles[i] + ".txt")).getAbsolutePath(), apaMatrices[i]); MatrixTools.saveMatrixTextNumpy( (new File(subFolder, apaDataTitles[i] + ".npy")).getAbsolutePath(), apaMatrices[i].getData()); } if (saveAllData) { APAUtils.saveListText((new File(subFolder, "enhancement.txt")).getAbsolutePath(), givenEnhancement); APAUtils.saveMeasures((new File(subFolder, "measures.txt")).getAbsolutePath(), apaMatrices[0], currentRegionWidth); } } public static void clearAllData() { axesRange = null; dataDirectory = null; genomeWideVariablesNotSet = true; gwAPAMatrix = null; gwNormedAPAMatrix = null; gwCenterNormedAPAMatrix = null; gwRankAPAMatrix = null; gwEnhancement = null; } public void addData(RealMatrix newData) { MatrixTools.cleanUpNaNs(newData); APAMatrix = APAMatrix.add(newData); normedAPAMatrix = normedAPAMatrix.add(APAUtils.standardNormalization(newData)); centerNormedAPAMatrix = centerNormedAPAMatrix.add(APAUtils.centerNormalization(newData)); rankAPAMatrix = rankAPAMatrix.add(APAUtils.rankPercentile(newData)); enhancement.add(APAUtils.peakEnhancement(newData)); } public synchronized void updateGenomeWideData() { synchronized (key) { gwAPAMatrix = gwAPAMatrix.add(APAMatrix); gwNormedAPAMatrix = gwNormedAPAMatrix.add(normedAPAMatrix); gwCenterNormedAPAMatrix = gwCenterNormedAPAMatrix.add(centerNormedAPAMatrix); gwRankAPAMatrix = gwRankAPAMatrix.add(rankAPAMatrix); gwEnhancement.addAll(enhancement); } } public void exportDataSet(String subFolderName, Integer[] peakNumbers, int currentRegionWidth, boolean saveAllData, boolean dontIncludePlots) { double nPeaksUsedInv = 1. / peakNumbers[0]; normedAPAMatrix = normedAPAMatrix.scalarMultiply(nPeaksUsedInv); centerNormedAPAMatrix = centerNormedAPAMatrix.scalarMultiply(nPeaksUsedInv); rankAPAMatrix = rankAPAMatrix.scalarMultiply(nPeaksUsedInv); RealMatrix[] matrices = {APAMatrix, normedAPAMatrix, centerNormedAPAMatrix, rankAPAMatrix}; String[] titles = {"APA", "normedAPA", "centerNormedAPA", "rankAPA", "enhancement", "measures"}; saveDataSet(subFolderName, matrices, titles, enhancement, peakNumbers, currentRegionWidth, saveAllData, dontIncludePlots); } public void thresholdPlots(int val) { MatrixTools.thresholdValues(APAMatrix, val); } } ================================================ FILE: src/juicebox/tools/utils/juicer/apa/APAPlotter.java ================================================ /* * The MIT License (MIT) * * Copyright (c) 2011-2020 Broad Institute, Aiden Lab, Rice University, Baylor College of Medicine * * Permission is hereby granted, free of charge, to any person obtaining a copy * of this software and associated documentation files (the "Software"), to deal * in the Software without restriction, including without limitation the rights * to use, copy, modify, merge, publish, distribute, sublicense, and/or sell * copies of the Software, and to permit persons to whom the Software is * furnished to do so, subject to the following conditions: * * The above copyright notice and this permission notice shall be included in * all copies or substantial portions of the Software. * * THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR * IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, * FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE * AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER * LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, * OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN * THE SOFTWARE. */ package juicebox.tools.utils.juicer.apa; import juicebox.tools.utils.common.MatrixTools; import org.apache.commons.math.linear.RealMatrix; import org.tc33.jheatchart.HeatChart; import javax.imageio.ImageIO; import javax.swing.*; import java.awt.*; import java.awt.image.BufferedImage; import java.io.File; import java.io.IOException; import java.text.DecimalFormat; /** * Helper class to wrap heat map plotting and handle apa plots * The static plot method should be called all the necessary inputs. */ class APAPlotter { /** * apa heat map plots range between red (max value) and white (0) */ private static final Color[] gradientColors = {Color.RED, Color.WHITE}; private static final float[] gradientFractions = {0.0f, 1.0f}; /** * used for comparisons */ private static final double epsilon = 1e-6; /** * heat map dimension defaults */ private static int fullHeight = 500; private static int heatmapWidth = 500; private static int colorScaleWidth = 40; private static int colorScaleHorizontalMargin = 10; private static int colorScaleVerticalMargin = 100; private static int extraWidthBuffer = 20; private static int fullWidth = heatmapWidth + colorScaleWidth + extraWidthBuffer; private static int numDivisions = 6; /** * Method for plotting apa data * * @param dataOriginal for heat map * @param axesRange initial values and increments to annotate axes [x0, dx, y0, dy] * @param outputFile where image will saved */ public static void plot(RealMatrix dataOriginal, int[] axesRange, File outputFile, String title, int currentRegionWidth, boolean useCellPlottingStandards) { // As noted in the Cell supplement: // "The color scale in all APA plots is set as follows. // The minimum of the color range is 0. The maximum is 5 x UR, where // UR is the mean value of the bins in the upper-right corner of the matrix. // The upper-right corner of the 10 kb resolution APA // plots is a 6 x 6 window (or 3 x 3 for 5 kb resolution APA plots)." // TODO RealMatrix data = dataOriginal.copy(); // don't want original edited APARegionStatistics apaStats = new APARegionStatistics(data, currentRegionWidth); DecimalFormat df = new DecimalFormat("0.000"); title += ", P2LL = " + df.format(apaStats.getPeak2LL()); Color lowColor; Color highColor; double maxAllowedValueCell = 5 * apaStats.getMeanUR(); double minAllowedValueCell = 0; if (useCellPlottingStandards) { double dataMin = MatrixTools.calculateMin(data); double dataMax = MatrixTools.calculateMax(data); if (dataMax > maxAllowedValueCell) { dataMax = maxAllowedValueCell; } if (dataMin < minAllowedValueCell) { dataMin = minAllowedValueCell; } MatrixTools.thresholdValuesDouble(data, minAllowedValueCell, maxAllowedValueCell); int lowColorGB = (int) (255 - dataMin / maxAllowedValueCell * 255); int highColorGB = (int) (255 - dataMax / maxAllowedValueCell * 255); lowColor = new Color(255, lowColorGB, lowColorGB); highColor = new Color(255, highColorGB, highColorGB); } else { lowColor = Color.white; highColor = Color.red; } // initialize heat map HeatChart map = new HeatChart(data.getData()); map.setXValues(axesRange[0], axesRange[1]); map.setYValues(axesRange[2], axesRange[3]); map.setTitle(title); map.setLowValueColour(lowColor); map.setHighValueColour(highColor); try { // calculate dimensions for plot wrapper initializeSizes(map); // create blank white image BufferedImage apaImage = new BufferedImage(fullWidth, fullHeight, BufferedImage.TYPE_INT_ARGB); Graphics2D g2 = apaImage.createGraphics(); g2.setBackground(Color.WHITE); g2.fillRect(0, 0, fullWidth, fullHeight); // plot in heat map, color bar, etc g2.drawImage(map.getChartImage(), 0, 0, heatmapWidth, fullHeight, null); drawHeatMapBorder(g2, map); plotColorScaleBar(g2); if (useCellPlottingStandards) { plotSpecialColorScaleValues(g2, map, minAllowedValueCell, maxAllowedValueCell); } else { plotColorScaleValues(g2, map); } // top left, top right, bottom left, bottom right values (from apa) drawCornerRegions(g2, map, new Dimension(currentRegionWidth, currentRegionWidth), apaStats.getRegionCornerValues()); // save data ImageIO.write(apaImage, "png", outputFile); } catch (IOException e) { e.printStackTrace(); } } /** * Initialize dimensions used for plotting apa data * * @param heatMap object */ private static void initializeSizes(HeatChart heatMap) { Dimension mapDimensions = getImageDimensions(heatMap.getChartImage()); //fullHeight = (int) (mapDimensions.height*((double)heatmapWidth)/mapDimensions.width); fullHeight = mapDimensions.height; heatmapWidth = mapDimensions.width; colorScaleWidth = 40; colorScaleHorizontalMargin = 10; colorScaleVerticalMargin = fullHeight / 5; extraWidthBuffer = 30; fullWidth = heatmapWidth + colorScaleWidth + extraWidthBuffer; numDivisions = calculateIdealNumDivisions(heatMap.getPermissiveIntRange()); } /** * Calculate raw dimensions of image * * @param image * @return dimension (x,y) size of image in pixels */ private static Dimension getImageDimensions(Image image) { ImageIcon icon = new ImageIcon(image); return new Dimension(icon.getIconWidth(), icon.getIconHeight()); } /** * Calculate optimal number of color map divisions based on range * * @param range of heat map data (max - min) * @return optimal number of color map divisions */ private static int calculateIdealNumDivisions(int range) { // 33 ~ minimum number of pixels per division for (int n = fullHeight / 33; n > 3; n--) { if (range % n == 0) return n; } return 5; } /** * @param g2 graphics2D object */ private static void plotColorScaleBar(Graphics2D g2) { // calculate color scale bar dimensions & location Point csBarTL = new Point(heatmapWidth + colorScaleHorizontalMargin, colorScaleVerticalMargin); Point csBarBL = new Point(heatmapWidth + colorScaleHorizontalMargin, fullHeight - colorScaleVerticalMargin); Rectangle csBar = new Rectangle(csBarTL.x, csBarTL.y, colorScaleWidth - 2 * colorScaleHorizontalMargin, fullHeight - 2 * colorScaleVerticalMargin); // plot the color scale linear gradient LinearGradientPaint gradient = new LinearGradientPaint(csBarTL, csBarBL, gradientFractions, gradientColors); g2.setPaint(gradient); g2.fill(csBar); // plot a border around color scale g2.setColor(Color.black); g2.drawRect(csBar.x, csBar.y, csBar.width, csBar.height); } /** * Plot number value axis for color scale bar. * * @param g2 graphics2D object * @param heatMap object */ private static void plotColorScaleValues(Graphics2D g2, HeatChart heatMap) { // size, increment calculations double valIncrement = Math.max(heatMap.getDataRange() / ((double) numDivisions), epsilon); double depthIncrement = ((double) (fullHeight - 2 * colorScaleVerticalMargin)) / ((double) numDivisions); int verticalDepth = fullHeight - colorScaleVerticalMargin; int csBarRightEdgeX = fullWidth - colorScaleHorizontalMargin - extraWidthBuffer; // formatting g2.setFont(heatMap.getAxisValuesFont()); DecimalFormat df = new DecimalFormat("0.#"); // draw each tick mark and its value for (double i = heatMap.getLowValue(); i <= heatMap.getHighValue(); i += valIncrement, verticalDepth -= depthIncrement) { if (i > heatMap.getHighValue() - epsilon) verticalDepth = colorScaleVerticalMargin; g2.drawString(df.format(i), csBarRightEdgeX + 5, verticalDepth); // value g2.drawLine(csBarRightEdgeX - 5, verticalDepth, csBarRightEdgeX, verticalDepth); // tick mark } } /** * Plot number value axis for color scale bar. * * @param g2 graphics2D object * @param heatMap object */ private static void plotSpecialColorScaleValues(Graphics2D g2, HeatChart heatMap, double minColor, double maxColor) { // size, increment calculations double valIncrement = Math.max((maxColor - minColor) / ((double) numDivisions), epsilon); double depthIncrement = ((double) (fullHeight - 2 * colorScaleVerticalMargin)) / ((double) numDivisions); int verticalDepth = fullHeight - colorScaleVerticalMargin; int csBarRightEdgeX = fullWidth - colorScaleHorizontalMargin - extraWidthBuffer; // formatting g2.setFont(heatMap.getAxisValuesFont()); DecimalFormat df = new DecimalFormat("0.#"); // draw each tick mark and its value for (double i = minColor; i <= maxColor; i += valIncrement, verticalDepth -= depthIncrement) { if (i > maxColor - epsilon) verticalDepth = colorScaleVerticalMargin; g2.drawString(df.format(i), csBarRightEdgeX + 5, verticalDepth); // value g2.drawLine(csBarRightEdgeX - 5, verticalDepth, csBarRightEdgeX, verticalDepth); // tick mark } } /** * Draw black border around main heat map * * @param g2 graphics2D object * @param heatMap object */ private static void drawHeatMapBorder(Graphics2D g2, HeatChart heatMap) { // calculate corners of heat map rectangle Point heatMapTL = heatMap.getHeatMapTL(); Point heatMapBR = heatMap.getHeatMapBR(); // plot border around heat map g2.setColor(Color.BLACK); g2.drawRect(heatMapTL.x, heatMapTL.y, heatMapBR.x - heatMapTL.x, heatMapBR.y - heatMapTL.y); } /** * Draw the corner boxes and their values as calculated by apa overlayed above the existing heat map * * @param g2 graphics2D oObject * @param map heat map object * @param regionCellDimensions dimensions for the corner regions to be plotted in units of cells, not pixels * where each cell corresponds to a data point, usually 20px-by-20px (default) * @param regionAPAValues apa results for each region in order of TL TR BL BR */ private static void drawCornerRegions(Graphics2D g2, HeatChart map, Dimension regionCellDimensions, double[] regionAPAValues) { // retrieve corners of heat map Point topLeft = map.getHeatMapTL(); Point topRight = map.getHeatMapTR(); Point bottomLeft = map.getHeatMapBL(); Point bottomRight = map.getHeatMapBR(); // calculate dimensions of corner regions Dimension cellSize = map.getCellSize(); int cornerWidth = regionCellDimensions.width * cellSize.width, cornerHeight = regionCellDimensions.height * cellSize.height; // slide to top left corner within each region topRight.translate(-cornerWidth, 0); bottomLeft.translate(0, -cornerHeight); bottomRight.translate(-cornerWidth, -cornerHeight); // plot the four region TL TR BL BR and their values Point[] points = {topLeft, topRight, bottomLeft, bottomRight}; g2.setColor(Color.black); for (int i = 0; i < 4; i++) { // plot rectangle from upper left corner Point currPoint = points[i]; g2.drawRect(currPoint.x, currPoint.y, cornerWidth, cornerHeight); // translate to center of rectangle currPoint.translate(cornerWidth / 2, cornerHeight / 2); drawCenteredDouble(g2, regionAPAValues[i], currPoint); } } /** * Plot double centered at a point (rather than from the upper left corner as is the default) * * @param g2 graphics2D object * @param value to be plotted * @param position for value to be centered at */ private static void drawCenteredDouble(Graphics2D g2, Double value, Point position) { DecimalFormat df = new DecimalFormat("0.000"); drawCenteredString(g2, df.format(value), position); } /** * Plot text centered at a point (rather than from the upper left corner as is the default) * * @param g2 graphics2D object * @param text to be plotted * @param position of where text will be centered at */ private static void drawCenteredString(Graphics2D g2, String text, Point position) { FontMetrics fm = g2.getFontMetrics(); int x2 = position.x - fm.stringWidth(text) / 2; int y2 = fm.getAscent() + (position.y - (fm.getAscent() + fm.getDescent()) / 2); g2.drawString(text, x2, y2); } } ================================================ FILE: src/juicebox/tools/utils/juicer/apa/APARegionStatistics.java ================================================ /* * The MIT License (MIT) * * Copyright (c) 2011-2020 Broad Institute, Aiden Lab, Rice University, Baylor College of Medicine * * Permission is hereby granted, free of charge, to any person obtaining a copy * of this software and associated documentation files (the "Software"), to deal * in the Software without restriction, including without limitation the rights * to use, copy, modify, merge, publish, distribute, sublicense, and/or sell * copies of the Software, and to permit persons to whom the Software is * furnished to do so, subject to the following conditions: * * The above copyright notice and this permission notice shall be included in * all copies or substantial portions of the Software. * * THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR * IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, * FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE * AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER * LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, * OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN * THE SOFTWARE. */ package juicebox.tools.utils.juicer.apa; import juicebox.tools.utils.common.MatrixTools; import org.apache.commons.math.linear.RealMatrix; import org.apache.commons.math.stat.descriptive.DescriptiveStatistics; /** * Created by muhammadsaadshamim on 5/4/15. */ public class APARegionStatistics { //public static int regionWidth = 6; //width of boxes //int totWidth = x.getColumnDimension(); //float widthp5 = width + .5f; //float half_width = width/2f; //private int mdpt, max; //private double centralVal; private final double peak2mean; private final double peak2UL; private final double avgUR; private final double peak2UR; private final double peak2LL; private final double peak2LR; private final double ZscoreLL; public APARegionStatistics(RealMatrix data, int regionWidth) { int max = data.getColumnDimension(); int midPoint = max / 2; double centralVal = data.getEntry(midPoint, midPoint); /** NOTE - indices are inclusive in java, but in python the second index is not inclusive */ double mean = (MatrixTools.sum(data.getData()) - centralVal) / (data.getRowDimension() * data.getColumnDimension() - 1); peak2mean = centralVal / mean; double avgUL = mean(data.getSubMatrix(0, regionWidth - 1, 0, regionWidth - 1).getData()); peak2UL = centralVal / avgUL; avgUR = mean(data.getSubMatrix(0, regionWidth - 1, max - regionWidth, max - 1).getData()); peak2UR = centralVal / avgUR; double avgLL = mean(data.getSubMatrix(max - regionWidth, max - 1, 0, regionWidth - 1).getData()); peak2LL = centralVal / avgLL; double avgLR = mean(data.getSubMatrix(max - regionWidth, max - 1, max - regionWidth, max - 1).getData()); peak2LR = centralVal / avgLR; DescriptiveStatistics yStats = statistics(data.getSubMatrix(max - regionWidth, max - 1, 0, regionWidth - 1).getData()); ZscoreLL = (centralVal - yStats.getMean()) / yStats.getStandardDeviation(); } public static DescriptiveStatistics statistics(double[][] x) { DescriptiveStatistics stats = new DescriptiveStatistics(); for (double[] row : x) for (double val : row) stats.addValue(val); return stats; } private static double mean(double[][] x) { return statistics(x).getMean(); } public double getPeak2mean() { return peak2mean; } public double getPeak2UL() { return peak2UL; } public double getPeak2UR() { return peak2UR; } public double getPeak2LL() { return peak2LL; } public double getPeak2LR() { return peak2LR; } public double getZscoreLL() { return ZscoreLL; } public double[] getRegionCornerValues() { return new double[]{peak2UL, peak2UR, peak2LL, peak2LR}; } public double getMeanUR() { return avgUR; } } ================================================ FILE: src/juicebox/tools/utils/juicer/apa/APAUtils.java ================================================ /* * The MIT License (MIT) * * Copyright (c) 2011-2020 Broad Institute, Aiden Lab, Rice University, Baylor College of Medicine * * Permission is hereby granted, free of charge, to any person obtaining a copy * of this software and associated documentation files (the "Software"), to deal * in the Software without restriction, including without limitation the rights * to use, copy, modify, merge, publish, distribute, sublicense, and/or sell * copies of the Software, and to permit persons to whom the Software is * furnished to do so, subject to the following conditions: * * The above copyright notice and this permission notice shall be included in * all copies or substantial portions of the Software. * * THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR * IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, * FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE * AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER * LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, * OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN * THE SOFTWARE. */ package juicebox.tools.utils.juicer.apa; import juicebox.data.HiCFileTools; import juicebox.data.MatrixZoomData; import juicebox.tools.utils.common.MatrixTools; import juicebox.tools.utils.common.StatPercentile; import juicebox.track.feature.Feature2D; import juicebox.windowui.NormalizationType; import org.apache.commons.math.linear.Array2DRowRealMatrix; import org.apache.commons.math.linear.RealMatrix; import java.io.*; import java.nio.charset.StandardCharsets; import java.util.ArrayList; import java.util.List; /** * Created by Muhammad Shamim on 1/21/15. */ public class APAUtils { /** * @param filename * @param matrix */ public static void saveMeasures(String filename, RealMatrix matrix, int currentRegionWidth) { Writer writer = null; APARegionStatistics apaStats = new APARegionStatistics(matrix, currentRegionWidth); try { writer = new BufferedWriter(new OutputStreamWriter(new FileOutputStream(filename), StandardCharsets.UTF_8)); writer.write("P2M" + '\t' + apaStats.getPeak2mean() + '\n'); writer.write("P2UL" + '\t' + apaStats.getPeak2UL() + '\n'); writer.write("P2UR" + '\t' + apaStats.getPeak2UR() + '\n'); writer.write("P2LL" + '\t' + apaStats.getPeak2LL() + '\n'); writer.write("P2LR" + '\t' + apaStats.getPeak2LR() + '\n'); writer.write("ZscoreLL" + '\t' + apaStats.getZscoreLL()); } catch (IOException ex) { ex.printStackTrace(); } finally { try { if (writer != null) writer.close(); } catch (Exception ex) { ex.printStackTrace(); } } } public static void saveListText(String filename, List array) { Writer writer = null; try { writer = new BufferedWriter(new OutputStreamWriter(new FileOutputStream(filename), StandardCharsets.UTF_8)); for (double val : array) { writer.write(val + " "); } writer.write("\n"); } catch (IOException ex) { ex.printStackTrace(); } finally { try { if (writer != null) writer.close(); } catch (Exception ex) { ex.printStackTrace(); } } } public static RealMatrix standardNormalization(RealMatrix matrix) { return matrix.copy().scalarMultiply(1. / Math.max(1., MatrixTools.mean(matrix))); } public static RealMatrix centerNormalization(RealMatrix matrix) { int center = matrix.getRowDimension() / 2; double centerVal = matrix.getEntry(center, center); if (centerVal == 0) { centerVal = MatrixTools.minimumPositive(matrix); if (centerVal == 0) centerVal = 1; } return matrix.copy().scalarMultiply(1. / centerVal); } public static double peakEnhancement(RealMatrix matrix) { int rows = matrix.getRowDimension(); int center = rows / 2; double centerVal = matrix.getEntry(center, center); double remainingSum = MatrixTools.sum(matrix.getData()) - centerVal; double remainingAverage = remainingSum / (rows * rows - 1); return centerVal / remainingAverage; } /** * @param data * @return */ public static RealMatrix rankPercentile(RealMatrix data) { int n = data.getColumnDimension(); StatPercentile percentile = new StatPercentile(MatrixTools.flattenedRowMajorOrderMatrix(data)); RealMatrix matrix = new Array2DRowRealMatrix(n, n); for (int r = 0; r < n; r++) { for (int c = 0; c < n; c++) { double currValue = data.getEntry(r, c); if (currValue == 0) { matrix.setEntry(r, c, 0); } else { matrix.setEntry(r, c, percentile.evaluate(currValue)); } //matrix.setEntry(r, c, percentile.evaluate()); } } return matrix; } /** * Size filtering of loops * * @param features * @param minPeakDist * @param maxPeakDist * @return */ public static ArrayList filterFeaturesBySize(List features, double minPeakDist, double maxPeakDist, int resolution) { ArrayList sizeFilteredFeatures = new ArrayList<>(); for (Feature2D feature : features) { double xMidPt = feature.getMidPt1(); double yMidPt = feature.getMidPt2(); int dist = (int) Math.round(Math.abs(xMidPt - yMidPt) / resolution); if (dist >= minPeakDist) { if (dist <= maxPeakDist) { sizeFilteredFeatures.add(feature); } } } return new ArrayList<>(sizeFilteredFeatures); } public static RealMatrix extractLocalizedData(MatrixZoomData zd, Feature2D loop, int L, int resolution, int window, NormalizationType norm) throws IOException { long loopX = loop.getMidPt1() / resolution; long loopY = loop.getMidPt2() / resolution; long binXStart = loopX - window; long binXEnd = loopX + (window + 1); long binYStart = loopY - window; long binYEnd = loopY + (window + 1); return HiCFileTools.extractLocalBoundedRegion(zd, binXStart, binXEnd, binYStart, binYEnd, L, L, norm, false); } public static RealMatrix extractLocalizedDataForAFA(MatrixZoomData zd, Feature2D loop, int resolution, int window, NormalizationType norm) throws IOException { long loopX = loop.getMidPt1() / resolution; long loopY = loop.getMidPt2() / resolution; long binXStart = loopY; long binXEnd = loopX + (window + 1); long binYStart = loopY - window; long binYEnd = loopX + 1; int L = (int) (binXStart - binXEnd); int dis = zd.getBinSize(); /*int loopX = loop.getMidPt1() / resolution; int loopY = loop.getMidPt2() / resolution; int binXStart = loopX - window; int binXEnd = loopY+1; int binYStart = loopX; int binYEnd = loopY + window; L = binXStart - binXEnd;*/ return HiCFileTools.extractLocalBoundedRegion(zd, binXStart, binXEnd, binYStart, binYEnd, L, L, norm, false); } public static RealMatrix linearInterpolation (RealMatrix original, int targetNumRows, int targetNumCols){ int r, c, i = 0, j = 0; //i is index of newRPos, j is index of newCPos int[] newRPos = new int [original.getRowDimension()]; int[] newCPos = new int [original.getColumnDimension()]; int rowFolds, colFolds, cSpan, rSpan; //cSpan is distance of 2 nearby original entries of the same row in resized matrix //rSpan is distance of 2 nearby original entries of the same column in resized matrix double value; //Resizing (magnifying) matrix using linear interpolation // initialize final matrix RealMatrix resizedMatrix = MatrixTools.cleanArray2DMatrix(targetNumRows, targetNumCols); //For every entries in the original matrix add it to the resized matrix rowFolds = targetNumRows / original.getRowDimension(); colFolds = targetNumCols / original.getColumnDimension(); for (r = 0; r < original.getRowDimension(); r++){ newRPos [r] = r*rowFolds; for (c = 0; c < original.getColumnDimension(); c++) { newCPos[c] = c * colFolds; resizedMatrix.addToEntry(newRPos[r], newCPos[c], original.getEntry(r, c)); } } cSpan = newCPos [1] - newCPos[0]; rSpan = newRPos [1] - newRPos[0]; //For every entry in the row that contains the entries from the original matrix, calculate and add its value using linear interpolation double currentOgEntry = 0; double nextOgEntry = 0; double fraction = 0; for (i = 0; i < newRPos.length; i ++){ r = newRPos[i]; for (c = 0; c < resizedMatrix.getColumnDimension(); c++) { if (c >= newCPos[newCPos.length - 1]) { resizedMatrix.addToEntry(r, c, resizedMatrix.getEntry(r, newCPos[newCPos.length - 1])); } else { currentOgEntry = resizedMatrix.getEntry(r, c - c%cSpan); nextOgEntry = resizedMatrix.getEntry(r, c + cSpan - c%cSpan); fraction = (((double)cSpan) - (double)(c%cSpan)) / (double)cSpan; value = currentOgEntry * fraction + nextOgEntry * (1.0 - fraction); resizedMatrix.addToEntry(r, c, value); } } } //For every other entry in the resized matrix, calculate its value using linear interpolation i = 0; j = 0; for (r = 0; r < resizedMatrix.getRowDimension(); r++){ if (r != newRPos[i] && r < newRPos[newRPos.length-1]) { for (c = 0; c < resizedMatrix.getColumnDimension(); c++) { currentOgEntry = resizedMatrix.getEntry(r - r%rSpan, c); nextOgEntry = resizedMatrix.getEntry(r + rSpan - r%rSpan, c); fraction = (double)(r%rSpan) / (double)rSpan; value = currentOgEntry * (1.0 - fraction) + nextOgEntry * fraction; resizedMatrix.addToEntry(r, c, value); } } else { for (c = 0; c < resizedMatrix.getColumnDimension(); c++) { resizedMatrix.addToEntry(r, c, resizedMatrix.getEntry(newRPos[newRPos.length-1], c)); } } } return resizedMatrix; } public static RealMatrix expandWithZeros (RealMatrix original, int targetNumRows, int targetNumCols){ int r, c; RealMatrix newMatrix = MatrixTools.cleanArray2DMatrix(targetNumRows, targetNumCols); for (r = 0; r < original.getRowDimension(); r++){ for (c = 0; c < original.getColumnDimension(); c++){ newMatrix.addToEntry(r, c, original.getEntry(r, c)); } } return newMatrix; } public static RealMatrix boxSampling (RealMatrix original, int targetNumRows, int targetNumCols){ //This method scale down a matrix using box sampling RealMatrix resizedMatrix = MatrixTools.cleanArray2DMatrix(targetNumRows, targetNumCols); int rowScale = original.getRowDimension() / resizedMatrix.getRowDimension(); int colScale = original.getColumnDimension() / resizedMatrix.getColumnDimension(); RealMatrix tile = MatrixTools.cleanArray2DMatrix(rowScale, colScale); int r, c, i, j; double value; for (r = 0; r < resizedMatrix.getRowDimension(); r += rowScale) { for (c = 0; c < resizedMatrix.getColumnDimension(); c += colScale){ //add values to entries in tile matrix for (i = 0; i < rowScale; i ++){ for (j = 0; j < colScale; j++){ tile.addToEntry(i, j, original.getEntry(r+i, c+j)); } } value = maxInMatrix(tile); resizedMatrix.addToEntry(r/rowScale, c/colScale, value); } } return resizedMatrix; } public static double maxInMatrix (RealMatrix matrix){ double result = matrix.getEntry(0,0); int r, c; double entry; for (r = 0; r < matrix.getRowDimension(); r++){ for (c = 0; c < matrix.getColumnDimension(); c++){ entry = matrix.getEntry(r, c); if (result < entry) result = entry; } } return result; } static int lcm (int a, int b){ return (a*b)/gcd (a, b); } static int gcd (int a, int b){ if (a == 0 || b == 0) return 0; if (a == b) return a; if (a > b) return gcd (a-b, b); return gcd (b-a, a); } public static RealMatrix matrixScaling (RealMatrix original, int targetNumRows, int targetNumCols){ int intermediateRowDimention = lcm (original.getRowDimension(), targetNumRows); int intermediateColDimention = lcm (original.getColumnDimension(), targetNumCols); RealMatrix intermediateMatrix = linearInterpolation(original, intermediateRowDimention, intermediateColDimention); // scale the intermediate down with box sampling RealMatrix resizedMatrix = boxSampling(intermediateMatrix, targetNumRows, targetNumCols); return resizedMatrix; } } ================================================ FILE: src/juicebox/tools/utils/juicer/arrowhead/ArrowheadScore.java ================================================ /* * The MIT License (MIT) * * Copyright (c) 2011-2020 Broad Institute, Aiden Lab, Rice University, Baylor College of Medicine * * Permission is hereby granted, free of charge, to any person obtaining a copy * of this software and associated documentation files (the "Software"), to deal * in the Software without restriction, including without limitation the rights * to use, copy, modify, merge, publish, distribute, sublicense, and/or sell * copies of the Software, and to permit persons to whom the Software is * furnished to do so, subject to the following conditions: * * The above copyright notice and this permission notice shall be included in * all copies or substantial portions of the Software. * * THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR * IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, * FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE * AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER * LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, * OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN * THE SOFTWARE. */ package juicebox.tools.utils.juicer.arrowhead; import juicebox.track.feature.Feature2D; import java.awt.*; import java.util.Arrays; import java.util.HashMap; import java.util.Map; /** * Container class for Arrowhead blocks */ public class ArrowheadScore { final long[] indices = new long[4]; double score = Double.NaN; boolean isActive = false; public ArrowheadScore(long[] indices) { System.arraycopy(indices, 0, this.indices, 0, 4); } /** * use for deep copying * * @param arrowheadScore */ public ArrowheadScore(ArrowheadScore arrowheadScore) { System.arraycopy(arrowheadScore.indices, 0, this.indices, 0, 4); this.score = arrowheadScore.score; this.isActive = arrowheadScore.isActive; } public void updateScore(double score) { if (Double.isNaN(this.score)) this.score = score; else if (!Double.isNaN(score)) this.score = Math.max(score, this.score); } /** * @param limStart * @param limEnd * @param resolution * @return true if block is fully contained within given bounds */ public boolean isWithin(int limStart, int limEnd, int resolution) { boolean containedInBounds = true; for (long index : indices) { long scaledIndex = index / resolution; containedInBounds = containedInBounds && scaledIndex >= limStart && scaledIndex <= limEnd; } return containedInBounds; } public boolean equivalentTo(ArrowheadScore mScore) { return Arrays.equals(indices, mScore.indices); } public Feature2D toFeature2D(String chrName) { Map attributes = new HashMap<>(); attributes.put("score", Double.toString(score)); return new Feature2D(Feature2D.FeatureType.DOMAIN, chrName, indices[0], indices[1], chrName, indices[2], indices[3], Color.yellow, attributes); } } ================================================ FILE: src/juicebox/tools/utils/juicer/arrowhead/ArrowheadScoreList.java ================================================ /* * The MIT License (MIT) * * Copyright (c) 2011-2020 Broad Institute, Aiden Lab, Rice University, Baylor College of Medicine * * Permission is hereby granted, free of charge, to any person obtaining a copy * of this software and associated documentation files (the "Software"), to deal * in the Software without restriction, including without limitation the rights * to use, copy, modify, merge, publish, distribute, sublicense, and/or sell * copies of the Software, and to permit persons to whom the Software is * furnished to do so, subject to the following conditions: * * The above copyright notice and this permission notice shall be included in * all copies or substantial portions of the Software. * * THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR * IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, * FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE * AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER * LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, * OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN * THE SOFTWARE. */ package juicebox.tools.utils.juicer.arrowhead; import juicebox.data.basics.Chromosome; import juicebox.tools.utils.common.MatrixTools; import juicebox.track.feature.Feature2D; import juicebox.track.feature.Feature2DList; import org.apache.commons.math.linear.RealMatrix; import java.util.ArrayList; import java.util.List; /** * Created by muhammadsaadshamim on 7/20/15. */ public class ArrowheadScoreList { private int resolution = -1; private List arrowheadScores = new ArrayList<>(); public ArrowheadScoreList(int resolution) { this.resolution = resolution; } public ArrowheadScoreList(Feature2DList features, Chromosome chr, int resolution) { this.resolution = resolution; if (features.getNumTotalFeatures() > 0) { for (Feature2D feature : features.get(chr.getIndex(), chr.getIndex())) { arrowheadScores.add(feature.toArrowheadScore()); } } } public ArrowheadScoreList deepCopy() { ArrowheadScoreList copy = new ArrowheadScoreList(resolution); for (ArrowheadScore data : arrowheadScores) { copy.arrowheadScores.add(new ArrowheadScore(data)); } return copy; } public ArrowheadScoreList updateActiveIndexScores(RealMatrix blockScore, int limStart, int limEnd) { setActiveListElements(limStart, limEnd); ArrowheadScoreList scoredList = new ArrowheadScoreList(resolution); for (ArrowheadScore score : arrowheadScores) { if (score.isActive) { int[] transformedIndices = scaleAndTranslateIndices(score.indices, resolution, limStart); score.updateScore(MatrixTools.calculateMax(MatrixTools.getSubMatrix(blockScore, transformedIndices))); scoredList.arrowheadScores.add(new ArrowheadScore(score)); } } return scoredList; } private int[] scaleAndTranslateIndices(long[] indices, int resolution, int limStart) { int[] transformedIndices = new int[indices.length]; for (int i = 0; i < indices.length; i++) { // casting should be ok for Arrowhead transformedIndices[i] = (int) (indices[i] / resolution - limStart); } return transformedIndices; } private void setActiveListElements(int limStart, int limEnd) { for (ArrowheadScore score : arrowheadScores) { score.isActive = false; } for (ArrowheadScore score : arrowheadScores) { if (score.isWithin(limStart, limEnd, resolution)) { score.isActive = true; } } } public void addAll(ArrowheadScoreList arrowheadScoreList) { arrowheadScores.addAll(arrowheadScoreList.arrowheadScores); } public void mergeScores() { List mergedScores = new ArrayList<>(); for (ArrowheadScore aScore : arrowheadScores) { boolean valueNotFound = true; for (ArrowheadScore mScore : mergedScores) { if (aScore.equivalentTo(mScore)) { mScore.updateScore(aScore.score); valueNotFound = false; break; } } if (valueNotFound) { mergedScores.add(aScore); } } arrowheadScores = mergedScores; } public Feature2DList toFeature2DList(int chrIndex, String chrName) { Feature2DList feature2DList = new Feature2DList(); for (ArrowheadScore score : arrowheadScores) { feature2DList.add(chrIndex, chrIndex, score.toFeature2D(chrName)); } return feature2DList; } } ================================================ FILE: src/juicebox/tools/utils/juicer/arrowhead/BinnedScore.java ================================================ /* * The MIT License (MIT) * * Copyright (c) 2011-2020 Broad Institute, Aiden Lab, Rice University, Baylor College of Medicine * * Permission is hereby granted, free of charge, to any person obtaining a copy * of this software and associated documentation files (the "Software"), to deal * in the Software without restriction, including without limitation the rights * to use, copy, modify, merge, publish, distribute, sublicense, and/or sell * copies of the Software, and to permit persons to whom the Software is * furnished to do so, subject to the following conditions: * * The above copyright notice and this permission notice shall be included in * all copies or substantial portions of the Software. * * THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR * IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, * FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE * AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER * LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, * OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN * THE SOFTWARE. */ package juicebox.tools.utils.juicer.arrowhead; import com.google.common.primitives.Doubles; import juicebox.tools.utils.common.ArrayTools; import java.util.ArrayList; import java.util.List; /** * Bin scores based on the connected components found in arrowhead */ class BinnedScore { private final List scores = new ArrayList<>(); private final List uVarScores = new ArrayList<>(); private final List lVarScores = new ArrayList<>(); private final List upSigns = new ArrayList<>(); private final List loSigns = new ArrayList<>(); private int minX; private int maxX; private int minY; private int maxY; public BinnedScore(HighScore score) { minX = score.getI(); maxX = score.getI(); minY = score.getJ(); maxY = score.getJ(); appendDataValues(score); } public static List convertBinnedScoresToHighScores(List binnedScores) { List highScores = new ArrayList<>(); for (BinnedScore score : binnedScores) { highScores.add(score.convertToHighScore()); } return highScores; } /** * @return true if given data point is spatially proximate to this data bin */ public boolean isNear(HighScore score, int distanceThreshold) { return (Math.abs(minX - score.getI()) < distanceThreshold || Math.abs(maxX - score.getI()) < distanceThreshold) && (Math.abs(minY - score.getJ()) < distanceThreshold || Math.abs(maxY - score.getJ()) < distanceThreshold); } /** * Add given data point to this bin and update region bounds and scores/signs */ public void addScoreToBin(HighScore score) { if (score.getI() < minX) minX = score.getI(); else if (score.getI() > maxX) maxX = score.getI(); if (score.getJ() < minY) minY = score.getJ(); else if (score.getJ() > maxY) maxY = score.getJ(); appendDataValues(score); } /** * Add given data point's scores/signs to cumulative list */ private void appendDataValues(HighScore score) { scores.add(score.getScore()); uVarScores.add(score.getuVarScore()); lVarScores.add(score.getlVarScore()); upSigns.add(score.getUpSign()); loSigns.add(score.getLoSign()); } /** * @return statistical summary of data points in this bin */ private HighScore convertToHighScore() { return new HighScore(maxX, maxY, ArrayTools.mean(Doubles.toArray(scores)), ArrayTools.mean(Doubles.toArray(uVarScores)), ArrayTools.mean(Doubles.toArray(lVarScores)), ArrayTools.mean(Doubles.toArray(upSigns)), ArrayTools.mean(Doubles.toArray(loSigns))); } } ================================================ FILE: src/juicebox/tools/utils/juicer/arrowhead/BlockBuster.java ================================================ /* * The MIT License (MIT) * * Copyright (c) 2011-2020 Broad Institute, Aiden Lab, Rice University, Baylor College of Medicine * * Permission is hereby granted, free of charge, to any person obtaining a copy * of this software and associated documentation files (the "Software"), to deal * in the Software without restriction, including without limitation the rights * to use, copy, modify, merge, publish, distribute, sublicense, and/or sell * copies of the Software, and to permit persons to whom the Software is * furnished to do so, subject to the following conditions: * * The above copyright notice and this permission notice shall be included in * all copies or substantial portions of the Software. * * THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR * IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, * FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE * AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER * LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, * OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN * THE SOFTWARE. */ package juicebox.tools.utils.juicer.arrowhead; import juicebox.HiCGlobals; import juicebox.data.HiCFileTools; import juicebox.data.MatrixZoomData; import juicebox.data.basics.Chromosome; import juicebox.tools.utils.common.MatrixTools; import juicebox.track.feature.Feature2DList; import juicebox.track.feature.Feature2DParser; import juicebox.windowui.NormalizationType; import org.apache.commons.math.linear.RealMatrix; import java.io.IOException; import java.util.*; /** * Created by muhammadsaadshamim on 6/3/15. */ public class BlockBuster { public static double varThreshold = 0.2; public static double highSignThreshold = 0.5; public static double maxLowSignThreshold = 0.4; public static double minLowSignThreshold = 0; public static double decrementLowSignThreshold = 0.1; public static int minBlockSize = 60; /** * Actual Arrowhead algorithm - should be called separately for each chromosome * * @return contact domain list and scores for given list/control */ public static void run(Chromosome chrom, int resolution, int matrixWidth, MatrixZoomData zd, NormalizationType norm, ArrowheadScoreList list, ArrowheadScoreList control, Feature2DList contactDomainsGenomeWide, Feature2DList contactDomainListScoresGenomeWide, Feature2DList contactDomainControlScoresGenomeWide) { int chrIndex = chrom.getIndex(); String chrName = chrom.getName(); long chrLength = chrom.getLength(); // used for sliding window across diagonal int increment = matrixWidth / 2; int maxDataLengthAtResolution = (int) Math.ceil(((double) chrLength) / resolution); try { // get large number of blocks (lower confidence) CumulativeBlockResults results = null; for (double signThreshold = maxLowSignThreshold; signThreshold >= minLowSignThreshold; signThreshold -= decrementLowSignThreshold) { results = callSubBlockbuster(zd, maxDataLengthAtResolution, Double.NaN, signThreshold, matrixWidth, increment, list, control, norm, resolution); if (results.getCumulativeResults().size() > 0) { break; } } // high variance threshold, fewer blocks, high confidence CumulativeBlockResults highConfidenceResults = callSubBlockbuster(zd, maxDataLengthAtResolution, varThreshold, highSignThreshold, matrixWidth, increment, new ArrowheadScoreList(resolution), new ArrowheadScoreList(resolution), norm, resolution); List uniqueBlocks = orderedSetDifference(results.getCumulativeResults(), highConfidenceResults.getCumulativeResults()); // remove the blocks that are small List filteredUniqueBlocks = filterBlocksBySize(uniqueBlocks, minBlockSize); appendNonConflictingBlocks(highConfidenceResults.getCumulativeResults(), filteredUniqueBlocks); // merge the high/low confidence results results.setCumulativeResults(highConfidenceResults.getCumulativeResults()); results.mergeScores(); // prior to this point, everything should be in terms of i,j indices in a binned matrix results.scaleIndicesByResolution(resolution); // if any contact domains are found if (results.getCumulativeResults().size() > 0) { if (HiCGlobals.printVerboseComments) { System.out.println("Initial # of contact domains: " + results.getCumulativeResults().size()); } // merge/bin domains in very close proximity List binnedScores = binScoresByDistance(results.getCumulativeResults(), 5 * resolution); binnedScores = binScoresByDistance(binnedScores, 10 * resolution); binnedScores.sort(Collections.reverseOrder()); // convert to Feature2DList format Feature2DList blockResults = Feature2DParser.parseHighScoreList(chrIndex, chrName, resolution, binnedScores); Feature2DList blockResultListScores = Feature2DParser.parseArrowheadScoreList(chrIndex, chrName, results.getCumulativeInternalList()); Feature2DList blockResultControlScores = Feature2DParser.parseArrowheadScoreList(chrIndex, chrName, results.getCumulativeInternalControl()); // add results to genome-wide accumulator contactDomainsGenomeWide.add(blockResults); contactDomainListScoresGenomeWide.add(blockResultListScores); contactDomainControlScoresGenomeWide.add(blockResultControlScores); } else { if (HiCGlobals.printVerboseComments) { System.out.println("No contact domains found for chromosome " + chrName); } } } catch (IOException e) { System.err.println("Data not available for this chromosome."); } } /** * Runs blockbuster for a sliding window along the diagonal of the matrix * * @param zd - zoomData from hic file * @param chrLength * @param varThreshold * @param signThreshold * @param matrixWidth * @param increment * @param list * @param control * @return contact domain results for given thresholds and parameters */ private static CumulativeBlockResults callSubBlockbuster(MatrixZoomData zd, int chrLength, double varThreshold, double signThreshold, int matrixWidth, int increment, ArrowheadScoreList list, ArrowheadScoreList control, NormalizationType norm, int resolution) throws IOException { // container for results CumulativeBlockResults cumulativeBlockResults = new CumulativeBlockResults(resolution); if (HiCGlobals.printVerboseComments) { System.out.println("Loading incr " + increment + " chrLength " + chrLength); } // slide across chromosome diagonal for (int limStart = 0; limStart < chrLength; limStart += increment) { // appropriate boundaries of window int adjustedLimStart = limStart; int limEnd = Math.min(limStart + matrixWidth, chrLength); if (limEnd == chrLength) { if (chrLength > increment) { adjustedLimStart = limEnd - matrixWidth; } } if (HiCGlobals.printVerboseComments) { System.out.println("Reading " + limStart + ":" + limEnd); } // get data for window from hic file int n = limEnd - adjustedLimStart + 1; RealMatrix observed = HiCFileTools.extractLocalBoundedRegion(zd, limStart, limEnd, n, norm, false); observed = MatrixTools.fillLowerLeftTriangle(observed); // get contact domains in window BlockResults results = new BlockResults(observed, varThreshold, signThreshold, list, control, adjustedLimStart, limEnd); if (HiCGlobals.printVerboseComments) { System.out.println("Found " + results.getResults().size() + " blocks"); } // accumulate results across the windows results.offsetResultsIndex(limStart); // +1? because genome index should start at 1 not 0? cumulativeBlockResults.add(results); if (HiCGlobals.printVerboseComments) { System.out.print("."); } } if (HiCGlobals.printVerboseComments) { System.out.println("."); } return cumulativeBlockResults; } /** * @param scores * @param dist * @return list of scores binned within distance */ private static List binScoresByDistance(List scores, int dist) { List binnedScores = new ArrayList<>(); for (HighScore score : scores) { boolean scoreNotBinned = true; for (BinnedScore binnedScore : binnedScores) { if (binnedScore.isNear(score, dist)) { binnedScore.addScoreToBin(score); scoreNotBinned = false; break; } } if (scoreNotBinned) { binnedScores.add(new BinnedScore(score)); } } return BinnedScore.convertBinnedScoresToHighScores(binnedScores); } /** * Check possibleAdditions for domains which do not overlap with the mainList * and append them * * @param mainList * @param possibleAdditions */ private static void appendNonConflictingBlocks(List mainList, List possibleAdditions) { Map blockEdges = new HashMap<>(); for (HighScore score : mainList) { blockEdges.put(score.getI(), score); blockEdges.put(score.getJ(), score); } for (HighScore score : possibleAdditions) { boolean doesNotConflict = true; for (int k = score.getI(); k <= score.getJ(); k++) { if (blockEdges.containsKey(k)) { doesNotConflict = false; break; } } if (doesNotConflict) { mainList.add(score); blockEdges.put(score.getI(), score); blockEdges.put(score.getJ(), score); } } } /** * @param blockList * @param minWidth * @return blockList with small blocks (i.e. < minWidth) removed */ private static List filterBlocksBySize(List blockList, int minWidth) { List filteredList = new ArrayList<>(); for (HighScore score : blockList) { if (score.getWidth() > minWidth) { filteredList.add(score); } } return filteredList; } /** * Set difference - returns the high scores in longerList that are not in shorterList. * * @param listA * @param listB * @return set difference */ private static List orderedSetDifference(List listA, List listB) { // remove duplicates Set setA = new HashSet<>(listA); Set setB = new HashSet<>(listB); List diffSet = new ArrayList<>(); for (HighScore score : setA) { if (!setB.contains(score)) { diffSet.add(score); } } return diffSet; } } ================================================ FILE: src/juicebox/tools/utils/juicer/arrowhead/BlockResults.java ================================================ /* * The MIT License (MIT) * * Copyright (c) 2011-2020 Broad Institute, Aiden Lab, Rice University, Baylor College of Medicine * * Permission is hereby granted, free of charge, to any person obtaining a copy * of this software and associated documentation files (the "Software"), to deal * in the Software without restriction, including without limitation the rights * to use, copy, modify, merge, publish, distribute, sublicense, and/or sell * copies of the Software, and to permit persons to whom the Software is * furnished to do so, subject to the following conditions: * * The above copyright notice and this permission notice shall be included in * all copies or substantial portions of the Software. * * THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR * IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, * FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE * AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER * LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, * OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN * THE SOFTWARE. */ package juicebox.tools.utils.juicer.arrowhead; import com.google.common.collect.Lists; import com.google.common.primitives.Doubles; import juicebox.tools.utils.common.MatrixTools; import org.apache.commons.math.linear.RealMatrix; import java.awt.*; import java.util.ArrayList; import java.util.Arrays; import java.util.List; import java.util.Set; /** * Created by muhammadsaadshamim on 6/5/15. */ class BlockResults { private final ArrowheadScoreList internalList; private final ArrowheadScoreList internalControl; private List results = new ArrayList<>(); public BlockResults(RealMatrix observed, double varThreshold, double signThreshold, ArrowheadScoreList list, ArrowheadScoreList control, int limStart, int limEnd) { int n = Math.min(observed.getRowDimension(), observed.getColumnDimension()); int gap = 7; RealMatrix dUpstream = calculateDirectionalityIndexUpstream(observed, n, gap); MatrixTriangles triangles = new MatrixTriangles(dUpstream); triangles.generateBlockScoreCalculations(); internalList = triangles.updateScoresUsingList(list, limStart, limEnd); internalControl = triangles.updateScoresUsingList(control, limStart, limEnd); triangles.thresholdScoreValues(varThreshold, signThreshold); List> connectedComponents = triangles.extractConnectedComponents(); //System.out.println("CC "+connectedComponents.size()); results = triangles.calculateResults(connectedComponents); // TODO plotArrowheadFigures(); } /** * calculate D upstream, directionality index upstream * * @param observed * @param n * @param gap * @return dUpstream */ private RealMatrix calculateDirectionalityIndexUpstream(RealMatrix observed, int n, int gap) { RealMatrix dUpstream = MatrixTools.cleanArray2DMatrix(n); for (int i = 0; i < n; i++) { // choose smaller window of two: from 0 to (i-gap) or from (i+gap) to n int window = Math.min(n - (i + gap), i - gap); window = Math.min(window, n); if (window >= gap) { double[] row = observed.getRow(i); // in MATLAB second index inclusive, but for java need +1 double[] A = Doubles.toArray(Lists.reverse(Doubles.asList(Arrays.copyOfRange(row, i - window, i - gap + 1)))); double[] B = Arrays.copyOfRange(row, i + gap, i + window + 1); double[] preference = new double[A.length]; for (int j = 0; j < A.length; j++) { preference[j] = (A[j] - B[j]) / (A[j] + B[j]); } int index = 0; for (int j = i + gap; j < i + window + 1; j++) { dUpstream.setEntry(i, j, preference[index]); index++; } } } return dUpstream; } /** * @return block results */ public List getResults() { return results; } public ArrowheadScoreList getInternalList() { return internalList; } public ArrowheadScoreList getInternalControl() { return internalControl; } public void offsetResultsIndex(int offset) { for (HighScore score : results) { score.offsetIndex(offset); } } } ================================================ FILE: src/juicebox/tools/utils/juicer/arrowhead/CumulativeBlockResults.java ================================================ /* * The MIT License (MIT) * * Copyright (c) 2011-2020 Broad Institute, Aiden Lab, Rice University, Baylor College of Medicine * * Permission is hereby granted, free of charge, to any person obtaining a copy * of this software and associated documentation files (the "Software"), to deal * in the Software without restriction, including without limitation the rights * to use, copy, modify, merge, publish, distribute, sublicense, and/or sell * copies of the Software, and to permit persons to whom the Software is * furnished to do so, subject to the following conditions: * * The above copyright notice and this permission notice shall be included in * all copies or substantial portions of the Software. * * THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR * IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, * FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE * AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER * LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, * OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN * THE SOFTWARE. */ package juicebox.tools.utils.juicer.arrowhead; import java.util.ArrayList; import java.util.List; /** * Created by muhammadsaadshamim on 7/22/15. */ class CumulativeBlockResults { private final ArrowheadScoreList cumulativeInternalList; private final ArrowheadScoreList cumulativeInternalControl; private List cumulativeResults = new ArrayList<>(); public CumulativeBlockResults(int resolution) { cumulativeInternalList = new ArrowheadScoreList(resolution); cumulativeInternalControl = new ArrowheadScoreList(resolution); } public void add(BlockResults blockResults) { cumulativeResults.addAll(blockResults.getResults()); cumulativeInternalControl.addAll(blockResults.getInternalControl()); cumulativeInternalList.addAll(blockResults.getInternalList()); } public ArrowheadScoreList getCumulativeInternalControl() { return cumulativeInternalControl; } public List getCumulativeResults() { return cumulativeResults; } public void setCumulativeResults(List cumulativeResults) { this.cumulativeResults = new ArrayList<>(cumulativeResults); } public ArrowheadScoreList getCumulativeInternalList() { return cumulativeInternalList; } public void mergeScores() { cumulativeInternalControl.mergeScores(); cumulativeInternalList.mergeScores(); } public void scaleIndicesByResolution(int resolution) { for (HighScore hs : cumulativeResults) { hs.scaleIndicesByResolution(resolution); } } } ================================================ FILE: src/juicebox/tools/utils/juicer/arrowhead/DynamicProgrammingUtils.java ================================================ /* * The MIT License (MIT) * * Copyright (c) 2011-2020 Broad Institute, Aiden Lab, Rice University, Baylor College of Medicine * * Permission is hereby granted, free of charge, to any person obtaining a copy * of this software and associated documentation files (the "Software"), to deal * in the Software without restriction, including without limitation the rights * to use, copy, modify, merge, publish, distribute, sublicense, and/or sell * copies of the Software, and to permit persons to whom the Software is * furnished to do so, subject to the following conditions: * * The above copyright notice and this permission notice shall be included in * all copies or substantial portions of the Software. * * THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR * IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, * FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE * AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER * LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, * OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN * THE SOFTWARE. */ package juicebox.tools.utils.juicer.arrowhead; import juicebox.tools.utils.common.MatrixTools; import org.apache.commons.math.linear.RealMatrix; /** * Created by muhammadsaadshamim on 6/3/15. */ class DynamicProgrammingUtils { /** * Calculate cumulative sums across upper right matrix * iterative result is entry to left + entry below + orig value - diagonal down (else we double count) * * @param matrix * @param superDiagonal * @return */ public static RealMatrix sum(RealMatrix matrix, int superDiagonal) { int n = Math.min(matrix.getRowDimension(), matrix.getColumnDimension()); RealMatrix diagMatrix = MatrixTools.cleanArray2DMatrix(matrix.getRowDimension(), matrix.getColumnDimension()); if (superDiagonal <= 0) { diagMatrix = MatrixTools.extractDiagonal(matrix); superDiagonal = 1; } // d = distance from diagonal for (int d = superDiagonal; d < n; d++) { // i = row, column is i +d; for (int i = 0; i < n - d; i++) { diagMatrix.setEntry(i, i + d, diagMatrix.getEntry(i, i + d - 1) + diagMatrix.getEntry(i + 1, i + d) + matrix.getEntry(i, i + d) - diagMatrix.getEntry(i + 1, i + d - 1)); } } return diagMatrix; } /** * Dynamic programming to calculate "right" matrix * Initialize by setting the diagonal to the diagonal of original * Iterate to the right and up. * * @param matrix * @param maxSize * @return rightMatrix */ public static RealMatrix right(RealMatrix matrix, int maxSize) { RealMatrix rightMatrix = MatrixTools.extractDiagonal(matrix); int n = rightMatrix.getRowDimension(); // j is column, i is row for (int j = 1; j < n; j++) { int endPoint = Math.max(j - 1 - maxSize, 0); for (int i = j - 1; i >= endPoint; i--) { rightMatrix.setEntry(i, j, matrix.getEntry(i, j) + rightMatrix.getEntry(i + 1, j)); } } return rightMatrix; } /** * Dynamic programming to calculate "upper" matrix * Initialize by setting the diagonal to the diagonal of original * Iterate down (for each row) and to the left. * * @param matrix * @param maxSize * @return upperMatrix */ public static RealMatrix upper(RealMatrix matrix, int maxSize) { RealMatrix upperMatrix = MatrixTools.extractDiagonal(matrix); int n = upperMatrix.getRowDimension(); // j is column, i is row for (int i = 0; i < n; i++) { int endPoint = Math.min(i + 1 + maxSize, n - 1); for (int j = i + 1; j <= endPoint; j++) { upperMatrix.setEntry(i, j, matrix.getEntry(i, j) + upperMatrix.getEntry(i, j - 1)); } } return upperMatrix; } } ================================================ FILE: src/juicebox/tools/utils/juicer/arrowhead/HighScore.java ================================================ /* * The MIT License (MIT) * * Copyright (c) 2011-2020 Broad Institute, Aiden Lab, Rice University, Baylor College of Medicine * * Permission is hereby granted, free of charge, to any person obtaining a copy * of this software and associated documentation files (the "Software"), to deal * in the Software without restriction, including without limitation the rights * to use, copy, modify, merge, publish, distribute, sublicense, and/or sell * copies of the Software, and to permit persons to whom the Software is * furnished to do so, subject to the following conditions: * * The above copyright notice and this permission notice shall be included in * all copies or substantial portions of the Software. * * THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR * IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, * FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE * AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER * LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, * OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN * THE SOFTWARE. */ package juicebox.tools.utils.juicer.arrowhead; import juicebox.track.feature.Feature2D; import java.awt.*; import java.util.HashMap; import java.util.Map; import java.util.Objects; /** * Wrapper for arrowhead blockbuster results * Created by muhammadsaadshamim on 6/8/15. */ public class HighScore implements Comparable { private final double score; private final double uVarScore; private final double lVarScore; private final double upSign; private final double loSign; private int i; private int j; public HighScore(int i, int j, double score, double uVarScore, double lVarScore, double upSign, double loSign) { this.i = i; this.j = j; this.score = score; this.uVarScore = uVarScore; this.lVarScore = lVarScore; this.upSign = upSign; this.loSign = loSign; } public String toString() { return "" + i + "\t" + j + "\t" + score + "\t" + uVarScore + "\t" + lVarScore + "\t" + upSign + "\t" + loSign; } public void offsetIndex(int offset) { this.i += offset; this.j += offset; } public void scaleIndicesByResolution(int resolution) { i *= resolution; j *= resolution; } public int getWidth() { return Math.abs(j - i); } public int getI() { return i; } public int getJ() { return j; } public double getLoSign() { return loSign; } public double getScore() { return score; } public double getuVarScore() { return uVarScore; } public double getlVarScore() { return lVarScore; } public double getUpSign() { return upSign; } @Override public boolean equals(Object object) { if (this == object) return true; if (object == null) return false; if (getClass() != object.getClass()) return false; final HighScore o = (HighScore) object; return i == o.getI() && j == o.getJ() && score == o.getScore() && uVarScore == o.getuVarScore() && lVarScore == o.getlVarScore() && upSign == o.getUpSign() && loSign == o.getLoSign(); } @Override public int hashCode() { return Objects.hash(i, j, score, uVarScore, lVarScore, upSign, loSign); } @Override public int compareTo(HighScore o) { return Double.compare(this.sortValue(), o.sortValue()); } private double sortValue() { return uVarScore + lVarScore; } public Feature2D toFeature2D(String chrName, int res) { Map attributes = new HashMap<>(); attributes.put("score", Double.toString(score)); attributes.put("uVarScore", Double.toString(uVarScore)); attributes.put("lVarScore", Double.toString(lVarScore)); attributes.put("upSign", Double.toString(upSign)); attributes.put("loSign", Double.toString(loSign)); return new Feature2D(Feature2D.FeatureType.DOMAIN, chrName, i, j, chrName, i, j, Color.yellow, attributes); } } ================================================ FILE: src/juicebox/tools/utils/juicer/arrowhead/MatrixTriangles.java ================================================ /* * The MIT License (MIT) * * Copyright (c) 2011-2020 Broad Institute, Aiden Lab, Rice University, Baylor College of Medicine * * Permission is hereby granted, free of charge, to any person obtaining a copy * of this software and associated documentation files (the "Software"), to deal * in the Software without restriction, including without limitation the rights * to use, copy, modify, merge, publish, distribute, sublicense, and/or sell * copies of the Software, and to permit persons to whom the Software is * furnished to do so, subject to the following conditions: * * The above copyright notice and this permission notice shall be included in * all copies or substantial portions of the Software. * * THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR * IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, * FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE * AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER * LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, * OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN * THE SOFTWARE. */ package juicebox.tools.utils.juicer.arrowhead; import juicebox.tools.utils.common.MatrixTools; import juicebox.tools.utils.juicer.arrowhead.connectedcomponents.BinaryConnectedComponents; import org.apache.commons.math.linear.RealMatrix; import java.awt.*; import java.util.ArrayList; import java.util.List; import java.util.Set; /** * Created by muhammadsaadshamim on 6/5/15. */ class MatrixTriangles { private boolean initialMatricesNotGenerated = true; private boolean blockScoresNotCalculated = true; private boolean blockScoresNotThresholded = true; private RealMatrix up; private RealMatrix upSign; private RealMatrix upSquared; private RealMatrix lo; private RealMatrix loSign; private RealMatrix loSquared; private RealMatrix upVar; private RealMatrix loVar; private RealMatrix blockScore; /** * calculate Bnew, the block score matrix. it's a combination of 3 matrices * * @param matrix */ public MatrixTriangles(RealMatrix matrix) { int n = Math.min(matrix.getRowDimension(), matrix.getColumnDimension()); up = MatrixTools.cleanArray2DMatrix(n); upSign = MatrixTools.cleanArray2DMatrix(n); upSquared = MatrixTools.cleanArray2DMatrix(n); lo = MatrixTools.cleanArray2DMatrix(n); loSign = MatrixTools.cleanArray2DMatrix(n); loSquared = MatrixTools.cleanArray2DMatrix(n); MatrixTools.setNaNs(matrix, 0); //int window= matrix.getRowDimension(); // TODO What? -> "not using this because it messed things up" RealMatrix matrixElementwiseSquared = MatrixTools.elementBasedMultiplication(matrix, matrix); RealMatrix signMatrix = MatrixTools.sign(matrix); RealMatrix onesMatrix = MatrixTools.ones(n); //System.out.println("msign "+ matrix.getNorm()); //System.out.println("sign " + signMatrix.getNorm()); // Matrices used as dynamic programming lookups. // "R" matrices are sums of the columns up to that point: R(1,5) is sum of // column 5 from diagonal (row 5) up to row 1 // "U" matrices are sums of the rows up to the point: U(1,5) is sum of row 5 // from diagonal (col 1) up to col 5 // We want mean, mean of sign, and variance, so we are doing the sum then // dividing by counts RealMatrix rSum = DynamicProgrammingUtils.right(matrix, n); RealMatrix rSign = DynamicProgrammingUtils.right(signMatrix, n); RealMatrix rSquared = DynamicProgrammingUtils.right(matrixElementwiseSquared, n); RealMatrix rCount = DynamicProgrammingUtils.right(onesMatrix, n); RealMatrix uSum = DynamicProgrammingUtils.upper(matrix, n); RealMatrix uSign = DynamicProgrammingUtils.upper(signMatrix, n); RealMatrix uSquared = DynamicProgrammingUtils.upper(matrixElementwiseSquared, n); RealMatrix uCount = DynamicProgrammingUtils.upper(onesMatrix, n); RealMatrix upCount = MatrixTools.cleanArray2DMatrix(n); RealMatrix loCount = MatrixTools.cleanArray2DMatrix(n); // Upper triangle for (int i = 0; i < n; i++) { for (int j = i + 1; j < n; j++) { int bottom = (int) Math.floor((j - i + 1) / 2); // add half of column up.setEntry(i, j, up.getEntry(i, j - 1) + rSum.getEntry(i, j) - rSum.getEntry(i + bottom, j)); upSign.setEntry(i, j, upSign.getEntry(i, j - 1) + rSign.getEntry(i, j) - rSign.getEntry(i + bottom, j)); upSquared.setEntry(i, j, upSquared.getEntry(i, j - 1) + rSquared.getEntry(i, j) - rSquared.getEntry(i + bottom, j)); upCount.setEntry(i, j, upCount.getEntry(i, j - 1) + rCount.getEntry(i, j) - rCount.getEntry(i + bottom, j)); } } // Normalize MatrixTools.replaceValue(upCount, 0, 1); up = MatrixTools.elementBasedDivision(up, upCount); upSign = MatrixTools.elementBasedDivision(upSign, upCount); upSquared = MatrixTools.elementBasedDivision(upSquared, upCount); // Lower triangle for (int a = 0; a < n; a++) { for (int b = a + 1; b < n; b++) { int val = (int) Math.floor((b - a + 1) / 2); int endpt = Math.min(2 * b - a, n - 1); loCount.setEntry(a, b, loCount.getEntry(a, b - 1) + uCount.getEntry(b, endpt) - rCount.getEntry(a + val, b)); lo.setEntry(a, b, lo.getEntry(a, b - 1) + uSum.getEntry(b, endpt) - rSum.getEntry(a + val, b)); loSign.setEntry(a, b, loSign.getEntry(a, b - 1) + uSign.getEntry(b, endpt) - rSign.getEntry(a + val, b)); loSquared.setEntry(a, b, loSquared.getEntry(a, b - 1) + uSquared.getEntry(b, endpt) - rSquared.getEntry(a + val, b)); } } // Normalize MatrixTools.replaceValue(loCount, 0, 1); lo = MatrixTools.elementBasedDivision(lo, loCount); loSign = MatrixTools.elementBasedDivision(loSign, loCount); loSquared = MatrixTools.elementBasedDivision(loSquared, loCount); initialMatricesNotGenerated = false; } /** * Calculate block scores */ public void generateBlockScoreCalculations() { if (initialMatricesNotGenerated) { System.out.println("Initial matrices have not been generated"); System.exit(45); } upVar = upSquared.subtract(MatrixTools.elementBasedMultiplication(up, up)); loVar = loSquared.subtract(MatrixTools.elementBasedMultiplication(lo, lo)); RealMatrix diff = MatrixTools.normalizeByMax(lo.subtract(up)); RealMatrix diffSign = MatrixTools.normalizeByMax(loSign.subtract(upSign)); RealMatrix diffSquared = MatrixTools.normalizeByMax((upVar).add(loVar)); blockScore = (diff.add(diffSign)).subtract(diffSquared); blockScoresNotCalculated = false; } /** * Use give thresholds to eliminate extremes * * @param varThreshold * @param signThreshold */ public void thresholdScoreValues(double varThreshold, double signThreshold) { if (blockScoresNotCalculated) { System.out.println("Block scores not calculated"); System.exit(46); } signThresholdInternalValues(blockScore, upSign, loSign, signThreshold); if (!Double.isNaN(varThreshold)) { varThresholdInternalValues(blockScore, upVar.add(loVar), varThreshold); } blockScoresNotThresholded = false; } /** * Threshold values in block score matrix, set extremes to zero * * @param matrix * @param thresholdSums * @param threshold */ private void varThresholdInternalValues(RealMatrix matrix, RealMatrix thresholdSums, double threshold) { for (int i = 0; i < matrix.getRowDimension(); i++) { for (int j = 0; j < matrix.getColumnDimension(); j++) { if (thresholdSums.getEntry(i, j) > threshold) { matrix.setEntry(i, j, 0); } } } } /** * Threshold sign values in block score matrix, set extremes at either end to zero * * @param matrix * @param upSign * @param loSign * @param threshold */ private void signThresholdInternalValues(RealMatrix matrix, RealMatrix upSign, RealMatrix loSign, double threshold) { for (int i = 0; i < matrix.getRowDimension(); i++) { for (int j = 0; j < matrix.getColumnDimension(); j++) { //System.out.println(upSign.getEntry(i, j)+" "+loSign.getEntry(i, j)+" "+threshold); if ((-upSign.getEntry(i, j)) < threshold || loSign.getEntry(i, j) < threshold) { matrix.setEntry(i, j, 0); } } } } /** * extract block scores from regions specified in the provided list * * @return */ public ArrowheadScoreList updateScoresUsingList(ArrowheadScoreList scoreList, int limStart, int limEnd) { if (blockScoresNotCalculated) { System.out.println("Block scores not calculated"); System.exit(47); } return scoreList.updateActiveIndexScores(blockScore, limStart, limEnd); } public List> extractConnectedComponents() { if (blockScoresNotThresholded) { System.out.println("Scores not fixed for threshold"); System.exit(48); } //System.out.println("Norm "+blockScore.getNorm()); return BinaryConnectedComponents.detection(blockScore.getData(), 0); } public List calculateResults(List> connectedComponents) { /* for each connected component, get result for highest scoring point */ ArrayList results = new ArrayList<>(); for (Set connectedComponent : connectedComponents) { Point score = getHighestScoringPoint(blockScore, connectedComponent); int i = score.x, j = score.y; results.add(new HighScore(i, j, blockScore.getEntry(i, j), upVar.getEntry(i, j), loVar.getEntry(i, j), -upSign.getEntry(i, j), loSign.getEntry(i, j))); } return results; } /** * Find the point within the connected component with the highest block score * * @param blockScore * @param component * @return scorePoint */ private Point getHighestScoringPoint(RealMatrix blockScore, Set component) { Point scorePoint = component.iterator().next(); double highestScore = blockScore.getEntry(scorePoint.x, scorePoint.y); for (Point point : component) { double score = blockScore.getEntry(point.x, point.y); if (score > highestScore) { highestScore = score; scorePoint = new Point(point); } } return new Point(scorePoint); } } ================================================ FILE: src/juicebox/tools/utils/juicer/arrowhead/connectedcomponents/BinaryConnectedComponents.java ================================================ /* * The MIT License (MIT) * * Copyright (c) 2011-2020 Broad Institute, Aiden Lab, Rice University, Baylor College of Medicine * * Permission is hereby granted, free of charge, to any person obtaining a copy * of this software and associated documentation files (the "Software"), to deal * in the Software without restriction, including without limitation the rights * to use, copy, modify, merge, publish, distribute, sublicense, and/or sell * copies of the Software, and to permit persons to whom the Software is * furnished to do so, subject to the following conditions: * * The above copyright notice and this permission notice shall be included in * all copies or substantial portions of the Software. * * THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR * IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, * FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE * AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER * LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, * OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN * THE SOFTWARE. */ package juicebox.tools.utils.juicer.arrowhead.connectedcomponents; import java.awt.*; import java.util.List; import java.util.Queue; import java.util.*; import java.util.concurrent.LinkedBlockingQueue; /** * Implementation of 2-pass algorithm for finding connected components */ public class BinaryConnectedComponents { // unique labels for components, start at 0 private static Integer nextLabel = 0; /** * @param image * @param threshold * @return list of connected components in image */ public synchronized static List> detection(double[][] image, double threshold) { int r = image.length; int c = image[0].length; // pixel label matrix int[][] labels = new int[r][c]; List indices = new ArrayList<>(); indices.add(new IndexNode(-1)); nextLabel = 1; // 1st pass for (int i = 0; i < r; i++) { for (int j = 0; j < c; j++) { if (image[i][j] > threshold) { processNeighbors(labels, indices, i, j, Math.max(i - 1, 0), Math.min(i + 1, r - 1), Math.max(j - 1, 0), Math.min(j + 1, c - 1)); } } } return processLabeledIndices(indices); } /** * 2nd pass of algorithm * * @param indices * @return connected components */ private static List> processLabeledIndices(List indices) { List> components = new ArrayList<>(); for (int i = 1; i < nextLabel; i++) { IndexNode current = indices.get(i); if (current.hasNotBeenIndexed()) { Set points = new HashSet<>(current.getMatrixIndices()); Queue queue = new LinkedBlockingQueue<>(current.getConnectedNodes()); current.index(); while (!queue.isEmpty()) { IndexNode node = queue.poll(); if (node.hasNotBeenIndexed()) { points.addAll(node.getMatrixIndices()); node.index(); for (IndexNode node2 : node.getConnectedNodes()) { if (node2.hasNotBeenIndexed()) queue.add(node2); } } } components.add(points); } } return components; } /** * Label the neighbors of the pixel * * @param labels * @param indices * @param i * @param j * @param left * @param right * @param top * @param bottom */ private static void processNeighbors(int[][] labels, List indices, int i, int j, int left, int right, int top, int bottom) { // 8 - point connectivity int[][] neighborLabels = getSubMatrix(labels, left, right, top, bottom); // 0 - means none found Set allPosVals = positiveValues(neighborLabels); int lowestLabel = 0; if (allPosVals.size() > 0) lowestLabel = Collections.min(new ArrayList<>(allPosVals)); if (lowestLabel <= 0) { lowestLabel = nextLabel; indices.add(new IndexNode(lowestLabel)); nextLabel++; } labels[i][j] = lowestLabel; IndexNode current = indices.get(lowestLabel); current.addPoint(new Point(i, j)); for (Integer k : allPosVals) { IndexNode other = indices.get(k); other.addConnections(current); current.addConnections(other); } } private static int[][] getSubMatrix(int[][] matrix, int left, int right, int top, int bottom) { int[][] subMatrix = new int[right - left + 1][bottom - top + 1]; for (int i = 0; i < subMatrix.length; i++) { System.arraycopy(matrix[left + i], top, subMatrix[i], 0, subMatrix[0].length); } return subMatrix; } private static Set positiveValues(int[][] matrix) { Set values = new HashSet<>(); for (int[] row : matrix) { for (int val : row) { if (val > 0) { values.add(val); } } } return values; } } ================================================ FILE: src/juicebox/tools/utils/juicer/arrowhead/connectedcomponents/IndexNode.java ================================================ /* * The MIT License (MIT) * * Copyright (c) 2011-2020 Broad Institute, Aiden Lab, Rice University, Baylor College of Medicine * * Permission is hereby granted, free of charge, to any person obtaining a copy * of this software and associated documentation files (the "Software"), to deal * in the Software without restriction, including without limitation the rights * to use, copy, modify, merge, publish, distribute, sublicense, and/or sell * copies of the Software, and to permit persons to whom the Software is * furnished to do so, subject to the following conditions: * * The above copyright notice and this permission notice shall be included in * all copies or substantial portions of the Software. * * THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR * IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, * FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE * AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER * LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, * OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN * THE SOFTWARE. */ package juicebox.tools.utils.juicer.arrowhead.connectedcomponents; import java.awt.*; import java.util.HashSet; import java.util.Set; /** * Created by muhammadsaadshamim on 6/5/15. */ class IndexNode { private final int n; private final Set connectedNodes = new HashSet<>(); private final Set matrixIndices = new HashSet<>(); private boolean hasNotBeenIndexed = true; public IndexNode(int n) { this.n = n; } public void addConnections(IndexNode node) { connectedNodes.add(node); } public void addPoint(Point point) { matrixIndices.add(point); } public Set getMatrixIndices() { return matrixIndices; } public void index() { hasNotBeenIndexed = false; } public boolean hasNotBeenIndexed() { return hasNotBeenIndexed; } public Set getConnectedNodes() { return connectedNodes; } public int getIndex() { return n; } } ================================================ FILE: src/juicebox/tools/utils/juicer/hiccups/GPUController.java ================================================ /* * The MIT License (MIT) * * Copyright (c) 2011-2020 Broad Institute, Aiden Lab, Rice University, Baylor College of Medicine * * Permission is hereby granted, free of charge, to any person obtaining a copy * of this software and associated documentation files (the "Software"), to deal * in the Software without restriction, including without limitation the rights * to use, copy, modify, merge, publish, distribute, sublicense, and/or sell * copies of the Software, and to permit persons to whom the Software is * furnished to do so, subject to the following conditions: * * The above copyright notice and this permission notice shall be included in * all copies or substantial portions of the Software. * * THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR * IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, * FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE * AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER * LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, * OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN * THE SOFTWARE. */ package juicebox.tools.utils.juicer.hiccups; import com.google.common.primitives.Doubles; import com.google.common.primitives.Floats; import jcuda.Pointer; import jcuda.Sizeof; import jcuda.driver.CUdeviceptr; import jcuda.utils.KernelLauncher; import juicebox.data.HiCFileTools; import juicebox.data.MatrixZoomData; import juicebox.tools.clt.juicer.HiCCUPS; import juicebox.tools.clt.juicer.HiCCUPSRegionHandler; import juicebox.tools.utils.common.ArrayTools; import juicebox.tools.utils.common.MatrixTools; import juicebox.windowui.HiCZoom; import juicebox.windowui.NormalizationType; import org.apache.commons.math.linear.RealMatrix; import java.io.BufferedReader; import java.io.IOException; import java.io.InputStreamReader; import java.util.Arrays; import static jcuda.driver.JCudaDriver.cuMemcpyDtoH; public class GPUController { private static final int blockSize = 16; //number of threads in block private final KernelLauncher kernelLauncher; private final boolean useCPUVersionHiCCUPS; private final int windowCPU; private final int matrixSizeCPU; private final int peakWidthCPU; public GPUController(int window, int matrixSize, int peakWidth, boolean useCPUVersionHiCCUPS) { windowCPU = window; matrixSizeCPU = matrixSize; peakWidthCPU = peakWidth; this.useCPUVersionHiCCUPS = useCPUVersionHiCCUPS; if (useCPUVersionHiCCUPS) { kernelLauncher = null; } else { String kernelCode = readCuFile("HiCCUPSKernel.cu", window, matrixSize, peakWidth); kernelLauncher = KernelLauncher.compile(kernelCode, "BasicPeakCallingKernel"); //KernelLauncher.create() //threads per block = block_size*block_size kernelLauncher.setBlockSize(blockSize, blockSize, 1); // for grid of blocks int gridSize = (int) Math.ceil(matrixSize * 1.0 / blockSize); kernelLauncher.setGridSize(gridSize, gridSize); } } private static String readCuFile(String fileName, int window, int matrixSize, int peakWidth) { StringBuilder contentBuilder = new StringBuilder(); try (BufferedReader br = new BufferedReader(new InputStreamReader(GPUController.class.getResourceAsStream(fileName)))) { String sCurrentLine; while ((sCurrentLine = br.readLine()) != null) { contentBuilder.append(sCurrentLine).append("\n"); } } catch (IOException e) { e.printStackTrace(); } String cuFileText = contentBuilder.toString(); cuFileText = cuFileText.replaceAll("HiCCUPS_WINDOW", "" + window); cuFileText = cuFileText.replaceAll("HiCCUPS_MATRIX_SIZE", "" + matrixSize); cuFileText = cuFileText.replaceAll("HiCCUPS_PEAK_WIDTH", "" + peakWidth); cuFileText = cuFileText.replaceAll("HiCCUPS_REGION_MARGIN", "" + (HiCCUPS.regionMargin)); cuFileText = cuFileText.replaceAll("HiCCUPS_W1_MAX_INDX", "" + (HiCCUPS.w1 - 1)); return cuFileText; } public GPUOutputContainer process(HiCCUPSRegionHandler regionHandler, HiCCUPSRegionContainer regionContainer, int matrixSize, float[] thresholdBL, float[] thresholdDonut, float[] thresholdH, float[] thresholdV, NormalizationType normalizationType, HiCZoom zoom) throws NegativeArraySizeException, IOException { MatrixZoomData zd = regionHandler.getZoomData(regionContainer, zoom); double[] normalizationVector = regionHandler.getNormalizationVector(regionContainer, zoom); double[] expectedVector = regionHandler.getExpectedVector(regionContainer, zoom); int[] rowBounds = regionContainer.getRowBounds(); int[] columnBounds = regionContainer.getColumnBounds(); RealMatrix localizedRegionData = HiCFileTools.extractLocalBoundedRegion(zd, rowBounds[0], rowBounds[1], columnBounds[0], columnBounds[1], matrixSize, matrixSize, normalizationType, false); float[] observedVals = Floats.toArray(Doubles.asList(MatrixTools.flattenedRowMajorOrderMatrix(localizedRegionData))); // slice KR vector to localized region float[] distanceExpectedKRVector = Floats.toArray(Doubles.asList(expectedVector)); float[] kr1CPU = Floats.toArray(Doubles.asList(Arrays.copyOfRange(normalizationVector, rowBounds[0], rowBounds[1]))); float[] kr2CPU = Floats.toArray(Doubles.asList(Arrays.copyOfRange(normalizationVector, columnBounds[0], columnBounds[1]))); if (kr1CPU.length < matrixSize) kr1CPU = ArrayTools.padEndOfArray(kr1CPU, matrixSize, Float.NaN); if (kr2CPU.length < matrixSize) kr2CPU = ArrayTools.padEndOfArray(kr2CPU, matrixSize, Float.NaN); float[] boundRowIndex = new float[1]; boundRowIndex[0] = rowBounds[0]; float[] boundColumnIndex = new float[1]; boundColumnIndex[0] = columnBounds[0]; if (useCPUVersionHiCCUPS) { return runCPUVersion(localizedRegionData.getData(), distanceExpectedKRVector, kr1CPU, kr2CPU, boundRowIndex, boundColumnIndex, thresholdBL, thresholdDonut, thresholdH, thresholdV, rowBounds, columnBounds); } // transfer host (CPU) memory to device (GPU) memory CUdeviceptr observedKRGPU = GPUHelper.allocateInput(observedVals); CUdeviceptr expectedDistanceVectorGPU = GPUHelper.allocateInput(distanceExpectedKRVector); CUdeviceptr kr1GPU = GPUHelper.allocateInput(kr1CPU); CUdeviceptr kr2GPU = GPUHelper.allocateInput(kr2CPU); CUdeviceptr thresholdBLGPU = GPUHelper.allocateInput(thresholdBL); CUdeviceptr thresholdDonutGPU = GPUHelper.allocateInput(thresholdDonut); CUdeviceptr thresholdHGPU = GPUHelper.allocateInput(thresholdH); CUdeviceptr thresholdVGPU = GPUHelper.allocateInput(thresholdV); CUdeviceptr boundRowIndexGPU = GPUHelper.allocateInput(boundRowIndex); CUdeviceptr boundColumnIndexGPU = GPUHelper.allocateInput(boundColumnIndex); // create empty gpu arrays for the results int flattenedSize = matrixSize * matrixSize; CUdeviceptr expectedBLGPU = GPUHelper.allocateOutput(flattenedSize, Sizeof.FLOAT); CUdeviceptr expectedDonutGPU = GPUHelper.allocateOutput(flattenedSize, Sizeof.FLOAT); CUdeviceptr expectedHGPU = GPUHelper.allocateOutput(flattenedSize, Sizeof.FLOAT); CUdeviceptr expectedVGPU = GPUHelper.allocateOutput(flattenedSize, Sizeof.FLOAT); CUdeviceptr binBLGPU = GPUHelper.allocateOutput(flattenedSize, Sizeof.FLOAT); CUdeviceptr binDonutGPU = GPUHelper.allocateOutput(flattenedSize, Sizeof.FLOAT); CUdeviceptr binHGPU = GPUHelper.allocateOutput(flattenedSize, Sizeof.FLOAT); CUdeviceptr binVGPU = GPUHelper.allocateOutput(flattenedSize, Sizeof.FLOAT); CUdeviceptr observedGPU = GPUHelper.allocateOutput(flattenedSize, Sizeof.FLOAT); CUdeviceptr peakGPU = GPUHelper.allocateOutput(flattenedSize, Sizeof.FLOAT); // call the kernel on the card kernelLauncher.call( // inputs observedKRGPU, // output expectedBLGPU, expectedDonutGPU, expectedHGPU, expectedVGPU, observedGPU, binBLGPU, binDonutGPU, binHGPU, binVGPU, peakGPU, // thresholds thresholdBLGPU, thresholdDonutGPU, thresholdHGPU, thresholdVGPU, // distance expected expectedDistanceVectorGPU, // kr kr1GPU, kr2GPU, // bounds boundRowIndexGPU, boundColumnIndexGPU); // initialize memory to store GPU results float[] expectedBLResult = new float[flattenedSize]; float[] expectedDonutResult = new float[flattenedSize]; float[] expectedHResult = new float[flattenedSize]; float[] expectedVResult = new float[flattenedSize]; float[] binBLResult = new float[flattenedSize]; float[] binDonutResult = new float[flattenedSize]; float[] binHResult = new float[flattenedSize]; float[] binVResult = new float[flattenedSize]; float[] observedResult = new float[flattenedSize]; float[] peakResult = new float[flattenedSize]; // transfer device (GPU) memory to host (CPU) memory cuMemcpyDtoH(Pointer.to(expectedBLResult), expectedBLGPU, flattenedSize * Sizeof.FLOAT); cuMemcpyDtoH(Pointer.to(expectedDonutResult), expectedDonutGPU, flattenedSize * Sizeof.FLOAT); cuMemcpyDtoH(Pointer.to(expectedHResult), expectedHGPU, flattenedSize * Sizeof.FLOAT); cuMemcpyDtoH(Pointer.to(expectedVResult), expectedVGPU, flattenedSize * Sizeof.FLOAT); cuMemcpyDtoH(Pointer.to(binBLResult), binBLGPU, flattenedSize * Sizeof.FLOAT); cuMemcpyDtoH(Pointer.to(binDonutResult), binDonutGPU, flattenedSize * Sizeof.FLOAT); cuMemcpyDtoH(Pointer.to(binHResult), binHGPU, flattenedSize * Sizeof.FLOAT); cuMemcpyDtoH(Pointer.to(binVResult), binVGPU, flattenedSize * Sizeof.FLOAT); cuMemcpyDtoH(Pointer.to(observedResult), observedGPU, flattenedSize * Sizeof.FLOAT); cuMemcpyDtoH(Pointer.to(peakResult), peakGPU, flattenedSize * Sizeof.FLOAT); GPUHelper.freeUpMemory(new CUdeviceptr[]{observedKRGPU, expectedDistanceVectorGPU, kr1GPU, kr2GPU, thresholdBLGPU, thresholdDonutGPU, thresholdHGPU, thresholdVGPU, boundRowIndexGPU, boundColumnIndexGPU, expectedBLGPU, expectedDonutGPU, expectedHGPU, expectedVGPU, binBLGPU, binDonutGPU, binHGPU, binVGPU, observedGPU, peakGPU}); //long gpu_time2 = System.currentTimeMillis(); //System.out.println("GPU Time: " + (gpu_time2-gpu_time1)); int finalWidthX = rowBounds[5] - rowBounds[4]; int finalWidthY = columnBounds[5] - columnBounds[4]; // x2, y2 not inclusive here int x1 = rowBounds[2]; int y1 = columnBounds[2]; int x2 = x1 + finalWidthX; int y2 = y1 + finalWidthY; //System.out.println("flat = "+flattenedSize+" n = "+matrixSize+" x1 = "+x1+" x2 = "+x2+" y1 = "+y1+" y2 ="+y2); float[][] observedDenseCPU = GPUHelper.GPUArraytoCPUMatrix(observedResult, matrixSize, x1, x2, y1, y2); float[][] peakDenseCPU = GPUHelper.GPUArraytoCPUMatrix(peakResult, matrixSize, x1, x2, y1, y2); float[][] binBLDenseCPU = GPUHelper.GPUArraytoCPUMatrix(binBLResult, matrixSize, x1, x2, y1, y2); float[][] binDonutDenseCPU = GPUHelper.GPUArraytoCPUMatrix(binDonutResult, matrixSize, x1, x2, y1, y2); float[][] binHDenseCPU = GPUHelper.GPUArraytoCPUMatrix(binHResult, matrixSize, x1, x2, y1, y2); float[][] binVDenseCPU = GPUHelper.GPUArraytoCPUMatrix(binVResult, matrixSize, x1, x2, y1, y2); float[][] expectedBLDenseCPU = GPUHelper.GPUArraytoCPUMatrix(expectedBLResult, matrixSize, x1, x2, y1, y2); float[][] expectedDonutDenseCPU = GPUHelper.GPUArraytoCPUMatrix(expectedDonutResult, matrixSize, x1, x2, y1, y2); float[][] expectedHDenseCPU = GPUHelper.GPUArraytoCPUMatrix(expectedHResult, matrixSize, x1, x2, y1, y2); float[][] expectedVDenseCPU = GPUHelper.GPUArraytoCPUMatrix(expectedVResult, matrixSize, x1, x2, y1, y2); return new GPUOutputContainer(observedDenseCPU, peakDenseCPU, binBLDenseCPU, binDonutDenseCPU, binHDenseCPU, binVDenseCPU, expectedBLDenseCPU, expectedDonutDenseCPU, expectedHDenseCPU, expectedVDenseCPU); } /** * just a direct implementation from the CUDA kernel * todo clean up and optimize after debugging and testing */ private GPUOutputContainer runCPUVersion(double[][] c, float[] d, float[] kr1, float[] kr2, float[] bound1, float[] bound3, float[] thresholdBL, float[] thresholdDonut, float[] thresholdH, float[] thresholdV, int[] rowBounds, int[] columnBounds) { float[][] observedDenseCPU = new float[matrixSizeCPU][matrixSizeCPU]; float[][] peakDenseCPU = new float[matrixSizeCPU][matrixSizeCPU]; float[][] binBLDenseCPU = new float[matrixSizeCPU][matrixSizeCPU]; float[][] binDonutDenseCPU = new float[matrixSizeCPU][matrixSizeCPU]; float[][] binHDenseCPU = new float[matrixSizeCPU][matrixSizeCPU]; float[][] binVDenseCPU = new float[matrixSizeCPU][matrixSizeCPU]; float[][] expectedBLDenseCPU = new float[matrixSizeCPU][matrixSizeCPU]; float[][] expectedDonutDenseCPU = new float[matrixSizeCPU][matrixSizeCPU]; float[][] expectedHDenseCPU = new float[matrixSizeCPU][matrixSizeCPU]; float[][] expectedVDenseCPU = new float[matrixSizeCPU][matrixSizeCPU]; //int t_col = threadIdx.x + blockIdx.x * blockDim.x;\n" + //" int t_row = threadIdx.y + blockIdx.y * blockDim.y;\n" + for (int t_row = HiCCUPS.regionMargin; t_row < matrixSizeCPU - HiCCUPS.regionMargin; t_row++) { for (int t_col = HiCCUPS.regionMargin; t_col < matrixSizeCPU - HiCCUPS.regionMargin; t_col++) { // Evalue is used to store the element of the matrix // that is computed by the thread float Evalue_bl = 0; float Edistvalue_bl = 0; float Evalue_donut = 0; float Edistvalue_donut = 0; float Evalue_h = 0; float Edistvalue_h = 0; float Evalue_v = 0; float Edistvalue_v = 0; float e_bl = 0; float e_donut = 0; float e_h = 0; float e_v = 0; float o = 0; float sbtrkt = 0; float bvalue_bl = 0; float bvalue_donut = 0; float bvalue_h = 0; float bvalue_v = 0; int wsize = windowCPU; int msize = matrixSizeCPU; int pwidth = peakWidthCPU; int buffer_width = HiCCUPS.regionMargin; int diff = (int) (bound1[0] - bound3[0]); int diagDist = Math.abs(t_row + diff - t_col); int maxIndex = msize - buffer_width; wsize = Math.min(wsize, (diagDist - 1) / 2); if (wsize <= pwidth) { wsize = pwidth + 1; } wsize = Math.min(wsize, buffer_width); // only run if within central window (not in data buffer margins) if (t_row >= buffer_width && t_row < maxIndex && t_col >= buffer_width && t_col < maxIndex) { // calculate initial bottom left box for (int i = t_row + 1; i <= t_row + wsize; i++) { for (int j = t_col - wsize; j < t_col; j++) { if (!Double.isNaN(c[i][j])) { if (i + diff - j < 0) { Evalue_bl += c[i][j]; Edistvalue_bl += d[Math.abs(i + diff - j)]; } } } } //Subtract off the middle peak for (int i = t_row + 1; i <= t_row + pwidth; i++) { for (int j = t_col - pwidth; j < t_col; j++) { if (!Double.isNaN(c[i][j])) { if (i + diff - j < 0) { Evalue_bl -= c[i][j]; Edistvalue_bl -= d[Math.abs(i + diff - j)]; } } } } //fix box dimensions while (Evalue_bl < 16) { Evalue_bl = 0; Edistvalue_bl = 0; wsize += 1; //dvisor = powf(wsize,2.0) - powf(pwidth,2.0); for (int i = t_row + 1; i <= t_row + wsize; i++) { for (int j = t_col - wsize; j < t_col; j++) { if (!Double.isNaN(c[i][j])) { if (i + diff - j < 0) { Evalue_bl += c[i][j]; int distVal = Math.abs(i + diff - j); Edistvalue_bl += d[distVal]; if (i >= t_row + 1) { if (i < t_row + pwidth + 1) { if (j >= t_col - pwidth) { if (j < t_col) { Evalue_bl -= c[i][j]; Edistvalue_bl -= d[distVal]; } } } } } } } } if (wsize >= buffer_width) { break; } if (2 * wsize >= diagDist) { break; } } // calculate donut for (int i = t_row - wsize; i <= t_row + wsize; ++i) { for (int j = t_col - wsize; j <= t_col + wsize; ++j) { if (!Double.isNaN(c[i][j])) { if (i + diff - j < 0) { Evalue_donut += c[i][j]; Edistvalue_donut += d[Math.abs(i + diff - j)]; } } } } //Subtract off the middle peak for (int i = t_row - pwidth; i <= t_row + pwidth; ++i) { for (int j = t_col - pwidth; j <= t_col + pwidth; ++j) { if (!Double.isNaN(c[i][j])) { if (i + diff - j < 0) { Evalue_donut -= c[i][j]; Edistvalue_donut -= d[Math.abs(i + diff - j)]; } } } } //Subtract off the cross hairs left side for (int i = t_row - wsize; i < t_row - pwidth; i++) { if (!Double.isNaN(c[i][t_col])) { Evalue_donut -= c[i][t_col]; Edistvalue_donut -= d[Math.abs(i + diff - t_col)]; } for (int j = -1; j <= 1; j++) { Evalue_v += c[i][t_col + j]; Edistvalue_v += d[Math.abs(i + diff - t_col - j)]; } } //Subtract off the cross hairs right side for (int i = t_row + pwidth + 1; i <= t_row + wsize; ++i) { if (!Double.isNaN(c[i][t_col])) { Evalue_donut -= c[i][t_col]; Edistvalue_donut -= d[Math.abs(i + diff - t_col)]; } for (int j = -1; j <= 1; ++j) { Evalue_v += c[i][t_col + j]; Edistvalue_v += d[Math.abs(i + diff - t_col - j)]; } } //Subtract off the cross hairs top side for (int j = t_col - wsize; j < t_col - pwidth; ++j) { if (!Double.isNaN(c[t_row][j])) { Evalue_donut -= c[t_row][j]; Edistvalue_donut -= d[Math.abs(t_row + diff - j)]; } for (int i = -1; i <= 1; ++i) { Evalue_h += c[t_row + i][j]; Edistvalue_h += d[Math.abs(t_row + i + diff - j)]; } } //Subtract off the cross hairs bottom side for (int j = t_col + pwidth + 1; j <= t_col + wsize; ++j) { if (!Double.isNaN(c[t_row][j])) { Evalue_donut -= c[t_row][j]; Edistvalue_donut -= d[Math.abs(t_row + diff - j)]; } for (int i = -1; i <= 1; ++i) { Evalue_h += c[t_row + i][j]; Edistvalue_h += d[Math.abs(t_row + i + diff - j)]; } } } e_bl = ((Evalue_bl * d[diagDist]) / Edistvalue_bl) * kr1[t_row] * kr2[t_col]; e_donut = ((Evalue_donut * d[diagDist]) / Edistvalue_donut) * kr1[t_row] * kr2[t_col]; e_h = ((Evalue_h * d[diagDist]) / Edistvalue_h) * kr1[t_row] * kr2[t_col]; e_v = ((Evalue_v * d[diagDist]) / Edistvalue_v) * kr1[t_row] * kr2[t_col]; float lognorm = (float) Math.log(Math.pow(2.0, .33)); if (!Float.isNaN(e_bl) && !Float.isInfinite(e_bl)) { if (e_bl <= 1) { bvalue_bl = 0; } else { bvalue_bl = (float) Math.floor(Math.log(e_bl) / lognorm); } } if (!Float.isNaN(e_donut) && !Float.isInfinite(e_donut)) { if (e_donut <= 1) { bvalue_donut = 0; } else { bvalue_donut = (float) Math.floor(Math.log(e_donut) / lognorm); } } if (!Float.isNaN(e_h) && !Float.isInfinite(e_h)) { if (e_h <= 1) { bvalue_h = 0; } else { bvalue_h = (float) Math.floor(Math.log(e_h) / lognorm); } } if (!Float.isNaN(e_v) && !Float.isInfinite(e_v)) { if (e_v <= 1) { bvalue_v = 0; } else { bvalue_v = (float) Math.floor(Math.log(e_v) / lognorm); } } // todo why are bin values exceeding w1 in cpu version? // do they exceed in gpu version as well bvalue_bl = Math.min(bvalue_bl, HiCCUPS.w1 - 1); bvalue_donut = Math.min(bvalue_donut, HiCCUPS.w1 - 1); bvalue_h = Math.min(bvalue_h, HiCCUPS.w1 - 1); bvalue_v = Math.min(bvalue_v, HiCCUPS.w1 - 1); // Write the matrix to device memory; // each thread writes one element expectedBLDenseCPU[t_row][t_col] = e_bl; expectedDonutDenseCPU[t_row][t_col] = e_donut; expectedHDenseCPU[t_row][t_col] = e_h; expectedVDenseCPU[t_row][t_col] = e_v; o = Math.round(c[t_row][t_col] * kr1[t_row] * kr2[t_col]); observedDenseCPU[t_row][t_col] = o; binBLDenseCPU[t_row][t_col] = bvalue_bl; binDonutDenseCPU[t_row][t_col] = bvalue_donut; binHDenseCPU[t_row][t_col] = bvalue_h; binVDenseCPU[t_row][t_col] = bvalue_v; //System.out.println("thresholdBL "+thresholdBL.length+" thresholdDonut "+thresholdDonut.length); //System.out.println("a "+bvalue_bl+" b "+bvalue_donut); sbtrkt = Math.max(thresholdBL[(int) bvalue_bl], thresholdDonut[(int) bvalue_donut]); sbtrkt = Math.max(sbtrkt, thresholdH[(int) bvalue_h]); sbtrkt = Math.max(sbtrkt, thresholdV[(int) bvalue_v]); peakDenseCPU[t_row][t_col] = o - sbtrkt; } } // x2, y2 not inclusive here int finalWidthX = rowBounds[5] - rowBounds[4]; int finalWidthY = columnBounds[5] - columnBounds[4]; // x2, y2 not inclusive here int x1 = rowBounds[2]; int y1 = columnBounds[2]; int x2 = x1 + finalWidthX; int y2 = y1 + finalWidthY; //System.out.println("flat = "+flattenedSize+" n = "+matrixSize+" x1 = "+x1+" x2 = "+x2+" y1 = "+y1+" y2 ="+y2); observedDenseCPU = MatrixTools.extractLocalMatrixRegion(observedDenseCPU, x1, x2, y1, y2); peakDenseCPU = MatrixTools.extractLocalMatrixRegion(peakDenseCPU, x1, x2, y1, y2); binBLDenseCPU = MatrixTools.extractLocalMatrixRegion(binBLDenseCPU, x1, x2, y1, y2); binDonutDenseCPU = MatrixTools.extractLocalMatrixRegion(binDonutDenseCPU, x1, x2, y1, y2); binHDenseCPU = MatrixTools.extractLocalMatrixRegion(binHDenseCPU, x1, x2, y1, y2); binVDenseCPU = MatrixTools.extractLocalMatrixRegion(binVDenseCPU, x1, x2, y1, y2); expectedBLDenseCPU = MatrixTools.extractLocalMatrixRegion(expectedBLDenseCPU, x1, x2, y1, y2); expectedDonutDenseCPU = MatrixTools.extractLocalMatrixRegion(expectedDonutDenseCPU, x1, x2, y1, y2); expectedHDenseCPU = MatrixTools.extractLocalMatrixRegion(expectedHDenseCPU, x1, x2, y1, y2); expectedVDenseCPU = MatrixTools.extractLocalMatrixRegion(expectedVDenseCPU, x1, x2, y1, y2); return new GPUOutputContainer(observedDenseCPU, peakDenseCPU, binBLDenseCPU, binDonutDenseCPU, binHDenseCPU, binVDenseCPU, expectedBLDenseCPU, expectedDonutDenseCPU, expectedHDenseCPU, expectedVDenseCPU); } } ================================================ FILE: src/juicebox/tools/utils/juicer/hiccups/GPUController2.java ================================================ /* * The MIT License (MIT) * * Copyright (c) 2011-2019 Broad Institute, Aiden Lab * * Permission is hereby granted, free of charge, to any person obtaining a copy * of this software and associated documentation files (the "Software"), to deal * in the Software without restriction, including without limitation the rights * to use, copy, modify, merge, publish, distribute, sublicense, and/or sell * copies of the Software, and to permit persons to whom the Software is * furnished to do so, subject to the following conditions: * * The above copyright notice and this permission notice shall be included in * all copies or substantial portions of the Software. * * THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR * IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, * FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE * AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER * LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, * OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN * THE SOFTWARE. */ package juicebox.tools.utils.juicer.hiccups; import com.google.common.primitives.Doubles; import com.google.common.primitives.Floats; import jcuda.CudaException; import jcuda.Pointer; import jcuda.Sizeof; import jcuda.driver.*; import jcuda.runtime.JCuda; import jcuda.utils.KernelLauncher; import juicebox.data.HiCFileTools; import juicebox.data.MatrixZoomData; import juicebox.tools.clt.juicer.HiCCUPS; import juicebox.tools.clt.juicer.HiCCUPSRegionHandler; import juicebox.tools.utils.common.ArrayTools; import juicebox.tools.utils.common.MatrixTools; import juicebox.windowui.HiCZoom; import juicebox.windowui.NormalizationType; import org.apache.commons.math.linear.RealMatrix; import java.io.BufferedReader; import java.io.IOException; import java.io.InputStreamReader; import java.util.Arrays; import java.util.Random; import static jcuda.driver.JCudaDriver.*; public class GPUController2 { private static final int blockSize = 16; //number of threads in block private final KernelLauncher kernelLauncher; private final boolean useCPUVersionHiCCUPS; private final int windowCPU; private final int matrixSizeCPU; private final int peakWidthCPU; public GPUController2(int window, int res, int matrixSize, int peakWidth, boolean useCPUVersionHiCCUPS) { windowCPU = window; matrixSizeCPU = matrixSize; peakWidthCPU = peakWidth; this.useCPUVersionHiCCUPS = useCPUVersionHiCCUPS; if (useCPUVersionHiCCUPS) { kernelLauncher = null; } else { String kernelCode = readCuFile("HiCCUPS2Kernel_1kb.cu", window, matrixSize, peakWidth); System.out.println("You are using the default kernel."); kernelLauncher = KernelLauncher.compile(kernelCode, "BasicPeakCallingKernel"); //KernelLauncher.create() //threads per block = block_size*block_size kernelLauncher.setBlockSize(blockSize, blockSize, 1); // for grid of blocks int gridSize = (int) Math.ceil(matrixSize * 1.0 / blockSize); kernelLauncher.setGridSize(gridSize, gridSize); } } private static String readCuFile(String fileName, int window, int matrixSize, int peakWidth) { StringBuilder contentBuilder = new StringBuilder(); try (BufferedReader br = new BufferedReader(new InputStreamReader(GPUController2.class.getResourceAsStream(fileName)))) { String sCurrentLine; while ((sCurrentLine = br.readLine()) != null) { contentBuilder.append(sCurrentLine).append("\n"); } } catch (IOException e) { e.printStackTrace(); } String cuFileText = contentBuilder.toString(); cuFileText = cuFileText.replaceAll("HiCCUPS_WINDOW", "" + window); cuFileText = cuFileText.replaceAll("HiCCUPS_MATRIX_SIZE", "" + matrixSize); cuFileText = cuFileText.replaceAll("HiCCUPS_PEAK_WIDTH", "" + peakWidth); cuFileText = cuFileText.replaceAll("HiCCUPS_REGION_MARGIN", "" + (HiCCUPS.regionMargin)); cuFileText = cuFileText.replaceAll("HiCCUPS_W1_MAX_INDX", "" + (HiCCUPS.w1 - 1)); return cuFileText; } public GPUOutputContainer2 process(HiCCUPSRegionHandler regionHandler, HiCCUPSRegionContainer regionContainer, int matrixSize, float[] thresholdBL, float[] thresholdDonut, float[] thresholdH, float[] thresholdV, NormalizationType normalizationType, HiCZoom zoom) throws NegativeArraySizeException, IOException { MatrixZoomData zd = regionHandler.getZoomData(regionContainer, zoom); double[] normalizationVector = regionHandler.getNormalizationVector(regionContainer, zoom); double[] expectedVector = regionHandler.getExpectedVector(regionContainer, zoom); int[] rowBounds = regionContainer.getRowBounds(); int[] columnBounds = regionContainer.getColumnBounds(); RealMatrix localizedRegionData = HiCFileTools.extractLocalBoundedRegion(zd, rowBounds[0], rowBounds[1], columnBounds[0], columnBounds[1], matrixSize, matrixSize, normalizationType, false); float[] observedVals = Floats.toArray(Doubles.asList(MatrixTools.flattenedRowMajorOrderMatrix(localizedRegionData))); // slice KR vector to localized region float[] distanceExpectedKRVector = Floats.toArray(Doubles.asList(expectedVector)); float[] kr1CPU = Floats.toArray(Doubles.asList(Arrays.copyOfRange(normalizationVector, rowBounds[0], rowBounds[1]))); float[] kr2CPU = Floats.toArray(Doubles.asList(Arrays.copyOfRange(normalizationVector, columnBounds[0], columnBounds[1]))); if (kr1CPU.length < matrixSize) kr1CPU = ArrayTools.padEndOfArray(kr1CPU, matrixSize, Float.NaN); if (kr2CPU.length < matrixSize) kr2CPU = ArrayTools.padEndOfArray(kr2CPU, matrixSize, Float.NaN); float[] boundRowIndex = new float[1]; boundRowIndex[0] = rowBounds[0]; float[] boundColumnIndex = new float[1]; boundColumnIndex[0] = columnBounds[0]; //if (useCPUVersionHiCCUPS) { // return runCPUVersion(localizedRegionData.getData(), distanceExpectedKRVector, kr1CPU, kr2CPU, // boundRowIndex, boundColumnIndex, thresholdBL, thresholdDonut, thresholdH, thresholdV, // rowBounds, columnBounds); //} //JCuda.cudaSetDevice(device); // transfer host (CPU) memory to device (GPU) memory CUdeviceptr observedKRGPU = GPUHelper.allocateInput(observedVals); CUdeviceptr expectedDistanceVectorGPU = GPUHelper.allocateInput(distanceExpectedKRVector); CUdeviceptr kr1GPU = GPUHelper.allocateInput(kr1CPU); CUdeviceptr kr2GPU = GPUHelper.allocateInput(kr2CPU); CUdeviceptr thresholdBLGPU = GPUHelper.allocateInput(thresholdBL); CUdeviceptr thresholdDonutGPU = GPUHelper.allocateInput(thresholdDonut); CUdeviceptr thresholdHGPU = GPUHelper.allocateInput(thresholdH); CUdeviceptr thresholdVGPU = GPUHelper.allocateInput(thresholdV); CUdeviceptr boundRowIndexGPU = GPUHelper.allocateInput(boundRowIndex); CUdeviceptr boundColumnIndexGPU = GPUHelper.allocateInput(boundColumnIndex); // create empty gpu arrays for the results int flattenedSize = matrixSize * matrixSize; CUdeviceptr expectedBLGPU = GPUHelper.allocateOutput(flattenedSize, Sizeof.FLOAT); CUdeviceptr expectedDonutGPU = GPUHelper.allocateOutput(flattenedSize, Sizeof.FLOAT); CUdeviceptr expectedHGPU = GPUHelper.allocateOutput(flattenedSize, Sizeof.FLOAT); CUdeviceptr expectedVGPU = GPUHelper.allocateOutput(flattenedSize, Sizeof.FLOAT); CUdeviceptr binBLGPU = GPUHelper.allocateOutput(flattenedSize, Sizeof.FLOAT); CUdeviceptr binDonutGPU = GPUHelper.allocateOutput(flattenedSize, Sizeof.FLOAT); CUdeviceptr binHGPU = GPUHelper.allocateOutput(flattenedSize, Sizeof.FLOAT); CUdeviceptr binVGPU = GPUHelper.allocateOutput(flattenedSize, Sizeof.FLOAT); CUdeviceptr observedGPU = GPUHelper.allocateOutput(flattenedSize, Sizeof.FLOAT); CUdeviceptr peakGPU = GPUHelper.allocateOutput(flattenedSize, Sizeof.FLOAT); CUdeviceptr pvalBLGPU = GPUHelper.allocateOutput(flattenedSize, Sizeof.FLOAT); CUdeviceptr pvalDonutGPU = GPUHelper.allocateOutput(flattenedSize, Sizeof.FLOAT); CUdeviceptr pvalHGPU = GPUHelper.allocateOutput(flattenedSize, Sizeof.FLOAT); CUdeviceptr pvalVGPU = GPUHelper.allocateOutput(flattenedSize, Sizeof.FLOAT); // call the kernel on the card kernelLauncher.call( // inputs observedKRGPU, // output expectedBLGPU, expectedDonutGPU, expectedHGPU, expectedVGPU, observedGPU, binBLGPU, binDonutGPU, binHGPU, binVGPU, peakGPU, pvalBLGPU, pvalDonutGPU, pvalHGPU, pvalVGPU, // thresholds thresholdBLGPU, thresholdDonutGPU, thresholdHGPU, thresholdVGPU, // distance expected expectedDistanceVectorGPU, // kr kr1GPU, kr2GPU, // bounds boundRowIndexGPU, boundColumnIndexGPU); // initialize memory to store GPU results float[] expectedBLResult = new float[flattenedSize]; float[] expectedDonutResult = new float[flattenedSize]; float[] expectedHResult = new float[flattenedSize]; float[] expectedVResult = new float[flattenedSize]; float[] binBLResult = new float[flattenedSize]; float[] binDonutResult = new float[flattenedSize]; float[] binHResult = new float[flattenedSize]; float[] binVResult = new float[flattenedSize]; float[] observedResult = new float[flattenedSize]; float[] peakResult = new float[flattenedSize]; float[] pvalBLResult = new float[flattenedSize]; float[] pvalDonutResult = new float[flattenedSize]; float[] pvalHResult = new float[flattenedSize]; float[] pvalVResult = new float[flattenedSize]; // transfer device (GPU) memory to host (CPU) memory cuMemcpyDtoH(Pointer.to(expectedBLResult), expectedBLGPU, flattenedSize * Sizeof.FLOAT); cuMemcpyDtoH(Pointer.to(expectedDonutResult), expectedDonutGPU, flattenedSize * Sizeof.FLOAT); cuMemcpyDtoH(Pointer.to(expectedHResult), expectedHGPU, flattenedSize * Sizeof.FLOAT); cuMemcpyDtoH(Pointer.to(expectedVResult), expectedVGPU, flattenedSize * Sizeof.FLOAT); cuMemcpyDtoH(Pointer.to(binBLResult), binBLGPU, flattenedSize * Sizeof.FLOAT); cuMemcpyDtoH(Pointer.to(binDonutResult), binDonutGPU, flattenedSize * Sizeof.FLOAT); cuMemcpyDtoH(Pointer.to(binHResult), binHGPU, flattenedSize * Sizeof.FLOAT); cuMemcpyDtoH(Pointer.to(binVResult), binVGPU, flattenedSize * Sizeof.FLOAT); cuMemcpyDtoH(Pointer.to(observedResult), observedGPU, flattenedSize * Sizeof.FLOAT); cuMemcpyDtoH(Pointer.to(peakResult), peakGPU, flattenedSize * Sizeof.FLOAT); cuMemcpyDtoH(Pointer.to(pvalBLResult), pvalBLGPU, flattenedSize * Sizeof.FLOAT); cuMemcpyDtoH(Pointer.to(pvalDonutResult), pvalDonutGPU, flattenedSize * Sizeof.FLOAT); cuMemcpyDtoH(Pointer.to(pvalHResult), pvalHGPU, flattenedSize * Sizeof.FLOAT); cuMemcpyDtoH(Pointer.to(pvalVResult), pvalVGPU, flattenedSize * Sizeof.FLOAT); GPUHelper.freeUpMemory(new CUdeviceptr[]{observedKRGPU, expectedDistanceVectorGPU, kr1GPU, kr2GPU, thresholdBLGPU, thresholdDonutGPU, thresholdHGPU, thresholdVGPU, boundRowIndexGPU, boundColumnIndexGPU, expectedBLGPU, expectedDonutGPU, expectedHGPU, expectedVGPU, binBLGPU, binDonutGPU, binHGPU, binVGPU, observedGPU, peakGPU, pvalBLGPU, pvalDonutGPU, pvalHGPU, pvalVGPU}); //long gpu_time2 = System.currentTimeMillis(); //System.out.println("GPU Time: " + (gpu_time2-gpu_time1)); int finalWidthX = rowBounds[5] - rowBounds[4]; int finalWidthY = columnBounds[5] - columnBounds[4]; // x2, y2 not inclusive here int x1 = rowBounds[2]; int y1 = columnBounds[2]; int x2 = x1 + finalWidthX; int y2 = y1 + finalWidthY; //System.out.println("flat = "+flattenedSize+" n = "+matrixSize+" x1 = "+x1+" x2 = "+x2+" y1 = "+y1+" y2 ="+y2); float[][] observedDenseCPU = GPUHelper.GPUArraytoCPUMatrix(observedResult, matrixSize, x1, x2, y1, y2); float[][] peakDenseCPU = GPUHelper.GPUArraytoCPUMatrix(peakResult, matrixSize, x1, x2, y1, y2); float[][] binBLDenseCPU = GPUHelper.GPUArraytoCPUMatrix(binBLResult, matrixSize, x1, x2, y1, y2); float[][] binDonutDenseCPU = GPUHelper.GPUArraytoCPUMatrix(binDonutResult, matrixSize, x1, x2, y1, y2); float[][] binHDenseCPU = GPUHelper.GPUArraytoCPUMatrix(binHResult, matrixSize, x1, x2, y1, y2); float[][] binVDenseCPU = GPUHelper.GPUArraytoCPUMatrix(binVResult, matrixSize, x1, x2, y1, y2); float[][] expectedBLDenseCPU = GPUHelper.GPUArraytoCPUMatrix(expectedBLResult, matrixSize, x1, x2, y1, y2); float[][] expectedDonutDenseCPU = GPUHelper.GPUArraytoCPUMatrix(expectedDonutResult, matrixSize, x1, x2, y1, y2); float[][] expectedHDenseCPU = GPUHelper.GPUArraytoCPUMatrix(expectedHResult, matrixSize, x1, x2, y1, y2); float[][] expectedVDenseCPU = GPUHelper.GPUArraytoCPUMatrix(expectedVResult, matrixSize, x1, x2, y1, y2); float[][] pvalBLDenseCPU = GPUHelper.GPUArraytoCPUMatrix(pvalBLResult, matrixSize, x1, x2, y1, y2); float[][] pvalDonutDenseCPU = GPUHelper.GPUArraytoCPUMatrix(pvalDonutResult, matrixSize, x1, x2, y1, y2); float[][] pvalHDenseCPU = GPUHelper.GPUArraytoCPUMatrix(pvalHResult, matrixSize, x1, x2, y1, y2); float[][] pvalVDenseCPU = GPUHelper.GPUArraytoCPUMatrix(pvalVResult, matrixSize, x1, x2, y1, y2); return new GPUOutputContainer2(observedDenseCPU, peakDenseCPU, binBLDenseCPU, binDonutDenseCPU, binHDenseCPU, binVDenseCPU, expectedBLDenseCPU, expectedDonutDenseCPU, expectedHDenseCPU, expectedVDenseCPU, pvalBLDenseCPU, pvalDonutDenseCPU, pvalHDenseCPU, pvalVDenseCPU); } /** * just a direct implementation from the CUDA kernel * todo clean up and optimize after debugging and testing */ private GPUOutputContainer runCPUVersion(double[][] c, float[] d, float[] kr1, float[] kr2, float[] bound1, float[] bound3, float[] thresholdBL, float[] thresholdDonut, float[] thresholdH, float[] thresholdV, int[] rowBounds, int[] columnBounds) { float[][] observedDenseCPU = new float[matrixSizeCPU][matrixSizeCPU]; float[][] peakDenseCPU = new float[matrixSizeCPU][matrixSizeCPU]; float[][] binBLDenseCPU = new float[matrixSizeCPU][matrixSizeCPU]; float[][] binDonutDenseCPU = new float[matrixSizeCPU][matrixSizeCPU]; float[][] binHDenseCPU = new float[matrixSizeCPU][matrixSizeCPU]; float[][] binVDenseCPU = new float[matrixSizeCPU][matrixSizeCPU]; float[][] expectedBLDenseCPU = new float[matrixSizeCPU][matrixSizeCPU]; float[][] expectedDonutDenseCPU = new float[matrixSizeCPU][matrixSizeCPU]; float[][] expectedHDenseCPU = new float[matrixSizeCPU][matrixSizeCPU]; float[][] expectedVDenseCPU = new float[matrixSizeCPU][matrixSizeCPU]; //int t_col = threadIdx.x + blockIdx.x * blockDim.x;\n" + //" int t_row = threadIdx.y + blockIdx.y * blockDim.y;\n" + for (int t_row = HiCCUPS.regionMargin; t_row < matrixSizeCPU - HiCCUPS.regionMargin; t_row++) { for (int t_col = HiCCUPS.regionMargin; t_col < matrixSizeCPU - HiCCUPS.regionMargin; t_col++) { // Evalue is used to store the element of the matrix // that is computed by the thread float Evalue_bl = 0; float Edistvalue_bl = 0; float Evalue_donut = 0; float Edistvalue_donut = 0; float Evalue_h = 0; float Edistvalue_h = 0; float Evalue_v = 0; float Edistvalue_v = 0; float e_bl = 0; float e_donut = 0; float e_h = 0; float e_v = 0; float o = 0; float sbtrkt = 0; float bvalue_bl = 0; float bvalue_donut = 0; float bvalue_h = 0; float bvalue_v = 0; int wsize = windowCPU; int msize = matrixSizeCPU; int pwidth = peakWidthCPU; int buffer_width = HiCCUPS.regionMargin; int diff = (int) (bound1[0] - bound3[0]); int diagDist = Math.abs(t_row + diff - t_col); int maxIndex = msize - buffer_width; wsize = Math.min(wsize, (diagDist - 1) / 2); if (wsize <= pwidth) { wsize = pwidth + 1; } wsize = Math.min(wsize, buffer_width); // only run if within central window (not in data buffer margins) if (t_row >= buffer_width && t_row < maxIndex && t_col >= buffer_width && t_col < maxIndex) { // calculate initial bottom left box for (int i = t_row + 1; i <= t_row + wsize; i++) { for (int j = t_col - wsize; j < t_col; j++) { if (!Double.isNaN(c[i][j])) { if (i + diff - j < 0) { Evalue_bl += c[i][j]; Edistvalue_bl += d[Math.abs(i + diff - j)]; } } } } //Subtract off the middle peak for (int i = t_row + 1; i <= t_row + pwidth; i++) { for (int j = t_col - pwidth; j < t_col; j++) { if (!Double.isNaN(c[i][j])) { if (i + diff - j < 0) { Evalue_bl -= c[i][j]; Edistvalue_bl -= d[Math.abs(i + diff - j)]; } } } } //fix box dimensions while (Evalue_bl < 16) { Evalue_bl = 0; Edistvalue_bl = 0; wsize += 1; //dvisor = powf(wsize,2.0) - powf(pwidth,2.0); for (int i = t_row + 1; i <= t_row + wsize; i++) { for (int j = t_col - wsize; j < t_col; j++) { if (!Double.isNaN(c[i][j])) { if (i + diff - j < 0) { Evalue_bl += c[i][j]; int distVal = Math.abs(i + diff - j); Edistvalue_bl += d[distVal]; if (i >= t_row + 1) { if (i < t_row + pwidth + 1) { if (j >= t_col - pwidth) { if (j < t_col) { Evalue_bl -= c[i][j]; Edistvalue_bl -= d[distVal]; } } } } } } } } if (wsize >= buffer_width) { break; } if (2 * wsize >= diagDist) { break; } } // calculate donut for (int i = t_row - wsize; i <= t_row + wsize; ++i) { for (int j = t_col - wsize; j <= t_col + wsize; ++j) { if (!Double.isNaN(c[i][j])) { if (i + diff - j < 0) { Evalue_donut += c[i][j]; Edistvalue_donut += d[Math.abs(i + diff - j)]; } } } } //Subtract off the middle peak for (int i = t_row - pwidth; i <= t_row + pwidth; ++i) { for (int j = t_col - pwidth; j <= t_col + pwidth; ++j) { if (!Double.isNaN(c[i][j])) { if (i + diff - j < 0) { Evalue_donut -= c[i][j]; Edistvalue_donut -= d[Math.abs(i + diff - j)]; } } } } //Subtract off the cross hairs left side for (int i = t_row - wsize; i < t_row - pwidth; i++) { if (!Double.isNaN(c[i][t_col])) { Evalue_donut -= c[i][t_col]; Edistvalue_donut -= d[Math.abs(i + diff - t_col)]; } for (int j = -1; j <= 1; j++) { Evalue_v += c[i][t_col + j]; Edistvalue_v += d[Math.abs(i + diff - t_col - j)]; } } //Subtract off the cross hairs right side for (int i = t_row + pwidth + 1; i <= t_row + wsize; ++i) { if (!Double.isNaN(c[i][t_col])) { Evalue_donut -= c[i][t_col]; Edistvalue_donut -= d[Math.abs(i + diff - t_col)]; } for (int j = -1; j <= 1; ++j) { Evalue_v += c[i][t_col + j]; Edistvalue_v += d[Math.abs(i + diff - t_col - j)]; } } //Subtract off the cross hairs top side for (int j = t_col - wsize; j < t_col - pwidth; ++j) { if (!Double.isNaN(c[t_row][j])) { Evalue_donut -= c[t_row][j]; Edistvalue_donut -= d[Math.abs(t_row + diff - j)]; } for (int i = -1; i <= 1; ++i) { Evalue_h += c[t_row + i][j]; Edistvalue_h += d[Math.abs(t_row + i + diff - j)]; } } //Subtract off the cross hairs bottom side for (int j = t_col + pwidth + 1; j <= t_col + wsize; ++j) { if (!Double.isNaN(c[t_row][j])) { Evalue_donut -= c[t_row][j]; Edistvalue_donut -= d[Math.abs(t_row + diff - j)]; } for (int i = -1; i <= 1; ++i) { Evalue_h += c[t_row + i][j]; Edistvalue_h += d[Math.abs(t_row + i + diff - j)]; } } } e_bl = ((Evalue_bl * d[diagDist]) / Edistvalue_bl) * kr1[t_row] * kr2[t_col]; e_donut = ((Evalue_donut * d[diagDist]) / Edistvalue_donut) * kr1[t_row] * kr2[t_col]; e_h = ((Evalue_h * d[diagDist]) / Edistvalue_h) * kr1[t_row] * kr2[t_col]; e_v = ((Evalue_v * d[diagDist]) / Edistvalue_v) * kr1[t_row] * kr2[t_col]; float lognorm = (float) Math.log(Math.pow(2.0, .33)); if (!Float.isNaN(e_bl) && !Float.isInfinite(e_bl)) { if (e_bl <= 1) { bvalue_bl = 0; } else { bvalue_bl = (float) Math.floor(Math.log(e_bl) / lognorm); } } if (!Float.isNaN(e_donut) && !Float.isInfinite(e_donut)) { if (e_donut <= 1) { bvalue_donut = 0; } else { bvalue_donut = (float) Math.floor(Math.log(e_donut) / lognorm); } } if (!Float.isNaN(e_h) && !Float.isInfinite(e_h)) { if (e_h <= 1) { bvalue_h = 0; } else { bvalue_h = (float) Math.floor(Math.log(e_h) / lognorm); } } if (!Float.isNaN(e_v) && !Float.isInfinite(e_v)) { if (e_v <= 1) { bvalue_v = 0; } else { bvalue_v = (float) Math.floor(Math.log(e_v) / lognorm); } } // todo why are bin values exceeding w1 in cpu version? // do they exceed in gpu version as well bvalue_bl = Math.min(bvalue_bl, HiCCUPS.w1 - 1); bvalue_donut = Math.min(bvalue_donut, HiCCUPS.w1 - 1); bvalue_h = Math.min(bvalue_h, HiCCUPS.w1 - 1); bvalue_v = Math.min(bvalue_v, HiCCUPS.w1 - 1); // Write the matrix to device memory; // each thread writes one element expectedBLDenseCPU[t_row][t_col] = e_bl; expectedDonutDenseCPU[t_row][t_col] = e_donut; expectedHDenseCPU[t_row][t_col] = e_h; expectedVDenseCPU[t_row][t_col] = e_v; o = Math.round(c[t_row][t_col] * kr1[t_row] * kr2[t_col]); observedDenseCPU[t_row][t_col] = o; binBLDenseCPU[t_row][t_col] = bvalue_bl; binDonutDenseCPU[t_row][t_col] = bvalue_donut; binHDenseCPU[t_row][t_col] = bvalue_h; binVDenseCPU[t_row][t_col] = bvalue_v; //System.out.println("thresholdBL "+thresholdBL.length+" thresholdDonut "+thresholdDonut.length); //System.out.println("a "+bvalue_bl+" b "+bvalue_donut); sbtrkt = Math.max(thresholdBL[(int) bvalue_bl], thresholdDonut[(int) bvalue_donut]); sbtrkt = Math.max(sbtrkt, thresholdH[(int) bvalue_h]); sbtrkt = Math.max(sbtrkt, thresholdV[(int) bvalue_v]); peakDenseCPU[t_row][t_col] = o - sbtrkt; } } // x2, y2 not inclusive here int finalWidthX = rowBounds[5] - rowBounds[4]; int finalWidthY = columnBounds[5] - columnBounds[4]; // x2, y2 not inclusive here int x1 = rowBounds[2]; int y1 = columnBounds[2]; int x2 = x1 + finalWidthX; int y2 = y1 + finalWidthY; //System.out.println("flat = "+flattenedSize+" n = "+matrixSize+" x1 = "+x1+" x2 = "+x2+" y1 = "+y1+" y2 ="+y2); observedDenseCPU = MatrixTools.extractLocalMatrixRegion(observedDenseCPU, x1, x2, y1, y2); peakDenseCPU = MatrixTools.extractLocalMatrixRegion(peakDenseCPU, x1, x2, y1, y2); binBLDenseCPU = MatrixTools.extractLocalMatrixRegion(binBLDenseCPU, x1, x2, y1, y2); binDonutDenseCPU = MatrixTools.extractLocalMatrixRegion(binDonutDenseCPU, x1, x2, y1, y2); binHDenseCPU = MatrixTools.extractLocalMatrixRegion(binHDenseCPU, x1, x2, y1, y2); binVDenseCPU = MatrixTools.extractLocalMatrixRegion(binVDenseCPU, x1, x2, y1, y2); expectedBLDenseCPU = MatrixTools.extractLocalMatrixRegion(expectedBLDenseCPU, x1, x2, y1, y2); expectedDonutDenseCPU = MatrixTools.extractLocalMatrixRegion(expectedDonutDenseCPU, x1, x2, y1, y2); expectedHDenseCPU = MatrixTools.extractLocalMatrixRegion(expectedHDenseCPU, x1, x2, y1, y2); expectedVDenseCPU = MatrixTools.extractLocalMatrixRegion(expectedVDenseCPU, x1, x2, y1, y2); return new GPUOutputContainer(observedDenseCPU, peakDenseCPU, binBLDenseCPU, binDonutDenseCPU, binHDenseCPU, binVDenseCPU, expectedBLDenseCPU, expectedDonutDenseCPU, expectedHDenseCPU, expectedVDenseCPU); } } ================================================ FILE: src/juicebox/tools/utils/juicer/hiccups/GPUHelper.java ================================================ /* * The MIT License (MIT) * * Copyright (c) 2011-2020 Broad Institute, Aiden Lab, Rice University, Baylor College of Medicine * * Permission is hereby granted, free of charge, to any person obtaining a copy * of this software and associated documentation files (the "Software"), to deal * in the Software without restriction, including without limitation the rights * to use, copy, modify, merge, publish, distribute, sublicense, and/or sell * copies of the Software, and to permit persons to whom the Software is * furnished to do so, subject to the following conditions: * * The above copyright notice and this permission notice shall be included in * all copies or substantial portions of the Software. * * THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR * IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, * FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE * AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER * LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, * OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN * THE SOFTWARE. */ package juicebox.tools.utils.juicer.hiccups; import jcuda.Pointer; import jcuda.Sizeof; import jcuda.driver.CUdeviceptr; import juicebox.tools.utils.common.MatrixTools; import static jcuda.driver.JCudaDriver.*; /** * Created by muhammadsaadshamim on 5/8/15. */ class GPUHelper { public static CUdeviceptr allocateOutput(int size, int typeSize) { CUdeviceptr dOutput = new CUdeviceptr(); cuMemAlloc(dOutput, size * typeSize); return dOutput; } public static CUdeviceptr allocateInput(float[] input) { int typeSize = Sizeof.FLOAT; Pointer ptr = Pointer.to(input); int size = input.length; CUdeviceptr dInput = new CUdeviceptr(); cuMemAlloc(dInput, size * Sizeof.FLOAT); cuMemcpyHtoD(dInput, ptr, size * typeSize); return dInput; } public static void freeUpMemory(CUdeviceptr[] pointers) { for (CUdeviceptr pointer : pointers) { cuMemFree(pointer); } } public static float[][] GPUArraytoCPUMatrix(float[] result, int n, int x1, int x2, int y1, int y2) { return MatrixTools.extractLocalMatrixRegion( MatrixTools.reshapeFlatMatrix(result, n), x1, x2, y1, y2); } } ================================================ FILE: src/juicebox/tools/utils/juicer/hiccups/GPUOutputContainer.java ================================================ /* * The MIT License (MIT) * * Copyright (c) 2011-2020 Broad Institute, Aiden Lab, Rice University, Baylor College of Medicine * * Permission is hereby granted, free of charge, to any person obtaining a copy * of this software and associated documentation files (the "Software"), to deal * in the Software without restriction, including without limitation the rights * to use, copy, modify, merge, publish, distribute, sublicense, and/or sell * copies of the Software, and to permit persons to whom the Software is * furnished to do so, subject to the following conditions: * * The above copyright notice and this permission notice shall be included in * all copies or substantial portions of the Software. * * THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR * IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, * FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE * AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER * LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, * OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN * THE SOFTWARE. */ package juicebox.tools.utils.juicer.hiccups; import juicebox.HiCGlobals; import juicebox.tools.utils.common.ArrayTools; import juicebox.track.feature.Feature2D; import juicebox.track.feature.Feature2DList; import java.util.List; /** * Created by muhammadsaadshamim on 5/12/15. */ public class GPUOutputContainer { private final float[][] observed; private final float[][] peak; private final float[][] binBL; private final float[][] binDonut; private final float[][] binH; private final float[][] binV; private final float[][] expectedBL; private final float[][] expectedDonut; private final float[][] expectedH; private final float[][] expectedV; private final int numRows; private final int numColumns; public GPUOutputContainer(float[][] observed, float[][] peak, float[][] binBL, float[][] binDonut, float[][] binH, float[][] binV, float[][] expectedBL, float[][] expectedDonut, float[][] expectedH, float[][] expectedV) { this.observed = ArrayTools.deepCopy(observed); this.peak = ArrayTools.deepCopy(peak); this.numRows = observed.length; this.numColumns = observed[0].length; this.binBL = ArrayTools.deepCopy(binBL); this.binDonut = ArrayTools.deepCopy(binDonut); this.binH = ArrayTools.deepCopy(binH); this.binV = ArrayTools.deepCopy(binV); this.expectedBL = ArrayTools.deepCopy(expectedBL); this.expectedDonut = ArrayTools.deepCopy(expectedDonut); this.expectedH = ArrayTools.deepCopy(expectedH); this.expectedV = ArrayTools.deepCopy(expectedV); } /** * Ensure NaN entries are uniform across the various arrays */ public void cleanUpBinNans() { for (int i = 0; i < numRows; i++) { for (int j = 0; j < numColumns; j++) { if (Float.isNaN(expectedBL[i][j]) || Float.isNaN(expectedDonut[i][j]) || Float.isNaN(expectedH[i][j]) || Float.isNaN(expectedV[i][j])) { binBL[i][j] = Float.NaN; binDonut[i][j] = Float.NaN; binH[i][j] = Float.NaN; binV[i][j] = Float.NaN; } } } } public void cleanUpPeakNaNs() { for (int i = 0; i < numRows; i++) { for (int j = 0; j < numColumns; j++) { if (Float.isNaN(expectedBL[i][j]) || Float.isNaN(expectedDonut[i][j]) || Float.isNaN(expectedH[i][j]) || Float.isNaN(expectedV[i][j])) { peak[i][j] = Float.NaN; } } } } public synchronized void updateHistograms(long[][] histBL, long[][] histDonut, long[][] histH, long[][] histV, int maxRows, int maxColumns) { for (int i = 0; i < numRows; i++) { for (int j = 0; j < numColumns; j++) { if (Float.isNaN(observed[i][j]) || Float.isInfinite(observed[i][j])) continue; int val = (int) observed[i][j]; processHistogramValue(binBL[i][j], val, histBL, maxRows, maxColumns); processHistogramValue(binDonut[i][j], val, histDonut, maxRows, maxColumns); processHistogramValue(binH[i][j], val, histH, maxRows, maxColumns); processHistogramValue(binV[i][j], val, histV, maxRows, maxColumns); } } } private void processHistogramValue(float potentialRowIndex, int columnIndex, long[][] histogram, int maxRows, int maxColumns) { if (Float.isNaN(potentialRowIndex)) return; int rowIndex = (int) potentialRowIndex; if (rowIndex >= 0 && rowIndex < maxRows) { if (columnIndex >= 0 && columnIndex < maxColumns) { histogram[rowIndex][columnIndex] += 1; if (HiCGlobals.printVerboseComments && histogram[rowIndex][columnIndex] < 0) { System.out.println("earlier source row " + rowIndex + " col " + columnIndex + " -- " + histogram[rowIndex][columnIndex]); } } } } public void cleanUpBinDiagonal(int relativeDiagonal) { // correction for diagonal (don't need to double number of calculations) if (relativeDiagonal >= (-1 * numRows)) { // TODO optimize so only necessary region eliminated for (int i = 0; i < numRows; i++) { for (int j = 0; j < numColumns; j++) { if (j - i <= relativeDiagonal) { binBL[i][j] = Float.NaN; binDonut[i][j] = Float.NaN; binH[i][j] = Float.NaN; binV[i][j] = Float.NaN; } } } } } public void cleanUpPeakDiagonal(int relativeDiagonal) { if (relativeDiagonal >= (-1 * numRows)) { // TODO optimize so only necessary region eliminated for (int i = 0; i < numRows; i++) { for (int j = 0; j < numColumns; j++) { if (j - i <= relativeDiagonal) { peak[i][j] = Float.NaN; } } } } } public Feature2DList extractPeaks(int chrIndex, String chrName, int w1, int w2, int rowOffset, int columnOffset, int resolution) { Feature2DList peaks = new Feature2DList(); for (int i = 0; i < numRows; i++) { for (int j = 0; j < numColumns; j++) { float peakVal = peak[i][j]; if (Float.isNaN(peakVal) || peakVal <= 0) continue; float observedVal = observed[i][j]; float expectedBLVal = expectedBL[i][j]; float expectedDonutVal = expectedDonut[i][j]; float expectedHVal = expectedH[i][j]; float expectedVVal = expectedV[i][j]; float binBLVal = binBL[i][j]; float binDonutVal = binDonut[i][j]; float binHVal = binH[i][j]; float binVVal = binV[i][j]; int rowPos = (i + rowOffset) * resolution; int colPos = (j + columnOffset) * resolution; if (!(Float.isNaN(observedVal) || Float.isNaN(expectedBLVal) || Float.isNaN(expectedDonutVal) || Float.isNaN(expectedHVal) || Float.isNaN(expectedVVal) || Float.isNaN(binBLVal) || Float.isNaN(binDonutVal) || Float.isNaN(binHVal) || Float.isNaN(binVVal))) { if (observedVal < w2 && binBLVal < w1 && binDonutVal < w1 && binHVal < w1 && binVVal < w1) { peaks.add(chrIndex, chrIndex, HiCCUPSUtils.generatePeak(chrName, observedVal, peakVal, rowPos, colPos, expectedBLVal, expectedDonutVal, expectedHVal, expectedVVal, binBLVal, binDonutVal, binHVal, binVVal, resolution)); } } } } return peaks; } public Feature2DList extractPeaksListGiven(int chrIndex, String chrName, int w1, int w2, int rowOffset, int columnOffset, int resolution, List inputListFoundFeatures) { Feature2DList peaks = new Feature2DList(); for (Feature2D f : inputListFoundFeatures) { int i = (int) ((f.getStart1() + f.getEnd1()) / (2 * resolution)) - rowOffset; int j = (int) ((f.getStart2() + f.getEnd2()) / (2 * resolution)) - columnOffset; float peakVal = peak[i][j]; float observedVal = observed[i][j]; float expectedBLVal = expectedBL[i][j]; float expectedDonutVal = expectedDonut[i][j]; float expectedHVal = expectedH[i][j]; float expectedVVal = expectedV[i][j]; float binBLVal = binBL[i][j]; float binDonutVal = binDonut[i][j]; float binHVal = binH[i][j]; float binVVal = binV[i][j]; int rowPos = (i + rowOffset) * resolution; int colPos = (j + columnOffset) * resolution; if (!(Float.isNaN(observedVal) || Float.isNaN(expectedBLVal) || Float.isNaN(expectedDonutVal) || Float.isNaN(expectedHVal) || Float.isNaN(expectedVVal) || Float.isNaN(binBLVal) || Float.isNaN(binDonutVal) || Float.isNaN(binHVal) || Float.isNaN(binVVal))) { if (observedVal < w2 && binBLVal < w1 && binDonutVal < w1 && binHVal < w1 && binVVal < w1) { peaks.add(chrIndex, chrIndex, HiCCUPSUtils.generatePeak(chrName, observedVal, peakVal, rowPos, colPos, expectedBLVal, expectedDonutVal, expectedHVal, expectedVVal, binBLVal, binDonutVal, binHVal, binVVal, resolution)); } } } return peaks; } } ================================================ FILE: src/juicebox/tools/utils/juicer/hiccups/GPUOutputContainer2.java ================================================ /* * The MIT License (MIT) * * Copyright (c) 2011-2020 Broad Institute, Aiden Lab * * Permission is hereby granted, free of charge, to any person obtaining a copy * of this software and associated documentation files (the "Software"), to deal * in the Software without restriction, including without limitation the rights * to use, copy, modify, merge, publish, distribute, sublicense, and/or sell * copies of the Software, and to permit persons to whom the Software is * furnished to do so, subject to the following conditions: * * The above copyright notice and this permission notice shall be included in * all copies or substantial portions of the Software. * * THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR * IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, * FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE * AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER * LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, * OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN * THE SOFTWARE. */ package juicebox.tools.utils.juicer.hiccups; import juicebox.HiCGlobals; import juicebox.tools.utils.common.ArrayTools; import juicebox.track.feature.Feature2D; import juicebox.track.feature.Feature2DList; import java.util.ArrayList; import java.util.List; import java.util.Map; /** * Created by muhammadsaadshamim on 5/12/15. */ public class GPUOutputContainer2 { private final float[][] observed; private final float[][] peak; private final float[][] binBL; private final float[][] binDonut; private final float[][] binH; private final float[][] binV; private final float[][] expectedBL; private final float[][] expectedDonut; private final float[][] expectedH; private final float[][] expectedV; private final float[][] pvalBL; private final float[][] pvalDonut; private final float[][] pvalH; private final float[][] pvalV; private final int numRows; private final int numColumns; public GPUOutputContainer2(float[][] observed, float[][] peak, float[][] binBL, float[][] binDonut, float[][] binH, float[][] binV, float[][] expectedBL, float[][] expectedDonut, float[][] expectedH, float[][] expectedV, float[][] pvalBL, float[][] pvalDonut, float[][] pvalH, float[][] pvalV) { this.observed = ArrayTools.deepCopy(observed); this.peak = ArrayTools.deepCopy(peak); this.numRows = observed.length; this.numColumns = observed[0].length; this.binBL = ArrayTools.deepCopy(binBL); this.binDonut = ArrayTools.deepCopy(binDonut); this.binH = ArrayTools.deepCopy(binH); this.binV = ArrayTools.deepCopy(binV); this.expectedBL = ArrayTools.deepCopy(expectedBL); this.expectedDonut = ArrayTools.deepCopy(expectedDonut); this.expectedH = ArrayTools.deepCopy(expectedH); this.expectedV = ArrayTools.deepCopy(expectedV); this.pvalBL = ArrayTools.deepCopy(pvalBL); this.pvalDonut = ArrayTools.deepCopy(pvalDonut); this.pvalH = ArrayTools.deepCopy(pvalH); this.pvalV = ArrayTools.deepCopy(pvalV); } /** * Ensure NaN entries are uniform across the various arrays */ public void cleanUpBinNans() { for (int i = 0; i < numRows; i++) { for (int j = 0; j < numColumns; j++) { if (Float.isNaN(expectedBL[i][j]) || Float.isNaN(expectedDonut[i][j]) || Float.isNaN(expectedH[i][j]) || Float.isNaN(expectedV[i][j])) { binBL[i][j] = Float.NaN; binDonut[i][j] = Float.NaN; binH[i][j] = Float.NaN; binV[i][j] = Float.NaN; } } } } public void cleanUpPvalNans() { for (int i = 0; i < numRows; i++) { for (int j = 0; j < numColumns; j++) { if (Float.isNaN(expectedBL[i][j]) || Float.isNaN(expectedDonut[i][j]) || Float.isNaN(expectedH[i][j]) || Float.isNaN(expectedV[i][j])) { pvalBL[i][j] = Float.NaN; pvalDonut[i][j] = Float.NaN; pvalH[i][j] = Float.NaN; pvalV[i][j] = Float.NaN; } if (expectedBL[i][j] == 0 || expectedDonut[i][j] == 0 || expectedH[i][j] == 0 || expectedV[i][j] == 0) { pvalBL[i][j] = Float.NaN; pvalDonut[i][j] = Float.NaN; pvalH[i][j] = Float.NaN; pvalV[i][j] = Float.NaN; } } } } public void cleanUpPeakNaNs() { for (int i = 0; i < numRows; i++) { for (int j = 0; j < numColumns; j++) { if (Float.isNaN(expectedBL[i][j]) || Float.isNaN(expectedDonut[i][j]) || Float.isNaN(expectedH[i][j]) || Float.isNaN(expectedV[i][j])) { peak[i][j] = Float.NaN; } } } } public synchronized void updateHistograms(long[][] histBL, long[][] histDonut, long[][] histH, long[][] histV, int maxRows) { for (int i = 0; i < numRows; i++) { for (int j = 0; j < numColumns; j++) { if (Float.isNaN(observed[i][j]) || Float.isInfinite(observed[i][j])) continue; int val = (int) observed[i][j]; processHistogramValue(binBL[i][j], val, histBL, maxRows); processHistogramValue(binDonut[i][j], val, histDonut, maxRows); processHistogramValue(binH[i][j], val, histH, maxRows); processHistogramValue(binV[i][j], val, histV, maxRows); } } } private void processHistogramValue(float potentialRowIndex, int columnIndex, long[][] histogram, int maxRows) { if (Float.isNaN(potentialRowIndex)) return; int rowIndex = (int) potentialRowIndex; if (rowIndex >= 0 && rowIndex < maxRows) { histogram[rowIndex][0] += 1; if (HiCGlobals.printVerboseComments && histogram[rowIndex][0] < 0) { System.out.println("earlier source row " + rowIndex + " col " + columnIndex + " -- " + histogram[rowIndex][0]); } } } public synchronized void updatePvalLists(Map> pvalBLMap, Map> pvalDonutMap, Map> pvalHMap, Map> pvalVMap, long[][] histBL, long[][] histDonut, long[][] histH, long[][] histV, int maxRows, double FDRthreshold) { for (int i = 0; i < numRows; i++) { for (int j = 0; j < numColumns; j++) { if (Float.isNaN(observed[i][j]) || Float.isInfinite(observed[i][j])) continue; processPValue(binBL[i][j], pvalBL[i][j], histBL, pvalBLMap, maxRows, FDRthreshold); processPValue(binDonut[i][j], pvalDonut[i][j], histDonut, pvalDonutMap, maxRows, FDRthreshold); processPValue(binH[i][j], pvalH[i][j], histH, pvalHMap, maxRows, FDRthreshold); processPValue(binV[i][j], pvalV[i][j], histV, pvalVMap, maxRows, FDRthreshold); } } } private synchronized void processPValue(float potentialRowIndex, float potentialPValue, long[][] hist, Map> kHist, int maxRows, double FDRthreshold) { if (Float.isNaN(potentialRowIndex)) return; if (Float.isNaN(potentialPValue)) return; int rowIndex = (int) potentialRowIndex; if (rowIndex >= 0 && rowIndex < maxRows) { if (potentialPValue < FDRthreshold) { hist[rowIndex][1]++; double ktemp = (potentialPValue * hist[rowIndex][0]) / FDRthreshold; long k = ktemp == Math.ceil(ktemp) ? (long) ktemp + 1 : (long) ktemp; if (kHist.get(rowIndex).get(k) == null) { kHist.get(rowIndex).put(k, 1); } else { kHist.get(rowIndex).put(k, kHist.get(rowIndex).get(k) + 1); } } } } public void cleanUpBinDiagonal(int relativeDiagonal) { // correction for diagonal (don't need to double number of calculations) if (relativeDiagonal >= (-1 * numRows)) { // TODO optimize so only necessary region eliminated for (int i = 0; i < numRows; i++) { for (int j = 0; j < numColumns; j++) { if (j - i <= relativeDiagonal) { binBL[i][j] = Float.NaN; binDonut[i][j] = Float.NaN; binH[i][j] = Float.NaN; binV[i][j] = Float.NaN; } } } } } public void cleanUpPeakDiagonal(int relativeDiagonal) { if (relativeDiagonal >= (-1 * numRows)) { // TODO optimize so only necessary region eliminated for (int i = 0; i < numRows; i++) { for (int j = 0; j < numColumns; j++) { if (j - i <= relativeDiagonal) { peak[i][j] = Float.NaN; } } } } } public Feature2DList extractPeaks(int chrIndex, String chrName, int w1, int w2, int rowOffset, int columnOffset, int resolution) { Feature2DList peaks = new Feature2DList(); for (int i = 0; i < numRows; i++) { for (int j = 0; j < numColumns; j++) { float peakVal = peak[i][j]; if (Float.isNaN(peakVal) || peakVal <= 0 || Float.isNaN(pvalBL[i][j]) || Float.isNaN(pvalDonut[i][j]) || Float.isNaN(pvalH[i][j]) || Float.isNaN(pvalV[i][j])) continue; float observedVal = observed[i][j]; float expectedBLVal = expectedBL[i][j]; float expectedDonutVal = expectedDonut[i][j]; float expectedHVal = expectedH[i][j]; float expectedVVal = expectedV[i][j]; float binBLVal = binBL[i][j]; float binDonutVal = binDonut[i][j]; float binHVal = binH[i][j]; float binVVal = binV[i][j]; float pvalBLVal = pvalBL[i][j]; float pvalDonutVal = pvalDonut[i][j]; float pvalHVal = pvalH[i][j]; float pvalVVal = pvalV[i][j]; int rowPos = (i + rowOffset) * resolution; int colPos = (j + columnOffset) * resolution; if (!(Float.isNaN(observedVal) || Float.isNaN(expectedBLVal) || Float.isNaN(expectedDonutVal) || Float.isNaN(expectedHVal) || Float.isNaN(expectedVVal) || Float.isNaN(binBLVal) || Float.isNaN(binDonutVal) || Float.isNaN(binHVal) || Float.isNaN(binVVal) || Float.isNaN(pvalBLVal) || Float.isNaN(pvalDonutVal) || Float.isNaN(pvalHVal) || Float.isNaN(pvalVVal))) { if (observedVal < w2 && binBLVal < w1 && binDonutVal < w1 && binHVal < w1 && binVVal < w1) { peaks.add(chrIndex, chrIndex, HiCCUPSUtils.generatePeak(chrName, observedVal, peakVal, rowPos, colPos, expectedBLVal, expectedDonutVal, expectedHVal, expectedVVal, binBLVal, binDonutVal, binHVal, binVVal, resolution, pvalBLVal, pvalDonutVal, pvalHVal, pvalVVal)); } } } } return peaks; } public Feature2DList extractPeaksListGiven(int chrIndex, String chrName, int w1, int w2, int rowOffset, int columnOffset, int resolution, List inputListFoundFeatures) { Feature2DList peaks = new Feature2DList(); for (Feature2D f : inputListFoundFeatures) { int i = (int) ((f.getStart1() + f.getEnd1()) / (2 * resolution)) - rowOffset; int j = (int) ((f.getStart2() + f.getEnd2()) / (2 * resolution)) - columnOffset; float peakVal = peak[i][j]; float observedVal = observed[i][j]; float expectedBLVal = expectedBL[i][j]; float expectedDonutVal = expectedDonut[i][j]; float expectedHVal = expectedH[i][j]; float expectedVVal = expectedV[i][j]; float binBLVal = binBL[i][j]; float binDonutVal = binDonut[i][j]; float binHVal = binH[i][j]; float binVVal = binV[i][j]; float pvalBLVal = pvalBL[i][j]; float pvalDonutVal = pvalDonut[i][j]; float pvalHVal = pvalH[i][j]; float pvalVVal = pvalV[i][j]; int rowPos = (i + rowOffset) * resolution; int colPos = (j + columnOffset) * resolution; if (!(Float.isNaN(observedVal) || Float.isNaN(expectedBLVal) || Float.isNaN(expectedDonutVal) || Float.isNaN(expectedHVal) || Float.isNaN(expectedVVal) || Float.isNaN(binBLVal) || Float.isNaN(binDonutVal) || Float.isNaN(binHVal) || Float.isNaN(binVVal))) { if (observedVal < w2 && binBLVal < w1 && binDonutVal < w1 && binHVal < w1 && binVVal < w1) { peaks.add(chrIndex, chrIndex, HiCCUPSUtils.generatePeak(chrName, observedVal, peakVal, rowPos, colPos, expectedBLVal, expectedDonutVal, expectedHVal, expectedVVal, binBLVal, binDonutVal, binHVal, binVVal, resolution, pvalBLVal, pvalDonutVal, pvalHVal, pvalVVal)); } } } return peaks; } } ================================================ FILE: src/juicebox/tools/utils/juicer/hiccups/GPUTesting.java ================================================ /* * The MIT License (MIT) * * Copyright (c) 2011-2020 Broad Institute, Aiden Lab, Rice University, Baylor College of Medicine * * Permission is hereby granted, free of charge, to any person obtaining a copy * of this software and associated documentation files (the "Software"), to deal * in the Software without restriction, including without limitation the rights * to use, copy, modify, merge, publish, distribute, sublicense, and/or sell * copies of the Software, and to permit persons to whom the Software is * furnished to do so, subject to the following conditions: * * The above copyright notice and this permission notice shall be included in * all copies or substantial portions of the Software. * * THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR * IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, * FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE * AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER * LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, * OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN * THE SOFTWARE. */ package juicebox.tools.utils.juicer.hiccups; import jcuda.Pointer; import jcuda.Sizeof; import jcuda.driver.CUdeviceptr; import jcuda.driver.JCudaDriver; import jcuda.utils.KernelLauncher; import java.util.Arrays; import static jcuda.driver.JCudaDriver.cuMemFree; import static jcuda.driver.JCudaDriver.cuMemcpyDtoH; /** * Created by muhammadsaadshamim on 5/7/15. */ class GPUTesting { public static void test() { JCudaDriver.setExceptionsEnabled(true); String sourceCode = "extern \"C\"" + "\n" + "__global__ void add(float *result, float *a, float *b)" + "\n" + "{" + "\n" + " int i = threadIdx.x;" + "\n" + " result[i] = a[i] + b[i];" + "\n" + "}"; // Prepare the kernel System.out.println("Preparing the KernelLauncher..."); KernelLauncher kernelLauncher = KernelLauncher.compile(sourceCode, "add"); // Create the input data System.out.println("Creating input data..."); int size = 10; float[] result = new float[size]; float[] a = new float[size]; float[] b = new float[size]; for (int i = 0; i < size; i++) { a[i] = i; b[i] = i; } // Allocate the device memory and copy the input // data to the device System.out.println("Initializing device memory..."); CUdeviceptr dResult = GPUHelper.allocateOutput(size, Sizeof.FLOAT); CUdeviceptr dA = GPUHelper.allocateInput(a); CUdeviceptr dB = GPUHelper.allocateInput(b); System.out.println("Calling the kernel..."); kernelLauncher.setBlockSize(size, 1, 1); kernelLauncher.call(dResult, dA, dB); // Copy the result from the device to the host System.out.println("Obtaining results..."); cuMemcpyDtoH(Pointer.to(result), dResult, size * Sizeof.FLOAT); System.out.println("Result: " + Arrays.toString(result)); // Clean up cuMemFree(dA); cuMemFree(dB); cuMemFree(dResult); } } ================================================ FILE: src/juicebox/tools/utils/juicer/hiccups/HiCCUPS2Kernel_1kb.cu ================================================ /** * Returns the incomplete gamma function P(a,x), evaluated by its series * representation. Assumes a > 0 and x >= 0. */ __device__ float gser(float a, float x){ int GAMMA_ITMAX = 200; float GAMMA_EPS = 2.22e-16; float ap, del, sum; int i; ap = a; del = 1.0/a; sum = del; for (i = 1; i <= GAMMA_ITMAX; ++ i) { ap += 1.0; del *= x/ap; sum += del; if (fabsf(del) < fabsf(sum)*GAMMA_EPS) { return sum*expf(-x + a*logf(x) - lgammaf(a)); } } return 1.0; // Too many iterations } /** * Returns the complementary incomplete gamma function Q(a,x), evaluated by its * continued fraction representation. Assumes a > 0 and x >= 0. */ __device__ float gcf(float a, float x){ int GAMMA_ITMAX = 200; float GAMMA_EPS = 2.22e-16; float GAMMA_FPMIN = (1.18e-38/GAMMA_EPS); float b, c, d, h, an, del; int i; b = x + 1.0 - a; c = 1.0/GAMMA_FPMIN; d = 1.0/b; h = d; for (i = 1; i <= GAMMA_ITMAX; ++ i) { an = -i*(i - a); b += 2.0; d = an*d + b; if (fabsf(d) < GAMMA_FPMIN) d = GAMMA_FPMIN; c = b + an/c; if (fabsf(c) < GAMMA_FPMIN) c = GAMMA_FPMIN; d = 1.0/d; del = d*c; h *= del; if (fabsf(del - 1.0) < GAMMA_EPS) { return expf(-x + a*logf(x) - lgammaf(a))*h; } } return 0.0; // Too many iterations } /** * Returns the incomplete gamma function P(a,x). */ __device__ float gammp(float a, float x){ //if (a <= 0.0) die ("gammp(): a illegal"); //if (x < 0.0) die ("gammp(): x illegal"); return x == 0.0 ? 0.0 : x < a + 1.0 ? gser(a,x) : 1.0 - gcf(a,x); } /** * Returns the complementary incomplete gamma function Q(a,x) = 1 - P(a,x). */ __device__ float gammq(float a, float x){ //if (a <= 0.0) die ("gammq(): a illegal"); //if (x < 0.0) die ("gammq(): x illegal"); if (x <= powf(2.0,-3.33)) { return x == 0.0 ? 1.0 : x < a + 1.0 ? 1.0 - gser(a,powf(2.0,-3.33)) : gcf(a, powf(2.0,-3.33)); } else { return x == 0.0 ? 1.0 : x < a + 1.0 ? 1.0 - gser(a,x) : gcf(a,x); } } __device__ void ensure_appropriate_values(float e_value, float lognormval, float* bvalue){ if (!isnan(e_value) && !isinf(e_value)) { if (e_value<=powf(2.0,-3.33)) { *bvalue = 0; } else { *bvalue = floorf(logf(e_value)/lognormval)+11; } } *bvalue = (float) min((int) *bvalue, HiCCUPS_W1_MAX_INDX ); } __device__ void process_masks_lr(int i_start, int i_max_p1, int msize, int t_col, float *c,float *d, int diff, float* evalue_d, float* evalue_dist_d, float* evalue_v, float* evalue_dist_v){ for (int i = i_start; i < i_max_p1; i++) { int index = i * msize + t_col; if (!isnan(c[index])) { *evalue_d -= c[index]; *evalue_dist_d -= d[abs(i+diff-t_col)]; } for (int j = -1; j < 2; j++) { *evalue_v += c[index + j]; *evalue_dist_v += d[abs(i+diff-t_col-j)]; } } } __device__ void process_masks_tb(int j_start, int j_max_p1, int msize, int t_row, float *c,float *d, int diff, float* evalue_d, float* evalue_dist_d, float* evalue_h, float* evalue_dist_h){ for (int j = j_start; j < j_max_p1; j++) { int index = t_row * msize + j; if (!isnan(c[index])) { *evalue_d -= c[index]; *evalue_dist_d -= d[abs(t_row+diff-j)]; } for (int i = -1; i < 2; i++) { *evalue_h += c[(t_row+i) * msize + j]; *evalue_dist_h += d[abs(t_row+i+diff-j)]; } } } extern "C" __global__ void BasicPeakCallingKernel(float *c, float *expectedbl, float *expecteddonut, float *expectedh, float *expectedv, float *observed, float *b_bl, float *b_donut, float *b_h, float *b_v, float *p, float *p_bl, float *p_donut, float *p_h, float *p_v, float *tbl, float *td, float *th, float *tv, float *d, float *kr1, float *kr2, float *bound1, float *bound3) { // 2D Thread ID int t_col = threadIdx.x + blockIdx.x * blockDim.x; int t_row = threadIdx.y + blockIdx.y * blockDim.y; // Evalue is used to store the element of the matrix // that is computed by the thread float Evalue_bl = 0; float Edistvalue_bl = 0; float Evalue_donut = 0; float Edistvalue_donut = 0; float Evalue_h = 0; float Edistvalue_h = 0; float Evalue_v = 0; float Edistvalue_v = 0; float e_bl = 0; float e_donut = 0; float e_h = 0; float e_v = 0; float o = 0; float bvalue_bl = 0; float bvalue_donut = 0; float bvalue_h = 0; float bvalue_v = 0; float pvalue_bl = 1; float pvalue_donut = 1; float pvalue_h = 1; float pvalue_v = 1; int wsize = HiCCUPS_WINDOW; int msize = HiCCUPS_MATRIX_SIZE; int pwidth = HiCCUPS_PEAK_WIDTH; int buffer_width = HiCCUPS_REGION_MARGIN; int diff = bound1[0] - bound3[0]; int diagDist = abs(t_row+diff-t_col); int maxIndex = msize-buffer_width; wsize = min(wsize, (abs(t_row+diff-t_col)-1)/2); if (wsize <= pwidth) { wsize = pwidth + 1; } wsize = min(wsize, buffer_width); // only run if within central window (not in data buffer margins) if (t_row >= buffer_width && t_row= buffer_width && t_col t_row && i < t_row+pwidth+1 && j > t_col-pwidth-1 && j < t_col) { Evalue_bl -= c[index]; Edistvalue_bl -= d[abs(i+diff-j)]; } } } } if (wsize >= buffer_width) { break; } if (2*wsize>= abs(t_row+diff-t_col)) { break; } } // calculate donut for (int i = t_row-wsize; i <= t_row+wsize; ++i) { for (int j = t_col-wsize; j <= t_col+wsize; ++j) { int index = i * msize + j; if (!isnan(c[index])) { if (i+diff-j<0) { Evalue_donut += c[index]; Edistvalue_donut += d[abs(i+diff-j)]; } } } } //Subtract off the middle peak for (int i = t_row-pwidth; i <= t_row+pwidth; ++i) { for (int j = t_col-pwidth; j <= t_col+pwidth; ++j) { int index = i * msize + j; if (!isnan(c[index])) { if (i+diff-j<0) { Evalue_donut -= c[index]; Edistvalue_donut -= d[abs(i+diff-j)]; } } } } //Subtract off the cross hairs left side process_masks_lr(t_row-wsize, t_row-pwidth, msize, t_col, c, d, diff, &Evalue_donut, &Edistvalue_donut, &Evalue_v, &Edistvalue_v); //Subtract off the cross hairs right side process_masks_lr(t_row+pwidth+1, t_row+wsize+1, msize, t_col, c, d, diff, &Evalue_donut, &Edistvalue_donut, &Evalue_v, &Edistvalue_v); //Subtract off the cross hairs top side process_masks_tb(t_col-wsize, t_col-pwidth, msize, t_row, c, d, diff, &Evalue_donut, &Edistvalue_donut, &Evalue_h, &Edistvalue_h); //Subtract off the cross hairs bottom side process_masks_tb(t_col+pwidth+1, t_col+wsize+1, msize, t_row, c, d, diff, &Evalue_donut, &Edistvalue_donut, &Evalue_h, &Edistvalue_h); e_bl = ((Evalue_bl*d[diagDist])/Edistvalue_bl)*kr1[t_row]*kr2[t_col]; e_donut = ((Evalue_donut*d[diagDist])/Edistvalue_donut)*kr1[t_row]*kr2[t_col]; e_h = ((Evalue_h*d[diagDist])/Edistvalue_h)*kr1[t_row]*kr2[t_col]; e_v = ((Evalue_v*d[diagDist])/Edistvalue_v)*kr1[t_row]*kr2[t_col]; float lognorm = logf(powf(2.0,0.33)); ensure_appropriate_values(e_bl, lognorm, &bvalue_bl); ensure_appropriate_values(e_donut, lognorm, &bvalue_donut); ensure_appropriate_values(e_h, lognorm, &bvalue_h); ensure_appropriate_values(e_v, lognorm, &bvalue_v); int val_index = t_row * msize + t_col; o = roundf(c[val_index]*kr1[t_row]*kr2[t_col]); pvalue_bl = 1 - gammq(o, e_bl); pvalue_donut = 1 - gammq(o, e_donut); pvalue_h = 1 - gammq(o, e_h); pvalue_v = 1 - gammq(o, e_v); // Write the matrix to device memory; // each thread writes one element expectedbl[val_index] = e_bl; expecteddonut[val_index] = e_donut; expectedh[val_index] = e_h; expectedv[val_index] = e_v; observed[val_index] = o; b_bl[val_index] = bvalue_bl; b_donut[val_index] = bvalue_donut; b_h[val_index] = bvalue_h; b_v[val_index] = bvalue_v; if (pvalue_bl <= tbl[(int) bvalue_bl] && pvalue_donut <= td[(int) bvalue_donut] && pvalue_h <= th[(int) bvalue_h] && pvalue_v <= tv[(int) bvalue_v]) { p[val_index] = 1; } else { p[val_index] = 0; } p_bl[val_index] = pvalue_bl; p_donut[val_index] = pvalue_donut; p_h[val_index] = pvalue_h; p_v[val_index] = pvalue_v; } } ================================================ FILE: src/juicebox/tools/utils/juicer/hiccups/HiCCUPSConfiguration.java ================================================ /* * The MIT License (MIT) * * Copyright (c) 2011-2021 Broad Institute, Aiden Lab, Rice University, Baylor College of Medicine * * Permission is hereby granted, free of charge, to any person obtaining a copy * of this software and associated documentation files (the "Software"), to deal * in the Software without restriction, including without limitation the rights * to use, copy, modify, merge, publish, distribute, sublicense, and/or sell * copies of the Software, and to permit persons to whom the Software is * furnished to do so, subject to the following conditions: * * The above copyright notice and this permission notice shall be included in * all copies or substantial portions of the Software. * * THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR * IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, * FITNESS FOR A PARTICULAR PURPOSE AND NON-INFRINGEMENT. IN NO EVENT SHALL THE * AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER * LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, * OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN * THE SOFTWARE. */ package juicebox.tools.utils.juicer.hiccups; import juicebox.data.HiCFileTools; import juicebox.tools.clt.CommandLineParserForJuicer; import juicebox.tools.utils.common.ArrayTools; import juicebox.windowui.HiCZoom; import java.text.DecimalFormat; import java.util.*; /** * Created by muhammadsaadshamim on 10/8/15. */ public class HiCCUPSConfiguration { private final int resolution; private int windowWidth, peakWidth, clusterRadius; private double fdrThreshold; /* * Reasonable Commands * * fdr = 0.10 for all resolutions * peak width = 1 for 25kb, 2 for 10kb, 4 for 5kb * window = 3 for 25kb, 5 for 10kb, 7 for 5kb * * cluster radius is 20kb for 5kb and 10kb res and 50kb for 25kb res * fdrsumthreshold is 0.02 for all resolutions * oeThreshold1 = 1.5 for all res * oeThreshold2 = 1.75 for all res * oeThreshold3 = 2 for all res * * published GM12878 looplist was only generated with 5kb and 10kb resolutions * same with published IMR90 looplist * published CH12 looplist only generated with 10kb */ public HiCCUPSConfiguration(int resolution, double fdrThreshold, int peakWidth, int windowWidth, int clusterRadius) { this.resolution = resolution; this.fdrThreshold = fdrThreshold; this.windowWidth = windowWidth; this.peakWidth = peakWidth; this.clusterRadius = clusterRadius; } public static List extractConfigurationsFromCommandLine(CommandLineParserForJuicer juicerParser, List availableZooms, int version) { List resString = juicerParser.getMultipleResolutionOptions(); if (resString == null) return null; int[] resolutions = ArrayTools.extractIntegers(resString); Map configurationMap = new HashMap<>(); for (int res : resolutions) { if (res == 1000) { configurationMap.put(res, getHiCCUPS2ConfigFor1K()); } else if (res == 2000) { configurationMap.put(res, getHiCCUPS2ConfigFor2K()); } else if (res == 5000) { if (version == 1) { configurationMap.put(res, getDefaultConfigFor5K()); } else { configurationMap.put(res, getHiCCUPS2ConfigFor5K()); } } else if (res == 10000) { configurationMap.put(res, getDefaultConfigFor10K()); } else if (res == 25000) { configurationMap.put(res, getDefaultConfigFor25K()); } else { configurationMap.put(res, getDefaultBlankConfig(res)); } } double[] fdr = HiCCUPSUtils.extractFDRValues(juicerParser.getFDROptions(), resolutions.length, 0.1f); // becomes default 10 int[] peaks = HiCCUPSUtils.extractIntegerValues(juicerParser.getPeakOptions(), resolutions.length); int[] windows = HiCCUPSUtils.extractIntegerValues(juicerParser.getWindowOptions(), resolutions.length); int[] radii = HiCCUPSUtils.extractIntegerValues(juicerParser.getClusterRadiusOptions(), resolutions.length); for (int i = 0; i < resolutions.length; i++) { if (fdr != null) configurationMap.get(resolutions[i]).fdrThreshold = fdr[i]; if (peaks != null) configurationMap.get(resolutions[i]).peakWidth = peaks[i]; if (windows != null) configurationMap.get(resolutions[i]).windowWidth = windows[i]; if (radii != null) configurationMap.get(resolutions[i]).clusterRadius = radii[i]; } Set filteredResolutions = new HashSet<>(HiCFileTools.filterResolutions(availableZooms, resolutions)); for (int res : resolutions) { if (!filteredResolutions.contains(res)) { System.err.println("Resolution " + res + " not available."); } } List validConfigs = new ArrayList<>(); for (int res : filteredResolutions) { if (configurationMap.containsKey(res)) { HiCCUPSConfiguration config = configurationMap.get(res); if (config.isValid()) { validConfigs.add(config); } else { System.out.println("Discarding invalid configuration: " + config); } } } if (validConfigs.size() > 0) { System.out.println("Using the following configurations for HiCCUPS:"); for (HiCCUPSConfiguration config : validConfigs) { System.out.println(config); } } else { return null; } return validConfigs; } public static HiCCUPSConfiguration getHiCCUPS2ConfigFor1K() { return new HiCCUPSConfiguration(1000, 10, 5, 10, 3000); } public static HiCCUPSConfiguration getHiCCUPS2ConfigFor2K() { return new HiCCUPSConfiguration(2000, 10, 4, 10, 6000); } public static HiCCUPSConfiguration getHiCCUPS2ConfigFor5K() { return new HiCCUPSConfiguration(5000, 10, 4, 7, 10000); } public static HiCCUPSConfiguration getDefaultConfigFor5K() { return new HiCCUPSConfiguration(5000, 10, 4, 7, 20000); } public static HiCCUPSConfiguration getDefaultConfigFor10K() { return new HiCCUPSConfiguration(10000, 10, 2, 5, 20000); } public static HiCCUPSConfiguration getDefaultConfigFor25K() { return new HiCCUPSConfiguration(25000, 10, 1, 3, 50000); } private static HiCCUPSConfiguration getDefaultBlankConfig(int res) { return new HiCCUPSConfiguration(res, 10, -1, -1, -1); } public static List getDefaultSetOfConfigsForUsers() { List configurations = new ArrayList<>(); configurations.add(HiCCUPSConfiguration.getDefaultConfigFor5K()); configurations.add(HiCCUPSConfiguration.getDefaultConfigFor10K()); configurations.add(HiCCUPSConfiguration.getDefaultConfigFor25K()); System.out.println("Default settings for 5kb, 10kb, and 25kb being used"); return configurations; } public static List getHiCCUPS2DefaultSetOfConfigsForUsers() { List configurations = new ArrayList<>(); configurations.add(HiCCUPSConfiguration.getHiCCUPS2ConfigFor1K()); configurations.add(HiCCUPSConfiguration.getHiCCUPS2ConfigFor2K()); configurations.add(HiCCUPSConfiguration.getHiCCUPS2ConfigFor5K()); configurations.add(HiCCUPSConfiguration.getDefaultConfigFor10K()); System.out.println("Default HiCCUPS2 settings for 1kb, 2kb, 5kb, and 10kb are being used"); return configurations; } private boolean isValid() { return resolution > 0 && windowWidth > 0 && peakWidth > 0 && clusterRadius > 0 && windowWidth > peakWidth; } public int divisor() { return (windowWidth - peakWidth) * (windowWidth + peakWidth); } public int getResolution() { return resolution; } public int getClusterRadius() { return clusterRadius; } public int getWindowWidth() { return windowWidth; } public int getPeakWidth() { return peakWidth; } public double getFDRThreshold() { return fdrThreshold; } public String toString() { return "Config res: " + resolution + " peak: " + peakWidth + " window: " + windowWidth + " fdr: " + getFDRPercent() + " radius: " + clusterRadius; } private String getFDRPercent() { DecimalFormat format = new DecimalFormat("#.##"); return format.format(100. * (1. / fdrThreshold)) + "%"; } } ================================================ FILE: src/juicebox/tools/utils/juicer/hiccups/HiCCUPSKernel.cu ================================================ __device__ void ensure_appropriate_values(float e_value, float lognormval, float* bvalue){ if (!isnan(e_value) && !isinf(e_value)) { if (e_value<=1) { *bvalue = 0; } else { *bvalue = floorf(logf(e_value)/lognormval); } } *bvalue = (float) min((int) *bvalue, HiCCUPS_W1_MAX_INDX ); } __device__ void process_masks_lr(int i_start, int i_max_p1, int msize, int t_col, float *c,float *d, int diff, float* evalue_d, float* evalue_dist_d, float* evalue_v, float* evalue_dist_v){ for (int i = i_start; i < i_max_p1; i++) { int index = i * msize + t_col; if (!isnan(c[index])) { *evalue_d -= c[index]; *evalue_dist_d -= d[abs(i+diff-t_col)]; } for (int j = -1; j < 2; j++) { *evalue_v += c[index + j]; *evalue_dist_v += d[abs(i+diff-t_col-j)]; } } } __device__ void process_masks_tb(int j_start, int j_max_p1, int msize, int t_row, float *c,float *d, int diff, float* evalue_d, float* evalue_dist_d, float* evalue_h, float* evalue_dist_h){ for (int j = j_start; j < j_max_p1; j++) { int index = t_row * msize + j; if (!isnan(c[index])) { *evalue_d -= c[index]; *evalue_dist_d -= d[abs(t_row+diff-j)]; } for (int i = -1; i < 2; i++) { *evalue_h += c[(t_row+i) * msize + j]; *evalue_dist_h += d[abs(t_row+i+diff-j)]; } } } extern "C" __global__ void BasicPeakCallingKernel(float *c, float *expectedbl, float *expecteddonut, float *expectedh, float *expectedv, float *observed, float *b_bl, float *b_donut, float *b_h, float *b_v, float *p, float *tbl, float *td, float *th, float *tv, float *d, float *kr1, float *kr2, float *bound1, float *bound3) { // 2D Thread ID int t_col = threadIdx.x + blockIdx.x * blockDim.x; int t_row = threadIdx.y + blockIdx.y * blockDim.y; // Evalue is used to store the element of the matrix // that is computed by the thread float Evalue_bl = 0; float Edistvalue_bl = 0; float Evalue_donut = 0; float Edistvalue_donut = 0; float Evalue_h = 0; float Edistvalue_h = 0; float Evalue_v = 0; float Edistvalue_v = 0; float e_bl = 0; float e_donut = 0; float e_h = 0; float e_v = 0; float o = 0; float sbtrkt = 0; float bvalue_bl = 0; float bvalue_donut = 0; float bvalue_h = 0; float bvalue_v = 0; int wsize = HiCCUPS_WINDOW; int msize = HiCCUPS_MATRIX_SIZE; int pwidth = HiCCUPS_PEAK_WIDTH; int buffer_width = HiCCUPS_REGION_MARGIN; int diff = bound1[0] - bound3[0]; int diagDist = abs(t_row+diff-t_col); int maxIndex = msize-buffer_width; wsize = min(wsize, (abs(t_row+diff-t_col)-1)/2); if (wsize <= pwidth) { wsize = pwidth + 1; } wsize = min(wsize, buffer_width); // only run if within central window (not in data buffer margins) if (t_row >= buffer_width && t_row= buffer_width && t_col t_row && i < t_row+pwidth+1 && j > t_col-pwidth-1 && j < t_col) { Evalue_bl -= c[index]; Edistvalue_bl -= d[abs(i+diff-j)]; } } } } if (wsize >= buffer_width) { break; } if (2*wsize>= abs(t_row+diff-t_col)) { break; } } // calculate donut for (int i = t_row-wsize; i <= t_row+wsize; ++i) { for (int j = t_col-wsize; j <= t_col+wsize; ++j) { int index = i * msize + j; if (!isnan(c[index])) { if (i+diff-j<0) { Evalue_donut += c[index]; Edistvalue_donut += d[abs(i+diff-j)]; } } } } //Subtract off the middle peak for (int i = t_row-pwidth; i <= t_row+pwidth; ++i) { for (int j = t_col-pwidth; j <= t_col+pwidth; ++j) { int index = i * msize + j; if (!isnan(c[index])) { if (i+diff-j<0) { Evalue_donut -= c[index]; Edistvalue_donut -= d[abs(i+diff-j)]; } } } } //Subtract off the cross hairs left side process_masks_lr(t_row-wsize, t_row-pwidth, msize, t_col, c, d, diff, &Evalue_donut, &Edistvalue_donut, &Evalue_v, &Edistvalue_v); //Subtract off the cross hairs right side process_masks_lr(t_row+pwidth+1, t_row+wsize+1, msize, t_col, c, d, diff, &Evalue_donut, &Edistvalue_donut, &Evalue_v, &Edistvalue_v); //Subtract off the cross hairs top side process_masks_tb(t_col-wsize, t_col-pwidth, msize, t_row, c, d, diff, &Evalue_donut, &Edistvalue_donut, &Evalue_h, &Edistvalue_h); //Subtract off the cross hairs bottom side process_masks_tb(t_col+pwidth+1, t_col+wsize+1, msize, t_row, c, d, diff, &Evalue_donut, &Edistvalue_donut, &Evalue_h, &Edistvalue_h); e_bl = ((Evalue_bl*d[diagDist])/Edistvalue_bl)*kr1[t_row]*kr2[t_col]; e_donut = ((Evalue_donut*d[diagDist])/Edistvalue_donut)*kr1[t_row]*kr2[t_col]; e_h = ((Evalue_h*d[diagDist])/Edistvalue_h)*kr1[t_row]*kr2[t_col]; e_v = ((Evalue_v*d[diagDist])/Edistvalue_v)*kr1[t_row]*kr2[t_col]; float lognorm = logf(powf(2.0,.33)); ensure_appropriate_values(e_bl, lognorm, &bvalue_bl); ensure_appropriate_values(e_donut, lognorm, &bvalue_donut); ensure_appropriate_values(e_h, lognorm, &bvalue_h); ensure_appropriate_values(e_v, lognorm, &bvalue_v); // Write the matrix to device memory; // each thread writes one element int val_index = t_row * msize + t_col; expectedbl[val_index] = e_bl; expecteddonut[val_index] = e_donut; expectedh[val_index] = e_h; expectedv[val_index] = e_v; o = roundf(c[val_index]*kr1[t_row]*kr2[t_col]); observed[val_index] = o; b_bl[val_index] = bvalue_bl; b_donut[val_index] = bvalue_donut; b_h[val_index] = bvalue_h; b_v[val_index] = bvalue_v; sbtrkt = fmaxf(tbl[(int) bvalue_bl],td[(int) bvalue_donut]); sbtrkt = fmaxf(sbtrkt, th[(int) bvalue_h]); sbtrkt = fmaxf(sbtrkt, tv[(int) bvalue_v]); p[val_index] = o-sbtrkt; } } ================================================ FILE: src/juicebox/tools/utils/juicer/hiccups/HiCCUPSRegionContainer.java ================================================ /* * The MIT License (MIT) * * Copyright (c) 2011-2020 Broad Institute, Aiden Lab, Rice University, Baylor College of Medicine * * Permission is hereby granted, free of charge, to any person obtaining a copy * of this software and associated documentation files (the "Software"), to deal * in the Software without restriction, including without limitation the rights * to use, copy, modify, merge, publish, distribute, sublicense, and/or sell * copies of the Software, and to permit persons to whom the Software is * furnished to do so, subject to the following conditions: * * The above copyright notice and this permission notice shall be included in * all copies or substantial portions of the Software. * * THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR * IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, * FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE * AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER * LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, * OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN * THE SOFTWARE. */ package juicebox.tools.utils.juicer.hiccups; import juicebox.data.basics.Chromosome; public class HiCCUPSRegionContainer { private final Chromosome chromosome; private final int[] rowBounds; private final int[] columnBounds; public HiCCUPSRegionContainer(Chromosome chromosome, int[] rowBounds, int[] columnBounds) { this.chromosome = chromosome; this.rowBounds = rowBounds; this.columnBounds = columnBounds; } public int[] getRowBounds() { return rowBounds; } public int[] getColumnBounds() { return columnBounds; } public Chromosome getChromosome() { return chromosome; } } ================================================ FILE: src/juicebox/tools/utils/juicer/hiccups/HiCCUPSUtils.java ================================================ /* * The MIT License (MIT) * * Copyright (c) 2011-2022 Broad Institute, Aiden Lab, Rice University, Baylor College of Medicine * * Permission is hereby granted, free of charge, to any person obtaining a copy * of this software and associated documentation files (the "Software"), to deal * in the Software without restriction, including without limitation the rights * to use, copy, modify, merge, publish, distribute, sublicense, and/or sell * copies of the Software, and to permit persons to whom the Software is * furnished to do so, subject to the following conditions: * * The above copyright notice and this permission notice shall be included in * all copies or substantial portions of the Software. * * THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR * IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, * FITNESS FOR A PARTICULAR PURPOSE AND NON-INFRINGEMENT. IN NO EVENT SHALL THE * AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER * LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, * OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN * THE SOFTWARE. */ package juicebox.tools.utils.juicer.hiccups; import juicebox.HiCGlobals; import juicebox.data.ChromosomeHandler; import juicebox.data.Dataset; import juicebox.data.HiCFileTools; import juicebox.data.NormalizationVector; import juicebox.data.basics.Chromosome; import juicebox.tools.clt.juicer.HiCCUPS; import juicebox.tools.clt.juicer.HiCCUPS2; import juicebox.tools.utils.common.ArrayTools; import juicebox.track.feature.*; import juicebox.windowui.NormalizationType; import java.awt.*; import java.io.File; import java.io.IOException; import java.util.List; import java.util.*; /** * Utility class for HiCCUPS * Created by muhammadsaadshamim on 6/2/15. */ public class HiCCUPSUtils { public static final String OBSERVED = "observed"; // for debugging /* public static final String notNearCentroidAttr = "NotNearCentroid"; public static final String centroidAttr = "Centroid"; public static final String nearCentroidAttr = "NearCentroid"; public static final String nearDiagAttr = "NearDiag"; public static final String StrongAttr = "Strong"; public static final String FilterStage = "Stage"; */ private static final String PEAK = "peak"; private static final String EXPECTEDBL = "expectedBL"; private static final String EXPECTEDDONUT = "expectedDonut"; private static final String EXPECTEDH = "expectedH"; private static final String EXPECTEDV = "expectedV"; private static final String BINBL = "binBL"; private static final String BINDONUT = "binDonut"; private static final String BINH = "binH"; private static final String BINV = "binV"; private static final String FDRBL = "fdrBL"; private static final String FDRDONUT = "fdrDonut"; private static final String FDRH = "fdrH"; private static final String FDRV = "fdrV"; private static final String RADIUS = "radius"; private static final String CENTROID1 = "centroid1"; private static final String CENTROID2 = "centroid2"; private static final String NUMCOLLAPSED = "numCollapsed"; private static final String POST_PROCESSED = "postprocessed_pixels"; private static final String MERGED = "merged_loops.bedpe"; private static final String REQUESTED = "_from_requested_loops"; private static final String MERGED_REQUESTED = "merged" + REQUESTED + ".bedpe"; private static final String FDR_THRESHOLDS = "fdr_thresholds"; private static final String ENRICHED_PIXELS = "enriched_pixels"; private static final String REQUESTED_LIST = "requested_list"; /** * @return a Feature2D peak for a possible peak location from hiccups */ public static Feature2D generatePeak(String chrName, float observed, float peak, int rowPos, int colPos, float expectedBL, float expectedDonut, float expectedH, float expectedV, float binBL, float binDonut, float binH, float binV, int resolution) { Map attributes = new HashMap<>(); attributes.put(OBSERVED, String.valueOf(observed)); attributes.put(PEAK, String.valueOf(peak)); attributes.put(EXPECTEDBL, String.valueOf(expectedBL)); attributes.put(EXPECTEDDONUT, String.valueOf(expectedDonut)); attributes.put(EXPECTEDH, String.valueOf(expectedH)); attributes.put(EXPECTEDV, String.valueOf(expectedV)); attributes.put(BINBL, String.valueOf(binBL)); attributes.put(BINDONUT, String.valueOf(binDonut)); attributes.put(BINH, String.valueOf(binH)); attributes.put(BINV, String.valueOf(binV)); int pos1 = Math.min(rowPos, colPos); int pos2 = Math.max(rowPos, colPos); return new Feature2D(Feature2D.FeatureType.PEAK, chrName, pos1, pos1 + resolution, chrName, pos2, pos2 + resolution, Color.black, attributes); } public static Feature2D generatePeak(String chrName, float observed, float peak, int rowPos, int colPos, float expectedBL, float expectedDonut, float expectedH, float expectedV, float binBL, float binDonut, float binH, float binV, int resolution, float pvalBL, float pvalDonut, float pvalH, float pvalV) { Map attributes = new HashMap<>(); attributes.put(OBSERVED, String.valueOf(observed)); attributes.put(PEAK, String.valueOf(peak)); attributes.put(EXPECTEDBL, String.valueOf(expectedBL)); attributes.put(EXPECTEDDONUT, String.valueOf(expectedDonut)); attributes.put(EXPECTEDH, String.valueOf(expectedH)); attributes.put(EXPECTEDV, String.valueOf(expectedV)); attributes.put(BINBL, String.valueOf(binBL)); attributes.put(BINDONUT, String.valueOf(binDonut)); attributes.put(BINH, String.valueOf(binH)); attributes.put(BINV, String.valueOf(binV)); attributes.put(FDRBL, String.valueOf(pvalBL)); attributes.put(FDRDONUT, String.valueOf(pvalDonut)); attributes.put(FDRH, String.valueOf(pvalH)); attributes.put(FDRV, String.valueOf(pvalV)); int pos1 = Math.min(rowPos, colPos); int pos2 = Math.max(rowPos, colPos); return new Feature2D(Feature2D.FeatureType.PEAK, chrName, pos1, pos1 + resolution, chrName, pos2, pos2 + resolution, Color.black, attributes); } /** * Calculate fdr values for a given peak */ public static void calculateFDR(Feature2D feature, float[][] fdrLogBL, float[][] fdrLogDonut, float[][] fdrLogH, float[][] fdrLogV) { int observed = (int) feature.getFloatAttribute(OBSERVED); int binBL = (int) feature.getFloatAttribute(BINBL); int binDonut = (int) feature.getFloatAttribute(BINDONUT); int binH = (int) feature.getFloatAttribute(BINH); int binV = (int) feature.getFloatAttribute(BINV); if (binBL >= 0 && binDonut >= 0 && binH >= 0 && binV >= 0 && observed >= 0) { feature.addFloatAttribute(FDRBL, (fdrLogBL[binBL][observed])); feature.addFloatAttribute(FDRDONUT, (fdrLogDonut[binDonut][observed])); feature.addFloatAttribute(FDRH, (fdrLogH[binH][observed])); feature.addFloatAttribute(FDRV, (fdrLogV[binV][observed])); } else { System.out.println("Error in calculateFDR binBL=" + binBL + " binDonut=" + binDonut + " binH=" + binH + " binV=" + binV + " observed=" + observed); } } private static void removeLowMapQFeatures(Feature2DList list, final int resolution, final Dataset ds, final ChromosomeHandler chromosomeHandler, final NormalizationType norm) { final Map chrNameToIndex = new HashMap<>(); for (Chromosome chr : chromosomeHandler.getChromosomeArray()) { chrNameToIndex.put(Feature2DList.getKey(chr, chr), chr.getIndex()); } if (HiCGlobals.printVerboseComments) { System.out.println("Initial: " + list.getNumTotalFeatures()); } list.filterLists(new FeatureFilter() { @Override public List filter(String chr, List feature2DList) { try { return removeLowMapQ(resolution, chrNameToIndex.get(chr), ds, feature2DList, norm); } catch (Exception e) { System.err.println("Unable to remove low mapQ entries for " + chr); //e.printStackTrace(); } return new ArrayList<>(); } }); } private static void coalesceFeaturesToCentroid(Feature2DList list, final int resolution, final int centroidRadius) { list.filterLists(new FeatureFilter() { @Override public List filter(String chr, List feature2DList) { return coalescePixelsToCentroid(resolution, feature2DList, centroidRadius); } }); } public static void filterOutFeaturesByEnrichment(Feature2DList list, final float maxEnrich) { list.filterLists(new FeatureFilter() { @Override public List filter(String chr, List feature2DList) { return enrichmentThreshold(feature2DList, maxEnrich); } }); } private static List enrichmentThreshold(List feature2DList, final float maxEnrich) { List filtered = new ArrayList<>(); for (Feature2D feature : feature2DList) { if (enrichmentThresholdSatisfied(feature, maxEnrich)) filtered.add(feature); } return filtered; } private static void doFinalCleanUp(Feature2DList list) { list.filterLists(new FeatureFilter() { @Override public List filter(String chr, List feature2DList) { return finalCleanUp(feature2DList); } }); } private static List finalCleanUp(List feature2DList) { List filtered = new ArrayList<>(); for (Feature2D feature : feature2DList) { if (finalCleanSatisfied(feature)) filtered.add(feature); } return filtered; } private static void filterOutFeaturesByFDR(Feature2DList list, int version) { list.filterLists(new FeatureFilter() { @Override public List filter(String chr, List feature2DList) { return fdrThreshold(feature2DList, version); } }); } private static List fdrThreshold(List feature2DList, int version) { List filtered = new ArrayList<>(); for (Feature2D feature : feature2DList) { if (version == 1 ) { if (fdrThresholdsSatisfied(feature)) filtered.add(feature); } else if (version == 2) { if (fdrThresholds2Satisfied(feature)) filtered.add(feature); } } return filtered; } private static List removeLowMapQ(int res, int chrIndex, Dataset ds, List list, NormalizationType norm) throws IOException { List features = new ArrayList<>(); NormalizationVector normVectorContainer = ds.getNormalizationVector(chrIndex, ds.getZoomForBPResolution(res), norm); if (normVectorContainer == null) { HiCFileTools.triggerNormError(norm); } else { double[] normalizationVector = normVectorContainer.getData().getValues().get(0); for (Feature2D feature : list) { int index1 = (int) (feature.getStart1() / res); int index2 = (int) (feature.getStart2() / res); if (nearbyValuesClear(normalizationVector, index1) && nearbyValuesClear(normalizationVector, index2)) { features.add(feature); } } } return features; } private static boolean nearbyValuesClear(double[] normalizationVector, int index) { for (int i = index - HiCCUPS.krNeighborhood; i <= index + HiCCUPS.krNeighborhood; i++) { if (Double.isNaN(normalizationVector[i])) return false; } return true; } /** * @return list of pixels coalesced to centroid of enriched region */ private static List coalescePixelsToCentroid(int resolution, List feature2DList, int originalClusterRadius) { // HashSet intermediate for removing duplicates; LinkedList used so that we can pop out highest obs values LinkedList featureLL = new LinkedList<>(new HashSet<>(feature2DList)); List coalesced = new ArrayList<>(); while (!featureLL.isEmpty()) { // See Feature2D Collections.sort(featureLL); Collections.reverse(featureLL); Feature2D pixel = featureLL.pollFirst(); featureLL.remove(pixel); List pixelList = new ArrayList<>(); pixelList.add(pixel); int pixelListX = (int) pixel.getStart1(); int pixelListY = (int) pixel.getStart2(); double r = 0; double pixelClusterRadius = originalClusterRadius; for (Feature2D px : featureLL) { // TODO should likely reduce radius or at least start with default? //System.out.println("Radius " + HiCCUPS.pixelClusterRadius); if (hypotenuse(pixelListX - px.getStart1(), pixelListY - px.getStart2()) <= pixelClusterRadius) { pixelList.add(px); pixelListX = mean(pixelList, 1); pixelListY = mean(pixelList, 2); List distances = new ArrayList<>(); for (Feature2D px2 : pixelList) { double dist = hypotenuse(pixelListX - px2.getStart1(), pixelListY - px2.getStart2()); if (Double.isNaN(dist) || dist < 0) { System.err.println("Invalid distance while merging centroid"); System.exit(29); } distances.add(dist); } //System.out.println("Radii "+distances); r = Math.round(Collections.max(distances)); pixelClusterRadius = originalClusterRadius + r; } } pixel.setEnd1((int) pixel.getStart1() + resolution); pixel.setEnd2((int) pixel.getStart2() + resolution); pixel.addIntAttribute(RADIUS, (int) Math.round(r)); pixel.addIntAttribute(CENTROID1, (pixelListX + resolution / 2)); pixel.addIntAttribute(CENTROID2, (pixelListY + resolution / 2)); pixel.addIntAttribute(NUMCOLLAPSED, (pixelList.size())); setPixelColor(pixel); coalesced.add(pixel); featureLL.removeAll(pixelList); } return coalesced; } private static void setPixelColor(Feature2D pixel) { Color c = HiCCUPS.defaultPeakColor; if (HiCCUPS.shouldColorBeScaledByFDR) { double fdr = -Math.floor(Math.log10( Math.max(pixel.getFloatAttribute(BINBL), pixel.getFloatAttribute(BINDONUT)))); fdr = Math.max(Math.min(fdr, 10), 0) / 10; c = new Color((int) (fdr * c.getRed()), (int) (fdr * c.getGreen()), (int) (fdr * c.getBlue())); } pixel.setColor(c); } private static boolean fdrThresholdsSatisfied(Feature2D pixel) { double f = HiCCUPS.fdrsum; double t1 = HiCCUPS.oeThreshold1; double t2 = HiCCUPS.oeThreshold2; double t3 = HiCCUPS.oeThreshold3; int observed = Math.round(pixel.getFloatAttribute(OBSERVED)); int numCollapsed = Math.round(pixel.getFloatAttribute(NUMCOLLAPSED)); float expectedBL = pixel.getFloatAttribute(EXPECTEDBL); float expectedDonut = pixel.getFloatAttribute(EXPECTEDDONUT); float expectedH = pixel.getFloatAttribute(EXPECTEDH); float expectedV = pixel.getFloatAttribute(EXPECTEDV); float fdrBL = pixel.getFloatAttribute(FDRBL); float fdrDonut = pixel.getFloatAttribute(FDRDONUT); float fdrH = pixel.getFloatAttribute(FDRH); float fdrV = pixel.getFloatAttribute(FDRV); return observed > (t2 * expectedBL) && observed > (t2 * expectedDonut) && observed > (t1 * expectedH) && observed > (t1 * expectedV) && (observed > (t3 * expectedBL) || observed > (t3 * expectedDonut)) && (numCollapsed > 1 || (fdrBL + fdrDonut + fdrH + fdrV) <= f); } private static boolean fdrThresholds2Satisfied(Feature2D pixel) { double f2 = HiCCUPS2.fdrsum2; double t1 = HiCCUPS2.oeThreshold1; double t2 = HiCCUPS2.oeThreshold2; double t3 = HiCCUPS2.oeThreshold3; int observed = Math.round(pixel.getFloatAttribute(OBSERVED)); int numCollapsed = Math.round(pixel.getFloatAttribute(NUMCOLLAPSED)); float expectedBL = pixel.getFloatAttribute(EXPECTEDBL); float expectedDonut = pixel.getFloatAttribute(EXPECTEDDONUT); float expectedH = pixel.getFloatAttribute(EXPECTEDH); float expectedV = pixel.getFloatAttribute(EXPECTEDV); float fdrBL = pixel.getFloatAttribute(FDRBL); float fdrDonut = pixel.getFloatAttribute(FDRDONUT); float fdrH = pixel.getFloatAttribute(FDRH); float fdrV = pixel.getFloatAttribute(FDRV); return observed > (t2 * expectedBL) && observed > (t2 * expectedDonut) && observed > (t1 * expectedH) && observed > (t1 * expectedV) && (observed > (t3 * expectedBL) || observed > (t3 * expectedDonut)) && (numCollapsed > 1 || (fdrBL + fdrDonut + fdrH + fdrV) <= f2); } private static boolean finalCleanSatisfied(Feature2D pixel) { double f1 = HiCCUPS2.fdrsum1; double t4 = HiCCUPS2.oeThreshold4; long resolution = pixel.getWidth1(); int observed = Math.round(pixel.getFloatAttribute(OBSERVED)); int numCollapsed = Math.round(pixel.getFloatAttribute(NUMCOLLAPSED)); float expectedBL = pixel.getFloatAttribute(EXPECTEDBL); float expectedDonut = pixel.getFloatAttribute(EXPECTEDDONUT); float expectedH = pixel.getFloatAttribute(EXPECTEDH); float expectedV = pixel.getFloatAttribute(EXPECTEDV); float fdrBL = pixel.getFloatAttribute(FDRBL); float fdrDonut = pixel.getFloatAttribute(FDRDONUT); float fdrH = pixel.getFloatAttribute(FDRH); float fdrV = pixel.getFloatAttribute(FDRV); if (resolution >= 5000) { return (observed < (t4 * expectedDonut) && observed < (t4 * expectedBL) && observed < (t4 * expectedH) && observed < (t4 * expectedV)) && (numCollapsed > 1 || (fdrBL + fdrDonut + fdrH + fdrV) <= f1); } else { return (observed < (t4 * expectedDonut) && observed < (t4 * expectedBL) && observed < (t4 * expectedH) && observed < (t4 * expectedV)); } } private static boolean enrichmentThresholdSatisfied(Feature2D pixel, final float maxEnrich) { float observed = pixel.getFloatAttribute(OBSERVED); float expectedBL = pixel.getFloatAttribute(EXPECTEDBL); float expectedDonut = pixel.getFloatAttribute(EXPECTEDDONUT); float expectedH = pixel.getFloatAttribute(EXPECTEDH); float expectedV = pixel.getFloatAttribute(EXPECTEDV); return (observed < maxEnrich * expectedBL && observed < maxEnrich * expectedDonut && observed < maxEnrich * expectedH && observed < maxEnrich * expectedV); } private static int mean(List pixelList, int i) { int n = pixelList.size(); double total = 0; for (Feature2D px : pixelList) { if (i == 1) total += px.getStart1(); else if (i == 2) total += px.getStart2(); } return (int) (total / n); } public static double hypotenuse(double x, double y) { return Math.sqrt(x * x + y * y); } /** * Code to merge high resolution calls (i.e. when <5kb resolution is used) * * @return loop list merged across resolutions */ public static Feature2DList mergeHighResolutions(Map hiccupsLoopLists) { Feature2DList mergedList = new Feature2DList(); if (hiccupsLoopLists.containsKey(1000) && hiccupsLoopLists.containsKey(2000) && hiccupsLoopLists.containsKey(5000)) { mergedList.add(handleGenericThreeListMerger(hiccupsLoopLists.get(1000), hiccupsLoopLists.get(2000), hiccupsLoopLists.get(5000), 2000, 5000, 50000, 80000, 20, 40)); } else if (hiccupsLoopLists.containsKey(1000) && hiccupsLoopLists.containsKey(2000)) { mergedList.add(handleGenericTwoListMerger(hiccupsLoopLists.get(1000), hiccupsLoopLists.get(2000), 2000, 50000, 20)); } else if (hiccupsLoopLists.containsKey(1000) && hiccupsLoopLists.containsKey(5000)) { mergedList.add(handleGenericTwoListMerger(hiccupsLoopLists.get(1000), hiccupsLoopLists.get(5000), 5000, 80000, 20)); } else if (hiccupsLoopLists.containsKey(2000) && hiccupsLoopLists.containsKey(5000)) { mergedList.add(handleGenericTwoListMerger(hiccupsLoopLists.get(2000), hiccupsLoopLists.get(5000), 5000, 80000, 40)); } mergedList.removeDuplicates(); if (hiccupsLoopLists.containsKey(10000)) { handleExistingGenericMerger(mergedList, hiccupsLoopLists.get(10000), 10000); } mergedList.removeDuplicates(); return mergedList; } /** * Expected behavior is to merge 5, 10, and 25 kB lists as determined * If at least one of these resolutions are found, any other resolution (e.g. 50 kB) will be thrown out * If none of these expected resolutions are found, all remaining resolutions will be merged without any filtering * * @return loop list merged across resolutions */ public static Feature2DList mergeAllResolutions(Map hiccupsLooplists) { Feature2DList mergedList = new Feature2DList(); boolean listHasBeenAltered = false; if (hiccupsLooplists.containsKey(5000) || hiccupsLooplists.containsKey(10000)) { if (hiccupsLooplists.containsKey(5000) && hiccupsLooplists.containsKey(10000)) { if (HiCGlobals.printVerboseComments) { System.out.println("Merge 5k and 10k res loops"); } mergedList.add(handleFiveAndTenKBMerger(hiccupsLooplists.get(5000), hiccupsLooplists.get(10000))); } else if (hiccupsLooplists.containsKey(5000)) { if (HiCGlobals.printVerboseComments) { System.out.println("Retrieve 5k res loops"); } mergedList.add(hiccupsLooplists.get(5000)); } else { // i.e. (hiccupsLooplists.containsKey(10000)) if (HiCGlobals.printVerboseComments) { System.out.println("Retrieve 10k res loops"); } mergedList.add(hiccupsLooplists.get(10000)); } listHasBeenAltered = true; mergedList.removeDuplicates(); } if (hiccupsLooplists.containsKey(25000)) { if (listHasBeenAltered) { if (HiCGlobals.printVerboseComments) { System.out.println("Merge with 25k res loops"); } handleExistingMergerWithTwentyFiveKB(mergedList, hiccupsLooplists.get(25000)); } else { if (HiCGlobals.printVerboseComments) { System.out.println("Retrieve 25k res loops"); } mergedList.add(hiccupsLooplists.get(25000)); } mergedList.removeDuplicates(); listHasBeenAltered = true; } // neither 25kB, 10kB, or 5kB list processed if (!listHasBeenAltered) { System.out.println("25kB, 10kB, or 5kB lists not found\nDefault lists being merged without filtering"); for (Feature2DList list : hiccupsLooplists.values()) { mergedList.add(list); } mergedList.removeDuplicates(); } return mergedList; } private static void handleExistingGenericMerger(Feature2DList mergedList, Feature2DList list2, int radius) { // add peaks unique to list 2 Feature2DList centroidsList2 = Feature2DTools.extractReproducibleCentroids(mergedList, list2, 2 * radius); Feature2DList distantList2 = Feature2DTools.extractPeaksNotNearCentroids(list2, centroidsList2); mergedList.add(distantList2); } private static void handleExistingMergerWithTwentyFiveKB(Feature2DList mergedList, Feature2DList twentyFiveKBList) { // add peaks unique to 25 kB Feature2DList centroidsTwentyFiveKB = Feature2DTools.extractReproducibleCentroids(mergedList, twentyFiveKBList, 2 * 25000); Feature2DList distant25 = Feature2DTools.extractPeaksNotNearCentroids(twentyFiveKBList, centroidsTwentyFiveKB); mergedList.add(distant25); } private static Feature2DList handleGenericTwoListMerger(Feature2DList list1, Feature2DList list2, int radius1, int nearDiagonal1, int observedLimit1) { // add peaks from list1 commonly found between list1 and list2 within 2*radius1 Feature2DList centroidsList1List2 = Feature2DTools.extractReproducibleCentroids(list2, list1, 2 * radius1); Feature2DList mergedList = Feature2DTools.extractPeaksNearCentroids(list1, centroidsList1List2, "list12->centroids"); // add peaks unique to list 2 Feature2DList centroidsList2List1 = Feature2DTools.extractReproducibleCentroids(list1, list2, 2 * radius1); Feature2DList distantList2List1 = Feature2DTools.extractPeaksNotNearCentroids(list2, centroidsList2List1); mergedList.add(distantList2List1); // add peaks close to diagonal from list 1 Feature2DList nearDiagList1 = Feature2DTools.getPeaksNearDiagonal(list1, nearDiagonal1); mergedList.add(nearDiagList1); // add particularly strong peaks from list 1 Feature2DList strongList1 = Feature2DTools.getStrongPeaks(list1, observedLimit1); mergedList.add(strongList1); // TODO expand filter duplicates? mergedList.removeDuplicates(); return mergedList; } private static Feature2DList handleGenericThreeListMerger(Feature2DList list1, Feature2DList list2, Feature2DList list3, int radius1, int radius2, int nearDiagonal1, int nearDiagonal2, int observedLimit1, int observedLimit2) { // add peaks from list1 commonly found between list1 and list2 within 2*radius1 Feature2DList centroidsList1List2 = Feature2DTools.extractReproducibleCentroids(list2, list1, 2 * radius1); Feature2DList mergedList = Feature2DTools.extractPeaksNearCentroids(list1, centroidsList1List2, "list12->centroids"); // add peaks from list1 commonly found between list1 and list3 with 2*radius2 Feature2DList centroidsList1List3 = Feature2DTools.extractReproducibleCentroids(list3, list1, 2 * radius2); Feature2DList peaksList1List3 = Feature2DTools.extractPeaksNearCentroids(list1, centroidsList1List3, "list13->centroids"); mergedList.add(peaksList1List3); // add peaks from list2 not found in list1, but common to list3 within 2*radius2 Feature2DList centroidsList2List1 = Feature2DTools.extractReproducibleCentroids(list1, list2, 2 * radius1); Feature2DList distantList2List1 = Feature2DTools.extractPeaksNotNearCentroids(list2, centroidsList2List1); Feature2DList centroidsList2List3 = Feature2DTools.extractReproducibleCentroids(list3, distantList2List1, 2 * radius2); Feature2DList peaksList2List3 = Feature2DTools.extractPeaksNearCentroids(list2, centroidsList2List3, "list23->centroids"); mergedList.add(peaksList2List3); // add peaks unique to list 3 Feature2DList centroidsList3List1 = Feature2DTools.extractReproducibleCentroids(list1, list3, 2 * radius2); Feature2DList distantList3List1 = Feature2DTools.extractPeaksNotNearCentroids(list3, centroidsList3List1); Feature2DList centroidsList3List2 = Feature2DTools.extractReproducibleCentroids(list2, distantList3List1, 2 * radius2); Feature2DList distantList3List2 = Feature2DTools.extractPeaksNotNearCentroids(distantList3List1, centroidsList3List2); mergedList.add(distantList3List2); // add peaks close to diagonal from list 1 Feature2DList nearDiagList1 = Feature2DTools.getPeaksNearDiagonal(list1, nearDiagonal1); mergedList.add(nearDiagList1); // add peaks close to diagonal from list 2 Feature2DList nearDiagList2 = Feature2DTools.getPeaksNearDiagonal(distantList2List1, nearDiagonal2); mergedList.add(nearDiagList2); // add particularly strong peaks from list 1 Feature2DList strongList1 = Feature2DTools.getStrongPeaks(list1, observedLimit1); mergedList.add(strongList1); // add particularly strong peaks from list 2 Feature2DList strongList2 = Feature2DTools.getStrongPeaks(distantList2List1, observedLimit2); mergedList.add(strongList2); // TODO expand filter duplicates? mergedList.removeDuplicates(); return mergedList; } private static Feature2DList handleFiveAndTenKBMerger(Feature2DList fiveKBList, Feature2DList tenKBList) { // add peaks commonly found between 5 and 10 kB Feature2DList centroidsFiveKB = Feature2DTools.extractReproducibleCentroids(tenKBList, fiveKBList, 2 * 10000); Feature2DList mergedList = Feature2DTools.extractPeaksNearCentroids(fiveKBList, centroidsFiveKB, "5->centroids"); // add peaks unique to 10 kB Feature2DList centroidsTenKB = Feature2DTools.extractReproducibleCentroids(fiveKBList, tenKBList, 2 * 10000); Feature2DList distant10 = Feature2DTools.extractPeaksNotNearCentroids(tenKBList, centroidsTenKB); mergedList.add(distant10); // add peaks close to diagonal in 5kB Feature2DList nearDiag = Feature2DTools.getPeaksNearDiagonal(fiveKBList, 110000); mergedList.add(nearDiag); // add particularly strong peaks from 5kB Feature2DList strong = Feature2DTools.getStrongPeaks(fiveKBList, 100); mergedList.add(strong); // TODO expand filter duplicates? mergedList.removeDuplicates(); return mergedList; } public static int[] extractIntegerValues(List valList, int n) { if (valList != null && !valList.isEmpty()) { int[] result = ArrayTools.extractIntegers(valList); if (result.length == n) { return result; } else if (result.length == 1) { return ArrayTools.preInitializeIntArray(result[0], n); } else { System.err.println("Must pass " + n + " parameters in place of " + Arrays.toString(result)); System.exit(30); return new int[0]; } } return null; } public static double[] extractFDRValues(List fdrStrings, int n, float defaultVal) { if (fdrStrings != null && !fdrStrings.isEmpty()) { double[] fdrValues = extractDoubleValues(fdrStrings, n, defaultVal); return ArrayTools.inverseArrayValues(fdrValues); } return null; } public static double[] extractDoubleValues(List valList, int n, double defaultVal) { if (valList == null) { return ArrayTools.preInitializeDoubleArray(defaultVal, n); } else { // if < 0, just return whatever is extracted // if > 0, then verify lengths match up (to ensure 1-to-1 correspondence of resolution with other params) if (n < 0) return ArrayTools.extractDoubles(valList); else { double[] result = ArrayTools.extractDoubles(valList); if (result.length == n) { return result; } else if (result.length == 1) { return ArrayTools.preInitializeDoubleArray(result[0], n); } else { System.err.println("Must pass " + n + " parameters in place of " + Arrays.toString(result)); System.exit(31); } } } return null; } public static void postProcess(Map looplists, Dataset ds, ChromosomeHandler chromosomeHandler, List configurations, NormalizationType norm, File outputDirectory, boolean isRequested, File outputFile, int version) { for (HiCCUPSConfiguration conf : configurations) { int res = conf.getResolution(); removeLowMapQFeatures(looplists.get(res), res, ds, chromosomeHandler, norm); coalesceFeaturesToCentroid(looplists.get(res), res, conf.getClusterRadius()); filterOutFeaturesByFDR(looplists.get(res), version); looplists.get(res).exportFeatureList(new File(outputDirectory, getPostprocessedLoopsFileName(res, isRequested)), true, Feature2DList.ListFormat.FINAL); } Feature2DList mergedList; if (looplists.containsKey(1000) || looplists.containsKey(2000)) { mergedList = mergeHighResolutions(looplists); } else { mergedList = mergeAllResolutions(looplists); } if (version == 2) { doFinalCleanUp(mergedList); } mergedList.exportFeatureList(outputFile, true, Feature2DList.ListFormat.FINAL); } public static void calculateThresholdAndFDR(int index, int width, double fdr, float[] poissonPMF, long[][] rcsHist, float[] threshold, float[][] fdrLog) { if (rcsHist[index][0] > 0) { float[] expected = ArrayTools.scalarMultiplyArray(rcsHist[index][0], poissonPMF); float[] rcsExpected = ArrayTools.makeReverseCumulativeArray(expected); for (int j = 0; j < width; j++) { if (fdr * rcsExpected[j] <= rcsHist[index][j]) { if (j == 0) { threshold[index] = (width - 2); } else { threshold[index] = (j - 1); } break; } } for (int j = 0; j < width; j++) { float sum1 = rcsExpected[j]; float sum2 = rcsHist[index][j]; if (sum2 > 0) { fdrLog[index][j] = sum1 / sum2; } else { break; } } } else if (HiCGlobals.printVerboseComments) { System.out.println("poss err index: " + index + " rcsHist " + rcsHist[index][0]); } } public static long histogramPvals(Map kHist, long totalPValues, long mstar) { for (long i = totalPValues; i >= 1; i--) { if (kHist.get(i) != null) { mstar = mstar - kHist.get(i); } if (i == mstar) { return i; } } System.err.println("didn't converge"); return 0; } public static Feature2DList filterOutFeaturelistByEnrichment(List configs, String folderPath, float maxEnrich, ChromosomeHandler commonChromosomesHandler) { Feature2DList results = new Feature2DList(); for (HiCCUPSConfiguration config : configs) { String fname = folderPath + File.separator + getRequestedLoopsFileName(config.getResolution()); Feature2DList requestedList = Feature2DParser.loadFeatures(fname, commonChromosomesHandler, true, null, false); HiCCUPSUtils.filterOutFeaturesByEnrichment(requestedList, maxEnrich); results.add(requestedList); } return results; } public static String getEnrichedPixelFileName(int resolution) { return ENRICHED_PIXELS + "_" + resolution + ".bedpe"; } private static String getPostprocessedLoopsFileName(int resolution, boolean isRequested) { if (isRequested) { return POST_PROCESSED + "_" + getRequestedLoopsFileName(resolution); } else { return POST_PROCESSED + "_" + resolution + ".bedpe"; } } public static String getRequestedLoopsFileName(int resolution) { return REQUESTED_LIST + "_" + resolution + ".bedpe"; } public static String getMergedLoopsFileName() { return MERGED; } public static String getMergedRequestedLoopsFileName() { return MERGED_REQUESTED; } public static String getFDRThresholdsFilename(int resolution) { return FDR_THRESHOLDS + "_" + resolution; } } ================================================ FILE: src/juicebox/tools/utils/juicer/localizer/LocalizerUtils.java ================================================ /* * The MIT License (MIT) * * Copyright (c) 2011-2023 Broad Institute, Aiden Lab, Rice University, Baylor College of Medicine * * Permission is hereby granted, free of charge, to any person obtaining a copy * of this software and associated documentation files (the "Software"), to deal * in the Software without restriction, including without limitation the rights * to use, copy, modify, merge, publish, distribute, sublicense, and/or sell * copies of the Software, and to permit persons to whom the Software is * furnished to do so, subject to the following conditions: * * The above copyright notice and this permission notice shall be included in * all copies or substantial portions of the Software. * * THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR * IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, * FITNESS FOR A PARTICULAR PURPOSE AND NON-INFRINGEMENT. IN NO EVENT SHALL THE * AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER * LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, * OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN * THE SOFTWARE. */ package juicebox.tools.utils.juicer.localizer; import juicebox.HiCGlobals; import juicebox.data.Dataset; import juicebox.data.HiCFileTools; import juicebox.data.MatrixZoomData; import juicebox.data.NormalizationVector; import juicebox.data.basics.ListOfDoubleArrays; import juicebox.tools.utils.common.MatrixTools; import juicebox.track.feature.Feature2D; import juicebox.windowui.NormalizationType; import org.apache.commons.math.distribution.PoissonDistribution; import org.apache.commons.math.distribution.PoissonDistributionImpl; import org.apache.commons.math.linear.Array2DRowRealMatrix; import org.apache.commons.math.linear.RealMatrix; import java.io.File; import java.io.IOException; import java.time.Duration; import java.time.Instant; import java.util.ArrayList; import java.util.Collections; import java.util.List; import java.util.Random; public class LocalizerUtils { /** * Size filtering of loops * * @param features * @param minPeakDist * @param maxPeakDist * @return */ public static ArrayList filterFeaturesBySize(List features, double minPeakDist, double maxPeakDist, int resolution) { ArrayList sizeFilteredFeatures = new ArrayList<>(); for (Feature2D feature : features) { double xMidPt = feature.getMidPt1(); double yMidPt = feature.getMidPt2(); int dist = (int) Math.round(Math.abs(xMidPt - yMidPt) / resolution); if (dist >= minPeakDist) { if (dist <= maxPeakDist) { sizeFilteredFeatures.add(feature); } } } return new ArrayList<>(sizeFilteredFeatures); } public static RealMatrix extractLocalizedData(MatrixZoomData zd, Feature2D loop, int L, int resolution, int window, NormalizationType norm) throws IOException { long loopX = loop.getMidPt1() / resolution; long loopY = loop.getMidPt2() / resolution; long binXStart = loopX - window; long binXEnd = loopX + (window + 1); long binYStart = loopY - window; long binYEnd = loopY + (window + 1); return HiCFileTools.extractLocalBoundedRegion(zd, binXStart, binXEnd, binYStart, binYEnd, L, L, norm, false); } public static List> extractNormParts(Dataset ds, MatrixZoomData zd, Feature2D loop, int resolution, int window, NormalizationType norm) throws IOException { long loopX = loop.getMidPt1() / resolution; long loopY = loop.getMidPt2() / resolution; long binXStart = loopX - window; long binXEnd = loopX + (window + 1); long binYStart = loopY - window; long binYEnd = loopY + (window + 1); List normH = new ArrayList<>(); List normV = new ArrayList<>(); NormalizationVector nv1 = ds.getNormalizationVector(zd.getChr1Idx(), zd.getZoom(), norm); NormalizationVector nv2 = ds.getNormalizationVector(zd.getChr2Idx(), zd.getZoom(), norm); ListOfDoubleArrays nv1Data = nv1.getData(); ListOfDoubleArrays nv2Data = nv2.getData(); for (long i = binXStart; i < binXEnd; i++) { normH.add(nv1Data.get(i)); } for (long i = binYStart; i < binYEnd; i++) { normV.add(nv2Data.get(i)); } List> normParts = new ArrayList<>(); normParts.add(normH); normParts.add(normV); return normParts; } public static List> localMax(RealMatrix rawSource, List normH, List normV, int window, int numPeaks, double maxPval, File outputDirectory) { // calculate total number of contacts in local window double rawSourceSum = matrixSum(rawSource, 0, rawSource.getRowDimension(), 0, rawSource.getColumnDimension()); //MatrixTools.saveMatrixText(new File(outputDirectory, "inputData.txt").getPath(), rawSource); // create copy of raw data and box blur over requested window (rawSummedData) // multiply box blurred matrix by window size to bring back into contact space (rawSummedData) Instant A = Instant.now(); RealMatrix rawSourceCopy = rawSource.copy(); RealMatrix rawSummedData = new Array2DRowRealMatrix(rawSource.getRowDimension(), rawSource.getColumnDimension()); boxBlur(rawSourceCopy, rawSummedData, window); multiplyInPlaceRound(rawSummedData, (window + window + 1) * (window + window + 1)); Instant B = Instant.now(); if (HiCGlobals.printVerboseComments) { System.out.println("time to blur raw matrix: " + Duration.between(A, B).toMillis()); } // calculate normed local matrix using input local norm vectors (normSource) // calculate gaussian blurred normed local matrix over requested window (normBlurred), multiply in place by ratio of box blurred raw matrix to normed matrix in order to make sure same number of contacts RealMatrix normSource = calculateNormMatrix(rawSource, normH, normV); Instant C = Instant.now(); if (HiCGlobals.printVerboseComments) { System.out.println("time to calculate norm matrix: " + Duration.between(B, C).toMillis()); } //MatrixTools.saveMatrixText(new File(outputDirectory, "normInputData.txt").getPath(), normSource); RealMatrix normBlurred = gaussBlur(normSource, window); //new Array2DRowRealMatrix(rawSource.getRowDimension(), rawSource.getColumnDimension()); double rawSummedSum = matrixSum(rawSummedData, 0, rawSource.getRowDimension(), 0, rawSource.getColumnDimension()); double normBlurredSum = matrixSum(normBlurred, 0, rawSource.getRowDimension(), 0, rawSource.getColumnDimension()); multiplyInPlace(normBlurred, rawSummedSum / normBlurredSum); Instant D = Instant.now(); if (HiCGlobals.printVerboseComments) { System.out.println("time to blur norm matrix: " + Duration.between(C, D).toMillis()); } //MatrixTools.saveMatrixText(new File(outputDirectory, "summedData.txt").getPath(), rawSummedData); //MatrixTools.saveMatrixText(new File(outputDirectory, "normSummedData.txt").getPath(), normBlurred); // set a non-uniform expected based on ratio of raw data to normed data (normExpected) // multiply in place to make sure it has the same number of contacts as the boxBlurred raw matrix RealMatrix normExpected = setNormExpected(rawSummedData, normBlurred, normH, normV); double normExpectedSum = matrixSum(normExpected, 0, rawSource.getRowDimension(), 0, rawSource.getColumnDimension()); multiplyInPlace(normExpected, rawSummedSum / normExpectedSum); Instant E = Instant.now(); if (HiCGlobals.printVerboseComments) { System.out.println("time to set expected: " + Duration.between(D, E).toMillis()); } //MatrixTools.saveMatrixText(new File(outputDirectory, "normExpectedData.txt").getPath(), normExpected); //do local nonmaximum suppression using the Poisson Z-score [2*(sqrt(X)-sqrt(lambda))] RealMatrix localMaxData = nonmaxsuppressPoissonZ(rawSummedData, normExpected, window); Instant F = Instant.now(); if (HiCGlobals.printVerboseComments) { System.out.println("time to suppress non-max: " + Duration.between(E, F).toMillis()); } //MatrixTools.saveMatrixText(new File(outputDirectory, "localMaxData.txt").getPath(), localMaxData); // count non-zero entries for bonferroni correction int pValAdj = nonZeroEntries(localMaxData, window, rawSource.getRowDimension() - window, window, rawSource.getColumnDimension() - window); // rank localized peaks List> orderedPeaks = orderPeaksPoissonZ(localMaxData, normExpected, window, maxPval, pValAdj); Instant G = Instant.now(); if (HiCGlobals.printVerboseComments) { System.out.println("time to identify peaks: " + Duration.between(F, G).toMillis()); } // return localized peaks List finalPeaksR = new ArrayList<>(); List finalPeaksC = new ArrayList<>(); List finalPeaksP = new ArrayList<>(); List finalPeaksO = new ArrayList<>(); List finalPeaksZ = new ArrayList<>(); numPeaks = numPeaks > orderedPeaks.get(0).size() ? orderedPeaks.get(0).size() : numPeaks; for (int i = 0; i < numPeaks; i++) { double peakRow = orderedPeaks.get(0).get(i); double peakCol = orderedPeaks.get(1).get(i); double peakPVal = orderedPeaks.get(2).get(i); double peakObserved = orderedPeaks.get(3).get(i); double peakZscore = orderedPeaks.get(4).get(i); //System.out.println(peakRow + " " + peakCol + " " + peakEntry); finalPeaksR.add(peakRow); finalPeaksC.add(peakCol); finalPeaksP.add(peakPVal); finalPeaksO.add(peakObserved); finalPeaksZ.add(peakZscore); } List> finalPeaks = new ArrayList<>(); finalPeaks.add(finalPeaksR); finalPeaks.add(finalPeaksC); finalPeaks.add(finalPeaksP); finalPeaks.add(finalPeaksO); finalPeaks.add(finalPeaksZ); return finalPeaks; } public static RealMatrix calculateNormMatrix(RealMatrix inputData, List normH, List normV) { int numRows = inputData.getRowDimension(); int numCols = inputData.getColumnDimension(); Instant A = Instant.now(); RealMatrix normSource = new Array2DRowRealMatrix(numRows, numCols); for (int i = 0; i < numRows; i++) { for (int j = 0; j < numCols; j++) { double valI = normH.get(i); double valJ = normV.get(j); // todo == 0 probably not the best thing to do here if (valI != 0 && valJ != 0 && !Double.isNaN(valI) && !Double.isNaN(valJ)) { normSource.setEntry(i,j,inputData.getEntry(i,j) / (valI * valJ)); } else { normSource.setEntry(i,j,0); } } } return normSource; } public static RealMatrix setNormExpected(RealMatrix rawSummedData, RealMatrix normBlurred, List normH, List normV) { int numRows = rawSummedData.getRowDimension(); int numCols = rawSummedData.getColumnDimension(); Instant A = Instant.now(); RealMatrix normExpected = new Array2DRowRealMatrix(numRows, numCols); for (int i = 0; i < numRows; i++) { for (int j = 0; j < numCols; j++) { if (normBlurred.getEntry(i,j)<=0) { normBlurred.setEntry(i,j,0); rawSummedData.setEntry(i,j,0); } double valI = normH.get(i); double valJ = normV.get(j); // todo == 0 probably not the best thing to do here if (normBlurred.getEntry(i,j)!=0) { normExpected.setEntry(i,j,(rawSummedData.getEntry(i,j)/normBlurred.getEntry(i,j))); //System.out.println(rawSummedData.getEntry(i,j) + " " + normBlurred.getEntry(i,j) + " " + normExpected.getEntry(i,j)); } else { normExpected.setEntry(i,j,0); } } } return normExpected; } public static double matrixSum(RealMatrix inputData, int rowBound1, int rowBound2, int colBound1, int colBound2) { double inputDataSum = 0; for (int i = rowBound1; i < rowBound2; i++) { for (int j = colBound1; j < colBound2; j++) { inputDataSum += inputData.getEntry(i,j); } } return inputDataSum; } public static int nonZeroEntries(RealMatrix inputData, int rowBound1, int rowBound2, int colBound1, int colBound2) { int nonZeroEntries = 0; for (int i = rowBound1; i < rowBound2; i++) { for (int j = colBound1; j < colBound2; j++) { if (inputData.getEntry(i,j)>0) { nonZeroEntries++; } } } return nonZeroEntries; } public static void multiplyInPlace(RealMatrix inputData, double scaleRatio) { int numRows = inputData.getRowDimension(); int numCols = inputData.getColumnDimension(); for (int i = 0; i < numRows; i++) { for (int j = 0; j < numCols; j++) { inputData.multiplyEntry(i,j,scaleRatio); } } } public static void multiplyInPlaceRound(RealMatrix inputData, double scaleRatio) { int numRows = inputData.getRowDimension(); int numCols = inputData.getColumnDimension(); for (int i = 0; i < numRows; i++) { for (int j = 0; j < numCols; j++) { double val = inputData.getEntry(i,j); double multVal = (double) Math.round(val*scaleRatio); inputData.setEntry(i,j,multVal); } } } public static RealMatrix gaussBlur(RealMatrix inputData, int window) { //int numRows = inputData.getRowDimension() - window; //int numCols = inputData.getColumnDimension() - window; //RealMatrix outputData = MatrixTools.cleanArray2DMatrix(numRows, numCols); //RealMatrix outputData = MatrixTools.deepCopy(inputData); int numRows = inputData.getRowDimension(); int numCols = inputData.getColumnDimension(); RealMatrix outputData = new Array2DRowRealMatrix(numRows, numCols); int[] boxSizes = boxesForGauss(window, 3); boxBlur(inputData, outputData, (boxSizes[0]-1)/2); boxBlur(outputData, inputData, (boxSizes[1]-1)/2); boxBlur(inputData, outputData, (boxSizes[2]-1)/2); //double outputDataSum = 0; //for (int i = window/2; i < (numRows-window/2); i++) { // for (int j = window/2; j < (numCols-window/2); j++) { // double sumVal = 0; // for (int rowOffset = 0; rowOffset < window; rowOffset++) { // for (int colOffset = 0; colOffset < window; colOffset++) { // sumVal = sumVal + (inputData.getEntry(i - (int) window/2 + rowOffset, j - (int) window/2 + colOffset) * //Math.exp(-1*(Math.pow((0-window/2+rowOffset),2)+Math.pow((0-window/2+colOffset),2))/(2*Math.pow(window/3,2)))*(1.0d/(2*Math.PI*Math.pow(window/3,2)))); // } // } // outputData.setEntry(i-(window/2),j-(window/2), sumVal); // outputDataSum += sumVal; // } //} return outputData; } public static int[] boxesForGauss(int sigma, int numBoxes) { int wl = (int) Math.floor(Math.sqrt((12*sigma*sigma/numBoxes)+1)); if (wl % 2 == 0) { wl--; } int wu = wl+2; int m = Math.round(((12*sigma*sigma) - (numBoxes*wl*wl) - (4*numBoxes*wl) - (3*numBoxes))/((-4*wl) - 4)); int[] boxSizes = new int[numBoxes]; for (int i = 0; i < numBoxes; i++ ) { boxSizes[i] = i 0) { outputData.setEntry(i-window,j-window,gradientVal); } } } return outputData; } public static RealMatrix nonmaxsuppress(RealMatrix inputData, int window) { int numRows = inputData.getRowDimension(); int numCols = inputData.getColumnDimension(); RealMatrix outputData = MatrixTools.cleanArray2DMatrix(numRows, numCols); Random randomGenerator = new Random(0); for (int i = 0; i < numRows; i++) { for (int j = 0; j < numCols; j++) { if (inputData.getEntry(i,j) > 0 && outputData.getEntry(i,j) >= 0) { int minRow = Math.max(0, i - window); int minCol = Math.max(0, j - window); int maxRow = Math.min(i + window, numRows - 1); int maxCol = Math.min(j + window, numCols - 1); int maxValR = i; int maxValC = j; double maxVal = inputData.getEntry(i, j); outputData.setEntry(maxValR, maxValC, inputData.getEntry(i, j)); for (int nmsRow = minRow; nmsRow <= maxRow; nmsRow++) { for (int nmsCol = minCol; nmsCol <= maxCol; nmsCol++) { if (nmsRow != i || nmsCol != j) { if (inputData.getEntry(nmsRow, nmsCol) > maxVal) { outputData.setEntry(maxValR, maxValC, -1); } else if (inputData.getEntry(nmsRow, nmsCol) == maxVal) { float coinToss = randomGenerator.nextFloat(); if (coinToss < 0.5) { outputData.setEntry(maxValR, maxValC, -1); } else { outputData.setEntry(nmsRow, nmsCol, -1); } } else { outputData.setEntry(nmsRow, nmsCol, -1); } } } } } } } return outputData; } public static RealMatrix nonmaxsuppressPoissonZ(RealMatrix observedData, RealMatrix expectedData, int window) { int numRows = observedData.getRowDimension(); int numCols = observedData.getColumnDimension(); RealMatrix outputData = MatrixTools.cleanArray2DMatrix(numRows, numCols); Random randomGenerator = new Random(0); for (int i = 0; i < numRows; i++) { for (int j = 0; j < numCols; j++) { if (observedData.getEntry(i,j) > 0 && outputData.getEntry(i,j) >= 0) { int minRow = Math.max(0, i - window); int minCol = Math.max(0, j - window); int maxRow = Math.min(i + window, numRows - 1); int maxCol = Math.min(j + window, numCols - 1); int maxValR = i; int maxValC = j; double maxVal = 2 * (Math.sqrt(observedData.getEntry(i, j)) - Math.sqrt(expectedData.getEntry(i, j))); outputData.setEntry(maxValR, maxValC, observedData.getEntry(i, j)); for (int nmsRow = minRow; nmsRow <= maxRow; nmsRow++) { for (int nmsCol = minCol; nmsCol <= maxCol; nmsCol++) { if (nmsRow != i || nmsCol != j) { double testVal = 2 * (Math.sqrt(observedData.getEntry(nmsRow, nmsCol)) - Math.sqrt(expectedData.getEntry(nmsRow, nmsCol))); if (testVal > maxVal) { outputData.setEntry(maxValR, maxValC, -1); } else if (testVal == maxVal) { float coinToss = randomGenerator.nextFloat(); if (coinToss < 0.5) { outputData.setEntry(maxValR, maxValC, -1); } else { outputData.setEntry(nmsRow, nmsCol, -1); } } else { outputData.setEntry(nmsRow, nmsCol, -1); } } } } } } } return outputData; } public static List> orderPeaks(RealMatrix inputData, double sourceSum, List normH, List normV, int window, double maxPval, int pValAdj) { List> peaks = new ArrayList<>(); peaks.add(new ArrayList<>()); peaks.add(new ArrayList<>()); peaks.add(new ArrayList<>()); peaks.add(new ArrayList<>()); int numRows = inputData.getRowDimension(); int numCols = inputData.getColumnDimension(); Instant A = Instant.now(); RealMatrix normExpected = new Array2DRowRealMatrix(numRows, numCols); for (int i = 0; i < numRows; i++) { for (int j = 0; j < numCols; j++) { normExpected.setEntry(i,j, sourceSum*normH.get(i)*normV.get(j)/(numRows*numCols)); } } Instant B = Instant.now(); double normSum = matrixSum(normExpected, 0, numRows, 0, numCols); Instant C = Instant.now(); multiplyInPlace(normExpected, sourceSum/normSum); Instant D = Instant.now(); RealMatrix normSummed = new Array2DRowRealMatrix(numRows, numCols); boxBlur(normExpected, normSummed, window); Instant E = Instant.now(); multiplyInPlace(normSummed, (window+window+1)*(window+window+1)); Instant F = Instant.now(); for (int i = window/2; i < inputData.getRowDimension()-window/2; i++) { for (int j = window/2; j < inputData.getColumnDimension()-window/2; j++) { if (inputData.getEntry(i,j) > 0) { Instant H = Instant.now(); PoissonDistribution dist = new PoissonDistributionImpl(normSummed.getEntry(i,j)); double pVal = 0; try { pVal = 1-dist.cumulativeProbability((int) inputData.getEntry(i,j)-1); } catch (Exception e) { e.printStackTrace(); System.err.println("error calculating p value"); } pVal = pVal * pValAdj; Instant I = Instant.now(); if (pVal <= maxPval) { //System.out.println(i + " " + j + " " + inputData.getEntry(i,j) + " " + normSummed.getEntry(i,j) + " " + pVal); int insertionPoint = Collections.binarySearch(peaks.get(2), pVal); if (insertionPoint < 0) { insertionPoint = -1 * (insertionPoint + 1); } else if (insertionPoint >= 0) { if (inputData.getEntry(i,j) <= peaks.get(3).get(insertionPoint)) { insertionPoint = insertionPoint+1; } } peaks.get(0).add(insertionPoint, (double) i); peaks.get(1).add(insertionPoint, (double) j); peaks.get(2).add(insertionPoint, pVal); peaks.get(3).add(insertionPoint, inputData.getEntry(i,j)); } Instant J = Instant.now(); //System.out.println("individual pval: " + Duration.between(H,I).toNanos()); //System.out.println("individual sort: " + Duration.between(I,J).toNanos()); } } } Instant G = Instant.now(); //System.out.println("norm set: " + Duration.between(A,B).toMillis()); //System.out.println("norm sum: " + Duration.between(B,C).toMillis()); //System.out.println("norm multiply: " + Duration.between(C,D).toMillis()); //System.out.println("norm sliding: " + Duration.between(D,E).toMillis()); //System.out.println("norm multiply 2: " + Duration.between(E,F).toMillis()); //System.out.println("norm pval: " + Duration.between(F,G).toMillis()); return peaks; } public static List> orderPeaksPoissonZ(RealMatrix inputData, RealMatrix expectedData, int window, double maxPval, int pValAdj) { List> peaks = new ArrayList<>(); peaks.add(new ArrayList<>()); peaks.add(new ArrayList<>()); peaks.add(new ArrayList<>()); peaks.add(new ArrayList<>()); peaks.add(new ArrayList<>()); for (int i = window; i < inputData.getRowDimension()-window; i++) { for (int j = window; j < inputData.getColumnDimension()-window; j++) { if (inputData.getEntry(i,j) > 0) { Instant H = Instant.now(); PoissonDistribution dist = new PoissonDistributionImpl(expectedData.getEntry(i,j)); double pVal = 0; try { pVal = 1-dist.cumulativeProbability((int) inputData.getEntry(i,j)-1); } catch (Exception e) { e.printStackTrace(); System.err.println("error calculating p value"); } pVal = pVal * pValAdj; Instant I = Instant.now(); if (pVal <= maxPval) { //System.out.println(i + " " + j + " " + inputData.getEntry(i,j) + " " + normSummed.getEntry(i,j) + " " + pVal); double zscore = 2*(Math.sqrt(inputData.getEntry(i, j)) - Math.sqrt(expectedData.getEntry(i,j))); int insertionPoint = Collections.binarySearch(peaks.get(4), zscore, Collections.reverseOrder()); if (insertionPoint < 0) { insertionPoint = -1 * (insertionPoint + 1); } //else if (insertionPoint >= 0) { // if (2*(Math.sqrt(inputData.getEntry(i, j)) - Math.sqrt(expectedData.getEntry(i,j))) <= peaks.get(4).get(insertionPoint)) { // insertionPoint = insertionPoint+1; // } //} peaks.get(0).add(insertionPoint, (double) i); peaks.get(1).add(insertionPoint, (double) j); peaks.get(2).add(insertionPoint, pVal); peaks.get(3).add(insertionPoint, inputData.getEntry(i,j)); peaks.get(4).add(insertionPoint, zscore); } Instant J = Instant.now(); //System.out.println("individual pval: " + Duration.between(H,I).toNanos()); //System.out.println("individual sort: " + Duration.between(I,J).toNanos()); } } } Instant G = Instant.now(); //System.out.println("norm set: " + Duration.between(A,B).toMillis()); //System.out.println("norm sum: " + Duration.between(B,C).toMillis()); //System.out.println("norm multiply: " + Duration.between(C,D).toMillis()); //System.out.println("norm sliding: " + Duration.between(D,E).toMillis()); //System.out.println("norm multiply 2: " + Duration.between(E,F).toMillis()); //System.out.println("norm pval: " + Duration.between(F,G).toMillis()); return peaks; } } ================================================ FILE: src/juicebox/tools/utils/norm/CustomNormVectorFileHandler.java ================================================ /* * The MIT License (MIT) * * Copyright (c) 2011-2021 Broad Institute, Aiden Lab, Rice University, Baylor College of Medicine * * Permission is hereby granted, free of charge, to any person obtaining a copy * of this software and associated documentation files (the "Software"), to deal * in the Software without restriction, including without limitation the rights * to use, copy, modify, merge, publish, distribute, sublicense, and/or sell * copies of the Software, and to permit persons to whom the Software is * furnished to do so, subject to the following conditions: * * The above copyright notice and this permission notice shall be included in * all copies or substantial portions of the Software. * * THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR * IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, * FITNESS FOR A PARTICULAR PURPOSE AND NON-INFRINGEMENT. IN NO EVENT SHALL THE * AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER * LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, * OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN * THE SOFTWARE. */ package juicebox.tools.utils.norm; import juicebox.HiC; import juicebox.HiCGlobals; import juicebox.data.*; import juicebox.data.basics.Chromosome; import juicebox.data.basics.ListOfDoubleArrays; import juicebox.gui.SuperAdapter; import juicebox.tools.utils.original.ExpectedValueCalculation; import juicebox.windowui.HiCZoom; import juicebox.windowui.NormalizationHandler; import juicebox.windowui.NormalizationType; import org.broad.igv.tdf.BufferedByteWriter; import java.io.*; import java.nio.charset.StandardCharsets; import java.util.*; import java.util.concurrent.ExecutorService; import java.util.zip.GZIPInputStream; public class CustomNormVectorFileHandler extends NormVectorUpdater { public static void updateHicFile(String path, String vectorPath, int numCPUThreads) throws IOException { DatasetReaderV2 reader = new DatasetReaderV2(path); Dataset ds = reader.read(); HiCGlobals.verifySupportedHiCFileVersion(reader.getVersion()); String[] vectorPaths = vectorPath.split(","); NormVectorInfo normVectorInfo = completeCalculationsNecessaryForUpdatingCustomNormalizations(ds, vectorPaths, true, numCPUThreads); writeNormsToUpdateFile(reader, path, false, null, normVectorInfo.getExpectedValueFunctionMap(), normVectorInfo.getNormVectorIndices(), normVectorInfo.getNormVectorBuffers(), "Finished adding another normalization."); System.out.println("all custom norms added"); } public static void unsafeHandleUpdatingOfNormalizations(SuperAdapter superAdapter, File[] files, boolean isControl, int numCPUThreads) { Dataset ds = superAdapter.getHiC().getDataset(); if (isControl) { ds = superAdapter.getHiC().getControlDataset(); } String[] filePaths = new String[files.length]; for (int i = 0; i < filePaths.length; i++) { filePaths[i] = files[i].getAbsolutePath(); } try { NormVectorInfo normVectorInfo = completeCalculationsNecessaryForUpdatingCustomNormalizations(ds, filePaths, false, numCPUThreads); for (NormalizationType customNormType : normVectorInfo.getNormalizationVectorsMap().keySet()) { ds.addNormalizationType(customNormType); for (NormalizationVector normalizationVector : normVectorInfo.getNormalizationVectorsMap().get(customNormType).values()) { if (normalizationVector == null) { System.out.println("error encountered"); } ds.addNormalizationVectorDirectlyToRAM(normalizationVector); } } System.out.println("all custom norms added v2"); } catch (Exception e) { e.printStackTrace(); } } private static NormVectorInfo completeCalculationsNecessaryForUpdatingCustomNormalizations( final Dataset ds, String[] filePaths, boolean overwriteHicFileFooter, int numCPUThreads) throws IOException { Map> normalizationVectorMap = readVectorFile(filePaths, ds.getChromosomeHandler(), ds.getNormalizationHandler()); ChromosomeHandler chromosomeHandler = ds.getChromosomeHandler(); Map fragCountMap = ds.getFragmentCounts(); List resolutions = ds.getAllPossibleResolutions(); List normVectorBuffers = new ArrayList<>(); List normVectorIndices = new ArrayList<>(); Map expectedValueFunctionMap = ds.getExpectedValueFunctionMap(); for (Iterator> it = expectedValueFunctionMap.entrySet().iterator(); it.hasNext(); ) { Map.Entry entry = it.next(); if (entry.getKey().contains("NONE")) { it.remove(); } } // Get existing norm vectors so we don't lose them if (overwriteHicFileFooter) { for (HiCZoom zoom : resolutions) { for (NormalizationType type : NormalizationHandler.getAllNormTypes()) { for (Chromosome chr : chromosomeHandler.getChromosomeArrayWithoutAllByAll()) { NormalizationVector existingNorm = ds.getNormalizationVector(chr.getIndex(), zoom, type); if (existingNorm != null) { long position = 0; for (int i=0; i < normVectorBuffers.size(); i++) { position += normVectorBuffers.get(i).bytesWritten(); } // todo @suhas putFloatArraysIntoBufferList(normVectorBuffers, existingNorm.getData().convertToFloats().getValues()); long newPos = 0; for (int i=0; i < normVectorBuffers.size(); i++) { newPos += normVectorBuffers.get(i).bytesWritten(); } int sizeInBytes = (int) (newPos - position); normVectorIndices.add(new NormalizationVectorIndexEntry( type.toString(), chr.getIndex(), zoom.getUnit().toString(), zoom.getBinSize(), position, sizeInBytes)); } } } } } System.out.println("loaded existing norms"); ExecutorService executor = HiCGlobals.newFixedThreadPool(); for (NormalizationType customNormType : normalizationVectorMap.keySet()) { final Map normVectorsByChrAndZoom = normalizationVectorMap.get(customNormType); final Set keySet = new HashSet<>(normVectorsByChrAndZoom.keySet()); final Map chrAndResolutionWhichFailed = new HashMap<>(); for (final String key : keySet) { final NormalizationVector nv = normVectorsByChrAndZoom.get(key); if (chrAndResolutionWhichFailed.containsKey(nv.getChrIdx()) && nv.getResolution() < chrAndResolutionWhichFailed.get(nv.getChrIdx())) { normVectorsByChrAndZoom.remove(key); continue; } if (nv.doesItNeedToBeScaledTo()) { Runnable worker = new Runnable() { @Override public void run() { NormalizationVector newScaledVector = nv.mmbaScaleToVector(ds); synchronized (normVectorsByChrAndZoom) { if (newScaledVector != null) { normVectorsByChrAndZoom.put(key, newScaledVector); } else { normVectorsByChrAndZoom.remove(key); int currResolution = nv.getResolution(); int chrIndx = nv.getChrIdx(); if (currResolution < chrAndResolutionWhichFailed.get(chrIndx)) { chrAndResolutionWhichFailed.put(chrIndx, currResolution); } } } } }; executor.execute(worker); } } } executor.shutdown(); // Wait until all threads finish while (!executor.isTerminated()) { } for (HiCZoom zoom : resolutions) { Map fcm = zoom.getUnit() == HiC.Unit.FRAG ? fragCountMap : null; for (NormalizationType customNormType : normalizationVectorMap.keySet()) { ExpectedValueCalculation evLoaded = new ExpectedValueCalculation(chromosomeHandler, zoom.getBinSize(), fcm, customNormType); String key = ExpectedValueFunctionImpl.getKey(zoom, customNormType); // Loop through chromosomes for (Chromosome chr : chromosomeHandler.getChromosomeArrayWithoutAllByAll()) { MatrixZoomData zd = HiCFileTools.getMatrixZoomData(ds, chr, chr, zoom); if (zd == null) continue; handleLoadedVector(customNormType, chr.getIndex(), zoom, normalizationVectorMap.get(customNormType), normVectorBuffers, normVectorIndices, zd, evLoaded, fragCountMap, chromosomeHandler, numCPUThreads); } expectedValueFunctionMap.put(key, evLoaded.getExpectedValueFunction()); } } ds.setExpectedValueFunctionMap(expectedValueFunctionMap); return new NormVectorInfo(normalizationVectorMap, normVectorBuffers, normVectorIndices, expectedValueFunctionMap); } private static void handleLoadedVector(NormalizationType customNormType, final int chrIndx, HiCZoom zoom, Map normVectors, List normVectorBuffers, List normVectorIndex, MatrixZoomData zd, ExpectedValueCalculation evLoaded, Map fragmentCountMap, ChromosomeHandler chromosomeHandler, int numCPUThreads) throws IOException { String key = NormalizationVector.getKey(customNormType, chrIndx, zoom.getUnit().toString(), zoom.getBinSize()); if (normVectors.containsKey(key)) { NormalizationVector vector = normVectors.get(key); if (vector == null || vector.getData() == null) return; // Write custom norm long position = 0; for (int i=0; i < normVectorBuffers.size(); i++) { position += normVectorBuffers.get(i).bytesWritten(); } // todo @suhas putFloatArraysIntoBufferList(normVectorBuffers, vector.getData().convertToFloats().getValues()); long newPos = 0; for (int i=0; i < normVectorBuffers.size(); i++) { newPos += normVectorBuffers.get(i).bytesWritten(); } int sizeInBytes = (int) (newPos - position); normVectorIndex.add(new NormalizationVectorIndexEntry( customNormType.toString(), chrIndx, zoom.getUnit().toString(), zoom.getBinSize(), position, sizeInBytes)); evLoaded.addDistancesFromZD(zd, fragmentCountMap, chromosomeHandler, numCPUThreads); System.out.println("done with "+key); } } private static Map> readVectorFile(String[] fnames, ChromosomeHandler chromosomeHandler, NormalizationHandler normalizationHandler) throws IOException { Map> normVectors = new HashMap<>(); for (String fname : fnames) { BufferedReader vectorReader; if (fname.endsWith(".gz")) { InputStream fileStream = new FileInputStream(fname); InputStream gzipStream = new GZIPInputStream(fileStream); Reader decoder = new InputStreamReader(gzipStream, StandardCharsets.UTF_8); vectorReader = new BufferedReader(decoder, 4194304); } else { //this.reader = org.broad.igv.util.ParsingUtils.openBufferedReader(path); vectorReader = new BufferedReader(new InputStreamReader(new FileInputStream(fname)), HiCGlobals.bufferSize); } Chromosome chr = null; int resolution = -1; HiC.Unit unit = null; NormalizationType customNormType = null; boolean needsToBeScaledTo = false; String nextLine = vectorReader.readLine(); while (nextLine != null) { // Header: vector type chr1 2048000 BP if (nextLine.startsWith("vector")) { String[] tokens = nextLine.split("\\s+"); chr = chromosomeHandler.getChromosomeFromName(tokens[2]); if (chr == null) { System.err.println("Skipping " + tokens[2] + " which isn't in dataset"); nextLine = skipLinesUntilTextEncountered(vectorReader, "vector"); continue; } customNormType = normalizationHandler.getNormTypeFromString(tokens[1]); resolution = Integer.parseInt(tokens[3]); unit = HiC.Unit.valueOf(tokens[4]); needsToBeScaledTo = tokens[0].toLowerCase().contains("scale"); } if (chr != null && customNormType != null) { if (HiCGlobals.printVerboseComments) { System.out.println("Adding norm " + customNormType + " for chr " + chr.getName() + " at " + resolution + " " + unit + " resolution."); } // Now do work on loaded norm vector // Create the new vector by looping through the loaded vector file line by line // assume custom norm vectors aren't for indices requiring long long size = (chr.getLength() / resolution + 1); ListOfDoubleArrays data = new ListOfDoubleArrays(size); int i = 0; nextLine = vectorReader.readLine(); // List data = new ArrayList(); while (nextLine != null && !(nextLine.startsWith("vector"))) { if (nextLine.equalsIgnoreCase("nan") || nextLine.equals(".")) { data.set(i, Double.NaN); } else { data.set(i, Double.parseDouble(nextLine)); } i++; if (i > size) { throw new IOException("More values than resolution would indicate"); } nextLine = vectorReader.readLine(); } if (!normVectors.containsKey(customNormType)) { normVectors.put(customNormType, new HashMap<>()); } NormalizationVector vector = new NormalizationVector(customNormType, chr.getIndex(), unit, resolution, data, needsToBeScaledTo); normVectors.get(customNormType).put(vector.getKey(), vector); } else { System.err.println("Chromosome vector null"); // this shouldn't happen due to continue above } } } return normVectors; } private static String skipLinesUntilTextEncountered(BufferedReader vectorReader, String string) throws IOException { String nextLine = vectorReader.readLine(); while (nextLine != null && !(nextLine.startsWith(string))) { nextLine = vectorReader.readLine(); } return nextLine; } } ================================================ FILE: src/juicebox/tools/utils/norm/ExternalNormalizationVectorLoader.java ================================================ /* * The MIT License (MIT) * * Copyright (c) 2011-2020 Broad Institute, Aiden Lab, Rice University, Baylor College of Medicine * * Permission is hereby granted, free of charge, to any person obtaining a copy * of this software and associated documentation files (the "Software"), to deal * in the Software without restriction, including without limitation the rights * to use, copy, modify, merge, publish, distribute, sublicense, and/or sell * copies of the Software, and to permit persons to whom the Software is * furnished to do so, subject to the following conditions: * * The above copyright notice and this permission notice shall be included in * all copies or substantial portions of the Software. * * THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR * IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, * FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE * AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER * LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, * OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN * THE SOFTWARE. */ package juicebox.tools.utils.norm; class ExternalNormalizationVectorLoader { } ================================================ FILE: src/juicebox/tools/utils/norm/GenomeWideNormalizationVectorUpdater.java ================================================ /* * The MIT License (MIT) * * Copyright (c) 2011-2021 Broad Institute, Aiden Lab, Rice University, Baylor College of Medicine * * Permission is hereby granted, free of charge, to any person obtaining a copy * of this software and associated documentation files (the "Software"), to deal * in the Software without restriction, including without limitation the rights * to use, copy, modify, merge, publish, distribute, sublicense, and/or sell * copies of the Software, and to permit persons to whom the Software is * furnished to do so, subject to the following conditions: * * The above copyright notice and this permission notice shall be included in * all copies or substantial portions of the Software. * * THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR * IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, * FITNESS FOR A PARTICULAR PURPOSE AND NON-INFRINGEMENT. IN NO EVENT SHALL THE * AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER * LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, * OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN * THE SOFTWARE. */ package juicebox.tools.utils.norm; import juicebox.HiCGlobals; import juicebox.data.*; import juicebox.data.basics.Chromosome; import juicebox.data.basics.ListOfFloatArrays; import juicebox.data.iterator.IteratorContainer; import juicebox.data.iterator.ListOfListGenerator; import juicebox.tools.utils.original.ExpectedValueCalculation; import juicebox.windowui.HiCZoom; import juicebox.windowui.NormalizationHandler; import juicebox.windowui.NormalizationType; import org.broad.igv.tdf.BufferedByteWriter; import org.broad.igv.util.Pair; import java.io.IOException; import java.util.*; public class GenomeWideNormalizationVectorUpdater extends NormVectorUpdater { // todo remove /* public static void addGWNorm(String path, int genomeWideResolution) throws IOException { DatasetReaderV2 reader = new DatasetReaderV2(path); Dataset ds = reader.read(); HiCGlobals.verifySupportedHiCFileVersion(reader.getVersion()); List resolutions = new ArrayList<>(); resolutions.addAll(ds.getBpZooms()); resolutions.addAll(ds.getFragZooms()); List normVectorBuffers = new ArrayList<>(); List normVectorIndex = new ArrayList<>(); Map expectedValueFunctionMap = ds.getExpectedValueFunctionMap(); for (Iterator> it = expectedValueFunctionMap.entrySet().iterator(); it.hasNext(); ) { Map.Entry entry = it.next(); if (entry.getKey().contains("NONE")) { it.remove(); } } // Loop through resolutions for (HiCZoom zoom : resolutions) { // compute genome-wide normalization // TODO make this dependent on memory, do as much as possible if (genomeWideResolution >= 10000 && zoom.getUnit() == HiC.Unit.BP && zoom.getBinSize() >= genomeWideResolution) { for (NormalizationType normType : NormalizationHandler.getAllGWNormTypes(false)) { Pair, ExpectedValueCalculation> wgVectors = getWGVectors(ds, zoom, normType); if (wgVectors != null) { Map nvMap = wgVectors.getFirst(); for (Chromosome chromosome : nvMap.keySet()) { updateNormVectorIndexWithVector(normVectorIndex, normVectorBuffers, nvMap.get(chromosome).getData().convertToFloats(), chromosome.getIndex(), normType, zoom); } ExpectedValueCalculation calculation = wgVectors.getSecond(); String key = ExpectedValueFunctionImpl.getKey(zoom, normType); expectedValueFunctionMap.put(key, calculation.getExpectedValueFunction()); } } } System.out.println(); System.out.print("Calculating norms for zoom " + zoom); // Integer is either limit on genome wide resolution or limit on what fragment resolution to calculate // if (genomeWideResolution == 0 && zoom.getUnit() == HiC.Unit.FRAG) continue; // if (genomeWideResolution < 10000 && zoom.getUnit() == HiC.Unit.FRAG && zoom.getBinSize() <= genomeWideResolution) continue; // Loop through chromosomes for (Chromosome chr : ds.getChromosomeHandler().getChromosomeArrayWithoutAllByAll()) { Matrix matrix = ds.getMatrix(chr, chr); if (matrix == null) continue; for (NormalizationType normType : NormalizationHandler.getAllNormTypes()) { NormalizationVector vector = ds.getNormalizationVector(chr.getIndex(), zoom, normType); if (vector != null) { updateNormVectorIndexWithVector(normVectorIndex, normVectorBuffers, vector.getData().convertToFloats(), chr.getIndex(), normType, zoom); } } } } int version = reader.getVersion(); long filePosition = reader.getNormFilePosition(); long nviHeaderPosition = reader.getNviHeaderPosition(); System.out.println(); NormalizationVectorUpdater.update(path, version, filePosition, expectedValueFunctionMap, normVectorIndex, normVectorBuffers, nviHeaderPosition); System.out.println("Finished normalization"); } */ public static void updateHicFileForGWfromPreAddNormOnly(Dataset ds, HiCZoom zoom, List normalizationsToBuild, Map resolutionsToBuildTo, List normVectorIndices, List normVectorBuffers, List expectedValueCalculations) throws IOException { for (NormalizationType normType : normalizationsToBuild) { if (NormalizationHandler.isGenomeWideNorm(normType)) { if (zoom.getBinSize() >= resolutionsToBuildTo.get(normType)) { if (HiCGlobals.printVerboseComments) { System.out.println("Now Doing " + normType.getLabel()); } long currentTime = System.currentTimeMillis(); Pair, ExpectedValueCalculation> wgVectors = getWGVectors(ds, zoom, normType); if (HiCGlobals.printVerboseComments) { System.out.println("\n" + normType.getLabel() + " normalization genome wide at " + zoom + " took " + (System.currentTimeMillis() - currentTime) + " milliseconds"); } if (wgVectors != null) { Map nvMap = wgVectors.getFirst(); List chromosomes = new ArrayList<>(nvMap.keySet()); Collections.sort(chromosomes, Comparator.comparingInt(Chromosome::getIndex)); for (Chromosome chromosome : chromosomes) { updateNormVectorIndexWithVector(normVectorIndices, normVectorBuffers, nvMap.get(chromosome).getData().convertToFloats(), chromosome.getIndex(), normType, zoom); } expectedValueCalculations.add(wgVectors.getSecond()); } } } } } /** * Compute the whole-genome normalization and expected value vectors and return as a pair (normalization vector first) */ private static Pair, ExpectedValueCalculation> getWGVectors(Dataset dataset, HiCZoom zoom, NormalizationType norm) { boolean includeIntraData = NormalizationHandler.isGenomeWideNormIntra(norm); // default INTER type final ChromosomeHandler chromosomeHandler = dataset.getChromosomeHandler(); final int resolution = zoom.getBinSize(); final IteratorContainer ic = ListOfListGenerator.createForWholeGenome(dataset, chromosomeHandler, zoom, includeIntraData); NormalizationCalculations calculations = new NormalizationCalculations(ic); ListOfFloatArrays vector = calculations.getNorm(norm); if (vector == null) { return null; } ExpectedValueCalculation expectedValueCalculation = new ExpectedValueCalculation(chromosomeHandler, resolution, null, norm); int addY = 0; // Loop through chromosomes for (Chromosome chr : chromosomeHandler.getChromosomeArrayWithoutAllByAll()) { MatrixZoomData zd = HiCFileTools.getMatrixZoomData(dataset, chr, chr, zoom); if (zd == null) continue; final int chrIdx = chr.getIndex(); Iterator iterator = zd.getFromFileIteratorContainer().getNewContactRecordIterator(); while (iterator.hasNext()) { ContactRecord cr = iterator.next(); int x = cr.getBinX(); int y = cr.getBinY(); final float vx = vector.get(x + addY); final float vy = vector.get(y + addY); if (isValidNormValue(vx) && isValidNormValue(vy)) { double value = cr.getCounts() / (vx * vy); expectedValueCalculation.addDistance(chrIdx, x, y, value); } } addY += chr.getLength() / resolution + 1; } // Split normalization vector by chromosome Map normVectorMap = NormalizationTools.parCreateNormVectorMap(chromosomeHandler, resolution, vector, norm, zoom); ic.clear(); return new Pair<>(normVectorMap, expectedValueCalculation); } } ================================================ FILE: src/juicebox/tools/utils/norm/MultithreadedNormalizationVectorUpdater.java ================================================ /* * The MIT License (MIT) * * Copyright (c) 2011-2021 Broad Institute, Aiden Lab, Rice University, Baylor College of Medicine * * Permission is hereby granted, free of charge, to any person obtaining a copy * of this software and associated documentation files (the "Software"), to deal * in the Software without restriction, including without limitation the rights * to use, copy, modify, merge, publish, distribute, sublicense, and/or sell * copies of the Software, and to permit persons to whom the Software is * furnished to do so, subject to the following conditions: * * The above copyright notice and this permission notice shall be included in * all copies or substantial portions of the Software. * * THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR * IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, * FITNESS FOR A PARTICULAR PURPOSE AND NON-INFRINGEMENT. IN NO EVENT SHALL THE * AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER * LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, * OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN * THE SOFTWARE. */ package juicebox.tools.utils.norm; import juicebox.HiC; import juicebox.HiCGlobals; import juicebox.data.*; import juicebox.data.basics.Chromosome; import juicebox.data.basics.ListOfFloatArrays; import juicebox.tools.utils.original.ExpectedValueCalculation; import juicebox.windowui.HiCZoom; import juicebox.windowui.NormalizationHandler; import juicebox.windowui.NormalizationType; import org.broad.igv.tdf.BufferedByteWriter; import java.io.IOException; import java.util.*; import java.util.concurrent.ConcurrentHashMap; import java.util.concurrent.ExecutorService; import java.util.concurrent.Executors; import java.util.concurrent.atomic.AtomicInteger; public class MultithreadedNormalizationVectorUpdater extends NormalizationVectorUpdater { protected Set synckrBPFailedChromosomes = Collections.synchronizedSet(krBPFailedChromosomes); protected Set synckrFragFailedChromosomes = Collections.synchronizedSet(krFragFailedChromosomes); protected Set syncmmbaBPFailedChromosomes = Collections.synchronizedSet(mmbaBPFailedChromosomes); protected Set syncmmbaFragFailedChromosomes = Collections.synchronizedSet(mmbaFragFailedChromosomes); protected Map> zoomSpecifickrBPFailedChromsomes = new ConcurrentHashMap<>(); protected Map> zoomSpecifickrFragFailedChromsomes = new ConcurrentHashMap<>(); protected Map> zoomSpecificmmbaBPFailedChromsomes = new ConcurrentHashMap<>(); protected Map> zoomSpecificmmbaFragFailedChromsomes = new ConcurrentHashMap<>(); protected static int numCPUThreads = 1; public MultithreadedNormalizationVectorUpdater(int numCPUThreads) { MultithreadedNormalizationVectorUpdater.numCPUThreads = numCPUThreads; } @Override public void updateHicFile(String path, List normalizationsToBuild, Map resolutionsToBuildTo, int genomeWideLowestResolutionAllowed, boolean noFrag) throws IOException { int minResolution = Integer.MAX_VALUE; for (Map.Entry entry : resolutionsToBuildTo.entrySet()) { if (entry.getValue() < minResolution) { minResolution = entry.getValue(); } } DatasetReaderV2 reader = new DatasetReaderV2(path); Dataset ds = reader.read(); HiCGlobals.verifySupportedHiCFileVersion(reader.getVersion()); ChromosomeHandler chromosomeHandler = ds.getChromosomeHandler(); Map fragCountMap = ds.getFragmentCounts(); List resolutions = ds.getAllPossibleResolutions(); reEvaluateWhichIntraNormsToBuild(normalizationsToBuild); normVectorBuffers.add(new BufferedByteWriter()); for (HiCZoom zoom : resolutions) { if (zoom.getBinSize() < minResolution) { System.out.println("skipping zoom" + zoom); continue; } if (noFrag && zoom.getUnit() == HiC.Unit.FRAG) continue; // compute genome-wide normalizations if (zoom.getUnit() == HiC.Unit.BP && zoom.getBinSize() >= genomeWideLowestResolutionAllowed) { GenomeWideNormalizationVectorUpdater.updateHicFileForGWfromPreAddNormOnly(ds, zoom, normalizationsToBuild, resolutionsToBuildTo, normVectorIndices, normVectorBuffers, expectedValueCalculations); } System.out.println(); System.out.print("Calculating norms for zoom " + zoom); Map fcm = zoom.getUnit() == HiC.Unit.FRAG ? fragCountMap : null; ExpectedValueCalculation evVC = new ExpectedValueCalculation(chromosomeHandler, zoom.getBinSize(), fcm, NormalizationHandler.VC); ExpectedValueCalculation evVCSqrt = new ExpectedValueCalculation(chromosomeHandler, zoom.getBinSize(), fcm, NormalizationHandler.VC_SQRT); ExpectedValueCalculation evKR = new ExpectedValueCalculation(chromosomeHandler, zoom.getBinSize(), fcm, NormalizationHandler.KR); ExpectedValueCalculation evSCALE = new ExpectedValueCalculation(chromosomeHandler, zoom.getBinSize(), fcm, NormalizationHandler.SCALE); Map withinZoomVCSumFactors = new ConcurrentHashMap<>(); Map withinZoomVCSQRTSumFactors = new ConcurrentHashMap<>(); Map withinZoomKRSumFactors = new ConcurrentHashMap<>(); Map withinZoomSCALESumFactors = new ConcurrentHashMap<>(); Map withinZoomVCVectors = new ConcurrentHashMap<>(); Map withinZoomVCSQRTVectors = new ConcurrentHashMap<>(); Map withinZoomKRVectors = new ConcurrentHashMap<>(); Map withinZoomSCALEVectors = new ConcurrentHashMap<>(); final AtomicInteger chromosomeIndex = new AtomicInteger(0); Set withinZoomSynckrBPFailedChromosomes = Collections.synchronizedSet(new HashSet<>()); Set withinZoomSynckrFragFailedChromosomes = Collections.synchronizedSet(new HashSet<>()); Set withinZoomSyncmmbaBPFailedChromosomes = Collections.synchronizedSet(new HashSet<>()); Set withinZoomSyncmmbaFragFailedChromosomes = Collections.synchronizedSet(new HashSet<>()); Map allChrZoomData = new ConcurrentHashMap<>(); ExecutorService executor = Executors.newFixedThreadPool(numCPUThreads); for (int l = 0; l < numCPUThreads; l++) { final int threadNum = l; Runnable worker = new Runnable() { @Override public void run() { try { DatasetReaderV2 localReader; Dataset localds; ChromosomeHandler localChromosomeHandler; synchronized(this){ localReader = new DatasetReaderV2(path); localds = localReader.read(); localChromosomeHandler = localds.getChromosomeHandler(); } runIndividualChromosomeCode(chromosomeIndex, localds, localChromosomeHandler, zoom, resolutionsToBuildTo, withinZoomVCSumFactors, withinZoomVCSQRTSumFactors, withinZoomKRSumFactors, withinZoomSCALESumFactors, withinZoomVCVectors, withinZoomVCSQRTVectors, withinZoomKRVectors, withinZoomSCALEVectors, withinZoomSynckrBPFailedChromosomes, withinZoomSynckrFragFailedChromosomes, withinZoomSyncmmbaBPFailedChromosomes, withinZoomSyncmmbaFragFailedChromosomes, allChrZoomData, threadNum); } catch (IOException e) { System.err.println("Error: " + e); } } //} }; executor.execute(worker); } executor.shutdown(); // Wait until all threads finish while (!executor.isTerminated()) { } // Loop through chromosomes for (Chromosome chr : chromosomeHandler.getChromosomeArrayWithoutAllByAll()) { if (allChrZoomData.get(chr.getIndex()) == null) continue; if (weShouldBuildVC && zoom.getBinSize() >= resolutionsToBuildTo.get(NormalizationHandler.VC)) { if (withinZoomVCSumFactors.get(chr.getIndex())!=null&&withinZoomVCVectors.get(chr.getIndex())!=null) { updateExpectedValueCalculationForChr(chr.getIndex(), withinZoomVCSumFactors.get(chr.getIndex()), withinZoomVCVectors.get(chr.getIndex()), NormalizationHandler.VC, zoom, allChrZoomData.get(chr.getIndex()), evVC, normVectorBuffers, normVectorIndices); } } if (weShouldBuildVCSqrt && zoom.getBinSize() >= resolutionsToBuildTo.get(NormalizationHandler.VC_SQRT)) { if (withinZoomVCSQRTSumFactors.get(chr.getIndex())!=null&&withinZoomVCSQRTVectors.get(chr.getIndex())!=null) { updateExpectedValueCalculationForChr(chr.getIndex(), withinZoomVCSQRTSumFactors.get(chr.getIndex()), withinZoomVCSQRTVectors.get(chr.getIndex()), NormalizationHandler.VC_SQRT, zoom, allChrZoomData.get(chr.getIndex()), evVCSqrt, normVectorBuffers, normVectorIndices); } } // KR normalization if (weShouldBuildKR && zoom.getBinSize() >= resolutionsToBuildTo.get(NormalizationHandler.KR)) { Set withinZoomFailureSetKR = zoom.getUnit() == HiC.Unit.FRAG ? withinZoomSynckrFragFailedChromosomes : withinZoomSynckrBPFailedChromosomes; if (!withinZoomFailureSetKR.contains(chr)&&withinZoomKRSumFactors.get(chr.getIndex())!=null&&withinZoomKRVectors.get(chr.getIndex())!=null) { updateExpectedValueCalculationForChr(chr.getIndex(), withinZoomKRSumFactors.get(chr.getIndex()), withinZoomKRVectors.get(chr.getIndex()), NormalizationHandler.KR, zoom, allChrZoomData.get(chr.getIndex()), evKR, normVectorBuffers, normVectorIndices); } } // Fast scaling normalization if (weShouldBuildScale && zoom.getBinSize() >= resolutionsToBuildTo.get(NormalizationHandler.SCALE)) { Set withinZoomFailureSetMMBA = zoom.getUnit() == HiC.Unit.FRAG ? withinZoomSyncmmbaFragFailedChromosomes : withinZoomSyncmmbaBPFailedChromosomes; if (!withinZoomFailureSetMMBA.contains(chr)&&withinZoomSCALESumFactors.get(chr.getIndex())!=null&&withinZoomSCALEVectors.get(chr.getIndex())!=null) { updateExpectedValueCalculationForChr(chr.getIndex(), withinZoomSCALESumFactors.get(chr.getIndex()), withinZoomSCALEVectors.get(chr.getIndex()), NormalizationHandler.SCALE, zoom, allChrZoomData.get(chr.getIndex()), evSCALE, normVectorBuffers, normVectorIndices); } } } if (weShouldBuildVC && evVC.hasData() && zoom.getBinSize() >= resolutionsToBuildTo.get(NormalizationHandler.VC)) { expectedValueCalculations.add(evVC); } if (weShouldBuildVCSqrt && evVCSqrt.hasData() && zoom.getBinSize() >= resolutionsToBuildTo.get(NormalizationHandler.VC_SQRT)) { expectedValueCalculations.add(evVCSqrt); } if (weShouldBuildKR && evKR.hasData() && zoom.getBinSize() >= resolutionsToBuildTo.get(NormalizationHandler.KR)) { expectedValueCalculations.add(evKR); } if (weShouldBuildScale && evSCALE.hasData() && zoom.getBinSize() >= resolutionsToBuildTo.get(NormalizationHandler.SCALE)) { expectedValueCalculations.add(evSCALE); } } writeNormsToUpdateFile(reader, path, true, expectedValueCalculations, null, normVectorIndices, normVectorBuffers, "Finished writing norms"); } protected static void updateExpectedValueCalculationForChr(final int chrIdx, double factor, ListOfFloatArrays vec, NormalizationType type, HiCZoom zoom, MatrixZoomData zd, ExpectedValueCalculation ev, List normVectorBuffers, List normVectorIndex) throws IOException { vec.multiplyEverythingBy(factor); updateNormVectorIndexWithVector(normVectorIndex, normVectorBuffers, vec, chrIdx, type, zoom); ev.addDistancesFromIterator(chrIdx, zd.getIteratorContainer(), vec); } protected void buildVCOrVCSQRT(boolean weShouldBuildVC, boolean weShouldBuildVCSqrt, Chromosome chr, NormalizationCalculations nc, HiCZoom zoom, Map withinZoomVCSumFactors, Map withinZoomVCVectors, Map withinZoomVCSQRTSumFactors, Map withinZoomVCSQRTVectors) throws IOException { final int chrIdx = chr.getIndex(); long currentTime = System.currentTimeMillis(); ListOfFloatArrays vc = nc.computeVC(); if (weShouldBuildVC) { withinZoomVCSumFactors.put(chrIdx, nc.getSumFactor(vc)); withinZoomVCVectors.put(chrIdx, vc); } if (weShouldBuildVCSqrt) { ListOfFloatArrays vcSqrt = new ListOfFloatArrays(vc.getLength()); for (long i = 0; i < vc.getLength(); i++) { vcSqrt.set(i, (float) Math.sqrt(vc.get(i))); } withinZoomVCSQRTSumFactors.put(chrIdx, nc.getSumFactor(vcSqrt)); withinZoomVCSQRTVectors.put(chrIdx, vcSqrt); } printNormTiming("VC and VC_SQRT", chr, zoom, currentTime); } protected void buildKR(Chromosome chr, NormalizationCalculations nc, HiCZoom zoom, Map withinZoomKRSumFactors, Map withinZoomKRVectors, Set withinZoomSynckrBPFailedChromosomes, Set withinZoomSynckrFragFailedChromosomes) throws IOException { Set failureSetKR = zoom.getUnit() == HiC.Unit.FRAG ? synckrFragFailedChromosomes : synckrBPFailedChromosomes; Set withinZoomFailureSetKR = zoom.getUnit() == HiC.Unit.FRAG ? withinZoomSynckrFragFailedChromosomes : withinZoomSynckrBPFailedChromosomes; final int chrIdx = chr.getIndex(); long currentTime = System.currentTimeMillis(); if (!failureSetKR.contains(chr)) { ListOfFloatArrays kr = nc.computeKR(); if (kr == null) { failureSetKR.add(chr); withinZoomFailureSetKR.add(chr); printNormTiming("FAILED KR", chr, zoom, currentTime); } else { withinZoomKRSumFactors.put(chrIdx, nc.getSumFactor(kr)); withinZoomKRVectors.put(chrIdx, kr); printNormTiming("KR", chr, zoom, currentTime); } } else { withinZoomFailureSetKR.add(chr); } } protected void buildScale(Chromosome chr, NormalizationCalculations nc, HiCZoom zoom, Map withinZoomSCALESumFactors, Map withinZoomSCALEVectors, Set withinZoomSyncmmbaBPFailedChromosomes, Set withinZoomSyncmmbaFragFailedChromosomes) throws IOException { Set failureSetMMBA = zoom.getUnit() == HiC.Unit.FRAG ? syncmmbaFragFailedChromosomes : syncmmbaBPFailedChromosomes; Set withinZoomFailureSetMMBA = zoom.getUnit() == HiC.Unit.FRAG ? withinZoomSyncmmbaFragFailedChromosomes : withinZoomSyncmmbaBPFailedChromosomes; final int chrIdx = chr.getIndex(); long currentTime = System.currentTimeMillis(); if (!failureSetMMBA.contains(chr)) { ListOfFloatArrays mmba = nc.computeMMBA(); if (mmba == null) { failureSetMMBA.add(chr); withinZoomFailureSetMMBA.add(chr); printNormTiming("FAILED SCALE", chr, zoom, currentTime); } else { withinZoomSCALESumFactors.put(chrIdx, nc.getSumFactor(mmba)); withinZoomSCALEVectors.put(chrIdx, mmba); printNormTiming("SCALE", chr, zoom, currentTime); } } else { withinZoomFailureSetMMBA.add(chr); } } protected void runIndividualChromosomeCode(AtomicInteger chromosomeIndex, Dataset ds, ChromosomeHandler chromosomeHandler, HiCZoom zoom, Map resolutionsToBuildTo, Map withinZoomVCSumFactors, Map withinZoomVCSQRTSumFactors, Map withinZoomKRSumFactors, Map withinZoomSCALESumFactors, Map withinZoomVCVectors, Map withinZoomVCSQRTVectors, Map withinZoomKRVectors, Map withinZoomSCALEVectors, Set withinZoomSynckrBPFailedChromosomes, Set withinZoomSynckrFragFailedChromosomes, Set withinZoomSyncmmbaBPFailedChromosomes, Set withinZoomSyncmmbaFragFailedChromosomes, Map allChrZoomData, int threadnum) throws IOException { int i = chromosomeIndex.getAndIncrement(); while (i < chromosomeHandler.getChromosomeArrayWithoutAllByAll().length) { Chromosome chr = chromosomeHandler.getChromosomeArrayWithoutAllByAll()[i]; MatrixZoomData zd = HiCFileTools.getMatrixZoomData(ds, chr, chr, zoom); if (zd == null) { i = chromosomeIndex.getAndIncrement(); continue; } NormalizationCalculations nc = new NormalizationCalculations(zd.getIteratorContainer()); if (!nc.isEnoughMemory()) { System.err.println("Not enough memory, skipping " + chr); i = chromosomeIndex.getAndIncrement(); continue; } allChrZoomData.put(chr.getIndex(), zd); if (weShouldBuildVC || weShouldBuildVCSqrt) { buildVCOrVCSQRT(weShouldBuildVC && zoom.getBinSize() >= resolutionsToBuildTo.get(NormalizationHandler.VC), weShouldBuildVCSqrt && zoom.getBinSize() >= resolutionsToBuildTo.get(NormalizationHandler.VC_SQRT), chr, nc, zoom, withinZoomVCSumFactors, withinZoomVCVectors, withinZoomVCSQRTSumFactors, withinZoomVCSQRTVectors); } if (weShouldBuildKR && zoom.getBinSize() >= resolutionsToBuildTo.get(NormalizationHandler.KR)) { buildKR(chr, nc, zoom, withinZoomKRSumFactors, withinZoomKRVectors, withinZoomSynckrBPFailedChromosomes, withinZoomSynckrFragFailedChromosomes); } if (weShouldBuildScale && zoom.getBinSize() >= resolutionsToBuildTo.get(NormalizationHandler.SCALE)) { buildScale(chr, nc, zoom, withinZoomSCALESumFactors, withinZoomSCALEVectors, withinZoomSyncmmbaBPFailedChromosomes, withinZoomSyncmmbaFragFailedChromosomes); } i = chromosomeIndex.getAndIncrement(); } } } ================================================ FILE: src/juicebox/tools/utils/norm/NormVectorInfo.java ================================================ /* * The MIT License (MIT) * * Copyright (c) 2011-2020 Broad Institute, Aiden Lab, Rice University, Baylor College of Medicine * * Permission is hereby granted, free of charge, to any person obtaining a copy * of this software and associated documentation files (the "Software"), to deal * in the Software without restriction, including without limitation the rights * to use, copy, modify, merge, publish, distribute, sublicense, and/or sell * copies of the Software, and to permit persons to whom the Software is * furnished to do so, subject to the following conditions: * * The above copyright notice and this permission notice shall be included in * all copies or substantial portions of the Software. * * THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR * IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, * FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE * AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER * LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, * OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN * THE SOFTWARE. */ package juicebox.tools.utils.norm; import juicebox.data.ExpectedValueFunction; import juicebox.data.NormalizationVector; import juicebox.windowui.NormalizationType; import org.broad.igv.tdf.BufferedByteWriter; import java.util.List; import java.util.Map; class NormVectorInfo { private final List normVectorBuffers; private final List normVectorIndices; private final Map expectedValueFunctionMap; private final Map> normalizationVectorsMap; NormVectorInfo(Map> normalizationVectorsMap, List normVectorBuffers, List normVectorIndices, Map expectedValueFunctionMap) { this.normalizationVectorsMap = normalizationVectorsMap; this.normVectorBuffers = normVectorBuffers; this.normVectorIndices = normVectorIndices; this.expectedValueFunctionMap = expectedValueFunctionMap; } public List getNormVectorBuffers() { return normVectorBuffers; } public List getNormVectorIndices() { return normVectorIndices; } public Map getExpectedValueFunctionMap() { return expectedValueFunctionMap; } public Map> getNormalizationVectorsMap() { return normalizationVectorsMap; } } ================================================ FILE: src/juicebox/tools/utils/norm/NormVectorUpdater.java ================================================ /* * The MIT License (MIT) * * Copyright (c) 2011-2021 Broad Institute, Aiden Lab, Rice University, Baylor College of Medicine * * Permission is hereby granted, free of charge, to any person obtaining a copy * of this software and associated documentation files (the "Software"), to deal * in the Software without restriction, including without limitation the rights * to use, copy, modify, merge, publish, distribute, sublicense, and/or sell * copies of the Software, and to permit persons to whom the Software is * furnished to do so, subject to the following conditions: * * The above copyright notice and this permission notice shall be included in * all copies or substantial portions of the Software. * * THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR * IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, * FITNESS FOR A PARTICULAR PURPOSE AND NON-INFRINGEMENT. IN NO EVENT SHALL THE * AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER * LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, * OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN * THE SOFTWARE. */ package juicebox.tools.utils.norm; import juicebox.HiC; import juicebox.data.DatasetReaderV2; import juicebox.data.ExpectedValueFunction; import juicebox.data.ExpectedValueFunctionImpl; import juicebox.data.basics.ListOfDoubleArrays; import juicebox.data.basics.ListOfFloatArrays; import juicebox.tools.utils.original.ExpectedValueCalculation; import juicebox.windowui.HiCZoom; import juicebox.windowui.NormalizationType; import org.broad.igv.tdf.BufferedByteWriter; import java.io.IOException; import java.io.RandomAccessFile; import java.util.ArrayList; import java.util.Collections; import java.util.List; import java.util.Map; public class NormVectorUpdater { static void updateNormVectorIndexWithVector(List normVectorIndex, List normVectorBufferList, ListOfFloatArrays vec, int chrIdx, NormalizationType type, HiCZoom zoom) throws IOException { long position = 0; for (int i=0; i < normVectorBufferList.size(); i++) { position += normVectorBufferList.get(i).bytesWritten(); } putFloatArraysIntoBufferList(normVectorBufferList, vec.getValues()); long newPos = 0; for (int i=0; i < normVectorBufferList.size(); i++) { newPos += normVectorBufferList.get(i).bytesWritten(); } int sizeInBytes = (int) (newPos - position); normVectorIndex.add(new NormalizationVectorIndexEntry(type.toString(), chrIdx, zoom.getUnit().toString(), zoom.getBinSize(), position, sizeInBytes)); } public static boolean isValidNormValue(float v) { return v > 0 && !Float.isNaN(v); } static void putFloatArraysIntoBufferList(List bufferList, List arrays) throws IOException { BufferedByteWriter buffer = getBufferWithEnoughSpace(bufferList, 8); long vectorLength = 0; for (float[] array : arrays) { vectorLength += array.length; } buffer.putLong(vectorLength); for (float[] array : arrays) { buffer = getBufferWithEnoughSpace(bufferList, 4 * array.length); for (float val : array) { buffer.putFloat(val); } } } private static void putMapValuesIntoBuffer(List bufferList, Map hashmap) throws IOException { int bytesNeeded = 4 + (8 * hashmap.size()); BufferedByteWriter buffer = getBufferWithEnoughSpace(bufferList, bytesNeeded); buffer.putInt(hashmap.size()); List keys = new ArrayList<>(hashmap.keySet()); Collections.sort(keys); for (Integer key : keys) { buffer.putInt(key); buffer.putFloat(hashmap.get(key).floatValue()); } } private static void writeExpectedToBuffer(RandomAccessFile raf, List expectedBuffers, long filePosition) throws IOException { raf.getChannel().position(filePosition); for (int i = 0; i < expectedBuffers.size(); i++) { byte[] evBytes = expectedBuffers.get(i).getBytes(); raf.write(evBytes); } } private static void handleVersionSix(RandomAccessFile raf, int version) throws IOException { if (version < 6) { // Update version // Master index raf.getChannel().position(4); BufferedByteWriter buffer = new BufferedByteWriter(); buffer.putInt(6); raf.write(buffer.getBytes()); } } /** * Compute the size of the index in bytes. This is needed to set offsets for the actual index entries. The * easiest way to do this is to write it to a buffer and check the size * * @param buffer Buffer to write to * @param normVectorIndex Normalization index to write */ static void writeNormIndex(BufferedByteWriter buffer, List normVectorIndex) throws IOException { buffer.putInt(normVectorIndex.size()); for (NormalizationVectorIndexEntry entry : normVectorIndex) { buffer.putNullTerminatedString(entry.type); buffer.putInt(entry.chrIdx); buffer.putNullTerminatedString(entry.unit); buffer.putInt(entry.resolution); buffer.putLong(entry.position); buffer.putLong(entry.sizeInBytes); } } static void writeNormsToUpdateFile(DatasetReaderV2 reader, String path, boolean useCalcNotFunc, List expectedValueCalculations, Map expectedValueFunctionMap, List normVectorIndices, List normVectorBuffers, String message) throws IOException { int version = reader.getVersion(); long filePosition = reader.getNormFilePosition(); long nviHeaderPosition = reader.getNviHeaderPosition(); try (RandomAccessFile raf = new RandomAccessFile(path, "rw")) { handleVersionSix(raf, version); List expectedBuffers = new ArrayList<>(); expectedBuffers.add(new BufferedByteWriter()); if (useCalcNotFunc) { writeExpectedValues(expectedBuffers, expectedValueCalculations); } else { writeExpectedValues(expectedBuffers, expectedValueFunctionMap); } writeExpectedToBuffer(raf, expectedBuffers, filePosition); writeNormsToBuffer(raf, normVectorIndices, normVectorBuffers, nviHeaderPosition); } System.out.println(message); } private static void writeExpectedValues(List expectedBuffers, List expectedValueCalculations) throws IOException { BufferedByteWriter buffer = getBufferWithEnoughSpace(expectedBuffers, 4); buffer.putInt(expectedValueCalculations.size()); for (ExpectedValueCalculation ev : expectedValueCalculations) { ev.computeDensity(); HiC.Unit unit = ev.isFrag ? HiC.Unit.FRAG : HiC.Unit.BP; appendExpectedValuesToBuffer(expectedBuffers, ev.getType(), unit, ev.getGridSize(), ev.getDensityAvg(), ev.getChrScaleFactors()); } } private static void writeExpectedValues(List expectedBuffers, Map expectedValueFunctionMap) throws IOException { BufferedByteWriter buffer = getBufferWithEnoughSpace(expectedBuffers, 4); buffer.putInt(expectedValueFunctionMap.size()); for (ExpectedValueFunction function : expectedValueFunctionMap.values()) { appendExpectedValuesToBuffer(expectedBuffers, function.getNormalizationType(), function.getUnit(), function.getBinSize(), function.getExpectedValuesNoNormalization(), ((ExpectedValueFunctionImpl) function).getNormFactors()); } } private static void appendExpectedValuesToBuffer(List expectedBuffers, NormalizationType normalizationType, HiC.Unit unit, int binSize, ListOfDoubleArrays expectedValuesNoNormalization, Map normFactors) throws IOException { int bytesNeeded = normalizationType.toString().length() + 1; bytesNeeded += unit.toString().length() + 1; bytesNeeded += 4; BufferedByteWriter buffer = getBufferWithEnoughSpace(expectedBuffers, bytesNeeded); buffer.putNullTerminatedString(normalizationType.toString()); buffer.putNullTerminatedString(unit.toString()); buffer.putInt(binSize); putFloatArraysIntoBufferList(expectedBuffers, expectedValuesNoNormalization.convertToFloats().getValues()); putMapValuesIntoBuffer(expectedBuffers, normFactors); } private static BufferedByteWriter getBufferWithEnoughSpace(List expectedBuffers, int bytesNeeded) { if (expectedBuffers.size()==0) { expectedBuffers.add(new BufferedByteWriter()); } BufferedByteWriter buffer = expectedBuffers.get(expectedBuffers.size() - 1); int freeBytes = Integer.MAX_VALUE - 10 - buffer.bytesWritten(); if (bytesNeeded >= freeBytes) { expectedBuffers.add(new BufferedByteWriter()); return expectedBuffers.get(expectedBuffers.size() - 1); } return buffer; } private static void writeNormsToBuffer(RandomAccessFile raf, List normVectorIndex, List normVectorBuffers, long nviHeaderPosition) throws IOException { // Get the size of the index in bytes, to compute an offset for the actual entries. BufferedByteWriter buffer = new BufferedByteWriter(); writeNormIndex(buffer, normVectorIndex); long normVectorStartPosition = raf.getChannel().position() + buffer.bytesWritten(); long size = buffer.bytesWritten(); long NVI = normVectorStartPosition - size; // write NVI, size raf.getChannel().position(nviHeaderPosition); BufferedByteWriter headerBuffer = new BufferedByteWriter(); headerBuffer.putLong(NVI); headerBuffer.putLong(size); raf.write(headerBuffer.getBytes()); // reset pointer to where we were raf.getChannel().position(NVI); // Update index entries for (NormalizationVectorIndexEntry entry : normVectorIndex) { entry.position += normVectorStartPosition; } // Now write for real buffer = new BufferedByteWriter(); writeNormIndex(buffer, normVectorIndex); raf.write(buffer.getBytes()); // Finally the norm vectors for (int i = 0; i < normVectorBuffers.size(); i++) { raf.write(normVectorBuffers.get(i).getBytes()); } } } ================================================ FILE: src/juicebox/tools/utils/norm/NormalizationCalculations.java ================================================ /* * The MIT License (MIT) * * Copyright (c) 2011-2021 Broad Institute, Aiden Lab, Rice University, Baylor College of Medicine * * Permission is hereby granted, free of charge, to any person obtaining a copy * of this software and associated documentation files (the "Software"), to deal * in the Software without restriction, including without limitation the rights * to use, copy, modify, merge, publish, distribute, sublicense, and/or sell * copies of the Software, and to permit persons to whom the Software is * furnished to do so, subject to the following conditions: * * The above copyright notice and this permission notice shall be included in * all copies or substantial portions of the Software. * * THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR * IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, * FITNESS FOR A PARTICULAR PURPOSE AND NON-INFRINGEMENT. IN NO EVENT SHALL THE * AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER * LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, * OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN * THE SOFTWARE. */ package juicebox.tools.utils.norm; import juicebox.data.ContactRecord; import juicebox.data.basics.ListOfDoubleArrays; import juicebox.data.basics.ListOfFloatArrays; import juicebox.data.basics.ListOfIntArrays; import juicebox.data.iterator.IteratorContainer; import juicebox.windowui.NormalizationType; import org.apache.commons.math3.stat.descriptive.DescriptiveStatistics; import java.util.Arrays; import java.util.Iterator; import java.util.List; import java.util.Random; /** * Class for computing VC ("Vanilla Coverage") and KR normalization vector. *

* Note: currently these are valid for square matrices only. * * @author jrobinso * Date: 1/25/13 * Time: 4:03 PM */ public class NormalizationCalculations { private final long matrixSize; // x and y symmetric private boolean isEnoughMemory = false; private final IteratorContainer ic; public NormalizationCalculations(IteratorContainer ic) { this.ic = ic; this.matrixSize = ic.getMatrixSize(); isEnoughMemory = ic.getIsThereEnoughMemoryForNormCalculation(); } private static ListOfDoubleArrays sparseMultiplyFromContactRecords(ListOfIntArrays offset, Iterator iterator, ListOfDoubleArrays vector) { ListOfDoubleArrays result = new ListOfDoubleArrays(vector.getLength()); while (iterator.hasNext()) { ContactRecord cr = iterator.next(); int row = cr.getBinX(); int col = cr.getBinY(); float value = cr.getCounts(); row = offset.get(row); col = offset.get(col); if (row != -1 && col != -1) { result.addTo(row, vector.get(col) * value); if (row != col) { result.addTo(col, vector.get(row) * value); } } } return result; } /* function [x,res] = bnewt(A,tol,x0,delta,fl) % BNEWT A balancing algorithm for symmetric matrices % % X = BNEWT(A) attempts to find a vector X such that % diag(X)*A*diag(X) is close to doubly stochastic. A must % be symmetric and nonnegative. % % X0: initial guess. TOL: error tolerance. % DEL: how close balancing vectors can get to the edge of the % positive cone. We use a relative measure on the size of elements. % FL: intermediate convergence statistics on/off. % RES: residual error, measured by norm(diag(x)*A*x - e). % Initialise [n,n]=size(A); e = ones(n,1); res=[]; if nargin < 5, fl = 0; end if nargin < 4, delta = 0.1; end if nargin < 3, x0 = e; end if nargin < 2, tol = 1e-6; end */ private ListOfDoubleArrays computeKRNormVector(ListOfIntArrays offset, double tol, ListOfDoubleArrays x0, double delta) { long n = x0.getLength(); ListOfDoubleArrays e = new ListOfDoubleArrays(n, 1); double g = 0.9; double etamax = 0.1; double eta = etamax; double rt = Math.pow(tol, 2); ListOfDoubleArrays v = sparseMultiplyFromContactRecords(offset, getIterator(), x0); ListOfDoubleArrays rk = new ListOfDoubleArrays(v.getLength()); for (long i = 0; i < v.getLength(); i++) { v.multiplyBy(i, x0.get(i)); rk.set(i, 1 - v.get(i)); } double rho_km1 = 0; for (double[] aRkArray : rk.getValues()) { for (double aRk : aRkArray) { rho_km1 += aRk * aRk; } } double rout = rho_km1; double rold = rout; int MVP = 0; // We'll count matrix vector products. int not_changing = 0; while (rout > rt && not_changing < 100) { // Outer iteration int k = 0; ListOfDoubleArrays y = e.deepClone(); ListOfDoubleArrays ynew = new ListOfDoubleArrays(e.getLength()); ListOfDoubleArrays Z = new ListOfDoubleArrays(e.getLength()); ListOfDoubleArrays p = new ListOfDoubleArrays(e.getLength()); ListOfDoubleArrays w = new ListOfDoubleArrays(e.getLength()); double alpha; double beta; double gamma; double rho_km2 = rho_km1; double innertol = Math.max(Math.pow(eta, 2) * rout, rt); while (rho_km1 > innertol) { // Inner iteration by CG k++; if (k == 1) { rho_km1 = 0; for (long i = 0; i < Z.getLength(); i++) { double rkVal = rk.get(i); double zVal = rkVal / v.get(i); Z.set(i, zVal); rho_km1 += rkVal * zVal; } p = Z.deepClone(); } else { beta = rho_km1 / rho_km2; p.multiplyEverythingBy(beta); for (long i = 0; i < p.getLength(); i++) { p.addTo(i, Z.get(i)); } } ListOfDoubleArrays tmp = new ListOfDoubleArrays(e.getLength()); for (long i = 0; i < tmp.getLength(); i++) { tmp.set(i, x0.get(i) * p.get(i)); } tmp = sparseMultiplyFromContactRecords(offset, getIterator(), tmp); alpha = 0; // Update search direction efficiently. for (long i = 0; i < tmp.getLength(); i++) { double pVal = p.get(i); double wVal = (x0.get(i) * tmp.get(i) + v.get(i) * pVal); w.set(i, wVal); alpha += pVal * wVal; } alpha = rho_km1 / alpha; double minynew = Double.MAX_VALUE; // Test distance to boundary of cone. for (long i = 0; i < p.getLength(); i++) { double yVal = y.get(i) + alpha * p.get(i); ynew.set(i, yVal); if (yVal < minynew) { minynew = yVal; } } if (minynew <= delta) { if (delta == 0) break; // break out of inner loop? gamma = Double.MAX_VALUE; for (long i = 0; i < ynew.getLength(); i++) { double pVal = p.get(i); if (alpha * pVal < 0) { double yVal = y.get(i); if ((delta - yVal) / (alpha * pVal) < gamma) { gamma = ((delta - yVal) / (alpha * pVal)); } } } for (long i = 0; i < y.getLength(); i++) { y.addTo(i, gamma * alpha * p.get(i)); } break; // break out of inner loop? } rho_km2 = rho_km1; rho_km1 = 0; y = ynew.deepClone(); for (long i = 0; i < y.getLength(); i++) { rk.addTo(i, -alpha * w.get(i)); double rkVal = rk.get(i); Z.set(i, rkVal / v.get(i)); rho_km1 += rkVal * Z.get(i); } } // end inner loop for (long i = 0; i < x0.getLength(); i++) { x0.multiplyBy(i, y.get(i)); } v = sparseMultiplyFromContactRecords(offset, getIterator(), x0); rho_km1 = 0; for (long i = 0; i < v.getLength(); i++) { v.multiplyBy(i, x0.get(i)); double rkVal = 1 - v.get(i); rk.set(i, rkVal); rho_km1 += rkVal * rkVal; } if (Math.abs(rho_km1 - rout) < 0.000001 || Double.isInfinite(rho_km1)) { not_changing++; } rout = rho_km1; MVP = MVP + k + 1; // Update inner iteration stopping criterion. double rat = rout / rold; rold = rout; double r_norm = Math.sqrt(rout); double eta_o = eta; eta = g * rat; if (g * Math.pow(eta_o, 2) > 0.1) { eta = Math.max(eta, g * Math.pow(eta_o, 2)); } eta = Math.max(Math.min(eta, etamax), 0.5 * tol / r_norm); } if (not_changing >= 100) { return null; } return x0; } private Iterator getIterator() { return ic.getNewContactRecordIterator(); } boolean isEnoughMemory() { return isEnoughMemory; } public ListOfFloatArrays getNorm(NormalizationType normOption) { ListOfFloatArrays norm; if (normOption.usesKR()) { norm = computeKR(); } else if (normOption.usesVC()) { norm = computeVC(); } else if (normOption.usesSCALE()) { norm = computeMMBA(); } else if (normOption.isNONE()) { return new ListOfFloatArrays(matrixSize, 1); } else { System.err.println("Not supported for normalization " + normOption); return null; } if (norm != null && norm.getLength() > 0) { double factor = getSumFactor(norm); norm.multiplyEverythingBy(factor); } return norm; } /** * Compute vanilla coverage norm, just the sum of the rows * * @return Normalization vector */ ListOfFloatArrays computeVC() { ListOfFloatArrays rowsums = new ListOfFloatArrays(matrixSize, 0); Iterator iterator = getIterator(); while (iterator.hasNext()) { ContactRecord cr = iterator.next(); int x = cr.getBinX(); int y = cr.getBinY(); float value = cr.getCounts(); rowsums.addTo(x, value); if (x != y) { rowsums.addTo(y, value); } } return rowsums; } /** * Get the sum of the normalized matrix * * @param norm Normalization vector * @return Square root of ratio of original to normalized vector */ public double getSumFactor(ListOfFloatArrays norm) { double[] normMatrixSums = getNormMatrixSumFactor(norm); return Math.sqrt(normMatrixSums[0] / normMatrixSums[1]); } public double[] getNormMatrixSumFactor(ListOfFloatArrays norm) { double matrix_sum = 0; double norm_sum = 0; Iterator iterator = getIterator(); while (iterator.hasNext()) { ContactRecord cr = iterator.next(); int x = cr.getBinX(); int y = cr.getBinY(); float value = cr.getCounts(); double valX = norm.get(x); double valY = norm.get(y); if (!Double.isNaN(valX) && !Double.isNaN(valY) && valX > 0 && valY > 0) { // want total sum of matrix, not just upper triangle if (x == y) { norm_sum += value / (valX * valY); matrix_sum += value; } else { norm_sum += 2 * value / (valX * valY); matrix_sum += 2 * value; } } } return new double[]{norm_sum, matrix_sum}; } public int getNumberOfValidEntriesInVector(double[] norm) { int counter = 0; for (double val : norm) { if (!Double.isNaN(val) && val > 0) { counter++; } } return counter; } ListOfFloatArrays computeKR() { boolean recalculate = true; ListOfIntArrays offset = getOffset(0); ListOfFloatArrays kr = null; int iteration = 1; while (recalculate && iteration <= 6) { // create new matrix indices upon every iteration, because we've thrown out rows // newSize is size of new sparse matrix (non-sparse rows) long newSize = 0; for (int[] array : offset.getValues()) { for (int offset1 : array) { if (offset1 != -1) newSize++; } } // initialize x0 for call the compute KR norm ListOfDoubleArrays x0 = new ListOfDoubleArrays(newSize, 1); x0 = computeKRNormVector(offset, 0.000001, x0, 0.1); // assume all went well and we don't need to recalculate recalculate = false; int rowsTossed = 0; if (x0 == null || iteration == 5) { // if x0 is no good, throw out some percentage of rows and reset the offset array that gives those rows recalculate = true; if (iteration < 5) { offset = getOffset(iteration); } else { offset = getOffset(10); } // System.out.print(" " + iteration + "%"); } else { // otherwise, check to be sure there are no tiny KR values // create true KR vector kr = new ListOfFloatArrays(matrixSize); int krIndex = 0; for (int[] offsetArray : offset.getValues()) { for (int offset1 : offsetArray) { if (offset1 == -1) { kr.set(krIndex++, Float.NaN); } else { kr.set(krIndex++, (float) (1.0f / x0.get(offset1))); } } } // find scaling factor double mySum = getSumFactor(kr); // if any values are too small, recalculate. set those rows to be thrown out and reset the offset // note that if no rows are thrown out, the offset should not change int index = 0; for (long i = 0; i < kr.getLength(); i++) { if (kr.get(i) * mySum < 0.01) { offset.set(i, -1); rowsTossed++; recalculate = true; } else { if (offset.get(i) != -1) { offset.set(i, index++); } } } // if (recalculate) System.out.print(" " + rowsTossed); } iteration++; System.gc(); } if (iteration > 6 && recalculate) { kr = new ListOfFloatArrays(matrixSize, Float.NaN); } return kr; } private ListOfIntArrays getOffset(double percent) { ListOfDoubleArrays rowSums = new ListOfDoubleArrays(matrixSize, 0); Iterator iterator = getIterator(); while (iterator.hasNext()) { ContactRecord cr = iterator.next(); int x = cr.getBinX(); int y = cr.getBinY(); float value = cr.getCounts(); rowSums.addTo(x, value); if (x != y) { rowSums.addTo(y, value); } } double thresh = 0; if (percent > 0) { // Get percent threshold from positive row sums (nonzero) DescriptiveStatistics stats = new DescriptiveStatistics(); rowSums.getValues().forEach(sum -> Arrays.stream(sum).filter(i-> i != 0).forEach(stats::addValue)); thresh = stats.getPercentile( percent); /* int j = 0; for (double[] array : rowSums.getValues()) { for (double sum : array) { if (sum != 0) { j++; } } } double[] posRowSums = new double[j]; j = 0; for (double[] array : rowSums.getValues()) { for (double sum : array) { if (sum != 0) { posRowSums[j++] = sum; } } } thresh = StatUtils.percentile(posRowSums, percent); */ } ListOfIntArrays offset = new ListOfIntArrays(rowSums.getLength()); int index = 0; for (long i = 0; i < rowSums.getLength(); i++) { if (rowSums.get(i) <= thresh) { offset.set(i, -1); } else { offset.set(i, index++); } } return offset; } public ListOfFloatArrays computeMMBA() { ListOfFloatArrays tempTargetVector = new ListOfFloatArrays(matrixSize, 1); return ZeroScale.mmbaScaleToVector(ic, tempTargetVector); } /*public BigContactRecordList booleanBalancing() { ListOfFloatArrays rowsums = new ListOfFloatArrays(totSize, 0); Map> rowsumIndices = new HashMap<>(); Map> rows = new HashMap<>(); //Map remainingContacts = new HashMap<>(); List thresholds = new ArrayList<>(Arrays.asList(1.1,1.2,1.3,1.4,1.5,1.6,1.7,1.8,1.9,2.0,3.0,4.0,5.0)); for (List localList : contactRecords) { for (ContactRecord cr : localList) { int x = cr.getBinX(); int y = cr.getBinY(); float value = cr.getCounts(); rowsums.addTo(x, value); if (x != y) { rowsums.addTo(y, value); } List row1 = rows.get((long) x); List row2 = rows.get((long) y); if (row1 == null) { row1 = new ArrayList<>(); rows.put((long) x, row1); //remainingContacts.put((long) x, new RandomizedCollection()); } if (row2 == null) { row2 = new ArrayList<>(); rows.put((long) y, row2); //remainingContacts.put((long) y, new RandomizedCollection()); } int xCurrentSize = row1.size(); int yCurrentSize = row2.size(); for (int i = 0; i < value; i++) { row1.add(new LinkedContactRecord(cr, yCurrentSize+i)); //remainingContacts.get((long) x).insert(xCurrentSize); if (x != y) { row2.add(new LinkedContactRecord(cr, xCurrentSize+i)); //remainingContacts.get((long) y).insert(yCurrentSize); } } } } System.out.println("loaded contacts for matrix: " + chr1 + "-" + chr2); int rowSumThreshold = (int) (1.0d / getSumFactor(rowsums)); List sortedRowSums = new ArrayList<>(); for (long i = 0; i < rowsums.getLength(); i++) { //Instant E = Instant.now(); Map sumIndexList = rowsumIndices.get(rowsums.get(i)); if (sumIndexList == null) { rowsumIndices.put(rowsums.get(i), new HashMap<>()); sumIndexList = rowsumIndices.get(rowsums.get(i)); } sumIndexList.put(i,1); sortedRowSums.add(rowsums.get(i)); //Instant F = Instant.now(); //System.err.println(Duration.between(E,F).toNanos()); } System.out.println("mapped row sums to rows indices for matrix: " + chr1 + "-" + chr2); Collections.sort(sortedRowSums); Map SumMap = new HashMap<>(); List SumKeys = new ArrayList<>(rowsumIndices.keySet()); Collections.sort(SumKeys); int keyCounter = 0; for (float key : SumKeys) { //Collections.sort(rowsumIndices.get(key)); while (sortedRowSums.get(keyCounter)!=key) { keyCounter++; } SumMap.put(key,keyCounter); } System.out.println("sorted row sums for matrix: " + chr1 + "-" + chr2); Instant A = Instant.now(); Map currentRows = rowsumIndices.get(sortedRowSums.get(sortedRowSums.size()-1)); long currentRow = currentRows.keySet().iterator().next(); //System.out.println(currentRows.keySet().size() + " " + sortedRowSums.get(sortedRowSums.size()-1) + " " + currentRow + " " + rowsums.get(currentRow)); Instant B = Instant.now(); //System.err.println(Duration.between(A,B).toNanos()); //System.err.println(rowSumThreshold + " " + getSumFactor(rowsums) + " " + rowsums.get(rowsums.getMaxRow())); Random randomNumberGenerator = new Random(0); while (rowsums.get(currentRow) > rowSumThreshold) { float currentRowSum = rowsums.get(currentRow); //Instant C = Instant.now(); //List removedContactList = new ArrayList<>(removedContacts.get(currentRow)); //Collections.sort(removedContactList); //int randomContact = getRandomWithExclusion(randomNumberGenerator, rows.get(currentRow).size(), removedContactList); //removedContacts.get(currentRow).add(randomContact); //int randomContact = remainingContacts.get(currentRow).getRandom(); int randomContact = (int) (rows.get(currentRow).size() * randomNumberGenerator.nextDouble()); //remainingContacts.get(currentRow).remove(randomContact); long firstRow, secondRow; if (rows.get(currentRow).get(randomContact).getContactRecord().getBinX() == currentRow) { firstRow = (long) rows.get(currentRow).get(randomContact).getContactRecord().getBinX(); secondRow = (long) rows.get(currentRow).get(randomContact).getContactRecord().getBinY(); } else { firstRow = (long) rows.get(currentRow).get(randomContact).getContactRecord().getBinY(); secondRow = (long) rows.get(currentRow).get(randomContact).getContactRecord().getBinX(); } //System.out.println(currentRow + " " + firstRow + " " + secondRow); float firstRowSum = rowsums.get(firstRow); int symmetricRandomContactPosition = rows.get(firstRow).get(randomContact).getLink(); long lastRow = rows.get(firstRow).get(rows.get(firstRow).size()-1).getContactRecord().getBinX() == firstRow? rows.get(firstRow).get(rows.get(firstRow).size()-1).getContactRecord().getBinY() : rows.get(firstRow).get(rows.get(firstRow).size()-1).getContactRecord().getBinX(); int lastLink = rows.get(firstRow).get(rows.get(firstRow).size()-1).getLink(); //System.out.println("initial values " + currentRow + " " + rows.get(firstRow).get(randomContact).getContactRecord().getBinX() + " " + rows.get(firstRow).get(randomContact).getContactRecord().getBinY() + " " + rows.get(firstRow).get(randomContact).getLink() + " " + rows.get(secondRow).get(symmetricRandomContactPosition).getContactRecord().getBinX() + " " + rows.get(secondRow).get(symmetricRandomContactPosition).getContactRecord().getBinY() + " " + rows.get(secondRow).get(symmetricRandomContactPosition).getLink() + " " + rows.get(firstRow).get(rows.get(firstRow).size()-1).getContactRecord().getBinX() + " " + rows.get(firstRow).get(rows.get(firstRow).size()-1).getContactRecord().getBinY() + " " + rows.get(firstRow).get(rows.get(firstRow).size()-1).getLink() + " " + rows.get(lastRow).get(lastLink).getContactRecord().getBinX() + " " + rows.get(lastRow).get(lastLink).getContactRecord().getBinY() + " " + rows.get(lastRow).get(lastLink).getLink()); rows.get(firstRow).get(randomContact).getContactRecord().incrementCount(-1); rows.get(firstRow).set(randomContact, rows.get(firstRow).get(rows.get(firstRow).size()-1)); //System.out.println("first row swapped " + currentRow + " " + rows.get(firstRow).get(randomContact).getContactRecord().getBinX() + " " + rows.get(firstRow).get(randomContact).getContactRecord().getBinY() + " " + rows.get(firstRow).get(randomContact).getLink() + " " + rows.get(secondRow).get(symmetricRandomContactPosition).getContactRecord().getBinX() + " " + rows.get(secondRow).get(symmetricRandomContactPosition).getContactRecord().getBinY() + " " + rows.get(secondRow).get(symmetricRandomContactPosition).getLink() + " " + rows.get(firstRow).get(rows.get(firstRow).size()-1).getContactRecord().getBinX() + " " + rows.get(firstRow).get(rows.get(firstRow).size()-1).getContactRecord().getBinY() + " " + rows.get(firstRow).get(rows.get(firstRow).size()-1).getLink() + " " + rows.get(lastRow).get(lastLink).getContactRecord().getBinX() + " " + rows.get(lastRow).get(lastLink).getContactRecord().getBinY() + " " + rows.get(lastRow).get(lastLink).getLink()); long partnerRow; int partnerLink = rows.get(firstRow).get(randomContact).getLink(); if (rows.get(firstRow).get(randomContact).getContactRecord().getBinX() == firstRow) { partnerRow = (long) rows.get(firstRow).get(randomContact).getContactRecord().getBinY(); } else { partnerRow = (long) rows.get(firstRow).get(randomContact).getContactRecord().getBinX(); } //System.out.println(firstRow + " " + rows.get(firstRow).get(randomContact).getContactRecord().getBinY() + " " + rows.get(firstRow).get(randomContact).getContactRecord().getBinX() + " " + partnerRow + " " + partnerLink + " " + symmetricRandomContactPosition); rows.get(partnerRow).get(partnerLink).setLink(randomContact); //System.out.println("partner link updated " + currentRow + " " + rows.get(firstRow).get(randomContact).getContactRecord().getBinX() + " " + rows.get(firstRow).get(randomContact).getContactRecord().getBinY() + " " + rows.get(firstRow).get(randomContact).getLink() + " " + rows.get(secondRow).get(symmetricRandomContactPosition).getContactRecord().getBinX() + " " + rows.get(secondRow).get(symmetricRandomContactPosition).getContactRecord().getBinY() + " " + rows.get(secondRow).get(symmetricRandomContactPosition).getLink() + " " + rows.get(firstRow).get(rows.get(firstRow).size()-1).getContactRecord().getBinX() + " " + rows.get(firstRow).get(rows.get(firstRow).size()-1).getContactRecord().getBinY() + " " + rows.get(firstRow).get(rows.get(firstRow).size()-1).getLink() + " " + rows.get(lastRow).get(lastLink).getContactRecord().getBinX() + " " + rows.get(lastRow).get(lastLink).getContactRecord().getBinY() + " " + rows.get(lastRow).get(lastLink).getLink()); rows.get(firstRow).remove(rows.get(firstRow).size()-1); //System.out.println("first row removed " + currentRow + " " + rows.get(firstRow).get(Math.min(randomContact,rows.get(firstRow).size()-1)).getContactRecord().getBinX() + " " + rows.get(firstRow).get(Math.min(randomContact,rows.get(firstRow).size()-1)).getContactRecord().getBinY() + " " + rows.get(firstRow).get(Math.min(randomContact,rows.get(firstRow).size()-1)).getLink() + " " + rows.get(secondRow).get(symmetricRandomContactPosition).getContactRecord().getBinX() + " " + rows.get(secondRow).get(symmetricRandomContactPosition).getContactRecord().getBinY() + " " + rows.get(secondRow).get(symmetricRandomContactPosition).getLink() + " " + rows.get(firstRow).get(rows.get(firstRow).size()-1).getContactRecord().getBinX() + " " + rows.get(firstRow).get(rows.get(firstRow).size()-1).getContactRecord().getBinY() + " " + rows.get(firstRow).get(rows.get(firstRow).size()-1).getLink() + " " + rows.get(lastRow).get(lastLink).getContactRecord().getBinX() + " " + rows.get(lastRow).get(lastLink).getContactRecord().getBinY() + " " + rows.get(lastRow).get(lastLink).getLink()); rowsums.addTo(firstRow, -1); float newFirstRowSum = rowsums.get(firstRow); //System.out.println(currentRowSum + " " + rowsums.get(currentRow) + " " + sortedRowSums.get(sortedRowSums.size()-1) ); rowsumIndices.get(currentRowSum).remove(currentRow); Map newRow1 = rowsumIndices.get(newFirstRowSum); if (newRow1 == null) { rowsumIndices.put(newFirstRowSum, new HashMap<>()); newRow1 = rowsumIndices.get(newFirstRowSum); newRow1.put(firstRow,1); } else { newRow1.put(firstRow,1); } int switchPlace1 = SumMap.get(firstRowSum); float potentialSwitchSum1 = sortedRowSums.get(switchPlace1); if (switchPlace1 == sortedRowSums.size()-1) { sortedRowSums.set(switchPlace1, newFirstRowSum); if (SumMap.get(newFirstRowSum) == null) { SumMap.put(newFirstRowSum, switchPlace1); } } else { sortedRowSums.set(sortedRowSums.size()-1, potentialSwitchSum1); sortedRowSums.set(switchPlace1, newFirstRowSum); SumMap.put(firstRowSum, switchPlace1+1); if (SumMap.get(newFirstRowSum) == null) { SumMap.put(newFirstRowSum, switchPlace1); } } //System.out.println(currentRowSum + " " + rowsums.get(currentRow) + " " + sortedRowSums.get(sortedRowSums.size()-1) ); if (firstRow != secondRow) { float secondRowSum = rowsums.get(secondRow); //removedContacts.get(secondRow).add(symmetricRandomContactPosition); //remainingContacts.get(secondRow).remove(symmetricRandomContactPosition); lastRow = rows.get(secondRow).get(rows.get(secondRow).size()-1).getContactRecord().getBinX() == secondRow? rows.get(secondRow).get(rows.get(secondRow).size()-1).getContactRecord().getBinY() : rows.get(secondRow).get(rows.get(secondRow).size()-1).getContactRecord().getBinX(); lastLink = rows.get(secondRow).get(rows.get(secondRow).size()-1).getLink(); //System.out.println("second row last check " + currentRow + " " + rows.get(secondRow).get(symmetricRandomContactPosition).getContactRecord().getBinX() + " " + rows.get(secondRow).get(symmetricRandomContactPosition).getContactRecord().getBinY() + " " + rows.get(secondRow).get(symmetricRandomContactPosition).getLink() + " " + rows.get(secondRow).get(rows.get(secondRow).size()-1).getContactRecord().getBinX() + " " + rows.get(secondRow).get(rows.get(secondRow).size()-1).getContactRecord().getBinY() + " " + rows.get(secondRow).get(rows.get(secondRow).size()-1).getLink() + " " + rows.get(lastRow).get(lastLink).getContactRecord().getBinX() + " " + rows.get(lastRow).get(lastLink).getContactRecord().getBinY() + " " + rows.get(lastRow).get(lastLink).getLink()); rows.get(secondRow).set(symmetricRandomContactPosition, rows.get(secondRow).get(rows.get(secondRow).size()-1)); //System.out.println("second row swapped " + currentRow + " " + rows.get(secondRow).get(symmetricRandomContactPosition).getContactRecord().getBinX() + " " + rows.get(secondRow).get(symmetricRandomContactPosition).getContactRecord().getBinY() + " " + rows.get(secondRow).get(symmetricRandomContactPosition).getLink() + " " + rows.get(secondRow).get(rows.get(secondRow).size()-1).getContactRecord().getBinX() + " " + rows.get(secondRow).get(rows.get(secondRow).size()-1).getContactRecord().getBinY() + " " + rows.get(secondRow).get(rows.get(secondRow).size()-1).getLink() + " " + rows.get(lastRow).get(lastLink).getContactRecord().getBinX() + " " + rows.get(lastRow).get(lastLink).getContactRecord().getBinY() + " " + rows.get(lastRow).get(lastLink).getLink()); partnerLink = rows.get(secondRow).get(symmetricRandomContactPosition).getLink(); if (rows.get(secondRow).get(symmetricRandomContactPosition).getContactRecord().getBinX() == secondRow) { partnerRow = (long) rows.get(secondRow).get(symmetricRandomContactPosition).getContactRecord().getBinY(); } else { partnerRow = (long) rows.get(secondRow).get(symmetricRandomContactPosition).getContactRecord().getBinX(); } if (symmetricRandomContactPosition!=rows.get(secondRow).size()-1) { rows.get(partnerRow).get(partnerLink).setLink(symmetricRandomContactPosition); } //System.out.println("partner link updated " + currentRow + " " + rows.get(secondRow).get(symmetricRandomContactPosition).getContactRecord().getBinX() + " " + rows.get(secondRow).get(symmetricRandomContactPosition).getContactRecord().getBinY() + " " + rows.get(secondRow).get(symmetricRandomContactPosition).getLink() + " " + rows.get(secondRow).get(rows.get(secondRow).size()-1).getContactRecord().getBinX() + " " + rows.get(secondRow).get(rows.get(secondRow).size()-1).getContactRecord().getBinY() + " " + rows.get(secondRow).get(rows.get(secondRow).size()-1).getLink() + " " + rows.get(lastRow).get(lastLink).getContactRecord().getBinX() + " " + rows.get(lastRow).get(lastLink).getContactRecord().getBinY() + " " + rows.get(lastRow).get(lastLink).getLink()); rows.get(secondRow).remove(rows.get(secondRow).size()-1); if (rows.get(secondRow).size()>0) { //System.out.println("second row removed " + currentRow + " " + rows.get(secondRow).get(Math.min(symmetricRandomContactPosition, rows.get(secondRow).size() - 1)).getContactRecord().getBinX() + " " + rows.get(secondRow).get(Math.min(symmetricRandomContactPosition, rows.get(secondRow).size() - 1)).getContactRecord().getBinY() + " " + rows.get(secondRow).get(Math.min(symmetricRandomContactPosition, rows.get(secondRow).size() - 1)).getLink() + " " + rows.get(secondRow).get(rows.get(secondRow).size() - 1).getContactRecord().getBinX() + " " + rows.get(secondRow).get(rows.get(secondRow).size() - 1).getContactRecord().getBinY() + " " + rows.get(secondRow).get(rows.get(secondRow).size() - 1).getLink() + " " + rows.get(lastRow).get(lastLink).getContactRecord().getBinX() + " " + rows.get(lastRow).get(lastLink).getContactRecord().getBinY() + " " + rows.get(lastRow).get(lastLink).getLink()); } rowsums.addTo(secondRow, -1); //System.out.println(currentRowSum + " " + rowsums.get(currentRow) + " " + sortedRowSums.get(sortedRowSums.size()-1) + " " + secondRowSum ); float newSecondRowSum = rowsums.get(secondRow); //int removeIndex2 = Collections.binarySearch(rowsumIndices.get(secondRowSum),secondRow); rowsumIndices.get(secondRowSum).remove(secondRow); Map newRow2 = rowsumIndices.get(newSecondRowSum); if (newRow2 == null) { rowsumIndices.put(newSecondRowSum, new HashMap<>()); newRow2 = rowsumIndices.get(newSecondRowSum); newRow2.put(secondRow,1); } else { newRow2.put(secondRow,1); } int switchPlace2 = SumMap.get(secondRowSum); if (switchPlace2 == 0) { sortedRowSums.set(0,newSecondRowSum); if (SumMap.get(newSecondRowSum) == null) { SumMap.put(newSecondRowSum,0); } if (sortedRowSums.get(1)==secondRowSum) { SumMap.put(secondRowSum,1); } else { SumMap.remove(secondRowSum); } } else { sortedRowSums.set(switchPlace2, newSecondRowSum); if (SumMap.get(newSecondRowSum) == null) { SumMap.put(newSecondRowSum,switchPlace2); } if (sortedRowSums.size() == switchPlace2+1) { SumMap.remove(secondRowSum); } else if (sortedRowSums.get(switchPlace2+1) == secondRowSum) { SumMap.put(secondRowSum, switchPlace2+1); } else { SumMap.remove(secondRowSum); } } } //System.out.println(currentRowSum + " " + rowsums.get(currentRow) + " " + sortedRowSums.get(sortedRowSums.size()-1) ); currentRows = rowsumIndices.get(sortedRowSums.get(sortedRowSums.size()-1)); currentRow = currentRows.keySet().iterator().next(); double maxRatio = (rowsums.get(currentRow)*1.0d)/rowSumThreshold; if (thresholds.size()>0 && maxRatio < thresholds.get(thresholds.size()-1)) { double passedThreshold = thresholds.get(thresholds.size()-1); while (thresholds.size()>0 && maxRatio < thresholds.get(thresholds.size()-1)) { passedThreshold = thresholds.remove(thresholds.size()-1); } System.out.println("passed threshold: " + passedThreshold + " for matrix: " + chr1 + "-" + chr2 + "(current max sum: " + rowsums.get(currentRow) + " , sum threshold: " + rowSumThreshold + ")"); } //Instant D = Instant.now(); //System.err.println(Duration.between(C,D).toMillis()); } return contactRecords; }*/ public int getRandomWithExclusion(Random rnd, int end, List exclude) { int random = 0; try { random = rnd.nextInt(end - exclude.size()); } catch (Exception e) { System.err.println(end + " " + exclude.size()); e.printStackTrace(); } for (int ex : exclude) { if (random < ex) { break; } random++; } return random; } } ================================================ FILE: src/juicebox/tools/utils/norm/NormalizationTools.java ================================================ /* * The MIT License (MIT) * * Copyright (c) 2011-2021 Broad Institute, Aiden Lab, Rice University, Baylor College of Medicine * * Permission is hereby granted, free of charge, to any person obtaining a copy * of this software and associated documentation files (the "Software"), to deal * in the Software without restriction, including without limitation the rights * to use, copy, modify, merge, publish, distribute, sublicense, and/or sell * copies of the Software, and to permit persons to whom the Software is * furnished to do so, subject to the following conditions: * * The above copyright notice and this permission notice shall be included in * all copies or substantial portions of the Software. * * THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR * IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, * FITNESS FOR A PARTICULAR PURPOSE AND NON-INFRINGEMENT. IN NO EVENT SHALL THE * AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER * LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, * OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN * THE SOFTWARE. */ package juicebox.tools.utils.norm; import juicebox.data.ChromosomeHandler; import juicebox.data.NormalizationVector; import juicebox.data.basics.Chromosome; import juicebox.data.basics.ListOfDoubleArrays; import juicebox.data.basics.ListOfFloatArrays; import juicebox.data.iterator.IteratorContainer; import juicebox.tools.dev.ParallelizedJuicerTools; import juicebox.windowui.HiCZoom; import juicebox.windowui.NormalizationType; import java.util.LinkedHashMap; import java.util.Map; import java.util.concurrent.atomic.AtomicInteger; public class NormalizationTools { public static Map parCreateNormVectorMap(ChromosomeHandler chromosomeHandler, int resolution, ListOfFloatArrays vector, NormalizationType norm, HiCZoom zoom) { final Map normVectorMap = new LinkedHashMap<>(); final AtomicInteger index = new AtomicInteger(0); Chromosome[] chromosomes = chromosomeHandler.getChromosomeArrayWithoutAllByAll(); long[] offsets = createOffsets(chromosomes, resolution); ParallelizedJuicerTools.launchParallelizedCode(IteratorContainer.numCPUMatrixThreads, () -> { int i = index.getAndIncrement(); while (i < (chromosomes).length) { Chromosome c1 = chromosomes[i]; long offset = offsets[i]; long chrBinned = c1.getLength() / resolution + 1; ListOfDoubleArrays chrNV = new ListOfDoubleArrays(chrBinned); for (long k = 0; k < chrNV.getLength(); k++) { // todo optimize a version with system.arraycopy and long chrNV.set(k, vector.get(offset + k)); } synchronized (normVectorMap) { normVectorMap.put(c1, new NormalizationVector(norm, c1.getIndex(), zoom.getUnit(), resolution, chrNV)); } i = index.getAndIncrement(); } }); return normVectorMap; } private static long[] createOffsets(Chromosome[] chromosomes, int resolution) { long[] offsets = new long[chromosomes.length]; offsets[0] = 0L; for (int i = 0; i < chromosomes.length - 1; i++) { offsets[i + 1] = offsets[i] + (chromosomes[i].getLength() / resolution) + 1; } return offsets; } } ================================================ FILE: src/juicebox/tools/utils/norm/NormalizationVectorIndexEntry.java ================================================ /* * The MIT License (MIT) * * Copyright (c) 2011-2020 Broad Institute, Aiden Lab, Rice University, Baylor College of Medicine * * Permission is hereby granted, free of charge, to any person obtaining a copy * of this software and associated documentation files (the "Software"), to deal * in the Software without restriction, including without limitation the rights * to use, copy, modify, merge, publish, distribute, sublicense, and/or sell * copies of the Software, and to permit persons to whom the Software is * furnished to do so, subject to the following conditions: * * The above copyright notice and this permission notice shall be included in * all copies or substantial portions of the Software. * * THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR * IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, * FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE * AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER * LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, * OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN * THE SOFTWARE. */ package juicebox.tools.utils.norm; class NormalizationVectorIndexEntry { final String type; final int chrIdx; final String unit; final int resolution; final long sizeInBytes; long position; NormalizationVectorIndexEntry(String type, int chrIdx, String unit, int resolution, long position, long sizeInBytes) { this.type = type; this.chrIdx = chrIdx; this.unit = unit; this.resolution = resolution; this.position = position; this.sizeInBytes = sizeInBytes; } @Override public String toString() { return type + " " + chrIdx + " " + unit + " " + resolution + " " + position + " " + sizeInBytes; } } ================================================ FILE: src/juicebox/tools/utils/norm/NormalizationVectorUpdater.java ================================================ /* * The MIT License (MIT) * * Copyright (c) 2011-2021 Broad Institute, Aiden Lab, Rice University, Baylor College of Medicine * * Permission is hereby granted, free of charge, to any person obtaining a copy * of this software and associated documentation files (the "Software"), to deal * in the Software without restriction, including without limitation the rights * to use, copy, modify, merge, publish, distribute, sublicense, and/or sell * copies of the Software, and to permit persons to whom the Software is * furnished to do so, subject to the following conditions: * * The above copyright notice and this permission notice shall be included in * all copies or substantial portions of the Software. * * THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR * IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, * FITNESS FOR A PARTICULAR PURPOSE AND NON-INFRINGEMENT. IN NO EVENT SHALL THE * AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER * LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, * OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN * THE SOFTWARE. */ package juicebox.tools.utils.norm; import juicebox.HiC; import juicebox.HiCGlobals; import juicebox.data.*; import juicebox.data.basics.Chromosome; import juicebox.data.basics.ListOfFloatArrays; import juicebox.tools.utils.original.ExpectedValueCalculation; import juicebox.windowui.HiCZoom; import juicebox.windowui.NormalizationHandler; import juicebox.windowui.NormalizationType; import org.broad.igv.tdf.BufferedByteWriter; import java.io.IOException; import java.util.*; /** * Update an existing hic file with new normalization vectors (included expected value vectors) * * @author jrobinso * @since 2/8/13 */ public class NormalizationVectorUpdater extends NormVectorUpdater { protected List normVectorBuffers = new ArrayList<>(); protected List normVectorIndices = new ArrayList<>(); protected List expectedValueCalculations = new ArrayList<>(); // Keep track of chromosomes that fail to converge, so we don't try them at higher resolutions. protected Set krBPFailedChromosomes = new HashSet<>(); protected Set krFragFailedChromosomes = new HashSet<>(); protected Set mmbaBPFailedChromosomes = new HashSet<>(); protected Set mmbaFragFailedChromosomes = new HashSet<>(); // norms to build; gets overwritten protected boolean weShouldBuildVC = true; protected boolean weShouldBuildVCSqrt = true; protected boolean weShouldBuildKR = true; protected boolean weShouldBuildScale = true; protected static void printNormTiming(String norm, Chromosome chr, HiCZoom zoom, long currentTime) { if (HiCGlobals.printVerboseComments) { System.out.println(norm + " normalization of " + chr + " at " + zoom + " took " + (System.currentTimeMillis() - currentTime) + " milliseconds"); } } protected static void updateExpectedValueCalculationForChr(final int chrIdx, NormalizationCalculations nc, ListOfFloatArrays vec, NormalizationType type, HiCZoom zoom, MatrixZoomData zd, ExpectedValueCalculation ev, List normVectorBuffers, List normVectorIndex) throws IOException { double factor = nc.getSumFactor(vec); vec.multiplyEverythingBy(factor); updateNormVectorIndexWithVector(normVectorIndex, normVectorBuffers, vec, chrIdx, type, zoom); ev.addDistancesFromIterator(chrIdx, zd.getIteratorContainer(), vec); } protected void reEvaluateWhichIntraNormsToBuild(List normalizationsToBuild) { weShouldBuildVC = normalizationsToBuild.contains(NormalizationHandler.VC); weShouldBuildVCSqrt = normalizationsToBuild.contains(NormalizationHandler.VC_SQRT); weShouldBuildKR = normalizationsToBuild.contains(NormalizationHandler.KR); weShouldBuildScale = normalizationsToBuild.contains(NormalizationHandler.SCALE); } protected void buildVCOrVCSQRT(boolean weShouldBuildVC, boolean weShouldBuildVCSqrt, Chromosome chr, NormalizationCalculations nc, HiCZoom zoom, MatrixZoomData zd, ExpectedValueCalculation evVC, ExpectedValueCalculation evVCSqrt) throws IOException { final int chrIdx = chr.getIndex(); ListOfFloatArrays vc = nc.computeVC(); ListOfFloatArrays vcSqrt = new ListOfFloatArrays(vc.getLength()); if (weShouldBuildVCSqrt) { for (int i = 0; i < vc.getLength(); i++) { vcSqrt.set(i, (float) Math.sqrt(vc.get(i))); } } if (weShouldBuildVC) { updateExpectedValueCalculationForChr(chrIdx, nc, vc, NormalizationHandler.VC, zoom, zd, evVC, normVectorBuffers, normVectorIndices); } if (weShouldBuildVCSqrt) { updateExpectedValueCalculationForChr(chrIdx, nc, vcSqrt, NormalizationHandler.VC_SQRT, zoom, zd, evVCSqrt, normVectorBuffers, normVectorIndices); } } protected void buildKR(Chromosome chr, NormalizationCalculations nc, HiCZoom zoom, MatrixZoomData zd, ExpectedValueCalculation evKR) throws IOException { Set failureSetKR = zoom.getUnit() == HiC.Unit.FRAG ? krFragFailedChromosomes : krBPFailedChromosomes; final int chrIdx = chr.getIndex(); long currentTime = System.currentTimeMillis(); if (!failureSetKR.contains(chr)) { ListOfFloatArrays kr = nc.computeKR(); if (kr == null) { failureSetKR.add(chr); printNormTiming("FAILED KR", chr, zoom, currentTime); } else { updateExpectedValueCalculationForChr(chrIdx, nc, kr, NormalizationHandler.KR, zoom, zd, evKR, normVectorBuffers, normVectorIndices); printNormTiming("KR", chr, zoom, currentTime); } } } public void updateHicFile(String path, List normalizationsToBuild, Map resolutionsToBuildTo, int genomeWideLowestResolutionAllowed, boolean noFrag) throws IOException { //System.out.println("test: using old norm code"); int minResolution = Integer.MAX_VALUE; for (Map.Entry entry : resolutionsToBuildTo.entrySet()) { if (entry.getValue() < minResolution) { minResolution = entry.getValue(); } } DatasetReaderV2 reader = new DatasetReaderV2(path); Dataset ds = reader.read(); HiCGlobals.verifySupportedHiCFileWritingVersion(reader.getVersion()); ChromosomeHandler chromosomeHandler = ds.getChromosomeHandler(); Map fragCountMap = ds.getFragmentCounts(); List resolutions = ds.getAllPossibleResolutions(); reEvaluateWhichIntraNormsToBuild(normalizationsToBuild); normVectorBuffers.add(new BufferedByteWriter()); for (HiCZoom zoom : resolutions) { if (zoom.getBinSize() < minResolution) { System.out.println("skipping zoom" + zoom); continue; } if (noFrag && zoom.getUnit() == HiC.Unit.FRAG) continue; System.out.println(); System.out.print("Calculating norms for zoom " + zoom); // compute genome-wide normalizations if (zoom.getUnit() == HiC.Unit.BP && zoom.getBinSize() >= genomeWideLowestResolutionAllowed) { GenomeWideNormalizationVectorUpdater.updateHicFileForGWfromPreAddNormOnly(ds, zoom, normalizationsToBuild, resolutionsToBuildTo, normVectorIndices, normVectorBuffers, expectedValueCalculations); } ds.clearCache(true, zoom); //System.out.println("genomewide normalization: " + Duration.between(A,B).toMillis()); Map fcm = zoom.getUnit() == HiC.Unit.FRAG ? fragCountMap : null; ExpectedValueCalculation evVC = new ExpectedValueCalculation(chromosomeHandler, zoom.getBinSize(), fcm, NormalizationHandler.VC); ExpectedValueCalculation evVCSqrt = new ExpectedValueCalculation(chromosomeHandler, zoom.getBinSize(), fcm, NormalizationHandler.VC_SQRT); ExpectedValueCalculation evKR = new ExpectedValueCalculation(chromosomeHandler, zoom.getBinSize(), fcm, NormalizationHandler.KR); ExpectedValueCalculation evSCALE = new ExpectedValueCalculation(chromosomeHandler, zoom.getBinSize(), fcm, NormalizationHandler.SCALE); // Loop through chromosomes for (Chromosome chr : chromosomeHandler.getChromosomeArrayWithoutAllByAll()) { MatrixZoomData zd = HiCFileTools.getMatrixZoomData(ds, chr, chr, zoom); if (zd == null) continue; if (HiCGlobals.printVerboseComments) { System.out.println("Now Doing " + chr.getName()); } NormalizationCalculations nc = new NormalizationCalculations(zd.getIteratorContainer()); if (!nc.isEnoughMemory()) { System.err.println("Not enough memory, skipping " + chr); continue; } if (weShouldBuildVC || weShouldBuildVCSqrt) { buildVCOrVCSQRT(weShouldBuildVC && zoom.getBinSize() >= resolutionsToBuildTo.get(NormalizationHandler.VC), weShouldBuildVCSqrt && zoom.getBinSize() >= resolutionsToBuildTo.get(NormalizationHandler.VC_SQRT), chr, nc, zoom, zd, evVC, evVCSqrt); } // KR normalization if (weShouldBuildKR && zoom.getBinSize() >= resolutionsToBuildTo.get(NormalizationHandler.KR)) { buildKR(chr, nc, zoom, zd, evKR); } // Fast scaling normalization if (weShouldBuildScale && zoom.getBinSize() >= resolutionsToBuildTo.get(NormalizationHandler.SCALE)) { buildScale(chr, nc, zoom, zd, evSCALE); } zd.clearCache(false); } if (weShouldBuildVC && evVC.hasData() && zoom.getBinSize() >= resolutionsToBuildTo.get(NormalizationHandler.VC)) { expectedValueCalculations.add(evVC); } if (weShouldBuildVCSqrt && evVCSqrt.hasData() && zoom.getBinSize() >= resolutionsToBuildTo.get(NormalizationHandler.VC_SQRT)) { expectedValueCalculations.add(evVCSqrt); } if (weShouldBuildKR && evKR.hasData() && zoom.getBinSize() >= resolutionsToBuildTo.get(NormalizationHandler.KR)) { expectedValueCalculations.add(evKR); } if (weShouldBuildScale && evSCALE.hasData() && zoom.getBinSize() >= resolutionsToBuildTo.get(NormalizationHandler.SCALE)) { expectedValueCalculations.add(evSCALE); } ds.clearCache(false, zoom); } writeNormsToUpdateFile(reader, path, true, expectedValueCalculations, null, normVectorIndices, normVectorBuffers, "Finished writing norms"); } protected void buildScale(Chromosome chr, NormalizationCalculations nc, HiCZoom zoom, MatrixZoomData zd, ExpectedValueCalculation evSCALE) throws IOException { Set failureSetMMBA = zoom.getUnit() == HiC.Unit.FRAG ? mmbaFragFailedChromosomes : mmbaBPFailedChromosomes; final int chrIdx = chr.getIndex(); long currentTime = System.currentTimeMillis(); if (!failureSetMMBA.contains(chr)) { ListOfFloatArrays mmba = nc.computeMMBA(); if (mmba == null) { failureSetMMBA.add(chr); printNormTiming("FAILED SCALE", chr, zoom, currentTime); } else { updateExpectedValueCalculationForChr(chrIdx, nc, mmba, NormalizationHandler.SCALE, zoom, zd, evSCALE, normVectorBuffers, normVectorIndices); printNormTiming("SCALE", chr, zoom, currentTime); } } } } ================================================ FILE: src/juicebox/tools/utils/norm/NormalizedSum.java ================================================ /* * The MIT License (MIT) * * Copyright (c) 2011-2020 Broad Institute, Aiden Lab, Rice University, Baylor College of Medicine * * Permission is hereby granted, free of charge, to any person obtaining a copy * of this software and associated documentation files (the "Software"), to deal * in the Software without restriction, including without limitation the rights * to use, copy, modify, merge, publish, distribute, sublicense, and/or sell * copies of the Software, and to permit persons to whom the Software is * furnished to do so, subject to the following conditions: * * The above copyright notice and this permission notice shall be included in * all copies or substantial portions of the Software. * * THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR * IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, * FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE * AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER * LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, * OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN * THE SOFTWARE. */ package juicebox.tools.utils.norm; class NormalizedSum { final String type; final int chr1Idx; final int chr2Idx; final String unit; final int resolution; final double value; public NormalizedSum(String type, int chr1Idx, int chr2Idx, String unit, int resolution, double value) { this.type = type; this.chr1Idx = chr1Idx; this.chr2Idx = chr2Idx; this.unit = unit; this.resolution = resolution; this.value = value; } } ================================================ FILE: src/juicebox/tools/utils/norm/UnusedFunctions.java ================================================ /* * The MIT License (MIT) * * Copyright (c) 2011-2021 Broad Institute, Aiden Lab, Rice University, Baylor College of Medicine * * Permission is hereby granted, free of charge, to any person obtaining a copy * of this software and associated documentation files (the "Software"), to deal * in the Software without restriction, including without limitation the rights * to use, copy, modify, merge, publish, distribute, sublicense, and/or sell * copies of the Software, and to permit persons to whom the Software is * furnished to do so, subject to the following conditions: * * The above copyright notice and this permission notice shall be included in * all copies or substantial portions of the Software. * * THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR * IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, * FITNESS FOR A PARTICULAR PURPOSE AND NON-INFRINGEMENT. IN NO EVENT SHALL THE * AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER * LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, * OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN * THE SOFTWARE. */ package juicebox.tools.utils.norm; import juicebox.data.DatasetReaderV2; import juicebox.tools.utils.original.LargeIndexEntry; import juicebox.windowui.NormalizationHandler; import juicebox.windowui.NormalizationType; import org.broad.igv.tdf.BufferedByteWriter; import java.io.IOException; import java.io.RandomAccessFile; import java.util.ArrayList; import java.util.List; import java.util.Map; class UnusedFunctions { /** * Main method is for internal testing and should not be used in general * * @param args If one argument, call updater code; if two, call dump index code * @throws IOException In case of error while reading or writing */ public static void internalTest(String[] args) throws IOException { /* String path = args[0]; if (args.length == 2) { CustomNormVectorFileHandler.updateHicFile(path, args[1]); } else { NormalizationVectorUpdater.updateHicFile(path, -100, false, true); } /* if (args.length > 1) { dumpNormalizationVectorIndex(path, args[1]); } else updateHicFile(path); */ } /* static void writeNormSums( List chromosomes, Dataset ds, List zooms, Map normVectors, BufferedByteWriter buffer) throws IOException { List sums = new ArrayList<>(); // Conventions: chromosomes[0] == Chr_ALL. Other chromosomes in increasing order for (int i = 1; i < chromosomes.size(); i++) { Chromosome chr1 = chromosomes.get(i); // Start at i+1, don't need this for intra for (int j = i; j < chromosomes.size(); j++) { // Normalized sums (used to compute averages for expected values) Chromosome chr2 = chromosomes.get(j); for (HiCZoom zoom : zooms) { MatrixZoomData zd2 = HiCFileTools.getMatrixZoomData(ds, chr1, chr2, zoom); if (zd2 == null) continue; BigContactRecordList contactRecords = zd2.getContactRecordList(); getNormalizedSumForNormalizationType(sums, contactRecords, normVectors, NormalizationHandler.VC, chr1, chr2, zoom); getNormalizedSumForNormalizationType(sums, contactRecords, normVectors, NormalizationHandler.VC_SQRT, chr1, chr2, zoom); getNormalizedSumForNormalizationType(sums, contactRecords, normVectors, NormalizationHandler.KR, chr1, chr2, zoom); getNormalizedSumForNormalizationType(sums, contactRecords, normVectors, NormalizationHandler.SCALE, chr1, chr2, zoom); } } } buffer.putInt(sums.size()); for (NormalizedSum sum : sums) { buffer.putNullTerminatedString(sum.type); buffer.putInt(sum.chr1Idx); buffer.putInt(sum.chr2Idx); buffer.putNullTerminatedString(sum.unit); buffer.putInt(sum.resolution); buffer.putDouble(sum.value); } } private static void getNormalizedSumForNormalizationType(List sums, BigContactRecordList recordLists, Map normVectors, NormalizationType vc, Chromosome chr1, Chromosome chr2, HiCZoom zoom) { String key1 = NormalizationVector.getKey(NormalizationHandler.VC, chr1.getIndex(), zoom.getUnit().toString(), zoom.getBinSize()); NormalizationVector vector1 = normVectors.get(key1); double[] vec1 = vector1.getData(); String key2 = NormalizationVector.getKey(NormalizationHandler.VC, chr2.getIndex(), zoom.getUnit().toString(), zoom.getBinSize()); NormalizationVector vector2 = normVectors.get(key2); double[] vec2 = vector2.getData(); double vecSum = 0; if (vec1 == null || vec2 == null) return; for (List recordList : recordLists) { for (ContactRecord cr : recordList) { int x = cr.getBinX(); int y = cr.getBinY(); if (!Double.isNaN(vec1[x]) && !Double.isNaN(vec2[y]) && vec1[x] > 0 && vec2[y] > 0) { // want total sum of matrix, not just upper triangle if (x == y) { vecSum += cr.getCounts() / (vec1[x] * vec2[y]); } else { vecSum += 2 * cr.getCounts() / (vec1[x] * vec2[y]); } } } } if (vecSum > 0) { sums.add(new NormalizedSum(NormalizationHandler.VC.getLabel(), chr1.getIndex(), chr2.getIndex(), zoom.getUnit().toString(), zoom.getBinSize(), vecSum)); } } */ static private void dumpNormalizationVectorIndex(String path, String outputFile, NormalizationHandler normalizationHandler) throws IOException { DatasetReaderV2 reader = new DatasetReaderV2(path); reader.read(); try (RandomAccessFile raf = new RandomAccessFile(outputFile, "rw")) { BufferedByteWriter buffer = new BufferedByteWriter(); // header: magic string HICNORM; version number 1; path String HIC_NORM = "HICNORM"; buffer.putNullTerminatedString(HIC_NORM); buffer.putInt(1); buffer.putNullTerminatedString(path); Map normVectorMap = reader.getNormVectorIndex(); List normList = new ArrayList<>(); for (Map.Entry entry : normVectorMap.entrySet()) { String[] parts = entry.getKey().split("_"); String strType; int chrIdx; String unit; int resolution; if (parts.length != 4) { NormalizationType type = normalizationHandler.getNormTypeFromString(parts[0] + "_" + parts[1]); strType = type.toString(); chrIdx = Integer.parseInt(parts[2]); unit = parts[3]; resolution = Integer.parseInt(parts[4]); } else { strType = parts[0]; chrIdx = Integer.parseInt(parts[1]); unit = parts[2]; resolution = Integer.parseInt(parts[3]); } NormalizationVectorIndexEntry newEntry = new NormalizationVectorIndexEntry(strType, chrIdx, unit, resolution, entry.getValue().position, entry.getValue().size); normList.add(newEntry); } NormalizationVectorUpdater.writeNormIndex(buffer, normList); raf.write(buffer.getBytes()); } } } ================================================ FILE: src/juicebox/tools/utils/norm/ZeroScale.java ================================================ /* * The MIT License (MIT) * * Copyright (c) 2011-2021 Broad Institute, Aiden Lab, Rice University, Baylor College of Medicine * * Permission is hereby granted, free of charge, to any person obtaining a copy * of this software and associated documentation files (the "Software"), to deal * in the Software without restriction, including without limitation the rights * to use, copy, modify, merge, publish, distribute, sublicense, and/or sell * copies of the Software, and to permit persons to whom the Software is * furnished to do so, subject to the following conditions: * * The above copyright notice and this permission notice shall be included in * all copies or substantial portions of the Software. * * THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR * IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, * FITNESS FOR A PARTICULAR PURPOSE AND NON-INFRINGEMENT. IN NO EVENT SHALL THE * AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER * LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, * OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN * THE SOFTWARE. */ package juicebox.tools.utils.norm; import juicebox.HiCGlobals; import juicebox.data.ContactRecord; import juicebox.data.basics.ListOfFloatArrays; import juicebox.data.iterator.IteratorContainer; import juicebox.tools.utils.norm.final2.FinalScale; import java.util.Iterator; public class ZeroScale { public static ListOfFloatArrays scale(IteratorContainer ic, ListOfFloatArrays targetVectorInitial, String key) { ListOfFloatArrays newVector = FinalScale.scaleToTargetVector(ic, targetVectorInitial); if (newVector == null && HiCGlobals.printVerboseComments) { System.err.println("Scaling result still null for " + key + "; vector did not converge"); } return newVector; } public static ListOfFloatArrays normalizeVectorByScaleFactor(ListOfFloatArrays newNormVector, IteratorContainer ic) { for (long k = 0; k < newNormVector.getLength(); k++) { float kVal = newNormVector.get(k); if (kVal <= 0 || Double.isNaN(kVal)) { newNormVector.set(k, Float.NaN); } else { newNormVector.set(k, 1.f / kVal); } } double normalizedSumTotal = 0, sumTotal = 0; Iterator iterator = ic.getNewContactRecordIterator(); while (iterator.hasNext()) { ContactRecord cr = iterator.next(); int x = cr.getBinX(); int y = cr.getBinY(); final float counts = cr.getCounts(); double valX = newNormVector.get(x); double valY = newNormVector.get(y); if (!Double.isNaN(valX) && !Double.isNaN(valY)) { double normalizedValue = counts / (valX * valY); normalizedSumTotal += normalizedValue; sumTotal += counts; if (x != y) { normalizedSumTotal += normalizedValue; sumTotal += counts; } } } double scaleFactor = Math.sqrt(normalizedSumTotal / sumTotal); newNormVector.multiplyEverythingBy(scaleFactor); return newNormVector; } public static ListOfFloatArrays mmbaScaleToVector(IteratorContainer ic, ListOfFloatArrays tempTargetVector) { ListOfFloatArrays newNormVector = scale(ic, tempTargetVector, "mmsa_scale"); if (newNormVector != null) { newNormVector = normalizeVectorByScaleFactor(newNormVector, ic); } return newNormVector; } } ================================================ FILE: src/juicebox/tools/utils/norm/final2/FinalScale.java ================================================ /* * The MIT License (MIT) * * Copyright (c) 2011-2021 Broad Institute, Aiden Lab, Rice University, Baylor College of Medicine * * Permission is hereby granted, free of charge, to any person obtaining a copy * of this software and associated documentation files (the "Software"), to deal * in the Software without restriction, including without limitation the rights * to use, copy, modify, merge, publish, distribute, sublicense, and/or sell * copies of the Software, and to permit persons to whom the Software is * furnished to do so, subject to the following conditions: * * The above copyright notice and this permission notice shall be included in * all copies or substantial portions of the Software. * * THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR * IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, * FITNESS FOR A PARTICULAR PURPOSE AND NON-INFRINGEMENT. IN NO EVENT SHALL THE * AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER * LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, * OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN * THE SOFTWARE. */ package juicebox.tools.utils.norm.final2; import juicebox.HiCGlobals; import juicebox.data.ContactRecord; import juicebox.data.basics.ListOfFloatArrays; import juicebox.data.basics.ListOfIntArrays; import juicebox.data.iterator.IteratorContainer; import java.util.Arrays; import java.util.Iterator; public class FinalScale { private final static float tol = .0005f; private final static boolean zerodiag = false; private final static boolean removeZerosOnDiag = false; private final static float percentLowRowSumExcluded = 0.0001f; private final static float dp = percentLowRowSumExcluded / 2; private final static float percentZValsToIgnore = 0;//0.0025f; private final static float dp1 = 0;//percentZValsToIgnore / 2; private final static float tolerance = .0005f; private final static int maxIter = 100; private final static int totalIterations = 3 * maxIter; private final static float minErrorThreshold = .02f; private static final float OFFSET = .5f; public static ListOfFloatArrays scaleToTargetVector(IteratorContainer ic, ListOfFloatArrays targetVectorInitial) { double low, zHigh, zLow; int rlind, zlind, zhind; float localPercentLowRowSumExcluded = percentLowRowSumExcluded; float localPercentZValsToIgnore = percentZValsToIgnore; // find the matrix dimensions long k = targetVectorInitial.getLength(); ListOfFloatArrays current = new ListOfFloatArrays(k); ListOfFloatArrays row, col; ListOfFloatArrays rowBackup = new ListOfFloatArrays(k); ListOfFloatArrays dr = new ListOfFloatArrays(k); ListOfFloatArrays dc = new ListOfFloatArrays(k); ListOfIntArrays bad; ListOfIntArrays bad1 = new ListOfIntArrays(k); ListOfFloatArrays s = new ListOfFloatArrays(k); double[] zz = new double[(int) Math.min(k, Integer.MAX_VALUE - 1)]; double[] r0 = new double[(int) Math.min(k, Integer.MAX_VALUE - 1)]; ListOfFloatArrays zTargetVector = targetVectorInitial.deepClone(); ListOfFloatArrays calculatedVectorB = new ListOfFloatArrays(k); ListOfFloatArrays one = new ListOfFloatArrays(k, 1); ListOfIntArrays numNonZero = new ListOfIntArrays(k, 0); double[] reportErrorForIteration = new double[totalIterations + 3]; int[] numItersForAllIterations = new int[totalIterations + 3]; int l = 0; for (long p = 0; p < k; p++) { if (Float.isNaN(zTargetVector.get(p))) continue; if (zTargetVector.get(p) > 0) { zz[l++] = zTargetVector.get(p); } } zz = dealWithSorting(zz, l); // unlikey to exceed max int for lind; hind // for now we will only sort one vector and hope that suffices zlind = (int) Math.max(0, l * localPercentZValsToIgnore + OFFSET); zhind = (int) Math.min(l - 1, l * (1.0 - localPercentZValsToIgnore) + OFFSET); zLow = zz[zlind]; zHigh = zz[zhind]; for (long p = 0; p < k; p++) { double valZ = zTargetVector.get(p); if (valZ > 0 && (valZ < zLow || valZ > zHigh)) { zTargetVector.set(p, Float.NaN); } } for (long p = 0; p < k; p++) { if (zTargetVector.get(p) == 0) { one.set(p, 0); } } if (removeZerosOnDiag) { bad = new ListOfIntArrays(k, 1); setBadValues(bad, ic); } else { bad = new ListOfIntArrays(k, 0); } // find rows sums setRowSums(numNonZero, ic); // find relevant percentiles int n0 = 0; for (long p = 0; p < k; p++) { int valP = numNonZero.get(p); if (valP > 0) { r0[n0++] = valP; } } r0 = dealWithSorting(r0, n0); rlind = (int) Math.max(0, n0 * localPercentLowRowSumExcluded + OFFSET); low = r0[rlind]; // find the "bad" rows and exclude them for (long p = 0; p < k; p++) { if ((numNonZero.get(p) < low && zTargetVector.get(p) > 0) || Float.isNaN(zTargetVector.get(p))) { bad.set(p, 1); zTargetVector.set(p, 1.0f); } } row = sparseMultiplyGetRowSums(ic, one, k); rowBackup = row.deepClone(); for (long p = 0; p < k; p++) { dr.set(p, 1 - bad.get(p)); } dc = dr.deepClone(); one = dr.deepClone(); // treat separately rows for which z[p] = 0 for (long p = 0; p < k; p++) { if (zTargetVector.get(p) == 0) { one.set(p, 0); } } for (long p = 0; p < k; p++) { bad1.set(p, (int) (1 - one.get(p))); } current = dr.deepClone(); // start iterations // row is the current rows sum; dr and dc are the current rows and columns scaling vectors double ber = 10.0 * (1.0 + tolerance); double err = ber; int iter = 0; int fail; int nerr = 0; double[] errors = new double[10000]; int allItersI = 0; // if perc or perc1 reached upper bound or the total number of iterationbs is too high, exit while ((ber > tolerance || err > 5.0 * tolerance) && iter < maxIter && allItersI < totalIterations && localPercentLowRowSumExcluded <= 0.2 && localPercentZValsToIgnore <= 0.1) { iter++; allItersI++; fail = 1; for (int p = 0; p < k; p++) { if (bad1.get(p) == 1) row.set(p, 1.0f); } for (int p = 0; p < k; p++) { s.set(p, zTargetVector.get(p) / row.get(p)); } for (long p = 0; p < k; p++) { dr.multiplyBy(p, s.get(p)); } // find column sums and update rows scaling vector col = sparseMultiplyGetRowSums(ic, dr, k); for (long p = 0; p < k; p++) col.multiplyBy(p, dc.get(p)); for (long p = 0; p < k; p++) if (bad1.get(p) == 1) col.set(p, 1.0f); for (long p = 0; p < k; p++) s.set(p, zTargetVector.get(p) / col.get(p)); for (long p = 0; p < k; p++) dc.multiplyBy(p, s.get(p)); // find row sums and update columns scaling vector row = sparseMultiplyGetRowSums(ic, dc, k); for (long p = 0; p < k; p++) row.multiplyBy(p, dr.get(p)); // calculate current scaling vector for (long p = 0; p < k; p++) { calculatedVectorB.set(p, (float) Math.sqrt(dr.get(p) * dc.get(p))); } // calculate the current error ber = 0; for (long p = 0; p < k; p++) { if (bad1.get(p) == 1) continue; double tempErr = Math.abs(calculatedVectorB.get(p) - current.get(p)); if (tempErr > ber) { ber = tempErr; } } reportErrorForIteration[allItersI - 1] = ber; numItersForAllIterations[allItersI - 1] = iter; // since calculating the error in row sums requires matrix-vector multiplication we are are doing this every 10 // iterations if (iter % 10 == 0) { col = sparseMultiplyGetRowSums(ic, calculatedVectorB, k); err = 0; for (long p = 0; p < k; p++) { if (bad1.get(p) == 1) continue; double tempErr = Math.abs((col.get(p) * calculatedVectorB.get(p) - zTargetVector.get(p))); if (err < tempErr) { err = tempErr; } } errors[nerr++] = err; } current = calculatedVectorB.deepClone(); // check whether convergence rate is satisfactory // if less than 5 iterations (so less than 5 errors) and less than 2 row sums errors, there is nothing to check if ((ber < tolerance) && (nerr < 2 || (nerr >= 2 && errors[nerr - 1] < 0.5 * errors[nerr - 2]))) continue; if (iter > 5) { for (int q = 1; q <= 5; q++) { if (reportErrorForIteration[allItersI - q] * (1.0 + minErrorThreshold) < reportErrorForIteration[allItersI - q - 1]) { fail = 0; } } if (nerr >= 2 && errors[nerr - 1] > 0.75 * errors[nerr - 2]) { fail = 1; } if (iter >= maxIter) { fail = 1; } if (fail == 1) { localPercentLowRowSumExcluded += dp; localPercentZValsToIgnore += dp1; nerr = 0; rlind = (int) Math.max(0, n0 * localPercentLowRowSumExcluded + OFFSET); low = r0[rlind]; zlind = (int) Math.max(0, l * localPercentZValsToIgnore + OFFSET); zhind = (int) Math.min(l - 1, l * (1.0 - localPercentZValsToIgnore) + OFFSET); zLow = zz[zlind]; zHigh = zz[zhind]; for (long p = 0; p < k; p++) { if (zTargetVector.get(p) > 0 && (zTargetVector.get(p) < zLow || zTargetVector.get(p) > zHigh)) { zTargetVector.set(p, Float.NaN); } } for (long p = 0; p < k; p++) { if ((numNonZero.get(p) < low && zTargetVector.get(p) > 0) || Float.isNaN(zTargetVector.get(p))) { bad.set(p, 1); bad1.set(p, 1); one.set(p, 0); zTargetVector.set(p, 1.0f); } } ber = 10.0 * (1.0 + tol); err = 10.0 * (1.0 + tol); // if the current error is larger than 5 iteration ago start from scratch, // otherwise continue from the current position if (reportErrorForIteration[allItersI - 1] > reportErrorForIteration[allItersI - 6]) { for (long p = 0; p < k; p++) { dr.set(p, 1 - bad.get(p)); } dc = dr.deepClone(); one = dr.deepClone(); current = dr.deepClone(); row = rowBackup.deepClone(); } else { for (long p = 0; p < k; p++) { dr.multiplyBy(p, (1 - bad.get(p))); } for (long p = 0; p < k; p++) { dc.multiplyBy(p, (1 - bad.get(p))); } } iter = 0; } } } // find the final error in row sums if (iter % 10 == 0) { col = sparseMultiplyGetRowSums(ic, calculatedVectorB, k); err = 0; for (int p = 0; p < k; p++) { if (bad1.get(p) == 1) continue; double tempErr = Math.abs(col.get(p) * calculatedVectorB.get(p) - zTargetVector.get(p)); if (err < tempErr) err = tempErr; } } reportErrorForIteration[allItersI + 1] = ber; reportErrorForIteration[allItersI + 2] = err; for (long p = 0; p < k; p++) { if (bad.get(p) == 1) { calculatedVectorB.set(p, Float.NaN); } } if (HiCGlobals.printVerboseComments) { System.out.println(allItersI); System.out.println(localPercentLowRowSumExcluded); System.out.println(localPercentZValsToIgnore); System.out.println(Arrays.toString(reportErrorForIteration)); } return calculatedVectorB; } private static void setRowSums(ListOfIntArrays numNonZero, IteratorContainer ic) { Iterator iterator = ic.getNewContactRecordIterator(); while (iterator.hasNext()) { ContactRecord cr = iterator.next(); int x = cr.getBinX(); int y = cr.getBinY(); numNonZero.addTo(x, 1); if (x != y) { numNonZero.addTo(y, 1); } } } private static void setBadValues(ListOfIntArrays bad, IteratorContainer ic) { Iterator iterator = ic.getNewContactRecordIterator(); while (iterator.hasNext()) { ContactRecord cr = iterator.next(); int x = cr.getBinX(); int y = cr.getBinY(); if (x == y) { bad.set(x, 0); } } } private static double[] dealWithSorting(double[] vector, int length) { double[] realVector = new double[length]; System.arraycopy(vector, 0, realVector, 0, length); Arrays.sort(realVector); return realVector; } private static ListOfFloatArrays sparseMultiplyGetRowSums(IteratorContainer ic, ListOfFloatArrays vector, long vectorLength) { return ic.sparseMultiply(vector, vectorLength); } } ================================================ FILE: src/juicebox/tools/utils/norm/final2/ScaleThreadObject.java ================================================ /* * The MIT License (MIT) * * Copyright (c) 2011-2020 Broad Institute, Aiden Lab, Rice University, Baylor College of Medicine * * Permission is hereby granted, free of charge, to any person obtaining a copy * of this software and associated documentation files (the "Software"), to deal * in the Software without restriction, including without limitation the rights * to use, copy, modify, merge, publish, distribute, sublicense, and/or sell * copies of the Software, and to permit persons to whom the Software is * furnished to do so, subject to the following conditions: * * The above copyright notice and this permission notice shall be included in * all copies or substantial portions of the Software. * * THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR * IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, * FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE * AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER * LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, * OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN * THE SOFTWARE. */ package juicebox.tools.utils.norm.final2; public class ScaleThreadObject { private final int[] iIndexes; private final int[] jIndexes; private final float[] xValues; private final float[] vVector; private final float[] result; public ScaleThreadObject(int[] iIndexes, int[] jIndexes, float[] xValues, float[] vVector, float[] result) { this.iIndexes = iIndexes; this.jIndexes = jIndexes; this.xValues = xValues; this.vVector = vVector; this.result = result; } public void execute() { for (int p = 0; p < xValues.length; p++) { result[iIndexes[p]] += xValues[p] * vVector[jIndexes[p]]; result[jIndexes[p]] += xValues[p] * vVector[iIndexes[p]]; } } } ================================================ FILE: src/juicebox/tools/utils/original/BigWigUtils.java ================================================ /* * The MIT License (MIT) * * Copyright (c) 2011-2020 Broad Institute, Aiden Lab, Rice University, Baylor College of Medicine * * Permission is hereby granted, free of charge, to any person obtaining a copy * of this software and associated documentation files (the "Software"), to deal * in the Software without restriction, including without limitation the rights * to use, copy, modify, merge, publish, distribute, sublicense, and/or sell * copies of the Software, and to permit persons to whom the Software is * furnished to do so, subject to the following conditions: * * The above copyright notice and this permission notice shall be included in * all copies or substantial portions of the Software. * * THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR * IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, * FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE * AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER * LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, * OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN * THE SOFTWARE. */ package juicebox.tools.utils.original; import org.broad.igv.bbfile.BBFileReader; import org.broad.igv.bbfile.BigWigIterator; import org.broad.igv.bbfile.WigItem; import java.io.IOException; /** * Some utils for querying bigwig files * * @author jrobinso * Date: 5/28/13 * Time: 3:27 PM */ public class BigWigUtils { public static void computeBins(String path, int windowSize) throws IOException { BBFileReader reader = new BBFileReader(path); for (String chr : reader.getChromosomeNames()) { computeBins(reader, chr, 0, Integer.MAX_VALUE, windowSize); } } public static void computeBins(String path, String chr, int start, int end, int windowSize) throws IOException { BBFileReader reader = new BBFileReader(path); boolean found = false; StringBuilder errString = new StringBuilder(); for (String chr1 : reader.getChromosomeNames()) { if (chr.equals(chr1)) found = true; errString.append("\"").append(chr1).append("\" "); } if (!found) { System.err.println("Chromosome \"" + chr + "\" not found in " + path); System.err.println("The chromosomes in " + path + " are " + errString); return; } computeBins(reader, chr, start, end, windowSize); } /** * Private method, does the actual work * * @param reader * @param chr * @param start * @param end * @param windowSize */ private static void computeBins(BBFileReader reader, String chr, int start, int end, int windowSize) { BigWigIterator iter = reader.getBigWigIterator(chr, start, chr, end, false); double sum = 0; int nPts = 0; double max = 0; int currentBin = 0; while (iter.hasNext()) { WigItem datum = iter.next(); int dPosition = (datum.getStartBase() + datum.getEndBase()) / 2; if (dPosition > (currentBin + 1) * windowSize) { // Output previous window // if (nPts > 0) { double mean = sum / nPts; int wStart = windowSize * currentBin; int wEnd = wStart + windowSize; // unclear why, but sometimes datum.getChromosome() is null //System.out.println(datum.getChromosome() + "\t" + wStart + "\t" + wEnd + "\t" + mean + "\t" + max); System.out.println(chr + "\t" + wStart + "\t" + wEnd + "\t" + mean + "\t" + max); currentBin++; // deal with empty bins while (currentBin < dPosition / windowSize) { wStart = windowSize * currentBin; wEnd = wStart + windowSize; mean = 0; max = 0; System.out.println(chr + "\t" + wStart + "\t" + wEnd + "\t" + mean + "\t" + max); // System.out.println(datum.getChromosome() + "\t" + wStart + "\t" + wEnd + "\t" + mean + "\t" + max); currentBin++; } // Start new window currentBin = dPosition / windowSize; sum = 0; nPts = 0; max = 0; } sum += datum.getWigValue(); max = Math.max(max, datum.getWigValue()); nPts++; } } /** * Example usage *

* First argument (required): path, either file or URL. * http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeUwTfbs/wgEncodeUwTfbsGm12878CtcfStdRawRep1.bigWig * /Users/jrobinso/projects/hic/data/wgEncodeUwTfbsGm12878CtcfStdRawRep1.bigWig * Second argument (required): windowSize in base pairs * 25000 * Third argument (optional): chromosome * Fourth argument (optional): start base -- if supplied end base must also be supplied * Firth argument (optional): end base */ // Example use public static void main(String[] args) throws Exception { if (args.length < 2) { System.err.println("Chromosome and window size are required"); System.exit(5); } String path = args[0]; int windowSize = Integer.parseInt(args[1]); if (args.length == 2) { computeBins(path, windowSize); } else { String chr = args[2]; if (args.length == 3) { computeBins(path, chr, 0, Integer.MAX_VALUE, windowSize); } else { int start = Integer.parseInt(args[3]) - 1; // Convert to "zero" based coords int end = Integer.parseInt(args[4]); computeBins(path, chr, start, end, windowSize); } } } } ================================================ FILE: src/juicebox/tools/utils/original/BlockPP.java ================================================ /* * The MIT License (MIT) * * Copyright (c) 2011-2020 Broad Institute, Aiden Lab, Rice University, Baylor College of Medicine * * Permission is hereby granted, free of charge, to any person obtaining a copy * of this software and associated documentation files (the "Software"), to deal * in the Software without restriction, including without limitation the rights * to use, copy, modify, merge, publish, distribute, sublicense, and/or sell * copies of the Software, and to permit persons to whom the Software is * furnished to do so, subject to the following conditions: * * The above copyright notice and this permission notice shall be included in * all copies or substantial portions of the Software. * * THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR * IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, * FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE * AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER * LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, * OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN * THE SOFTWARE. */ package juicebox.tools.utils.original; import java.awt.*; import java.util.HashMap; import java.util.Map; /** * Representation of a sparse matrix block used for preprocessing. */ class BlockPP { private final int number; // Key to the map is a Point representing the x,y coordinate for the cell. private final Map contactRecordMap; BlockPP(int number) { this.number = number; this.contactRecordMap = new HashMap<>(); } BlockPP(int number, Map contactRecordMap) { this.number = number; this.contactRecordMap = contactRecordMap; } int getNumber() { return number; } int getNumRecords() {return contactRecordMap.size();} void incrementCount(int col, int row, float score) { Point p = new Point(col, row); ContactCount rec = contactRecordMap.get(p); if (rec == null) { rec = new ContactCount(score); contactRecordMap.put(p, rec); } else { rec.incrementCount(score); } } Map getContactRecordMap() { return contactRecordMap; } void merge(BlockPP other) { for (Map.Entry entry : other.getContactRecordMap().entrySet()) { Point point = entry.getKey(); ContactCount otherValue = entry.getValue(); ContactCount value = contactRecordMap.get(point); if (value == null) { contactRecordMap.put(point, otherValue); } else { value.incrementCount(otherValue.getCounts()); } } } void clear() { contactRecordMap.clear(); } } ================================================ FILE: src/juicebox/tools/utils/original/BlockQueue.java ================================================ /* * The MIT License (MIT) * * Copyright (c) 2011-2020 Broad Institute, Aiden Lab, Rice University, Baylor College of Medicine * * Permission is hereby granted, free of charge, to any person obtaining a copy * of this software and associated documentation files (the "Software"), to deal * in the Software without restriction, including without limitation the rights * to use, copy, modify, merge, publish, distribute, sublicense, and/or sell * copies of the Software, and to permit persons to whom the Software is * furnished to do so, subject to the following conditions: * * The above copyright notice and this permission notice shall be included in * all copies or substantial portions of the Software. * * THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR * IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, * FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE * AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER * LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, * OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN * THE SOFTWARE. */ package juicebox.tools.utils.original; import java.io.IOException; interface BlockQueue { void advance() throws IOException; BlockPP getBlock(); } ================================================ FILE: src/juicebox/tools/utils/original/BlockQueueFB.java ================================================ /* * The MIT License (MIT) * * Copyright (c) 2011-2021 Broad Institute, Aiden Lab, Rice University, Baylor College of Medicine * * Permission is hereby granted, free of charge, to any person obtaining a copy * of this software and associated documentation files (the "Software"), to deal * in the Software without restriction, including without limitation the rights * to use, copy, modify, merge, publish, distribute, sublicense, and/or sell * copies of the Software, and to permit persons to whom the Software is * furnished to do so, subject to the following conditions: * * The above copyright notice and this permission notice shall be included in * all copies or substantial portions of the Software. * * THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR * IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, * FITNESS FOR A PARTICULAR PURPOSE AND NON-INFRINGEMENT. IN NO EVENT SHALL THE * AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER * LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, * OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN * THE SOFTWARE. */ package juicebox.tools.utils.original; import htsjdk.tribble.util.LittleEndianInputStream; import java.awt.*; import java.io.*; import java.util.HashMap; import java.util.Map; class BlockQueueFB implements BlockQueue { final File file; BlockPP block; long filePosition; long fileLength; BlockQueueFB(File file) { this.file = file; fileLength = file.length(); try { advance(); } catch (IOException e) { e.printStackTrace(); //To change body of catch statement use File | Settings | File Templates. } } public void advance() throws IOException { if (filePosition >= fileLength) { block = null; return; } FileInputStream fis = null; try { fis = new FileInputStream(file); fis.getChannel().position(filePosition); LittleEndianInputStream lis = new LittleEndianInputStream(fis); int blockNumber = lis.readInt(); int nRecords = lis.readInt(); byte[] bytes = new byte[nRecords * 12]; readFully(bytes, fis); ByteArrayInputStream bis = new ByteArrayInputStream(bytes); lis = new LittleEndianInputStream(bis); Map contactRecordMap = new HashMap<>(nRecords); for (int i = 0; i < nRecords; i++) { int x = lis.readInt(); int y = lis.readInt(); float v = lis.readFloat(); ContactCount rec = new ContactCount(v); contactRecordMap.put(new Point(x, y), rec); } block = new BlockPP(blockNumber, contactRecordMap); // Update file position based on # of bytes read, for next block filePosition = fis.getChannel().position(); } finally { if (fis != null) fis.close(); } } public BlockPP getBlock() { return block; } /** * Read enough bytes to fill the input buffer */ void readFully(byte[] b, InputStream is) throws IOException { int len = b.length; if (len < 1) throw new IndexOutOfBoundsException(); int n = 0; while (n < len) { int count = is.read(b, n, len - n); if (count < 0) throw new EOFException(); n += count; } } } ================================================ FILE: src/juicebox/tools/utils/original/BlockQueueMem.java ================================================ /* * The MIT License (MIT) * * Copyright (c) 2011-2020 Broad Institute, Aiden Lab, Rice University, Baylor College of Medicine * * Permission is hereby granted, free of charge, to any person obtaining a copy * of this software and associated documentation files (the "Software"), to deal * in the Software without restriction, including without limitation the rights * to use, copy, modify, merge, publish, distribute, sublicense, and/or sell * copies of the Software, and to permit persons to whom the Software is * furnished to do so, subject to the following conditions: * * The above copyright notice and this permission notice shall be included in * all copies or substantial portions of the Software. * * THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR * IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, * FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE * AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER * LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, * OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN * THE SOFTWARE. */ package juicebox.tools.utils.original; import java.util.ArrayList; import java.util.Collection; import java.util.Comparator; import java.util.List; class BlockQueueMem implements BlockQueue { final List blocks; int idx = 0; BlockQueueMem(Collection blockCollection) { this.blocks = new ArrayList<>(blockCollection); blocks.sort(new Comparator() { @Override public int compare(BlockPP o1, BlockPP o2) { return o1.getNumber() - o2.getNumber(); } }); } public void advance() { idx++; } public BlockPP getBlock() { if (idx >= blocks.size()) { return null; } else { return blocks.get(idx); } } } ================================================ FILE: src/juicebox/tools/utils/original/Chunk.java ================================================ /* * The MIT License (MIT) * * Copyright (c) 2011-2021 Broad Institute, Aiden Lab, Rice University, Baylor College of Medicine * * Permission is hereby granted, free of charge, to any person obtaining a copy * of this software and associated documentation files (the "Software"), to deal * in the Software without restriction, including without limitation the rights * to use, copy, modify, merge, publish, distribute, sublicense, and/or sell * copies of the Software, and to permit persons to whom the Software is * furnished to do so, subject to the following conditions: * * The above copyright notice and this permission notice shall be included in * all copies or substantial portions of the Software. * * THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR * IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, * FITNESS FOR A PARTICULAR PURPOSE AND NON-INFRINGEMENT. IN NO EVENT SHALL THE * AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER * LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, * OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN * THE SOFTWARE. */ package juicebox.tools.utils.original; public class Chunk { public final long mndIndex; public final int mndChunk; public Chunk(long mndIndex, int mndChunk) { this.mndIndex = mndIndex; this.mndChunk = mndChunk; } public Chunk(String s1, String s2) { this(Long.parseLong(s1), Integer.parseInt(s2)); } } ================================================ FILE: src/juicebox/tools/utils/original/ContactCount.java ================================================ /* * The MIT License (MIT) * * Copyright (c) 2011-2020 Broad Institute, Aiden Lab, Rice University, Baylor College of Medicine * * Permission is hereby granted, free of charge, to any person obtaining a copy * of this software and associated documentation files (the "Software"), to deal * in the Software without restriction, including without limitation the rights * to use, copy, modify, merge, publish, distribute, sublicense, and/or sell * copies of the Software, and to permit persons to whom the Software is * furnished to do so, subject to the following conditions: * * The above copyright notice and this permission notice shall be included in * all copies or substantial portions of the Software. * * THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR * IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, * FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE * AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER * LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, * OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN * THE SOFTWARE. */ package juicebox.tools.utils.original; class ContactCount { float value; ContactCount(float value) { this.value = value; } void incrementCount(float increment) { value += increment; } float getCounts() { return value; } } ================================================ FILE: src/juicebox/tools/utils/original/ExpectedValueCalculation.java ================================================ /* * The MIT License (MIT) * * Copyright (c) 2011-2021 Broad Institute, Aiden Lab, Rice University, Baylor College of Medicine * * Permission is hereby granted, free of charge, to any person obtaining a copy * of this software and associated documentation files (the "Software"), to deal * in the Software without restriction, including without limitation the rights * to use, copy, modify, merge, publish, distribute, sublicense, and/or sell * copies of the Software, and to permit persons to whom the Software is * furnished to do so, subject to the following conditions: * * The above copyright notice and this permission notice shall be included in * all copies or substantial portions of the Software. * * THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR * IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, * FITNESS FOR A PARTICULAR PURPOSE AND NON-INFRINGEMENT. IN NO EVENT SHALL THE * AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER * LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, * OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN * THE SOFTWARE. */ package juicebox.tools.utils.original; import juicebox.HiC; import juicebox.data.ChromosomeHandler; import juicebox.data.ContactRecord; import juicebox.data.ExpectedValueFunctionImpl; import juicebox.data.MatrixZoomData; import juicebox.data.basics.Chromosome; import juicebox.data.basics.ListOfDoubleArrays; import juicebox.data.basics.ListOfFloatArrays; import juicebox.data.iterator.IteratorContainer; import juicebox.tools.utils.norm.NormVectorUpdater; import juicebox.windowui.NormalizationType; import java.util.Arrays; import java.util.Iterator; import java.util.Map; import java.util.concurrent.ConcurrentHashMap; /** * Computes an "expected" density vector. Essentially there are 3 steps to using this class *

* (1) instantiate it with a collection of Chromosomes (representing a genome) and a grid size * (2) loop through the pair data, calling addDistance for each pair, to accumulate all counts * (3) when data loop is complete, call computeDensity to do the calculation *

*

* Methods are provided to save the result of the calculation to a binary file, and restore it. See the * DensityUtil class for example usage. * * @author Jim Robinson * @since 11/27/11 */ public class ExpectedValueCalculation { private final int gridSize; private final int numberOfBins; /** * Map of chromosome index -> total count for that chromosome */ private final Map chromosomeCounts = new ConcurrentHashMap<>(); /** * Map of chromosome index -> "normalization factor", essentially a fudge factor to make * the "expected total" == observed total */ private final Map chrScaleFactors = new ConcurrentHashMap<>(); private final NormalizationType type; // A little redundant, for clarity public boolean isFrag = false; /** * Genome wide count of binned reads at a given distance */ private final double[] actualDistances; /** * Expected count at a given binned distance from diagonal */ private ListOfDoubleArrays densityAvg; /** * Chromosome in this genome, needed for normalizations */ private final Map chromosomesMap = new ConcurrentHashMap<>(); /** * Stores restriction site fragment information for fragment maps */ private final Map fragmentCountMap; /** * Instantiate a DensityCalculation. This constructor is used to compute the "expected" density from pair data. * * @param chromosomeHandler Handler for list of chromosomesMap, mainly used for size * @param gridSize Grid size, used for binning appropriately * @param fragmentCountMap Optional. Map of chromosome name -> number of fragments * @param type Identifies the observed matrix type, either NONE (observed), VC, or KR. */ public ExpectedValueCalculation(ChromosomeHandler chromosomeHandler, int gridSize, Map fragmentCountMap, NormalizationType type) { this.type = type; this.gridSize = gridSize; if (fragmentCountMap != null) { this.isFrag = true; this.fragmentCountMap = fragmentCountMap; } else { this.fragmentCountMap = null; } long maxLen = 0; for (Chromosome chr : chromosomeHandler.getChromosomeArrayWithoutAllByAll()) { if (chr != null) { chromosomesMap.put(chr.getIndex(), chr); try { maxLen = isFrag ? Math.max(maxLen, fragmentCountMap.get(chr.getName())) : Math.max(maxLen, chr.getLength()); } catch (NullPointerException error) { System.err.println("Problem with creating fragment-delimited maps, NullPointerException.\n" + "This could be due to a null fragment map or to a mismatch in the chromosome name in " + "the fragment map vis-a-vis the input file or chrom.sizes file.\n" + "Exiting."); System.exit(63); } catch (ArrayIndexOutOfBoundsException error) { System.err.println("Problem with creating fragment-delimited maps, ArrayIndexOutOfBoundsException.\n" + "This could be due to a null fragment map or to a mismatch in the chromosome name in " + "the fragment map vis-a-vis the input file or chrom.sizes file.\n" + "Exiting."); System.exit(22); } } } numberOfBins = (int) (maxLen / gridSize) + 1; actualDistances = new double[numberOfBins]; Arrays.fill(actualDistances, 0); } public int getGridSize() { return gridSize; } /** * Add an observed distance. This is called for each pair in the data set * * @param chrIdx index of chromosome where observed, so can increment count * @param bin1 Position1 observed in units of "bins" * @param bin2 Position2 observed in units of "bins" */ public synchronized void addDistance(Integer chrIdx, int bin1, int bin2, double weight) { // Ignore NaN values TODO -- is this the right thing to do? if (Double.isNaN(weight)) return; int dist; Chromosome chr = chromosomesMap.get(chrIdx); if (chr == null) return; Double count = chromosomeCounts.get(chrIdx); if (count == null) { chromosomeCounts.put(chrIdx, weight); } else { chromosomeCounts.put(chrIdx, count + weight); } dist = Math.abs(bin1 - bin2); actualDistances[dist] += weight; } public void merge(ExpectedValueCalculation otherEVCalc) { for (Map.Entry entry : otherEVCalc.chromosomesMap.entrySet()) { Chromosome chr = chromosomesMap.get(entry.getKey()); if (chr != null) { if (otherEVCalc.chromosomeCounts.get(entry.getKey()) != null) { Double count = chromosomeCounts.get(entry.getKey()); if (count == null) { chromosomeCounts.put(entry.getKey(), otherEVCalc.chromosomeCounts.get(entry.getKey())); } else { chromosomeCounts.put(entry.getKey(), count + otherEVCalc.chromosomeCounts.get(entry.getKey())); } } } } for (int i = 0; i < actualDistances.length; i++) { actualDistances[i] += otherEVCalc.actualDistances[i]; } } public boolean hasData() { return !chromosomeCounts.isEmpty(); } /** * Compute the "density" -- port of python function getDensityControls(). * The density is a measure of the average distribution of counts genome-wide for a ligated molecule. * The density will decrease as distance from the center diagonal increases. * First compute "possible distances" for each bin. * "possible distances" provides a way to normalize the counts. Basically it's the number of * slots available in the diagonal. The sum along the diagonal will then be the count at that distance, * an "expected" or average uniform density. */ public synchronized void computeDensity() { long maxNumBins = 0; //System.err.println("# of bins=" + numberOfBins); /** * Genome wide binned possible distances */ double[] possibleDistances = new double[numberOfBins]; for (Chromosome chr : chromosomesMap.values()) { // didn't see anything at all from a chromosome, then don't include it in possDists. if (chr == null || !chromosomeCounts.containsKey(chr.getIndex())) continue; // use correct units (bp or fragments) long len = isFrag ? fragmentCountMap.get(chr.getName()) : chr.getLength(); long nChrBins = len / gridSize; maxNumBins = Math.max(maxNumBins, nChrBins); for (int i = 0; i < nChrBins; i++) { possibleDistances[i] += (nChrBins - i); } } //System.err.println("max # bins " + maxNumBins); densityAvg = new ListOfDoubleArrays(maxNumBins); // Smoothing. Keep pointers to window size. When read counts drops below 400 (= 5% shot noise), smooth double numSum = actualDistances[0]; double denSum = possibleDistances[0]; int bound1 = 0; int bound2 = 0; for (long ii = 0; ii < maxNumBins; ii++) { if (numSum < 400) { while (numSum < 400 && bound2 < maxNumBins) { // increase window size until window is big enough. This code will only execute once; // after this, the window will always contain at least 400 reads. bound2++; numSum += actualDistances[bound2]; denSum += possibleDistances[bound2]; } } else if (numSum >= 400 && bound2 - bound1 > 0) { while (bound2 - bound1 > 0 && bound2 < numberOfBins && bound1 < numberOfBins && numSum - actualDistances[bound1] - actualDistances[bound2] >= 400) { numSum = numSum - actualDistances[bound1] - actualDistances[bound2]; denSum = denSum - possibleDistances[bound1] - possibleDistances[bound2]; bound1++; bound2--; } } densityAvg.set(ii, numSum / denSum); // Default case - bump the window size up by 2 to keep it centered for the next iteration if (bound2 + 2 < maxNumBins) { numSum += actualDistances[bound2 + 1] + actualDistances[bound2 + 2]; denSum += possibleDistances[bound2 + 1] + possibleDistances[bound2 + 2]; bound2 += 2; } else if (bound2 + 1 < maxNumBins) { numSum += actualDistances[bound2 + 1]; denSum += possibleDistances[bound2 + 1]; bound2++; } // Otherwise, bound2 is at limit already } // Compute fudge factors for each chromosome so the total "expected" count for that chromosome == the observed for (Chromosome chr : chromosomesMap.values()) { if (chr == null || !chromosomeCounts.containsKey(chr.getIndex())) { continue; } //int len = isFrag ? fragmentCalculation.getNumberFragments(chr.getName()) : chr.getLength(); long len = isFrag ? fragmentCountMap.get(chr.getName()) : chr.getLength(); long nChrBins = len / gridSize; double expectedCount = 0; for (long n = 0; n < nChrBins; n++) { if (n < maxNumBins) { final double v = densityAvg.get(n); // this is the sum of the diagonal for this particular chromosome. // the value in each bin is multiplied by the length of the diagonal to get expected count // the total at the end should be the sum of the expected matrix for this chromosome // i.e., for each chromosome, we calculate sum (genome-wide actual)/(genome-wide possible) == v // then multiply it by the chromosome-wide possible == nChrBins - n. expectedCount += (nChrBins - n) * v; } } double observedCount = chromosomeCounts.get(chr.getIndex()); double f = expectedCount / observedCount; chrScaleFactors.put(chr.getIndex(), f); } } /** * Accessor for the normalization factors * * @return The normalization factors */ public Map getChrScaleFactors() { return chrScaleFactors; } /** * Accessor for the densities * * @return The densities */ public ListOfDoubleArrays getDensityAvg() { return densityAvg; } /** * Accessor for the normalization type * * @return The normalization type */ public NormalizationType getType() { return type; } public ExpectedValueFunctionImpl getExpectedValueFunction() { computeDensity(); return new ExpectedValueFunctionImpl(type, isFrag ? HiC.Unit.FRAG : HiC.Unit.BP, gridSize, densityAvg, chrScaleFactors); } // TODO: this is often inefficient, we have all of the contact records when we leave norm calculations, should do this there if possible public void addDistancesFromIterator(int chrIndx, IteratorContainer ic, ListOfFloatArrays vector) { Iterator iterator = ic.getNewContactRecordIterator(); while (iterator.hasNext()) { ContactRecord cr = iterator.next(); int x = cr.getBinX(); int y = cr.getBinY(); final float counts = cr.getCounts(); float xVal = vector.get(x); float yVal = vector.get(y); if (NormVectorUpdater.isValidNormValue(xVal) & NormVectorUpdater.isValidNormValue(yVal)) { double value = counts / (xVal * yVal); addDistance(chrIndx, x, y, value); } } } public void addDistancesFromZD(MatrixZoomData zd, Map fragmentCountMap, ChromosomeHandler chromosomeHandler, int numCPUThreads) { this.merge(zd.computeExpected(true, fragmentCountMap, chromosomeHandler, numCPUThreads)); } } // Smooth in 3 stages, the window sizes are tuned to human. // // Smooth (1) // final int smoothingWidow1 = 15000000; // int start = smoothingWidow1 / gridSize; // int window = (int) (5 * (2000000f / gridSize)); // if (window == 0) window = 1; // for (int i = start; i < numberOfBins; i++) { // int kMin = i - window; // int kMax = Math.min(i + window, numberOfBins); // double sum = 0; // for (int k = kMin; k < kMax; k++) { // sum += density[k]; // } // densityAvg[i] = sum / (kMax - kMin); // } // // // Smooth (2) // start = 70000000 / gridSize; // window = (int)(20 * (2000000f / gridSize)); // for (int i = start; i < numberOfBins; i++) { // int kMin = i - window; // int kMax = Math.min(i + window, numberOfBins); // double sum = 0; // for (int k = kMin; k < kMax; k++) { // sum += density[k]; // } // densityAvg[i] = sum / (kMax - kMin); // } // // // Smooth (3) // start = 170000000 / gridSize; // for (int i = start; i < numberOfBins; i++) { // densityAvg[i] = densityAvg[start]; // } /* --- Code above based on the following Python gridSize => grid (or bin) size == 10^6 actualDistances => array of actual distances, each element represents a bin possibleDistances => array of possible distances, each element represents a bin jdists => outer distances between pairs for each jdist actualDistance[jdist]++; for each chromosome chrlen = chromosome length numberOfBins = chrlen / gridSize for each i from 0 to numberOfBins possibleDistances[i] += (numberOfBins - i) for each i from 0 to maxGrid density[i] = actualDistance[i] / possibleDistances[i] for each i from 0 to len(density) density_avg[i] = density[i] for each i from 15000000/gridsize to len(density_avg) sum1 = 0 for each k from (i - 5*((2*10^6) / gridSize) to (i + 5*((2*10^6)/gridsize)) sum1 += density[k] density_avg[i] = sum1 / (10*((2*10^6)/gridsize)) for each i from 70000000/gridsize to len(density_avg) sum2 = 0 for each k from (i - 20*((2*10^6) / gridSize) to (i + 20*((2*10^6)/gridsize)) sum2 += density[k] density_avg[i] = sum2 / (40*((2*10^6)/gridsize)) for each i from 170000000/gridsize to len(density_avg) density_avg[i]=density_avg[170000000/gridsize] */ ================================================ FILE: src/juicebox/tools/utils/original/FragmentCalculation.java ================================================ /* * The MIT License (MIT) * * Copyright (c) 2011-2021 Broad Institute, Aiden Lab, Rice University, Baylor College of Medicine * * Permission is hereby granted, free of charge, to any person obtaining a copy * of this software and associated documentation files (the "Software"), to deal * in the Software without restriction, including without limitation the rights * to use, copy, modify, merge, publish, distribute, sublicense, and/or sell * copies of the Software, and to permit persons to whom the Software is * furnished to do so, subject to the following conditions: * * The above copyright notice and this permission notice shall be included in * all copies or substantial portions of the Software. * * THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR * IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, * FITNESS FOR A PARTICULAR PURPOSE AND NON-INFRINGEMENT. IN NO EVENT SHALL THE * AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER * LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, * OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN * THE SOFTWARE. */ package juicebox.tools.utils.original; import juicebox.HiCGlobals; import juicebox.data.ChromosomeHandler; import java.io.*; import java.util.LinkedHashMap; import java.util.Map; import java.util.regex.Pattern; /** * @author nchernia * Date: 8/26/12 */ public class FragmentCalculation { private final Map sitesMap; private FragmentCalculation(Map sitesMap) { this.sitesMap = sitesMap; } private static FragmentCalculation readFragments(InputStream is, ChromosomeHandler handler) throws IOException { Pattern pattern = Pattern.compile("\\s"); BufferedReader reader = new BufferedReader(new InputStreamReader(is), HiCGlobals.bufferSize); String nextLine; Map sitesMap = new LinkedHashMap<>(); while ((nextLine = reader.readLine()) != null) { String[] tokens = pattern.split(nextLine); if (tokens.length > 1) { String key = tokens[0]; int[] sites = new int[tokens.length - 1]; for (int i = 1; i < tokens.length; i++) { sites[i - 1] = Integer.parseInt(tokens[i]); } if (handler != null) { sitesMap.put(handler.cleanUpName(key), sites); } else { sitesMap.put(key, sites); } } else { System.out.println("Skipping line: " + nextLine); } } return new FragmentCalculation(sitesMap); } public static FragmentCalculation readFragments(String filename, ChromosomeHandler handler, String parentCommand) { InputStream is = null; try { File file = new File(filename); is = new FileInputStream(file); return readFragments(is, handler); } catch (Exception e) { System.err.println("Warning: Unable to process fragment file. " + parentCommand + " will continue without fragment file."); return null; } finally { try { if (is != null) { is.close(); } } catch (IOException e) { } } } /** * Return fragment that this position lies on. Fragment 0 means position < sites[0]. * Fragment 1 means position >= sites[0] and < sites[1]. * * @param sites The sorted array of fragment sites for the chromosome * @param position The position to search for within that array * @return The fragment location such that position >= sites[retVal-1] and position < sites[retVal] */ public static int binarySearch(int[] sites, int position) { int lo = 0; int hi = sites.length - 1; while (lo <= hi) { // Base case - found range int mid = lo + (hi - lo) / 2; if (position > sites[mid]) lo = mid + 1; else if (position < sites[mid]) hi = mid - 1; else return mid + 1; } return lo; } public int[] getSites(String chrName) { return sitesMap.get(chrName); } public int getNumberFragments(String chrName) { int[] sites = sitesMap.get(chrName); if (sites == null) // for "All" return 1; return sites.length; } public Map getSitesMap() { return sitesMap; } } ================================================ FILE: src/juicebox/tools/utils/original/HiCDBUtils.java ================================================ /* * The MIT License (MIT) * * Copyright (c) 2011-2020 Broad Institute, Aiden Lab, Rice University, Baylor College of Medicine * * Permission is hereby granted, free of charge, to any person obtaining a copy * of this software and associated documentation files (the "Software"), to deal * in the Software without restriction, including without limitation the rights * to use, copy, modify, merge, publish, distribute, sublicense, and/or sell * copies of the Software, and to permit persons to whom the Software is * furnished to do so, subject to the following conditions: * * The above copyright notice and this permission notice shall be included in * all copies or substantial portions of the Software. * * THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR * IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, * FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE * AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER * LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, * OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN * THE SOFTWARE. */ package juicebox.tools.utils.original; import juicebox.HiC; import juicebox.HiCGlobals; import org.broad.igv.Globals; import org.broad.igv.util.ParsingUtils; import java.io.BufferedReader; import java.io.FileReader; import java.io.IOException; import java.io.InputStreamReader; import java.sql.*; import java.util.regex.Pattern; /** * @author jrobinso * Date: 10/29/12 * Time: 10:50 AM */ public class HiCDBUtils { private static String DB_DRIVER; private static String DB_URL; private static String DB_USER; private static String DB_PASSWORD; public static void main(String[] args) throws IOException, SQLException { String cmd = args[0]; if (HiC.valueOfUnit(cmd) == HiC.Unit.FRAG) { String f = args[1]; insertFragments(f); } else if (cmd.equals("annot")) { String f = args[1]; insertAnnotationList(f); updateFragmentAnnotations(); } else if (cmd.equals("update")) { updateFragmentAnnotations(); } else { // TODO ? throw new IOException("Command not clear"); } } private static void insertAnnotationList(String annotListFile) throws IOException, SQLException { BufferedReader reader = null; try { //reader = ParsingUtils.openBufferedReader(annotListFile); reader = new BufferedReader(new InputStreamReader(ParsingUtils.openInputStream(annotListFile)), HiCGlobals.bufferSize); String nextLine; while ((nextLine = reader.readLine()) != null) { if (!nextLine.startsWith("#")) { System.out.print("Processing " + nextLine); insertAnnotations(nextLine); System.out.println(" DONE"); } } } finally { if (reader != null) reader.close(); } } private static void insertAnnotations(String line) throws IOException, SQLException { Connection dbConnection = null; String insertAnnotationSql = "INSERT INTO IGV.ANNOTATION " + "(CHR, BEG, END, NAME, TYPE, SUBTYPE, CELL_TYPE, ALT_NAME, SCORE, ANTIBODY, SOURCE, REPLICATE, LINE) " + "VALUES (?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?)"; PreparedStatement ps = null; String[] tk = Globals.whitespacePattern.split(line); String fragmentFile = tk[0]; String celltype = tk[1]; String altname = tk[2]; String type = tk[3]; String subtype = tk[4]; String antibody = tk[5]; String source = tk[6]; String replicate = tk.length > 7 ? tk[7] : ""; BufferedReader annotationReader = null; try { //annotationReader = ParsingUtils.openBufferedReader(fragmentFile); annotationReader = new BufferedReader(new InputStreamReader(ParsingUtils.openInputStream(fragmentFile)), HiCGlobals.bufferSize); dbConnection = getDBConnection(); ps = dbConnection.prepareStatement(insertAnnotationSql); dbConnection.setAutoCommit(false); String nextLine; int count = 0; while ((nextLine = annotationReader.readLine()) != null) { String[] tokens = Globals.whitespacePattern.split(nextLine); String chr = tokens[0]; int beg = Integer.parseInt(tokens[1]); int end = Integer.parseInt(tokens[2]); String name = tokens[3]; int score = Integer.parseInt(tokens[4]); ps.setString(1, chr); ps.setInt(2, beg); ps.setInt(3, end); ps.setString(4, name); ps.setString(5, type); ps.setString(6, subtype); ps.setString(7, celltype); ps.setString(8, altname); ps.setInt(9, score); ps.setString(10, antibody); ps.setString(11, source); ps.setString(12, replicate); ps.setString(13, nextLine); ps.addBatch(); count++; if (count % 1000 == 0) { ps.executeBatch(); count = 0; } } if (count > 0) ps.executeBatch(); dbConnection.commit(); annotationReader.close(); annotationReader = null; } finally { if (ps != null) ps.close(); if (dbConnection != null) dbConnection.close(); if (annotationReader != null) annotationReader.close(); } } private static void insertFragments(String fragmentFile) throws IOException, SQLException { Connection dbConnection = null; String insertTableSQL = "INSERT INTO IGV.FRAGMENT " + "(TYPE, CHR, BEG, END, IDX) VALUES" + "(?,?,?,?, ?)"; PreparedStatement ps = null; BufferedReader fragmentReader = null; Pattern pattern = Pattern.compile("\\s"); try { fragmentReader = new BufferedReader(new FileReader(fragmentFile), HiCGlobals.bufferSize); dbConnection = getDBConnection(); ps = dbConnection.prepareStatement(insertTableSQL); dbConnection.setAutoCommit(false); String nextLine; while ((nextLine = fragmentReader.readLine()) != null) { String[] tokens = pattern.split(nextLine); // A hack, could use IGV's genome alias definitions String chr = getChrAlias(tokens[0]); System.out.println("Processing " + chr); int beg = 0; int idx = 0; for (int i = 1; i < tokens.length; i++) { int end = Integer.parseInt(tokens[i]); ps.setString(1, "MboI_5frag"); //ps.setString(1, "HindIII"); ps.setString(2, chr); ps.setInt(3, beg); ps.setInt(4, end); ps.setInt(5, idx); ps.addBatch(); beg = end; idx++; } ps.executeBatch(); } dbConnection.commit(); } finally { assert dbConnection != null; dbConnection.close(); assert fragmentReader != null; fragmentReader.close(); } } private static void updateFragmentAnnotations() throws SQLException { String selectLastSQL = "SELECT MAX(ANNOTATION_ID) FROM FRAGMENT_ANNOTATION"; String selectAnnotationSql = "SELECT ID, CHR, BEG, END FROM ANNOTATION WHERE ID > ? ORDER BY ID"; String selectFragSql = "SELECT ID FROM FRAGMENT WHERE CHR = ? and BEG <= ? and END >= ?"; String updateSQL = "INSERT INTO FRAGMENT_ANNOTATION (FRAGMENT_ID, ANNOTATION_ID) VALUES (?, ?)"; Connection dbConnection = null; PreparedStatement lastIdPrepStat = null; PreparedStatement annotPrepStat = null; PreparedStatement fragPrepStat = null; PreparedStatement updatePrepStat = null; ResultSet lastIdRS = null; ResultSet annotRS = null; ResultSet fragRS = null; try { dbConnection = getDBConnection(); dbConnection.setAutoCommit(false); annotPrepStat = dbConnection.prepareStatement(selectAnnotationSql); fragPrepStat = dbConnection.prepareStatement(selectFragSql); updatePrepStat = dbConnection.prepareStatement(updateSQL); int updateCount = 0; lastIdPrepStat = dbConnection.prepareStatement(selectLastSQL); lastIdRS = lastIdPrepStat.executeQuery(); int lastIDProcessed = 0; if (lastIdRS.next()) lastIDProcessed = lastIdRS.getInt(1); System.out.println("Last id processed = " + lastIDProcessed); annotPrepStat.setInt(1, lastIDProcessed); annotRS = annotPrepStat.executeQuery(); while (annotRS.next()) { int annotID = annotRS.getInt(1); String chr = annotRS.getString(2); int beg = annotRS.getInt(3); int end = annotRS.getInt(4); fragPrepStat.setString(1, chr); fragPrepStat.setInt(2, end); fragPrepStat.setInt(3, beg); fragRS = fragPrepStat.executeQuery(); while (fragRS.next()) { int fragID = fragRS.getInt(1); updatePrepStat.setInt(1, fragID); updatePrepStat.setInt(2, annotID); updatePrepStat.addBatch(); updateCount++; if (updateCount % 100 == 0) { //System.out.println("Updating"); updatePrepStat.executeBatch(); updateCount = 0; dbConnection.commit(); } } fragRS.close(); fragRS = null; } if (updateCount > 0) updatePrepStat.executeBatch(); dbConnection.commit(); } finally { if (annotRS != null) annotRS.close(); if (lastIdRS != null) lastIdRS.close(); if (fragRS != null) fragRS.close(); if (lastIdPrepStat != null) lastIdPrepStat.close(); if (annotPrepStat != null) annotPrepStat.close(); if (updatePrepStat != null) updatePrepStat.close(); if (fragPrepStat != null) fragPrepStat.close(); if (dbConnection != null) dbConnection.close(); } } private static Connection getDBConnection() { if (DB_DRIVER == null) { DB_DRIVER = System.getProperty("DB_DRIVER"); DB_URL = System.getProperty("DB_URL"); DB_USER = System.getProperty("DB_USER"); DB_PASSWORD = System.getProperty("DB_PASSWORD"); } Connection dbConnection = null; try { Class.forName(DB_DRIVER); } catch (ClassNotFoundException e) { System.out.println(e.getMessage()); } try { dbConnection = DriverManager.getConnection(DB_URL, DB_USER, DB_PASSWORD); //return dbConnection; } catch (SQLException e) { System.out.println(e.getMessage()); } return dbConnection; } private static String getChrAlias(String token) { if (token.equals("MT")) { return "chrM"; } else if (!token.startsWith("chr")) { return "chr" + token; } else { return token; } } } ================================================ FILE: src/juicebox/tools/utils/original/IndexEntry.java ================================================ /* * The MIT License (MIT) * * Copyright (c) 2011-2020 Broad Institute, Aiden Lab, Rice University, Baylor College of Medicine * * Permission is hereby granted, free of charge, to any person obtaining a copy * of this software and associated documentation files (the "Software"), to deal * in the Software without restriction, including without limitation the rights * to use, copy, modify, merge, publish, distribute, sublicense, and/or sell * copies of the Software, and to permit persons to whom the Software is * furnished to do so, subject to the following conditions: * * The above copyright notice and this permission notice shall be included in * all copies or substantial portions of the Software. * * THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR * IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, * FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE * AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER * LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, * OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN * THE SOFTWARE. */ package juicebox.tools.utils.original; public class IndexEntry { public final long position; public final int size; public int id; public IndexEntry(int id, long position, int size) { this.id = id; this.position = position; this.size = size; } public IndexEntry(long position, int size) { this.position = position; this.size = size; } } ================================================ FILE: src/juicebox/tools/utils/original/LargeIndexEntry.java ================================================ /* * The MIT License (MIT) * * Copyright (c) 2011-2020 Broad Institute, Aiden Lab, Rice University, Baylor College of Medicine * * Permission is hereby granted, free of charge, to any person obtaining a copy * of this software and associated documentation files (the "Software"), to deal * in the Software without restriction, including without limitation the rights * to use, copy, modify, merge, publish, distribute, sublicense, and/or sell * copies of the Software, and to permit persons to whom the Software is * furnished to do so, subject to the following conditions: * * The above copyright notice and this permission notice shall be included in * all copies or substantial portions of the Software. * * THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR * IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, * FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE * AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER * LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, * OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN * THE SOFTWARE. */ package juicebox.tools.utils.original; public class LargeIndexEntry { public final long position; public final long size; int id; LargeIndexEntry(int id, long position, long size) { this.id = id; this.position = position; this.size = size; } public LargeIndexEntry(long position, long size) { this.position = position; this.size = size; } } ================================================ FILE: src/juicebox/tools/utils/original/MTIndexHandler.java ================================================ /* * The MIT License (MIT) * * Copyright (c) 2011-2021 Broad Institute, Aiden Lab, Rice University, Baylor College of Medicine * * Permission is hereby granted, free of charge, to any person obtaining a copy * of this software and associated documentation files (the "Software"), to deal * in the Software without restriction, including without limitation the rights * to use, copy, modify, merge, publish, distribute, sublicense, and/or sell * copies of the Software, and to permit persons to whom the Software is * furnished to do so, subject to the following conditions: * * The above copyright notice and this permission notice shall be included in * all copies or substantial portions of the Software. * * THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR * IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, * FITNESS FOR A PARTICULAR PURPOSE AND NON-INFRINGEMENT. IN NO EVENT SHALL THE * AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER * LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, * OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN * THE SOFTWARE. */ package juicebox.tools.utils.original; import juicebox.HiCGlobals; import juicebox.data.ChromosomeHandler; import java.io.BufferedReader; import java.io.FileInputStream; import java.io.InputStreamReader; import java.util.ArrayList; import java.util.HashMap; import java.util.List; import java.util.Map; import java.util.concurrent.ConcurrentHashMap; public class MTIndexHandler { public static Map> readMndIndex(String mndIndexFile, Map chromosomePairIndexes) { FileInputStream is = null; Map> tempIndex = new HashMap<>(); Map> mndIndex = new ConcurrentHashMap<>(); try { is = new FileInputStream(mndIndexFile); BufferedReader reader = new BufferedReader(new InputStreamReader(is), HiCGlobals.bufferSize); String nextLine; while ((nextLine = reader.readLine()) != null) { String[] nextEntry = nextLine.split(","); if (nextEntry.length == 4) { // todo should probably just check if tempIndex.contains(nextEntry[0]) if (tempIndex.get(nextEntry[0]) == null) { tempIndex.put(nextEntry[0], new ArrayList<>()); } Chunk indexEntry = new Chunk(nextEntry[2], nextEntry[3]); tempIndex.get(nextEntry[0]).add(indexEntry); } else { System.err.println("Improperly formatted merged nodups index: " + nextLine); System.exit(70); } } if (tempIndex.isEmpty()) { System.err.println("Intermediate MNDIndex is empty or could not be read"); System.exit(44); } } catch (Exception e) { System.err.println("Unable to read merged nodups index"); System.exit(70); } for (Map.Entry entry : chromosomePairIndexes.entrySet()) { String reverseName = entry.getValue().split("-")[1] + "-" + entry.getValue().split("-")[0]; if (tempIndex.containsKey(entry.getValue())) { mndIndex.put(entry.getKey(), tempIndex.get(entry.getValue())); } else if (tempIndex.containsKey(reverseName)) { mndIndex.put(entry.getKey(), tempIndex.get(reverseName)); } else if (!reverseName.equalsIgnoreCase("all")) { System.err.println("Unable to find " + entry.getValue() + " or " + reverseName); } } if (mndIndex.isEmpty()) { System.err.println("MNDIndex is empty or could not be read"); System.exit(43); } return mndIndex; } public static Map populateChromosomeIndexes(ChromosomeHandler chromosomeHandler, int numCPUThreads) { Map chromosomeIndexes = new ConcurrentHashMap<>(chromosomeHandler.size(), 0.75f, numCPUThreads); for (int i = 0; i < chromosomeHandler.size(); i++) { chromosomeIndexes.put(chromosomeHandler.getChromosomeFromIndex(i).getName(), i); } return chromosomeIndexes; } public static int populateChromosomePairIndexes(ChromosomeHandler chromosomeHandler, Map chromosomePairIndexes, Map chromosomePairIndexesReverse, Map chromosomePairIndex1, Map chromosomePairIndex2) { int chromosomePairCounter = 0; String genomeWideName = chromosomeHandler.getChromosomeFromIndex(0).getName(); String genomeWidePairName = genomeWideName + "-" + genomeWideName; chromosomePairIndexes.put(chromosomePairCounter, genomeWidePairName); chromosomePairIndexesReverse.put(genomeWidePairName, chromosomePairCounter); chromosomePairIndex1.put(chromosomePairCounter, 0); chromosomePairIndex2.put(chromosomePairCounter, 0); chromosomePairCounter++; for (int i = 1; i < chromosomeHandler.size(); i++) { for (int j = i; j < chromosomeHandler.size(); j++) { String c1Name = chromosomeHandler.getChromosomeFromIndex(i).getName(); String c2Name = chromosomeHandler.getChromosomeFromIndex(j).getName(); String chromosomePairName = c1Name + "-" + c2Name; chromosomePairIndexes.put(chromosomePairCounter, chromosomePairName); chromosomePairIndexesReverse.put(chromosomePairName, chromosomePairCounter); chromosomePairIndex1.put(chromosomePairCounter, i); chromosomePairIndex2.put(chromosomePairCounter, j); chromosomePairCounter++; } } return chromosomePairCounter; } } ================================================ FILE: src/juicebox/tools/utils/original/MatrixPP.java ================================================ /* * The MIT License (MIT) * * Copyright (c) 2011-2021 Broad Institute, Aiden Lab, Rice University, Baylor College of Medicine * * Permission is hereby granted, free of charge, to any person obtaining a copy * of this software and associated documentation files (the "Software"), to deal * in the Software without restriction, including without limitation the rights * to use, copy, modify, merge, publish, distribute, sublicense, and/or sell * copies of the Software, and to permit persons to whom the Software is * furnished to do so, subject to the following conditions: * * The above copyright notice and this permission notice shall be included in * all copies or substantial portions of the Software. * * THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR * IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, * FITNESS FOR A PARTICULAR PURPOSE AND NON-INFRINGEMENT. IN NO EVENT SHALL THE * AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER * LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, * OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN * THE SOFTWARE. */ package juicebox.tools.utils.original; import juicebox.HiC; import juicebox.data.ChromosomeHandler; import juicebox.data.ContactRecord; import juicebox.data.basics.Chromosome; import juicebox.windowui.HiCZoom; import java.io.File; import java.io.IOException; import java.util.Map; public class MatrixPP { private static final int INTRA_CUTOFF = 500; private static final int INTER_CUTOFF = 5000; private final int MAX_SQRT = (int) Math.sqrt(Integer.MAX_VALUE); private final int chr1Idx; private final int chr2Idx; private final MatrixZoomDataPP[] zoomData; /** * Constructor for creating a matrix and initializing zoomed data at predefined resolution scales. This * constructor is used when parsing alignment files. * c * * @param chr1Idx Chromosome 1 * @param chromosomeHandler * @param bpBinSizes * @param fragmentCalculation * @param fragBinSizes * @param chr2Idx Chromosome 2 */ public MatrixPP(int chr1Idx, int chr2Idx, ChromosomeHandler chromosomeHandler, int[] bpBinSizes, FragmentCalculation fragmentCalculation, int[] fragBinSizes, int countThreshold, int v9DepthBase, int BLOCK_CAPACITY) { this.chr1Idx = chr1Idx; this.chr2Idx = chr2Idx; int nResolutions = bpBinSizes.length; if (fragmentCalculation != null) { nResolutions += fragBinSizes.length; } zoomData = new MatrixZoomDataPP[nResolutions]; int zoom = 0; // for (int idx = 0; idx < bpBinSizes.length; idx++) { int binSize = bpBinSizes[zoom]; Chromosome chrom1 = chromosomeHandler.getChromosomeFromIndex(chr1Idx); Chromosome chrom2 = chromosomeHandler.getChromosomeFromIndex(chr2Idx); // Size block (submatrices) to be ~500 bins wide. long len = Math.max(chrom1.getLength(), chrom2.getLength()); // for now, this will not be a long int nBins = (int) (len / binSize + 1); // Size of chrom in bins int nColumns; if (chrom1.equals(chrom2)) { nColumns = getNumColumnsFromNumBins(nBins, binSize, INTRA_CUTOFF); } else { nColumns = getNumColumnsFromNumBins(nBins, binSize, INTER_CUTOFF); } zoomData[idx] = new MatrixZoomDataPP(chrom1, chrom2, binSize, nColumns, zoom, false, fragmentCalculation, countThreshold, v9DepthBase, BLOCK_CAPACITY); zoom++; } if (fragmentCalculation != null) { Chromosome chrom1 = chromosomeHandler.getChromosomeFromIndex(chr1Idx); Chromosome chrom2 = chromosomeHandler.getChromosomeFromIndex(chr2Idx); int nFragBins1 = Math.max(fragmentCalculation.getNumberFragments(chrom1.getName()), fragmentCalculation.getNumberFragments(chrom2.getName())); zoom = 0; for (int idx = bpBinSizes.length; idx < nResolutions; idx++) { int binSize = fragBinSizes[zoom]; int nBins = nFragBins1 / binSize + 1; int nColumns = getNumColumnsFromNumBins(nBins, binSize, 0); zoomData[idx] = new MatrixZoomDataPP(chrom1, chrom2, binSize, nColumns, zoom, true, fragmentCalculation, countThreshold, v9DepthBase); zoom++; } } } private int getNumColumnsFromNumBins(int nBins, int binSize, int cutoff) { int nColumns = nBins / Preprocessor.BLOCK_SIZE + 1; if (binSize < cutoff) { long numerator = (long) nBins * binSize; long denominator = (long) Preprocessor.BLOCK_SIZE * cutoff; nColumns = (int) (numerator / denominator) + 1; } return Math.min(nColumns, MAX_SQRT - 1); } /** * Constructor for creating a matrix with a single zoom level at a specified bin size. This is provided * primarily for constructing a whole-genome view. * * @param chr1Idx Chromosome 1 * @param chr2Idx Chromosome 2 * @param binSize Bin size */ MatrixPP(int chr1Idx, int chr2Idx, int binSize, int blockColumnCount, ChromosomeHandler chromosomeHandler, FragmentCalculation fragmentCalculation, int countThreshold, int v9DepthBase) { this.chr1Idx = chr1Idx; this.chr2Idx = chr2Idx; zoomData = new MatrixZoomDataPP[1]; zoomData[0] = new MatrixZoomDataPP(chromosomeHandler.getChromosomeFromIndex(chr1Idx), chromosomeHandler.getChromosomeFromIndex(chr2Idx), binSize, blockColumnCount, 0, false, fragmentCalculation, countThreshold, v9DepthBase); } String getKey() { return "" + chr1Idx + "_" + chr2Idx; } void incrementCount(int pos1, int pos2, int frag1, int frag2, float score, Map expectedValueCalculations, File tmpDir) throws IOException { for (MatrixZoomDataPP aZoomData : zoomData) { if (aZoomData.isFrag) { aZoomData.incrementCount(frag1, frag2, score, expectedValueCalculations, tmpDir); } else { aZoomData.incrementCount(pos1, pos2, score, expectedValueCalculations, tmpDir); } } } public void incrementCount(ContactRecord cr, Map expectedValueCalculations, File tmpDir, HiCZoom zoom) throws IOException { for (MatrixZoomDataPP aZoomData : zoomData) { if (aZoomData.isFrag && zoom.getUnit().equals(HiC.Unit.FRAG)) { aZoomData.incrementCount(cr, expectedValueCalculations, tmpDir, zoom); } else if (!aZoomData.isFrag && zoom.getUnit().equals(HiC.Unit.BP)) { aZoomData.incrementCount(cr, expectedValueCalculations, tmpDir, zoom); } } } public void parsingComplete() { for (MatrixZoomDataPP zd : zoomData) { if (zd != null) // fragment level could be null zd.parsingComplete(); } } int getChr1Idx() { return chr1Idx; } int getChr2Idx() { return chr2Idx; } MatrixZoomDataPP[] getZoomData() { return zoomData; } /** * used by multithreaded code */ public void mergeMatrices(MatrixPP otherMatrix) { if (otherMatrix != null) { for (MatrixZoomDataPP aZoomData : zoomData) { for (MatrixZoomDataPP bZoomData : otherMatrix.zoomData) { if (aZoomData.getZoom() == bZoomData.getZoom()) { aZoomData.mergeMatrices(bZoomData); } } } } } } ================================================ FILE: src/juicebox/tools/utils/original/MatrixZoomDataPP.java ================================================ /* * The MIT License (MIT) * * Copyright (c) 2011-2022 Broad Institute, Aiden Lab, Rice University, Baylor College of Medicine * * Permission is hereby granted, free of charge, to any person obtaining a copy * of this software and associated documentation files (the "Software"), to deal * in the Software without restriction, including without limitation the rights * to use, copy, modify, merge, publish, distribute, sublicense, and/or sell * copies of the Software, and to permit persons to whom the Software is * furnished to do so, subject to the following conditions: * * The above copyright notice and this permission notice shall be included in * all copies or substantial portions of the Software. * * THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR * IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, * FITNESS FOR A PARTICULAR PURPOSE AND NON-INFRINGEMENT. IN NO EVENT SHALL THE * AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER * LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, * OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN * THE SOFTWARE. */ package juicebox.tools.utils.original; import htsjdk.tribble.util.LittleEndianInputStream; import htsjdk.tribble.util.LittleEndianOutputStream; import juicebox.HiC; import juicebox.HiCGlobals; import juicebox.data.ContactRecord; import juicebox.data.basics.Chromosome; import juicebox.data.v9depth.V9Depth; import juicebox.windowui.HiCZoom; import org.apache.commons.math3.stat.descriptive.DescriptiveStatistics; import org.broad.igv.tdf.BufferedByteWriter; import org.broad.igv.util.collections.DownsampledDoubleArrayList; import java.awt.*; import java.io.*; import java.util.List; import java.util.*; import java.util.concurrent.ConcurrentHashMap; import java.util.concurrent.ExecutorService; import java.util.concurrent.Executors; import java.util.zip.Deflater; public class MatrixZoomDataPP { final boolean isFrag; final Set blockNumbers; // The only reason for this is to get a count final ConcurrentHashMap blockNumRecords; final List tmpFiles; final Map> tmpFilesByBlockNumber; private final Chromosome chr1; // Redundant, but convenient BinDatasetReader private final Chromosome chr2; // Redundant, but convenient private final int zoom; private final int binSize; // bin size in bp private final int blockBinCount; // block size in bins private final int blockColumnCount; // number of block columns private final LinkedHashMap blocks; private final int countThreshold; long blockIndexPosition; private double sum = 0; private double numRecords = 0; private double cellCount = 0; private double percent5; private double percent95; private int BLOCK_CAPACITY = 1000; private final V9Depth v9Depth; /** * Representation of MatrixZoomData used for preprocessing * * @param chr1 index of first chromosome (x-axis) * @param chr2 index of second chromosome * @param binSize size of each grid bin in bp * @param blockColumnCount number of block columns * @param zoom integer zoom (resolution) level index. TODO Is this needed? */ MatrixZoomDataPP(Chromosome chr1, Chromosome chr2, int binSize, int blockColumnCount, int zoom, boolean isFrag, FragmentCalculation fragmentCalculation, int countThreshold, int v9BaseDepth) { this.tmpFiles = new ArrayList<>(); this.tmpFilesByBlockNumber = new ConcurrentHashMap<>(); this.blockNumbers = Collections.synchronizedSet(new HashSet<>(BLOCK_CAPACITY)); this.blockNumRecords = new ConcurrentHashMap<>(BLOCK_CAPACITY); this.countThreshold = countThreshold; this.chr1 = chr1; this.chr2 = chr2; this.binSize = binSize; this.blockColumnCount = blockColumnCount; this.zoom = zoom; this.isFrag = isFrag; // Get length in proper units Chromosome longChr = chr1.getLength() > chr2.getLength() ? chr1 : chr2; long len = isFrag ? fragmentCalculation.getNumberFragments(longChr.getName()) : longChr.getLength(); int nBinsX = (int) (len / binSize + 1); blockBinCount = nBinsX / blockColumnCount + 1; blocks = new LinkedHashMap<>(blockColumnCount); v9Depth = V9Depth.setDepthMethod(v9BaseDepth, blockBinCount); } MatrixZoomDataPP(Chromosome chr1, Chromosome chr2, int binSize, int blockColumnCount, int zoom, boolean isFrag, FragmentCalculation fragmentCalculation, int countThreshold, int v9BaseDepth, int BLOCK_CAPACITY) { this.tmpFiles = new ArrayList<>(); this.tmpFilesByBlockNumber = new ConcurrentHashMap<>(); this.BLOCK_CAPACITY = BLOCK_CAPACITY; this.blockNumbers = Collections.synchronizedSet(new HashSet<>(BLOCK_CAPACITY)); this.blockNumRecords = new ConcurrentHashMap<>(BLOCK_CAPACITY); this.countThreshold = countThreshold; this.chr1 = chr1; this.chr2 = chr2; this.binSize = binSize; this.blockColumnCount = blockColumnCount; this.zoom = zoom; this.isFrag = isFrag; // Get length in proper units Chromosome longChr = chr1.getLength() > chr2.getLength() ? chr1 : chr2; long len = isFrag ? fragmentCalculation.getNumberFragments(longChr.getName()) : longChr.getLength(); int nBinsX = (int) (len / binSize + 1); blockBinCount = nBinsX / blockColumnCount + 1; blocks = new LinkedHashMap<>(blockColumnCount); v9Depth = V9Depth.setDepthMethod(v9BaseDepth, blockBinCount); } HiC.Unit getUnit() { return isFrag ? HiC.Unit.FRAG : HiC.Unit.BP; } double getSum() { return sum; } double getOccupiedCellCount() { return cellCount; } double getPercent95() { return percent95; } double getPercent5() { return percent5; } int getBinSize() { return binSize; } Chromosome getChr1() { return chr1; } Chromosome getChr2() { return chr2; } int getZoom() { return zoom; } int getBlockBinCount() { return blockBinCount; } int getBlockColumnCount() { return blockColumnCount; } Map getBlocks() { return blocks; } /** * Increment the count for the bin represented by the GENOMIC position (pos1, pos2) */ void incrementCount(int pos1, int pos2, float score, Map expectedValueCalculations, File tmpDir) throws IOException { sum += score; // Convert to proper units, fragments or base-pairs if (pos1 < 0 || pos2 < 0) return; int xBin = pos1 / binSize; int yBin = pos2 / binSize; int blockNumber; // Intra chromosome -- we'll store lower diagonal only if (chr1.equals(chr2)) { int b1 = Math.min(xBin, yBin); int b2 = Math.max(xBin, yBin); xBin = b1; yBin = b2; if (b1 != b2) { sum += score; // <= count for mirror cell. } if (expectedValueCalculations != null) { String evKey = (isFrag ? "FRAG_" : "BP_") + binSize; ExpectedValueCalculation ev = expectedValueCalculations.get(evKey); if (ev != null) { ev.addDistance(chr1.getIndex(), xBin, yBin, score); } } //compute intra chromosomal block number (version 9 and up) int depth = v9Depth.getDepth(xBin, yBin); int positionAlongDiagonal = ((xBin + yBin) / 2 / blockBinCount); blockNumber = depth * blockColumnCount + positionAlongDiagonal; } else { // compute interchromosomal block number (version 9 and up, first block is zero) int blockCol = xBin / blockBinCount; int blockRow = yBin / blockBinCount; blockNumber = blockColumnCount * blockRow + blockCol; } BlockPP block = blocks.get(blockNumber); if (block == null) { block = new BlockPP(blockNumber); blocks.put(blockNumber, block); } block.incrementCount(xBin, yBin, score); // If too many blocks write to tmp directory if (blocks.size() > BLOCK_CAPACITY) { File tmpfile = tmpDir == null ? File.createTempFile("blocks", "bin") : File.createTempFile("blocks", "bin", tmpDir); //System.out.println(chr1.getName() + "-" + chr2.getName() + " Dumping blocks to " + tmpfile.getAbsolutePath()); dumpBlocks(tmpfile); tmpFiles.add(tmpfile); tmpfile.deleteOnExit(); } } /** * Increment the count for the bin represented by the CONTACT RECORD for a given ZOOM */ public void incrementCount(ContactRecord cr, Map expectedValueCalculations, File tmpDir, HiCZoom recordZoom) throws IOException { float score = cr.getCounts(); sum += score; // Convert to proper units, fragments or base-pairs if (cr.getBinX() < 0 || cr.getBinY() < 0) return; if (recordZoom.getBinSize() > binSize) return; //if (binSize % recordZoom.getBinSize() > 0) return; float rescale = (float) binSize / (float) recordZoom.getBinSize(); float thresholdX; float thresholdY; Random generator = new Random(0); int xBin; int yBin; if ( binSize % recordZoom.getBinSize() == 0) { xBin = (int) ((float) cr.getBinX() / rescale); yBin = (int) ((float) cr.getBinY() / rescale); } else { if ((int) ((float) cr.getBinX() / rescale) == (int) ((float) cr.getBinX()+1 / rescale)) { xBin = (int) ((float) cr.getBinX() / rescale); } else { thresholdX = ((int) ((float) cr.getBinX() / rescale) + 1) * rescale - cr.getBinX(); if (generator.nextFloat() < thresholdX) { xBin = (int) ((float) cr.getBinX() / rescale); } else { xBin = (int) ((float) cr.getBinX() / rescale) + 1; } } if ((int) ((float) cr.getBinY() / rescale) == (int) ((float) cr.getBinY()+1 / rescale)) { yBin = (int) ((float) cr.getBinY() / rescale); } else { thresholdY = ((int) ((float) cr.getBinY() / rescale) + 1) * rescale - cr.getBinY(); if (generator.nextFloat() < thresholdY) { yBin = (int) ((float) cr.getBinY() / rescale); } else { yBin = (int) ((float) cr.getBinY() / rescale) + 1; } } } int blockNumber; // Intra chromosome -- we'll store lower diagonal only if (chr1.equals(chr2)) { int b1 = Math.min(xBin, yBin); int b2 = Math.max(xBin, yBin); xBin = b1; yBin = b2; if (b1 != b2) { sum += score; // <= count for mirror cell. } if (expectedValueCalculations != null) { String evKey = (isFrag ? "FRAG_" : "BP_") + binSize; ExpectedValueCalculation ev = expectedValueCalculations.get(evKey); if (ev != null) { ev.addDistance(chr1.getIndex(), xBin, yBin, score); } } //compute intra chromosomal block number (version 9 and up) int depth = v9Depth.getDepth(xBin, yBin); int positionAlongDiagonal = ((xBin + yBin) / 2 / blockBinCount); blockNumber = depth * blockColumnCount + positionAlongDiagonal; } else { // compute interchromosomal block number (version 9 and up, first block is zero) int blockCol = xBin / blockBinCount; int blockRow = yBin / blockBinCount; blockNumber = blockColumnCount * blockRow + blockCol; } BlockPP block = blocks.get(blockNumber); if (block == null) { block = new BlockPP(blockNumber); blocks.put(blockNumber, block); } block.incrementCount(xBin, yBin, score); // If too many blocks write to tmp directory if (blocks.size() > BLOCK_CAPACITY) { File tmpfile = tmpDir == null ? File.createTempFile("blocks", "bin") : File.createTempFile("blocks", "bin", tmpDir); //System.out.println(chr1.getName() + "-" + chr2.getName() + " Dumping blocks to " + tmpfile.getAbsolutePath()); dumpBlocks(tmpfile); tmpFiles.add(tmpfile); tmpfile.deleteOnExit(); } } /** * Dump the blocks calculated so far to a temporary file * * @param file File to write to * @throws IOException */ private void dumpBlocks(File file) throws IOException { LittleEndianOutputStream los = null; try { if (HiCGlobals.printVerboseComments) { System.err.println("Used Memory prior to dumping blocks " + binSize); System.err.println(Runtime.getRuntime().totalMemory() - Runtime.getRuntime().freeMemory()); } los = new LittleEndianOutputStream(new BufferedOutputStream(new FileOutputStream(file), 4194304)); List blockList = new ArrayList<>(blocks.values()); Collections.sort(blockList, new Comparator() { @Override public int compare(BlockPP o1, BlockPP o2) { return o1.getNumber() - o2.getNumber(); } }); for (BlockPP b : blockList) { // Remove from map blocks.remove(b.getNumber()); int number = b.getNumber(); blockNumbers.add(number); if (!blockNumRecords.containsKey(number)) { blockNumRecords.put(number, b.getNumRecords()); } else { blockNumRecords.put(number, blockNumRecords.get(number)+b.getNumRecords()); } numRecords += b.getNumRecords(); if (tmpFilesByBlockNumber.get(number)==null) { tmpFilesByBlockNumber.put(number, new ConcurrentHashMap<>()); } tmpFilesByBlockNumber.get(number).put(file, los.getWrittenCount()); los.writeInt(number); Map records = b.getContactRecordMap(); los.writeInt(records.size()); for (Map.Entry entry : records.entrySet()) { Point point = entry.getKey(); ContactCount count = entry.getValue(); los.writeInt(point.x); los.writeInt(point.y); los.writeFloat(count.getCounts()); } b.clear(); } blocks.clear(); if (HiCGlobals.printVerboseComments) { System.err.println("Used Memory after dumping blocks " + binSize); System.err.println(Runtime.getRuntime().totalMemory() - Runtime.getRuntime().freeMemory()); } } finally { if (los != null) los.close(); } } // Merge and write out blocks one at a time. protected List mergeAndWriteBlocks(LittleEndianOutputStream los, Deflater compressor) throws IOException { DownsampledDoubleArrayList sampledData = new DownsampledDoubleArrayList(10000, 10000); List activeList = new ArrayList<>(); // Initialize queues -- first whatever is left over in memory if (blocks.size() > 0) { BlockQueue bqInMem = new BlockQueueMem(blocks.values()); activeList.add(bqInMem); } // Now from files for (File file : tmpFiles) { BlockQueue bq = new BlockQueueFB(file); if (bq.getBlock() != null) { activeList.add(bq); } } List indexEntries = new ArrayList<>(); if (activeList.size() == 0) { throw new RuntimeException("No reads in Hi-C contact matrices. This could be because the MAPQ filter is set too high (-q) or because all reads map to the same fragment."); } do { activeList.sort(new Comparator() { @Override public int compare(BlockQueue o1, BlockQueue o2) { return o1.getBlock().getNumber() - o2.getBlock().getNumber(); } }); BlockQueue topQueue = activeList.get(0); BlockPP currentBlock = topQueue.getBlock(); topQueue.advance(); int num = currentBlock.getNumber(); for (int i = 1; i < activeList.size(); i++) { BlockQueue blockQueue = activeList.get(i); BlockPP block = blockQueue.getBlock(); if (block.getNumber() == num) { currentBlock.merge(block); blockQueue.advance(); } } Iterator iterator = activeList.iterator(); while (iterator.hasNext()) { if (iterator.next().getBlock() == null) { iterator.remove(); } } // Output block long position = los.getWrittenCount(); writeBlock(currentBlock, sampledData, los, compressor); long size = los.getWrittenCount() - position; indexEntries.add(new IndexEntry(num, position, (int) size)); } while (activeList.size() > 0); for (File f : tmpFiles) { boolean result = f.delete(); if (!result) { System.out.println("Error while deleting file"); } } computeStats(sampledData); return indexEntries; } // Merge and write out blocks multithreaded. protected List mergeAndWriteBlocks(LittleEndianOutputStream[] losArray, Deflater compressor, int whichZoom, int numResolutions) { DownsampledDoubleArrayList sampledData = new DownsampledDoubleArrayList(10000, 10000); Integer[] sortedBlockNumbers = new Integer[blockNumbers.size()]; blockNumbers.toArray(sortedBlockNumbers); Arrays.sort(sortedBlockNumbers); int numCPUThreads = (losArray.length - 1) / numResolutions; ExecutorService executor = Executors.newFixedThreadPool(numCPUThreads); Map blockChunkSizes = new ConcurrentHashMap<>(numCPUThreads); Map> chunkBlockIndexes = new ConcurrentHashMap<>(numCPUThreads); int startBlock =0, endBlock = 0; for (int l = 0; l < numCPUThreads; l++) { final int threadNum = l; final int whichLos = numCPUThreads * whichZoom + threadNum; final int numOfRecordsPerThread = 2 * (int) Math.floor(numRecords / numCPUThreads); final int maxNumOfBlocksPerThread = (int) Math.floor((double) sortedBlockNumbers.length / numCPUThreads); if (l>0) { startBlock = endBlock; } int numOfRecords = 0; for (int i = startBlock; i < sortedBlockNumbers.length; i++) { numOfRecords += blockNumRecords.get(sortedBlockNumbers[i]); if (numOfRecords > numOfRecordsPerThread || i - startBlock > maxNumOfBlocksPerThread) { endBlock = i; // i always less than sortedBlockNumbers.length from for loop //endBlock = Math.min(i, sortedBlockNumbers.length); break; } } if (l + 1 == numCPUThreads && endBlock < sortedBlockNumbers.length) { endBlock = sortedBlockNumbers.length; } //System.err.println(binSize + " " + blockNumbers.size() + " " + sortedBlockNumbers.length + " " + startBlock + " " + endBlock); if (startBlock >= endBlock) { blockChunkSizes.put(threadNum,(long) 0); continue; } final Integer[] threadBlocks = Arrays.copyOfRange(sortedBlockNumbers, startBlock, endBlock); final LinkedHashMap threadSafeBlocks = new LinkedHashMap(blocks); List indexEntries = new ArrayList<>(); Runnable worker = new Runnable() { @Override public void run() { try { writeBlockChunk(threadBlocks, threadSafeBlocks, losArray, whichLos, indexEntries, sampledData); threadSafeBlocks.clear(); } catch (Exception e) { e.printStackTrace(); } chunkBlockIndexes.put(whichLos,indexEntries); } }; executor.execute(worker); } executor.shutdown(); blocks.clear(); // Wait until all threads finish while (!executor.isTerminated()) { try { Thread.sleep(50); } catch (InterruptedException e) { System.err.println(e.getLocalizedMessage()); } } long adjust = 0; for (int i = 0; i < losArray.length; i++) { blockChunkSizes.put(i, losArray[i].getWrittenCount()); if (i < numCPUThreads*whichZoom) { adjust += blockChunkSizes.get(i); } } List finalIndexEntries = new ArrayList<>(); for (int i = numCPUThreads*whichZoom ; i < numCPUThreads * (whichZoom + 1); i++) { adjust += blockChunkSizes.get(i); if (chunkBlockIndexes.get(i) != null) { for (int j = 0; j < chunkBlockIndexes.get(i).size(); j++) { finalIndexEntries.add(new IndexEntry(chunkBlockIndexes.get(i).get(j).id, chunkBlockIndexes.get(i).get(j).position + adjust, chunkBlockIndexes.get(i).get(j).size)); } } } for (File f : tmpFiles) { boolean result = f.delete(); if (!result) { System.out.println("Error while deleting file"); } } if (HiCGlobals.printVerboseComments) { System.err.println("Used Memory after writing zoom"); System.err.println(Runtime.getRuntime().totalMemory() - Runtime.getRuntime().freeMemory()); } computeStats(sampledData); return finalIndexEntries; } private void writeBlockChunk(Integer[] threadBlocks, Map threadSafeBlocks,LittleEndianOutputStream[] losArray, int threadNum, List indexEntries, DownsampledDoubleArrayList sampledData ) throws IOException{ Deflater compressor = new Deflater(); compressor.setLevel(Deflater.DEFAULT_COMPRESSION); //System.err.println(threadBlocks.length); for (int i = 0; i < threadBlocks.length; i++) { BlockPP currentBlock = null; int num = threadBlocks[i]; if (threadSafeBlocks.get(num) != null ){ currentBlock = threadSafeBlocks.get(num); threadSafeBlocks.remove(num); if (tmpFilesByBlockNumber.get(num) != null) { for (Map.Entry entry : tmpFilesByBlockNumber.get(num).entrySet()) { readAndMerge(currentBlock, entry); } } } else if (tmpFilesByBlockNumber.get(num) != null) { Iterator> iter = tmpFilesByBlockNumber.get(num).entrySet().iterator(); if (iter.hasNext()) { Map.Entry firstEntry = iter.next(); currentBlock = readTmpBlock(firstEntry.getKey(), firstEntry.getValue()); if (currentBlock != null) { while (iter.hasNext()) { readAndMerge(currentBlock, iter.next()); } } } } if (currentBlock != null) { long position = losArray[threadNum + 1].getWrittenCount(); writeBlock(currentBlock, sampledData, losArray[threadNum + 1], compressor); long size = losArray[threadNum + 1].getWrittenCount() - position; indexEntries.add(new IndexEntry(num, position, (int) size)); } currentBlock.clear(); if (HiCGlobals.printVerboseComments) { System.err.println("Used Memory after writing block " + i); System.err.println(Runtime.getRuntime().totalMemory() - Runtime.getRuntime().freeMemory()); } } threadSafeBlocks.clear(); } private void readAndMerge(BlockPP currentBlock, Map.Entry entry) throws IOException { BlockPP tmpBlock = readTmpBlock(entry.getKey(), entry.getValue()); if (tmpBlock != null) { currentBlock.merge(tmpBlock); } } private BlockPP readTmpBlock(File file, long filePosition) throws IOException { if (filePosition >= file.length()) { return null; } FileInputStream fis = null; try { fis = new FileInputStream(file); fis.getChannel().position(filePosition); LittleEndianInputStream lis = new LittleEndianInputStream(fis); int blockNumber = lis.readInt(); int nRecords = lis.readInt(); byte[] bytes = new byte[nRecords * 12]; int len = bytes.length; if (len < 0) throw new IndexOutOfBoundsException(); int n = 0; while (n < len) { int count = fis.read(bytes, n, len - n); if (count < 0) throw new EOFException(); n += count; } ByteArrayInputStream bis = new ByteArrayInputStream(bytes); lis = new LittleEndianInputStream(bis); Map contactRecordMap = new HashMap<>(nRecords); for (int i = 0; i < nRecords; i++) { int x = lis.readInt(); int y = lis.readInt(); float v = lis.readFloat(); ContactCount rec = new ContactCount(v); contactRecordMap.put(new Point(x, y), rec); } return new BlockPP(blockNumber, contactRecordMap); } finally { if (fis != null) fis.close(); } } private void computeStats(DownsampledDoubleArrayList sampledData) { DescriptiveStatistics stats = new DescriptiveStatistics(sampledData.toArray()); this.percent5 = stats.getPercentile(5); this.percent95 = stats.getPercentile(95); } void parsingComplete() { // Add the block numbers still in memory for (BlockPP block : blocks.values()) { int number = block.getNumber(); blockNumbers.add(number); if (!blockNumRecords.containsKey(number)) { blockNumRecords.put(number, block.getNumRecords()); } else { blockNumRecords.put(number, blockNumRecords.get(number)+block.getNumRecords()); } numRecords += block.getNumRecords(); } } /** * used by multithreaded code * * @param otherMatrixZoom */ void mergeMatrices(MatrixZoomDataPP otherMatrixZoom) { sum += otherMatrixZoom.sum; numRecords += otherMatrixZoom.numRecords; for (Map.Entry otherBlock : otherMatrixZoom.blocks.entrySet()) { int blockNumber = otherBlock.getKey(); BlockPP block = blocks.get(blockNumber); if (block == null) { blocks.put(blockNumber, otherBlock.getValue()); blockNumbers.add(blockNumber); } else { block.merge(otherBlock.getValue()); blockNumRecords.put(blockNumber, block.getNumRecords()); } } for (int blockNumber : otherMatrixZoom.blockNumbers) { blockNumbers.add(blockNumber); if (!blockNumRecords.containsKey(blockNumber)) { blockNumRecords.put(blockNumber, otherMatrixZoom.blockNumRecords.get(blockNumber)); } else { blockNumRecords.put(blockNumber, blockNumRecords.get(blockNumber) + otherMatrixZoom.blockNumRecords.get(blockNumber)); } } tmpFiles.addAll(otherMatrixZoom.tmpFiles); for (Map.Entry> entry : otherMatrixZoom.tmpFilesByBlockNumber.entrySet()) { if (!tmpFilesByBlockNumber.containsKey(entry.getKey())) { tmpFilesByBlockNumber.put(entry.getKey(), entry.getValue()); } else { for (Map.Entry tmpFile : entry.getValue().entrySet()) { tmpFilesByBlockNumber.get(entry.getKey()).put(tmpFile.getKey(), tmpFile.getValue()); } } } //System.err.println(binSize + " " + blockNumbers.size() + " " + otherMatrixZoom.blockNumbers.size()); } /** * Note -- compressed * * @param block Block to write * @param sampledData Array to hold a sample of the data (to compute statistics) * @throws IOException */ protected void writeBlock(BlockPP block, DownsampledDoubleArrayList sampledData, LittleEndianOutputStream los, Deflater compressor) throws IOException { final Map records = block.getContactRecordMap();// getContactRecords(); // System.out.println("Write contact records : records count = " + records.size()); // Count records first int nRecords; if (countThreshold > 0) { nRecords = 0; for (ContactCount rec : records.values()) { if (rec.getCounts() >= countThreshold) { nRecords++; } } } else { nRecords = records.size(); } BufferedByteWriter buffer = new BufferedByteWriter(nRecords * 12); buffer.putInt(nRecords); incrementCellCount(nRecords); // Find extents of occupied cells int binXOffset = Integer.MAX_VALUE; int binYOffset = Integer.MAX_VALUE; int binXMax = 0; int binYMax = 0; for (Map.Entry entry : records.entrySet()) { Point point = entry.getKey(); binXOffset = Math.min(binXOffset, point.x); binYOffset = Math.min(binYOffset, point.y); binXMax = Math.max(binXMax, point.x); binYMax = Math.max(binYMax, point.y); } buffer.putInt(binXOffset); buffer.putInt(binYOffset); // Sort keys in row-major order List keys = new ArrayList<>(records.keySet()); keys.sort(new Comparator() { @Override public int compare(Point o1, Point o2) { if (o1.y != o2.y) { return o1.y - o2.y; } else { return o1.x - o2.x; } } }); Point lastPoint = keys.get(keys.size() - 1); final short w = (short) (binXMax - binXOffset + 1); final int w1 = binXMax - binXOffset + 1; final int w2 = binYMax - binYOffset + 1; boolean isInteger = true; float maxCounts = 0; LinkedHashMap> rows = new LinkedHashMap<>(); for (Point point : keys) { final ContactCount contactCount = records.get(point); float counts = contactCount.getCounts(); if (counts >= countThreshold) { isInteger = isInteger && (Math.floor(counts) == counts); maxCounts = Math.max(counts, maxCounts); final int px = point.x - binXOffset; final int py = point.y - binYOffset; List row = rows.get(py); if (row == null) { row = new ArrayList<>(10); rows.put(py, row); } row.add(new ContactRecord(px, py, counts)); } } // Compute size for each representation and choose smallest boolean useShort = isInteger && (maxCounts < Short.MAX_VALUE); boolean useShortBinX = w1 < Short.MAX_VALUE; boolean useShortBinY = w2 < Short.MAX_VALUE; int valueSize = useShort ? 2 : 4; int lorSize = 0; int nDensePts = (lastPoint.y - binYOffset) * w + (lastPoint.x - binXOffset) + 1; int denseSize = nDensePts * valueSize; for (List row : rows.values()) { lorSize += 4 + row.size() * valueSize; } buffer.put((byte) (useShort ? 0 : 1)); buffer.put((byte) (useShortBinX ? 0 : 1)); buffer.put((byte) (useShortBinY ? 0 : 1)); //dense calculation is incorrect for v9 denseSize = Integer.MAX_VALUE; if (lorSize < denseSize) { buffer.put((byte) 1); // List of rows representation if (useShortBinY) { buffer.putShort((short) rows.size()); // # of rows } else { buffer.putInt(rows.size()); // # of rows } for (Map.Entry> entry : rows.entrySet()) { int py = entry.getKey(); List row = entry.getValue(); if (useShortBinY) { buffer.putShort((short) py); // Row number } else { buffer.putInt(py); // Row number } if (useShortBinX) { buffer.putShort((short) row.size()); // size of row } else { buffer.putInt(row.size()); // size of row } for (ContactRecord contactRecord : row) { if (useShortBinX) { buffer.putShort((short) (contactRecord.getBinX())); } else { buffer.putInt(contactRecord.getBinX()); } final float counts = contactRecord.getCounts(); if (useShort) { buffer.putShort((short) counts); } else { buffer.putFloat(counts); } synchronized(sampledData) { sampledData.add(counts); } incrementSum(counts); } } } else { buffer.put((byte) 2); // Dense matrix buffer.putInt(nDensePts); buffer.putShort(w); int lastIdx = 0; for (Point p : keys) { int idx = (p.y - binYOffset) * w + (p.x - binXOffset); for (int i = lastIdx; i < idx; i++) { // Filler value if (useShort) { buffer.putShort(Short.MIN_VALUE); } else { buffer.putFloat(Float.NaN); } } float counts = records.get(p).getCounts(); if (useShort) { buffer.putShort((short) counts); } else { buffer.putFloat(counts); } lastIdx = idx + 1; synchronized(sampledData) { sampledData.add(counts); } incrementSum(counts); } } byte[] bytes = buffer.getBytes(); byte[] compressedBytes = compress(bytes, compressor); los.write(compressedBytes); } private synchronized void incrementSum(float counts) { sum += counts; } private synchronized void incrementCellCount(int nRecords) { cellCount += nRecords; } /** * todo should this be synchronized? * * @param data * @param compressor * @return */ protected byte[] compress(byte[] data, Deflater compressor) { // Give the compressor the data to compress compressor.reset(); compressor.setInput(data); compressor.finish(); // Create an expandable byte array to hold the compressed data. // You cannot use an array that's the same size as the orginal because // there is no guarantee that the compressed data will be smaller than // the uncompressed data. ByteArrayOutputStream bos = new ByteArrayOutputStream(data.length); // Compress the data byte[] buf = new byte[1024]; while (!compressor.finished()) { int count = compressor.deflate(buf); bos.write(buf, 0, count); } try { bos.close(); } catch (IOException e) { System.err.println("Error clossing ByteArrayOutputStream"); e.printStackTrace(); } return bos.toByteArray(); } } ================================================ FILE: src/juicebox/tools/utils/original/MultithreadedPreprocessor.java ================================================ /* * The MIT License (MIT) * * Copyright (c) 2011-2021 Broad Institute, Aiden Lab, Rice University, Baylor College of Medicine * * Permission is hereby granted, free of charge, to any person obtaining a copy * of this software and associated documentation files (the "Software"), to deal * in the Software without restriction, including without limitation the rights * to use, copy, modify, merge, publish, distribute, sublicense, and/or sell * copies of the Software, and to permit persons to whom the Software is * furnished to do so, subject to the following conditions: * * The above copyright notice and this permission notice shall be included in * all copies or substantial portions of the Software. * * THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR * IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, * FITNESS FOR A PARTICULAR PURPOSE AND NON-INFRINGEMENT. IN NO EVENT SHALL THE * AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER * LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, * OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN * THE SOFTWARE. */ package juicebox.tools.utils.original; import htsjdk.tribble.util.LittleEndianOutputStream; import juicebox.HiCGlobals; import juicebox.data.ChromosomeHandler; import juicebox.tools.utils.original.mnditerator.AlignmentPair; import juicebox.tools.utils.original.mnditerator.AsciiPairIterator; import juicebox.tools.utils.original.mnditerator.PairIterator; import juicebox.windowui.NormalizationHandler; import org.broad.igv.util.Pair; import java.io.*; import java.util.*; import java.util.concurrent.ConcurrentHashMap; import java.util.concurrent.ExecutorService; import java.util.concurrent.Executors; import java.util.concurrent.atomic.AtomicInteger; import java.util.zip.Deflater; public class MultithreadedPreprocessor extends Preprocessor { public static final String CAT_SCRIPT = "_cat_outputs.sh"; private final Map chromosomePairIndexes = new ConcurrentHashMap<>(); private final Map chromosomePairIndexesReverse = new ConcurrentHashMap<>(); private final Map chromosomePairIndex1 = new ConcurrentHashMap<>(); private final Map chromosomePairIndex2 = new ConcurrentHashMap<>(); private int chromosomePairCounter = 0; private final Map nonemptyChromosomePairs = new ConcurrentHashMap<>(); private final Map> wholeGenomeMatrixParts = new ConcurrentHashMap<>(); private final Map localMatrixPositions = new ConcurrentHashMap<>(); private final Map matrixSizes = new ConcurrentHashMap<>(); private final Map>> chromosomePairBlockIndexes; protected static int numCPUThreads = 1; private final Map> allLocalExpectedValueCalculations; protected static Map> mndIndex = null; private final AtomicInteger chunkCounter = new AtomicInteger(0); private int totalChunks = 0; private int totalChrPairToWrite = 0; private final AtomicInteger totalChrPairsWritten = new AtomicInteger(0); private final ConcurrentHashMap completedChunksPerChrPair = new ConcurrentHashMap<>(); private final ConcurrentHashMap numChunksPerChrPair = new ConcurrentHashMap<>(); private final ConcurrentHashMap chrPairCompleted = new ConcurrentHashMap<>(); private final ConcurrentHashMap chrPairAvailableThreads = new ConcurrentHashMap<>(); private final ConcurrentHashMap chrPairBlockCapacities = new ConcurrentHashMap<>(); private final ConcurrentHashMap chunkCounterToChrPairMap = new ConcurrentHashMap<>(); private final ConcurrentHashMap chunkCounterToChrChunkMap = new ConcurrentHashMap<>(); private final ConcurrentHashMap, MatrixPP>>> threadSpecificChrPairMatrices = new ConcurrentHashMap<>(); private final ConcurrentHashMap finalChrMatrices = new ConcurrentHashMap<>(); public MultithreadedPreprocessor(File outputFile, String genomeId, ChromosomeHandler chromosomeHandler, double hicFileScalingFactor, int numCPUThreads, String mndIndexFile) throws IOException { super(outputFile, genomeId, chromosomeHandler, hicFileScalingFactor); MultithreadedPreprocessor.numCPUThreads = numCPUThreads; chromosomeIndexes = MTIndexHandler.populateChromosomeIndexes(chromosomeHandler, numCPUThreads); chromosomePairCounter = MTIndexHandler.populateChromosomePairIndexes(chromosomeHandler, chromosomePairIndexes, chromosomePairIndexesReverse, chromosomePairIndex1, chromosomePairIndex2); setMndIndex(mndIndexFile, chromosomePairIndexes); this.chromosomePairBlockIndexes = new ConcurrentHashMap<>(chromosomePairCounter, (float) 0.75, numCPUThreads); this.allLocalExpectedValueCalculations = new ConcurrentHashMap<>(numCPUThreads, (float) 0.75, numCPUThreads); } public void setMndIndex(String mndIndexFile, Map chromosomePairIndexes) throws IOException { if (mndIndexFile != null && mndIndexFile.length() > 1) { mndIndex = MTIndexHandler.readMndIndex(mndIndexFile, chromosomePairIndexes); } else { throw new IOException("No mndIndex provided"); } } @Override public void preprocess(final String inputFile, String ignore1, String ignore2, Map> ignore3) throws IOException { super.preprocess(inputFile, outputFile + "_header", outputFile + "_footer", mndIndex); try { PrintWriter finalOutput = new PrintWriter(outputFile + CAT_SCRIPT); StringBuilder catOutputLine = new StringBuilder(); StringBuilder removeLine = new StringBuilder(); catOutputLine.append("cat ").append(outputFile + "_header"); removeLine.append("rm ").append(outputFile + "_header"); for (int i = 0; i < chromosomePairCounter; i++) { if ((nonemptyChromosomePairs.containsKey(i) && chromosomePairBlockIndexes.containsKey(i) && mndIndex.containsKey(i)) || i == 0) { catOutputLine.append(" ").append(outputFile).append("_").append(chromosomePairIndexes.get(i)); removeLine.append(" ").append(outputFile).append("_").append(chromosomePairIndexes.get(i)); if (i > 0) { int numOfNeededThreads = chrPairAvailableThreads.get(i).get(); if (numOfNeededThreads > 1) { for (int j = 1; j <= numOfNeededThreads * numResolutions; j++) { catOutputLine.append(" ").append(outputFile).append("_").append(chromosomePairIndexes.get(i)).append("_").append(j); removeLine.append(" ").append(outputFile).append("_").append(chromosomePairIndexes.get(i)).append("_").append(j); } } } } } catOutputLine.append(" ").append(outputFile + "_footer").append(" > ").append(outputFile).append("\n"); removeLine.append(" ").append(outputFile + "_footer\n"); finalOutput.println(catOutputLine.toString()); finalOutput.println(removeLine.toString()); finalOutput.close(); } catch (Exception e) { e.printStackTrace(); System.err.println("Unable to write to catOutputs.sh"); System.exit(70); } } private int getGenomicPosition(int chr, int pos, ChromosomeHandler localChromosomeHandler) { long len = 0; for (int i = 1; i < chr; i++) { len += localChromosomeHandler.getChromosomeFromIndex(i).getLength(); } len += pos; return (int) (len / 1000); } private Pair, MatrixPP> processIndividualMatrixChunk(String inputFile, int chunkNumber, int currentChrPair, Set syncWrittenMatrices, Map localExpectedValueCalculations, int threadNum) throws IOException { MatrixPP wholeGenomeMatrix = getInitialGenomeWideMatrixPP(chromosomeHandler); int i = chunkNumber; int chunksProcessed = 0; String currentMatrixName = null; int currentPairIndex = -1; int currentChr1 = -1; int currentChr2 = -1; MatrixPP currentMatrix = null; String currentMatrixKey = null; while (i < totalChunks) { int chrPair = chunkCounterToChrPairMap.get(i); if (chrPair != currentChrPair) { break; } int chrChunk = chunkCounterToChrChunkMap.get(i); List chunkPositions = mndIndex.get(chrPair); PairIterator iter = null; if (mndIndex == null) { System.err.println("No index for merged nodups file."); System.exit(67); } else { iter = new AsciiPairIterator(inputFile, chromosomeIndexes, chunkPositions.get(chrChunk), chromosomeHandler); } while (iter.hasNext()) { AlignmentPair pair = iter.next(); // skip pairs that mapped to contigs if (!pair.isContigPair()) { if (shouldSkipContact(pair)) continue; // Flip pair if needed so chr1 < chr2 int chr1, chr2, bp1, bp2, frag1, frag2; if (pair.getChr1() < pair.getChr2()) { bp1 = pair.getPos1(); bp2 = pair.getPos2(); frag1 = pair.getFrag1(); frag2 = pair.getFrag2(); chr1 = pair.getChr1(); chr2 = pair.getChr2(); } else { bp1 = pair.getPos2(); bp2 = pair.getPos1(); frag1 = pair.getFrag2(); frag2 = pair.getFrag1(); chr1 = pair.getChr2(); chr2 = pair.getChr1(); } bp1 = ensureFitInChromosomeBounds(bp1, chr1); bp2 = ensureFitInChromosomeBounds(bp2, chr2); // Randomize position within fragment site if (allowPositionsRandomization && fragmentCalculation != null) { Pair newBPos12 = getRandomizedPositions(chr1, chr2, frag1, frag2, bp1, bp2); bp1 = newBPos12.getFirst(); bp2 = newBPos12.getSecond(); } // only increment if not intraFragment and passes the mapq threshold if (!(currentChr1 == chr1 && currentChr2 == chr2)) { // Start the next matrix currentChr1 = chr1; currentChr2 = chr2; currentMatrixKey = currentChr1 + "_" + currentChr2; currentMatrixName = chromosomeHandler.getChromosomeFromIndex(chr1).getName() + "-" + chromosomeHandler.getChromosomeFromIndex(chr2).getName(); currentPairIndex = chromosomePairIndexesReverse.get(currentMatrixName); if (currentPairIndex != currentChrPair) { break; } if (syncWrittenMatrices.contains(currentMatrixKey)) { System.err.println("Error: the chromosome combination " + currentMatrixKey + " appears in multiple blocks"); if (outputFile != null) outputFile.deleteOnExit(); System.exit(58); } currentMatrix = new MatrixPP(currentChr1, currentChr2, chromosomeHandler, bpBinSizes, fragmentCalculation, fragBinSizes, countThreshold, v9DepthBase, chrPairBlockCapacities.get(currentChrPair)); } currentMatrix.incrementCount(bp1, bp2, frag1, frag2, pair.getScore(), localExpectedValueCalculations, tmpDir); int pos1 = getGenomicPosition(chr1, bp1, chromosomeHandler); int pos2 = getGenomicPosition(chr2, bp2, chromosomeHandler); wholeGenomeMatrix.incrementCount(pos1, pos2, pos1, pos2, pair.getScore(), localExpectedValueCalculations, tmpDir); } } if (iter != null) iter.close(); chunksProcessed++; i = chunkCounter.getAndIncrement(); } if (currentMatrix != null) { currentMatrix.parsingComplete(); //LittleEndianOutputStream[] localLos = {new LittleEndianOutputStream(new BufferedOutputStream(new FileOutputStream(outputFile + "_" + chromosomePairIndexes.get(currentPairIndex)), HiCGlobals.bufferSize))}; //writeMatrix(currentMatrix, localLos, getDefaultCompressor(), localMatrixPositions, currentPairIndex, true); } wholeGenomeMatrixParts.get(currentChrPair).put(threadNum, wholeGenomeMatrix); return new Pair<>(new Pair<>(i, chunksProcessed), currentMatrix); } @Override protected void writeBody(String inputFile, Map> mndIndex) throws IOException { Set syncWrittenMatrices = Collections.synchronizedSet(new HashSet<>()); final AtomicInteger freeThreads = new AtomicInteger(numCPUThreads); for (int chrPair = 1; chrPair < chromosomePairCounter; chrPair++) { if (mndIndex.containsKey(chrPair)) { int numOfChunks = mndIndex.get(chrPair).size(); totalChrPairToWrite++; completedChunksPerChrPair.put(chrPair, new AtomicInteger(0)); numChunksPerChrPair.put(chrPair, numOfChunks); chrPairCompleted.put(chrPair, new AtomicInteger(0)); chrPairAvailableThreads.put(chrPair, new AtomicInteger(0)); chrPairBlockCapacities.put(chrPair, BLOCK_CAPACITY/Math.min(numCPUThreads,numOfChunks)); threadSpecificChrPairMatrices.put(chrPair, new ConcurrentHashMap<>()); wholeGenomeMatrixParts.put(chrPair, new ConcurrentHashMap<>()); for (int i=0; i localExpectedValueCalculations = null; if (expectedVectorFile == null) { localExpectedValueCalculations = new LinkedHashMap<>(); for (int bBinSize : bpBinSizes) { ExpectedValueCalculation calc = new ExpectedValueCalculation(chromosomeHandler, bBinSize, null, NormalizationHandler.NONE); String key = "BP_" + bBinSize; localExpectedValueCalculations.put(key, calc); } if (fragmentCalculation != null) { // Create map of chr name -> # of fragments Map sitesMap = fragmentCalculation.getSitesMap(); Map fragmentCountMap = new HashMap<>(); for (Map.Entry entry : sitesMap.entrySet()) { int fragCount = entry.getValue().length + 1; String chr = entry.getKey(); fragmentCountMap.put(chr, fragCount); } for (int fBinSize : fragBinSizes) { ExpectedValueCalculation calc = new ExpectedValueCalculation(chromosomeHandler, fBinSize, fragmentCountMap, NormalizationHandler.NONE); String key = "FRAG_" + fBinSize; localExpectedValueCalculations.put(key, calc); } } } while (currentChunk < totalChunks) { int currentChrPair = chunkCounterToChrPairMap.get(currentChunk); threadSpecificChrPairMatrices.get(currentChrPair).put(threadNum, processIndividualMatrixChunk(inputFile, currentChunk, currentChrPair, syncWrittenMatrices, localExpectedValueCalculations, threadNum)); synchronized(finalChrMatrices) { if (!finalChrMatrices.containsKey(currentChrPair)) { int currentChr1 = chromosomePairIndex1.get(currentChrPair); int currentChr2 = chromosomePairIndex2.get(currentChrPair); finalChrMatrices.put(currentChrPair, new MatrixPP(currentChr1, currentChr2, chromosomeHandler, bpBinSizes, fragmentCalculation, fragBinSizes, countThreshold, v9DepthBase, chrPairBlockCapacities.get(currentChrPair))); } synchronized(finalChrMatrices.get(currentChrPair)) { finalChrMatrices.get(currentChrPair).mergeMatrices(threadSpecificChrPairMatrices.get(currentChrPair).get(threadNum).getSecond()); } } for (int completedChunks = 0; completedChunks < threadSpecificChrPairMatrices.get(currentChrPair).get(threadNum).getFirst().getSecond(); completedChunks++) { completedChunksPerChrPair.get(currentChrPair).getAndIncrement(); } //System.err.println(currentChrPair + " " + threadSpecificChrPairMatrices.get(currentChrPair).get(threadNum).getFirst().getSecond() + " " + Duration.between(A,B).toMillis() + " " + Duration.between(B,C).toMillis() + " " + completedChunksPerChrPair.get(currentChrPair).get()); currentChunk = threadSpecificChrPairMatrices.get(currentChrPair).get(threadNum).getFirst().getFirst(); int currentAvailableThreads = chrPairAvailableThreads.get(currentChrPair).incrementAndGet(); if (completedChunksPerChrPair.get(currentChrPair).get() == numChunksPerChrPair.get(currentChrPair)) { WriteIndividualMatrix(currentChrPair, currentAvailableThreads); finalChrMatrices.remove(currentChrPair); threadSpecificChrPairMatrices.remove(currentChrPair); chrPairCompleted.get(currentChrPair).getAndIncrement(); //System.err.println(currentChrPair + " " + Duration.between(D,E).toMillis()); } while (chrPairCompleted.get(currentChrPair).get() == 0) { try { Thread.sleep(1000); } catch (InterruptedException e) { System.err.println(e.getLocalizedMessage()); } } } allLocalExpectedValueCalculations.put(threadNum, localExpectedValueCalculations); } catch (Exception e) { e.printStackTrace(); } } }; executor.execute(worker); } executor.shutdown(); // Wait until all threads finish while (!executor.isTerminated()) { try { Thread.sleep(50); } catch (InterruptedException e) { System.err.println(e.getLocalizedMessage()); } } if (expectedVectorFile == null) { for (int i = 0; i < numCPUThreads; i++) { if (allLocalExpectedValueCalculations.get(i) != null) { for (Map.Entry entry : allLocalExpectedValueCalculations.get(i).entrySet()) { expectedValueCalculations.get(entry.getKey()).merge(entry.getValue()); } } } } MatrixPP wholeGenomeMatrix = getInitialGenomeWideMatrixPP(chromosomeHandler); for (int i = 1; i < chromosomePairCounter; i++) { if (nonemptyChromosomePairs.containsKey(i)) { if (wholeGenomeMatrixParts.containsKey(i)) { for (Map.Entry entry : wholeGenomeMatrixParts.get(i).entrySet()) { wholeGenomeMatrix.mergeMatrices(entry.getValue()); } } } } // just making this more readable FileOutputStream tempFOS = new FileOutputStream(outputFile + "_" + chromosomePairIndexes.get(0)); LittleEndianOutputStream tempLOS = new LittleEndianOutputStream(new BufferedOutputStream(tempFOS, HiCGlobals.bufferSize)); LittleEndianOutputStream[] localLos = {tempLOS}; writeMatrix(wholeGenomeMatrix, localLos, getDefaultCompressor(), localMatrixPositions, 0, true); nonemptyChromosomePairs.put(0, 1); long currentPosition = losArray[0].getWrittenCount(); long nextMatrixPosition = 0; String currentMatrixKey = null; for (int i = 0; i < chromosomePairCounter; i++) { if (nonemptyChromosomePairs.containsKey(i) && chromosomePairBlockIndexes.containsKey(i)) { for (Map.Entry> entry : chromosomePairBlockIndexes.get(i).entrySet()) { updateIndexPositions(entry.getValue(), null, false, new File(outputFile + "_" + chromosomePairIndexes.get(i)), currentPosition, entry.getKey()); } nextMatrixPosition = localMatrixPositions.get("" + i).position + currentPosition; currentMatrixKey = chromosomePairIndex1.get(i) + "_" + chromosomePairIndex2.get(i); matrixPositions.put(currentMatrixKey, new IndexEntry(nextMatrixPosition, localMatrixPositions.get("" + i).size)); currentPosition += matrixSizes.get(i); } } masterIndexPosition = currentPosition; } void WriteIndividualMatrix(Integer chromosomePair, int numOfNeededThreads) throws IOException { int chr1 = chromosomePairIndex1.get(chromosomePair); int chr2 = chromosomePairIndex2.get(chromosomePair); if (includedChromosomes != null) { String c1Name = chromosomeHandler.getChromosomeFromIndex(chr1).getName(); String c2Name = chromosomeHandler.getChromosomeFromIndex(chr2).getName(); if (includedChromosomes.contains(c1Name) || includedChromosomes.contains(c2Name)) { nonemptyChromosomePairs.put(chromosomePair, 1); } } else { nonemptyChromosomePairs.put(chromosomePair, 1); } LittleEndianOutputStream[] localLos; if (numOfNeededThreads == 1) { localLos = new LittleEndianOutputStream[1]; localLos[0] = new LittleEndianOutputStream(new BufferedOutputStream(new FileOutputStream(outputFile + "_" + chromosomePairIndexes.get(chromosomePair)), HiCGlobals.bufferSize)); } else { localLos = new LittleEndianOutputStream[(numOfNeededThreads * numResolutions) + 1]; localLos[0] = new LittleEndianOutputStream(new BufferedOutputStream(new FileOutputStream(outputFile + "_" + chromosomePairIndexes.get(chromosomePair)), HiCGlobals.bufferSize)); for (int i = 1; i <= numOfNeededThreads * numResolutions; i++) { localLos[i] = new LittleEndianOutputStream(new BufferedOutputStream(new FileOutputStream(outputFile + "_" + chromosomePairIndexes.get(chromosomePair) + "_" + i), HiCGlobals.bufferSize)); } } writeMatrix(finalChrMatrices.get(chromosomePair), localLos, getDefaultCompressor(), localMatrixPositions, chromosomePair, true); } @Override // MatrixPP matrix, LittleEndianOutputStream los, Deflater compressor protected Pair>, Long> writeMatrix(MatrixPP matrix, LittleEndianOutputStream[] localLos, Deflater localCompressor, Map localMatrixPositions, int chromosomePairIndex, boolean doMultiThreadedBehavior) throws IOException { Pair>, Long> localBlockIndexes = super.writeMatrix(matrix, localLos, localCompressor, localMatrixPositions, chromosomePairIndex, true); chromosomePairBlockIndexes.put(chromosomePairIndex, localBlockIndexes.getFirst()); long size = 0 - localBlockIndexes.getSecond(); for (int i = 0; i < localLos.length; i++) { size += localLos[i].getWrittenCount(); localLos[i].close(); } matrixSizes.put(chromosomePairIndex, size); //System.out.print("."); return localBlockIndexes; } } ================================================ FILE: src/juicebox/tools/utils/original/MultithreadedPreprocessorHic.java ================================================ /* * The MIT License (MIT) * * Copyright (c) 2011-2022 Broad Institute, Aiden Lab, Rice University, Baylor College of Medicine * * Permission is hereby granted, free of charge, to any person obtaining a copy * of this software and associated documentation files (the "Software"), to deal * in the Software without restriction, including without limitation the rights * to use, copy, modify, merge, publish, distribute, sublicense, and/or sell * copies of the Software, and to permit persons to whom the Software is * furnished to do so, subject to the following conditions: * * The above copyright notice and this permission notice shall be included in * all copies or substantial portions of the Software. * * THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR * IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, * FITNESS FOR A PARTICULAR PURPOSE AND NON-INFRINGEMENT. IN NO EVENT SHALL THE * AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER * LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, * OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN * THE SOFTWARE. */ package juicebox.tools.utils.original; import htsjdk.tribble.util.LittleEndianOutputStream; import juicebox.HiC; import juicebox.HiCGlobals; import juicebox.data.*; import juicebox.tools.utils.original.merge.HiCMergeTools; import juicebox.windowui.HiCZoom; import org.broad.igv.util.Pair; import java.io.BufferedOutputStream; import java.io.File; import java.io.IOException; import java.io.PrintWriter; import java.nio.file.Files; import java.nio.file.Paths; import java.util.Arrays; import java.util.HashMap; import java.util.List; import java.util.Map; import java.util.concurrent.ConcurrentHashMap; public class MultithreadedPreprocessorHic extends Preprocessor { public static final String CAT_SCRIPT = "_cat_outputs.sh"; private final Map chromosomePairIndexes = new ConcurrentHashMap<>(); private final Map chromosomePairIndex1 = new ConcurrentHashMap<>(); private final Map chromosomePairIndex2 = new ConcurrentHashMap<>(); private final int chromosomePairCounter; private final Map nonemptyChromosomePairs = new ConcurrentHashMap<>(); private final Map>> chromosomePairBlockIndexes; protected static int numCPUThreads = 1; protected static Map> mndIndex = null; private Dataset ds; private long currentPosition; public MultithreadedPreprocessorHic(File outputFile, String genomeId, ChromosomeHandler chromosomeHandler, double hicFileScalingFactor, int numCPUThreads) { super(outputFile, genomeId, chromosomeHandler, hicFileScalingFactor); MultithreadedPreprocessorHic.numCPUThreads = numCPUThreads; chromosomeIndexes = MTIndexHandler.populateChromosomeIndexes(chromosomeHandler, numCPUThreads); Map chromosomePairIndexesReverse = new ConcurrentHashMap<>(); chromosomePairCounter = MTIndexHandler.populateChromosomePairIndexes(chromosomeHandler, chromosomePairIndexes, chromosomePairIndexesReverse, chromosomePairIndex1, chromosomePairIndex2); this.chromosomePairBlockIndexes = new ConcurrentHashMap<>(chromosomePairCounter, (float) 0.75, numCPUThreads); } @Override public void preprocess(final String inputFile, String ignore1, String ignore2, Map> ignore3) throws IOException { List summedHiCFiles = Arrays.asList(inputFile.split("\\+")); HiCMergeTools.mergeStatsAndGraphs(summedHiCFiles, this, outputFile.getAbsolutePath()); ds = HiCFileTools.extractDatasetForCLT(summedHiCFiles, true); super.preprocess(inputFile, outputFile + "_header", outputFile + "_footer", mndIndex); try { PrintWriter finalOutput = new PrintWriter(outputFile + CAT_SCRIPT); StringBuilder catOutputLine = new StringBuilder(); catOutputLine.append("cat ").append(outputFile).append("_header").append(" > ").append(outputFile).append("\n"); catOutputLine.append("rm ").append(outputFile).append("_header\n"); for (int i = 0; i < chromosomePairCounter; i++) { if ((nonemptyChromosomePairs.containsKey(i) && chromosomePairBlockIndexes.containsKey(i)) || i == 0) { catOutputLine.append("cat ").append(outputFile).append("_").append(chromosomePairIndexes.get(i)).append(" >> ").append(outputFile).append("\n"); catOutputLine.append("rm ").append(outputFile).append("_").append(chromosomePairIndexes.get(i)).append("\n"); if (i > 0) { int numOfNeededThreads = numCPUThreads; if (numOfNeededThreads > 1) { for (int j = 1; j <= numOfNeededThreads * numResolutions; j++) { catOutputLine.append("cat ").append(outputFile).append("_").append(chromosomePairIndexes.get(i)).append("_").append(j).append(" >> ").append(outputFile).append("\n"); catOutputLine.append("rm ").append(outputFile).append("_").append(chromosomePairIndexes.get(i)).append("_").append(j).append("\n"); } } } } } catOutputLine.append("cat ").append(outputFile).append("_footer").append(" >> ").append(outputFile).append("\n"); catOutputLine.append("rm ").append(outputFile).append("_footer\n"); finalOutput.println(catOutputLine); finalOutput.close(); } catch (Exception e) { e.printStackTrace(); System.err.println("Unable to write to catOutputs.sh"); System.exit(70); } } @Override protected void writeBody(String inputFile, Map> mndIndex) throws IOException { currentPosition = losArray[0].getWrittenCount(); Map fragmentCountMap = null; boolean calculateExpecteds = false; if (expectedVectorFile == null) { if (fragmentCalculation != null) { // Create map of chr name -> # of fragments Map sitesMap = fragmentCalculation.getSitesMap(); fragmentCountMap = new HashMap<>(); for (Map.Entry entry : sitesMap.entrySet()) { int fragCount = entry.getValue().length + 1; String chr = entry.getKey(); fragmentCountMap.put(chr, fragCount); } } calculateExpecteds = true; } writeIndividualMatrix(0, 1, false, fragmentCountMap); for (int chrPair = 1; chrPair < chromosomePairCounter; chrPair++) { writeIndividualMatrix(chrPair, numCPUThreads, calculateExpecteds, fragmentCountMap); } masterIndexPosition = currentPosition; } void writeIndividualMatrix(Integer chromosomePair, int numOfNeededThreads, boolean calculateExpecteds, Map fragmentCountMap) throws IOException { int chr1 = chromosomePairIndex1.get(chromosomePair); int chr2 = chromosomePairIndex2.get(chromosomePair); Matrix combinedMatrix = ds.getMatrix(chromosomeHandler.getChromosomeFromIndex(chr1), chromosomeHandler.getChromosomeFromIndex(chr2)); if (includedChromosomes != null && combinedMatrix != null) { String c1Name = chromosomeHandler.getChromosomeFromIndex(chr1).getName(); String c2Name = chromosomeHandler.getChromosomeFromIndex(chr2).getName(); if (includedChromosomes.contains(c1Name) || includedChromosomes.contains(c2Name)) { nonemptyChromosomePairs.put(chromosomePair, 1); } } else { nonemptyChromosomePairs.put(chromosomePair, 1); } if (combinedMatrix!=null && nonemptyChromosomePairs.containsKey(chromosomePair)) { LittleEndianOutputStream[] localLos; if (numOfNeededThreads == 1) { localLos = new LittleEndianOutputStream[1]; localLos[0] = new LittleEndianOutputStream(new BufferedOutputStream(Files.newOutputStream(Paths.get(outputFile + "_" + chromosomePairIndexes.get(chromosomePair))), HiCGlobals.bufferSize)); } else { localLos = new LittleEndianOutputStream[(numOfNeededThreads * numResolutions) + 1]; localLos[0] = new LittleEndianOutputStream(new BufferedOutputStream(Files.newOutputStream(Paths.get(outputFile + "_" + chromosomePairIndexes.get(chromosomePair))), HiCGlobals.bufferSize)); for (int i = 1; i <= numOfNeededThreads * numResolutions; i++) { localLos[i] = new LittleEndianOutputStream(new BufferedOutputStream(Files.newOutputStream(Paths.get(outputFile + "_" + chromosomePairIndexes.get(chromosomePair) + "_" + i)), HiCGlobals.bufferSize)); } } LittleEndianOutputStream los = localLos[0]; long position = los.getWrittenCount(); los.writeInt(combinedMatrix.getChr1Idx()); los.writeInt(combinedMatrix.getChr2Idx()); int numResolutions = 0; for (int i = 0; i < bpBinSizes.length; i++) { MatrixZoomData zd = combinedMatrix.getZoomData(new HiCZoom(HiC.Unit.BP, bpBinSizes[i])); if (zd != null) { numResolutions += 1; } if (chromosomePair == 0) { break; } } for (int i = 0; i < fragBinSizes.length; i++) { MatrixZoomData zd = combinedMatrix.getZoomData(new HiCZoom(HiC.Unit.FRAG, fragBinSizes[i])); if (chromosomePair > 0) { if (zd != null) { numResolutions += 1; } } } los.writeInt(numResolutions); for (int i = 0; i < numResolutions; i++) { MatrixZoomData zd; if (i < bpBinSizes.length) { zd = combinedMatrix.getZoomData(new HiCZoom(HiC.Unit.BP, bpBinSizes[i])); } else { zd = combinedMatrix.getZoomData(new HiCZoom(HiC.Unit.FRAG, fragBinSizes[i - bpBinSizes.length])); } if (zd != null) if (i < bpBinSizes.length) { writeZoomHeader(zd, los, i); } else { writeZoomHeader(zd, los, i - bpBinSizes.length); } } long size = los.getWrittenCount() - position; matrixPositions.put(combinedMatrix.getKey(), new IndexEntry(currentPosition + position, (int) size)); final Map> localBlockIndexes = new ConcurrentHashMap<>(); for (int i = 0; i < numResolutions; i++) { MatrixZoomData zd; if (i < bpBinSizes.length) { zd = combinedMatrix.getZoomData(new HiCZoom(HiC.Unit.BP, bpBinSizes[i])); } else { zd = combinedMatrix.getZoomData(new HiCZoom(HiC.Unit.FRAG, fragBinSizes[i - bpBinSizes.length])); } if (zd != null) { Pair, ExpectedValueCalculation> zdOutput; if (localLos.length > 1) { zdOutput = zd.mergeAndWriteBlocks(localLos, compressor, i, numResolutions, calculateExpecteds, fragmentCountMap, chromosomeHandler, subsampleFraction, randomSubsampleGenerator); } else { zdOutput = zd.mergeAndWriteBlocks(localLos[0], compressor, calculateExpecteds, fragmentCountMap, chromosomeHandler, subsampleFraction, randomSubsampleGenerator); } localBlockIndexes.put(zd.blockIndexPosition, zdOutput.getFirst()); if (calculateExpecteds) { ExpectedValueCalculation tmpCalc = zdOutput.getSecond(); String key; if (zd.getZoom().getUnit() == HiC.Unit.BP) { key = "BP_" + zd.getZoom().getBinSize(); } else { key = "FRAG_" + zd.getZoom().getBinSize(); } expectedValueCalculations.get(key).merge(tmpCalc); tmpCalc = null; } } } long matrixSize = 0; for (int i = 0; i < localLos.length; i++) { matrixSize += localLos[i].getWrittenCount(); localLos[i].close(); } chromosomePairBlockIndexes.put(chromosomePair, localBlockIndexes); for (Map.Entry> entry : localBlockIndexes.entrySet()) { updateIndexPositions(entry.getValue(), null, false, new File(outputFile + "_" + chromosomePairIndexes.get(chromosomePair)), currentPosition, entry.getKey()); } currentPosition += matrixSize; System.out.print("."); } } protected void writeZoomHeader(MatrixZoomData zd, LittleEndianOutputStream los, int zoom) throws IOException { int numberOfBlocks = zd.getBlockNumbers().size(); los.writeString(zd.getZoom().getUnit().toString()); // Unit los.writeInt(zoom); // zoom index, lowest res is zero los.writeFloat((float) zd.getSumCount()); // sum los.writeFloat((float) 0); los.writeFloat((float) 0); los.writeFloat((float) 0); los.writeInt(zd.getBinSize()); los.writeInt(zd.getBlockBinCount()); los.writeInt(zd.getBlockColumnCount()); los.writeInt(numberOfBlocks); zd.blockIndexPosition = los.getWrittenCount(); // Placeholder for block index for (int i = 0; i < numberOfBlocks; i++) { los.writeInt(0); los.writeLong(0L); los.writeInt(0); } } } ================================================ FILE: src/juicebox/tools/utils/original/Preprocessor.java ================================================ /* * The MIT License (MIT) * * Copyright (c) 2011-2022 Broad Institute, Aiden Lab, Rice University, Baylor College of Medicine * * Permission is hereby granted, free of charge, to any person obtaining a copy * of this software and associated documentation files (the "Software"), to deal * in the Software without restriction, including without limitation the rights * to use, copy, modify, merge, publish, distribute, sublicense, and/or sell * copies of the Software, and to permit persons to whom the Software is * furnished to do so, subject to the following conditions: * * The above copyright notice and this permission notice shall be included in * all copies or substantial portions of the Software. * * THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR * IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, * FITNESS FOR A PARTICULAR PURPOSE AND NON-INFRINGEMENT. IN NO EVENT SHALL THE * AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER * LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, * OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN * THE SOFTWARE. */ package juicebox.tools.utils.original; //import juicebox.MainWindow; import htsjdk.tribble.util.LittleEndianOutputStream; import juicebox.HiC; import juicebox.HiCGlobals; import juicebox.data.ChromosomeHandler; import juicebox.data.basics.Chromosome; import juicebox.data.basics.ListOfDoubleArrays; import juicebox.tools.clt.CommandLineParser.Alignment; import juicebox.tools.utils.common.UNIXTools; import juicebox.tools.utils.original.mnditerator.AlignmentPair; import juicebox.tools.utils.original.mnditerator.PairIterator; import juicebox.windowui.NormalizationHandler; import org.broad.igv.tdf.BufferedByteWriter; import org.broad.igv.util.Pair; import java.io.*; import java.util.*; import java.util.concurrent.ConcurrentHashMap; import java.util.zip.Deflater; /** * @author jrobinso * @since Aug 16, 2010 */ public class Preprocessor { protected static final int VERSION = 9; protected static final int BLOCK_SIZE = 1000; public static final String V9_DEPTH_BASE = "v9-depth-base"; protected int v9DepthBase = 2; public static final String HIC_FILE_SCALING = "hicFileScalingFactor"; public static final String STATISTICS = "statistics"; public static final String GRAPHS = "graphs"; public static final String SOFTWARE = "software"; protected static final String NVI_INDEX = "nviIndex"; protected static final String NVI_LENGTH = "nviLength"; protected final ChromosomeHandler chromosomeHandler; protected Map chromosomeIndexes; protected final File outputFile; protected final Map matrixPositions; protected String genomeId; protected final Deflater compressor; protected LittleEndianOutputStream[] losArray = new LittleEndianOutputStream[1]; protected long masterIndexPosition; protected int countThreshold = 0; protected int mapqThreshold = 0; protected boolean diagonalsOnly = false; protected String fragmentFileName = null; protected String statsFileName = null; protected String graphFileName = null; protected String expectedVectorFile = null; protected Set randomizeFragMapFiles = null; protected FragmentCalculation fragmentCalculation = null; protected Set includedChromosomes; protected ArrayList fragmentCalculationsForRandomization = null; protected Alignment alignmentFilter; protected static final Random random = new Random(5); protected static boolean allowPositionsRandomization = false; protected static boolean throwOutIntraFrag = false; public static int BLOCK_CAPACITY = 1000; protected double subsampleFraction = 1; protected Random randomSubsampleGenerator = new Random(0); protected static boolean fromHIC = false; // Base-pair resolutions protected int[] bpBinSizes = {2500000, 1000000, 500000, 250000, 100000, 50000, 25000, 10000, 5000, 1000}; // Fragment resolutions protected int[] fragBinSizes = {500, 200, 100, 50, 20, 5, 2, 1}; // number of resolutions protected int numResolutions = bpBinSizes.length + fragBinSizes.length; // hic scaling factor value protected double hicFileScalingFactor = 1; protected Long normVectorIndex = 0L, normVectorLength = 0L; /** * The position of the field containing the masterIndex position */ protected long masterIndexPositionPosition; protected long normVectorIndexPosition; protected long normVectorLengthPosition; protected Map expectedValueCalculations; protected File tmpDir; public Preprocessor(File outputFile, String genomeId, ChromosomeHandler chromosomeHandler, double hicFileScalingFactor) { this.genomeId = genomeId; this.outputFile = outputFile; this.matrixPositions = new LinkedHashMap<>(); this.chromosomeHandler = chromosomeHandler; chromosomeIndexes = new Hashtable<>(); for (int i = 0; i < chromosomeHandler.size(); i++) { chromosomeIndexes.put(chromosomeHandler.getChromosomeFromIndex(i).getName(), i); } compressor = getDefaultCompressor(); this.tmpDir = createTempFolder(outputFile.getAbsolutePath() + "_tmp_folder"); if (hicFileScalingFactor > 0) { this.hicFileScalingFactor = hicFileScalingFactor; } } public void setCountThreshold(int countThreshold) { this.countThreshold = countThreshold; } public void setV9DepthBase(int v9DepthBase) { if (v9DepthBase > 1 || v9DepthBase < 0) { this.v9DepthBase = v9DepthBase; } } public void setMapqThreshold(int mapqThreshold) { this.mapqThreshold = mapqThreshold; } public void setDiagonalsOnly(boolean diagonalsOnly) { this.diagonalsOnly = diagonalsOnly; } public void setIncludedChromosomes(Set includedChromosomes) { if (includedChromosomes != null && includedChromosomes.size() > 0) { this.includedChromosomes = Collections.synchronizedSet(new HashSet<>()); for (String name : includedChromosomes) { this.includedChromosomes.add(chromosomeHandler.cleanUpName(name)); } } } public void setFragmentFile(String fragmentFileName) { this.fragmentFileName = fragmentFileName; } public void setExpectedVectorFile(String expectedVectorFile) { this.expectedVectorFile = expectedVectorFile; } public void setGraphFile(String graphFileName) { this.graphFileName = graphFileName; } public void setGenome(String genome) { if (genome != null) { this.genomeId = genome; } } public void setResolutions(List resolutions) { if (resolutions != null) { ArrayList fragResolutions = new ArrayList<>(); ArrayList bpResolutions = new ArrayList<>(); for (String str : resolutions) { boolean fragment = false; int index = str.indexOf("f"); if (index != -1) { str = str.substring(0, index); fragment = true; } Integer myInt = null; try { myInt = Integer.valueOf(str); } catch (NumberFormatException exception) { System.err.println("Resolution improperly formatted. It must be in the form of a number, such as 1000000 for 1M bp,"); System.err.println("or a number followed by 'f', such as 25f for 25 fragment"); System.exit(1); } if (fragment) fragResolutions.add(myInt); else bpResolutions.add(myInt); } boolean resolutionsSet = false; if (fragResolutions.size() > 0) { resolutionsSet = true; Collections.sort(fragResolutions); Collections.reverse(fragResolutions); int[] frags = new int[fragResolutions.size()]; for (int i=0; i 0) { resolutionsSet = true; Collections.sort(bpResolutions); Collections.reverse(bpResolutions); int[] bps = new int[bpResolutions.size()]; for (int i = 0; i < bps.length; i++) { bps[i] = bpResolutions.get(i); } bpBinSizes = bps; } else { bpBinSizes = new int[0]; } if (!resolutionsSet) { System.err.println("No valid resolutions sent in"); System.exit(1); } } } public void setAlignmentFilter(Alignment al) { this.alignmentFilter = al; } public void setRandomizeFragMaps(Set fragMaps) { this.randomizeFragMapFiles = fragMaps; } public void setSubsampler(double subsampleFraction) { if (subsampleFraction == -1) { this.subsampleFraction = 1; } else { this.subsampleFraction = subsampleFraction; } } protected static int randomizePos(FragmentCalculation fragmentCalculation, String chr, int frag) { int low = 1; int high = 1; if (frag == 0) { high = fragmentCalculation.getSites(chr)[frag]; } else if (frag >= fragmentCalculation.getNumberFragments(chr)) { high = fragmentCalculation.getSites(chr)[frag - 1]; low = fragmentCalculation.getSites(chr)[frag - 2]; } else { high = fragmentCalculation.getSites(chr)[frag]; low = fragmentCalculation.getSites(chr)[frag - 1]; } return random.nextInt(high - low + 1) + low; } public void setRandomizePosition(boolean allowPositionsRandomization) { Preprocessor.allowPositionsRandomization = allowPositionsRandomization; } public void setThrowOutIntraFragOption(boolean throwOutIntraFrag) { Preprocessor.throwOutIntraFrag = throwOutIntraFrag; } protected static FragmentCalculation findFragMap(List maps, String chr, int bp, int frag) { //potential maps that this strand could come from ArrayList mapsFound = new ArrayList<>(); for (FragmentCalculation fragmentCalculation : maps) { int low = 1; int high = 1; if (frag > fragmentCalculation.getNumberFragments(chr)) { // definitely not this restriction site file for certain continue; } try { if (frag == 0) { high = fragmentCalculation.getSites(chr)[frag]; } else if (frag == fragmentCalculation.getNumberFragments(chr)) { high = fragmentCalculation.getSites(chr)[frag - 1]; low = fragmentCalculation.getSites(chr)[frag - 2]; } else { high = fragmentCalculation.getSites(chr)[frag]; low = fragmentCalculation.getSites(chr)[frag - 1]; } } catch (Exception e) { e.printStackTrace(); System.out.println(String.format("fragment: %d, number of frags: %d", frag, fragmentCalculation.getNumberFragments(chr))); } // does bp fit in this range? if (bp >= low && bp <= high) { mapsFound.add(fragmentCalculation); } } if (mapsFound.size() == 1) { return mapsFound.get(0); } return null; } public void setFromHIC(boolean fromHIC) { Preprocessor.fromHIC = fromHIC; } public void preprocess(final String inputFile, final String headerFile, final String footerFile, Map> mndIndex) throws IOException { if (!fromHIC) { File file = new File(inputFile); if (!file.exists() || file.length() == 0) { System.err.println(inputFile + " does not exist or does not contain any reads."); System.exit(57); } } try { StringBuilder stats = null; StringBuilder graphs = null; StringBuilder hicFileScaling = new StringBuilder().append(hicFileScalingFactor); if (fragmentFileName != null) { fragmentCalculation = FragmentCalculation.readFragments(fragmentFileName, chromosomeHandler, "Pre"); } else { System.out.println("Not including fragment map"); } if (allowPositionsRandomization) { if (randomizeFragMapFiles != null) { fragmentCalculationsForRandomization = new ArrayList<>(); for (String fragmentFileName : randomizeFragMapFiles) { try { FragmentCalculation fragmentCalculation = FragmentCalculation.readFragments(fragmentFileName, chromosomeHandler, "PreWithRand"); fragmentCalculationsForRandomization.add(fragmentCalculation); System.out.println(String.format("added %s", fragmentFileName)); } catch (Exception e) { System.err.println(String.format("Warning: Unable to process fragment file %s. Randomization will continue without fragment file %s.", fragmentFileName, fragmentFileName)); } } } else { System.out.println("Using default fragment map for randomization"); } } else if (randomizeFragMapFiles != null) { System.err.println("Position randomizer seed not set, disregarding map options"); } if (statsFileName != null) { FileInputStream is = null; try { is = new FileInputStream(statsFileName); BufferedReader reader = new BufferedReader(new InputStreamReader(is), HiCGlobals.bufferSize); stats = new StringBuilder(); String nextLine; while ((nextLine = reader.readLine()) != null) { stats.append(nextLine).append("\n"); } } catch (IOException e) { System.err.println("Error while reading stats file: " + e); stats = null; } finally { if (is != null) { is.close(); } } } if (graphFileName != null) { FileInputStream is = null; try { is = new FileInputStream(graphFileName); BufferedReader reader = new BufferedReader(new InputStreamReader(is), HiCGlobals.bufferSize); graphs = new StringBuilder(); String nextLine; while ((nextLine = reader.readLine()) != null) { graphs.append(nextLine).append("\n"); } } catch (IOException e) { System.err.println("Error while reading graphs file: " + e); graphs = null; } finally { if (is != null) { is.close(); } } } if (expectedVectorFile == null) { expectedValueCalculations = Collections.synchronizedMap(new LinkedHashMap<>()); for (int bBinSize : bpBinSizes) { ExpectedValueCalculation calc = new ExpectedValueCalculation(chromosomeHandler, bBinSize, null, NormalizationHandler.NONE); String key = "BP_" + bBinSize; expectedValueCalculations.put(key, calc); } } if (fragmentCalculation != null) { // Create map of chr name -> # of fragments Map sitesMap = fragmentCalculation.getSitesMap(); Map fragmentCountMap = new HashMap<>(); for (Map.Entry entry : sitesMap.entrySet()) { int fragCount = entry.getValue().length + 1; String chr = entry.getKey(); fragmentCountMap.put(chr, fragCount); } if (expectedVectorFile == null) { for (int fBinSize : fragBinSizes) { ExpectedValueCalculation calc = new ExpectedValueCalculation(chromosomeHandler, fBinSize, fragmentCountMap, NormalizationHandler.NONE); String key = "FRAG_" + fBinSize; expectedValueCalculations.put(key, calc); } } } LittleEndianOutputStream[] losFooter = new LittleEndianOutputStream[1]; try { losArray[0] = new LittleEndianOutputStream(new BufferedOutputStream(new FileOutputStream(headerFile), HiCGlobals.bufferSize)); if (footerFile.equalsIgnoreCase(headerFile)) { losFooter = losArray; } else { losFooter[0] = new LittleEndianOutputStream(new BufferedOutputStream(new FileOutputStream(footerFile), HiCGlobals.bufferSize)); } } catch (Exception e) { System.err.println("Unable to write to " + outputFile); System.exit(70); } System.out.println("Start preprocess"); System.out.println("Writing header"); writeHeader(stats, graphs, hicFileScaling); System.out.println("Writing body"); writeBody(inputFile, mndIndex); System.out.println(); System.out.println("Writing footer"); writeFooter(losFooter); if (losFooter != null && losFooter[0] != null) { losFooter[0].close(); } } finally { if (losArray != null && losArray[0] != null) { losArray[0].close(); } } updateMasterIndex(headerFile); System.out.println("\nFinished preprocess"); } protected void writeHeader(StringBuilder stats, StringBuilder graphs, StringBuilder hicFileScaling) throws IOException { // Magic number byte[] magicBytes = "HIC".getBytes(); LittleEndianOutputStream los = losArray[0]; los.write(magicBytes[0]); los.write(magicBytes[1]); los.write(magicBytes[2]); los.write(0); // VERSION los.writeInt(VERSION); // Placeholder for master index position, replaced with actual position after all contents are written masterIndexPositionPosition = los.getWrittenCount(); los.writeLong(0L); // Genome ID los.writeString(genomeId); // Add NVI info //los.writeString(NVI_INDEX); normVectorIndexPosition = los.getWrittenCount(); los.writeLong(0L); //los.writeString(NVI_LENGTH); normVectorLengthPosition = los.getWrittenCount(); los.writeLong(0L); // Attribute dictionary int nAttributes = 1; if (stats != null) nAttributes += 1; if (graphs != null) nAttributes += 1; if (hicFileScaling != null) nAttributes += 1; if (v9DepthBase != 2) nAttributes += 1; los.writeInt(nAttributes); los.writeString(SOFTWARE); los.writeString("Juicer Tools Version " + HiCGlobals.versionNum); if (stats != null) { los.writeString(STATISTICS); los.writeString(stats.toString()); } if (graphs != null) { los.writeString(GRAPHS); los.writeString(graphs.toString()); } if (hicFileScaling != null) { los.writeString(HIC_FILE_SCALING); los.writeString(hicFileScaling.toString()); } if (v9DepthBase != 2) { los.writeString(V9_DEPTH_BASE); los.writeString("" + v9DepthBase); } // Sequence dictionary int nChrs = chromosomeHandler.size(); los.writeInt(nChrs); for (Chromosome chromosome : chromosomeHandler.getChromosomeArray()) { los.writeString(chromosome.getName()); los.writeLong(chromosome.getLength()); } //BP resolution levels int nBpRes = bpBinSizes.length; los.writeInt(nBpRes); for (int bpBinSize : bpBinSizes) { los.writeInt(bpBinSize); } //fragment resolutions int nFragRes = fragmentCalculation == null ? 0 : fragBinSizes.length; los.writeInt(nFragRes); for (int i = 0; i < nFragRes; i++) { los.writeInt(fragBinSizes[i]); } numResolutions = nBpRes + nFragRes; // fragment sites if (nFragRes > 0) { for (Chromosome chromosome : chromosomeHandler.getChromosomeArray()) { int[] sites = fragmentCalculation.getSites(chromosome.getName()); int nSites = sites == null ? 0 : sites.length; los.writeInt(nSites); for (int i = 0; i < nSites; i++) { los.writeInt(sites[i]); } } } } public void setPositionRandomizerSeed(long randomSeed) { random.setSeed(randomSeed); } protected MatrixPP getInitialGenomeWideMatrixPP(ChromosomeHandler chromosomeHandler) { long genomeLength = chromosomeHandler.getChromosomeFromIndex(0).getLength(); // <= whole genome in KB int binSize = (int) (genomeLength / 500); // todo if (binSize == 0) binSize = 1; int nBinsX = (int) (genomeLength / binSize + 1); // todo int nBlockColumns = nBinsX / BLOCK_SIZE + 1; return new MatrixPP(0, 0, binSize, nBlockColumns, chromosomeHandler, fragmentCalculation, countThreshold, v9DepthBase); } /** * @param file List of files to read * @return Matrix with counts in each bin * @throws IOException */ private MatrixPP computeWholeGenomeMatrix(String file) throws IOException { MatrixPP matrix = getInitialGenomeWideMatrixPP(chromosomeHandler); PairIterator iter = null; //int belowMapq = 0; //int intraFrag = 0; int totalRead = 0; int contig = 0; int hicContact = 0; // Create an index the first time through try { iter = PairIterator.getIterator(file, chromosomeIndexes, chromosomeHandler); while (iter.hasNext()) { totalRead++; AlignmentPair pair = iter.next(); if (pair.isContigPair()) { contig++; } else { int bp1 = pair.getPos1(); int bp2 = pair.getPos2(); int chr1 = pair.getChr1(); int chr2 = pair.getChr2(); int pos1, pos2; if (shouldSkipContact(pair)) continue; pos1 = getGenomicPosition(chr1, bp1); pos2 = getGenomicPosition(chr2, bp2); matrix.incrementCount(pos1, pos2, pos1, pos2, pair.getScore(), expectedValueCalculations, tmpDir); hicContact++; } } } finally { if (iter != null) iter.close(); } /* Intra-fragment Reads: 2,321 (0.19% / 0.79%) Below MAPQ Threshold: 44,134 (3.57% / 15.01%) Hi-C Contacts: 247,589 (20.02% / 84.20%) Ligation Motif Present: 99,245 (8.03% / 33.75%) 3' Bias (Long Range): 73% - 27% Pair Type %(L-I-O-R): 25% - 25% - 25% - 25% Inter-chromosomal: 58,845 (4.76% / 20.01%) Intra-chromosomal: 188,744 (15.27% / 64.19%) Short Range (<20Kb): 48,394 (3.91% / 16.46%) Long Range (>20Kb): 140,350 (11.35% / 47.73%) System.err.println("contig: " + contig + " total: " + totalRead + " below mapq: " + belowMapq + " intra frag: " + intraFrag); */ matrix.parsingComplete(); return matrix; } protected boolean alignmentsAreEqual(Alignment alignment, Alignment alignmentStandard) { if (alignment == alignmentStandard) { return true; } if (alignmentStandard == Alignment.TANDEM) { return alignment == Alignment.LL || alignment == Alignment.RR; } return false; } protected int getGenomicPosition(int chr, int pos) { long len = 0; for (int i = 1; i < chr; i++) { len += chromosomeHandler.getChromosomeFromIndex(i).getLength(); } len += pos; return (int) (len / 1000); } protected static Alignment calculateAlignment(AlignmentPair pair) { if (pair.getStrand1() == pair.getStrand2()) { if (pair.getStrand1()) { return Alignment.RR; } else { return Alignment.LL; } } else if (pair.getStrand1()) { if (pair.getPos1() < pair.getPos2()) { return Alignment.INNER; } else { return Alignment.OUTER; } } else { if (pair.getPos1() < pair.getPos2()) { return Alignment.OUTER; } else { return Alignment.INNER; } } } protected void writeBody(String inputFile, Map> mndIndex) throws IOException { MatrixPP wholeGenomeMatrix = computeWholeGenomeMatrix(inputFile); writeMatrix(wholeGenomeMatrix, losArray, compressor, matrixPositions, -1, false); PairIterator iter = PairIterator.getIterator(inputFile, chromosomeIndexes, chromosomeHandler); Set writtenMatrices = Collections.synchronizedSet(new HashSet<>()); int currentChr1 = -1; int currentChr2 = -1; MatrixPP currentMatrix = null; String currentMatrixKey = null; while (iter.hasNext()) { AlignmentPair pair = iter.next(); // skip pairs that mapped to contigs if (!pair.isContigPair()) { if (shouldSkipContact(pair)) continue; // Flip pair if needed so chr1 < chr2 int chr1, chr2, bp1, bp2, frag1, frag2; if (pair.getChr1() < pair.getChr2()) { bp1 = pair.getPos1(); bp2 = pair.getPos2(); frag1 = pair.getFrag1(); frag2 = pair.getFrag2(); chr1 = pair.getChr1(); chr2 = pair.getChr2(); } else { bp1 = pair.getPos2(); bp2 = pair.getPos1(); frag1 = pair.getFrag2(); frag2 = pair.getFrag1(); chr1 = pair.getChr2(); chr2 = pair.getChr1(); } bp1 = ensureFitInChromosomeBounds(bp1, chr1); bp2 = ensureFitInChromosomeBounds(bp2, chr2); // Randomize position within fragment site if (allowPositionsRandomization && fragmentCalculation != null) { Pair newBPos12 = getRandomizedPositions(chr1, chr2, frag1, frag2, bp1, bp2); bp1 = newBPos12.getFirst(); bp2 = newBPos12.getSecond(); } // only increment if not intraFragment and passes the mapq threshold if (!(currentChr1 == chr1 && currentChr2 == chr2)) { // Starting a new matrix if (currentMatrix != null) { currentMatrix.parsingComplete(); writeMatrix(currentMatrix, losArray, compressor, matrixPositions, -1, false); writtenMatrices.add(currentMatrixKey); currentMatrix = null; System.gc(); //System.out.println("Available memory: " + RuntimeUtils.getAvailableMemory()); } // Start the next matrix currentChr1 = chr1; currentChr2 = chr2; currentMatrixKey = currentChr1 + "_" + currentChr2; if (writtenMatrices.contains(currentMatrixKey)) { System.err.println("Error: the chromosome combination " + currentMatrixKey + " appears in multiple blocks"); if (outputFile != null) outputFile.deleteOnExit(); System.exit(58); } currentMatrix = new MatrixPP(currentChr1, currentChr2, chromosomeHandler, bpBinSizes, fragmentCalculation, fragBinSizes, countThreshold, v9DepthBase, BLOCK_CAPACITY); } currentMatrix.incrementCount(bp1, bp2, frag1, frag2, pair.getScore(), expectedValueCalculations, tmpDir); } } /* if (fragmentCalculation != null && allowPositionsRandomization) { System.out.println(String.format("Randomization errors encountered: %d no map found, " + "%d two different maps found", noMapFoundCount, mapDifferentCount)); } */ if (currentMatrix != null) { currentMatrix.parsingComplete(); writeMatrix(currentMatrix, losArray, compressor, matrixPositions, -1, false); } if (iter != null) iter.close(); masterIndexPosition = losArray[0].getWrittenCount(); } protected int ensureFitInChromosomeBounds(int bp, int chrom) { if (bp < 0) { return 0; } long maxLength = chromosomeHandler.getChromosomeFromIndex(chrom).getLength(); if (bp > maxLength) { return (int) maxLength; } return bp; } protected Pair getRandomizedPositions(int chr1, int chr2, int frag1, int frag2, int bp1, int bp2) { FragmentCalculation fragMapToUse; if (fragmentCalculationsForRandomization != null) { FragmentCalculation fragMap1 = findFragMap(fragmentCalculationsForRandomization, chromosomeHandler.getChromosomeFromIndex(chr1).getName(), bp1, frag1); FragmentCalculation fragMap2 = findFragMap(fragmentCalculationsForRandomization, chromosomeHandler.getChromosomeFromIndex(chr2).getName(), bp2, frag2); if (fragMap1 == null && fragMap2 == null) { //noMapFoundCount += 1; return null; } else if (fragMap1 != null && fragMap2 != null && fragMap1 != fragMap2) { //mapDifferentCount += 1; return null; } if (fragMap1 != null) { fragMapToUse = fragMap1; } else { fragMapToUse = fragMap2; } } else { // use default map fragMapToUse = fragmentCalculation; } int newBP1 = randomizePos(fragMapToUse, chromosomeHandler.getChromosomeFromIndex(chr1).getName(), frag1); int newBP2 = randomizePos(fragMapToUse, chromosomeHandler.getChromosomeFromIndex(chr2).getName(), frag2); return new Pair<>(newBP1, newBP2); } protected boolean shouldSkipContact(AlignmentPair pair) { int chr1 = pair.getChr1(); int chr2 = pair.getChr2(); if (diagonalsOnly && chr1 != chr2) return true; if (includedChromosomes != null && chr1 != 0) { String c1Name = chromosomeHandler.getChromosomeFromIndex(chr1).getName(); String c2Name = chromosomeHandler.getChromosomeFromIndex(chr2).getName(); if (!includedChromosomes.contains(c1Name) || !includedChromosomes.contains(c2Name)) { return true; } } if (alignmentFilter != null && !alignmentsAreEqual(calculateAlignment(pair), alignmentFilter)) { return true; } int mapq = Math.min(pair.getMapq1(), pair.getMapq2()); if (mapq < mapqThreshold) return true; int frag1 = pair.getFrag1(); int frag2 = pair.getFrag2(); if (throwOutIntraFrag && chr1 == chr2 && frag1 == frag2) {return true;} if ( subsampleFraction < 1 && subsampleFraction > 0) { return randomSubsampleGenerator.nextDouble() > subsampleFraction; } else { return false; } } protected void updateMasterIndex(String headerFile) throws IOException { RandomAccessFile raf = null; try { raf = new RandomAccessFile(headerFile, "rw"); // Master index raf.getChannel().position(masterIndexPositionPosition); BufferedByteWriter buffer = new BufferedByteWriter(); buffer.putLong(masterIndexPosition); raf.write(buffer.getBytes()); System.out.println("masterIndexPosition: " + masterIndexPosition); } finally { if (raf != null) raf.close(); } } private void updateNormVectorIndexInfo() throws IOException { RandomAccessFile raf = null; try { raf = new RandomAccessFile(outputFile, "rw"); // NVI index raf.getChannel().position(normVectorIndexPosition); BufferedByteWriter buffer = new BufferedByteWriter(); buffer.putLong(normVectorIndex); // todo raf.write(buffer.getBytes()); // NVI length raf.getChannel().position(normVectorLengthPosition); buffer = new BufferedByteWriter(); buffer.putLong(normVectorLength); // todo raf.write(buffer.getBytes()); } finally { if (raf != null) raf.close(); } } protected void writeFooter(LittleEndianOutputStream[] los) throws IOException { // Index List bufferList = new ArrayList<>(); bufferList.add(new BufferedByteWriter()); bufferList.get(bufferList.size()-1).putInt(matrixPositions.size()); for (Map.Entry entry : matrixPositions.entrySet()) { if (Integer.MAX_VALUE - bufferList.get(bufferList.size()-1).bytesWritten() < 1000) { bufferList.add(new BufferedByteWriter()); } bufferList.get(bufferList.size()-1).putNullTerminatedString(entry.getKey()); bufferList.get(bufferList.size()-1).putLong(entry.getValue().position); bufferList.get(bufferList.size()-1).putInt(entry.getValue().size); } // Vectors (Expected values, other). /*** NEVA ***/ if (expectedVectorFile == null) { if (Integer.MAX_VALUE - bufferList.get(bufferList.size()-1).bytesWritten() < 1000) { bufferList.add(new BufferedByteWriter()); } bufferList.get(bufferList.size()-1).putInt(expectedValueCalculations.size()); for (Map.Entry entry : expectedValueCalculations.entrySet()) { ExpectedValueCalculation ev = entry.getValue(); ev.computeDensity(); int binSize = ev.getGridSize(); HiC.Unit unit = ev.isFrag ? HiC.Unit.FRAG : HiC.Unit.BP; bufferList.get(bufferList.size()-1).putNullTerminatedString(unit.toString()); bufferList.get(bufferList.size()-1).putInt(binSize); // The density values ListOfDoubleArrays expectedValues = ev.getDensityAvg(); // todo @Suhas to handle buffer overflow bufferList.get(bufferList.size()-1).putLong(expectedValues.getLength()); for (double[] expectedArray : expectedValues.getValues()) { bufferList.add(new BufferedByteWriter()); for (double value : expectedArray) { if (Integer.MAX_VALUE - bufferList.get(bufferList.size()-1).bytesWritten() < 1000000) { bufferList.add(new BufferedByteWriter()); } bufferList.get(bufferList.size()-1).putFloat( (float) value); } } // Map of chromosome index -> normalization factor Map normalizationFactors = ev.getChrScaleFactors(); if (Integer.MAX_VALUE - bufferList.get(bufferList.size()-1).bytesWritten() < 1000000) { bufferList.add(new BufferedByteWriter()); } bufferList.get(bufferList.size()-1).putInt(normalizationFactors.size()); for (Map.Entry normFactor : normalizationFactors.entrySet()) { bufferList.get(bufferList.size()-1).putInt(normFactor.getKey()); bufferList.get(bufferList.size()-1).putFloat(normFactor.getValue().floatValue()); //System.out.println(normFactor.getKey() + " " + normFactor.getValue()); } } } else { // read in expected vector file. to get # of resolutions, might have to read twice. int count=0; try (Reader reader = new FileReader(expectedVectorFile); BufferedReader bufferedReader = new BufferedReader(reader)) { String line; while ((line = bufferedReader.readLine()) != null) { if (line.startsWith("fixedStep")) count++; if (line.startsWith("variableStep")) { System.err.println("Expected vector file must be in wiggle fixedStep format"); System.exit(19); } } } bufferList.get(bufferList.size()-1).putInt(count); try (Reader reader = new FileReader(expectedVectorFile); BufferedReader bufferedReader = new BufferedReader(reader)) { String line; while ((line = bufferedReader.readLine()) != null) { if (line.startsWith("fixedStep")) { String[] words = line.split("\\s+"); for (String str:words){ if (str.contains("chrom")){ String[] chrs = str.split("="); } } } } } } long nBytesV5 = 0; for (int i = 0; i>, Long> writeMatrix(MatrixPP matrix, LittleEndianOutputStream[] losArray, Deflater compressor, Map matrixPositions, int chromosomePairIndex, boolean doMultiThreadedBehavior) throws IOException { if (HiCGlobals.printVerboseComments) { System.err.println("Used Memory for matrix"); System.err.println(Runtime.getRuntime().totalMemory() - Runtime.getRuntime().freeMemory()); } LittleEndianOutputStream los = losArray[0]; long position = los.getWrittenCount(); los.writeInt(matrix.getChr1Idx()); los.writeInt(matrix.getChr2Idx()); int numResolutions = 0; for (MatrixZoomDataPP zd : matrix.getZoomData()) { if (zd != null) { numResolutions++; } } los.writeInt(numResolutions); //fos.writeInt(matrix.getZoomData().length); for ( int i = 0; i < matrix.getZoomData().length; i++) { MatrixZoomDataPP zd = matrix.getZoomData()[i]; if (zd != null) writeZoomHeader(zd, los); } long size = los.getWrittenCount() - position; if (chromosomePairIndex > -1) { matrixPositions.put("" + chromosomePairIndex, new IndexEntry(position, (int) size)); } else { matrixPositions.put(matrix.getKey(), new IndexEntry(position, (int) size)); } final Map> localBlockIndexes = new ConcurrentHashMap<>(); for (int i = matrix.getZoomData().length-1 ; i >= 0; i--) { MatrixZoomDataPP zd = matrix.getZoomData()[i]; if (zd != null) { List blockIndex = null; if (doMultiThreadedBehavior) { if (losArray.length > 1) { blockIndex = zd.mergeAndWriteBlocks(losArray, compressor, i, matrix.getZoomData().length); } else { blockIndex = zd.mergeAndWriteBlocks(losArray[0], compressor); } localBlockIndexes.put(zd.blockIndexPosition, blockIndex); } else { blockIndex = zd.mergeAndWriteBlocks(losArray[0], compressor); updateIndexPositions(blockIndex, losArray, true, outputFile, 0, zd.blockIndexPosition); } } } System.out.print("."); return new Pair<>(localBlockIndexes, position); } protected void updateIndexPositions(List blockIndex, LittleEndianOutputStream[] losArray, boolean doRestore, File outputFile, long currentPosition, long blockIndexPosition) throws IOException { // Temporarily close output stream. Remember position long losPos = 0; if (doRestore) { losPos = losArray[0].getWrittenCount(); losArray[0].close(); } RandomAccessFile raf = null; try { raf = new RandomAccessFile(outputFile, "rw"); // Block indices long pos = blockIndexPosition; raf.getChannel().position(pos); // Write as little endian BufferedByteWriter buffer = new BufferedByteWriter(); for (IndexEntry aBlockIndex : blockIndex) { buffer.putInt(aBlockIndex.id); buffer.putLong(aBlockIndex.position + currentPosition); buffer.putInt(aBlockIndex.size); } raf.write(buffer.getBytes()); } finally { if (raf != null) raf.close(); } if (doRestore) { FileOutputStream fos = new FileOutputStream(outputFile, true); fos.getChannel().position(losPos); losArray[0] = new LittleEndianOutputStream(new BufferedOutputStream(fos, HiCGlobals.bufferSize)); losArray[0].setWrittenCount(losPos); } } private void writeZoomHeader(MatrixZoomDataPP zd, LittleEndianOutputStream los) throws IOException { int numberOfBlocks = zd.blockNumbers.size(); los.writeString(zd.getUnit().toString()); // Unit los.writeInt(zd.getZoom()); // zoom index, lowest res is zero los.writeFloat((float) zd.getSum()); // sum los.writeFloat((float) zd.getOccupiedCellCount()); los.writeFloat((float) zd.getPercent5()); los.writeFloat((float) zd.getPercent95()); los.writeInt(zd.getBinSize()); los.writeInt(zd.getBlockBinCount()); los.writeInt(zd.getBlockColumnCount()); los.writeInt(numberOfBlocks); zd.blockIndexPosition = los.getWrittenCount(); // Placeholder for block index for (int i = 0; i < numberOfBlocks; i++) { los.writeInt(0); los.writeLong(0L); los.writeInt(0); } } public void setTmpdir(String tmpDirName) { if (tmpDirName != null) { createTempFolder(tmpDirName); } } private File createTempFolder(String newPath) { this.tmpDir = new File(newPath); if (!tmpDir.exists()) { UNIXTools.makeDir(tmpDir); tmpDir.deleteOnExit(); } return tmpDir; } public void setStatisticsFile(String statsOption) { statsFileName = statsOption; } } ================================================ FILE: src/juicebox/tools/utils/original/merge/HiCMergeTools.java ================================================ /* * The MIT License (MIT) * * Copyright (c) 2011-2022 Broad Institute, Aiden Lab, Rice University, Baylor College of Medicine * * Permission is hereby granted, free of charge, to any person obtaining a copy * of this software and associated documentation files (the "Software"), to deal * in the Software without restriction, including without limitation the rights * to use, copy, modify, merge, publish, distribute, sublicense, and/or sell * copies of the Software, and to permit persons to whom the Software is * furnished to do so, subject to the following conditions: * * The above copyright notice and this permission notice shall be included in * all copies or substantial portions of the Software. * * THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR * IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, * FITNESS FOR A PARTICULAR PURPOSE AND NON-INFRINGEMENT. IN NO EVENT SHALL THE * AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER * LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, * OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN * THE SOFTWARE. */ package juicebox.tools.utils.original.merge; import juicebox.data.Dataset; import juicebox.data.HiCFileTools; import juicebox.tools.utils.original.Preprocessor; import juicebox.tools.utils.original.merge.merger.GraphsMerger; import juicebox.tools.utils.original.merge.merger.Merger; import juicebox.tools.utils.original.merge.merger.PairedAlignmentStatsMerger; import juicebox.tools.utils.original.merge.merger.SingleAlignmentStatsMerger; import java.util.ArrayList; import java.util.List; public class HiCMergeTools { public static void mergeStatsAndGraphs(List dsPaths, Preprocessor builder, String stem) { List statsList = new ArrayList<>(); List graphsList = new ArrayList<>(); for (String dsPath : dsPaths) { List newList = new ArrayList<>(); newList.add(dsPath); Dataset ds = HiCFileTools.extractDatasetForCLT(newList, false); addToListIfValidString(ds.getStatistics(), statsList); addToListIfValidString(ds.getGraphs(), graphsList); } if (statsList.size() > 0) { boolean isSingleAlignment = confirmAllSingleAlignment(statsList); String statsPath = stem + "merged_stats.txt"; if (isSingleAlignment) { StatsUtils.merge(statsList, new SingleAlignmentStatsMerger(), statsPath); } else { StatsUtils.merge(statsList, new PairedAlignmentStatsMerger(), statsPath); } builder.setStatisticsFile(statsPath); } if (graphsList.size() > 0) { String graphsPath = stem + "merged_graphs_hists.m"; StatsUtils.merge(graphsList, new GraphsMerger(), graphsPath); builder.setGraphFile(graphsPath); } } private static void addToListIfValidString(String info, List infoList) { if (info != null && info.length() > 1) { infoList.add(info); } } private static boolean confirmAllSingleAlignment(List statsList) { boolean hasSingleAlignment = false; boolean hasPairedAlignment = false; for (String s : statsList) { hasSingleAlignment = hasSingleAlignment | Merger.containsIgnoreCase(s, "Read type: Single End"); hasPairedAlignment = hasPairedAlignment | Merger.containsIgnoreCase(s, "Read type: Paired End"); } if (hasSingleAlignment && hasPairedAlignment) { System.err.println("Cannot mix single-end and paired-end files together"); System.exit(9); } return hasSingleAlignment; } } ================================================ FILE: src/juicebox/tools/utils/original/merge/StatsUtils.java ================================================ /* * The MIT License (MIT) * * Copyright (c) 2011-2022 Broad Institute, Aiden Lab, Rice University, Baylor College of Medicine * * Permission is hereby granted, free of charge, to any person obtaining a copy * of this software and associated documentation files (the "Software"), to deal * in the Software without restriction, including without limitation the rights * to use, copy, modify, merge, publish, distribute, sublicense, and/or sell * copies of the Software, and to permit persons to whom the Software is * furnished to do so, subject to the following conditions: * * The above copyright notice and this permission notice shall be included in * all copies or substantial portions of the Software. * * THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR * IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, * FITNESS FOR A PARTICULAR PURPOSE AND NON-INFRINGEMENT. IN NO EVENT SHALL THE * AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER * LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, * OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN * THE SOFTWARE. */ package juicebox.tools.utils.original.merge; import juicebox.tools.utils.original.merge.merger.Merger; import java.util.List; public class StatsUtils { public static void merge(List statsList, Merger merger, String filename) { for (String s : statsList) { merger.parse(s); } merger.printToMergedFile(filename); } } ================================================ FILE: src/juicebox/tools/utils/original/merge/merger/GraphsMerger.java ================================================ /* * The MIT License (MIT) * * Copyright (c) 2011-2022 Broad Institute, Aiden Lab, Rice University, Baylor College of Medicine * * Permission is hereby granted, free of charge, to any person obtaining a copy * of this software and associated documentation files (the "Software"), to deal * in the Software without restriction, including without limitation the rights * to use, copy, modify, merge, publish, distribute, sublicense, and/or sell * copies of the Software, and to permit persons to whom the Software is * furnished to do so, subject to the following conditions: * * The above copyright notice and this permission notice shall be included in * all copies or substantial portions of the Software. * * THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR * IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, * FITNESS FOR A PARTICULAR PURPOSE AND NON-INFRINGEMENT. IN NO EVENT SHALL THE * AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER * LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, * OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN * THE SOFTWARE. */ package juicebox.tools.utils.original.merge.merger; import java.io.BufferedWriter; import java.io.FileWriter; import java.io.IOException; import java.util.Scanner; public class GraphsMerger extends Merger { private final long[] A = new long[2000]; private final long[][] B = new long[3][200]; private final long[][] D = new long[4][100]; private final long[] x = new long[100]; @Override public void parse(String s) { Scanner scanner = new Scanner(s); try { skipUntilNextArray(scanner); addTo1DArray(A, scanner); skipUntilNextArray(scanner); addTo2DArray(B, scanner); skipUntilNextArray(scanner); addTo2DArray(D, scanner); skipUntilNextArray(scanner); for (int idx = 0; idx < x.length; idx++) { long newX = scanner.nextLong(); if (x[idx] > 0L) { if (x[idx] != newX) { System.err.println("X mismatch error? " + x[idx] + " - " + newX); } } x[idx] = newX; } } catch (Exception e) { e.printStackTrace(); } } @Override public void printToMergedFile(String filename) { try { BufferedWriter histWriter = new BufferedWriter(new FileWriter(filename)); histWriter.write("A = [\n"); write1DArray(A, histWriter); histWriter.write("\n];\n"); histWriter.write("B = [\n"); write2DArray(B, histWriter); histWriter.write("\n];\n"); histWriter.write("D = [\n"); write2DArray(D, histWriter); histWriter.write("\n];"); histWriter.write("x = [\n"); write1DArray(x, histWriter); histWriter.write("\n];\n"); histWriter.close(); } catch (IOException error) { error.printStackTrace(); } } private void addTo1DArray(long[] arr, Scanner scanner) { for (int idx = 0; idx < arr.length; idx++) { arr[idx] += scanner.nextLong(); } } private void write1DArray(long[] arr, BufferedWriter histWriter) throws IOException { for (long tmp : arr) { histWriter.write(tmp + " "); } } private void addTo2DArray(long[][] arr, Scanner scanner) { int numRows = arr.length; int len = arr[0].length; for (int idx = 0; idx < len; idx++) { for (int r = 0; r < numRows; r++) { try { arr[r][idx] += scanner.nextLong(); } catch (Exception e) { System.err.println(scanner.next()); e.printStackTrace(); } } } } private void write2DArray(long[][] arr, BufferedWriter histWriter) throws IOException { int numRows = arr.length; int len = arr[0].length; for (int idx = 0; idx < len; idx++) { StringBuilder s = new StringBuilder("" + arr[0][idx]); for (int r = 1; r < numRows; r++) { s.append(" ").append(arr[r][idx]); } histWriter.write(s + "\n"); } } private void skipUntilNextArray(Scanner scanner) { while (!scanner.next().equals("[")) ; } } ================================================ FILE: src/juicebox/tools/utils/original/merge/merger/Merger.java ================================================ /* * The MIT License (MIT) * * Copyright (c) 2011-2022 Broad Institute, Aiden Lab, Rice University, Baylor College of Medicine * * Permission is hereby granted, free of charge, to any person obtaining a copy * of this software and associated documentation files (the "Software"), to deal * in the Software without restriction, including without limitation the rights * to use, copy, modify, merge, publish, distribute, sublicense, and/or sell * copies of the Software, and to permit persons to whom the Software is * furnished to do so, subject to the following conditions: * * The above copyright notice and this permission notice shall be included in * all copies or substantial portions of the Software. * * THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR * IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, * FITNESS FOR A PARTICULAR PURPOSE AND NON-INFRINGEMENT. IN NO EVENT SHALL THE * AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER * LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, * OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN * THE SOFTWARE. */ package juicebox.tools.utils.original.merge.merger; public abstract class Merger { public static boolean containsIgnoreCase(String main, String word) { return main.toLowerCase().contains(word.toLowerCase()); } public abstract void parse(String s); public abstract void printToMergedFile(String filename); } ================================================ FILE: src/juicebox/tools/utils/original/merge/merger/PairedAlignmentStatsMerger.java ================================================ /* * The MIT License (MIT) * * Copyright (c) 2011-2022 Broad Institute, Aiden Lab, Rice University, Baylor College of Medicine * * Permission is hereby granted, free of charge, to any person obtaining a copy * of this software and associated documentation files (the "Software"), to deal * in the Software without restriction, including without limitation the rights * to use, copy, modify, merge, publish, distribute, sublicense, and/or sell * copies of the Software, and to permit persons to whom the Software is * furnished to do so, subject to the following conditions: * * The above copyright notice and this permission notice shall be included in * all copies or substantial portions of the Software. * * THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR * IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, * FITNESS FOR A PARTICULAR PURPOSE AND NON-INFRINGEMENT. IN NO EVENT SHALL THE * AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER * LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, * OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN * THE SOFTWARE. */ package juicebox.tools.utils.original.merge.merger; import java.io.BufferedWriter; import java.io.FileWriter; import java.io.IOException; public class PairedAlignmentStatsMerger extends StatsMerger { @Override public void printToMergedFile(String filename) { try { BufferedWriter out = new BufferedWriter(new FileWriter(filename)); out.write("Read type: Paired End\n"); long denom1 = getStatistic(STATS_LABEL.TOTAL_SEQ); write(out, "Sequenced Read Pairs: ", STATS_LABEL.TOTAL_SEQ, -1, -1); write(out, "No chimera found: ", STATS_LABEL.NO_CHIMERA, denom1, -1); write(out, "One or both reads unmapped: ", STATS_LABEL.UNMAPPED, denom1, -1); write(out, "2 alignments: ", STATS_LABEL.TWO_ALIGN, denom1, -1); write(out, "\t2 alignments (A...B): ", STATS_LABEL.TWO_ALIGN_A, denom1, -1); write(out, "\t2 alignments (A1...A2B; A1B2...B1A2): ", STATS_LABEL.TWO_ALIGN_B, denom1, -1); write(out, "3 or more alignments: ", STATS_LABEL.THREE_PLUS, denom1, -1); write(out, "Ligation Motif Present: ", STATS_LABEL.LIGATION_MOTIF, denom1, -1); long denomAlignable = getStatistic(STATS_LABEL.TWO_ALIGN); long denom2AUniq = getStatistic(STATS_LABEL.TOTAL_UNIQUE); write(out, "Total Unique: ", STATS_LABEL.TOTAL_UNIQUE, denom1, denomAlignable); write(out, "Total Duplicates: ", STATS_LABEL.TOTAL_DUPS, denom1, denomAlignable); write(out, "Below MAPQ Threshold: ", STATS_LABEL.BELOW_MAPQ, denom1, denom2AUniq); write(out, "Hi-C Contacts: ", STATS_LABEL.HIC_CONTACTS, denom1, denom2AUniq); write(out, "\t3' Bias (Long Range): ", STATS_LABEL.THREE_BIAS, denom1, denom2AUniq); if (getStatistic(STATS_LABEL.PAIR_PERCENTS) == 25L) { out.write("\tPair Type %(L-I-O-R): 25% - 25% - 25% - 25%\n"); write(out, "\tL-I-O-R Convergence: ", STATS_LABEL.CONVERGENCE, -1, -1); } write(out, "Inter-chromosomal: ", STATS_LABEL.INTER, denom1, denom2AUniq); write(out, "Intra-chromosomal: ", STATS_LABEL.INTRA, denom1, denom2AUniq); out.write("Short Range (<20Kb):\n"); write(out, "\t<500BP: ", STATS_LABEL.FIVE_HUNDRED_BP, denom1, denom2AUniq); write(out, "\t500BP-5kB: ", STATS_LABEL.FIVE_KB, denom1, denom2AUniq); write(out, "\t5kB-20kB: ", STATS_LABEL.TWENTY_KB, denom1, denom2AUniq); write(out, "Long Range (>20Kb): ", STATS_LABEL.LONG_RANGE, denom1, denom2AUniq); out.close(); } catch (IOException error) { error.printStackTrace(); } } @Override protected STATS_LABEL parseLabel(String s) { if (containsIgnoreCase(s, "Sequenced Read Pairs:")) return STATS_LABEL.TOTAL_SEQ; if (containsIgnoreCase(s, "One or both reads unmapped:")) return STATS_LABEL.UNMAPPED; if (containsIgnoreCase(s, "2 alignments:")) return STATS_LABEL.TWO_ALIGN; if (containsIgnoreCase(s, "2 alignments (A...B):")) return STATS_LABEL.TWO_ALIGN_A; if (containsIgnoreCase(s, "2 alignments (A1...A2B; A1B2...B1A2):")) return STATS_LABEL.TWO_ALIGN_B; if (containsIgnoreCase(s, "Average insert size:")) return STATS_LABEL.IGNORE; return super.parseLabel(s); } } ================================================ FILE: src/juicebox/tools/utils/original/merge/merger/SingleAlignmentStatsMerger.java ================================================ /* * The MIT License (MIT) * * Copyright (c) 2011-2022 Broad Institute, Aiden Lab, Rice University, Baylor College of Medicine * * Permission is hereby granted, free of charge, to any person obtaining a copy * of this software and associated documentation files (the "Software"), to deal * in the Software without restriction, including without limitation the rights * to use, copy, modify, merge, publish, distribute, sublicense, and/or sell * copies of the Software, and to permit persons to whom the Software is * furnished to do so, subject to the following conditions: * * The above copyright notice and this permission notice shall be included in * all copies or substantial portions of the Software. * * THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR * IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, * FITNESS FOR A PARTICULAR PURPOSE AND NON-INFRINGEMENT. IN NO EVENT SHALL THE * AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER * LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, * OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN * THE SOFTWARE. */ package juicebox.tools.utils.original.merge.merger; import java.io.BufferedWriter; import java.io.FileWriter; import java.io.IOException; public class SingleAlignmentStatsMerger extends StatsMerger { @Override public void printToMergedFile(String filename) { try { BufferedWriter out = new BufferedWriter(new FileWriter(filename)); out.write("Read type: Single End\n"); write(out, "Sequenced Reads: ", STATS_LABEL.TOTAL_SEQ, -1, -1); long denom1 = getStatistic(STATS_LABEL.TOTAL_SEQ); write(out, "No chimera found: ", STATS_LABEL.NO_CHIMERA, denom1, -1); write(out, "0 alignments: ", STATS_LABEL.UNMAPPED, denom1, -1); write(out, "1 alignment: ", STATS_LABEL.ONE_ALIGN, denom1, -1); long denom1A = getStatistic(STATS_LABEL.ONE_ALIGN); write(out, "\t1 alignment unique: ", STATS_LABEL.ONE_UNIQUE, denom1, denom1A); write(out, "\t1 alignment duplicates: ", STATS_LABEL.ONE_DUPS, denom1, denom1A); write(out, "2 alignments: ", STATS_LABEL.TWO_ALIGN, denom1, -1); long denom2A = getStatistic(STATS_LABEL.TWO_ALIGN); write(out, "\t2 alignment unique: ", STATS_LABEL.TWO_UNIQUE, denom1, denom2A); write(out, "\t2 alignment duplicates: ", STATS_LABEL.TWO_DUPS, denom1, denom2A); write(out, "3 or more alignments: ", STATS_LABEL.THREE_PLUS, denom1, -1); write(out, "Ligation Motif Present: ", STATS_LABEL.LIGATION_MOTIF, denom1, -1); long denomAlignable = denom1A + denom2A; long denom2AUniq = getStatistic(STATS_LABEL.TWO_UNIQUE); write(out, "Total Unique: ", STATS_LABEL.TOTAL_UNIQUE, denom1, denomAlignable); write(out, "Total Duplicates: ", STATS_LABEL.TOTAL_DUPS, denom1, denomAlignable); write(out, "Below MAPQ Threshold: ", STATS_LABEL.BELOW_MAPQ, denom1, denom2AUniq); write(out, "Hi-C Contacts: ", STATS_LABEL.HIC_CONTACTS, denom1, denom2AUniq); write(out, "\t3' Bias (Long Range): ", STATS_LABEL.THREE_BIAS, denom1, denom2AUniq); if (getStatistic(STATS_LABEL.PAIR_PERCENTS) == 25L) { out.write("\tPair Type %(L-I-O-R): 25% - 25% - 25% - 25%\n"); write(out, "\tL-I-O-R Convergence: ", STATS_LABEL.CONVERGENCE, -1, -1); } write(out, "Inter-chromosomal: ", STATS_LABEL.INTER, denom1, denom2AUniq); write(out, "Intra-chromosomal: ", STATS_LABEL.INTRA, denom1, denom2AUniq); out.write("Short Range (<20Kb):\n"); write(out, "\t<500BP: ", STATS_LABEL.FIVE_HUNDRED_BP, denom1, denom2AUniq); write(out, "\t500BP-5kB: ", STATS_LABEL.FIVE_KB, denom1, denom2AUniq); write(out, "\t5kB-20kB: ", STATS_LABEL.TWENTY_KB, denom1, denom2AUniq); write(out, "Long Range (>20Kb): ", STATS_LABEL.LONG_RANGE, denom1, denom2AUniq); out.close(); } catch (IOException error) { error.printStackTrace(); } } @Override protected STATS_LABEL parseLabel(String s) { if (containsIgnoreCase(s, "Sequenced Reads:")) return STATS_LABEL.TOTAL_SEQ; if (containsIgnoreCase(s, "0 alignments:")) return STATS_LABEL.UNMAPPED; if (containsIgnoreCase(s, "1 alignment:")) return STATS_LABEL.ONE_ALIGN; if (containsIgnoreCase(s, "2 alignments:")) return STATS_LABEL.TWO_ALIGN; if (containsIgnoreCase(s, "1 alignment unique")) return STATS_LABEL.ONE_UNIQUE; if (containsIgnoreCase(s, "1 alignment duplicates")) return STATS_LABEL.ONE_DUPS; if (containsIgnoreCase(s, "2 alignment unique")) return STATS_LABEL.TWO_UNIQUE; if (containsIgnoreCase(s, "2 alignment duplicates")) return STATS_LABEL.TWO_DUPS; return super.parseLabel(s); } } ================================================ FILE: src/juicebox/tools/utils/original/merge/merger/StatsMerger.java ================================================ /* * The MIT License (MIT) * * Copyright (c) 2011-2022 Broad Institute, Aiden Lab, Rice University, Baylor College of Medicine * * Permission is hereby granted, free of charge, to any person obtaining a copy * of this software and associated documentation files (the "Software"), to deal * in the Software without restriction, including without limitation the rights * to use, copy, modify, merge, publish, distribute, sublicense, and/or sell * copies of the Software, and to permit persons to whom the Software is * furnished to do so, subject to the following conditions: * * The above copyright notice and this permission notice shall be included in * all copies or substantial portions of the Software. * * THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR * IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, * FITNESS FOR A PARTICULAR PURPOSE AND NON-INFRINGEMENT. IN NO EVENT SHALL THE * AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER * LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, * OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN * THE SOFTWARE. */ package juicebox.tools.utils.original.merge.merger; import java.io.BufferedWriter; import java.io.IOException; import java.text.NumberFormat; import java.util.Locale; import java.util.StringTokenizer; public abstract class StatsMerger extends Merger { public static int NUM_FIELDS = 28; private final NumberFormat nf = NumberFormat.getNumberInstance(Locale.US); private final long[] statistics = new long[NUM_FIELDS]; public void parse(String s) { StringTokenizer lines = new StringTokenizer(s, "\n"); while (lines.hasMoreTokens()) { String current = lines.nextToken(); processLine(current); } } protected long getStatistic(STATS_LABEL label) { return statistics[label.ordinal()]; } protected void processLine(String current) { int key = parseLabel(current).ordinal(); if (key == STATS_LABEL.IGNORE.ordinal()) return; String[] colonSplit = current.split(":"); if (colonSplit.length == 2) { if (hasNA(colonSplit[1])) return; String[] parenthesesSplit = colonSplit[1].split("\\("); if (key == STATS_LABEL.PAIR_PERCENTS.ordinal()) { if (statistics[key] != -1) { if (checkAll25(colonSplit[1])) { statistics[key] = 25; } else { statistics[key] = -1; } } } else { try { long value = Long.parseLong(parenthesesSplit[0].replaceAll(",", "").trim()); if (key == STATS_LABEL.CONVERGENCE.ordinal()) { statistics[key] = Math.max(statistics[key], value); } else { statistics[key] += value; } } catch (Exception e) { e.printStackTrace(); } } } else { // Appears to be correct format, convert files as appropriate System.err.println("Incorrect form in original statistics attribute. Offending line:"); System.err.println(current); } } private boolean checkAll25(String s) { int start = s.length(); int end = s.replaceAll("25%", "").length(); return start - end == 12; } private boolean hasNA(String s) { String na = "N/A"; return s.toLowerCase().contains(na.toLowerCase()); } protected STATS_LABEL parseLabel(String s) { if (containsIgnoreCase(s, "No chimera found:")) return STATS_LABEL.NO_CHIMERA; if (containsIgnoreCase(s, "3 or more alignments")) return STATS_LABEL.THREE_PLUS; if (containsIgnoreCase(s, "Ligation Motif Present:")) return STATS_LABEL.LIGATION_MOTIF; if (containsIgnoreCase(s, "Total Unique:")) return STATS_LABEL.TOTAL_UNIQUE; if (containsIgnoreCase(s, "Total Duplicates:")) return STATS_LABEL.TOTAL_DUPS; if (containsIgnoreCase(s, "Library Complexity")) return STATS_LABEL.IGNORE; if (containsIgnoreCase(s, "Intra-fragment Reads:")) return STATS_LABEL.INTRA_FRAG_READS; if (containsIgnoreCase(s, "Below MAPQ Threshold:")) return STATS_LABEL.BELOW_MAPQ; if (containsIgnoreCase(s, "Hi-C Contacts:")) return STATS_LABEL.HIC_CONTACTS; if (containsIgnoreCase(s, "3' Bias (Long Range):")) return STATS_LABEL.THREE_BIAS; if (containsIgnoreCase(s, "Pair Type %(L-I-O-R):")) return STATS_LABEL.PAIR_PERCENTS; if (containsIgnoreCase(s, "L-I-O-R Convergence:")) return STATS_LABEL.CONVERGENCE; if (containsIgnoreCase(s, "Inter-chromosomal:")) return STATS_LABEL.INTER; if (containsIgnoreCase(s, "Intra-chromosomal:")) return STATS_LABEL.INTRA; if (containsIgnoreCase(s, "Short Range (<20Kb):")) return STATS_LABEL.IGNORE; if (containsIgnoreCase(s, "<500BP:")) return STATS_LABEL.FIVE_HUNDRED_BP; if (containsIgnoreCase(s, "500BP-5kB:")) return STATS_LABEL.FIVE_KB; if (containsIgnoreCase(s, "5kB-20kB:")) return STATS_LABEL.TWENTY_KB; if (containsIgnoreCase(s, "Long Range (>20Kb):")) return STATS_LABEL.LONG_RANGE; return STATS_LABEL.IGNORE; } protected void write(BufferedWriter statsOut, String description, STATS_LABEL valType, long denom, long denom2) throws IOException { long value = statistics[valType.ordinal()]; if (value > 0) { String valString = commify(value); if (denom > 0) { if (denom2 > 0) { statsOut.write(description + valString + " (" + percent(value, denom) + " / " + percent(value, denom2) + ")\n"); } else { statsOut.write(description + valString + " (" + percent(value, denom) + ")\n"); } } else { statsOut.write(description + valString + "\n"); } } } private String percent(long num, long total) { return String.format("%.2f", num * 100f / total) + "%"; } private String commify(long value) { return nf.format(value); } public enum STATS_LABEL { TOTAL_SEQ, UNMAPPED, TWO_ALIGN, TWO_ALIGN_A, TWO_ALIGN_B, ONE_ALIGN, ONE_UNIQUE, ONE_DUPS, TWO_UNIQUE, TWO_DUPS, IGNORE, NO_CHIMERA, THREE_PLUS, LIGATION_MOTIF, TOTAL_UNIQUE, TOTAL_DUPS, INTRA_FRAG_READS, BELOW_MAPQ, HIC_CONTACTS, THREE_BIAS, PAIR_PERCENTS, CONVERGENCE, INTER, INTRA, FIVE_HUNDRED_BP, FIVE_KB, TWENTY_KB, LONG_RANGE } } ================================================ FILE: src/juicebox/tools/utils/original/mnditerator/AlignmentPair.java ================================================ /* * The MIT License (MIT) * * Copyright (c) 2011-2021 Broad Institute, Aiden Lab, Rice University, Baylor College of Medicine * * Permission is hereby granted, free of charge, to any person obtaining a copy * of this software and associated documentation files (the "Software"), to deal * in the Software without restriction, including without limitation the rights * to use, copy, modify, merge, publish, distribute, sublicense, and/or sell * copies of the Software, and to permit persons to whom the Software is * furnished to do so, subject to the following conditions: * * The above copyright notice and this permission notice shall be included in * all copies or substantial portions of the Software. * * THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR * IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, * FITNESS FOR A PARTICULAR PURPOSE AND NON-INFRINGEMENT. IN NO EVENT SHALL THE * AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER * LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, * OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN * THE SOFTWARE. */ package juicebox.tools.utils.original.mnditerator; //import htsjdk.tribble.util.LittleEndianOutputStream; //import java.io.IOException; public class AlignmentPair { private boolean strand1 = true; // true if forward strand private boolean strand2 = false; private int frag1 = 0; private int frag2 = 1; private final int chr1; private final int pos1; private final int chr2; private final int pos2; private int mapq1 = 1000; private int mapq2 = 1000; private float score = 1.0f; // The score (or count) private boolean isContigPair; private boolean isValidForStats = true; public AlignmentPair(boolean strand1, int chr1, int pos1, int frag1, int mapq1, boolean strand2, int chr2, int pos2, int frag2, int mapq2) { this.strand1 = strand1; this.chr1 = chr1; this.pos1 = pos1; this.frag1 = frag1; this.mapq1 = mapq1; this.strand2 = strand2; this.chr2 = chr2; this.pos2 = pos2; this.frag2 = frag2; this.mapq2 = mapq2; isContigPair = false; } public AlignmentPair() { this(false, -1, -1, -1, -1, false, -1, -1, -1, -1); isContigPair = true; isValidForStats = false; } public AlignmentPair(boolean ignore) { this(); isContigPair = false; isValidForStats = false; } public AlignmentPair(int chr1, int pos1, int chr2, int pos2) { this.chr1 = chr1; this.pos1 = pos1; this.chr2 = chr2; this.pos2 = pos2; isContigPair = false; } public AlignmentPair(boolean strand1, int chr1, int pos1, int frag1, boolean strand2, int chr2, int pos2, int frag2) { this.strand1 = strand1; this.chr1 = chr1; this.pos1 = pos1; this.frag1 = frag1; this.strand2 = strand2; this.chr2 = chr2; this.pos2 = pos2; this.frag2 = frag2; isContigPair = false; } public int getChr1() { return chr1; } public int getPos1() { return pos1; } public int getChr2() { return chr2; } public int getPos2() { return pos2; } public int getMapq1() { return mapq1; } public int getMapq2() { return mapq2; } public boolean getStrand1() { return strand1; } private int getStrand1AsInt() { return strand1 ? 0 : 16; // 0 is the forward strand, so true; 16 is the reverse strand } private int getStrand2AsInt() { return strand2 ? 0 : 16; // 0 is the forward strand, so true; 16 is the reverse strand } public boolean getStrand2() { return strand2; } public int getFrag1() { return frag1; } public int getFrag2() { return frag2; } public float getScore() { return score; } public void setScore(float score1) { this.score = score1; } public String toString() { int str1 = getStrand1AsInt(); int str2 = getStrand2AsInt(); return str1 + "\t" + chr1 + "\t" + pos1 + "\t" + frag1 + "\t" + mapq1 + "\t" + str2 + "\t" + chr2 + "\t" + pos2 + "\t" + frag2 + "\t" + mapq2 + "\t" + score; } public boolean isContigPair() { return this.isContigPair; } public boolean isValid() { return isValidForStats; } public boolean isShort() { return mapq1 == 1000 && mapq2 == 1000; } public void updateFragments(int frag1, int frag2) { this.frag1 = frag1; this.frag2 = frag2; } public void updateStrands(boolean strand1, boolean strand2) { this.strand1 = strand1; this.strand2 = strand2; } public void updateMAPQs(int mapq1, int mapq2) { this.mapq1 = mapq1; this.mapq2 = mapq2; } } ================================================ FILE: src/juicebox/tools/utils/original/mnditerator/AlignmentPairLong.java ================================================ /* * The MIT License (MIT) * * Copyright (c) 2011-2021 Broad Institute, Aiden Lab, Rice University, Baylor College of Medicine * * Permission is hereby granted, free of charge, to any person obtaining a copy * of this software and associated documentation files (the "Software"), to deal * in the Software without restriction, including without limitation the rights * to use, copy, modify, merge, publish, distribute, sublicense, and/or sell * copies of the Software, and to permit persons to whom the Software is * furnished to do so, subject to the following conditions: * * The above copyright notice and this permission notice shall be included in * all copies or substantial portions of the Software. * * THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR * IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, * FITNESS FOR A PARTICULAR PURPOSE AND NON-INFRINGEMENT. IN NO EVENT SHALL THE * AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER * LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, * OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN * THE SOFTWARE. */ package juicebox.tools.utils.original.mnditerator; public class AlignmentPairLong extends AlignmentPair { private final String seq1; private final String seq2; public AlignmentPairLong(boolean strand1, int chr1, int pos1, int frag1, int mapq1, String seq1, boolean strand2, int chr2, int pos2, int frag2, int mapq2, String seq2) { super(strand1, chr1, pos1, frag1, mapq1, strand2, chr2, pos2, frag2, mapq2); this.seq1 = seq1; this.seq2 = seq2; } public AlignmentPairLong(AlignmentPair np, String seq1, String seq2) { this(np.getStrand1(), np.getChr1(), np.getPos1(), np.getFrag1(), np.getMapq1(), seq1, np.getStrand2(), np.getChr2(), np.getPos2(), np.getFrag2(), np.getMapq2(), seq2); } public String getSeq1() { return seq1; } public String getSeq2() { return seq2; } } ================================================ FILE: src/juicebox/tools/utils/original/mnditerator/AsciiPairIterator.java ================================================ /* * The MIT License (MIT) * * Copyright (c) 2011-2021 Broad Institute, Aiden Lab, Rice University, Baylor College of Medicine * * Permission is hereby granted, free of charge, to any person obtaining a copy * of this software and associated documentation files (the "Software"), to deal * in the Software without restriction, including without limitation the rights * to use, copy, modify, merge, publish, distribute, sublicense, and/or sell * copies of the Software, and to permit persons to whom the Software is * furnished to do so, subject to the following conditions: * * The above copyright notice and this permission notice shall be included in * all copies or substantial portions of the Software. * * THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR * IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, * FITNESS FOR A PARTICULAR PURPOSE AND NON-INFRINGEMENT. IN NO EVENT SHALL THE * AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER * LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, * OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN * THE SOFTWARE. */ package juicebox.tools.utils.original.mnditerator; import juicebox.HiCGlobals; import juicebox.data.ChromosomeHandler; import juicebox.tools.utils.original.Chunk; import org.broad.igv.util.ParsingUtils; import java.io.*; import java.nio.charset.StandardCharsets; import java.util.Map; import java.util.zip.GZIPInputStream; public class AsciiPairIterator extends GenericPairIterator implements PairIterator { private int mndChunkSize = 0; private int mndChunkCounter = 0; private boolean stopAfterChunk = false; public AsciiPairIterator(String path, Map chromosomeOrdinals, ChromosomeHandler handler, boolean allowNewChroms) throws IOException { super(new MNDFileParser(new ComplexLineParser(chromosomeOrdinals, handler, allowNewChroms, true))); if (path.endsWith(".gz")) { InputStream gzipStream = new GZIPInputStream(new FileInputStream(path)); Reader decoder = new InputStreamReader(gzipStream, StandardCharsets.UTF_8); this.reader = new BufferedReader(decoder, 4194304); } else { this.reader = new BufferedReader(new InputStreamReader(ParsingUtils.openInputStream(path)), HiCGlobals.bufferSize); } advance(); } public AsciiPairIterator(String path, Map chromosomeOrdinals, Chunk chunk, ChromosomeHandler handler) throws IOException { super(new MNDFileParser(new ComplexLineParser(chromosomeOrdinals, handler, false, false))); if (path.endsWith(".gz")) { System.err.println("Multithreading with indexed mnd currently only works with unzipped mnd"); System.exit(70); } else { FileInputStream fis = new FileInputStream(path); fis.getChannel().position(chunk.mndIndex); this.reader = new BufferedReader(new InputStreamReader(fis), HiCGlobals.bufferSize); //this.mndStart = chunk.mndIndex; this.mndChunkSize = chunk.mndChunk; this.stopAfterChunk = true; } advance(); } @Override protected String validateLine(String nextLine) { if (nextLine != null) { mndChunkCounter += nextLine.length() + 1; if (stopAfterChunk) { if (mndChunkCounter > mndChunkSize) { return null; } } } return nextLine; } } ================================================ FILE: src/juicebox/tools/utils/original/mnditerator/AsciiToBinConverter.java ================================================ /* * The MIT License (MIT) * * Copyright (c) 2011-2021 Broad Institute, Aiden Lab, Rice University, Baylor College of Medicine * * Permission is hereby granted, free of charge, to any person obtaining a copy * of this software and associated documentation files (the "Software"), to deal * in the Software without restriction, including without limitation the rights * to use, copy, modify, merge, publish, distribute, sublicense, and/or sell * copies of the Software, and to permit persons to whom the Software is * furnished to do so, subject to the following conditions: * * The above copyright notice and this permission notice shall be included in * all copies or substantial portions of the Software. * * THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR * IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, * FITNESS FOR A PARTICULAR PURPOSE AND NON-INFRINGEMENT. IN NO EVENT SHALL THE * AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER * LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, * OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN * THE SOFTWARE. */ package juicebox.tools.utils.original.mnditerator; import htsjdk.tribble.util.LittleEndianOutputStream; import juicebox.data.ChromosomeHandler; import juicebox.data.basics.Chromosome; import java.io.*; import java.util.HashMap; import java.util.Map; /** * Utility class for converting an asscii "pair" file to a compact binary format. Can greatly speed up calculation * of "hic" file * Input: D0J8AACXX120130:6:1101:1003:8700/1 15 61559113 0 D0J8AACXX120130:6:1101:1003:8700/2 15 61559309 16 * Output: [chr1 index][pos1][chr2 index][pos 2] (int, int, int, int)/ * * @author Jim Robinson * @since 4/7/12 */ public class AsciiToBinConverter { /** * @param inputPath * @param outputFile * @param chromosomeHandler */ public static void convert(String inputPath, String outputFile, ChromosomeHandler chromosomeHandler) throws IOException { Map chromosomeOrdinals = new HashMap<>(); for (Chromosome c : chromosomeHandler.getChromosomeArray()) { chromosomeOrdinals.put(c.getName(), c.getIndex()); } AsciiPairIterator iter = null; BufferedOutputStream bos = null; try { bos = new BufferedOutputStream(new FileOutputStream(outputFile)); LittleEndianOutputStream les = new LittleEndianOutputStream(bos); iter = new AsciiPairIterator(inputPath, chromosomeOrdinals, chromosomeHandler, true); if (outputFile.endsWith(".bn")) { writeOutShortBinaryFormat(iter, les); } else { writeOutStandardBinaryFormat(iter, les); } les.flush(); bos.flush(); } finally { if (iter != null) iter.close(); if (bos != null) bos.close(); } } private static void writeOutShortBinaryFormat(AsciiPairIterator iter, LittleEndianOutputStream les) throws IOException { while (iter.hasNext()) { AlignmentPair pair = iter.next(); les.writeInt(pair.getChr1()); les.writeInt(pair.getPos1()); les.writeInt(pair.getChr2()); les.writeInt(pair.getPos2()); les.writeFloat(pair.getScore()); } } private static void writeOutStandardBinaryFormat(AsciiPairIterator iter, LittleEndianOutputStream les) throws IOException { while (iter.hasNext()) { AlignmentPair pair = iter.next(); les.writeBoolean(pair.getStrand1()); les.writeInt(pair.getChr1()); les.writeInt(pair.getPos1()); les.writeInt(pair.getFrag1()); les.writeBoolean(pair.getStrand2()); les.writeInt(pair.getChr2()); les.writeInt(pair.getPos2()); les.writeInt(pair.getFrag2()); } } public static void convertBack(String inputPath, String outputFile) throws IOException { PrintWriter pw = null; try { File f = new File(outputFile); FileWriter fw = new FileWriter(f); pw = new PrintWriter(fw); BinPairIterator iter; if (inputPath.endsWith(".bn")) { iter = new ShortBinPairIterator(inputPath); } else { iter = new BinPairIterator(inputPath); } while (iter.hasNext()) { AlignmentPair pair = iter.next(); pw.println(pair); } } finally { if (pw != null) { pw.close(); } } } } ================================================ FILE: src/juicebox/tools/utils/original/mnditerator/BAMPairIterator.java ================================================ /* * The MIT License (MIT) * * Copyright (c) 2011-2021 Broad Institute, Aiden Lab, Rice University, Baylor College of Medicine * * Permission is hereby granted, free of charge, to any person obtaining a copy * of this software and associated documentation files (the "Software"), to deal * in the Software without restriction, including without limitation the rights * to use, copy, modify, merge, publish, distribute, sublicense, and/or sell * copies of the Software, and to permit persons to whom the Software is * furnished to do so, subject to the following conditions: * * The above copyright notice and this permission notice shall be included in * all copies or substantial portions of the Software. * * THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR * IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, * FITNESS FOR A PARTICULAR PURPOSE AND NON-INFRINGEMENT. IN NO EVENT SHALL THE * AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER * LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, * OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN * THE SOFTWARE. */ package juicebox.tools.utils.original.mnditerator; import htsjdk.samtools.util.CloseableIterator; import org.broad.igv.sam.Alignment; import org.broad.igv.sam.ReadMate; import org.broad.igv.sam.reader.AlignmentReader; import org.broad.igv.sam.reader.AlignmentReaderFactory; import java.io.IOException; import java.util.Map; /** * TODO - should this be deleted? * Also, the chromosomeOrdinals map seems to always be empty * * @author Jim Robinson * @since 9/24/11 */ public class BAMPairIterator implements PairIterator { private AlignmentPair nextPair = null; private AlignmentPair preNext = null; private final CloseableIterator iterator; private final AlignmentReader reader; // Map of name -> index private Map chromosomeOrdinals; public BAMPairIterator(String path) throws IOException { this.reader = AlignmentReaderFactory.getReader(path, false); this.iterator = reader.iterator(); advance(); } private void advance() { while (iterator.hasNext()) { Alignment alignment = (Alignment) iterator.next(); final ReadMate mate = alignment.getMate(); if (alignment.isPaired() && alignment.isMapped() && alignment.getMappingQuality() > 0 && mate != null && mate.isMapped()) { // Skip "normal" insert sizes if ((!alignment.getChr().equals(mate.getChr())) || alignment.getInferredInsertSize() > 1000) { // Each pair is represented twice in the file, keep the record with the "leftmost" coordinate if ((alignment.getChr().equals(mate.getChr()) && alignment.getStart() < mate.getStart()) || (alignment.getChr().compareTo(mate.getChr()) < 0)) { final String chrom1 = alignment.getChr(); final String chrom2 = mate.getChr(); if (chromosomeOrdinals.containsKey(chrom1) && chromosomeOrdinals.containsKey(chrom2)) { int chr1 = chromosomeOrdinals.get(chrom1); int chr2 = chromosomeOrdinals.get(chrom2); // nextPair = new AlignmentPair(chr1, alignment.getStart(), chr2, mate.getStart()); } return; } } } } nextPair = null; } public boolean hasNext() { return preNext != null || nextPair != null; //To change body of implemented methods use File | Settings | File Templates. } public AlignmentPair next() { AlignmentPair p; if (preNext == null) { p = nextPair; advance(); } else { p = preNext; preNext = null; } return p; } public void remove() { // Not implemented } public void close() { iterator.close(); try { reader.close(); } catch (IOException e) { e.printStackTrace(); //To change body of catch statement use File | Settings | File Templates. } } } ================================================ FILE: src/juicebox/tools/utils/original/mnditerator/BinPairIterator.java ================================================ /* * The MIT License (MIT) * * Copyright (c) 2011-2021 Broad Institute, Aiden Lab, Rice University, Baylor College of Medicine * * Permission is hereby granted, free of charge, to any person obtaining a copy * of this software and associated documentation files (the "Software"), to deal * in the Software without restriction, including without limitation the rights * to use, copy, modify, merge, publish, distribute, sublicense, and/or sell * copies of the Software, and to permit persons to whom the Software is * furnished to do so, subject to the following conditions: * * The above copyright notice and this permission notice shall be included in * all copies or substantial portions of the Software. * * THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR * IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, * FITNESS FOR A PARTICULAR PURPOSE AND NON-INFRINGEMENT. IN NO EVENT SHALL THE * AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER * LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, * OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN * THE SOFTWARE. */ package juicebox.tools.utils.original.mnditerator; import htsjdk.tribble.util.LittleEndianInputStream; import java.io.BufferedInputStream; import java.io.EOFException; import java.io.FileInputStream; import java.io.IOException; /** * @author Jim Robinson * @since 4/7/12 */ public class BinPairIterator implements PairIterator { protected final LittleEndianInputStream is; protected AlignmentPair next; private AlignmentPair preNext; /** * TODO -- chromosomeIndexes is ignored for now, but should be used to map the chromosome stored in the * TODO -- bin pair file with an integer index. The current assumption is the chromosome map in * TODO -- the bin pair file is the same being used for the hic file, a fragile assumption. * * @param path * @throws IOException */ public BinPairIterator(String path) throws IOException { is = new LittleEndianInputStream(new BufferedInputStream(new FileInputStream(path))); advance(); } public boolean hasNext() { return preNext != null || next != null; //To change body of implemented methods use File | Settings | File Templates. } public AlignmentPair next() { AlignmentPair retValue; if (preNext == null) { retValue = next; advance(); } else { retValue = preNext; preNext = null; } return retValue; } public void remove() { } public void close() { if (is != null) try { is.close(); } catch (IOException e) { e.printStackTrace(); } } protected void advance() { try { boolean str1 = (is.readByte() != 0); int chr1 = is.readInt(); int pos1 = is.readInt(); int frag1 = is.readInt(); boolean str2 = (is.readByte() != 0); int chr2 = is.readInt(); int pos2 = is.readInt(); int frag2 = is.readInt(); next = new AlignmentPair(str1, chr1, pos1, frag1, str2, chr2, pos2, frag2); } catch (IOException e) { next = null; if (!(e instanceof EOFException)) { e.printStackTrace(); } } } } ================================================ FILE: src/juicebox/tools/utils/original/mnditerator/ComplexLineParser.java ================================================ /* * The MIT License (MIT) * * Copyright (c) 2011-2021 Broad Institute, Aiden Lab, Rice University, Baylor College of Medicine * * Permission is hereby granted, free of charge, to any person obtaining a copy * of this software and associated documentation files (the "Software"), to deal * in the Software without restriction, including without limitation the rights * to use, copy, modify, merge, publish, distribute, sublicense, and/or sell * copies of the Software, and to permit persons to whom the Software is * furnished to do so, subject to the following conditions: * * The above copyright notice and this permission notice shall be included in * all copies or substantial portions of the Software. * * THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR * IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, * FITNESS FOR A PARTICULAR PURPOSE AND NON-INFRINGEMENT. IN NO EVENT SHALL THE * AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER * LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, * OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN * THE SOFTWARE. */ package juicebox.tools.utils.original.mnditerator; import juicebox.data.ChromosomeHandler; import java.util.Map; public class ComplexLineParser extends MNDLineParser { private final Map chromosomeOrdinals; private final boolean allowNewChroms; private final ChromosomeHandler handler; private int chromCounter = -1; ComplexLineParser(Map chromosomeOrdinals, ChromosomeHandler handler, boolean allowNewChroms, boolean shouldUpdateCounter) { this.chromosomeOrdinals = chromosomeOrdinals; this.allowNewChroms = allowNewChroms; this.handler = handler; if (shouldUpdateCounter) { updateChromCounter(); } } @Override protected int getChromosomeOrdinal(String chrom) { return chromosomeOrdinals.get(chrom); } @Override public AlignmentPair generateBasicPair(String[] tokens, int chrom1Index, int chrom2Index, int pos1Index, int pos2Index) { String chrom1 = handler.cleanUpName(getInternedString(tokens[chrom1Index])); String chrom2 = handler.cleanUpName(getInternedString(tokens[chrom2Index])); if (isValid(chrom1, chrom2)) { return createPair(tokens, chrom1, chrom2, pos1Index, pos2Index); } return new AlignmentPair(); // sets dummy values, sets isContigPair } @Override public String getChromosomeNameFromIndex(int chrIndex) { return handler.getChromosomeFromIndex(chrIndex).getName(); } private void updateOrdinalsMap(String chrom) { if (!chromosomeOrdinals.containsKey(chrom)) { chromosomeOrdinals.put(chrom, chromCounter++); } } private void updateChromCounter() { for (Integer val : chromosomeOrdinals.values()) { chromCounter = Math.max(chromCounter, val); } chromCounter++; } private boolean isValid(String chrom1, String chrom2) { if (chromosomeOrdinals.containsKey(chrom1) && chromosomeOrdinals.containsKey(chrom2)) { return true; } if (allowNewChroms) { updateOrdinalsMap(chrom1); updateOrdinalsMap(chrom2); return true; } return false; } } ================================================ FILE: src/juicebox/tools/utils/original/mnditerator/GenericPairIterator.java ================================================ /* * The MIT License (MIT) * * Copyright (c) 2011-2021 Broad Institute, Aiden Lab, Rice University, Baylor College of Medicine * * Permission is hereby granted, free of charge, to any person obtaining a copy * of this software and associated documentation files (the "Software"), to deal * in the Software without restriction, including without limitation the rights * to use, copy, modify, merge, publish, distribute, sublicense, and/or sell * copies of the Software, and to permit persons to whom the Software is * furnished to do so, subject to the following conditions: * * The above copyright notice and this permission notice shall be included in * all copies or substantial portions of the Software. * * THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR * IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, * FITNESS FOR A PARTICULAR PURPOSE AND NON-INFRINGEMENT. IN NO EVENT SHALL THE * AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER * LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, * OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN * THE SOFTWARE. */ package juicebox.tools.utils.original.mnditerator; import java.io.BufferedReader; import java.io.IOException; public abstract class GenericPairIterator implements PairIterator { protected final MNDFileParser mndFileParser; protected AlignmentPair nextPair = null; protected BufferedReader reader; public GenericPairIterator(MNDFileParser mndFileParser) { this.mndFileParser = mndFileParser; } public boolean hasNext() { return nextPair != null; } public AlignmentPair next() { AlignmentPair p = nextPair; advance(); return p; } protected void advance() { try { String nextLine = reader.readLine(); nextLine = validateLine(nextLine); if (nextLine != null) { nextPair = mndFileParser.parse(nextLine); return; } } catch (IOException e) { e.printStackTrace(); } nextPair = null; } protected String validateLine(String nextLine) { return nextLine; } public void remove() { // Not implemented } public void close() { try { reader.close(); } catch (IOException e) { e.printStackTrace(); //To change body of catch statement use File | Settings | File Templates. } } } ================================================ FILE: src/juicebox/tools/utils/original/mnditerator/MNDFileParser.java ================================================ /* * The MIT License (MIT) * * Copyright (c) 2011-2021 Broad Institute, Aiden Lab, Rice University, Baylor College of Medicine * * Permission is hereby granted, free of charge, to any person obtaining a copy * of this software and associated documentation files (the "Software"), to deal * in the Software without restriction, including without limitation the rights * to use, copy, modify, merge, publish, distribute, sublicense, and/or sell * copies of the Software, and to permit persons to whom the Software is * furnished to do so, subject to the following conditions: * * The above copyright notice and this permission notice shall be included in * all copies or substantial portions of the Software. * * THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR * IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, * FITNESS FOR A PARTICULAR PURPOSE AND NON-INFRINGEMENT. IN NO EVENT SHALL THE * AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER * LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, * OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN * THE SOFTWARE. */ package juicebox.tools.utils.original.mnditerator; import juicebox.tools.clt.JuiceboxCLT; import java.io.IOException; public class MNDFileParser { protected static final int dcicF1 = 0, dcicF2 = 1, dcicM1 = 2, dcicM2 = 3; public static String[] dcicCategories = new String[]{"frag1", "frag2", "mapq1", "mapq2"}; protected final int[] dcicIndices = new int[]{-1, -1, -1, -1}; private final MNDLineParser pg; private Format format = null; MNDFileParser(MNDLineParser pg) { this.pg = pg; } public static Format getFileFormat(int nTokens, String nextLine) throws IOException { if (nTokens == 4) { return Format.SUPER_SHORT; } else if (nTokens == 5) { return Format.SUPER_SHORT_WITH_SCORE; } else if (nTokens == 8) { return Format.SHORT; } else if (nTokens == 9) { return Format.SHORT_WITH_SCORE; } else if (nTokens == 16) { return Format.LONG; } else if (nTokens == 11) { return Format.MEDIUM; } else { throw new IOException("Unexpected number of columns: " + nTokens + "\n" + "Check line containing:\n" + nextLine); } } /** * formats detailed: https://github.com/aidenlab/juicer/wiki/Pre#file-format */ public AlignmentPair parse(String nextLine) throws IOException { String[] tokens = JuiceboxCLT.splitToList(nextLine); if (format == null) { int nTokens = tokens.length; if (nextLine.startsWith("#")) { // header line, skip; DCIC files MUST have header format = Format.DCIC; updateDCICIndicesIfApplicable(nextLine, tokens); return new AlignmentPair(true); } else { format = getFileFormat(nTokens, nextLine); } } if (format == Format.MEDIUM) { return parseMediumFormat(tokens); } else if (format == Format.LONG) { return parseLongFormat(tokens); } else if (format == Format.DCIC) { return parseDCICFormat(tokens); } else if (format == Format.SUPER_SHORT || format == Format.SUPER_SHORT_WITH_SCORE) { return parseSuperShortFormat(tokens, format == Format.SUPER_SHORT_WITH_SCORE); } else { return parseShortFormat(tokens, format == Format.SHORT_WITH_SCORE); } } public void updateDCICIndicesIfApplicable(String nextLine, String[] tokens) { if (nextLine.contains("column")) { for (int i = 0; i < tokens.length; i++) { for (int k = 0; k < MNDFileParser.dcicCategories.length; k++) { if (tokens[i].contains(MNDFileParser.dcicCategories[k])) { dcicIndices[k] = i - 1; } } } } } public AlignmentPair parseShortFormat(String[] tokens, boolean includeScore) { AlignmentPair nextPair = pg.generateBasicPair(tokens, 1, 5, 2, 6); pg.updatePairScoreIfNeeded(includeScore, nextPair, tokens, 8); pg.updateFragmentsForPair(nextPair, tokens, 3, 7); pg.updateStrandsForPair(nextPair, tokens, 0, 4); return nextPair; } public AlignmentPair parseSuperShortFormat(String[] tokens, boolean includeScore) { AlignmentPair nextPair = pg.generateBasicPair(tokens, 0, 2, 1, 3); pg.updatePairScoreIfNeeded(includeScore, nextPair, tokens, 4); return nextPair; } public AlignmentPair parseDCICFormat(String[] tokens) { AlignmentPair nextPair = pg.generateBasicPair(tokens, 1, 3, 2, 4); pg.updateDCICStrandsForPair(nextPair, tokens, 5, 6); if (dcicIndices[dcicF1] != -1 && dcicIndices[dcicF2] != -1) { pg.updateFragmentsForPair(nextPair, tokens, dcicIndices[dcicF1], dcicIndices[dcicF2]); } if (dcicIndices[dcicM1] != -1 && dcicIndices[dcicM2] != -1) { pg.updateMAPQsForPair(nextPair, tokens, dcicIndices[dcicM1], dcicIndices[dcicM2]); } return nextPair; } public AlignmentPair parseLongFormat(String[] tokens) { AlignmentPair nextPair = pg.generateMediumPair(tokens, 1, 5, 2, 6, 3, 7, 8, 11, 0, 4); return new AlignmentPairLong(nextPair, tokens[10], tokens[13]); } public AlignmentPair parseMediumFormat(String[] tokens) { return pg.generateMediumPair(tokens, 2, 6, 3, 7, 4, 8, 9, 10, 1, 5); } public String getChromosomeNameFromIndex(int chrIndex) { return pg.getChromosomeNameFromIndex(chrIndex); } enum Format {SUPER_SHORT, SUPER_SHORT_WITH_SCORE, SHORT, LONG, MEDIUM, SHORT_WITH_SCORE, DCIC} } ================================================ FILE: src/juicebox/tools/utils/original/mnditerator/MNDLineParser.java ================================================ /* * The MIT License (MIT) * * Copyright (c) 2011-2021 Broad Institute, Aiden Lab, Rice University, Baylor College of Medicine * * Permission is hereby granted, free of charge, to any person obtaining a copy * of this software and associated documentation files (the "Software"), to deal * in the Software without restriction, including without limitation the rights * to use, copy, modify, merge, publish, distribute, sublicense, and/or sell * copies of the Software, and to permit persons to whom the Software is * furnished to do so, subject to the following conditions: * * The above copyright notice and this permission notice shall be included in * all copies or substantial portions of the Software. * * THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR * IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, * FITNESS FOR A PARTICULAR PURPOSE AND NON-INFRINGEMENT. IN NO EVENT SHALL THE * AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER * LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, * OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN * THE SOFTWARE. */ package juicebox.tools.utils.original.mnditerator; import java.util.HashMap; import java.util.Map; public abstract class MNDLineParser { /** * A map of chromosome name -> chromosome string. A private "intern" pool. The java "intern" pool stores string * in perm space, which is rather limited and can cause us to run out of memory. */ private final Map stringInternPool = new HashMap<>(); abstract protected int getChromosomeOrdinal(String chrom); abstract public String getChromosomeNameFromIndex(int chrIndex); public abstract AlignmentPair generateBasicPair(String[] tokens, int chrom1Index, int chrom2Index, int pos1Index, int pos2Index); protected AlignmentPair createPair(String[] tokens, String chrom1, String chrom2, int pos1Index, int pos2Index) { int chr1 = getChromosomeOrdinal(chrom1); int chr2 = getChromosomeOrdinal(chrom2); int pos1 = Integer.parseInt(tokens[pos1Index]); int pos2 = Integer.parseInt(tokens[pos2Index]); return new AlignmentPair(chr1, pos1, chr2, pos2); } public AlignmentPair generateMediumPair(String[] tokens, int chrom1Index, int chrom2Index, int pos1Index, int pos2Index, int frag1Index, int frag2Index, int mapq1Index, int mapq2Index, int strand1Index, int strand2Index) { AlignmentPair nextPair = generateBasicPair(tokens, chrom1Index, chrom2Index, pos1Index, pos2Index); updateFragmentsForPair(nextPair, tokens, frag1Index, frag2Index); updateMAPQsForPair(nextPair, tokens, mapq1Index, mapq2Index); updateStrandsForPair(nextPair, tokens, strand1Index, strand2Index); return nextPair; } public void updateStrandsForPair(AlignmentPair nextPair, String[] tokens, int strand1Index, int strand2Index) { boolean strand1 = Integer.parseInt(tokens[strand1Index]) == 0; boolean strand2 = Integer.parseInt(tokens[strand2Index]) == 0; nextPair.updateStrands(strand1, strand2); } public void updateDCICStrandsForPair(AlignmentPair nextPair, String[] tokens, int strand1Index, int strand2Index) { boolean strand1 = tokens[strand1Index].equals("+"); boolean strand2 = tokens[strand2Index].equals("+"); nextPair.updateStrands(strand1, strand2); } public void updateMAPQsForPair(AlignmentPair nextPair, String[] tokens, int mapq1Index, int mapq2Index) { int mapq1 = Integer.parseInt(tokens[mapq1Index]); int mapq2 = Integer.parseInt(tokens[mapq2Index]); nextPair.updateMAPQs(mapq1, mapq2); } public void updateFragmentsForPair(AlignmentPair nextPair, String[] tokens, int frag1Index, int frag2Index) { int frag1 = Integer.parseInt(tokens[frag1Index]); int frag2 = Integer.parseInt(tokens[frag2Index]); nextPair.updateFragments(frag1, frag2); } public void updatePairScoreIfNeeded(boolean includeScore, AlignmentPair nextPair, String[] tokens, int scoreIndex) { if (includeScore) { nextPair.setScore(Float.parseFloat(tokens[scoreIndex])); } } /** * Replace "aString" with a stored equivalent object, if it exists. If it does not store it. The purpose * of this class is to avoid running out of memory storing zillions of equivalent string. */ protected String getInternedString(String aString) { String s = stringInternPool.get(aString); if (s == null) { //noinspection RedundantStringConstructorCall s = new String(aString); // The "new" will break any dependency on larger strings if this is a "substring" stringInternPool.put(aString, s); } return s; } } ================================================ FILE: src/juicebox/tools/utils/original/mnditerator/PairIterator.java ================================================ /* * The MIT License (MIT) * * Copyright (c) 2011-2021 Broad Institute, Aiden Lab, Rice University, Baylor College of Medicine * * Permission is hereby granted, free of charge, to any person obtaining a copy * of this software and associated documentation files (the "Software"), to deal * in the Software without restriction, including without limitation the rights * to use, copy, modify, merge, publish, distribute, sublicense, and/or sell * copies of the Software, and to permit persons to whom the Software is * furnished to do so, subject to the following conditions: * * The above copyright notice and this permission notice shall be included in * all copies or substantial portions of the Software. * * THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR * IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, * FITNESS FOR A PARTICULAR PURPOSE AND NON-INFRINGEMENT. IN NO EVENT SHALL THE * AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER * LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, * OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN * THE SOFTWARE. */ package juicebox.tools.utils.original.mnditerator; import juicebox.data.ChromosomeHandler; import java.io.IOException; import java.util.Iterator; import java.util.Map; /** * @author Jim Robinson * @since 9/24/11 */ public interface PairIterator extends Iterator { boolean hasNext(); AlignmentPair next(); void remove(); void close(); static PairIterator getIterator(String file, Map chromosomeIndexes, ChromosomeHandler chromosomeHandler) throws IOException { if (file.endsWith(".bin")) { return new BinPairIterator(file); } else if (file.endsWith(".bn")) { return new ShortBinPairIterator(file); } else { return new AsciiPairIterator(file, chromosomeIndexes, chromosomeHandler, false); } } } ================================================ FILE: src/juicebox/tools/utils/original/mnditerator/RandomAccessAsciiPairIterator.java ================================================ /* * The MIT License (MIT) * * Copyright (c) 2011-2021 Broad Institute, Aiden Lab, Rice University, Baylor College of Medicine * * Permission is hereby granted, free of charge, to any person obtaining a copy * of this software and associated documentation files (the "Software"), to deal * in the Software without restriction, including without limitation the rights * to use, copy, modify, merge, publish, distribute, sublicense, and/or sell * copies of the Software, and to permit persons to whom the Software is * furnished to do so, subject to the following conditions: * * The above copyright notice and this permission notice shall be included in * all copies or substantial portions of the Software. * * THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR * IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, * FITNESS FOR A PARTICULAR PURPOSE AND NON-INFRINGEMENT. IN NO EVENT SHALL THE * AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER * LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, * OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN * THE SOFTWARE. */ package juicebox.tools.utils.original.mnditerator; import juicebox.data.ChromosomeHandler; import juicebox.tools.utils.original.Chunk; import java.io.IOException; import java.util.Map; /** * @author Jim Robinson * @since 9/24/11 */ public class RandomAccessAsciiPairIterator extends AsciiPairIterator { public RandomAccessAsciiPairIterator(String path, Map chromosomeOrdinals, long mndIndex, int mndChunk, ChromosomeHandler handler) throws IOException { super(path, chromosomeOrdinals, new Chunk(mndIndex, mndChunk), handler); } /* to use RandomAccessFile, we only need to adjust constructor below, don't duplicate all code from asciipairiterator however, since this isn't even being used, I'm just commenting it out - MSS public AsciiPairIterator(String path, Map chromosomeOrdinals, long mndIndex, int mndChunk, ChromosomeHandler handler) throws IOException { this.handler = handler; if (path.endsWith(".gz")) { System.err.println("Multithreading with indexed mnd currently only works with unzipped mnd"); System.exit(70); } else { reader = new RandomAccessFile(path, "r"); reader.getChannel().position(mndIndex); this.mndStart = mndIndex; this.mndChunkSize = mndChunk; this.stopAfterChunk = true; } this.chromosomeOrdinals = chromosomeOrdinals; advance(); } */ } ================================================ FILE: src/juicebox/tools/utils/original/mnditerator/ShortBinPairIterator.java ================================================ /* * The MIT License (MIT) * * Copyright (c) 2011-2021 Broad Institute, Aiden Lab, Rice University, Baylor College of Medicine * * Permission is hereby granted, free of charge, to any person obtaining a copy * of this software and associated documentation files (the "Software"), to deal * in the Software without restriction, including without limitation the rights * to use, copy, modify, merge, publish, distribute, sublicense, and/or sell * copies of the Software, and to permit persons to whom the Software is * furnished to do so, subject to the following conditions: * * The above copyright notice and this permission notice shall be included in * all copies or substantial portions of the Software. * * THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR * IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, * FITNESS FOR A PARTICULAR PURPOSE AND NON-INFRINGEMENT. IN NO EVENT SHALL THE * AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER * LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, * OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN * THE SOFTWARE. */ package juicebox.tools.utils.original.mnditerator; import java.io.EOFException; import java.io.IOException; public class ShortBinPairIterator extends BinPairIterator { public ShortBinPairIterator(String path) throws IOException { super(path); } @Override protected void advance() { try { int chr1 = is.readInt(); int pos1 = is.readInt(); int chr2 = is.readInt(); int pos2 = is.readInt(); next = new AlignmentPair(chr1, pos1, chr2, pos2); float score = is.readFloat(); next.setScore(score); } catch (IOException e) { next = null; if (!(e instanceof EOFException)) { e.printStackTrace(); } } } } ================================================ FILE: src/juicebox/tools/utils/original/mnditerator/SimpleAsciiPairIterator.java ================================================ /* * The MIT License (MIT) * * Copyright (c) 2011-2021 Broad Institute, Aiden Lab, Rice University, Baylor College of Medicine * * Permission is hereby granted, free of charge, to any person obtaining a copy * of this software and associated documentation files (the "Software"), to deal * in the Software without restriction, including without limitation the rights * to use, copy, modify, merge, publish, distribute, sublicense, and/or sell * copies of the Software, and to permit persons to whom the Software is * furnished to do so, subject to the following conditions: * * The above copyright notice and this permission notice shall be included in * all copies or substantial portions of the Software. * * THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR * IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, * FITNESS FOR A PARTICULAR PURPOSE AND NON-INFRINGEMENT. IN NO EVENT SHALL THE * AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER * LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, * OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN * THE SOFTWARE. */ package juicebox.tools.utils.original.mnditerator; import juicebox.HiCGlobals; import org.broad.igv.util.ParsingUtils; import java.io.*; import java.nio.charset.StandardCharsets; import java.util.zip.GZIPInputStream; public class SimpleAsciiPairIterator extends GenericPairIterator implements PairIterator { public SimpleAsciiPairIterator(String path) throws IOException { super(new MNDFileParser(new SimpleLineParser())); if (path.endsWith(".gz")) { InputStream gzipStream = new GZIPInputStream(new FileInputStream(path)); Reader decoder = new InputStreamReader(gzipStream, StandardCharsets.UTF_8); this.reader = new BufferedReader(decoder, 4194304); } else { this.reader = new BufferedReader(new InputStreamReader(ParsingUtils.openInputStream(path)), HiCGlobals.bufferSize); } advance(); } public String getChromosomeNameFromIndex(int chrIndex) { return mndFileParser.getChromosomeNameFromIndex(chrIndex); } } ================================================ FILE: src/juicebox/tools/utils/original/mnditerator/SimpleLineParser.java ================================================ /* * The MIT License (MIT) * * Copyright (c) 2011-2021 Broad Institute, Aiden Lab, Rice University, Baylor College of Medicine * * Permission is hereby granted, free of charge, to any person obtaining a copy * of this software and associated documentation files (the "Software"), to deal * in the Software without restriction, including without limitation the rights * to use, copy, modify, merge, publish, distribute, sublicense, and/or sell * copies of the Software, and to permit persons to whom the Software is * furnished to do so, subject to the following conditions: * * The above copyright notice and this permission notice shall be included in * all copies or substantial portions of the Software. * * THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR * IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, * FITNESS FOR A PARTICULAR PURPOSE AND NON-INFRINGEMENT. IN NO EVENT SHALL THE * AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER * LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, * OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN * THE SOFTWARE. */ package juicebox.tools.utils.original.mnditerator; import java.util.HashMap; import java.util.Map; public class SimpleLineParser extends MNDLineParser { private final Map chrNameToIndex = new HashMap<>(); private final Map chrIndexToName = new HashMap<>(); private int nextChromIndex = 1; @Override protected int getChromosomeOrdinal(String chrom) { if (!chrNameToIndex.containsKey(chrom)) { chrNameToIndex.put(chrom, nextChromIndex); chrNameToIndex.put(chrom.toLowerCase(), nextChromIndex); chrNameToIndex.put(chrom.toUpperCase(), nextChromIndex); chrIndexToName.put(nextChromIndex, chrom); nextChromIndex++; } return chrNameToIndex.get(chrom); } @Override public AlignmentPair generateBasicPair(String[] tokens, int chrom1Index, int chrom2Index, int pos1Index, int pos2Index) { String chrom1 = getInternedString(tokens[chrom1Index]); String chrom2 = getInternedString(tokens[chrom2Index]); return createPair(tokens, chrom1, chrom2, pos1Index, pos2Index); } @Override public String getChromosomeNameFromIndex(int chrIndex) { return chrIndexToName.get(chrIndex); } } ================================================ FILE: src/juicebox/tools/utils/original/stats/LoneStatisticsWorker.java ================================================ /* * The MIT License (MIT) * * Copyright (c) 2011-2021 Broad Institute, Aiden Lab, Rice University, Baylor College of Medicine * * Permission is hereby granted, free of charge, to any person obtaining a copy * of this software and associated documentation files (the "Software"), to deal * in the Software without restriction, including without limitation the rights * to use, copy, modify, merge, publish, distribute, sublicense, and/or sell * copies of the Software, and to permit persons to whom the Software is * furnished to do so, subject to the following conditions: * * The above copyright notice and this permission notice shall be included in * all copies or substantial portions of the Software. * * THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR * IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, * FITNESS FOR A PARTICULAR PURPOSE AND NON-INFRINGEMENT. IN NO EVENT SHALL THE * AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER * LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, * OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN * THE SOFTWARE. */ package juicebox.tools.utils.original.stats; import juicebox.tools.utils.original.FragmentCalculation; import juicebox.tools.utils.original.mnditerator.SimpleAsciiPairIterator; import java.io.IOException; import java.util.List; public class LoneStatisticsWorker extends StatisticsWorker { private SimpleAsciiPairIterator fileIterator; public LoneStatisticsWorker(String siteFile, List statsFiles, List mapqThresholds, String ligationJunction, String inFile, FragmentCalculation fragmentCalculation) { super(siteFile, statsFiles, mapqThresholds, ligationJunction, inFile, fragmentCalculation); } public void infileStatistics() { try { fileIterator = new SimpleAsciiPairIterator(inFile); while (fileIterator.hasNext()) { processSingleEntry(fileIterator.next(), "", false); } } catch (IOException e) { e.printStackTrace(); } } protected String getChromosomeNameFromIndex(int chr) { return fileIterator.getChromosomeNameFromIndex(chr); } } ================================================ FILE: src/juicebox/tools/utils/original/stats/ParallelStatistics.java ================================================ /* * The MIT License (MIT) * * Copyright (c) 2011-2021 Broad Institute, Aiden Lab, Rice University, Baylor College of Medicine * * Permission is hereby granted, free of charge, to any person obtaining a copy * of this software and associated documentation files (the "Software"), to deal * in the Software without restriction, including without limitation the rights * to use, copy, modify, merge, publish, distribute, sublicense, and/or sell * copies of the Software, and to permit persons to whom the Software is * furnished to do so, subject to the following conditions: * * The above copyright notice and this permission notice shall be included in * all copies or substantial portions of the Software. * * THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR * IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, * FITNESS FOR A PARTICULAR PURPOSE AND NON-INFRINGEMENT. IN NO EVENT SHALL THE * AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER * LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, * OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN * THE SOFTWARE. */ package juicebox.tools.utils.original.stats; import juicebox.data.ChromosomeHandler; import juicebox.tools.utils.original.Chunk; import juicebox.tools.utils.original.FragmentCalculation; import java.util.List; import java.util.concurrent.ExecutorService; import java.util.concurrent.Executors; import java.util.concurrent.atomic.AtomicInteger; public class ParallelStatistics { private final static Object mergerLock = new Object(); private final int numThreads; private final StatisticsContainer mergedContainer; private final AtomicInteger threadCounter = new AtomicInteger(); private final List mndChunks; private final String siteFile; private final List statsFiles; private final List mapqThresholds; private final String ligationJunction; private final String inFile; private final ChromosomeHandler localHandler; private final FragmentCalculation fragmentCalculation; public ParallelStatistics(int numThreads, StatisticsContainer mergedContainer, List mndChunks, String siteFile, List statsFiles, List mapqThresholds, String ligationJunction, String inFile, ChromosomeHandler localHandler, FragmentCalculation fragmentCalculation) { this.numThreads = numThreads; this.mergedContainer = mergedContainer; this.mndChunks = mndChunks; this.siteFile = siteFile; this.statsFiles = statsFiles; this.mapqThresholds = mapqThresholds; this.ligationJunction = ligationJunction; this.inFile = inFile; this.localHandler = localHandler; this.fragmentCalculation = fragmentCalculation; } public void launchThreads() { ExecutorService executor = Executors.newFixedThreadPool(numThreads); for (int l = 0; l < numThreads; l++) { executor.execute(() -> runParallelizedStatistics(mergedContainer)); } executor.shutdown(); // Wait until all threads finish while (!executor.isTerminated()) { } } public void runParallelizedStatistics(final StatisticsContainer mergedContainer) { int currentCount = threadCounter.getAndIncrement(); while (currentCount < mndChunks.size()) { Chunk chunk = mndChunks.get(currentCount); try { ParallelStatisticsWorker runner = new ParallelStatisticsWorker(siteFile, statsFiles, mapqThresholds, ligationJunction, inFile, localHandler, fragmentCalculation); runner.infileStatistics(chunk); synchronized (mergerLock) { mergedContainer.add(runner.getResultsContainer(), statsFiles.size()); } } catch (Exception e2) { e2.printStackTrace(); } currentCount = threadCounter.getAndIncrement(); } } } ================================================ FILE: src/juicebox/tools/utils/original/stats/ParallelStatisticsWorker.java ================================================ /* * The MIT License (MIT) * * Copyright (c) 2011-2021 Broad Institute, Aiden Lab, Rice University, Baylor College of Medicine * * Permission is hereby granted, free of charge, to any person obtaining a copy * of this software and associated documentation files (the "Software"), to deal * in the Software without restriction, including without limitation the rights * to use, copy, modify, merge, publish, distribute, sublicense, and/or sell * copies of the Software, and to permit persons to whom the Software is * furnished to do so, subject to the following conditions: * * The above copyright notice and this permission notice shall be included in * all copies or substantial portions of the Software. * * THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR * IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, * FITNESS FOR A PARTICULAR PURPOSE AND NON-INFRINGEMENT. IN NO EVENT SHALL THE * AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER * LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, * OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN * THE SOFTWARE. */ package juicebox.tools.utils.original.stats; import juicebox.data.ChromosomeHandler; import juicebox.tools.utils.original.Chunk; import juicebox.tools.utils.original.FragmentCalculation; import juicebox.tools.utils.original.mnditerator.AlignmentPairLong; import juicebox.tools.utils.original.mnditerator.AsciiPairIterator; import java.io.IOException; import java.util.HashMap; import java.util.List; import java.util.Map; public class ParallelStatisticsWorker extends StatisticsWorker { private final ChromosomeHandler localHandler; public ParallelStatisticsWorker(String siteFile, List statsFiles, List mapqThresholds, String ligationJunction, String inFile, ChromosomeHandler localHandler, FragmentCalculation chromosomes) { super(siteFile, statsFiles, mapqThresholds, ligationJunction, inFile, chromosomes); this.localHandler = localHandler; } public void infileStatistics(Chunk chunk) { //read in infile and calculate statistics try { //create index for AsciiIterator Map chromosomeIndexes = new HashMap<>(); for (int i = 0; i < localHandler.size(); i++) { chromosomeIndexes.put(localHandler.getChromosomeFromIndex(i).getName(), i); } //iterate through input file AsciiPairIterator files = new AsciiPairIterator(inFile, chromosomeIndexes, chunk, localHandler); if (files.hasNext()) { AlignmentPairLong firstPair = (AlignmentPairLong) files.next(); String previousBlock = firstPair.getChr1() + "_" + firstPair.getChr2(); processSingleEntry(firstPair, previousBlock, true); while (files.hasNext()) { AlignmentPairLong pair = (AlignmentPairLong) files.next(); if (processSingleEntry(pair, previousBlock, true)) { break; } } } } catch (IOException e) { e.printStackTrace(); } } protected String getChromosomeNameFromIndex(int chr) { return localHandler.getChromosomeFromIndex(chr).getName(); } } ================================================ FILE: src/juicebox/tools/utils/original/stats/StatisticsContainer.java ================================================ /* * The MIT License (MIT) * * Copyright (c) 2011-2021 Broad Institute, Aiden Lab, Rice University, Baylor College of Medicine * * Permission is hereby granted, free of charge, to any person obtaining a copy * of this software and associated documentation files (the "Software"), to deal * in the Software without restriction, including without limitation the rights * to use, copy, modify, merge, publish, distribute, sublicense, and/or sell * copies of the Software, and to permit persons to whom the Software is * furnished to do so, subject to the following conditions: * * The above copyright notice and this permission notice shall be included in * all copies or substantial portions of the Software. * * THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR * IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, * FITNESS FOR A PARTICULAR PURPOSE AND NON-INFRINGEMENT. IN NO EVENT SHALL THE * AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER * LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, * OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN * THE SOFTWARE. */ package juicebox.tools.utils.original.stats; import juicebox.tools.clt.old.LibraryComplexity; import java.io.*; import java.text.NumberFormat; import java.util.*; public class StatisticsContainer { private final static float CONVERGENCE_THRESHOLD = 0.01f; private final static int CONVERGENCE_REGION = 3; private final static int SEQ_INDEX = 0, DUPS_INDEX = 1, UNIQUE_INDEX = 2; private final static int LC_INDEX = 3, SINGLE_ALIGNMENT_INDEX = 4; private final static int SINGLE_ALIGN_DUPS_INDEX = 5, SINGLE_ALIGN_UNIQUE_INDEX = 6; private final static int NUM_TO_READ = 7; private final NumberFormat nf = NumberFormat.getNumberInstance(Locale.US); //Variables for calculating statistics public final List> hindIII = new ArrayList<>(); public final List> mapQ = new ArrayList<>(); public final List> mapQInter = new ArrayList<>(); public final List> mapQIntra = new ArrayList<>(); public final List> innerM = new ArrayList<>(); public final List> outerM = new ArrayList<>(); public final List> rightM = new ArrayList<>(); public final List> leftM = new ArrayList<>(); private final List convergenceIndices = new ArrayList<>(); public long unique = 0; public long[] intraFragment = new long[2]; public long[] threePrimeEnd = new long[2]; public long[] fivePrimeEnd = new long[2]; public long[] dangling = new long[2]; public long[] ligation = new long[2]; public long[] inner = new long[2]; public long[] outer = new long[2]; public long[] left = new long[2]; public long[] right = new long[2]; public long[] intra = new long[2]; public long[] inter = new long[2]; public long[] interDangling = new long[2]; public long[] trueDanglingIntraSmall = new long[2]; public long[] trueDanglingIntraLarge = new long[2]; public long[] trueDanglingInter = new long[2]; public long[] totalCurrent = new long[2]; public long[] underMapQ = new long[2]; public long[] fiveHundredBPRes = new long[2]; public long[] fiveHundredBPResDangling = new long[2]; public long[] fiveKBRes = new long[2]; public long[] fiveKBResDangling = new long[2]; public long[] twentyKBRes = new long[2]; public long[] twentyKBResDangling = new long[2]; public long[] large = new long[2]; public long[] largeDangling = new long[2]; private static final long[] bins = {10, 12, 15, 19, 23, 28, 35, 43, 53, 66, 81, 100, 123, 152, 187, 231, 285, 351, 433, 534, 658, 811, 1000, 1233, 1520, 1874, 2310, 2848, 3511, 4329, 5337, 6579, 8111, 10000, 12328, 15199, 18738, 23101, 28480, 35112, 43288, 53367, 65793, 81113, 100000, 123285, 151991, 187382, 231013, 284804, 351119, 432876, 533670, 657933, 811131, 1000000, 1232847, 1519911, 1873817, 2310130, 2848036, 3511192, 4328761, 5336699, 6579332, 8111308, 10000000, 12328467, 15199111, 18738174, 23101297, 28480359, 35111917, 43287613, 53366992, 65793322, 81113083, 100000000, 123284674, 151991108, 187381742, 231012970, 284803587, 351119173, 432876128, 533669923, 657933225, 811130831, 1000000000, 1232846739, 1519911083, 1873817423, 2310129700L, 2848035868L, 3511191734L, 4328761281L, 5336699231L, 6579332247L, 8111308308L, 10000000000L}; public StatisticsContainer() { for (int i = 0; i < 2; i++) { hindIII.add(new HashMap<>()); mapQ.add(new HashMap<>()); mapQInter.add(new HashMap<>()); mapQIntra.add(new HashMap<>()); innerM.add(new HashMap<>()); outerM.add(new HashMap<>()); rightM.add(new HashMap<>()); leftM.add(new HashMap<>()); } } public void add(StatisticsContainer individualContainer, int numberOfMapQValues) { unique += individualContainer.unique; for (int j=0; j statsFiles) { for (int i = 0; i < statsFiles.size(); i++) { File statFile = new File(statsFiles.get(i)); //output statistics file for first mapq calculation boolean[] valsWereFound = new boolean[NUM_TO_READ]; long[] valsFound = new long[NUM_TO_READ]; // seqReads, duplicates attempReadingDataFromExistingFile(valsWereFound, valsFound, statFile); // if (statFile.exists()) { try { BufferedWriter statsOut = new BufferedWriter(new FileWriter(statFile, true)); writeLibComplexityIfNeeded(valsWereFound, valsFound, statsOut); if (unique == 0) unique = 1; writeOut(statsOut, "Intra-fragment Reads: ", valsWereFound, intraFragment[i], valsFound, unique, true); //if (!isUTLibrary(valsWereFound, valsFound, underMapQ[i])) { attemptMapqCorrection(valsWereFound, valsFound, underMapQ, unique, i); writeOut(statsOut, "Below MAPQ Threshold: ", valsWereFound, underMapQ[i], valsFound, unique, true); //} writeOut(statsOut, "Hi-C Contacts: ", valsWereFound, totalCurrent[i], valsFound, unique, false); //writeOut(statsOut, " Ligation Motif Present: ", valsWereFound, ligation[i], valsFound, unique, true); appendPairTypeStatsOutputToFile(i, statsOut); writeOut(statsOut, "Inter-chromosomal: ", valsWereFound, inter[i], valsFound, unique, false); writeOut(statsOut, "Intra-chromosomal: ", valsWereFound, intra[i], valsFound, unique, false); statsOut.write("Short Range (<20Kb):\n"); writeOut(statsOut, " <500BP: ", valsWereFound, fiveHundredBPRes[i], valsFound, unique, false); writeOut(statsOut, " 500BP-5kB: ", valsWereFound, fiveKBRes[i], valsFound, unique, false); writeOut(statsOut, " 5kB-20kB: ", valsWereFound, twentyKBRes[i], valsFound, unique, false); writeOut(statsOut, "Long Range (>20Kb): ", valsWereFound, large[i], valsFound, unique, false); statsOut.close(); } catch (IOException error) { error.printStackTrace(); } // } } } private boolean isUTLibrary(boolean[] valsWereFound, long[] valsFound, long belowMapQ) { return valsWereFound[SINGLE_ALIGNMENT_INDEX] && valsFound[SINGLE_ALIGNMENT_INDEX] > 0 && belowMapQ < 1; } private void writeLibComplexityIfNeeded(boolean[] valsWereFound, long[] valsFound, BufferedWriter statsOut) throws IOException { if (!valsWereFound[LC_INDEX]) { boolean isUTExperiment = false; long lcTotal = 0L; if (valsWereFound[SINGLE_ALIGN_UNIQUE_INDEX] && valsWereFound[SINGLE_ALIGN_DUPS_INDEX]) { long resultLC1 = LibraryComplexity.estimateLibrarySize(valsFound[SINGLE_ALIGN_DUPS_INDEX], valsFound[SINGLE_ALIGN_UNIQUE_INDEX]); isUTExperiment = true; if (resultLC1 > 0) { lcTotal += resultLC1; statsOut.write("Library Complexity Estimate (1 alignment)*: " + commify(resultLC1) + "\n"); } else { statsOut.write("Library Complexity Estimate (1 alignment)*: N/A\n"); } } if (valsWereFound[UNIQUE_INDEX] && valsWereFound[DUPS_INDEX]) { long resultLC2 = LibraryComplexity.estimateLibrarySize(valsFound[DUPS_INDEX], valsFound[UNIQUE_INDEX]); String description = ""; if (isUTExperiment) { description = " (2 alignments)"; } if (resultLC2 > 0) { lcTotal += resultLC2; statsOut.write("Library Complexity Estimate" + description + "*: " + commify(resultLC2) + "\n"); } else { statsOut.write("Library Complexity Estimate" + description + "*: N/A\n"); } } if (isUTExperiment) { if (lcTotal > 0) { statsOut.write("Library Complexity Estimate (1+2 above)*: " + commify(lcTotal) + "\n"); } else { statsOut.write("Library Complexity Estimate (1+2 above)*: N/A\n"); } } } } private void attempReadingDataFromExistingFile(boolean[] valsWereFound, long[] valsFound, File statFile) { Arrays.fill(valsWereFound, false); Arrays.fill(valsFound, 0); if (statFile.exists()) { try { BufferedReader stats = new BufferedReader(new FileReader(statFile)); String statsData = stats.readLine(); while (statsData != null) { statsData = statsData.toLowerCase(); if (statsData.contains("sequenced")) { populateFoundVals(statsData, valsWereFound, valsFound, SEQ_INDEX); } else if (statsData.contains("unique")) { if (isSingleAlignment(statsData)) { populateFoundVals(statsData, valsWereFound, valsFound, SINGLE_ALIGN_UNIQUE_INDEX); } else { populateFoundVals(statsData, valsWereFound, valsFound, UNIQUE_INDEX); } } else if (statsData.contains("duplicate") && !statsData.contains("optical")) { if (isSingleAlignment(statsData)) { populateFoundVals(statsData, valsWereFound, valsFound, SINGLE_ALIGN_DUPS_INDEX); } else { populateFoundVals(statsData, valsWereFound, valsFound, DUPS_INDEX); } } else if (statsData.contains("complexity")) { populateFoundVals(statsData, valsWereFound, valsFound, LC_INDEX); } else if (statsData.contains("single") && statsData.contains("alignment")) { populateFoundVals(statsData, valsWereFound, valsFound, SINGLE_ALIGNMENT_INDEX); } statsData = stats.readLine(); } stats.close(); } catch (IOException error) { error.printStackTrace(); } } } private boolean isSingleAlignment(String text) { String[] tokens = text.split(":"); String description = tokens[0].toLowerCase(); return (description.contains("1") || description.contains("one")) && description.contains("alignment"); } private void populateFoundVals(String statsData, boolean[] valsWereFound, long[] valsFound, int index) { if (!valsWereFound[index]) { valsWereFound[index] = true; String[] tokens = statsData.split(":"); String substring1 = tokens[1].replaceAll("[, ]", ""); if (substring1.contains("(")) { substring1 = substring1.split("\\(")[0]; } valsFound[index] = Long.parseLong(substring1.trim()); } } private void attemptMapqCorrection(boolean[] valsWereGiven, long[] valsFound, long[] underMapQ, long unique, int i) { if (underMapQ[i] < 1 && valsWereGiven[UNIQUE_INDEX]) { underMapQ[i] = valsFound[UNIQUE_INDEX] - unique; } } void appendPairTypeStatsOutputToFile(int i, BufferedWriter statsOut) throws IOException { if ((fivePrimeEnd[i] + threePrimeEnd[i]) > 0) { statsOut.write(" 3' Bias (Long Range): " + wholePercentify(threePrimeEnd[i], threePrimeEnd[i] + fivePrimeEnd[i])); statsOut.write(" - " + wholePercentify(fivePrimeEnd[i], threePrimeEnd[i] + fivePrimeEnd[i]) + "\n"); } else { statsOut.write(" 3' Bias (Long Range): N/A\n"); } if (large[i] > 0) { statsOut.write(" Pair Type %(L-I-O-R): " + wholePercentify(left[i], large[i])); statsOut.write(" - " + wholePercentify(inner[i], large[i])); statsOut.write(" - " + wholePercentify(outer[i], large[i])); statsOut.write(" - " + wholePercentify(right[i], large[i]) + "\n"); statsOut.write(" L-I-O-R Convergence: " + bins[convergenceIndices.get(i)] + "\n"); } else { statsOut.write(" Pair Type %(L-I-O-R): N/A\n"); } } private void writeOut(BufferedWriter statsOut, String description, boolean[] valsWereGiven, long value, long[] valsFound, long unique, boolean checkNA) throws IOException { if (!checkNA || value > 0) { if (valsWereGiven[SEQ_INDEX] && valsWereGiven[UNIQUE_INDEX]) { statsOut.write(description + commify(value) + " (" + percentify(value, valsFound[SEQ_INDEX]) + " / " + percentify(value, valsFound[UNIQUE_INDEX]) + ")\n"); } else { statsOut.write(description + commify(value) + " (" + percentify(value, unique) + ")\n"); } } else { statsOut.write(description + "N/A\n"); } } public void writeHistFile(List statsFiles) { //write for mapq if file exists for (int j = 0; j < statsFiles.size(); j++) { if (new File(statsFiles.get(j)).exists()) { //separate stats file name int index = statsFiles.get(j).lastIndexOf("\\"); String statsFilePath = statsFiles.get(j).substring(0, index + 1); //directories String statsFileName = statsFiles.get(j).substring(index + 1).replaceAll(".txt", ""); //filename String histsFile = statsFilePath + statsFileName + "_hists.m"; try { BufferedWriter hist = new BufferedWriter(new FileWriter(histsFile, false)); hist.write("A = [\n"); for (int i = 1; i <= 2000; i++) { long tmp = hindIII.get(j).getOrDefault(i, 0L); hist.write(tmp + " "); } hist.write("\n];\n"); hist.write("B = [\n"); for (int i = 1; i <= 200; i++) { long tmp = mapQ.get(j).getOrDefault(i, 0L); long tmp2 = mapQIntra.get(j).getOrDefault(i, 0L); long tmp3 = mapQInter.get(j).getOrDefault(i, 0L); hist.write(tmp + " " + tmp2 + " " + tmp3 + "\n"); } hist.write("\n];\n"); hist.write("D = [\n"); for (int i = 0; i < bins.length; i++) { long tmp = innerM.get(j).getOrDefault(i, 0L); long tmp2 = outerM.get(j).getOrDefault(i, 0L); long tmp3 = rightM.get(j).getOrDefault(i, 0L); long tmp4 = leftM.get(j).getOrDefault(i, 0L); hist.write(tmp + " " + tmp2 + " " + tmp3 + " " + tmp4 + "\n"); } hist.write("\n];"); hist.write("x = [\n"); for (long bin : bins) { hist.write(bin + " "); } hist.write("\n];\n"); hist.close(); } catch (IOException error) { error.printStackTrace(); } } } } public void calculateConvergence(int numMapQs) { convergenceIndices.clear(); for (int q = 0; q < numMapQs; q++) { int index = -1; boolean solutionFound = false; while (!solutionFound && index < bins.length - 1) { index++; if (getConvergenceError(q, index) < CONVERGENCE_THRESHOLD) { solutionFound = confirmConvergenceMaintained(q, index + 1, bins.length); } } convergenceIndices.add(index); } } private boolean confirmConvergenceMaintained(int q, int startIndex, int maxIndex) { boolean convergenceMaintained = true; for (int i = startIndex; i < Math.min(startIndex + CONVERGENCE_REGION, maxIndex); i++) { double error = getConvergenceError(q, i); convergenceMaintained &= (error < CONVERGENCE_THRESHOLD); } return convergenceMaintained; } private double getConvergenceError(int q, int i) { long[] vals = new long[]{ innerM.get(q).getOrDefault(i, 0L), outerM.get(q).getOrDefault(i, 0L), rightM.get(q).getOrDefault(i, 0L), leftM.get(q).getOrDefault(i, 0L)}; double total = 0.0; for (long val : vals) { total += val; } if (total < 1) return 1e3; double logAvg = Math.log(total / 4.0); double error = 0; for (long val : vals) { double tempErr = (logAvg - Math.log(val)) / logAvg; error = Math.max(error, Math.abs(tempErr)); } return error; } } ================================================ FILE: src/juicebox/tools/utils/original/stats/StatisticsWorker.java ================================================ /* * The MIT License (MIT) * * Copyright (c) 2011-2021 Broad Institute, Aiden Lab, Rice University, Baylor College of Medicine * * Permission is hereby granted, free of charge, to any person obtaining a copy * of this software and associated documentation files (the "Software"), to deal * in the Software without restriction, including without limitation the rights * to use, copy, modify, merge, publish, distribute, sublicense, and/or sell * copies of the Software, and to permit persons to whom the Software is * furnished to do so, subject to the following conditions: * * The above copyright notice and this permission notice shall be included in * all copies or substantial portions of the Software. * * THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR * IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, * FITNESS FOR A PARTICULAR PURPOSE AND NON-INFRINGEMENT. IN NO EVENT SHALL THE * AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER * LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, * OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN * THE SOFTWARE. */ package juicebox.tools.utils.original.stats; import juicebox.tools.utils.original.FragmentCalculation; import juicebox.tools.utils.original.mnditerator.AlignmentPair; import juicebox.tools.utils.original.mnditerator.AlignmentPairLong; import java.util.List; import java.util.Map; public abstract class StatisticsWorker { protected static final int TWENTY_KB = 20000; protected static final int FIVE_HUNDRED_BP = 500; protected static final int FIVE_KB = 5000; protected static final int distThreshold = 2000; protected static final int mapqValThreshold = 200; protected static final long[] bins = {10, 12, 15, 19, 23, 28, 35, 43, 53, 66, 81, 100, 123, 152, 187, 231, 285, 351, 433, 534, 658, 811, 1000, 1233, 1520, 1874, 2310, 2848, 3511, 4329, 5337, 6579, 8111, 10000, 12328, 15199, 18738, 23101, 28480, 35112, 43288, 53367, 65793, 81113, 100000, 123285, 151991, 187382, 231013, 284804, 351119, 432876, 533670, 657933, 811131, 1000000, 1232847, 1519911, 1873817, 2310130, 2848036, 3511192, 4328761, 5336699, 6579332, 8111308, 10000000, 12328467, 15199111, 18738174, 23101297, 28480359, 35111917, 43287613, 53366992, 65793322, 81113083, 100000000, 123284674, 151991108, 187381742, 231012970, 284803587, 351119173, 432876128, 533669923, 657933225, 811130831, 1000000000, 1232846739, 1519911083, 1873817423, 2310129700L, 2848035868L, 3511191734L, 4328761281L, 5336699231L, 6579332247L, 8111308308L, 10000000000L}; //variables for getting parameters of input file, flags set to default initially protected final String siteFile; protected final String inFile; protected final String danglingJunction; protected final String ligationJunction; protected final List statsFiles; protected final List mapqThresholds; protected final FragmentCalculation fragmentCalculation; protected final StatisticsContainer resultsContainer; public StatisticsWorker(String siteFile, List statsFiles, List mapqThresholds, String ligationJunction, String inFile, FragmentCalculation fragmentCalculation) { this.inFile = inFile; this.siteFile = siteFile; this.statsFiles = statsFiles; this.mapqThresholds = mapqThresholds; this.ligationJunction = ligationJunction; this.fragmentCalculation = fragmentCalculation; this.resultsContainer = new StatisticsContainer(); this.danglingJunction = ligationJunction.substring(ligationJunction.length() / 2); } public StatisticsContainer getResultsContainer() { return resultsContainer; } protected boolean processSingleEntry(AlignmentPair pair, String blockKey, boolean multithread) { int chr1, chr2, pos1, pos2, frag1, frag2, mapq1, mapq2; boolean str1, str2; chr1 = pair.getChr1(); chr2 = pair.getChr2(); String currentBlock = chr1 + "_" + chr2; if (multithread && !currentBlock.equals(blockKey)) { return true; } pos1 = pair.getPos1(); pos2 = pair.getPos2(); frag1 = pair.getFrag1(); frag2 = pair.getFrag2(); mapq1 = pair.getMapq1(); mapq2 = pair.getMapq2(); str1 = pair.getStrand1(); str2 = pair.getStrand2(); resultsContainer.unique++; //don't count as Hi-C contact if fails mapq or intra fragment test for(int ind=0; ind= 0 && mapq2 >= 0) { int mapqValue = Math.min(mapq1, mapq2); if (mapqValue < mapqThresholds.get(ind)) { resultsContainer.underMapQ[ind]++; countMe = false; } } //calculate statistics for mapq threshold if (countMe && statsFiles.get(ind) != null) { resultsContainer.totalCurrent[ind]++; //position distance int posDist = Math.abs(pos1 - pos2); int histDist = bSearch(posDist); boolean isDangling = false; //one part of read pair has unligated end if (pair instanceof AlignmentPairLong) { AlignmentPairLong longPair = (AlignmentPairLong) pair; String seq1 = longPair.getSeq1(); String seq2 = longPair.getSeq2(); if ((seq1 != null && seq2 != null) && (seq1.startsWith(danglingJunction) || seq2.startsWith(danglingJunction))) { resultsContainer.dangling[ind]++; isDangling = true; } } //look at chromosomes if (chr1 == chr2) { resultsContainer.intra[ind]++; //determine right/left/inner/outer ordering of chromosomes/strands boolean distGT20KB = posDist >= TWENTY_KB; if (str1 == str2) { if (str1) { populateLIOR(distGT20KB, resultsContainer.right, resultsContainer.rightM, ind, histDist); } else { populateLIOR(distGT20KB, resultsContainer.left, resultsContainer.leftM, ind, histDist); } } else { if (str1) { if (pos1 < pos2) { populateLIOR(distGT20KB, resultsContainer.inner, resultsContainer.innerM, ind, histDist); } else { populateLIOR(distGT20KB, resultsContainer.outer, resultsContainer.outerM, ind, histDist); } } else { if (pos1 < pos2) { populateLIOR(distGT20KB, resultsContainer.outer, resultsContainer.outerM, ind, histDist); } else { populateLIOR(distGT20KB, resultsContainer.inner, resultsContainer.innerM, ind, histDist); } } } //intra reads less than 20KB apart if (posDist < FIVE_HUNDRED_BP) { populateDist(resultsContainer.fiveHundredBPRes, resultsContainer.fiveHundredBPResDangling, ind, isDangling); } else if (posDist < FIVE_KB) { populateDist(resultsContainer.fiveKBRes, resultsContainer.fiveKBResDangling, ind, isDangling); } else if (posDist < TWENTY_KB) { populateDist(resultsContainer.twentyKBRes, resultsContainer.twentyKBResDangling, ind, isDangling); } else { populateDist(resultsContainer.large, resultsContainer.largeDangling, ind, isDangling); } } else { populateDist(resultsContainer.inter, resultsContainer.interDangling, ind, isDangling); } if (pair instanceof AlignmentPairLong) { AlignmentPairLong longPair = (AlignmentPairLong) pair; String seq1 = longPair.getSeq1(); String seq2 = longPair.getSeq2(); if ((seq1 != null && seq2 != null) && (mapq1 >= 0 && mapq2 >= 0)) { int mapqVal = Math.min(mapq1, mapq2); if (mapqVal <= mapqValThreshold) { resultsContainer.mapQ.get(ind).put(mapqVal, resultsContainer.mapQ.get(ind).getOrDefault(mapqVal, 0L) + 1); if (chr1 == chr2) { resultsContainer.mapQIntra.get(ind).put(mapqVal, resultsContainer.mapQIntra.get(ind).getOrDefault(mapqVal, 0L) + 1); } else { resultsContainer.mapQInter.get(ind).put(mapqVal, resultsContainer.mapQInter.get(ind).getOrDefault(mapqVal, 0L) + 1); } } //read pair contains ligation junction if (seq1.contains(ligationJunction) || seq2.contains(ligationJunction)) { resultsContainer.ligation[ind]++; } } } //determine distance from nearest HindIII site, add to histogram if (!siteFile.contains("none") && fragmentCalculation != null) { try { boolean report = ((chr1 != chr2) || (posDist >= TWENTY_KB)); int dist = distHindIII(str1, chr1, pos1, frag1, report, ind); if (dist <= distThreshold) { resultsContainer.hindIII.get(ind).put(dist, resultsContainer.hindIII.get(ind).getOrDefault(dist, 0L) + 1); } dist = distHindIII(str2, chr2, pos2, frag2, report, ind); if (dist <= distThreshold) { resultsContainer.hindIII.get(ind).put(dist, resultsContainer.hindIII.get(ind).getOrDefault(dist, 0L) + 1); } } catch (Exception e) { // System.err.println(e.getLocalizedMessage()); // do nothing, fail gracefully; likely a chromosome issue } } if (pair instanceof AlignmentPairLong && fragmentCalculation != null) { AlignmentPairLong longPair = (AlignmentPairLong) pair; String seq1 = longPair.getSeq1(); String seq2 = longPair.getSeq2(); if (isDangling) { try { int dist; if (seq1.startsWith(danglingJunction)) { dist = distHindIII(str1, chr1, pos1, frag1, true, ind); } else { dist = distHindIII(str2, chr2, pos2, frag2, true, ind); } //$record[13] =~ m/^$danglingJunction/ if (dist == 1) { if (chr1 == chr2) { if (posDist < TWENTY_KB) { resultsContainer.trueDanglingIntraSmall[ind]++; } else { resultsContainer.trueDanglingIntraLarge[ind]++; } } else { resultsContainer.trueDanglingInter[ind]++; } } } catch (Exception e) { // do nothing, fail gracefully; likely a chromosome issue } } } } } return false; } private void populateDist(long[] array, long[] arrayDangling, int ind, boolean isDangling) { array[ind]++; if (isDangling) { arrayDangling[ind]++; } } private void populateLIOR(boolean distGT20KB, long[] array, List> arrayM, int ind, int histDist) { if (distGT20KB) { array[ind]++; } arrayM.get(ind).put(histDist, arrayM.get(ind).getOrDefault(histDist, 0L) + 1); } /* private void fragmentSearch() { try { BufferedReader files = new BufferedReader(new FileReader(inFile)); BufferedWriter fragOut = new BufferedWriter(new FileWriter(outFile, false)); String file = files.readLine(); while (file != null) { String[] record = file.split("\\s+"); int indexOne = FragmentCalculation.binarySearch(fragmentCalculation.getSites(localHandler.cleanUpName(record[1])),Integer.parseInt(record[2])); int indexTwo = FragmentCalculation.binarySearch(fragmentCalculation.getSites(localHandler.cleanUpName(record[4])),Integer.parseInt(record[5])); fragOut.write(record[0] + " " + record[1] + " " + record[2] + " " + indexOne + " "); fragOut.write(record[3] + " " + record[4] + " " + record[5] + " " + indexTwo + " "); for (int i = 6; i < record.length; i++) { fragOut.write(record[i] + " "); } fragOut.write("\n"); file = files.readLine(); } files.close(); fragOut.close(); } catch (IOException error){ error.printStackTrace(); } } */ private int distHindIII(boolean strand, int chrIndex, int pos, int frag, boolean rep, int index) { //Find distance to nearest HindIII restriction site //find upper index of position in sites array via binary search //get distance to each end of HindIII fragment int dist1; int dist2; int[] sites = fragmentCalculation.getSites(getChromosomeNameFromIndex(chrIndex)); int arr = sites.length; if (frag >= arr) { return 0; } if (frag == 0) { //# first fragment, distance is position dist1 = pos; } else { dist1 = Math.abs(pos - sites[frag - 1]); } dist2 = Math.abs(pos - sites[frag]); //get minimum value -- if (dist1 <= dist2), it's dist1, else dist2 int retVal = Math.min(dist1, dist2); //get which end of the fragment this is, 3' or 5' (depends on strand) if ((retVal == dist1) && (rep)) { if (strand) { resultsContainer.fivePrimeEnd[index]++; } else { resultsContainer.threePrimeEnd[index]++; } } else if ((retVal == dist2) && (rep)) { if (!strand) { resultsContainer.fivePrimeEnd[index]++; } else { resultsContainer.threePrimeEnd[index]++; } } return retVal; } protected abstract String getChromosomeNameFromIndex(int chr); private static int bSearch(int distance) { //search for int distance in array binary int lower = 0; int upper = bins.length - 1; int index; while (lower <= upper) { index = (lower + upper) / 2; if (bins[index] < distance) { lower = index + 1; } else if (bins[index]>distance) { upper=index-1; } else { return index; } } return lower; } } ================================================ FILE: src/juicebox/track/CategoryPanel.java ================================================ /* * The MIT License (MIT) * * Copyright (c) 2011-2021 Broad Institute, Aiden Lab, Rice University, Baylor College of Medicine * * Permission is hereby granted, free of charge, to any person obtaining a copy * of this software and associated documentation files (the "Software"), to deal * in the Software without restriction, including without limitation the rights * to use, copy, modify, merge, publish, distribute, sublicense, and/or sell * copies of the Software, and to permit persons to whom the Software is * furnished to do so, subject to the following conditions: * * The above copyright notice and this permission notice shall be included in * all copies or substantial portions of the Software. * * THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR * IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, * FITNESS FOR A PARTICULAR PURPOSE AND NON-INFRINGEMENT. IN NO EVENT SHALL THE * AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER * LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, * OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN * THE SOFTWARE. */ package juicebox.track; import com.jidesoft.swing.ButtonStyle; import com.jidesoft.swing.JideButton; import org.broad.igv.util.ResourceLocator; import javax.swing.*; import java.awt.*; import java.awt.event.ActionEvent; import java.awt.event.ActionListener; import java.awt.event.MouseAdapter; import java.awt.event.MouseEvent; import java.util.ArrayList; import java.util.Collection; import java.util.List; import java.util.Set; //import javax.swing.border.Border; //import javax.swing.border.LineBorder; //import java.awt.geom.Path2D; //import java.awt.geom.Rectangle2D; //import java.awt.geom.RoundRectangle2D; /** * @author Jim Robinson * @since 5/8/12 */ class CategoryPanel extends JPanel { private static final long serialVersionUID = 900006; private final JPanel listPanel; private final JPanel labelBar; int nColumns = 5; private boolean expanded; public CategoryPanel(String name, List locatorList, Set loadedTrackNames) { expanded = true; setLayout(new BoxLayout(this, BoxLayout.Y_AXIS)); setAlignmentX(LEFT_ALIGNMENT); //setLayout(null); labelBar = new JPanel(); //labelBar.setBackground(Color.blue); labelBar.setLayout(new BoxLayout(labelBar, BoxLayout.X_AXIS)); labelBar.setBorder(BorderFactory.createRaisedBevelBorder()); // new LabelBorder(Color.black)); labelBar.setAlignmentX(LEFT_ALIGNMENT); JideButton toggleButton = new JideButton(expanded ? " - " : " + "); toggleButton.setButtonStyle(ButtonStyle.HYPERLINK_STYLE); labelBar.add(toggleButton); labelBar.add(new JLabel(name)); this.add(labelBar); listPanel = new JPanel(); listPanel.setLayout(new GridLayout(0, 4)); for (ResourceLocator loc : locatorList) { final String trackName = loc.getTrackName(); JCheckBox cb = new JCheckBox(trackName); cb.setSelected(loadedTrackNames.contains(trackName)); listPanel.add(cb); } this.add(listPanel); toggleButton.addActionListener(new ActionListener() { @Override public void actionPerformed(ActionEvent actionEvent) { expanded = !expanded; listPanel.setVisible(expanded); } }); labelBar.addMouseListener(new MouseAdapter() { @Override public void mouseClicked(MouseEvent mouseEvent) { expanded = !expanded; listPanel.setVisible(expanded); } }); } public Collection getSelectedTracks() { List selectedTracks = new ArrayList<>(); for (Component c : listPanel.getComponents()) { if (c instanceof JCheckBox && ((JCheckBox) c).isSelected()) { selectedTracks.add(((JCheckBox) c).getText()); } } return selectedTracks; } /** * If the preferredSize has been set to a * non-null value just returns it. * If the UI delegate's getPreferredSize * method returns a non null value then return that; * otherwise defer to the component's layout manager. * * @return the value of the preferredSize property * @see #setPreferredSize * @see javax.swing.plaf.ComponentUI */ @Override public Dimension getPreferredSize() { if (listPanel == null) { return super.getPreferredSize(); } else { Dimension d = listPanel.getPreferredSize(); Component p = getRootPane(); int h = listPanel.isVisible() ? d.height : 0; int w = p == null ? d.width : getParent().getWidth(); return new Dimension(w, 3 + 3 + 30 + h); } } /** * If the minimum size has been set to a non-null value * just returns it. If the UI delegate's getMinimumSize * method returns a non-null value then return that; otherwise * defer to the component's layout manager. * * @return the value of the minimumSize property * @see #setMinimumSize * @see javax.swing.plaf.ComponentUI */ @Override public Dimension getMinimumSize() { return getPreferredSize(); } @Override public void doLayout() { if (labelBar == null || listPanel == null) return; Dimension d = listPanel.getPreferredSize(); Component p = getParent(); int w = p == null ? d.width : getParent().getWidth(); int y = 0; labelBar.setBounds(0, y, w, 30); y += 30; //noinspection SuspiciousNameCombination listPanel.setBounds(y, 33, w, d.height); } } ================================================ FILE: src/juicebox/track/EigenvectorTrack.java ================================================ /* * The MIT License (MIT) * * Copyright (c) 2011-2020 Broad Institute, Aiden Lab, Rice University, Baylor College of Medicine * * Permission is hereby granted, free of charge, to any person obtaining a copy * of this software and associated documentation files (the "Software"), to deal * in the Software without restriction, including without limitation the rights * to use, copy, modify, merge, publish, distribute, sublicense, and/or sell * copies of the Software, and to permit persons to whom the Software is * furnished to do so, subject to the following conditions: * * The above copyright notice and this permission notice shall be included in * all copies or substantial portions of the Software. * * THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR * IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, * FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE * AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER * LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, * OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN * THE SOFTWARE. */ package juicebox.track; import juicebox.Context; import juicebox.HiC; import juicebox.data.MatrixZoomData; import juicebox.gui.SuperAdapter; import juicebox.tools.utils.common.ArrayTools; import org.apache.commons.math3.stat.descriptive.DescriptiveStatistics; import org.broad.igv.renderer.GraphicUtils; import org.broad.igv.renderer.Renderer; import org.broad.igv.ui.FontManager; import org.broad.igv.util.ResourceLocator; import org.broad.igv.util.collections.LRUCache; import javax.swing.*; import java.awt.*; import java.awt.event.ActionEvent; import java.awt.event.ActionListener; import java.awt.geom.AffineTransform; import java.util.HashMap; import java.util.Map; /** * @author Jim Robinson * @since 4/13/12 */ public class EigenvectorTrack extends HiCTrack { // actual dataset object saves more; we will just save 6 most recent ones here private final LRUCache dataCache = new LRUCache<>(6); //private final Map dataCache = new HashMap<>(); private final Map dataMaxCache = new HashMap<>(); private final Map medianCache = new HashMap<>(); private final Map flippingRecordCache = new HashMap<>(); private final HiC hic; private int currentZoomBinSize = -1; private String name; private boolean isControl = false; public EigenvectorTrack(String id, String name, HiC hic, boolean isControl) { super(new ResourceLocator(id)); this.hic = hic; this.name = name; this.isControl = isControl; } private double[] loadData(int chrIdxPreCtrlInt, int zoomBinSize) { double[] data = hic.getEigenvector(chrIdxPreCtrlInt, 0, isControl); currentZoomBinSize = zoomBinSize; String cacheKey = getCacheKey(chrIdxPreCtrlInt, zoomBinSize); if (data != null && data.length > 0) { int flipVal = 1; if (flippingRecordCache.containsKey(cacheKey)) { flipVal = flippingRecordCache.get(cacheKey); if (flipVal == -1) { data = ArrayTools.flipArrayValues(data); } } else { flippingRecordCache.put(cacheKey, flipVal); } dataCache.put(cacheKey, data); DescriptiveStatistics stats = new DescriptiveStatistics(); for (double datum : data) { if (!Double.isNaN(datum)) { stats.addValue(datum); } } medianCache.put(cacheKey, stats.getPercentile(50)); double max = 0; for (double aData : stats.getValues()) { if (Math.abs(aData) > max) max = Math.abs(aData); } dataMaxCache.put(cacheKey, max); } return data; } private String getCacheKey(int chrIdx, int zoomBinSize) { String key = "observed_"; if (isControl) { key = "control_"; } return key + chrIdx + "_" + zoomBinSize; } @Override public String getToolTipText(int x, int y, TrackPanel.Orientation orientation) { return ""; // if (data == null) return null; // // int binOrigin = hic.xContext.getBinOrigin(); // int bin = binOrigin + (int) (x / hic.xContext.getScaleFactor()); // // return bin < data.length ? String.valueOf(data[bin]) : null; } @Override public JPopupMenu getPopupMenu(final TrackPanel trackPanel, final SuperAdapter superAdapter, final TrackPanel.Orientation orientation) { JPopupMenu menu = super.getPopupMenu(trackPanel, superAdapter, orientation); menu.addSeparator(); JMenuItem menuItem = new JMenuItem("Flip Eigenvector"); menuItem.addActionListener(new ActionListener() { @Override public void actionPerformed(ActionEvent e) { MatrixZoomData zd = getAppropriateZD(); if (zd == null) return; int chrIdx = orientation == TrackPanel.Orientation.X ? zd.getChr1Idx() : zd.getChr2Idx(); flipEigenvector(chrIdx, superAdapter.getHiC().getZoom().getBinSize()); hic.refreshEigenvectorTrackIfExists(); } }); menu.add(menuItem); return menu; } protected void flipEigenvector(int chrIdx, int zoomBinSize) { String cacheKey = getCacheKey(chrIdx, zoomBinSize); int currFlipVal = flippingRecordCache.get(cacheKey); flippingRecordCache.put(cacheKey, -1 * currFlipVal); } /** * Render the track in the supplied rectangle. It is the responsibility of the track to draw within the * bounds of the rectangle. * * @param g the graphics context * @param rect the track bounds, relative to the enclosing DataPanel bounds. * @param gridAxis */ @Override public void render(Graphics g, Context context, Rectangle rect, TrackPanel.Orientation orientation, HiCGridAxis gridAxis) { g.setColor(getPosColor()); int height = orientation == TrackPanel.Orientation.X ? rect.height : rect.width; int width = orientation == TrackPanel.Orientation.X ? rect.width : rect.height; int y = orientation == TrackPanel.Orientation.X ? rect.y : rect.x; int x = orientation == TrackPanel.Orientation.X ? rect.x : rect.y; MatrixZoomData zd = getAppropriateZD(); if (zd == null) return; int zoomBinSize = hic.getZoom().getBinSize(); int chrIdx = orientation == TrackPanel.Orientation.X ? zd.getChr1Idx() : zd.getChr2Idx(); String cacheKey = getCacheKey(chrIdx, zoomBinSize); double[] eigen = dataCache.get(cacheKey); if (eigen == null) { eigen = loadData(chrIdx, zoomBinSize); } if (eigen == null || eigen.length == 0) { Font original = g.getFont(); g.setFont(FontManager.getFont(12)); if (orientation == TrackPanel.Orientation.X) { GraphicUtils.drawCenteredText("Eigenvector not available at this resolution", rect, g); } else { drawRotatedString((Graphics2D) g, "Eigenvector not available at this resolution", (2 * rect.height) / 3, rect.x + 15); } g.setFont(original); return; } double dataMax = dataMaxCache.get(cacheKey); double median = medianCache.get(cacheKey); int h = height / 2; for (int bin = (int) context.getBinOrigin(); bin < eigen.length; bin++) { if (Double.isNaN(eigen[bin])) continue; int xPixelLeft = x + (int) ((bin - context.getBinOrigin()) * hic.getScaleFactor()); int xPixelRight = x + (int) ((bin + 1 - context.getBinOrigin()) * hic.getScaleFactor()); if (xPixelRight < x) { continue; } else if (xPixelLeft > x + width) { break; } double x2 = eigen[bin] - median; double max = dataMax - median; int myh = (int) ((x2 / max) * h); if (x2 > 0) { g.setColor(getPosColor()); g.fillRect(xPixelLeft, y + h - myh, (xPixelRight - xPixelLeft), myh); } else { g.setColor(getNegColor()); g.fillRect(xPixelLeft, y + h, (xPixelRight - xPixelLeft), -myh); } } } private MatrixZoomData getAppropriateZD() { try { if (isControl) { return hic.getControlZd(); } else { return hic.getZd(); } } catch (Exception e) { return null; } } public String getName() { return name; } @Override public void setName(String text) { this.name = text; } public Renderer getRenderer() { return null; //TODO change body of implemented methods use File | Settings | File Templates. } public void forceRefreshCache() { currentZoomBinSize = -1; dataCache.clear(); dataMaxCache.clear(); medianCache.clear(); } private void drawRotatedString(Graphics2D g2, String string, float x, float y) { AffineTransform orig = g2.getTransform(); g2.rotate(0); g2.setColor(Color.BLUE); g2.translate(x, 0); g2.scale(-1, 1); g2.translate(-x, 0); g2.drawString(string, x, y); g2.setTransform(orig); //g2.translate(0,0); //g2.scale(1,1); } } ================================================ FILE: src/juicebox/track/HiCCoverageDataSource.java ================================================ /* * The MIT License (MIT) * * Copyright (c) 2011-2020 Broad Institute, Aiden Lab, Rice University, Baylor College of Medicine * * Permission is hereby granted, free of charge, to any person obtaining a copy * of this software and associated documentation files (the "Software"), to deal * in the Software without restriction, including without limitation the rights * to use, copy, modify, merge, publish, distribute, sublicense, and/or sell * copies of the Software, and to permit persons to whom the Software is * furnished to do so, subject to the following conditions: * * The above copyright notice and this permission notice shall be included in * all copies or substantial portions of the Software. * * THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR * IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, * FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE * AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER * LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, * OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN * THE SOFTWARE. */ package juicebox.track; import juicebox.HiC; import juicebox.data.Dataset; import juicebox.data.MatrixZoomData; import juicebox.data.NormalizationVector; import juicebox.data.basics.Chromosome; import juicebox.windowui.HiCZoom; import juicebox.windowui.NormalizationType; import org.apache.commons.math.stat.StatUtils; import org.apache.commons.math3.stat.descriptive.DescriptiveStatistics; import org.broad.igv.renderer.DataRange; import org.broad.igv.track.WindowFunction; import java.awt.*; import java.util.ArrayList; import java.util.Collection; /** * @author jrobinso * Date: 8/1/13 * Time: 7:53 PM */ public class HiCCoverageDataSource implements HiCDataSource { private final HiC hic; private final NormalizationType normalizationType; private String name; private Color color = new Color(97, 184, 209); private Color altcolor = color; private DataRange dataRange; private final boolean isControl; public HiCCoverageDataSource(HiC hic, NormalizationType no, boolean isControl) { this.name = no.getDescription(); if (isControl) { this.name += " (Control)"; } this.hic = hic; this.normalizationType = no; this.isControl = isControl; } private void initDataRange() { MatrixZoomData zd; try { zd = hic.getZd(); } catch (Exception e) { return; } if (zd != null) { int chrIdx = zd.getChr1Idx(); HiCZoom zoom = zd.getZoom(); NormalizationVector nv = hic.getDataset().getNormalizationVector(chrIdx, zoom, normalizationType); if (nv == null) { setDataRange(new DataRange(0, 1)); } else { DescriptiveStatistics stats = new DescriptiveStatistics(nv.getData().getValues().get(0)); double max = stats.getPercentile(95); setDataRange(new DataRange(0, (float) max)); } } } public DataRange getDataRange() { if (dataRange == null) { initDataRange(); } return dataRange; } public void setDataRange(DataRange dataRange) { this.dataRange = dataRange; } public String getName() { return name; } public void setName(String name) { this.name = name; } public Color getPosColor() { return color; } public void setColor(Color color) { this.color = color; } public Color getNegColor() { return altcolor; } public void setNegColor(Color color) { this.altcolor = color; } public boolean isLog() { return false; } public Collection getAvailableWindowFunctions() { return new ArrayList<>(); } public HiCDataPoint[] getData(Chromosome chr, int startBin, int endBin, HiCGridAxis gridAxis, double scaleFactor, WindowFunction windowFunction) { HiCZoom zoom; Dataset dataset; try { if (isControl) { zoom = hic.getControlZd().getZoom(); dataset = hic.getControlDataset(); } else { zoom = hic.getZd().getZoom(); dataset = hic.getDataset(); } } catch (Exception e) { return null; } NormalizationVector nv = dataset.getNormalizationVector(chr.getIndex(), zoom, normalizationType); if (nv == null) return null; double[] data = nv.getData().getValues().get(0); CoverageDataPoint[] dataPoints = new CoverageDataPoint[endBin - startBin + 1]; for (int b = startBin; b <= endBin; b++) { long gStart = gridAxis.getGenomicStart(b); long gEnd = gridAxis.getGenomicEnd(b); int idx = b - startBin; double value = b < data.length ? data[b] : 0; dataPoints[idx] = new CoverageDataPoint(b, gStart, gEnd, value); } return dataPoints; } public static class CoverageDataPoint implements HiCDataPoint { final int binNumber; public final long genomicStart; public final long genomicEnd; public final double value; public CoverageDataPoint(int binNumber, long genomicStart, long genomicEnd, double value) { this.binNumber = binNumber; this.genomicEnd = genomicEnd; this.genomicStart = genomicStart; this.value = value; } @Override public double getBinNumber() { return binNumber; } @Override public double getWithInBins() { return 1; } @Override public long getGenomicStart() { return genomicStart; } @Override public double getValue(WindowFunction windowFunction) { return value; } @Override public long getGenomicEnd() { return genomicEnd; } } } ================================================ FILE: src/juicebox/track/HiCDataAdapter.java ================================================ /* * The MIT License (MIT) * * Copyright (c) 2011-2021 Broad Institute, Aiden Lab, Rice University, Baylor College of Medicine * * Permission is hereby granted, free of charge, to any person obtaining a copy * of this software and associated documentation files (the "Software"), to deal * in the Software without restriction, including without limitation the rights * to use, copy, modify, merge, publish, distribute, sublicense, and/or sell * copies of the Software, and to permit persons to whom the Software is * furnished to do so, subject to the following conditions: * * The above copyright notice and this permission notice shall be included in * all copies or substantial portions of the Software. * * THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR * IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, * FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE * AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER * LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, * OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN * THE SOFTWARE. */ package juicebox.track; import juicebox.HiC; import juicebox.data.basics.Chromosome; import org.broad.igv.feature.LocusScore; import org.broad.igv.track.WindowFunction; import java.util.List; /** * An adapter class to serve as a bridge between an IGV data source and a HiC track. HiC tracks differ from IGV tracks * in that the coordinate system is based on "bins", each of which can correspond to a variable genomic length. * * @author jrobinso Date: 9/10/12 */ public abstract class HiCDataAdapter implements HiCDataSource { private final double log2 = Math.log(2); private final HiC hic; private LoadedDataInterval loadedDataInterval; HiCDataAdapter(HiC hic) { this.hic = hic; } @Override public boolean isLog() { return getDataRange() != null && getDataRange().isLog(); } @Override public HiCDataPoint[] getData( Chromosome chr, int startBin, int endBin, HiCGridAxis gridAxis, double scaleFactor, WindowFunction windowFunction) { String zoom; try { zoom = hic.getZd().getZoom().getKey(); } catch (Exception e) { zoom = "null"; } String axisType = gridAxis.getClass().getName(); if (loadedDataInterval != null && loadedDataInterval.contains(zoom, (int) scaleFactor, axisType, windowFunction, chr.getName(), startBin, endBin)) { // another method is setting loadedDataInterval return loadedDataInterval.getData(); } else { // Expand starBin and endBin by 50% to facilitate panning //TODO: pass in expanded scaffolds instead of expanding here? int f = (endBin - startBin) / 2; startBin = Math.max(0, startBin - f); endBin = endBin + f; int igvZoom = gridAxis.getIGVZoom(); int subCount = (int) scaleFactor; // Increase zoom level for "super-zoom" (=> get higher resolution data if (subCount > 1) { int z = (int) (Math.log(scaleFactor) / log2); igvZoom += (z + 1); } DataAccumulator[] tmp = new DataAccumulator[(endBin - startBin + 1) * subCount]; long gStart = gridAxis.getGenomicStart(startBin); long gEnd = gridAxis.getGenomicEnd(endBin); List scores = getLocusScores(chr.getName(), gStart, gEnd, igvZoom, windowFunction); if (scores == null) { return null; } int nPts = 0; for (LocusScore locusScore : scores) { int bs = Math.max(startBin, gridAxis.getBinNumberForGenomicPosition(locusScore.getStart())); int be = Math.min(endBin, gridAxis.getBinNumberForGenomicPosition(locusScore.getEnd() - 1)); for (int b = bs; b <= be; b++) { long bStart = gridAxis.getGenomicStart(b); long bEnd = gridAxis.getGenomicEnd(b); double delta = ((double) (bEnd - bStart)) / subCount; int subBin0 = b == bs ? (int) ((locusScore.getStart() - bStart) / delta) : 0; int subBin1 = b == be ? (int) ((locusScore.getEnd() - bStart) / delta) : subCount - 1; for (int subBin = subBin0; subBin <= subBin1; subBin++) { final double subBinWidth = 1.0 / subCount; int idx = (b - startBin) * subCount + subBin; if (idx < 0 || idx >= tmp.length) { continue; } DataAccumulator dataBin = tmp[idx]; if (dataBin == null) { double bPrime = b + ((double) subBin) / subCount; int g0 = (int) (bStart + subBin * delta); int g1 = (int) (bStart + (subBin + 1) * delta); dataBin = new DataAccumulator(bPrime, subBinWidth, g0, g1); // bStart, bEnd); tmp[idx] = dataBin; nPts++; } dataBin.addScore(locusScore); } } } // Copy data, leaving out null values DataAccumulator[] data; if (nPts == tmp.length) { data = tmp; } else { data = new DataAccumulator[nPts]; int idx = 0; for (DataAccumulator sum : tmp) { if (sum != null) { data[idx++] = sum; } } } loadedDataInterval = new LoadedDataInterval(zoom, (int) scaleFactor, axisType, windowFunction, chr.getName(), startBin, endBin, data); return data; // should only return number of points in aggregate scaffold } } @Override public void setName(String text) { } protected abstract List getLocusScores(String chr, long gStart, long gEnd, int zoom, WindowFunction windowFunction); public static class DataAccumulator implements HiCDataPoint { final double binNumber; public double width = 1; public int nPts = 0; //set after public double weightedSum = 0; //set after public double max = 0; //set after public long genomicStart; public long genomicEnd; public DataAccumulator(double binNumber) { this.binNumber = binNumber; } public DataAccumulator(double binNumber, double delta, long genomicStart, long genomicEnd) { this.binNumber = binNumber; this.width = delta; this.genomicStart = genomicStart; this.genomicEnd = genomicEnd; } @Override public double getBinNumber() { return binNumber; } @Override public double getWithInBins() { return width; } @Override public long getGenomicEnd() { return genomicEnd; } @Override public long getGenomicStart() { return genomicStart; } @Override public double getValue(WindowFunction windowFunction) { return windowFunction == WindowFunction.max ? max : (nPts == 0 ? 0 : (float) (weightedSum / nPts)); } void addScore(LocusScore ls) { // if (ls.getStart() >= genomicEnd || ls.getEnd() < genomicStart) return; // double weight = ((double) (Math.min(genomicEnd, ls.getEnd()) - Math.max(genomicStart, ls.getStart()))) / // (genomicEnd - genomicStart); double weight = 1; final float score = ls.getScore(); weightedSum += weight * score; nPts++; max = score > max ? score : max; } } class LoadedDataInterval { final String zoom; final int scaleFactor; final String axisType; final WindowFunction windowFunction; final String chr; final int startBin; final int endBin; final DataAccumulator[] data; LoadedDataInterval(String zoom, int scaleFactor, String axisType, WindowFunction windowFunction, String chr, int startBin, int endBin, DataAccumulator[] data) { this.zoom = zoom; this.scaleFactor = scaleFactor; this.axisType = axisType; this.windowFunction = windowFunction; this.chr = chr; this.startBin = startBin; this.endBin = endBin; this.data = data; } boolean contains(String zoom, int scaleFactor, String axisType, WindowFunction windowFunction, String chr, int startBin, int endBin) { return zoom.equals(this.zoom) && scaleFactor == this.scaleFactor && axisType.equals(this.axisType) && windowFunction == this.windowFunction && chr.equals(this.chr) && startBin >= this.startBin && endBin <= this.endBin; } DataAccumulator[] getData() { return data; } } } ================================================ FILE: src/juicebox/track/HiCDataPoint.java ================================================ /* * The MIT License (MIT) * * Copyright (c) 2011-2020 Broad Institute, Aiden Lab, Rice University, Baylor College of Medicine * * Permission is hereby granted, free of charge, to any person obtaining a copy * of this software and associated documentation files (the "Software"), to deal * in the Software without restriction, including without limitation the rights * to use, copy, modify, merge, publish, distribute, sublicense, and/or sell * copies of the Software, and to permit persons to whom the Software is * furnished to do so, subject to the following conditions: * * The above copyright notice and this permission notice shall be included in * all copies or substantial portions of the Software. * * THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR * IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, * FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE * AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER * LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, * OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN * THE SOFTWARE. */ package juicebox.track; import org.broad.igv.track.WindowFunction; /** * @author jrobinso * Date: 8/1/13 * Time: 6:45 PM */ public interface HiCDataPoint { double getBinNumber(); long getGenomicStart(); long getGenomicEnd(); double getValue(WindowFunction windowFunction); double getWithInBins(); } ================================================ FILE: src/juicebox/track/HiCDataSource.java ================================================ /* * The MIT License (MIT) * * Copyright (c) 2011-2020 Broad Institute, Aiden Lab, Rice University, Baylor College of Medicine * * Permission is hereby granted, free of charge, to any person obtaining a copy * of this software and associated documentation files (the "Software"), to deal * in the Software without restriction, including without limitation the rights * to use, copy, modify, merge, publish, distribute, sublicense, and/or sell * copies of the Software, and to permit persons to whom the Software is * furnished to do so, subject to the following conditions: * * The above copyright notice and this permission notice shall be included in * all copies or substantial portions of the Software. * * THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR * IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, * FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE * AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER * LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, * OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN * THE SOFTWARE. */ package juicebox.track; import juicebox.data.basics.Chromosome; import org.broad.igv.renderer.DataRange; import org.broad.igv.track.WindowFunction; import java.awt.*; import java.util.Collection; /** * @author jrobinso * Date: 8/1/13 * Time: 7:51 PM */ public interface HiCDataSource { String getName(); void setName(String text); Color getPosColor(); void setColor(Color selectedColor); Color getNegColor(); void setNegColor(Color selectedColor); DataRange getDataRange(); void setDataRange(DataRange dataRange); boolean isLog(); HiCDataPoint[] getData(Chromosome chr, int startBin, int endBin, HiCGridAxis gridAxis, double scaleFactor, WindowFunction windowFunction); Collection getAvailableWindowFunctions(); } ================================================ FILE: src/juicebox/track/HiCDataTrack.java ================================================ /* * The MIT License (MIT) * * Copyright (c) 2011-2020 Broad Institute, Aiden Lab, Rice University, Baylor College of Medicine * * Permission is hereby granted, free of charge, to any person obtaining a copy * of this software and associated documentation files (the "Software"), to deal * in the Software without restriction, including without limitation the rights * to use, copy, modify, merge, publish, distribute, sublicense, and/or sell * copies of the Software, and to permit persons to whom the Software is * furnished to do so, subject to the following conditions: * * The above copyright notice and this permission notice shall be included in * all copies or substantial portions of the Software. * * THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR * IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, * FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE * AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER * LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, * OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN * THE SOFTWARE. */ package juicebox.track; import juicebox.Context; import juicebox.HiC; import juicebox.assembly.OneDimAssemblyTrackLifter; import juicebox.data.censoring.OneDimTrackCensoring; import juicebox.gui.SuperAdapter; import org.broad.igv.renderer.DataRange; import org.broad.igv.track.WindowFunction; import org.broad.igv.util.ResourceLocator; import javax.swing.*; import java.awt.*; import java.awt.event.ActionEvent; import java.awt.event.ActionListener; import java.text.NumberFormat; import java.util.Arrays; import java.util.Collection; import java.util.Comparator; /** * @author jrobinso * Date: 11/2/12 * Time: 9:41 AM */ public class HiCDataTrack extends HiCTrack { private static final int TRACK_MARGIN = 2; private final HiC hic; private final HiCDataSource dataSource; private final NumberFormat formatter = NumberFormat.getInstance(); private final float[] dash = {8.0f}; private final BasicStroke dashedStroke = new BasicStroke(0.5f, BasicStroke.CAP_BUTT, BasicStroke.JOIN_MITER, 2.0f, dash, 0.0f); private final Color dashColor = new Color(120, 120, 120); private boolean logScale = false; private HiCDataPoint[] data; private WindowFunction windowFunction = WindowFunction.mean; public HiCDataTrack(HiC hic, ResourceLocator locator, HiCDataSource da) { super(locator); this.hic = hic; this.dataSource = da; this.logScale = dataSource.isLog(); } @Override public void render(Graphics g, Context context, Rectangle rect, TrackPanel.Orientation orientation, HiCGridAxis gridAxis) { int height = orientation == TrackPanel.Orientation.X ? rect.height : rect.width; int width = orientation == TrackPanel.Orientation.X ? rect.width : rect.height; int y = orientation == TrackPanel.Orientation.X ? rect.y : rect.x; int x = orientation == TrackPanel.Orientation.X ? rect.x : rect.y; Graphics2D g2d = (Graphics2D) g; double startBin = context.getBinOrigin(); double endBin = startBin + (width / hic.getScaleFactor()); // only show parts of things if (hic.getChromosomeHandler().isCustomChromosome(context.getChromosome())) { data = OneDimTrackCensoring.getFilteredData(dataSource, hic, context.getChromosome(), (int) startBin, (int) endBin + 1, gridAxis, hic.getScaleFactor(), windowFunction); // fix this case w ordering modifications } else if (SuperAdapter.assemblyModeCurrentlyActive) { data = OneDimAssemblyTrackLifter.liftDataArray(dataSource, hic, context.getChromosome(), (int) startBin, (int) endBin + 1, gridAxis, hic.getScaleFactor(), windowFunction); } else { data = dataSource.getData(context.getChromosome(), (int) startBin, (int) endBin + 1, gridAxis, hic.getScaleFactor(), windowFunction); } if (data == null) return; Color posColor = dataSource.getPosColor(); Color negColor = dataSource.getNegColor(); // Get the Y axis definition, consisting of minimum, maximum, and base value. Often // the base value is == min value which is == 0. DataRange dataRange = dataSource.getDataRange(); float maxValue = dataRange.getMaximum(); float baseValue = dataRange.getBaseline(); float minValue = dataRange.getMinimum(); boolean isLog = dataRange.isLog(); if (isLog) { minValue = (float) (minValue == 0 ? 0 : Math.log10(minValue)); maxValue = (float) Math.log10(maxValue); } // Calculate the Y scale factor. double delta = (maxValue - minValue); double yScaleFactor = (height - TRACK_MARGIN) / delta; // Calculate the Y position in pixels of the base value. Clip to bounds of rectangle double baseDelta = maxValue - baseValue; int baseY = (int) (y + baseDelta * yScaleFactor); if (baseY < y) { baseY = y; } else if (baseY > y + (height - TRACK_MARGIN)) { baseY = y + (height - TRACK_MARGIN); } //for (int i = 0; i < data.length; i++) { for (HiCDataPoint d : data) { //HiCDataPoint d = data[i]; if (d == null) continue; double bin = d.getBinNumber() - startBin; double widthInBIns = d.getWithInBins(); int xPixelLeft = x + (int) Math.round(bin * hic.getScaleFactor()); //context.getScreenPosition (genomicPosition); int dx = (int) Math.max(1, widthInBIns * hic.getScaleFactor()); int xPixelRight = xPixelLeft + dx; if (xPixelRight < x) { continue; } else if (xPixelLeft > x + width) { break; } double dataY = d.getValue(windowFunction); if (isLog && dataY <= 0) { continue; } if (!Double.isNaN(dataY)) { // Compute the pixel y location. Clip to bounds of rectangle. double dy = isLog ? Math.log10(dataY) - baseValue : (dataY - baseValue); int pY = baseY - (int) (dy * yScaleFactor); if (pY < y) { pY = y; } else if (pY > y + (height - TRACK_MARGIN)) { pY = y + (height - TRACK_MARGIN); } Color color = (dataY >= baseValue) ? posColor : negColor; g.setColor(color); if (dx <= 1) { g.drawLine(xPixelLeft, baseY, xPixelLeft, pY); } else { if (pY > baseY) { g.fillRect(xPixelLeft, baseY, dx, pY - baseY); } else { g.fillRect(xPixelLeft, pY, dx, baseY - pY); } } } } if (minValue < 0) { g.setColor(dashColor); g2d.setStroke(dashedStroke); g.drawLine(0, baseY, width, baseY); } } public WindowFunction getWindowFunction() { return windowFunction; } public void setWindowFunction(WindowFunction windowFunction) { this.windowFunction = windowFunction; } public String getName() { return dataSource.getName(); } @Override public void setName(String text) { dataSource.setName(text); } @Override public String getToolTipText(int x, int y, TrackPanel.Orientation orientation) { StringBuilder txt = new StringBuilder(); txt.append(""); txt.append(getName()); txt.append(""); if (data == null) return txt.toString(); Context context = orientation == TrackPanel.Orientation.X ? hic.getXContext() : hic.getYContext(); double binOrigin = context.getBinOrigin(); final double scaleFactor = hic.getScaleFactor(); final double substepSize = 1.0 / scaleFactor; double bin = (binOrigin + (x / scaleFactor)); HiCDataPoint target = new HiCDataAdapter.DataAccumulator(bin); int idx = Arrays.binarySearch(data, target, new Comparator() { @Override public int compare(HiCDataPoint weightedSum, HiCDataPoint weightedSum1) { final double binNumber = weightedSum.getBinNumber(); final double binNumber1 = weightedSum1.getBinNumber(); int bin = (int) binNumber; int bin1 = (int) binNumber1; if (bin == bin1) { double rem = binNumber - bin; double rem1 = binNumber1 - bin; if (Math.abs(rem - rem1) < substepSize) { return 0; } else { if (rem > rem1) return 1; else return -1; } } else { return bin - bin1; } } }); txt.append(""); if (idx < 0) { txt.append("
bin: ").append(formatter.format((int) bin)); } else { HiCDataPoint ws = data[idx]; if (ws == null) return null; txt.append("
").append(formatter.format(ws.getGenomicStart())) .append("-") .append(formatter.format(ws.getGenomicEnd())) .append("
bin: ") .append(formatter.format(ws.getBinNumber())) .append("
value: ") .append(formatter.format(ws.getValue(windowFunction))); } txt.append(""); return txt.toString(); } @Override public JPopupMenu getPopupMenu(final TrackPanel trackPanel, final SuperAdapter superAdapter, TrackPanel.Orientation orientation) { JPopupMenu menu = super.getPopupMenu(trackPanel, superAdapter, orientation); menu.addSeparator(); JMenuItem menuItem = new JMenuItem("Configure track..."); menuItem.addActionListener(new ActionListener() { @Override public void actionPerformed(ActionEvent e) { final TrackConfigDialog trackConfigDialog = new TrackConfigDialog(superAdapter.getMainWindow(), HiCDataTrack.this); trackConfigDialog.setVisible(true); if (trackConfigDialog.isNotCanceled()) { superAdapter.updateTrackPanel(); } } }); menu.add(menuItem); return menu; } public DataRange getDataRange() { return dataSource.getDataRange(); //To change body of created methods use File | Settings | File Templates. } public void setDataRange(DataRange dataRange) { dataSource.setDataRange(dataRange); } @Override public Color getPosColor() { return dataSource.getPosColor(); } @Override public void setPosColor(Color selectedColor) { dataSource.setColor(selectedColor); } @Override public Color getNegColor() { return dataSource.getNegColor(); } @Override public void setNegColor(Color selectedColor) { dataSource.setNegColor(selectedColor); } public Collection getAvailableWindowFunctions() { return dataSource.getAvailableWindowFunctions(); } } ================================================ FILE: src/juicebox/track/HiCFeatureTrack.java ================================================ /* * The MIT License (MIT) * * Copyright (c) 2011-2020 Broad Institute, Aiden Lab, Rice University, Baylor College of Medicine * * Permission is hereby granted, free of charge, to any person obtaining a copy * of this software and associated documentation files (the "Software"), to deal * in the Software without restriction, including without limitation the rights * to use, copy, modify, merge, publish, distribute, sublicense, and/or sell * copies of the Software, and to permit persons to whom the Software is * furnished to do so, subject to the following conditions: * * The above copyright notice and this permission notice shall be included in * all copies or substantial portions of the Software. * * THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR * IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, * FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE * AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER * LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, * OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN * THE SOFTWARE. */ package juicebox.track; import htsjdk.tribble.Feature; import juicebox.Context; import juicebox.HiC; import juicebox.assembly.IGVFeatureCopy; import juicebox.assembly.OneDimAssemblyTrackLifter; import juicebox.gui.SuperAdapter; import org.broad.igv.feature.Exon; import org.broad.igv.feature.FeatureUtils; import org.broad.igv.feature.IGVFeature; import org.broad.igv.feature.Strand; import org.broad.igv.track.FeatureSource; import org.broad.igv.ui.FontManager; import org.broad.igv.util.BrowserLauncher; import org.broad.igv.util.ResourceLocator; import java.awt.*; import java.io.IOException; import java.util.ArrayList; import java.util.Comparator; import java.util.Iterator; import java.util.List; /** * @author jrobinso * Date: 12/1/12 * Time: 12:34 AM */ public class HiCFeatureTrack extends HiCTrack { private static final int BLOCK_HEIGHT = 14; private static final int ARROW_SPACING = 10; private final Font font; private final HiC hic; private final FeatureSource featureSource; private String name; public HiCFeatureTrack(HiC hic, ResourceLocator locator, FeatureSource featureSource) { super(locator); this.hic = hic; this.featureSource = featureSource; font = FontManager.getFont(6); } public static double getFractionalBin(int position, double scaleFactor, HiCGridAxis gridAxis) { double bin1 = gridAxis.getBinNumberForGenomicPosition(position); // Fractional bin (important for "super-zoom") if (scaleFactor > 1) { double bw1 = gridAxis.getGenomicEnd(bin1) - gridAxis.getGenomicStart(bin1); bin1 += (position - gridAxis.getGenomicStart(bin1)) / bw1; } return bin1; } @Override public void render(Graphics g, Context context, Rectangle rect, TrackPanel.Orientation orientation, HiCGridAxis gridAxis) { int height = orientation == TrackPanel.Orientation.X ? rect.height : rect.width; int width = orientation == TrackPanel.Orientation.X ? rect.width : rect.height; int y = orientation == TrackPanel.Orientation.X ? rect.y : rect.x; int x = orientation == TrackPanel.Orientation.X ? rect.x : rect.y; String chr = context.getChromosome().getName(); double startBin = context.getBinOrigin(); final double scaleFactor = hic.getScaleFactor(); double endBin = startBin + (width / scaleFactor); // todo igv int gStart = (int) gridAxis.getGenomicStart(startBin); int gEnd = (int) gridAxis.getGenomicEnd(endBin); int fh = Math.min(height - 2, BLOCK_HEIGHT); int fy = y + (height - fh) / 2; int fCenter = y + height / 2; g.setFont(font); g.setColor(getPosColor()); //Graphics strGraphics = g.create(); g.setColor(new Color(0, 150, 0)); Iterator iter; if (SuperAdapter.assemblyModeCurrentlyActive) { // Update features according to current assembly status gStart = 0; gEnd = (int) context.getChrLength(); } try { iter = featureSource.getFeatures(chr, gStart, gEnd); if (!iter.hasNext()) { // if empty probably because "chr" missing at start of chromosome // TODO mitochondrial genes may be an issue here? iter = featureSource.getFeatures("chr" + chr, gStart, gEnd); } } catch (IOException error) { System.err.println("Error getting feature source " + error); return; } //handles bed and gff files only for now if (SuperAdapter.assemblyModeCurrentlyActive && (getLocator().getPath().toLowerCase().endsWith(".bed") || getLocator().getPath().toLowerCase().endsWith(".gff"))) { // update features according to assembly status ArrayList iterItems = new ArrayList<>(); while (iter.hasNext()) { IGVFeature feature = (IGVFeature) iter.next(); iterItems.add(feature); } List newFeatureList = OneDimAssemblyTrackLifter.liftIGVFeatures(hic, context.getChromosome(), (int) startBin, (int) endBin + 1, gridAxis, iterItems, getLocator().getPath().toLowerCase().endsWith(".bed")); iter = newFeatureList.iterator(); } while (iter.hasNext()) { IGVFeature feature = (IGVFeature) iter.next(); final Color featureColor = feature.getColor(); if (featureColor != null) { g.setColor(featureColor); } int startPoint = feature.getStart(); int endPoint = feature.getEnd(); double bin1 = getFractionalBin(startPoint, scaleFactor, gridAxis); double bin2 = getFractionalBin(endPoint, scaleFactor, gridAxis); if (bin2 < startBin) { continue; } else if (bin1 > endBin) { break; } int xPixelLeft = x + (int) ((bin1 - startBin) * scaleFactor); int xPixelRight = x + (int) ((bin2 - startBin) * scaleFactor); int fw = Math.max(1, xPixelRight - xPixelLeft); if (fw < 5 || feature.getExons() == null || feature.getExons().size() == 0) { g.fillRect(xPixelLeft, fy, fw, fh); } else { // intron g.drawLine(xPixelLeft, fCenter, xPixelRight, fCenter); // arrows if (fw > 20) { if (feature.getStrand() == Strand.POSITIVE) { for (int p = xPixelLeft + 5; p < xPixelLeft + fw; p += 10) { g.drawLine(p - 2, fCenter - 2, p, fCenter); g.drawLine(p - 2, fCenter + 2, p, fCenter); } } else if (feature.getStrand() == Strand.NEGATIVE) { for (int p = xPixelLeft + fw - 5; p > xPixelLeft; p -= 10) { g.drawLine(p + 2, fCenter - 2, p, fCenter); g.drawLine(p + 2, fCenter + 2, p, fCenter); } } } for (Exon exon : feature.getExons()) { bin1 = getFractionalBin(exon.getStart(), scaleFactor, gridAxis); bin2 = getFractionalBin(exon.getEnd(), scaleFactor, gridAxis); xPixelLeft = (int) ((bin1 - startBin) * scaleFactor); fw = (int) ((bin2 - bin1 + 1) * scaleFactor); g.fillRect(xPixelLeft, fy, fw, fh); } } } } @Override public String getToolTipText(int x, int y, TrackPanel.Orientation orientation) { Context context = orientation == TrackPanel.Orientation.X ? hic.getXContext() : hic.getYContext(); StringBuilder txt = new StringBuilder(); txt.append(""); txt.append(getName()); txt.append(""); IGVFeature f = getFeatureAtPixel(x, context, orientation); if (f != null) { // && (f.getEnd() > start && f.getStart() < end)) { txt.append("
"); txt.append(f.getDescription()); txt.append(""); } return txt.toString(); } private IGVFeature getFeatureAtPixel(int x, Context context, TrackPanel.Orientation orientation) { HiCGridAxis gridAxis; try { gridAxis = orientation == TrackPanel.Orientation.X ? hic.getZd().getXGridAxis() : hic.getZd().getYGridAxis(); } catch (Exception e) { return null; } int binOrigin = (int) (context.getBinOrigin()); int bin = binOrigin + (int) (x / hic.getScaleFactor()); int start = (int) gridAxis.getGenomicStart(bin); int end = (int) gridAxis.getGenomicEnd(bin); int middle = (int) gridAxis.getGenomicMid(bin); String chr = context.getChromosome().getName(); int b1 = Math.max(0, bin - 2); int b2 = bin + 2; int buffer = (int) ((gridAxis.getGenomicEnd(b2) - gridAxis.getGenomicStart(b1)) / 2); // The maximum length of all features in this collection. Used to insure we consider all features that // might overlap the position (feature are sorted by start position, but length is variable) int maxFeatureLength = 284000; // TTN gene Iterator iter; try { iter = featureSource.getFeatures(chr, start, end); if (!iter.hasNext()) { // if empty, probably because "chr" missing at start of chromosome // TODO mitochondrial genes may be an issue here? iter = featureSource.getFeatures("chr" + chr, start, end); } } catch (IOException error) { System.err.println("Error getting feature source " + error); return null; } List allFeatures = new ArrayList<>(); while (iter.hasNext()) { allFeatures.add((Feature) iter.next()); } List featuresAtMouse = FeatureUtils.getAllFeaturesAt(middle, maxFeatureLength, buffer, allFeatures); // Return the most specific (smallest); if (featuresAtMouse != null && featuresAtMouse.size() > 0) { featuresAtMouse.sort(new Comparator() { @Override public int compare(Feature feature, Feature feature1) { return ((feature.getEnd() - feature.getStart()) - (feature1.getEnd() - feature1.getStart())); } }); return (IGVFeature) featuresAtMouse.get(0); } return null; } @Override public String getName() { return name; //To change body of implemented methods use File | Settings | File Templates. } public void setName(String name) { this.name = name; } protected void drawStrandArrows(Strand strand, int startX, int endX, int startY, Graphics2D g2D) { // Don't draw strand arrows for very small regions int distance = endX - startX; if ((distance < 6)) { return; } int sz = strand.equals(Strand.POSITIVE) ? -3 : 3; final int asz = Math.abs(sz); for (int ii = startX + ARROW_SPACING / 2; ii < endX; ii += ARROW_SPACING) { g2D.drawLine(ii, startY, ii + sz, startY + asz); g2D.drawLine(ii, startY, ii + sz, startY - asz); } } public void mouseClicked(int x, int y, Context context, TrackPanel.Orientation orientation) { IGVFeature f = getFeatureAtPixel(x, context, orientation); String url = ""; if (f != null) { try { url = "http://www.genecards.org/cgi-bin/carddisp.pl?gene=" + f.getName(); BrowserLauncher.openURL(url); } catch (IOException e) { System.err.println("Error opening gene link: " + url + " " + e.getLocalizedMessage()); } } } } ================================================ FILE: src/juicebox/track/HiCFixedGridAxis.java ================================================ /* * The MIT License (MIT) * * Copyright (c) 2011-2021 Broad Institute, Aiden Lab, Rice University, Baylor College of Medicine * * Permission is hereby granted, free of charge, to any person obtaining a copy * of this software and associated documentation files (the "Software"), to deal * in the Software without restriction, including without limitation the rights * to use, copy, modify, merge, publish, distribute, sublicense, and/or sell * copies of the Software, and to permit persons to whom the Software is * furnished to do so, subject to the following conditions: * * The above copyright notice and this permission notice shall be included in * all copies or substantial portions of the Software. * * THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR * IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, * FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE * AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER * LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, * OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN * THE SOFTWARE. */ package juicebox.track; /** * @author jrobinso * Date: 9/14/12 * Time: 8:54 AM */ public class HiCFixedGridAxis implements HiCGridAxis { private final long binCount; private final int binSize; private final int igvZoom; private final int[] sites; private final double log2 = Math.log(2.0D); public HiCFixedGridAxis(long binCount, int binSize, int[] sites) { this.binCount = binCount; this.binSize = binSize; this.sites = sites; // Compute an approximate igv zoom level igvZoom = Math.max(0, (int) (Math.log(binCount / 700) / log2)); } @Override public int getBinSize() { return binSize; } @Override public long getGenomicStart(double binNumber) { return (long) (binNumber * binSize); } @Override public long getGenomicEnd(double binNumber) { return (long) ((binNumber + 1) * binSize); } @Override public long getGenomicMid(double binNumber) { return (long) ((binNumber + 0.5) * binSize); } @Override public int getIGVZoom() { return igvZoom; } @Override public int getBinNumberForGenomicPosition(long genomicPosition) { return (int) (genomicPosition / ((double) binSize)); } @Override public int getBinNumberForFragment(int fragment) { if (fragment < sites.length && fragment >= 0) { int genomicPosition = sites[fragment]; return getBinNumberForGenomicPosition(genomicPosition); } throw new RuntimeException("Fragment: " + fragment + " is out of range"); } @Override public long getBinCount() { return binCount; } } ================================================ FILE: src/juicebox/track/HiCFragmentAxis.java ================================================ /* * The MIT License (MIT) * * Copyright (c) 2011-2021 Broad Institute, Aiden Lab, Rice University, Baylor College of Medicine * * Permission is hereby granted, free of charge, to any person obtaining a copy * of this software and associated documentation files (the "Software"), to deal * in the Software without restriction, including without limitation the rights * to use, copy, modify, merge, publish, distribute, sublicense, and/or sell * copies of the Software, and to permit persons to whom the Software is * furnished to do so, subject to the following conditions: * * The above copyright notice and this permission notice shall be included in * all copies or substantial portions of the Software. * * THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR * IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, * FITNESS FOR A PARTICULAR PURPOSE AND NON-INFRINGEMENT. IN NO EVENT SHALL THE * AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER * LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, * OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN * THE SOFTWARE. */ package juicebox.track; /** * @author jrobinso * Date: 9/14/12 * Time: 8:49 AM */ public class HiCFragmentAxis implements HiCGridAxis { private final int binSize; // bin size in fragments private final int igvZoom; private final int[] sites; private final long chrLength; private final double log2 = Math.log(2.0D); /** * @param sites ordered by start position. Its assumed bins are contiguous, no gaps and no overlap. * @param chrLength */ public HiCFragmentAxis(int binSize, int[] sites, long chrLength) { this.binSize = binSize; this.sites = sites; this.chrLength = chrLength; // Compute an approximate igv zoom level double averageBinSizeInBP = ((double) this.chrLength) / (sites.length + 1) * binSize; igvZoom = (int) (Math.log((this.chrLength / 700) / averageBinSizeInBP) / log2); } @Override public long getGenomicStart(double binNumber) { int fragNumber = (int) binNumber * binSize; int siteIdx = Math.min(fragNumber, sites.length - 1); if (binNumber >= sites.length) { binNumber = sites.length - 1; } return binNumber == 0 ? 0 : sites[siteIdx - 1]; } @Override public long getGenomicEnd(double binNumber) { int fragNumber = (int) (binNumber + 1) * binSize - 1; int siteIdx = Math.min(fragNumber, sites.length - 1); return siteIdx < sites.length ? sites[siteIdx] : chrLength; } // @Override // public int getGenomicStart(double binNumber) { // // // if (binNumber >= sites.length) { // binNumber = sites.length - 1; // } // // int bin = (int) binNumber; // double remainder = binNumber % bin; // // double start = binNumber == 0 ? 0 : sites[bin-1]; // double end = sites[bin]; // double delta = end - start; // // return (int) (start + remainder * delta); // // } // // @Override // public int getGenomicEnd(double binNumber) { // // if (binNumber >= sites.length) { // return chrLength; // } // // int bin = (int) binNumber; // double remainder = binNumber % bin; // // double start = binNumber == 0 ? 0 : sites[bin-1]; // double end = sites[bin]; // // return sites[bin]; // // // } @Override public long getGenomicMid(double binNumber) { return (getGenomicStart(binNumber) + getGenomicEnd(binNumber)) / 2; } @Override public int getIGVZoom() { return igvZoom; } /** * Return bin that this position lies on. Fragment 0 means position < sites[0]. * Fragment 1 means position >= sites[0] and < sites[1]. * * @param position The genome position to search for within that array * @return The fragment location such that position >= sites[retVal-1] and position < sites[retVal] */ @Override public int getBinNumberForGenomicPosition(long position) { return getFragmentNumberForGenomicPosition((int) position) / binSize; // should not exceed max int size } /** * Return bin that this position lies on. Fragment 0 means position < sites[0]. * Fragment 1 means position >= sites[0] and < sites[1]. * * @param position The genome position to search for within that array * @return The fragment location such that position >= sites[retVal-1] and position < sites[retVal] */ private int getFragmentNumberForGenomicPosition(int position) { int lo = 0; int hi = sites.length - 1; // Eliminate the extreme cases if (position < sites[0]) return 0; if (position >= sites[hi]) return sites.length; while (lo <= hi) { int mid = (lo + hi) >>> 1; if (position >= sites[mid - 1] && position < sites[mid]) { return mid; } else if (position >= sites[mid]) { lo = mid + 1; } else { hi = mid; } } // Not found return -1; } @Override public int getBinNumberForFragment(int fragment) { if (fragment <= sites.length) { return fragment / binSize; } else { throw new RuntimeException("Fragment: " + fragment + " is out of range"); } } @Override public long getBinCount() { return (sites.length / binSize) + 1; } @Override public int getBinSize() { return binSize; } } ================================================ FILE: src/juicebox/track/HiCGridAxis.java ================================================ /* * The MIT License (MIT) * * Copyright (c) 2011-2020 Broad Institute, Aiden Lab, Rice University, Baylor College of Medicine * * Permission is hereby granted, free of charge, to any person obtaining a copy * of this software and associated documentation files (the "Software"), to deal * in the Software without restriction, including without limitation the rights * to use, copy, modify, merge, publish, distribute, sublicense, and/or sell * copies of the Software, and to permit persons to whom the Software is * furnished to do so, subject to the following conditions: * * The above copyright notice and this permission notice shall be included in * all copies or substantial portions of the Software. * * THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR * IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, * FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE * AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER * LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, * OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN * THE SOFTWARE. */ package juicebox.track; /** * @author jrobinso * Date: 9/14/12 * Time: 8:54 AM */ public interface HiCGridAxis { long getGenomicStart(double binNumber); long getGenomicEnd(double binNumber); long getGenomicMid(double binNumber); int getIGVZoom(); long getBinCount(); int getBinSize(); int getBinNumberForGenomicPosition(long genomePosition); int getBinNumberForFragment(int fragmentX); } ================================================ FILE: src/juicebox/track/HiCIGVDataAdapter.java ================================================ /* * The MIT License (MIT) * * Copyright (c) 2011-2020 Broad Institute, Aiden Lab, Rice University, Baylor College of Medicine * * Permission is hereby granted, free of charge, to any person obtaining a copy * of this software and associated documentation files (the "Software"), to deal * in the Software without restriction, including without limitation the rights * to use, copy, modify, merge, publish, distribute, sublicense, and/or sell * copies of the Software, and to permit persons to whom the Software is * furnished to do so, subject to the following conditions: * * The above copyright notice and this permission notice shall be included in * all copies or substantial portions of the Software. * * THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR * IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, * FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE * AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER * LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, * OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN * THE SOFTWARE. */ package juicebox.track; import juicebox.HiC; import org.broad.igv.feature.LocusScore; import org.broad.igv.renderer.DataRange; import org.broad.igv.track.DataTrack; import org.broad.igv.track.WindowFunction; import java.awt.*; import java.util.Collection; import java.util.List; /** * @author jrobinso * Date: 11/8/12 * Time: 10:16 AM */ public class HiCIGVDataAdapter extends HiCDataAdapter { private final DataTrack igvTrack; public HiCIGVDataAdapter(HiC hic, DataTrack igvTrack) { super(hic); this.igvTrack = igvTrack; } public double getMax() { return igvTrack.getDataRange().getMaximum(); } public String getName() { return igvTrack.getName(); } @Override public void setName(String text) { igvTrack.setName(text); } public Color getPosColor() { return igvTrack.getColor(); } @Override public void setColor(Color selectedColor) { igvTrack.setColor(selectedColor); } public boolean isLogScale() { return igvTrack.getDataRange().isLog(); } public Color getNegColor() { return igvTrack.getAltColor(); } @Override public void setNegColor(Color selectedColor) { igvTrack.setAltColor(selectedColor); } public DataRange getDataRange() { return igvTrack.getDataRange(); } @Override public void setDataRange(DataRange dataRange) { igvTrack.setDataRange(dataRange); } @Override public Collection getAvailableWindowFunctions() { return igvTrack.getAvailableWindowFunctions(); } protected List getLocusScores(String chr, long gStart, long gEnd, int zoom, WindowFunction windowFunction) { igvTrack.setWindowFunction(windowFunction); org.broad.igv.track.LoadedDataInterval> scores = igvTrack.getSummaryScores(chr, (int) gStart, (int) gEnd, zoom); // Problems with human not having the "chr". Return scores if not 0, otherwise try adding "chr" if (scores.getFeatures().size() > 0) return scores.getFeatures(); else return igvTrack.getSummaryScores("chr" + chr, (int) gStart, (int) gEnd, zoom).getFeatures(); } } ================================================ FILE: src/juicebox/track/HiCLoadDialog.java ================================================ /* * The MIT License (MIT) * * Copyright (c) 2011-2021 Broad Institute, Aiden Lab, Rice University, Baylor College of Medicine * * Permission is hereby granted, free of charge, to any person obtaining a copy * of this software and associated documentation files (the "Software"), to deal * in the Software without restriction, including without limitation the rights * to use, copy, modify, merge, publish, distribute, sublicense, and/or sell * copies of the Software, and to permit persons to whom the Software is * furnished to do so, subject to the following conditions: * * The above copyright notice and this permission notice shall be included in * all copies or substantial portions of the Software. * * THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR * IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, * FITNESS FOR A PARTICULAR PURPOSE AND NON-INFRINGEMENT. IN NO EVENT SHALL THE * AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER * LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, * OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN * THE SOFTWARE. */ package juicebox.track; //import org.broad.igv.track.Track; import org.broad.igv.util.ResourceLocator; import javax.swing.*; import javax.swing.border.EmptyBorder; import java.awt.*; import java.awt.event.ActionEvent; import java.awt.event.ActionListener; import java.util.List; import java.util.*; /** * @author Jim Robinson * @since 5/8/12 */ class HiCLoadDialog extends JDialog { private static final long serialVersionUID = 900004; private final Collection selectedTracks = new HashSet<>(); private boolean canceled = false; public HiCLoadDialog(Frame parent, Map> locators, List tracks) { super(parent); initComponents(locators, tracks); setModal(true); this.setSize(750, 800); } private void initComponents(Map> locators, List tracks) { Container contentPane = getContentPane(); contentPane.setLayout(new BorderLayout()); //======== dialogPane ======== JPanel dialogPane = new JPanel(); dialogPane.setBorder(new EmptyBorder(12, 12, 12, 12)); dialogPane.setLayout(new BorderLayout()); final Box mainPanel = new Box(BoxLayout.Y_AXIS); mainPanel.setAlignmentX(LEFT_ALIGNMENT); Set loadedTrackNames = new HashSet<>(tracks.size()); for (HiCTrack t : tracks) { loadedTrackNames.add(t.getName()); } for (Map.Entry> entry : locators.entrySet()) { String catName = entry.getKey(); List locatorList = entry.getValue(); mainPanel.add(new CategoryPanel(catName, locatorList, loadedTrackNames)); } JScrollPane sp = new JScrollPane(mainPanel); sp.setBackground(mainPanel.getBackground()); dialogPane.add(sp, BorderLayout.CENTER); contentPane.add(dialogPane, BorderLayout.CENTER); JPanel buttonBar = new JPanel(); buttonBar.setBorder(new EmptyBorder(12, 0, 0, 0)); buttonBar.setLayout(new GridBagLayout()); ((GridBagLayout) buttonBar.getLayout()).columnWidths = new int[]{0, 85, 80}; ((GridBagLayout) buttonBar.getLayout()).columnWeights = new double[]{1.0, 0.0, 0.0}; //---- okButton ---- JButton okButton = new JButton("OK"); okButton.addActionListener(new ActionListener() { @Override public void actionPerformed(ActionEvent actionEvent) { canceled = false; for (Component c : mainPanel.getComponents()) { if (c instanceof CategoryPanel) { selectedTracks.addAll(((CategoryPanel) c).getSelectedTracks()); } } setVisible(false); } }); //---- cancelButton ---- JButton cancelButton = new JButton("Cancel"); cancelButton.addActionListener(new ActionListener() { @Override public void actionPerformed(ActionEvent actionEvent) { canceled = true; setVisible(false); } }); buttonBar.add(cancelButton, new GridBagConstraints(2, 0, 1, 1, 0.0, 0.0, GridBagConstraints.CENTER, GridBagConstraints.BOTH, new Insets(0, 0, 0, 0), 0, 0)); buttonBar.add(okButton, new GridBagConstraints(1, 0, 1, 1, 0.0, 0.0, GridBagConstraints.CENTER, GridBagConstraints.BOTH, new Insets(0, 0, 0, 5), 0, 0)); contentPane.add(buttonBar, BorderLayout.SOUTH); pack(); setLocationRelativeTo(getOwner()); } public boolean isCanceled() { return canceled; } public Collection getSelectedTracks() { return selectedTracks; } } ================================================ FILE: src/juicebox/track/HiCTrack.java ================================================ /* * The MIT License (MIT) * * Copyright (c) 2011-2020 Broad Institute, Aiden Lab, Rice University, Baylor College of Medicine * * Permission is hereby granted, free of charge, to any person obtaining a copy * of this software and associated documentation files (the "Software"), to deal * in the Software without restriction, including without limitation the rights * to use, copy, modify, merge, publish, distribute, sublicense, and/or sell * copies of the Software, and to permit persons to whom the Software is * furnished to do so, subject to the following conditions: * * The above copyright notice and this permission notice shall be included in * all copies or substantial portions of the Software. * * THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR * IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, * FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE * AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER * LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, * OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN * THE SOFTWARE. */ package juicebox.track; import juicebox.Context; import juicebox.gui.SuperAdapter; import org.broad.igv.util.ResourceLocator; import javax.swing.*; import java.awt.*; import java.awt.event.ActionEvent; import java.awt.event.ActionListener; /** * @author jrobinso * Date: 9/10/12 * Time: 3:15 PM */ public abstract class HiCTrack{ private static int height = 25; private final ResourceLocator locator; private Color posColor = Color.blue.darker(); private Color negColor = Color.red.darker(); HiCTrack(ResourceLocator locator) { this.locator = locator; } public int getHeight() { return height; } public void setHeight(int height) { juicebox.track.HiCTrack.height = height; } public ResourceLocator getLocator() { return locator; } public void mouseClicked(int x, int y, Context context, TrackPanel.Orientation orientation) { // Ignore by default, override in subclasses } public JPopupMenu getPopupMenu(final TrackPanel trackPanel, final SuperAdapter superAdapter, TrackPanel.Orientation orientation) { JPopupMenu menu = new JPopupMenu(getName()); JMenuItem menuItem = new JMenuItem("Remove track"); menuItem.addActionListener(new ActionListener() { @Override public void actionPerformed(ActionEvent e) { trackPanel.removeTrack(HiCTrack.this); } }); menu.add(menuItem); JMenuItem menuItem2 = new JMenuItem("Move up..."); menuItem2.addActionListener(new ActionListener() { @Override public void actionPerformed(ActionEvent e) { trackPanel.moveTrackUp(HiCTrack.this); } }); //if track is on the top don't add to the menu if (trackPanel.getTrackList().indexOf(HiCTrack.this) != 0) { menu.add(menuItem2); } JMenuItem menuItem3 = new JMenuItem("Move down..."); menuItem3.addActionListener(new ActionListener() { @Override public void actionPerformed(ActionEvent e) { trackPanel.moveTrackDown(HiCTrack.this); } }); //if track is on the bottom don't add to the menu if (trackPanel.getTrackList().indexOf(HiCTrack.this) != trackPanel.getTrackList().size() - 1) { menu.add(menuItem3); } return menu; } public abstract String getName(); public abstract void setName(String text); public Color getPosColor() { return posColor; } public void setPosColor(Color posColor) { this.posColor = posColor; } public Color getNegColor() { return negColor; } public void setNegColor(Color negColor) { this.negColor = negColor; } public abstract void render(Graphics g2d, Context context, Rectangle trackRectangle, TrackPanel.Orientation orientation, HiCGridAxis gridAxis); public abstract String getToolTipText(int x, int y, TrackPanel.Orientation orientation); } ================================================ FILE: src/juicebox/track/HiCTrackManager.java ================================================ /* * The MIT License (MIT) * * Copyright (c) 2011-2021 Broad Institute, Aiden Lab, Rice University, Baylor College of Medicine * * Permission is hereby granted, free of charge, to any person obtaining a copy * of this software and associated documentation files (the "Software"), to deal * in the Software without restriction, including without limitation the rights * to use, copy, modify, merge, publish, distribute, sublicense, and/or sell * copies of the Software, and to permit persons to whom the Software is * furnished to do so, subject to the following conditions: * * The above copyright notice and this permission notice shall be included in * all copies or substantial portions of the Software. * * THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR * IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, * FITNESS FOR A PARTICULAR PURPOSE AND NON-INFRINGEMENT. IN NO EVENT SHALL THE * AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER * LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, * OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN * THE SOFTWARE. */ package juicebox.track; import juicebox.HiC; import juicebox.data.basics.Chromosome; import juicebox.gui.SuperAdapter; import juicebox.windowui.NormalizationType; import org.broad.igv.bbfile.BBFileReader; import org.broad.igv.bigwig.BigWigDataSource; import org.broad.igv.feature.genome.Genome; import org.broad.igv.feature.genome.GenomeManager; import org.broad.igv.feature.tribble.FeatureFileHeader; import org.broad.igv.feature.tribble.TribbleIndexNotFoundException; import org.broad.igv.track.*; import org.broad.igv.util.ResourceLocator; import javax.swing.*; import java.io.IOException; import java.util.*; /** * @author Jim Robinson * @since 5/8/12 */ public class HiCTrackManager { //static String path = "http://www.broadinstitute.org/igvdata/hic/tracksMenu.xml"; //static String path = "/Users/jrobinso/Documents/IGV/hg19_encode.xml"; private final List loadedTracks = new ArrayList<>(); private final Map coverageTracks = new HashMap<>(); private final Map controlCoverageTracks = new HashMap<>(); private final SuperAdapter superAdapter; private final HiC hic; public HiCTrackManager(SuperAdapter superAdapter, HiC hic) { this.superAdapter = superAdapter; this.hic = hic; org.broad.igv.Globals.setSuppressMessages(true); } public void unsafeLoadTrackDirectPath(final String path) { unsafeLoadTrackDirect(new ResourceLocator(path)); superAdapter.updateTrackPanel(); } public void loadCoverageTrack(NormalizationType no, boolean isControl) { if (isControl) { if (controlCoverageTracks.containsKey(no)) return; // Already loaded HiCDataSource source = new HiCCoverageDataSource(hic, no, isControl); ResourceLocator locator = new ResourceLocator(no.getDescription()); HiCDataTrack track = new HiCDataTrack(hic, locator, source); controlCoverageTracks.put(no, track); loadedTracks.add(track); } else { if (coverageTracks.containsKey(no)) return; // Already loaded HiCDataSource source = new HiCCoverageDataSource(hic, no, isControl); ResourceLocator locator = new ResourceLocator(no.getDescription()); HiCDataTrack track = new HiCDataTrack(hic, locator, source); coverageTracks.put(no, track); loadedTracks.add(track); } superAdapter.updateTrackPanel(); } public void unsafeTrackLoad(final List locators) { for (ResourceLocator locator : locators) { try { unsafeLoadTrackDirect(locator); } catch (Exception e) { SuperAdapter.showMessageDialog("Could not load resource:
" + e.getMessage()); System.out.println("Removing " + locator.getName()); hic.removeTrack(locator); } } superAdapter.updateTrackPanel(); } public void add(HiCTrack track) { loadedTracks.add(track); superAdapter.updateTrackPanel(); } private void unsafeLoadTrackDirect(final ResourceLocator locator) { Genome genome = loadGenome(); String path = locator.getPath(); String pathLC = path.toLowerCase(); int index = path.lastIndexOf('.'); if (index < 0) { SuperAdapter.showMessageDialog("File is missing extension"); return; } String extension = path.substring(index).toLowerCase(); // The below code is meant to solve problems recognizing the proper file type. The IGV code looks for // the location "type" in order to read the file properly if (extension.equals(".gz")) { // setting type to be the extension before the .gz int index2 = path.substring(0, index).lastIndexOf('.'); String str = path.substring(0, index).substring(index2); // special exception for refGene.txt.gz if (!str.equals(".txt")) { locator.setType(str); } } else { if (extension.equals(".txt") || extension.equals(".zip")) { SuperAdapter.showMessageDialog(".txt files are not a currently supported 1D track. " + "If you are trying to use refGene, make sure it is in the .txt.gz format. " + "If you are trying to load loops/domains, use the 2D Annotations panel."); return; } else { locator.setType(extension); } } if (pathLC.endsWith(".wig") || pathLC.endsWith(".wig.gz")) { HiCWigAdapter da = new HiCWigAdapter(hic, path); HiCDataTrack hicTrack = new HiCDataTrack(hic, locator, da); loadedTracks.add(hicTrack); } else if (pathLC.endsWith(".tdf") || pathLC.endsWith(".bigwig") || pathLC.endsWith(".bw") || pathLC.endsWith(".bedgraph") || pathLC.endsWith(".bedgraph.gz")) { List tracks = (new TrackLoader()).load(locator, genome); for (Track t : tracks) { HiCDataAdapter da = new HiCIGVDataAdapter(hic, (DataTrack) t); HiCDataTrack hicTrack = new HiCDataTrack(hic, locator, da); loadedTracks.add(hicTrack); } } else if (pathLC.endsWith(".bb") || pathLC.endsWith(".bigbed")) { try { BigWigDataSource src = new BigWigDataSource(new BBFileReader(locator.getPath()), genome); HiCFeatureTrack track = new HiCFeatureTrack(hic, locator, src); track.setName(locator.getTrackName()); loadedTracks.add(track); } catch (Exception e) { System.err.println("Error loading bb track: " + locator.getPath() + " " + e.getLocalizedMessage()); JOptionPane.showMessageDialog(superAdapter.getMainWindow(), "Error loading track. " + e.getMessage()); } } else { List tracks = new ArrayList<>(); try { loadTribbleFile(locator, tracks, genome); loadedTracks.addAll(tracks); } catch (Exception e) { System.err.println("Error loading tribble track: " + locator.getPath() + " " + e.getLocalizedMessage()); JOptionPane.showMessageDialog(superAdapter.getMainWindow(), "Error loading track. " + e.getMessage()); } /* FeatureCodec codec = CodecFactory.getCodec(locator, genome); if (codec != null) { AbstractFeatureReader bfs = AbstractFeatureReader.getFeatureReader(locator.getPath(), codec, false); try { // htsjdk.tribble.CloseableTribbleIterator iter = bfs.iterator(); // CloseableTribbleIterator extends java.lang.Iterator FeatureCollectionSource src = new FeatureCollectionSource(iter, genome); HiCFeatureTrack track = new HiCFeatureTrack(hic, locator, src); track.setName(locator.getTrackName()); loadedTracks.add(track); } catch (Exception e) { System.err.println("Error loading track: " + path, e); JOptionPane.showMessageDialog(superAdapter.getMainWindow(), "Error loading track. " + e.getMessage()); } //Object header = bfs.getHeader(); //TrackProperties trackProperties = getTrackProperties(header); } else { System.err.println("Error loading track: " + path); System.out.println("path: " + path);//DEBUGGING File file = new File(path); JOptionPane.showMessageDialog(superAdapter.getMainWindow(), "Error loading " + file.getName() + ".\n Does not appear to be a track file."); hic.removeTrack(new HiCFeatureTrack(hic, locator, null)); } */ } } public void removeTrack(HiCTrack track) { loadedTracks.remove(track); NormalizationType key = null; for (Map.Entry entry : coverageTracks.entrySet()) { if (entry.getValue() == track) { key = entry.getKey(); } } if (key != null) { coverageTracks.remove(key); } key = null; for (Map.Entry entry : controlCoverageTracks.entrySet()) { if (entry.getValue() == track) { key = entry.getKey(); } } if (key != null) { controlCoverageTracks.remove(key); } superAdapter.updateTrackPanel(); } public void removeTrack(ResourceLocator locator) { List tracks = new ArrayList<>(); for (HiCTrack tmp : loadedTracks) { if (tmp.getLocator().equals(locator)) { tracks.add(tmp); // for coverage tracks, can have more than one, so don't break } } for (HiCTrack track : tracks) { removeTrack(track); } } public void moveTrackUp(HiCTrack track) { int currentIdx = loadedTracks.indexOf(track); if (currentIdx != 0) { Collections.swap(loadedTracks, currentIdx, currentIdx - 1); superAdapter.updateTrackPanel(); } } public void moveTrackDown(HiCTrack track) { int currentIdx = loadedTracks.indexOf(track); if (currentIdx != loadedTracks.size() - 1) { Collections.swap(loadedTracks, currentIdx, currentIdx + 1); superAdapter.updateTrackPanel(); } } public List getLoadedTracks() { return loadedTracks; } public void clearTracks() { loadedTracks.clear(); coverageTracks.clear(); controlCoverageTracks.clear(); } /* TODO @zgire, is this old code that can be deleted? public Map getCoverageTracks() { return coverageTracks; } public List getReloadTracks(List reloadTracks) { for (HiCTrack reloadTrack : reloadTracks) reloadTrackNames.add(reloadTrack); return reloadTrackNames; } public List getReloadTrackNames() { return reloadTrackNames; } */ private Genome loadGenome() { Genome genome = GenomeManager.getInstance().getCurrentGenome(); if (genome == null) { if (hic.getDataset() != null) { List chrList = new ArrayList<>(Arrays.asList(hic.getDataset().getChromosomeHandler().getChromosomeArray())); Chromosome chrMT = hic.getDataset().getChromosomeHandler().getChromosomeFromName("MT"); if (chrMT != null) { chrList.add(new Chromosome(chrMT.getIndex(), "chrM", chrMT.getLength())); } List igvChrList = new ArrayList<>(); for (Chromosome chrom : chrList) { igvChrList.add(chrom.toIGVChromosome()); } genome = new Genome(hic.getDataset().getGenomeId(), igvChrList); } } return genome; } /** * Load the input file as a feature file. * Taken from IGV, but needed to be separate because our tracks are different. * * @param locator * @param newTracks */ private void loadTribbleFile(ResourceLocator locator, List newTracks, Genome genome) throws IOException, TribbleIndexNotFoundException { TribbleFeatureSource tribbleFeatureSource = TribbleFeatureSource.getFeatureSource(locator, genome); FeatureSource src = GFFFeatureSource.isGFF(locator.getPath()) ? new GFFFeatureSource(tribbleFeatureSource) : tribbleFeatureSource; // Create feature source and track HiCFeatureTrack t = new HiCFeatureTrack(hic, locator, src); t.setName(locator.getTrackName()); //t.setRendererClass(BasicTribbleRenderer.class); // Set track properties from header Object header = tribbleFeatureSource.getHeader(); if (header instanceof FeatureFileHeader) { FeatureFileHeader ffh = (FeatureFileHeader) header; /* if (ffh.getTrackType() != null) { t.setTrackType(ffh.getTrackType()); } if (ffh.getTrackProperties() != null) { t.setProperties(ffh.getTrackProperties()); }*/ if (ffh.getTrackType() == TrackType.REPMASK) { t.setHeight(15); } } /* if (locator.getPath().contains(".narrowPeak") || locator.getPath().contains(".broadPeak") || locator.getPath().contains(".gappedPeak")) { t.setUseScore(true); }*/ newTracks.add(t); } } ================================================ FILE: src/juicebox/track/HiCWigAdapter.java ================================================ /* * The MIT License (MIT) * * Copyright (c) 2011-2020 Broad Institute, Aiden Lab, Rice University, Baylor College of Medicine * * Permission is hereby granted, free of charge, to any person obtaining a copy * of this software and associated documentation files (the "Software"), to deal * in the Software without restriction, including without limitation the rights * to use, copy, modify, merge, publish, distribute, sublicense, and/or sell * copies of the Software, and to permit persons to whom the Software is * furnished to do so, subject to the following conditions: * * The above copyright notice and this permission notice shall be included in * all copies or substantial portions of the Software. * * THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR * IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, * FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE * AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER * LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, * OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN * THE SOFTWARE. */ package juicebox.track; import juicebox.HiC; import org.broad.igv.data.BasicScore; import org.broad.igv.data.WiggleDataset; import org.broad.igv.data.WiggleParser; import org.broad.igv.feature.LocusScore; import org.broad.igv.renderer.DataRange; import org.broad.igv.track.TrackProperties; import org.broad.igv.track.WindowFunction; import org.broad.igv.util.ResourceLocator; import java.awt.*; import java.util.List; import java.util.*; /** * @author jrobinso * Date: 11/8/12 * Time: 10:30 AM */ public class HiCWigAdapter extends HiCDataAdapter { private final Map> locusScoreMap = new HashMap<>(); private WiggleDataset dataset; private String trackName; private Color color; private Color altColor; private DataRange dataRange; public HiCWigAdapter(HiC hic, String path) { super(hic); init(path); } private void init(String path) { dataset = (new WiggleParser(new ResourceLocator(path), null)).parse(); trackName = dataset.getTrackNames()[0]; TrackProperties properties = dataset.getTrackProperties(); color = properties.getColor(); if (color == null) color = Color.blue.darker(); altColor = properties.getAltColor(); if (altColor == null) altColor = Color.red.darker(); float min = properties.getMinValue(); float max = properties.getMaxValue(); float mid = properties.getMidValue(); if (Float.isNaN(min) || Float.isNaN(max)) { mid = 0; min = dataset.getDataMin(); max = dataset.getDataMax(); // min = dataset.getPercent10(); // max = dataset.getPercent90(); if (min > 0 && max > 0) min = 0; else if (min < 0 && max < 0) max = 0; } else { if (Float.isNaN(mid)) { if (min >= 0) { mid = Math.max(min, 0); } else { mid = Math.min(max, 0); } } } dataRange = new DataRange(min, mid, max); if (properties.isLogScale()) { dataRange.setType(DataRange.Type.LOG); } } protected java.util.List getLocusScores(String chr, long gStart, long gEnd, int zoom, WindowFunction windowFunction) { List scores = locusScoreMap.get(chr); if (scores == null) { // Problems with human not having the "chr". Try adding "chr" scores = locusScoreMap.get("chr" + chr); } // neither option has been seen yet. try again with regular chr if (scores == null) { int[] startLocations = dataset.getStartLocations(chr); int[] endLocations = dataset.getEndLocations(chr); float[] values = dataset.getData(trackName, chr); if (values == null) { chr = "chr" + chr; startLocations = dataset.getStartLocations(chr); endLocations = dataset.getEndLocations(chr); values = dataset.getData(trackName, chr); } if (values == null) return null; scores = new ArrayList<>(values.length); for (int i = 0; i < values.length; i++) { BasicScore bs = new BasicScore(startLocations[i], endLocations[i], values[i]); scores.add(bs); } locusScoreMap.put(chr, scores); } return scores; } @Override public String getName() { return trackName; //To change body of implemented methods use File | Settings | File Templates. } @Override public void setName(String text) { this.trackName = text; } @Override public Color getPosColor() { return color; //To change body of implemented methods use File | Settings | File Templates. } @Override public void setColor(Color selectedColor) { this.color = selectedColor; } @Override public Color getNegColor() { return altColor; //To change body of implemented methods use File | Settings | File Templates. } @Override public void setNegColor(Color selectedColor) { this.altColor = selectedColor; } @Override public DataRange getDataRange() { return dataRange; //To change body of implemented methods use File | Settings | File Templates. } @Override public void setDataRange(DataRange dataRange) { this.dataRange = dataRange; } @Override public Collection getAvailableWindowFunctions() { return Arrays.asList(WindowFunction.mean, WindowFunction.max); } } ================================================ FILE: src/juicebox/track/LoadAction.java ================================================ /* * The MIT License (MIT) * * Copyright (c) 2011-2021 Broad Institute, Aiden Lab, Rice University, Baylor College of Medicine * * Permission is hereby granted, free of charge, to any person obtaining a copy * of this software and associated documentation files (the "Software"), to deal * in the Software without restriction, including without limitation the rights * to use, copy, modify, merge, publish, distribute, sublicense, and/or sell * copies of the Software, and to permit persons to whom the Software is * furnished to do so, subject to the following conditions: * * The above copyright notice and this permission notice shall be included in * all copies or substantial portions of the Software. * * THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR * IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, * FITNESS FOR A PARTICULAR PURPOSE AND NON-INFRINGEMENT. IN NO EVENT SHALL THE * AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER * LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, * OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN * THE SOFTWARE. */ package juicebox.track; import juicebox.HiC; import juicebox.MainWindow; import juicebox.gui.SuperAdapter; import org.apache.commons.io.FilenameUtils; import org.broad.igv.util.ResourceLocator; import org.broad.igv.util.Utilities; import org.w3c.dom.*; import org.xml.sax.SAXException; import javax.swing.*; import javax.xml.parsers.DocumentBuilderFactory; import javax.xml.parsers.ParserConfigurationException; import java.awt.event.ActionEvent; import java.io.File; import java.io.IOException; import java.io.InputStream; import java.net.URISyntaxException; import java.net.URL; import java.util.ArrayList; import java.util.Enumeration; import java.util.LinkedHashSet; import java.util.List; import java.util.jar.JarEntry; import java.util.jar.JarFile; /** * @author jrobinso */ public class LoadAction extends AbstractAction { private static final long serialVersionUID = 9000034; private final JFrame parentFrame; private final MainWindow mainWindow; private final HiC hic; private Runnable repaint1DLayersPanel = null; public LoadAction(String s, MainWindow mainWindow, HiC hic, Runnable repaint1DLayersPanel) { super(s); this.parentFrame = mainWindow; this.mainWindow = mainWindow; this.hic = hic; this.repaint1DLayersPanel = repaint1DLayersPanel; } private static Document createMasterDocument(String xmlUrl, JFrame parentFrame) throws ParserConfigurationException { StringBuffer buffer = new StringBuffer(); Document masterDocument = DocumentBuilderFactory.newInstance().newDocumentBuilder().newDocument(); try { Document xmlDocument = readXMLDocument(xmlUrl, buffer); if (xmlDocument != null) { Element global = xmlDocument.getDocumentElement(); masterDocument.appendChild(masterDocument.importNode(global, true)); } else { masterDocument = null; } } catch (Exception e) { String message = "Cannot create an XML Document from " + xmlUrl; System.err.println(message + " " + e.getLocalizedMessage()); } if (buffer.length() > 0) { String message = "The following urls could not be processed due to load failures:
" + buffer.toString(); JOptionPane.showMessageDialog(parentFrame, message); } return masterDocument; } private static Document readXMLDocument(String url, StringBuffer errors) { InputStream is; Document xmlDocument = null; is = LoadAction.class.getResourceAsStream(url); if (is == null) { System.err.println(url + " doesn't exist, so cannot read default annotations"); return null; } try { xmlDocument = Utilities.createDOMDocumentFromXmlStream(is); xmlDocument = resolveIncludes(xmlDocument, errors); } catch (SAXException e) { System.err.println("Invalid XML resource: " + url + " " + e.getLocalizedMessage()); errors.append(url).append("
").append(e.getMessage()); } catch (java.net.SocketTimeoutException e) { System.err.println("Connection time out " + e.getLocalizedMessage()); errors.append(url).append("
Connection time out"); } catch (IOException e) { System.err.println("Error accessing " + url + " " + e.getLocalizedMessage()); errors.append(url).append("
").append(e.getMessage()); } catch (ParserConfigurationException e) { System.err.println("Parser configuration error for:" + url + " " + e.getLocalizedMessage()); errors.append(url).append("
").append(e.getMessage()); } finally { try { is.close(); } catch (IOException e) { System.err.println("Error closing stream for: " + url + " " + e.getLocalizedMessage()); } } return xmlDocument; } private static Document resolveIncludes(Document document, StringBuffer errors) { NodeList includeNodes = document.getElementsByTagName("Include"); if (includeNodes.getLength() == 0) { return document; } int size = includeNodes.getLength(); // Copy the nodes as we'll be modifying the tree. This is neccessary! Node[] tmp = new Node[size]; for (int i = 0; i < size; i++) { tmp[i] = includeNodes.item(i); } for (Node item : tmp) { NamedNodeMap nodeMap = item.getAttributes(); if (nodeMap == null) { System.out.println("XML node " + item.getNodeName() + " has no attributes"); } else { Attr path = (Attr) item.getAttributes().getNamedItem("path"); if (path == null) { System.out.println("XML node " + item.getNodeName() + " is missing a path attribute"); } else { Node parent = item.getParentNode(); //System.out.println("Loading node " + path.getValue()); Document doc = readXMLDocument(path.getValue(), errors); if (doc != null) { Element global = doc.getDocumentElement(); Node expandedNode = parent.getOwnerDocument().importNode(global, true); parent.replaceChild(expandedNode, item); } } } } return document; } private String getXmlUrl() { String genome = hic.getDataset().getGenomeId(); if (genome == null) { genome = "hg19"; } return "tracksMenu_" + genome + ".xml"; } @Override public void actionPerformed(ActionEvent evt) { if (hic.getDataset() == null) { JOptionPane.showMessageDialog(parentFrame, "File must be loaded to load annotations", "Error", JOptionPane.ERROR_MESSAGE); return; } String genome = hic.getDataset().getGenomeId(); if (genome == null) { genome = "hg19"; } String xmlURL = "tracksMenu_" + genome + ".xml"; safeLoadNodes(xmlURL); } private void safeLoadNodes(final String xmlFile) { Runnable runnable = new Runnable() { @Override public void run() { List locators = unsafeLoadNodes(xmlFile); if (locators != null && !locators.isEmpty()) { // TODO MSS hic.unsafeLoadHostedTracks(locators); } if (repaint1DLayersPanel != null) { repaint1DLayersPanel.run(); } } }; mainWindow.executeLongRunningTask(runnable, "safe load nodes"); } public void checkBoxesForReload(String track) { // TODO MSS ResourceTree resourceTree = hic.getResourceTree(); try { if (resourceTree == null) { Document tempDoc = createMasterDocument(getXmlUrl(), parentFrame); resourceTree = new ResourceTree(hic, tempDoc); resourceTree.checkTrackBoxesForReloadState(track.trim()); } } catch (Exception e) { e.printStackTrace(); } resourceTree.checkTrackBoxesForReloadState(track); } private ArrayList getAvaliableXmlResourses() throws Exception { String resourses_path = "juicebox/track"; ArrayList resourses = new ArrayList<>(); File jarFile = new File(LoadAction.class.getProtectionDomain().getCodeSource() .getLocation().getPath()); if(jarFile.isFile()) { // Run with JAR file System.out.println("Within JAR"); final JarFile jar = new JarFile(jarFile); final Enumeration entries = jar.entries(); //gives ALL entries in jar while(entries.hasMoreElements()) { String name = entries.nextElement().getName(); if (name.startsWith(resourses_path + "/tracksMenu") && name.endsWith(".xml")) { //filter according to the path File f = new File(name); resourses.add(f.getName()); } } jar.close(); } else { // Run with IDE System.out.println("Within IDE"); URL url = MainWindow.class.getResource("/" + resourses_path); if (url != null) { try { final File apps = new File(url.toURI()); for (File app : apps.listFiles()) { System.out.println(app.toString()); if (app.toString().endsWith(".xml")) { resourses.add(FilenameUtils.getName(app.getPath())); } } } catch (URISyntaxException ex) { // never happens ex.fillInStackTrace(); } } } return resourses; } private List unsafeLoadNodes(String xmlFile) { // TODO MSS ResourceTree resourceTree = hic.getResourceTree(); try { if (resourceTree == null) { Document masterDocument = createMasterDocument(xmlFile, parentFrame); if (masterDocument == null){ ArrayList avaliable_resourses = getAvaliableXmlResourses(); if (avaliable_resourses.size()>0) { String[] options = new String[avaliable_resourses.size()]; options = avaliable_resourses.toArray(options); String selected_option = (String) JOptionPane.showInputDialog( null, "No tracks found for the genome \n " + "Would you like to use one of avaliable tracks below?" + hic.getDataset().getGenomeId(), "Please select genome", JOptionPane.QUESTION_MESSAGE, null, options, options[0] ); if (selected_option != null) { System.out.println("Using genome data from " + selected_option); masterDocument = createMasterDocument(selected_option, parentFrame); } } } resourceTree = new ResourceTree(hic, masterDocument); } } catch (Exception e) { System.err.println("Could not load from server" + e.getLocalizedMessage()); SuperAdapter.showMessageDialog("Could not load from server: " + e.getMessage()); return null; } resourceTree.showResourceTreeDialog(parentFrame); LinkedHashSet selectedLocators = resourceTree.getLocators(); LinkedHashSet deselectedLocators = resourceTree.getDeselectedLocators(); List newLoadList = new ArrayList<>(); boolean repaint = false; if (selectedLocators != null) { for (ResourceLocator locator : selectedLocators) { try { if (locator.getType() != null && locator.getType().equals("norm")) { hic.loadCoverageTrack(locator.getPath()); } else if (locator.getType() != null && locator.getType().equals("eigenvector")) { hic.loadEigenvectorTrack(); } else newLoadList.add(locator); } catch (Exception e) { System.err.println("Could not load selected locator" + e.getLocalizedMessage()); SuperAdapter.showMessageDialog("Could not load selection: " + e.getMessage()); deselectedLocators.add(locator); } } } if (deselectedLocators != null) { for (ResourceLocator locator : deselectedLocators) { System.out.println("Removing " + locator.getName()); hic.removeTrack(locator); resourceTree.remove(locator); } } if (repaint) { mainWindow.repaint(); } //hic.setShowLoops(true); return newLoadList; } } ================================================ FILE: src/juicebox/track/LoadEncodeAction.java ================================================ /* * The MIT License (MIT) * * Copyright (c) 2011-2021 Broad Institute, Aiden Lab, Rice University, Baylor College of Medicine * * Permission is hereby granted, free of charge, to any person obtaining a copy * of this software and associated documentation files (the "Software"), to deal * in the Software without restriction, including without limitation the rights * to use, copy, modify, merge, publish, distribute, sublicense, and/or sell * copies of the Software, and to permit persons to whom the Software is * furnished to do so, subject to the following conditions: * * The above copyright notice and this permission notice shall be included in * all copies or substantial portions of the Software. * * THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR * IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, * FITNESS FOR A PARTICULAR PURPOSE AND NON-INFRINGEMENT. IN NO EVENT SHALL THE * AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER * LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, * OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN * THE SOFTWARE. */ package juicebox.track; import juicebox.HiC; import juicebox.MainWindow; import juicebox.data.Dataset; import juicebox.encode.EncodeFileBrowser; import juicebox.encode.EncodeFileRecord; import org.broad.igv.track.AttributeManager; import org.broad.igv.util.ResourceLocator; import javax.swing.*; import java.awt.*; import java.awt.event.ActionEvent; import java.io.IOException; import java.util.List; import java.util.*; /** * @author jrobinso * Date: 3/13/14 * Time: 9:57 AM */ public class LoadEncodeAction extends AbstractAction { private static final long serialVersionUID = 9000035; private static final Map colors; static { colors = new HashMap<>(); colors.put("H3K27AC", new Color(200, 0, 0)); colors.put("H3K27ME3", new Color(200, 0, 0)); colors.put("H3K36ME3", new Color(0, 0, 150)); colors.put("H3K4ME1", new Color(0, 150, 0)); colors.put("H3K4ME2", new Color(0, 150, 0)); colors.put("H3K4ME3", new Color(0, 150, 0)); colors.put("H3K9AC", new Color(100, 0, 0)); colors.put("H3K9ME1", new Color(100, 0, 0)); } private final MainWindow mainWindow; private final HiC hic; private String genome; private HashSet loadedLocators; private Runnable updateLayerPanelRunnable = null; public LoadEncodeAction(String s, MainWindow mainWindow, HiC hic, Runnable updateLayerPanelRunnable) { super(s); this.mainWindow = mainWindow; this.hic = hic; this.genome = null; this.updateLayerPanelRunnable = updateLayerPanelRunnable; } public void checkEncodeBoxes(String track) { try { Dataset ds = hic.getDataset(); genome = ds.getGenomeId(); EncodeFileBrowser encodeFileBrowser = EncodeFileBrowser.getInstance(genome); assert encodeFileBrowser != null; encodeFileBrowser.checkEncodeTracks(track); } catch (IOException e) { e.printStackTrace(); } } @Override public void actionPerformed(ActionEvent e) { if (hic.getDataset() == null || hic.getDataset().getGenomeId() == null) { JOptionPane.showMessageDialog(mainWindow, "File must be loaded to load annotations", "Error", JOptionPane.ERROR_MESSAGE); return; } genome = hic.getDataset().getGenomeId(); hic.setEncodeAction(this); String[] visibleAttributes = {"dataType", "cell", "antibody", "lab"}; try { EncodeFileBrowser browser = EncodeFileBrowser.getInstance(genome); String response = genome; while ((browser == null) && (response != null)) { response = JOptionPane.showInputDialog("Encode tracks are not available for " + response + " enter another genome or press cancel to exit"); if (response != null) { browser = EncodeFileBrowser.getInstance(response); } } if (browser == null) return; browser.setVisible(true); if (browser.isCanceled()) return; List records = browser.getSelectedRecords(); safeLoadENCODETracks(records, visibleAttributes); } catch (IOException exc) { System.err.println("Error opening Encode browser " + exc.getLocalizedMessage()); } } private void safeLoadENCODETracks(final List records, final String[] visibleAttributes) { Runnable runnable = new Runnable() { @Override public void run() { unsafeLoadENCODETracks(records, visibleAttributes); if (updateLayerPanelRunnable != null) { updateLayerPanelRunnable.run(); } } }; mainWindow.executeLongRunningTask(runnable, "safe load encode tracks"); } private void unsafeLoadENCODETracks(List records, String[] visibleAttributes) { if (records.size() > 0) { if (loadedLocators == null) { loadedLocators = new HashSet<>(); } List locators = null; for (EncodeFileRecord record : records) { ResourceLocator rl = new ResourceLocator(record.getPath()); rl.setName(record.getTrackName()); final String antibody = record.getAttributeValue("antibody"); if (antibody != null) { rl.setColor(colors.get(antibody.toUpperCase())); } for (String name : visibleAttributes) { String value = record.getAttributeValue(name); if (value != null) { AttributeManager.getInstance().addAttribute(rl.getName(), name, value); } } if (!loadedLocators.contains(rl)) { if (locators == null) { locators = new ArrayList<>(); } locators.add(rl); loadedLocators.add(rl); } } if (locators != null) { hic.unsafeLoadHostedTracks(locators); } } } public void remove(ResourceLocator locator) { try { EncodeFileBrowser browser = EncodeFileBrowser.getInstance(genome); assert browser != null; browser.remove(locator); loadedLocators.remove(locator); } catch (IOException e) { e.printStackTrace(); } } } ================================================ FILE: src/juicebox/track/ResourceTree.java ================================================ /* * The MIT License (MIT) * * Copyright (c) 2011-2021 Broad Institute, Aiden Lab, Rice University, Baylor College of Medicine * * Permission is hereby granted, free of charge, to any person obtaining a copy * of this software and associated documentation files (the "Software"), to deal * in the Software without restriction, including without limitation the rights * to use, copy, modify, merge, publish, distribute, sublicense, and/or sell * copies of the Software, and to permit persons to whom the Software is * furnished to do so, subject to the following conditions: * * The above copyright notice and this permission notice shall be included in * all copies or substantial portions of the Software. * * THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR * IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, * FITNESS FOR A PARTICULAR PURPOSE AND NON-INFRINGEMENT. IN NO EVENT SHALL THE * AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER * LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, * OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN * THE SOFTWARE. */ package juicebox.track; import juicebox.HiC; import juicebox.HiCGlobals; import juicebox.gui.SuperAdapter; import juicebox.windowui.NormalizationType; import org.broad.igv.ui.color.ColorUtilities; import org.broad.igv.ui.util.FileDialogUtils; import org.broad.igv.ui.util.LinkCheckBox; import org.broad.igv.util.ResourceLocator; import org.w3c.dom.Document; import org.w3c.dom.Element; import org.w3c.dom.Node; import org.w3c.dom.NodeList; import javax.swing.*; import javax.swing.tree.*; import java.awt.*; import java.awt.event.*; import java.io.File; import java.util.List; import java.util.*; import static org.broad.igv.util.ResourceLocator.AttributeType.*; /** * Parses XML file of IGV resources, and displays them in tree format. * * @author eflakes */ public class ResourceTree { private static final String EIGENVECTOR = "Eigenvector"; private static final String SUBCOMPARTMENTS = "Subcompartments"; private static final String GLOBAL = "Global"; private final List leafResources = new ArrayList<>(); private final JTree dialogTree; private final Set loadedLocators; private JDialog dialog; private DefaultMutableTreeNode oneDFeatureRoot; private LinkedHashSet newLocators; private LinkedHashSet deselectedLocators; private LinkedHashSet addedNodes; private File openAnnotationPath = null; public ResourceTree(final HiC hic, Document document) { dialog = null; loadedLocators = new HashSet<>(); dialogTree = new JTree(new DefaultMutableTreeNode("Available feature sets")); dialogTree.setExpandsSelectedPaths(true); dialogTree.setCellRenderer(new NodeRenderer()); dialogTree.setCellEditor(new ResourceEditor(dialogTree)); dialogTree.setEditable(true); if (document != null) { DefaultMutableTreeNode node = createTreeFromDOM(document); ((DefaultMutableTreeNode) dialogTree.getModel().getRoot()).add(node); } createTreeFromDataset(hic, this); expandTree(); hic.setResourceTree(this); dialogTree.setRootVisible(false); MouseListener ml = new MouseAdapter() { public void mousePressed(MouseEvent e) { int selRow = dialogTree.getRowForLocation(e.getX(), e.getY()); final TreePath selPath = dialogTree.getPathForLocation(e.getX(), e.getY()); if (selRow != -1 && selPath != null) { if (SwingUtilities.isRightMouseButton(e)) { // removing (DefaultMutableTreeNode) cast to selpath.getlast... (revert if error) //noinspection SuspiciousMethodCalls if (addedNodes != null && addedNodes.contains(selPath.getLastPathComponent())) { JPopupMenu menu = new JPopupMenu("popup"); JMenuItem menuItem = new JMenuItem("Remove feature"); menuItem.addActionListener(new ActionListener() { @Override public void actionPerformed(ActionEvent e) { removeFeature((DefaultMutableTreeNode) selPath.getLastPathComponent()); } }); menu.add(menuItem); menu.show(dialogTree, e.getX(), e.getY()); } } } } }; dialogTree.addMouseListener(ml); } private static String getAttribute(Element element, String key) { String value = element.getAttribute(key); if (value != null) { if (value.trim().equals("")) { value = null; } } return value; } public LinkedHashSet getLocators() { return newLocators; } public LinkedHashSet getDeselectedLocators() { return deselectedLocators; } /** * Shows a tree of selectable resources. * * @param parent Parent window * @return the resources selected by user. */ public void showResourceTreeDialog(JFrame parent) { newLocators = new LinkedHashSet<>(); deselectedLocators = new LinkedHashSet<>(); dialog = new JDialog(parent, "Available Features", true); JPanel treePanel = new JPanel(new BorderLayout()); JScrollPane pane = new JScrollPane(dialogTree); treePanel.add(pane, BorderLayout.CENTER); pane.setPreferredSize(new Dimension(650, 500)); pane.setOpaque(true); Color backGroundColor = HiCGlobals.isDarkulaModeEnabled ? Color.BLACK : Color.WHITE; pane.setBackground(backGroundColor); pane.setViewportView(dialogTree); dialog.setBackground(backGroundColor); dialog.getContentPane().setBackground(backGroundColor); Component[] children = treePanel.getComponents(); if (children != null) { for (Component child : children) { child.setBackground(backGroundColor); } } JPanel buttonPanel = new JPanel(); JButton okButton = new JButton("OK"); JButton cancelButton = new JButton("Cancel"); cancelButton.addActionListener(new ActionListener() { @Override public void actionPerformed(ActionEvent actionEvent) { dialog.dispose(); // get selected locators LinkedHashSet selectedLocators = getSelectedResourceLocators(); LinkedHashSet newlyAddedLocators = new LinkedHashSet<>(); // these have been added from dialog open to hitting the "cancel" button for (ResourceLocator locator : selectedLocators) { if (!loadedLocators.contains(locator)) { newlyAddedLocators.add(locator); } } // roll back that change (remove the selected ones) for (ResourceLocator locator : newlyAddedLocators) { remove(locator); } // add back in anything that was deselected for (ResourceLocator locator : loadedLocators) { addBack(locator); } } }); okButton.addActionListener(new ActionListener() { @Override public void actionPerformed(ActionEvent actionEvent) { dialog.dispose(); LinkedHashSet selectedLocators = getSelectedResourceLocators(); for (ResourceLocator locator : selectedLocators) { if (!loadedLocators.contains(locator)) { newLocators.add(locator); } } for (ResourceLocator locator : loadedLocators) { if (!selectedLocators.contains(locator)) { deselectedLocators.add(locator); } } // add these to loaded ones for next use loadedLocators.addAll(newLocators); for (ResourceLocator locator : deselectedLocators) { loadedLocators.remove(locator); } dialogTree.clearSelection(); } }); buttonPanel.add(okButton); buttonPanel.add(cancelButton); dialog.add(treePanel); dialog.add(buttonPanel, BorderLayout.PAGE_END); dialog.setResizable(true); dialog.pack(); dialog.setLocationRelativeTo(parent); dialog.setVisible(true); } public boolean addLocalButtonActionPerformed(final SuperAdapter superAdapter) { boolean localFilesAdded = false; File[] oneDfiles = FileDialogUtils.chooseMultiple("Choose 1D Annotation file", openAnnotationPath, null); if (oneDfiles != null && oneDfiles.length > 0) { for (File file : oneDfiles) { if (file == null || !file.exists()) continue; localFilesAdded = true; String path = file.getAbsolutePath(); openAnnotationPath = new File(path); ResourceLocator locator = new ResourceLocator(path); locator.setName(file.getName()); locator.setType(file.getName()); CheckableResource resource = new CheckableResource(file.getName(), true, locator); DefaultMutableTreeNode treeNode = new DefaultMutableTreeNode(file); treeNode.setUserObject(resource); if (containsDuplicate(treeNode)) { if (HiCGlobals.guiIsCurrentlyActive) { int dialogResult = JOptionPane.showConfirmDialog(superAdapter.getMainWindow(), file.getName() + " is already loaded. Would you like to overwrite it?", "Warning", JOptionPane.YES_NO_OPTION); if (dialogResult == JOptionPane.YES_OPTION) { removeChildNodeFromAddedNodes(treeNode); removeChildNodeFromFeatureRoot(treeNode); removeResourceFromLeaf(resource, leafResources); } else { setSelectionForMatchingChildNodes(treeNode, true); continue; } } } leafResources.add(resource); oneDFeatureRoot.add(treeNode); ((CheckableResource) oneDFeatureRoot.getUserObject()).setSelected(true); if (addedNodes == null) { addedNodes = new LinkedHashSet<>(); } addedNodes.add(treeNode); expandTree(); dialogTree.updateUI(); } } return localFilesAdded; } private boolean containsDuplicate(DefaultMutableTreeNode treeNode) { return !getMatchingChildNodesFromAddedNodes(treeNode).isEmpty(); } private void setSelectionForMatchingChildNodes(DefaultMutableTreeNode treeNode, Boolean selectionBoolean) { List desiredChildNodes = getMatchingChildNodesFromAddedNodes(treeNode); for (DefaultMutableTreeNode childNode : desiredChildNodes) { if (childNode.getUserObject() instanceof CheckableResource) { ((CheckableResource) childNode.getUserObject()).setSelected(selectionBoolean); } } } private void removeResourceFromLeaf(CheckableResource resource, List leafResources) { List resourcesToRemove = new ArrayList<>(); for (CheckableResource res : leafResources) { if (res.getText().equals(resource.getText())) resourcesToRemove.add(res); } leafResources.removeAll(resourcesToRemove); } private void removeChildNodeFromFeatureRoot(DefaultMutableTreeNode treeNode) { List childNodesToRemove = new ArrayList<>(); if (!(treeNode.getUserObject() instanceof CheckableResource)) { return; } String targetTreeNodePath = ((CheckableResource) treeNode.getUserObject()).getResourceLocator().getPath(); Enumeration childNodesPresent = oneDFeatureRoot.children(); while (childNodesPresent.hasMoreElements()) { DefaultMutableTreeNode currentChildNode = (DefaultMutableTreeNode) childNodesPresent.nextElement(); if (currentChildNode.getUserObject() instanceof CheckableResource) { String currentChildNodePath = ((CheckableResource) currentChildNode.getUserObject()).getResourceLocator().getPath(); if (currentChildNodePath.equals(targetTreeNodePath)) { childNodesToRemove.add(currentChildNode); } } } for (DefaultMutableTreeNode childNode : childNodesToRemove) { oneDFeatureRoot.remove(childNode); } } private void removeChildNodeFromAddedNodes(DefaultMutableTreeNode treeNode) { List childNodesToRemove = getMatchingChildNodesFromAddedNodes(treeNode); for (DefaultMutableTreeNode childNode : childNodesToRemove) { addedNodes.remove(childNode); } } private List getMatchingChildNodesFromAddedNodes(DefaultMutableTreeNode treeNode) { List matchingChildNodes = new ArrayList<>(); if (addedNodes != null && treeNode.getUserObject() instanceof CheckableResource) { String targetPath = ((CheckableResource) treeNode.getUserObject()).getResourceLocator().getPath(); for (DefaultMutableTreeNode childNode : addedNodes) { if (childNode.getUserObject() instanceof CheckableResource) { String childPath = ((CheckableResource) childNode.getUserObject()).getResourceLocator().getPath(); if (childPath.equals(targetPath)) { matchingChildNodes.add(childNode); } } } } return matchingChildNodes; } private void removeFeature(DefaultMutableTreeNode node) { ((CheckableResource) node.getUserObject()).setSelected(false); ResourceEditor.checkOrUncheckParentNodesRecursively(node, false); addedNodes.remove(node); DefaultMutableTreeNode parent = (DefaultMutableTreeNode) node.getParent(); parent.remove(node); ResourceLocator locator = ((CheckableResource) node.getUserObject()).getResourceLocator(); // no longer needed? MSS //String path = locator.getPath(); //hic.removeLoadedAnnotation(path); // actually removes the entry (at least 2d annotation) so that it can be reloaded deselectedLocators.add(locator); loadedLocators.remove(locator); newLocators.remove(locator); removeResourceFromLeaf((CheckableResource) node.getUserObject(), leafResources); //leafResources.remove(node); dialogTree.updateUI(); } private void createTreeFromDataset(HiC hic, ResourceTree resourceTree) { oneDFeatureRoot = new DefaultMutableTreeNode("Dataset-specific 1D Features"); ResourceLocator locator = new ResourceLocator("Dataset-specific 1D Features"); locator.setName("Dataset-specific 1D Features"); locator.setType("norm"); CheckableResource rootResource = new CheckableResource("Dataset-specific 1D Features", false, locator); oneDFeatureRoot.setUserObject(rootResource); oneDFeatureRoot.setAllowsChildren(true); if (hic.getDataset().getVersion() >= 6) { if (hic.getDataset().getNormalizationTypes().size() > 0) { DefaultMutableTreeNode normNode = new DefaultMutableTreeNode("Coverage normalizations"); oneDFeatureRoot.add(normNode); locator = new ResourceLocator("Coverage normalizations"); locator.setName("Coverage normalizations"); locator.setType("norm"); CheckableResource resource = new CheckableResource("Coverage normalizations", false, locator); normNode.setUserObject(resource); normNode.setAllowsChildren(true); for (NormalizationType t : hic.getDataset().getNormalizationTypes()) { String label = t.getDescription(); locator = new ResourceLocator(label); locator.setType("norm"); locator.setName(label); resource = new CheckableResource(label, false, locator); DefaultMutableTreeNode treeNode = new DefaultMutableTreeNode(label); normNode.add(treeNode); treeNode.setUserObject(resource); resource.setEnabled(resourceTree.dialogTree.isEnabled()); treeNode.setAllowsChildren(false); leafResources.add(resource); } } } locator = new ResourceLocator(EIGENVECTOR); locator.setType(EIGENVECTOR.toLowerCase()); locator.setName(EIGENVECTOR); CheckableResource resource = new CheckableResource(EIGENVECTOR, false, locator); DefaultMutableTreeNode treeNode = new DefaultMutableTreeNode(EIGENVECTOR); oneDFeatureRoot.add(treeNode); treeNode.setUserObject(resource); resource.setEnabled(resourceTree.dialogTree.isEnabled()); treeNode.setAllowsChildren(false); leafResources.add(resource); locator = hic.getDataset().getSubcompartments(); if (locator != null) { resource = new CheckableResource(SUBCOMPARTMENTS, false, locator); treeNode = new DefaultMutableTreeNode(SUBCOMPARTMENTS); oneDFeatureRoot.add(treeNode); treeNode.setUserObject(resource); resource.setEnabled(resourceTree.dialogTree.isEnabled()); treeNode.setAllowsChildren(false); leafResources.add(resource); } ((DefaultMutableTreeNode) dialogTree.getModel().getRoot()).add(oneDFeatureRoot); } private DefaultMutableTreeNode createTreeFromDOM(Document document) { Element rootElement = (Element) document.getElementsByTagName(GLOBAL).item(0); if (rootElement == null) { return new DefaultMutableTreeNode(""); } String nodeName = rootElement.getNodeName(); if (!nodeName.equalsIgnoreCase(GLOBAL)) { throw new RuntimeException(rootElement + " is not the root of the xml document!"); } String rootLabel = getAttribute(rootElement, "name"); DefaultMutableTreeNode rootNode = new DefaultMutableTreeNode(rootLabel); // Build and attach descendants of the root node to the tree buildLocatorTree(rootNode, rootElement); return rootNode; } /** * Build a tree of all resources, placed under {@code treeNode}, starting * from {@code xmlNode}. * * @param treeNode * @param xmlNode */ private void buildLocatorTree(DefaultMutableTreeNode treeNode, Element xmlNode) { String name = getAttribute(xmlNode, NAME.getText()); ResourceLocator locator = new ResourceLocator( getAttribute(xmlNode, URL.getText()), getAttribute(xmlNode, PATH.getText()) ); locator.setName(name); if (xmlNode.getTagName().equalsIgnoreCase("Resource")) { String resourceType = getAttribute(xmlNode, RESOURCE_TYPE.getText()); locator.setType(resourceType); String infoLink = getAttribute(xmlNode, HYPERLINK.getText()); if (infoLink == null) { infoLink = getAttribute(xmlNode, INFOLINK.getText()); } locator.setFeatureInfoURL(infoLink); String sampleId = getAttribute(xmlNode, SAMPLE_ID.getText()); if (sampleId == null) { // legacy option sampleId = getAttribute(xmlNode, ID.getText()); } locator.setSampleId(sampleId); locator.setDescription(getAttribute(xmlNode, DESCRIPTION.getText())); locator.setTrackLine(getAttribute(xmlNode, TRACK_LINE.getText())); locator.setName(name); // Special element for alignment tracks locator.setCoverage(getAttribute(xmlNode, COVERAGE.getText())); String colorString = getAttribute(xmlNode, COLOR.getText()); if (colorString != null) { try { Color c = ColorUtilities.stringToColor(colorString); locator.setColor(c); } catch (Exception e) { System.err.println("Error setting color: " + e.getLocalizedMessage()); } } } NodeList nodeList = xmlNode.getChildNodes(); Node xmlChildNode; // If we have children treat it as a category not a leaf for (int i = 0; i < nodeList.getLength(); i++) { xmlChildNode = nodeList.item(i); String nodeName = xmlChildNode.getNodeName(); if (nodeName.equalsIgnoreCase("#text")) { continue; } // Need to check class of child node, its not necessarily an // element (could be a comment for example). if (xmlChildNode instanceof Element) { String categoryLabel = getAttribute((Element) xmlChildNode, NAME.getText()); DefaultMutableTreeNode treeChildNode = new DefaultMutableTreeNode(categoryLabel); treeNode.add(treeChildNode); buildLocatorTree(treeChildNode, (Element) xmlChildNode); } } // If it's a leaf set the checkbox to represent the resource if (treeNode.isLeaf()) { CheckableResource resource = new CheckableResource(name, false, locator); treeNode.setUserObject(resource); treeNode.setAllowsChildren(false); leafResources.add(resource); } else { locator = new ResourceLocator(name); CheckableResource resource = new CheckableResource(name, false, locator); treeNode.setUserObject(resource); treeNode.setAllowsChildren(true); } } public void remove(ResourceLocator locator) { //locator. loadedLocators.remove(locator); Enumeration enumeration = ((DefaultMutableTreeNode) dialogTree.getModel().getRoot()).preorderEnumeration(); // skip root enumeration.nextElement(); while (enumeration.hasMoreElements()) { try { DefaultMutableTreeNode node = (DefaultMutableTreeNode) enumeration.nextElement(); CheckableResource resource = (CheckableResource) node.getUserObject(); if (locator.equals(resource.getResourceLocator())) { resource.setSelected(false); ResourceEditor.checkOrUncheckParentNodesRecursively(node, false); } } catch (Exception e) { System.err.println("There appears to be an invalid node in the resource tree"); } } } private void addBack(ResourceLocator locator) { Enumeration enumeration = ((DefaultMutableTreeNode) dialogTree.getModel().getRoot()).preorderEnumeration(); // skip root enumeration.nextElement(); while (enumeration.hasMoreElements()) { DefaultMutableTreeNode node = (DefaultMutableTreeNode) enumeration.nextElement(); try { CheckableResource resource = (CheckableResource) node.getUserObject(); if (locator.equals(resource.getResourceLocator())) { resource.setSelected(true); ResourceEditor.checkOrUncheckParentNodesRecursively(node, true); } } catch (Exception ignored) { } } } private LinkedHashSet getSelectedResourceLocators() { LinkedHashSet resourceLocators = new LinkedHashSet<>(); for (CheckableResource resource : leafResources) { if (resource.isSelected()) { resourceLocators.add(resource.getResourceLocator()); } } return resourceLocators; } public void checkTrackBoxesForReloadState(String track) { Enumeration en = ((DefaultMutableTreeNode) dialogTree.getModel().getRoot()).preorderEnumeration(); //skip root en.nextElement(); while (en.hasMoreElements()) { try { DefaultMutableTreeNode node = (DefaultMutableTreeNode) en.nextElement(); CheckableResource resource = (CheckableResource) node.getUserObject(); if (node.isLeaf()) { if (resource.dataResourceLocator.getPath() != null) { if (resource.dataResourceLocator.getName().contains(track)) { resource.setSelected(true); resource.setEnabled(true); loadedLocators.add(resource.getResourceLocator()); ResourceEditor.checkOrUncheckParentNodesRecursively(node, true); //System.out.println("name: "+resource.dataResourceLocator.getName()); for debugging } } } } catch (Exception ignored) { } } } /** * Expands tree. */ private void expandTree() { TreeNode root = (TreeNode) dialogTree.getModel().getRoot(); TreePath rootPath = new TreePath(root); TreeNode node = (TreeNode) rootPath.getLastPathComponent(); for (Enumeration e = node.children(); e.hasMoreElements(); ) { TreePath childPath = rootPath.pathByAddingChild(e.nextElement()); if (!dialogTree.isExpanded(childPath)) { dialogTree.expandPath(childPath); } } if (!dialogTree.isExpanded(rootPath)) { dialogTree.expandPath(rootPath); } } /** * */ interface SelectableResource extends DataResource { boolean isSelected(); void setSelected(boolean newValue); } /** * */ interface DataResource { ResourceLocator getResourceLocator(); String getText(); void setText(String newValue); boolean isEnabled(); void setEnabled(boolean value); } /** * Node's Renderer */ static class NodeRenderer implements TreeCellRenderer { private final LinkCheckBox renderer = new LinkCheckBox(); private final Color selectionForeground; private final Color selectionBackground; private final Color textForeground; private final Color textBackground; NodeRenderer() { Font fontValue; fontValue = UIManager.getFont("Tree.font"); if (fontValue != null) { renderer.setFont(fontValue); } Boolean booleanValue = (Boolean) UIManager.get("Tree.drawsFocusBorderAroundIcon"); renderer.setFocusPainted( (booleanValue != null) && booleanValue); selectionForeground = UIManager.getColor("Tree.selectionForeground"); selectionBackground = UIManager.getColor("Tree.selectionBackground"); textForeground = UIManager.getColor("Tree.textForeground"); textBackground = UIManager.getColor("Tree.textBackground"); renderer.setSelected(false); } public Component getTreeCellRendererComponent(JTree tree, Object value, boolean isNodeSelected, boolean isNodeExpanded, boolean isLeaf, int row, boolean hasFocus) { // Convert value into a usable string String stringValue = ""; if (value != null) { String toStringValue = value.toString(); if (toStringValue != null) { stringValue = toStringValue; } } // Initialize checkbox state and selection renderer.setSelected(false); renderer.setText(stringValue); renderer.setEnabled(tree.isEnabled()); // Tell renderer how to highlight nodes on selection if (isNodeSelected) { renderer.setForeground(selectionForeground); renderer.setBackground(selectionBackground); } else { renderer.setForeground(textForeground); renderer.setBackground(textBackground); } if (value != null) { if (value instanceof DefaultMutableTreeNode) { DefaultMutableTreeNode node = (DefaultMutableTreeNode) value; Object userObject = node.getUserObject(); if (userObject instanceof CheckableResource) { CheckableResource resource = (CheckableResource) userObject; renderer.setText(resource.getText()); renderer.setSelected(resource.isSelected()); renderer.setEnabled(resource.isEnabled()); String hyperLink = resource.getResourceLocator().getFeatureInfoURL(); if (hyperLink == null) { renderer.showHyperLink(false); } else { renderer.setHyperLink(hyperLink); renderer.showHyperLink(true); } } } } return renderer; } LinkCheckBox getRendereringComponent() { return renderer; } } /** * Node's Resource Editor */ static class ResourceEditor extends AbstractCellEditor implements TreeCellEditor { private static final long serialVersionUID = 9000036; final NodeRenderer renderer = new NodeRenderer(); final JTree tree; ResourceEditor(JTree tree) { this.tree = tree; } /** * Call to recursively check or uncheck the parent ancestors of the * passed node. */ static void checkOrUncheckParentNodesRecursively(TreeNode node, boolean checkParentNode) { if (node == null) { return; } TreeNode parentNode = node.getParent(); if (parentNode == null) { return; } Object parentUserObject = ((DefaultMutableTreeNode) parentNode).getUserObject(); CheckableResource parentNodeResource = null; if (parentUserObject instanceof CheckableResource) { parentNodeResource = ((CheckableResource) parentUserObject); } if (parentNodeResource != null) { // If parent's current check state matchs what we want there // is nothing to do so just leave if (parentNodeResource.isSelected() == checkParentNode) { return; } else if (checkParentNode) { parentNodeResource.setSelected(true); } else { // Uncheck Only if their are no selected descendants if (doesNotHaveSelectedChildren(parentNode)) { parentNodeResource.setSelected(false); } } } checkOrUncheckParentNodesRecursively(parentNode, checkParentNode); } /* * Uncheck a node unless rule prevent this behavior. */ static boolean hasSelectedDescendants(TreeNode treeNode) { Enumeration children = treeNode.children(); while (children.hasMoreElements()) { TreeNode childNode = (TreeNode) children.nextElement(); Object childsUserObject = ((DefaultMutableTreeNode) childNode).getUserObject(); if (childsUserObject instanceof CheckableResource) { CheckableResource childResource = ((CheckableResource) childsUserObject); // If has selected say so if (childResource.isSelected()) { return true; } } // If has selected descendant say so if (hasSelectedDescendants(childNode)) { return true; } } return false; } static boolean doesNotHaveSelectedChildren(TreeNode treeNode) { Enumeration children = treeNode.children(); while (children.hasMoreElements()) { TreeNode childNode = (TreeNode) children.nextElement(); Object childsUserObject = ((DefaultMutableTreeNode) childNode).getUserObject(); if (childsUserObject instanceof CheckableResource) { CheckableResource childResource = ((CheckableResource) childsUserObject); if (childResource.isSelected()) { return false; } } } return true; } public Object getCellEditorValue() { CheckableResource resource = null; TreePath treePath = tree.getEditingPath(); if (treePath != null) { Object node = treePath.getLastPathComponent(); if ((node instanceof DefaultMutableTreeNode)) { LinkCheckBox checkbox = renderer.getRendereringComponent(); DefaultMutableTreeNode treeNode = (DefaultMutableTreeNode) node; Object userObject = treeNode.getUserObject(); resource = (CheckableResource) userObject; // Don't change resource if disabled if (!resource.isEnabled()) { return resource; } boolean isChecked = checkbox.isSelected(); // Check/Uncheck the selected node. This code ONLY handles // the clicked node. Not it's ancestors or decendants. if (isChecked) { resource.setSelected(true); } else { // See if we are allowed to unchecking this specific // node - if not, it won't be done. This does not // prevent it's children from being unchecked. uncheckCurrentNodeIfAllowed(resource, treeNode); } /* * Now we have to check or uncheck the descendants and * ancestors depending on what we did above. */ boolean checkRelatives = isChecked; // If we found a mix of select leave and selected but // but disabled leave we must be trying to toggle off // the children if (hasSelectedAndLockedDescendants(treeNode)) { checkRelatives = false; } // If we found only locked leave we must be trying to toggle // on the unlocked children else if (hasLockedDescendants(treeNode)) { checkRelatives = true; } // Otherwise, just use the value of the checkbox if (!treeNode.isLeaf()) { //check up and down the tree // If not a leaf check/uncheck children as requested checkOrUncheckChildNodesRecursively(treeNode, checkRelatives); // If not a leaf check/uncheck ancestors checkOrUncheckParentNodesRecursively(treeNode, resource.isSelected()); } else { // it must be a leaf - so check up the tree checkOrUncheckParentNodesRecursively(treeNode, checkRelatives); } } tree.treeDidChange(); } return resource; } private void uncheckCurrentNodeIfAllowed(CheckableResource resource, TreeNode treeNode) { // If we are unchecking a parent make sure there are // no checked children if (doesNotHaveSelectedChildren(treeNode)) { resource.setSelected(false); } else { // If node has selected children and has disabled descendants we // must not unselect // No disabled descendants so we can uncheck at will resource.setSelected(hasLockedDescendants(treeNode)); } } /** * Can only be called from getCellEditorValue() to recursively check * or uncheck the children of the passed parent node. */ private void checkOrUncheckChildNodesRecursively(TreeNode currentNode, boolean isCheckingNeeded) { Object parentUserObject = ((DefaultMutableTreeNode) currentNode).getUserObject(); CheckableResource currentTreeNodeResource = null; if (parentUserObject instanceof CheckableResource) { currentTreeNodeResource = ((CheckableResource) parentUserObject); } if (currentTreeNodeResource != null) { // Set all enabled children to the checked state of their parent Enumeration children = currentNode.children(); while (children.hasMoreElements()) { TreeNode childNode = (TreeNode) children.nextElement(); Object childsUserObject = ((DefaultMutableTreeNode) childNode).getUserObject(); if (childsUserObject instanceof CheckableResource) { CheckableResource childResource = ((CheckableResource) childsUserObject); if (childResource.isEnabled()) { // Child must be checked if it has selected // selected and disabled descendants if (hasLockedDescendants(childNode)) { childResource.setSelected(true); } else { // else check/uncheck as requested childResource.setSelected(isCheckingNeeded); } } } checkOrUncheckChildNodesRecursively(childNode, isCheckingNeeded); } } } boolean hasLockedDescendants(TreeNode treeNode) { Enumeration children = treeNode.children(); while (children.hasMoreElements()) { TreeNode childNode = (TreeNode) children.nextElement(); Object childsUserObject = ((DefaultMutableTreeNode) childNode).getUserObject(); if (childsUserObject instanceof CheckableResource) { CheckableResource childResource = ((CheckableResource) childsUserObject); // If disabled say so if (!childResource.isEnabled()) { return true; } } // If a descendant is disabled say so if (hasLockedDescendants(childNode)) { return true; } } return false; } /** * Return true if it find nodes that ar both selected and disabled * * @param treeNode * @return true if we are working with preselected nodes */ /* public boolean hasLockedChildren(TreeNode treeNode) { boolean hasSelectedAndDisabled = false; Enumeration children = treeNode.children(); while (children.hasMoreElements()) { TreeNode childNode = (TreeNode) children.nextElement(); Object childsUserObject = ((DefaultMutableTreeNode) childNode).getUserObject(); if (childsUserObject instanceof CheckableResource) { CheckableResource childResource = ((CheckableResource) childsUserObject); if (!childResource.isEnabled() && childResource.isSelected()) { hasSelectedAndDisabled = true; } if (hasSelectedAndDisabled) { break; } } } return (hasSelectedAndDisabled); } */ /** * @param treeNode * @return true if we are working with preselected nodes */ /* public boolean hasSelectedAndLockedChildren(TreeNode treeNode) { boolean hasSelected = false; boolean hasSelectedAndDisabled = false; Enumeration children = treeNode.children(); while (children.hasMoreElements()) { TreeNode childNode = (TreeNode) children.nextElement(); Object childsUserObject = ((DefaultMutableTreeNode) childNode).getUserObject(); if (childsUserObject instanceof CheckableResource) { CheckableResource childResource = ((CheckableResource) childsUserObject); if (childResource.isSelected() && childResource.isEnabled()) { hasSelected = true; } if (!childResource.isEnabled() && childResource.isSelected()) { hasSelectedAndDisabled = true; } if (hasSelected & hasSelectedAndDisabled) { break; } } } // If we have both we can return true return (hasSelected & hasSelectedAndDisabled); } /* /** * @param treeNode * @return true if we are working with preselected nodes */ boolean hasSelectedAndLockedDescendants(TreeNode treeNode) { boolean hasSelected = false; boolean hasSelectedAndDisabled = false; Enumeration children = treeNode.children(); while (children.hasMoreElements()) { TreeNode childNode = (TreeNode) children.nextElement(); Object childsUserObject = ((DefaultMutableTreeNode) childNode).getUserObject(); if (childsUserObject instanceof CheckableResource) { CheckableResource childResource = ((CheckableResource) childsUserObject); if (childResource.isSelected() && childResource.isEnabled()) { hasSelected = true; } if (!childResource.isEnabled() && childResource.isSelected()) { hasSelectedAndDisabled = true; } if (hasSelected & hasSelectedAndDisabled) { break; } } // If has a mix of selected and checked but disableddescendant if (hasSelectedAndLockedDescendants(childNode)) { return true; } } // If we have both we can return true return (hasSelected & hasSelectedAndDisabled); } @Override public boolean isCellEditable(EventObject event) { boolean returnValue = false; if (event instanceof MouseEvent) { MouseEvent mouseEvent = (MouseEvent) event; TreePath treePath = tree.getPathForLocation( mouseEvent.getX(), mouseEvent.getY()); if (treePath != null) { Object node = treePath.getLastPathComponent(); if ((node instanceof DefaultMutableTreeNode)) { DefaultMutableTreeNode treeNode = (DefaultMutableTreeNode) node; Object userObject = treeNode.getUserObject(); if (userObject instanceof CheckableResource) { returnValue = true; } } } } return returnValue; } public Component getTreeCellEditorComponent(JTree tree, Object value, boolean selected, boolean expanded, boolean leaf, int row) { Component rendererComponent = renderer.getTreeCellRendererComponent( tree, value, true, expanded, leaf, row, true); ItemListener itemListener = new ItemListener() { public void itemStateChanged(ItemEvent itemEvent) { if (stopCellEditing()) { fireEditingStopped(); } } }; if (rendererComponent instanceof LinkCheckBox) { ((LinkCheckBox) rendererComponent).addItemListener(itemListener); } return rendererComponent; } } public static class CheckableResource implements SelectableResource { final static Color partialSelectionColor = new Color(255, 128, 128); final boolean isParentOfPartiallySelectedChildren = false; final ResourceLocator dataResourceLocator; String text; boolean selected; boolean isEnabled = true; CheckableResource(String text, boolean selected, ResourceLocator dataResourceLocator) { this.text = text; this.selected = selected; this.dataResourceLocator = dataResourceLocator; } public boolean isSelected() { return selected; } public void setSelected(boolean newValue) { selected = newValue; } public boolean isEnabled() { return isEnabled; } public void setEnabled(boolean value) { isEnabled = value; } public String getText() { return text; } public void setText(String newValue) { text = newValue; } public ResourceLocator getResourceLocator() { return dataResourceLocator; } public boolean isParentOfPartiallySelectedChildren() { return isParentOfPartiallySelectedChildren; } @Override public String toString() { return text + ":" + selected; } } } ================================================ FILE: src/juicebox/track/TrackConfigDialog.java ================================================ /* * The MIT License (MIT) * * Copyright (c) 2011-2021 Broad Institute, Aiden Lab, Rice University, Baylor College of Medicine * * Permission is hereby granted, free of charge, to any person obtaining a copy * of this software and associated documentation files (the "Software"), to deal * in the Software without restriction, including without limitation the rights * to use, copy, modify, merge, publish, distribute, sublicense, and/or sell * copies of the Software, and to permit persons to whom the Software is * furnished to do so, subject to the following conditions: * * The above copyright notice and this permission notice shall be included in * all copies or substantial portions of the Software. * * THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR * IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, * FITNESS FOR A PARTICULAR PURPOSE AND NON-INFRINGEMENT. IN NO EVENT SHALL THE * AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER * LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, * OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN * THE SOFTWARE. */ package juicebox.track; import org.broad.igv.renderer.DataRange; import org.broad.igv.track.WindowFunction; import org.broad.igv.ui.color.ColorChooserPanel; import javax.swing.*; import javax.swing.border.EmptyBorder; import javax.swing.border.TitledBorder; import java.awt.*; import java.awt.event.ActionEvent; import java.awt.event.ActionListener; import java.awt.event.FocusAdapter; import java.awt.event.FocusEvent; /** * @author Jim Robinson */ class TrackConfigDialog extends JDialog { private static final long serialVersionUID = 900005; private final HiCTrack track; private boolean canceled = false; private ColorChooserPanel posColorChooser; private ColorChooserPanel altColorChooser; private JCheckBox logScaleCB; private JTextField minYField; private JTextField maxYField; private JRadioButton meanRB; private JRadioButton maxRB; private JTextField nameField; public TrackConfigDialog(Frame owner, HiCTrack track) { super(owner); initComponents(); this.track = track; nameField.setText(track.getName()); posColorChooser.setSelectedColor(track.getPosColor()); altColorChooser.setSelectedColor(track.getNegColor()); if (track instanceof EigenvectorTrack) { altColorChooser.setEnabled(true); } if (track instanceof HiCDataTrack) { minYField.setEnabled(true); maxYField.setEnabled(true); logScaleCB.setEnabled(true); altColorChooser.setEnabled(true); maxRB.setEnabled(true); meanRB.setEnabled(true); HiCDataTrack dataTrack = (HiCDataTrack) track; minYField.setText(String.valueOf(dataTrack.getDataRange().getMinimum())); maxYField.setText(String.valueOf(dataTrack.getDataRange().getMaximum())); logScaleCB.setSelected(dataTrack.getDataRange().isLog()); altColorChooser.setSelectedColor(dataTrack.getNegColor()); if (!dataTrack.getAvailableWindowFunctions().contains(WindowFunction.max)) { maxRB.setEnabled(false); } if (dataTrack.getWindowFunction() == WindowFunction.max) { maxRB.setSelected(true); } else { meanRB.setSelected(true); } } else { minYField.setEnabled(false); maxYField.setEnabled(false); logScaleCB.setEnabled(false); altColorChooser.setEnabled(false); maxRB.setEnabled(false); meanRB.setEnabled(false); } } private void minYFieldFocusLost(FocusEvent e) { if (track instanceof HiCDataTrack) { if (!validateNumeric(minYField.getText())) { DataRange dr = ((HiCDataTrack) track).getDataRange(); minYField.setText(String.valueOf(dr.getMinimum())); } } } private void maxYFieldFocusLost(FocusEvent e) { if (track instanceof HiCDataTrack) { if (!validateNumeric(maxYField.getText())) { DataRange dr = ((HiCDataTrack) track).getDataRange(); minYField.setText(String.valueOf(dr.getMaximum())); } } } public boolean isNotCanceled() { return !canceled; } private void okButtonActionPerformed(ActionEvent e) { if (validateNumeric(minYField.getText()) && validateNumeric(maxYField.getText())) { track.setName(nameField.getText()); track.setPosColor(posColorChooser.getSelectedColor()); if (track instanceof HiCDataTrack) { float newMin = Float.parseFloat(minYField.getText()); float newMax = Float.parseFloat(maxYField.getText()); DataRange newDataRange = new DataRange(newMin, newMax); if (newMin < 0 && newMax > 0) { newDataRange = new DataRange(newMin, 0f, newMax); } newDataRange.setType(logScaleCB.isSelected() ? DataRange.Type.LOG : DataRange.Type.LINEAR); ((HiCDataTrack) track).setDataRange(newDataRange); track.setNegColor(altColorChooser.getSelectedColor()); WindowFunction wf = maxRB.isSelected() ? WindowFunction.max : WindowFunction.mean; ((HiCDataTrack) track).setWindowFunction(wf); } canceled = false; setVisible(false); } } private void cancelButtonActionPerformed(ActionEvent e) { canceled = true; setVisible(false); } /* TODO @zgire, is this old code that can be deleted? private Color getReloadColors(String temp) { HashMap reloadColors = new HashMap(); for (HiCTrack tracks : trackManager.getReloadTrackNames()) { reloadColors.put(tracks.getName(), tracks.getPosColor()); } return reloadColors.get(temp); } /* public void setStateForReloadTracks(String currentTrack) { for (HiCTrack tracks : trackManager.getReloadTrackNames()) { String trackName = tracks.getName(); System.out.println(trackName); if (tracks.getLocator().getPath().contains(currentTrack)) { tracks.setColor(getReloadColors(trackName)); System.out.println("match"); tracks.setName(trackName); } } } */ private void initComponents() { // JFormDesigner - Component initialization - DO NOT MODIFY //GEN-BEGIN:initComponents // Generated using JFormDesigner non-commercial license nameField = new JTextField(); logScaleCB = new JCheckBox(); minYField = new JTextField(); maxYField = new JTextField(); posColorChooser = new ColorChooserPanel(); altColorChooser = new ColorChooserPanel(); meanRB = new JRadioButton(); maxRB = new JRadioButton(); JPanel dialogPane = new JPanel(); JPanel contentPanel = new JPanel(); JPanel panel4 = new JPanel(); JPanel panel1 = new JPanel(); JLabel label2 = new JLabel(); JLabel label3 = new JLabel(); JPanel panel2 = new JPanel(); JLabel label4 = new JLabel(); JLabel label5 = new JLabel(); JPanel panel3 = new JPanel(); JPanel buttonBar = new JPanel(); JButton okButton = new JButton(); JButton cancelButton = new JButton(); //======== this ======== setModalityType(Dialog.ModalityType.APPLICATION_MODAL); setDefaultCloseOperation(WindowConstants.DISPOSE_ON_CLOSE); setAlwaysOnTop(true); Container contentPane = getContentPane(); contentPane.setLayout(new BorderLayout()); //======== dialogPane ======== { dialogPane.setBorder(new EmptyBorder(12, 12, 12, 12)); dialogPane.setLayout(new BorderLayout()); //======== contentPanel ======== { contentPanel.setLayout(null); //======== panel4 ======== { panel4.setBorder(new TitledBorder("Track Name")); panel4.setLayout(null); panel4.add(nameField); nameField.setBounds(20, 25, 500, nameField.getPreferredSize().height); { // compute preferred size Dimension preferredSize = new Dimension(); for (int i = 0; i < panel4.getComponentCount(); i++) { Rectangle bounds = panel4.getComponent(i).getBounds(); preferredSize.width = Math.max(bounds.x + bounds.width, preferredSize.width); preferredSize.height = Math.max(bounds.y + bounds.height, preferredSize.height); } Insets insets = panel4.getInsets(); preferredSize.width += insets.right; preferredSize.height += insets.bottom; panel4.setMinimumSize(preferredSize); panel4.setPreferredSize(preferredSize); } } contentPanel.add(panel4); panel4.setBounds(0, 0, 535, 67); //======== panel1 ======== { panel1.setBorder(new TitledBorder("Y Axis")); panel1.setLayout(null); //---- label2 ---- label2.setText("Min"); panel1.add(label2); label2.setBounds(new Rectangle(new Point(30, 30), label2.getPreferredSize())); //---- label3 ---- label3.setText("Max"); panel1.add(label3); label3.setBounds(new Rectangle(new Point(30, 70), label3.getPreferredSize())); //---- logScaleCB ---- logScaleCB.setText("Log scale"); logScaleCB.setEnabled(false); panel1.add(logScaleCB); logScaleCB.setBounds(new Rectangle(new Point(30, 110), logScaleCB.getPreferredSize())); //---- minYField ---- minYField.addFocusListener(new FocusAdapter() { @Override public void focusLost(FocusEvent e) { minYFieldFocusLost(e); } }); panel1.add(minYField); minYField.setBounds(100, 24, 170, minYField.getPreferredSize().height); //---- maxYField ---- maxYField.addFocusListener(new FocusAdapter() { @Override public void focusLost(FocusEvent e) { maxYFieldFocusLost(e); } }); panel1.add(maxYField); maxYField.setBounds(100, 64, 170, 28); { // compute preferred size Dimension preferredSize = new Dimension(); for (int i = 0; i < panel1.getComponentCount(); i++) { Rectangle bounds = panel1.getComponent(i).getBounds(); preferredSize.width = Math.max(bounds.x + bounds.width, preferredSize.width); preferredSize.height = Math.max(bounds.y + bounds.height, preferredSize.height); } Insets insets = panel1.getInsets(); preferredSize.width += insets.right; preferredSize.height += insets.bottom; panel1.setMinimumSize(preferredSize); panel1.setPreferredSize(preferredSize); } } contentPanel.add(panel1); panel1.setBounds(0, 69, 535, 167); //======== panel2 ======== { panel2.setBorder(new TitledBorder("Colors")); panel2.setLayout(null); //---- label4 ---- label4.setText("Positive values"); panel2.add(label4); label4.setBounds(new Rectangle(new Point(25, 30), label4.getPreferredSize())); //---- label5 ---- label5.setText("Negative values"); panel2.add(label5); label5.setBounds(25, 60, 105, 16); panel2.add(posColorChooser); posColorChooser.setBounds(160, 27, 55, posColorChooser.getPreferredSize().height); panel2.add(altColorChooser); altColorChooser.setBounds(new Rectangle(new Point(160, 57), altColorChooser.getPreferredSize())); { // compute preferred size Dimension preferredSize = new Dimension(); for (int i = 0; i < panel2.getComponentCount(); i++) { Rectangle bounds = panel2.getComponent(i).getBounds(); preferredSize.width = Math.max(bounds.x + bounds.width, preferredSize.width); preferredSize.height = Math.max(bounds.y + bounds.height, preferredSize.height); } Insets insets = panel2.getInsets(); preferredSize.width += insets.right; preferredSize.height += insets.bottom; panel2.setMinimumSize(preferredSize); panel2.setPreferredSize(preferredSize); } } contentPanel.add(panel2); panel2.setBounds(0, 235, 535, 95); //======== panel3 ======== { panel3.setBorder(new TitledBorder("Data Reduction Function")); panel3.setAlignmentX(0.0F); panel3.setLayout(new FlowLayout(FlowLayout.LEFT)); //---- meanRB ---- meanRB.setText("Mean"); panel3.add(meanRB); //---- maxRB ---- maxRB.setText("Max"); panel3.add(maxRB); } contentPanel.add(panel3); panel3.setBounds(0, 335, 535, 89); { // compute preferred size Dimension preferredSize = new Dimension(); for (int i = 0; i < contentPanel.getComponentCount(); i++) { Rectangle bounds = contentPanel.getComponent(i).getBounds(); preferredSize.width = Math.max(bounds.x + bounds.width, preferredSize.width); preferredSize.height = Math.max(bounds.y + bounds.height, preferredSize.height); } Insets insets = contentPanel.getInsets(); preferredSize.width += insets.right; preferredSize.height += insets.bottom; contentPanel.setMinimumSize(preferredSize); contentPanel.setPreferredSize(preferredSize); } } dialogPane.add(contentPanel, BorderLayout.CENTER); //======== buttonBar ======== { buttonBar.setBorder(new EmptyBorder(12, 0, 0, 0)); buttonBar.setLayout(new GridBagLayout()); ((GridBagLayout) buttonBar.getLayout()).columnWidths = new int[]{0, 85, 80}; ((GridBagLayout) buttonBar.getLayout()).columnWeights = new double[]{1.0, 0.0, 0.0}; //---- okButton ---- okButton.setText("OK"); okButton.addActionListener(new ActionListener() { @Override public void actionPerformed(ActionEvent e) { okButtonActionPerformed(e); } }); buttonBar.add(okButton, new GridBagConstraints(1, 0, 1, 1, 0.0, 0.0, GridBagConstraints.CENTER, GridBagConstraints.BOTH, new Insets(0, 0, 0, 5), 0, 0)); //---- cancelButton ---- cancelButton.setText("Cancel"); cancelButton.addActionListener(new ActionListener() { @Override public void actionPerformed(ActionEvent e) { cancelButtonActionPerformed(e); } }); buttonBar.add(cancelButton, new GridBagConstraints(2, 0, 1, 1, 0.0, 0.0, GridBagConstraints.CENTER, GridBagConstraints.BOTH, new Insets(0, 0, 0, 0), 0, 0)); } dialogPane.add(buttonBar, BorderLayout.SOUTH); } contentPane.add(dialogPane, BorderLayout.CENTER); setSize(565, 510); setLocationRelativeTo(getOwner()); //---- dataReductionGroup ---- ButtonGroup dataReductionGroup = new ButtonGroup(); dataReductionGroup.add(meanRB); dataReductionGroup.add(maxRB); // JFormDesigner - End of component initialization //GEN-END:initComponents } private boolean validateNumeric(String text) { try { Double.parseDouble(text); return true; } catch (NumberFormatException e) { JOptionPane.showMessageDialog(this, "Error: numeric value required (" + text + ")"); return false; } } } ================================================ FILE: src/juicebox/track/TrackConfigDialog.jfd ================================================ JFDML JFormDesigner: "5.1.1.0.120" Java: "1.6.0_51" encoding: "UTF-8" new FormModel { contentType: "form/swing" root: new FormRoot { add( new FormWindow( "javax.swing.JDialog", new FormLayoutManager( class java.awt.BorderLayout ) ) { name: "this" "$sizePolicy": 1 "modalityType": enum java.awt.Dialog$ModalityType APPLICATION_MODAL "defaultCloseOperation": 2 "alwaysOnTop": true add( new FormContainer( "javax.swing.JPanel", new FormLayoutManager( class java.awt.BorderLayout ) ) { name: "dialogPane" "border": new javax.swing.border.EmptyBorder( 12, 12, 12, 12 ) add( new FormContainer( "javax.swing.JPanel", new FormLayoutManager( class com.jformdesigner.runtime.NullLayout ) ) { name: "contentPanel" add( new FormContainer( "javax.swing.JPanel", new FormLayoutManager( class com.jformdesigner.runtime.NullLayout ) ) { name: "panel4" "border": new javax.swing.border.TitledBorder( "Track Name" ) add( new FormComponent( "javax.swing.JTextField" ) { name: "nameField" }, new FormLayoutConstraints( class com.jformdesigner.runtime.NullConstraints ) { "width": 500 "x": 20 "y": 25 } ) }, new FormLayoutConstraints( class com.jformdesigner.runtime.NullConstraints ) { "width": 535 "height": 67 } ) add( new FormContainer( "javax.swing.JPanel", new FormLayoutManager( class com.jformdesigner.runtime.NullLayout ) ) { name: "panel1" "border": new javax.swing.border.TitledBorder( "Y Axis" ) add( new FormComponent( "javax.swing.JLabel" ) { name: "label2" "text": "Min" }, new FormLayoutConstraints( class com.jformdesigner.runtime.NullConstraints ) { "x": 30 "y": 30 } ) add( new FormComponent( "javax.swing.JLabel" ) { name: "label3" "text": "Max" }, new FormLayoutConstraints( class com.jformdesigner.runtime.NullConstraints ) { "x": 30 "y": 70 } ) add( new FormComponent( "javax.swing.JCheckBox" ) { name: "logScaleCB" "text": "Log scale" "enabled": false }, new FormLayoutConstraints( class com.jformdesigner.runtime.NullConstraints ) { "x": 30 "y": 110 } ) add( new FormComponent( "javax.swing.JTextField" ) { name: "minYField" addEvent( new FormEvent( "java.awt.event.FocusListener", "focusLost", "minYFieldFocusLost", true ) ) }, new FormLayoutConstraints( class com.jformdesigner.runtime.NullConstraints ) { "x": 100 "y": 24 "width": 170 } ) add( new FormComponent( "javax.swing.JTextField" ) { name: "maxYField" addEvent( new FormEvent( "java.awt.event.FocusListener", "focusLost", "maxYFieldFocusLost", true ) ) }, new FormLayoutConstraints( class com.jformdesigner.runtime.NullConstraints ) { "width": 170 "height": 28 "x": 100 "y": 64 } ) }, new FormLayoutConstraints( class com.jformdesigner.runtime.NullConstraints ) { "y": 69 "width": 535 "height": 167 "x": 0 } ) add( new FormContainer( "javax.swing.JPanel", new FormLayoutManager( class com.jformdesigner.runtime.NullLayout ) ) { name: "panel2" "border": new javax.swing.border.TitledBorder( "Colors" ) add( new FormComponent( "javax.swing.JLabel" ) { name: "label4" "text": "Positive values" }, new FormLayoutConstraints( class com.jformdesigner.runtime.NullConstraints ) { "x": 25 "y": 30 } ) add( new FormComponent( "javax.swing.JLabel" ) { name: "label5" "text": "Negative values" }, new FormLayoutConstraints( class com.jformdesigner.runtime.NullConstraints ) { "width": 105 "height": 16 "x": 25 "y": 60 } ) add( new FormComponent( "org.broad.igv.ui.color.ColorChooserPanel" ) { name: "posColorChooser" }, new FormLayoutConstraints( class com.jformdesigner.runtime.NullConstraints ) { "x": 160 "y": 27 "width": 55 } ) add( new FormComponent( "org.broad.igv.ui.color.ColorChooserPanel" ) { name: "altColorChooser" }, new FormLayoutConstraints( class com.jformdesigner.runtime.NullConstraints ) { "x": 160 "y": 57 } ) }, new FormLayoutConstraints( class com.jformdesigner.runtime.NullConstraints ) { "y": 235 "width": 535 "height": 95 "x": 0 } ) add( new FormContainer( "javax.swing.JPanel", new FormLayoutManager( class java.awt.FlowLayout ) { "alignment": 0 } ) { name: "panel3" "border": new javax.swing.border.TitledBorder( "Data Reduction Function" ) "alignmentX": 0.0f add( new FormComponent( "javax.swing.JRadioButton" ) { name: "meanRB" "text": "Mean" "$buttonGroup": new FormReference( "dataReductionGroup" ) } ) add( new FormComponent( "javax.swing.JRadioButton" ) { name: "maxRB" "text": "Max" "$buttonGroup": new FormReference( "dataReductionGroup" ) } ) }, new FormLayoutConstraints( class com.jformdesigner.runtime.NullConstraints ) { "x": 0 "y": 335 "width": 535 "height": 89 } ) }, new FormLayoutConstraints( class java.lang.String ) { "value": "Center" } ) add( new FormContainer( "javax.swing.JPanel", new FormLayoutManager( class java.awt.GridBagLayout ) { "$columnSpecs": "0:1.0, 80, 80" "$hGap": 5 "$vGap": 5 "$rowSpecs": "0" } ) { name: "buttonBar" "border": new javax.swing.border.EmptyBorder( 12, 0, 0, 0 ) add( new FormComponent( "javax.swing.JButton" ) { name: "okButton" "text": "OK" addEvent( new FormEvent( "java.awt.event.ActionListener", "actionPerformed", "okButtonActionPerformed", true ) ) }, new FormLayoutConstraints( class com.jformdesigner.runtime.GridBagConstraintsEx ) { "gridx": 1 } ) add( new FormComponent( "javax.swing.JButton" ) { name: "cancelButton" "text": "Cancel" addEvent( new FormEvent( "java.awt.event.ActionListener", "actionPerformed", "cancelButtonActionPerformed", true ) ) }, new FormLayoutConstraints( class com.jformdesigner.runtime.GridBagConstraintsEx ) { "gridx": 2 } ) }, new FormLayoutConstraints( class java.lang.String ) { "value": "South" } ) }, new FormLayoutConstraints( class java.lang.String ) { "value": "Center" } ) }, new FormLayoutConstraints( null ) { "location": new java.awt.Point( 0, 0 ) "size": new java.awt.Dimension( 565, 510 ) } ) add( new FormNonVisual( "javax.swing.ButtonGroup" ) { name: "dataReductionGroup" }, new FormLayoutConstraints( null ) { "location": new java.awt.Point( 0, 520 ) } ) } } ================================================ FILE: src/juicebox/track/TrackConfigPanel.java ================================================ /* * The MIT License (MIT) * * Copyright (c) 2011-2021 Broad Institute, Aiden Lab, Rice University, Baylor College of Medicine * * Permission is hereby granted, free of charge, to any person obtaining a copy * of this software and associated documentation files (the "Software"), to deal * in the Software without restriction, including without limitation the rights * to use, copy, modify, merge, publish, distribute, sublicense, and/or sell * copies of the Software, and to permit persons to whom the Software is * furnished to do so, subject to the following conditions: * * The above copyright notice and this permission notice shall be included in * all copies or substantial portions of the Software. * * THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR * IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, * FITNESS FOR A PARTICULAR PURPOSE AND NON-INFRINGEMENT. IN NO EVENT SHALL THE * AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER * LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, * OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN * THE SOFTWARE. */ package juicebox.track; import juicebox.gui.SuperAdapter; import org.broad.igv.renderer.DataRange; import org.broad.igv.track.WindowFunction; import org.broad.igv.ui.color.ColorChooserPanel; import javax.swing.*; import javax.swing.event.DocumentEvent; import javax.swing.event.DocumentListener; import java.awt.*; import java.awt.event.ActionEvent; import java.awt.event.ActionListener; import java.awt.event.FocusEvent; /** * @author Jim Robinson */ public class TrackConfigPanel extends JPanel { private static final long serialVersionUID = 900007; private final HiCTrack track; private final boolean canceled = false; private ColorChooserPanel posColorChooser; private ColorChooserPanel altColorChooser; private JCheckBox logScaleCB; private JTextField minYField; private JTextField maxYField; private JRadioButton meanRB; private JRadioButton maxRB; private JTextField nameField; public TrackConfigPanel(SuperAdapter superAdapter, HiCTrack track) { super(new FlowLayout()); this.track = track; initComponents(superAdapter); if (track instanceof EigenvectorTrack) { altColorChooser.setEnabled(true); } if (track instanceof HiCDataTrack) { minYField.setEnabled(true); maxYField.setEnabled(true); logScaleCB.setEnabled(true); altColorChooser.setEnabled(true); maxRB.setEnabled(true); meanRB.setEnabled(true); HiCDataTrack dataTrack = (HiCDataTrack) track; minYField.setText(String.valueOf(dataTrack.getDataRange().getMinimum())); maxYField.setText(String.valueOf(dataTrack.getDataRange().getMaximum())); logScaleCB.setSelected(dataTrack.getDataRange().isLog()); altColorChooser.setSelectedColor(dataTrack.getNegColor()); if (!dataTrack.getAvailableWindowFunctions().contains(WindowFunction.max)) { maxRB.setEnabled(false); } if (dataTrack.getWindowFunction() == WindowFunction.max) { maxRB.setSelected(true); } else { meanRB.setSelected(true); } } else { minYField.setEnabled(false); maxYField.setEnabled(false); logScaleCB.setEnabled(false); altColorChooser.setEnabled(false); maxRB.setEnabled(false); meanRB.setEnabled(false); } } private void minYFieldFocusLost(FocusEvent e) { if (track instanceof HiCDataTrack) { if (!validateNumeric(minYField.getText())) { DataRange dr = ((HiCDataTrack) track).getDataRange(); minYField.setText(String.valueOf(dr.getMinimum())); } } } private void maxYFieldFocusLost(FocusEvent e) { if (track instanceof HiCDataTrack) { if (!validateNumeric(maxYField.getText())) { DataRange dr = ((HiCDataTrack) track).getDataRange(); minYField.setText(String.valueOf(dr.getMaximum())); } } } private void initComponents(final SuperAdapter superAdapter) { // JFormDesigner - Component initialization - DO NOT MODIFY //GEN-BEGIN:initComponents // Generated using JFormDesigner non-commercial license nameField = new JTextField(track.getName(), 10); nameField.setToolTipText("Change the name for this annotation: " + nameField.getText()); nameField.setMaximumSize(new Dimension(100, 30)); nameField.getDocument().addDocumentListener(new DocumentListener() { private void action() { track.setName(nameField.getText()); nameField.setToolTipText("Change the name for this annotation: " + nameField.getText()); superAdapter.updateTrackPanel(); superAdapter.repaintTrackPanels(); superAdapter.repaint(); } @Override public void insertUpdate(DocumentEvent e) { action(); } @Override public void removeUpdate(DocumentEvent e) { action(); } @Override public void changedUpdate(DocumentEvent e) { action(); } }); add(nameField); add(new JLabel("Positive:")); posColorChooser = new ColorChooserPanel(); posColorChooser.setToolTipText("Change color for positive values"); posColorChooser.setSelectedColor(track.getPosColor()); posColorChooser.addActionListener(new ActionListener() { @Override public void actionPerformed(ActionEvent e) { Color color = posColorChooser.getSelectedColor(); if (color != null) { track.setPosColor(color); superAdapter.updateTrackPanel(); superAdapter.repaintTrackPanels(); } } }); add(posColorChooser); add(new JLabel("Negative:")); altColorChooser = new ColorChooserPanel(); altColorChooser.setToolTipText("Change color for negative values"); altColorChooser.setSelectedColor(track.getNegColor()); altColorChooser.addActionListener(new ActionListener() { @Override public void actionPerformed(ActionEvent e) { Color color = altColorChooser.getSelectedColor(); if (color != null) { track.setNegColor(color); superAdapter.updateTrackPanel(); superAdapter.repaintTrackPanels(); } } }); add(altColorChooser); add(new JLabel("Min:")); minYField = new JTextField("", 3); /*minYField.addFocusListener(new FocusAdapter() { @Override public void focusLost(FocusEvent e) { minYFieldFocusLost(e); superAdapter.updateTrackPanel(); superAdapter.repaintTrackPanels(); } });*/ add(minYField); minYField.getDocument().addDocumentListener(dataActionDocument(minYField, superAdapter)); add(new JLabel("Max:")); maxYField = new JTextField("", 3); /*maxYField.addFocusListener(new FocusAdapter() { @Override public void focusLost(FocusEvent e) { maxYFieldFocusLost(e); superAdapter.updateTrackPanel(); superAdapter.repaintTrackPanels(); } });*/ add(maxYField); maxYField.getDocument().addDocumentListener(dataActionDocument(maxYField, superAdapter)); logScaleCB = new JCheckBox(); logScaleCB.setText("Log"); logScaleCB.setToolTipText("Set logarithmic scaling"); logScaleCB.setEnabled(false); add(logScaleCB); logScaleCB.addActionListener(new ActionListener() { @Override public void actionPerformed(ActionEvent e) { performDataAction(superAdapter); } }); add(new JLabel("DRF")); meanRB = new JRadioButton("Mean"); meanRB.setToolTipText("Data Reduction Function"); maxRB = new JRadioButton("Max"); maxRB.setToolTipText("Data Reduction Function"); ButtonGroup dataReductionGroup = new ButtonGroup(); dataReductionGroup.add(meanRB); dataReductionGroup.add(maxRB); add(meanRB); add(maxRB); meanRB.addActionListener(new ActionListener() { @Override public void actionPerformed(ActionEvent e) { if (track instanceof HiCDataTrack) { WindowFunction wf = maxRB.isSelected() ? WindowFunction.max : WindowFunction.mean; ((HiCDataTrack) track).setWindowFunction(wf); superAdapter.updateTrackPanel(); superAdapter.repaintTrackPanels(); } } }); maxRB.addActionListener(new ActionListener() { @Override public void actionPerformed(ActionEvent e) { if (track instanceof HiCDataTrack) { WindowFunction wf = maxRB.isSelected() ? WindowFunction.max : WindowFunction.mean; ((HiCDataTrack) track).setWindowFunction(wf); superAdapter.updateTrackPanel(); superAdapter.repaintTrackPanels(); } } }); } private DocumentListener dataActionDocument(final JTextField field, final SuperAdapter superAdapter) { return new DocumentListener() { private void action() { field.setToolTipText("Change: " + field.getText()); if (isReasonableText(field.getText())) { performDataAction(superAdapter); } } @Override public void insertUpdate(DocumentEvent e) { action(); } @Override public void removeUpdate(DocumentEvent e) { action(); } @Override public void changedUpdate(DocumentEvent e) { action(); } }; } private void performDataAction(SuperAdapter superAdapter) { if (track instanceof HiCDataTrack && validateNumeric(minYField.getText()) && validateNumeric(maxYField.getText())) { float newMin = Float.parseFloat(minYField.getText()); float newMax = Float.parseFloat(maxYField.getText()); DataRange newDataRange = new DataRange(newMin, newMax); if (newMin < 0 && newMax > 0) { newDataRange = new DataRange(newMin, 0f, newMax); } newDataRange.setType(logScaleCB.isSelected() ? DataRange.Type.LOG : DataRange.Type.LINEAR); ((HiCDataTrack) track).setDataRange(newDataRange); superAdapter.updateTrackPanel(); superAdapter.repaintTrackPanels(); } } private boolean isReasonableText(String text) { return text.length() > 0 && !text.equals(".") && !text.equals("-"); } private boolean validateNumeric(String text) { try { if (isReasonableText(text)) { Double.parseDouble(text); return true; } } catch (NumberFormatException e) { JOptionPane.showMessageDialog(this, "Error: numeric value required (" + text + ")"); } return false; } } ================================================ FILE: src/juicebox/track/TrackLabelPanel.java ================================================ /* * The MIT License (MIT) * * Copyright (c) 2011-2021 Broad Institute, Aiden Lab, Rice University, Baylor College of Medicine * * Permission is hereby granted, free of charge, to any person obtaining a copy * of this software and associated documentation files (the "Software"), to deal * in the Software without restriction, including without limitation the rights * to use, copy, modify, merge, publish, distribute, sublicense, and/or sell * copies of the Software, and to permit persons to whom the Software is * furnished to do so, subject to the following conditions: * * The above copyright notice and this permission notice shall be included in * all copies or substantial portions of the Software. * * THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR * IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, * FITNESS FOR A PARTICULAR PURPOSE AND NON-INFRINGEMENT. IN NO EVENT SHALL THE * AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER * LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, * OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN * THE SOFTWARE. */ package juicebox.track; //import juicebox.Context; import juicebox.HiC; import juicebox.HiCGlobals; import javax.swing.*; import java.awt.*; import java.util.ArrayList; //import java.util.HashMap; //import java.util.Map; //import org.broad.igv.renderer.GraphicUtils; //import java.awt.geom.Rectangle2D; /** * @author jrobinso * Date: 8/3/13 * Time: 9:36 PM */ public class TrackLabelPanel extends JPanel { private static final long serialVersionUID = 9000037; private final HiC hic; final private int leftMargin = 10; final private int rightMargin = 5; private HiCTrack eigenvectorTrack; private final int numExtraBufferLinesSpaces = 2; public TrackLabelPanel(HiC hic) { this.hic = hic; setLayout(null); } @Override public void setBounds(int x, int y, int width, int height) { super.setBounds(x, y, width, height); for (Component c : this.getComponents()) { if (c instanceof JLabel) { Rectangle bounds = c.getBounds(); bounds.width = width - (leftMargin + rightMargin); c.setBounds(bounds); } } } public void updateLabels() { removeAll(); if (hic.getDataset() == null) { return; } java.util.List tracks = new ArrayList<>(hic.getLoadedTracks()); int trackCount = tracks.size() + (eigenvectorTrack == null ? 0 : 1); if (trackCount == 0) { return; } int top = 0; final int width = getWidth() - (leftMargin + rightMargin); for (HiCTrack hicTrack : tracks) { JLabel textLabel = getTrackLabel(hicTrack.getName(), true); textLabel.setBounds(leftMargin, top, width, hicTrack.getHeight()); textLabel.setBackground(Color.CYAN); add(textLabel); top += hicTrack.getHeight(); } } private JLabel getTrackLabel(String name, boolean addToolTip) { JLabel label = new JLabel(name); //, SwingConstants.RIGHT); label.setVerticalAlignment(SwingConstants.CENTER); label.setFont(HiCGlobals.font(10, false)); if (addToolTip) label.setToolTipText(name); return label; } } ================================================ FILE: src/juicebox/track/TrackPanel.java ================================================ /* * The MIT License (MIT) * * Copyright (c) 2011-2021 Broad Institute, Aiden Lab, Rice University, Baylor College of Medicine * * Permission is hereby granted, free of charge, to any person obtaining a copy * of this software and associated documentation files (the "Software"), to deal * in the Software without restriction, including without limitation the rights * to use, copy, modify, merge, publish, distribute, sublicense, and/or sell * copies of the Software, and to permit persons to whom the Software is * furnished to do so, subject to the following conditions: * * The above copyright notice and this permission notice shall be included in * all copies or substantial portions of the Software. * * THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR * IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, * FITNESS FOR A PARTICULAR PURPOSE AND NON-INFRINGEMENT. IN NO EVENT SHALL THE * AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER * LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, * OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN * THE SOFTWARE. */ package juicebox.track; import juicebox.Context; import juicebox.HiC; import juicebox.HiCGlobals; import juicebox.data.HiCFileTools; import juicebox.data.MatrixZoomData; import juicebox.gui.SuperAdapter; import juicebox.mapcolorui.FeatureRenderer; import juicebox.track.feature.Feature2D; import org.broad.igv.util.Pair; import javax.swing.*; import java.awt.*; import java.awt.event.MouseAdapter; import java.awt.event.MouseEvent; import java.awt.geom.AffineTransform; import java.util.ArrayList; import java.util.Collection; import java.util.List; /** * Created by IntelliJ IDEA. * User: neva * Date: 4/3/12 * Time: 4:08 PM * To change this template use File | Settings | File Templates. */ public class TrackPanel extends JPanel { private static final long serialVersionUID = 9000038; //private MouseAdapter mouseAdapter; private final HiC hic; private final Orientation orientation; // HiCTrack eigenvectorTrack; private final Collection> trackRectangles; private final SuperAdapter superAdapter; public TrackPanel(SuperAdapter superAdapter, HiC hiC, Orientation orientation) { this.superAdapter = superAdapter; this.hic = hiC; this.orientation = orientation; setAutoscrolls(true); trackRectangles = new ArrayList<>(); if (HiCGlobals.isDarkulaModeEnabled) { setBackground(Color.black); } else { setBackground(Color.white); } addMouseAdapter(superAdapter); //setToolTipText(""); // Has side affect of turning on tt text } public void removeTrack(HiCTrack track) { hic.removeTrack(track); superAdapter.revalidate(); superAdapter.repaint(); superAdapter.getLayersPanel().redraw1DLayerPanels(superAdapter); } public void moveTrackUp(HiCTrack track) { // Move up the track in the array by 1. hic.moveTrack(track, true); superAdapter.revalidate(); superAdapter.repaint(); } public void moveTrackDown(HiCTrack track) { // Move down the track in the array by 1. hic.moveTrack(track, false); superAdapter.revalidate(); superAdapter.repaint(); } public List getTrackList() { return hic.getLoadedTracks(); } private void addMouseAdapter(final SuperAdapter superAdapter) { MouseAdapter mouseAdapter = new MouseAdapter() { @Override public void mouseMoved(MouseEvent e) { TrackPanel.this.superAdapter.updateMainViewPanelToolTipText(tooltipText(e.getX(), e.getY(), true)); } @Override public void mouseReleased(MouseEvent mouseEvent) { if (mouseEvent.isPopupTrigger()) { handlePopupEvent(mouseEvent); } } @Override public void mouseClicked(MouseEvent mouseEvent) { Context context = orientation == Orientation.X ? hic.getXContext() : hic.getYContext(); if (mouseEvent.isPopupTrigger()) { handlePopupEvent(mouseEvent); } else if (mouseEvent.getClickCount() > 1) { int x = mouseEvent.getX(); int y = mouseEvent.getY(); if (orientation == Orientation.Y) { y = mouseEvent.getX(); x = mouseEvent.getY(); } for (Pair p : trackRectangles) { Rectangle r = p.getFirst(); if (y >= r.y && y < r.y + r.height) { HiCTrack track = p.getSecond(); track.mouseClicked(x, y, context, orientation); } } } } @Override public void mousePressed(MouseEvent mouseEvent) { if (mouseEvent.isPopupTrigger()) { handlePopupEvent(mouseEvent); } } private void handlePopupEvent(MouseEvent mouseEvent) { for (Pair p : trackRectangles) { Rectangle r = p.getFirst(); if (r.contains(mouseEvent.getPoint())) { HiCTrack track = p.getSecond(); JPopupMenu menu = track.getPopupMenu(TrackPanel.this, superAdapter, orientation); menu.show(mouseEvent.getComponent(), mouseEvent.getX(), mouseEvent.getY()); repaint(); // Collection selectedTracks = Arrays.asList(p.getSecond()); // TrackClickEvent te = new TrackClickEvent(mouseEvent, null); // IGVPopupMenu menu = TrackMenuUtils.getPopupMenu(selectedTracks, "", te); // menu.show(mouseEvent.getComponent(), mouseEvent.getX(), mouseEvent.getY()); } } } }; this.addMouseListener(mouseAdapter); this.addMouseMotionListener(mouseAdapter); } /** * Returns the current height of this component. * This method is preferable to writing * component.getBounds().height, or * component.getSize().height because it doesn't cause any * heap allocations. * * @return the current height of this component */ @Override public int getHeight() { if (orientation == Orientation.X) { int h = 0; for (HiCTrack t : hic.getLoadedTracks()) { h += t.getHeight(); } return h; } else { return super.getHeight(); } } @Override public int getWidth() { if (orientation == Orientation.Y) { int h = 0; for (HiCTrack t : hic.getLoadedTracks()) { h += t.getHeight(); } return h; } else { return super.getWidth(); } } /** * If the preferredSize has been set to a * non-null value just returns it. * If the UI delegate's getPreferredSize * method returns a non null value then return that; * otherwise defer to the component's layout manager. * * @return the value of the preferredSize property * @see #setPreferredSize * @see javax.swing.plaf.ComponentUI */ @Override public Dimension getPreferredSize() { return new Dimension(getWidth(), getHeight()); } protected void paintComponent(Graphics g) { super.paintComponent(g); Graphics2D g2d = (Graphics2D) g; g2d.setRenderingHint(RenderingHints.KEY_ANTIALIASING, RenderingHints.VALUE_ANTIALIAS_ON); AffineTransform originalTransform = g2d.getTransform(); if (orientation == Orientation.Y) { AffineTransform rotateTransform = new AffineTransform(); rotateTransform.quadrantRotate(1); rotateTransform.scale(1, -1); g2d.transform(rotateTransform); } trackRectangles.clear(); java.util.List tracks = new ArrayList<>(hic.getLoadedTracks()); if (tracks.isEmpty()) { return; } Rectangle rect = getBounds(); g.setColor(getBackground()); g.fillRect(rect.x, rect.y, rect.width, rect.height); //int rectBottom = orientation == Orientation.X ? rect.y + rect.height : rect.x + rect.width; int y = orientation == Orientation.X ? rect.y : rect.x; try { HiCGridAxis gridAxis = orientation == Orientation.X ? hic.getZd().getXGridAxis() : hic.getZd().getYGridAxis(); for (HiCTrack hicTrack : tracks) { if (hicTrack.getHeight() > 0) { int h = hicTrack.getHeight(); Rectangle trackRectangle; if (orientation == Orientation.X) { trackRectangle = new Rectangle(rect.x, y, rect.width, h); } else { //noinspection SuspiciousNameCombination trackRectangle = new Rectangle(y, rect.y, h, rect.height); } if (getContext() != null) { hicTrack.render(g, getContext(), trackRectangle, orientation, gridAxis); y += h; trackRectangles.add(new Pair<>(trackRectangle, hicTrack)); } } } } catch (Exception e) { if (HiCGlobals.printVerboseComments) e.printStackTrace(); } g2d.setTransform(originalTransform); Point cursorPoint = hic.getCursorPoint(); if (cursorPoint == null) { cursorPoint = hic.getDiagonalCursorPoint(); } if (cursorPoint != null) { if (HiCGlobals.isDarkulaModeEnabled) { g.setColor(HiCGlobals.DARKULA_RULER_LINE_COLOR); } else { g.setColor(HiCGlobals.RULER_LINE_COLOR); } if (orientation == Orientation.X) { g.drawLine(cursorPoint.x, 0, cursorPoint.x, getHeight()); } else { g.drawLine(0, cursorPoint.y, getWidth(), cursorPoint.y); } } try { List highlights = hic.getHighlightedFeatures(); if (highlights.size() > 0) { g.setColor(FeatureRenderer.HIGHLIGHT_COLOR); MatrixZoomData zd = hic.getZd(); HiCGridAxis xAxis = zd.getXGridAxis(); HiCGridAxis yAxis = zd.getYGridAxis(); double binOriginX = hic.getXContext().getBinOrigin(); double binOriginY = hic.getYContext().getBinOrigin(); for (Feature2D highlight : highlights) { int binStart1 = xAxis.getBinNumberForGenomicPosition(highlight.getStart1()); int binEnd1 = xAxis.getBinNumberForGenomicPosition(highlight.getEnd1()); int binStart2 = yAxis.getBinNumberForGenomicPosition(highlight.getStart2()); int binEnd2 = yAxis.getBinNumberForGenomicPosition(highlight.getEnd2()); double scaleFactor = hic.getScaleFactor(); if (orientation == Orientation.X) { if (HiCFileTools.equivalentChromosome(highlight.getChr1(), zd.getChr1())) { int x3 = (int) ((binStart1 - binOriginX) * scaleFactor); int h3 = (int) Math.max(1, scaleFactor * (binEnd1 - binStart1)); g.drawLine(x3, 0, x3, getHeight()); g.drawLine(x3 + h3, 0, x3 + h3, getHeight()); } } else if (HiCFileTools.equivalentChromosome(highlight.getChr2(), zd.getChr2())) { int y3 = (int) ((binStart2 - binOriginY) * scaleFactor); int w3 = (int) Math.max(1, scaleFactor * (binEnd2 - binStart2)); g.drawLine(0, y3, getWidth(), y3); g.drawLine(0, y3 + w3, getWidth(), y3 + w3); } } } } catch (Exception e2) { // } } private Context getContext() { return orientation == Orientation.X ? hic.getXContext() : hic.getYContext(); } public String tooltipText(int mx, int my, boolean isMouseDirectlyOnTrack) { if (isMouseDirectlyOnTrack) { int x = mx; int y = my; if (orientation == Orientation.Y) { y = mx; x = my; } for (Pair p : trackRectangles) { Rectangle r = p.getFirst(); if (r.contains(mx, my)) { return p.getSecond().getToolTipText(x, y, orientation); } } } else { StringBuilder toolTipText = new StringBuilder(); if (orientation == Orientation.X) { for (Pair p : trackRectangles) { Rectangle r = p.getFirst(); int y = r.y + r.height / 2; if (r.contains(mx, y)) { String tempText = p.getSecond().getToolTipText(mx, y, orientation); if (tempText.length() > 0) toolTipText.append("
").append(tempText); } } } else { for (Pair p : trackRectangles) { Rectangle r = p.getFirst(); int x = r.x + r.width / 2; if (r.contains(x, my)) { String tempText = p.getSecond().getToolTipText(my, x, orientation); if (tempText.length() > 0) toolTipText.append("
").append(tempText); } } } if (toolTipText.length() > 5) return "
" + toolTipText; } return null; } // @Override // public String getToolTipText(MouseEvent event) { // return tooltipText(event.getX(), event.getY()); // } public enum Orientation {X, Y} } ================================================ FILE: src/juicebox/track/feature/AnnotationLayer.java ================================================ /* * The MIT License (MIT) * * Copyright (c) 2011-2020 Broad Institute, Aiden Lab, Rice University, Baylor College of Medicine * * Permission is hereby granted, free of charge, to any person obtaining a copy * of this software and associated documentation files (the "Software"), to deal * in the Software without restriction, including without limitation the rights * to use, copy, modify, merge, publish, distribute, sublicense, and/or sell * copies of the Software, and to permit persons to whom the Software is * furnished to do so, subject to the following conditions: * * The above copyright notice and this permission notice shall be included in * all copies or substantial portions of the Software. * * THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR * IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, * FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE * AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER * LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, * OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN * THE SOFTWARE. */ package juicebox.track.feature; import juicebox.DirectoryManager; import juicebox.HiCGlobals; import juicebox.data.HiCFileTools; import juicebox.data.MatrixZoomData; import juicebox.mapcolorui.Feature2DHandler; import java.awt.*; import java.io.File; import java.io.PrintWriter; import java.util.ArrayList; import java.util.List; /** * Created by Marie on 6/3/15. * Modified by muhammadsaadshamim */ public class AnnotationLayer { private static int i; private final int id; private CustomAnnotationRTree2DHandler customAnnotationRTreeHandler; private boolean unsavedEdits; private boolean nothingSavedYet; private Feature2D lastItem; private int lastChr1Idx; private int lastChr2Idx; private PrintWriter tempWriter; private File tempFile; private ArrayList attributeKeys; private LayerType layerType; public AnnotationLayer() { id = i++; nothingSavedYet = true; reset(); layerType = LayerType.DEFAULT; } public AnnotationLayer(Feature2DList inputList) { this(); this.customAnnotationRTreeHandler = new CustomAnnotationRTree2DHandler(inputList); } public AnnotationLayer(Feature2DHandler feature2DHandler, LayerType layerType) { this(feature2DHandler.getFeatureList()); setLayerType(layerType); } // Clear all annotations private void reset() { nothingSavedYet = true; lastChr1Idx = -1; lastChr2Idx = -1; lastItem = null; unsavedEdits = false; customAnnotationRTreeHandler = new CustomAnnotationRTree2DHandler(new Feature2DList()); attributeKeys = new ArrayList<>(); // TODO make sure attributes get copied over } public void clearAnnotations() { reset(); deleteTempFile(); } public LayerType getLayerType() { return layerType; } public void setLayerType(LayerType layerType) { this.layerType = layerType; } //add annotation to feature2D list public void add(int chr1Idx, int chr2Idx, Feature2D feature) { if (feature == null) { return; } // Add attributes to feature List featureKeys = feature.getAttributeKeys(); for (String customKey : attributeKeys) { if (!featureKeys.contains(customKey)) { feature.addStringAttribute(customKey, "null"); //System.out.println("Added" + customKey); } } getAndAddAttributes(featureKeys); customAnnotationRTreeHandler.add(chr1Idx, chr2Idx, feature); lastChr1Idx = chr1Idx; lastChr2Idx = chr2Idx; lastItem = feature; // Autosave the information unsavedEdits = true; if (nothingSavedYet) { makeTempFile(); nothingSavedYet = false; } updateAutoSave(); } // Requires that lastItem is not null private void makeTempFile() { tempFile = getAutosaveFile(); tempWriter = HiCFileTools.openWriter(tempFile); Feature2D singleFeature = customAnnotationRTreeHandler.extractSingleFeature(); if (singleFeature == null) { tempWriter.println(Feature2D.getDefaultOutputFileHeader()); } else { tempWriter.println(singleFeature.getOutputFileHeader()); } } private void deleteTempFile() { if (tempWriter != null) { tempWriter.close(); } if (tempFile == null) { tempFile = getAutosaveFile(); } if (tempFile.exists()) { tempFile.delete(); } this.unsavedEdits = false; } public boolean getLayerVisibility() { return customAnnotationRTreeHandler.getLayerVisibility(); } // Set show loops public void setLayerVisibility(boolean newStatus) { customAnnotationRTreeHandler.setLayerVisibility(newStatus); } // Creates unique identifier for Feature2D based on start and end positions. private String getIdentifier(Feature2D feature) { return "" + feature.getStart1() + feature.getEnd1() + feature.getStart2() + feature.getEnd2(); } // Undo last move public void undo() { removeRecentFromList(lastChr1Idx, lastChr2Idx, lastItem); } /** * Export feature list to given file path */ private void updateAutoSave() { if (unsavedEdits && lastItem != null) { customAnnotationRTreeHandler.autoSaveNew(tempWriter, lastItem); } } /** * Export feature list to given file path, including header */ private void reSaveAll() { deleteTempFile(); makeTempFile(); customAnnotationRTreeHandler.autoSaveAll(tempWriter); } public boolean hasLoop(MatrixZoomData zd, int chrIdx1, int chrIdx2, int x, int y, int n, double binOriginX, double binOriginY, double scale, Feature2D feature) { if (chrIdx1 > 0 && chrIdx2 > 0) { List featureList = getNearbyFeatures(zd, chrIdx1, chrIdx2, x, y, n, binOriginX, binOriginY, scale); return featureList.contains(feature) || featureList.contains(feature.reflectionAcrossDiagonal()); } return false; } private void removeRecentFromList(int idx1, int idx2, Feature2D feature) { if (idx1 > 0 && idx2 > 0) { List lastList; String mirrorIdentity = "" + feature.getStart2() + feature.getEnd2() + feature.getStart1() + feature.getEnd1(); lastList = customAnnotationRTreeHandler.get(idx1, idx2); unsavedEdits = customAnnotationRTreeHandler.checkAndRemoveFeature(idx1, idx2, feature); if (!unsavedEdits) { Feature2D removeFeature = null; for (Feature2D aFeature : lastList) { if (getIdentifier(aFeature).compareTo(mirrorIdentity) == 0) { removeFeature = aFeature; unsavedEdits = true; } } customAnnotationRTreeHandler.checkAndRemoveFeature(idx1, idx2, removeFeature); } } reSaveAll(); } public void removeFromList(MatrixZoomData zd, int chrIdx1, int chrIdx2, int x, int y, int n, double binOriginX, double binOriginY, double scale, Feature2D feature) { if (chrIdx1 > 0 && chrIdx2 > 0) { List lastList; String mirrorIdentity = "" + feature.getStart2() + feature.getEnd2() + feature.getStart1() + feature.getEnd1(); lastList = getNearbyFeatures(zd, chrIdx1, chrIdx2, x, y, n, binOriginX, binOriginY, scale); unsavedEdits = customAnnotationRTreeHandler.checkAndRemoveFeature(chrIdx1, chrIdx2, feature); if (!unsavedEdits) { Feature2D removeFeature = null; for (Feature2D aFeature : lastList) { if (getIdentifier(aFeature).compareTo(mirrorIdentity) == 0) { removeFeature = aFeature; unsavedEdits = true; } } customAnnotationRTreeHandler.checkAndRemoveFeature(chrIdx1, chrIdx2, removeFeature); } } reSaveAll(); } // Export annotations public boolean exportAnnotations(String outputFilePath) { boolean somethingExported = customAnnotationRTreeHandler.exportFeatureList(new File(outputFilePath), false, Feature2DList.ListFormat.NA); if (somethingExported) { deleteTempFile(); } return somethingExported; } public boolean exportOverlap(Feature2DList otherAnnotations, String outputFilePath) { if (customAnnotationRTreeHandler.getOverlap(otherAnnotations).exportFeatureList( new File(outputFilePath), false, Feature2DList.ListFormat.NA)) { unsavedEdits = false; } return false; } private void getAndAddAttributes(List featureKeys) { // Add feature's unique attributes to all others for (String key : featureKeys) { if (!attributeKeys.contains(key)) { attributeKeys.add(key); customAnnotationRTreeHandler.addAttributeFieldToAll(key, "null"); } } } public void addAllAttributeValues(String key, String newValue) { attributeKeys.add(key); customAnnotationRTreeHandler.addAttributeFieldToAll(key, newValue); } public List getNearbyFeatures(MatrixZoomData zd, int chrIdx1, int chrIdx2, int x, int y, int n, double binOriginX, double binOriginY, double scale) { return customAnnotationRTreeHandler.getNearbyFeatures(zd, chrIdx1, chrIdx2, x, y, n, binOriginX, binOriginY, scale); } public List getIntersectingFeatures(int chrIdx1, int chrIdx2, net.sf.jsi.Rectangle selectionWindow) { return customAnnotationRTreeHandler.getIntersectingFeatures(chrIdx1, chrIdx2, selectionWindow, false); } public Feature2DHandler getFeatureHandler() { return customAnnotationRTreeHandler; } public int getId() { return id; } public void resetCounter() { i = 0; } public int getNumberOfFeatures() { return customAnnotationRTreeHandler.getNumberOfFeatures(); } public void setColorOfAllAnnotations(Color color) { customAnnotationRTreeHandler.setColorOfAllAnnotations(color); } public boolean getIsSparse() { return customAnnotationRTreeHandler.getIsSparsePlottingEnabled(); } public void setIsSparse(boolean isSparse) { customAnnotationRTreeHandler.setSparsePlottingEnabled(isSparse); } public void createMergedLoopLists(List lists) { customAnnotationRTreeHandler.createNewMergedLoopLists(lists); } public void createMergedLoopLists(Feature2DList list) { List lists = new ArrayList<>(); lists.add(list); customAnnotationRTreeHandler.createNewMergedLoopLists(lists); } public Feature2DList getFeatureList() { return customAnnotationRTreeHandler.getFeatureList(); } private String getAutosaveFilename() { return HiCGlobals.BACKUP_FILE_STEM + id + ".bedpe"; } private File getAutosaveFile() { return new File(DirectoryManager.getHiCDirectory(), getAutosaveFilename()); } public enum LayerType {DEFAULT, EDIT, SCAFFOLD, SUPERSCAFFOLD} } ================================================ FILE: src/juicebox/track/feature/AnnotationLayerHandler.java ================================================ /* * The MIT License (MIT) * * Copyright (c) 2011-2021 Broad Institute, Aiden Lab, Rice University, Baylor College of Medicine * * Permission is hereby granted, free of charge, to any person obtaining a copy * of this software and associated documentation files (the "Software"), to deal * in the Software without restriction, including without limitation the rights * to use, copy, modify, merge, publish, distribute, sublicense, and/or sell * copies of the Software, and to permit persons to whom the Software is * furnished to do so, subject to the following conditions: * * The above copyright notice and this permission notice shall be included in * all copies or substantial portions of the Software. * * THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR * IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, * FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE * AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER * LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, * OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN * THE SOFTWARE. */ package juicebox.track.feature; import juicebox.HiC; import juicebox.HiCGlobals; import juicebox.data.ChromosomeHandler; import juicebox.data.MatrixZoomData; import juicebox.gui.SuperAdapter; import juicebox.mapcolorui.Feature2DHandler; import juicebox.mapcolorui.FeatureRenderer; import juicebox.track.HiCGridAxis; import juicebox.windowui.layers.MiniAnnotationsLayerPanel; import juicebox.windowui.layers.PlottingStyleButton; import juicebox.windowui.layers.SaveAnnotationsDialog; import org.broad.igv.ui.color.ColorChooserPanel; import org.broad.igv.util.Pair; import javax.swing.*; import java.awt.*; import java.util.List; import java.util.*; /** * Created by Marie on 6/4/15. * Modified by muhammadsaadshamim */ public class AnnotationLayerHandler { private static boolean importAnnotationsEnabled = false; private Rectangle selectionRegion; private Feature2D.FeatureType featureType = Feature2D.FeatureType.NONE; private Feature2D lastResizeLoop = null; private int lastChr1Idx = -1; private int lastChr2Idx = -1; private Pair lastStarts = null; private Pair lastEnds = null; private AnnotationLayer annotationLayer; private String layerName; private FeatureRenderer.PlottingOption plottingStyle = FeatureRenderer.PlottingOption.EVERYTHING; private FeatureRenderer.LineStyle lineStyle = FeatureRenderer.LineStyle.SOLID; private boolean canExport = false, canUndo = false; private JButton exportButton, undoButton, importAnnotationsButton, deleteLayerButton, censorButton; private final List activeLayerButtons = new ArrayList<>(); private Color defaultColor = Color.BLUE; private final List plottingStyleButtons = new ArrayList<>(); private final List colorChooserPanels = new ArrayList<>(); private JTextField nameTextField; private JLabel miniNameLabel; public AnnotationLayerHandler() { annotationLayer = new AnnotationLayer(); resetSelection(); layerName = "Layer " + annotationLayer.getId(); } public AnnotationLayerHandler(Feature2DList feature2DList) { annotationLayer = new AnnotationLayer(feature2DList); resetSelection(); layerName = "Layer " + annotationLayer.getId(); } private void resetSelection() { selectionRegion = null; //selectionPoint = null; featureType = Feature2D.FeatureType.NONE; } public void doPeak() { featureType = Feature2D.FeatureType.PEAK; } private void doDomain() { featureType = Feature2D.FeatureType.DOMAIN; } public void setStationaryStart(long start1, long start2) { lastStarts = new Pair<>(start1, start2); lastEnds = null; } public void setStationaryEnd(long end1, long end2) { lastEnds = new Pair<>(end1, end2); lastStarts = null; } // Update selection region from new rectangle public void updateSelectionRegion(Rectangle newRegion) { doDomain(); selectionRegion = newRegion; } // // Update selection region from new coordinates // public Rectangle updateSelectionRegion(int x, int y, int deltaX, int deltaY) { // // int x2, y2; // doDomain(); // Rectangle lastRegion, damageRect; // // lastRegion = selectionRegion; // // if (deltaX == 0 || deltaY == 0) { // return null; // } // // x2 = deltaX > 0 ? x : x + deltaX; // y2 = deltaY > 0 ? y : y + deltaY; // selectionRegion = new Rectangle(x2, y2, Math.abs(deltaX), Math.abs(deltaY)); // // damageRect = lastRegion == null ? selectionRegion : selectionRegion.union(lastRegion); // damageRect.x--; // damageRect.y--; // damageRect.width += 2; // damageRect.height += 2; // return damageRect; // } public void setLastItem(int idx1, int idx2, Feature2D lastLoop) { lastChr1Idx = idx1; lastChr2Idx = idx2; lastResizeLoop = lastLoop; } private void clearLastItem() { lastChr1Idx = -1; lastChr2Idx = -1; lastResizeLoop = null; } /* public void updateSelectionPoint(int x, int y) { selectionPoint = new Point(x, y); } */ // Adds to lower lefthand side, for consistency. public Feature2D generateFeature(HiC hic) { if (selectionRegion == null) return null; long start1, start2, end1, end2; Feature2D newFeature; setExportAbility(true); setUndoAbility(true); clearLastItem(); String chr1 = hic.getXContext().getChromosome().getName(); String chr2 = hic.getYContext().getChromosome().getName(); int chr1Idx = hic.getXContext().getChromosome().getIndex(); int chr2Idx = hic.getYContext().getChromosome().getIndex(); HashMap attributes = new HashMap<>(); long rightBound = hic.getXContext().getChromosome().getLength(); long bottomBound = hic.getYContext().getChromosome().getLength(); int leftBound = 0; int x = selectionRegion.x; int y = selectionRegion.y; int width = selectionRegion.width; int height = selectionRegion.height; start1 = geneXPos(hic, x, 0); end1 = geneXPos(hic, x + width, 0); start2 = geneYPos(hic, y, 0); end2 = geneYPos(hic, y + height, 0); // System.out.println(start1 + "\t" + end1); // Snap if close to diagonal if (chr1Idx == chr2Idx && (pointsShouldSnapToDiagonal(hic, x, y, width, height) || regionsOverlapSignificantly(start1, end1, start2, end2, .6))) { if (start1 < start2) { // snap to the right i.e. use y values start1 = start2; end1 = end2; } else { // snap down i.e. use x values start2 = start1; end2 = end1; } } // Make sure bounds aren't unreasonable (out of HiC map) // int rightBound = hic.getChromosomes().get(0).getLength(); // int bottomBound = hic.getChromosomes().get(1).getLength(); start1 = Math.min(Math.max(start1, leftBound), rightBound); start2 = Math.min(Math.max(start2, leftBound), bottomBound); end1 = Math.max(Math.min(end1, rightBound), leftBound); end2 = Math.max(Math.min(end2, bottomBound), leftBound); // Check for anchored corners if (lastStarts != null) { if (lastStarts.getFirst() < end1 && lastStarts.getSecond() < end2) { start1 = lastStarts.getFirst(); start2 = lastStarts.getSecond(); } } else if (lastEnds != null) { if (start1 < lastEnds.getFirst() && start2 < lastEnds.getSecond()) { end1 = lastEnds.getFirst(); end2 = lastEnds.getSecond(); } } // Add new feature if (HiCGlobals.splitModeEnabled) { } newFeature = new Feature2D(Feature2D.FeatureType.DOMAIN, chr1, start1, end1, chr2, start2, end2, defaultColor, attributes); lastStarts = null; lastEnds = null; return newFeature; } public Feature2D addFeature(HiC hic) { // Add new feature Feature2D newFeature = generateFeature(hic); annotationLayer.add(hic.getXContext().getChromosome().getIndex(), hic.getYContext().getChromosome().getIndex(), newFeature); return newFeature; } private Feature2D generateTempSelectedGroup(List selectedFeatures, HiC hiC) { Collections.sort(selectedFeatures); Feature2D firstSelectedContig = selectedFeatures.get(0); Feature2D lastSelectedContig = selectedFeatures.get(selectedFeatures.size() - 1); String chrX = hiC.getXContext().getChromosome().getName(); String chrY = hiC.getYContext().getChromosome().getName(); long startX = firstSelectedContig.getStart1(); long startY = firstSelectedContig.getStart2(); long endX = lastSelectedContig.getEnd1(); long endY = lastSelectedContig.getEnd2(); HashMap attributes = new HashMap<>(); return new Feature2D(Feature2D.FeatureType.SELECTED_GROUP, chrX, startX, endX, chrY, startY, endY, getDefaultColor(), attributes); } public Feature2D addTempSelectedGroup(List selectedFeatures, HiC hiC) { Feature2D tempSelectedGroup = generateTempSelectedGroup(selectedFeatures, hiC); annotationLayer.add(hiC.getXContext().getChromosome().getIndex(), hiC.getYContext().getChromosome().getIndex(), tempSelectedGroup); return tempSelectedGroup; } private List getTempSelectedGroups(int chr1Idx, int chr2Idx) { List tempSelectedGroups = new ArrayList<>(); List allVisibleLoops = this.getAllVisibleLoops().getFeatureList(Feature2DList.getKey(chr1Idx, chr2Idx)); if (allVisibleLoops != null) { for (Feature2D feature2D : this.getAllVisibleLoops().getFeatureList(Feature2DList.getKey(chr1Idx, chr2Idx))) { if (feature2D.getFeatureType() == Feature2D.FeatureType.SELECTED_GROUP) { tempSelectedGroups.add(feature2D); } } } return tempSelectedGroups; } public void filterTempSelectedGroup(int chr1Idx, int chr2Idx) { List tempSelectedGroups = getTempSelectedGroups(chr1Idx, chr2Idx); for (Feature2D feature2D : tempSelectedGroups) { this.getAllVisibleLoops().checkAndRemoveFeature(chr1Idx, chr2Idx, feature2D); } } private boolean regionsOverlapSignificantly(long start1, long end1, long start2, long end2, double tolerance) { // must cross diagonal for overlap if ((start1 < end2 && end1 > start2) || (start1 > end2 && end1 < start2)) { double areaFeatureScaled = (end1 - start1) / 100.0 * (end2 - start2) / 100.0; double areaOverlapScaled = Math.pow((Math.min(end1, end2) - Math.max(start1, start2)) / 100.0, 2); return areaOverlapScaled / areaFeatureScaled > tolerance; } return false; } private boolean pointsShouldSnapToDiagonal(HiC hic, int x, int y, int width, int height) { return nearDiagonal(hic, x, y) && nearDiagonal(hic, x + width, y + height) && !allPointsAreOnSameSideOfDiagonal(hic, x, y, width, height); } /** * assumes that points are on same chromosome * * @param hic * @param x * @param y * @param width * @param height * @return */ private boolean allPointsAreOnSameSideOfDiagonal(HiC hic, int x, int y, int width, int height) { int x1 = getXBin(hic, x); int y1 = getYBin(hic, y); int x2 = getXBin(hic, x + width); int y2 = getYBin(hic, y + height); // if this has been called, we can assume that x1,y1 and x2,y2 are near the diagonal // now we need to check if x1,y2 and x2,y1 are on the same side of the diagonal or not // if they are on same side of diagonal, don't snap to grid // i.e. xy for all points // if x1,y2 and x2,y1 are on the same side, then x1,y1 and x2,y2 will be on that side as well (rectangle) return (x1 < y2 && x2 < y1) || (x1 > y2 && x2 > y1); } /* public void addVisibleLoops(HiC hic) { try { hic.getZd(); } catch (Exception e) { return; } if (hic.getXContext() == null || hic.getYContext() == null) return; java.util.List loops = hic.getAllVisibleLoops(); if (loops == null) return; if (customAnnotation == null) { System.err.println("Error! Custom annotations should not be null!"); return; } // Add each loop list to the custom annotation list if (loops.size() > 0) { setExportAbility(true); for (Feature2DList list : loops) { customAnnotation.addVisibleToCustom(list); } } } */ public void undo(JButton undoButton) { annotationLayer.undo(); if (lastResizeLoop != null) { annotationLayer.add(lastChr1Idx, lastChr2Idx, lastResizeLoop); resetSelection(); } undoButton.setEnabled(false); } private boolean nearDiagonal(HiC hic, int x, int y) { int start1 = getXBin(hic, x); int start2 = getYBin(hic, y); int threshold = 15; return Math.abs(start1 - start2) < threshold; } /* TODO - consider scaling threshold with resolution? private int getThreshold(HiC hic) { try{ return (int)Math.ceil(threshold*Math.log(hic.getZd().getBinSize())); } catch (Exception e){ return threshold; } } */ //helper for getannotatemenu private long geneXPos(HiC hic, int x, int displacement) { try { final MatrixZoomData zd = hic.getZd(); if (zd == null) return -1; HiCGridAxis xGridAxis = zd.getXGridAxis(); int binX = getXBin(hic, x) + displacement; return xGridAxis.getGenomicStart(binX); } catch (Exception e) { return -1; } } //helper for getannotatemenu private long geneYPos(HiC hic, int y, int displacement) { try { final MatrixZoomData zd = hic.getZd(); if (zd == null) return -1; HiCGridAxis yGridAxis = zd.getYGridAxis(); int binY = getYBin(hic, y) + displacement; return yGridAxis.getGenomicStart(binY); } catch (Exception e) { return -1; } } private int getXBin(HiC hic, int x) { return (int) (hic.getXContext().getBinOrigin() + x / hic.getScaleFactor()); } private int getYBin(HiC hic, int y) { return (int) (hic.getYContext().getBinOrigin() + y / hic.getScaleFactor()); } public boolean getLayerVisibility() { return annotationLayer.getLayerVisibility(); } public void setLayerVisibility(boolean showCustom) { annotationLayer.setLayerVisibility(showCustom); } public AnnotationLayer.LayerType getAnnotationLayerType() { return annotationLayer.getLayerType(); } public void clearAnnotations() { annotationLayer.clearAnnotations(); } public AnnotationLayer getAnnotationLayer() { return annotationLayer; } private void setAnnotationLayer(AnnotationLayer annotationLayer) { this.annotationLayer = annotationLayer; } public List getNearbyFeatures(MatrixZoomData zd, int chr1Idx, int chr2Idx, int centerX, int centerY, int numberOfLoopsToFind, double binOriginX, double binOriginY, double scaleFactor) { return annotationLayer.getNearbyFeatures(zd, chr1Idx, chr2Idx, centerX, centerY, numberOfLoopsToFind, binOriginX, binOriginY, scaleFactor); } private List getIntersectingFeatures(int chr1Idx, int chr2Idx, net.sf.jsi.Rectangle selectionWindow) { return annotationLayer.getIntersectingFeatures(chr1Idx, chr2Idx, selectionWindow); } /* * Gets the contained features within the selection region, including the features that the * selection starts and ends in */ public List getSelectedFeatures(HiC hic, int lastX, int lastY) { List selectedFeatures = new ArrayList<>(); int chr1Idx = hic.getXContext().getChromosome().getIndex(); int chr2Idx = hic.getYContext().getChromosome().getIndex(); boolean previousStatus = annotationLayer.getFeatureHandler().getIsSparsePlottingEnabled(); // Multiple regions selected if (selectionRegion != null) { long startX, endX; long startY, endY; int x = selectionRegion.x; int width = selectionRegion.width; int y = selectionRegion.y; int height = selectionRegion.height; // Get starting chrX and ending chrX and window startX = geneXPos(hic, x, 0); endX = geneXPos(hic, x + width, 0); // Get starting chrY and ending chrY and window startY = geneYPos(hic, y, 0); endY = geneYPos(hic, y + height, 0); net.sf.jsi.Rectangle selectionWindow = new net.sf.jsi.Rectangle(startX, startY, endX, endY); try { //annotationLayer.getFeatureHandler().setSparsePlottingEnabled(true); // Get features that are both contained by and touching (nearest single neighbor) // the selection rectangle List intersectingFeatures = getIntersectingFeatures(chr1Idx, chr2Idx, selectionWindow); selectedFeatures.addAll(intersectingFeatures); annotationLayer.getFeatureHandler().setSparsePlottingEnabled(previousStatus); } catch (Exception e) { //annotationLayer.getFeatureHandler().setSparsePlottingEnabled(false); selectionRegion = null; return selectedFeatures; } selectionRegion = null; return new ArrayList<>(new HashSet<>(selectedFeatures)); // Single region selected } else { try { // Find feature that contains selection point annotationLayer.getFeatureHandler().setSparsePlottingEnabled(true); selectedFeatures.addAll(selectSingleRegion(chr1Idx, chr2Idx, lastX, lastY, hic.getZd(), hic)); annotationLayer.getFeatureHandler().setSparsePlottingEnabled(previousStatus); } catch (Exception e) { System.out.println("error:" + e); annotationLayer.getFeatureHandler().setSparsePlottingEnabled(false); return selectedFeatures; } return selectedFeatures; } } private List selectSingleRegion(int chr1Idx, int chr2Idx, int unscaledX, int unscaledY, MatrixZoomData zd, HiC hic) { List selectedFeatures = new ArrayList<>(); final HiCGridAxis xAxis = zd.getXGridAxis(); final HiCGridAxis yAxis = zd.getYGridAxis(); final double binOriginX = hic.getXContext().getBinOrigin(); final double binOriginY = hic.getYContext().getBinOrigin(); final double scale = hic.getScaleFactor(); long x = (long) (((unscaledX / scale) + binOriginX) * xAxis.getBinSize()); long y = (long) (((unscaledY / scale) + binOriginY) * yAxis.getBinSize()); Feature2DList features = this.getAnnotationLayer().getFeatureHandler().getAllVisibleLoops(); List contigs = features.get(chr1Idx, chr2Idx); for (Feature2D feature2D : contigs) { if (feature2D.containsPoint(x, y)) { selectedFeatures.add(feature2D); } } return selectedFeatures; } public void removeFromList(MatrixZoomData zd, int chr1Idx, int chr2Idx, int centerX, int centerY, int numberOfLoopsToFind, double binOriginX, double binOriginY, double scaleFactor, Feature2D feature) { annotationLayer.removeFromList(zd, chr1Idx, chr2Idx, centerX, centerY, numberOfLoopsToFind, binOriginX, binOriginY, scaleFactor, feature); } public boolean hasLoop(MatrixZoomData zd, int chr1Idx, int chr2Idx, int centerX, int centerY, int numberOfLoopsToFind, double binOriginX, double binOriginY, double scaleFactor, Feature2D feature) { return annotationLayer.hasLoop(zd, chr1Idx, chr2Idx, centerX, centerY, numberOfLoopsToFind, binOriginX, binOriginY, scaleFactor, feature); } public String getLayerName() { return layerName; } public void setLayerNameAndOtherField(String layerName) { this.layerName = layerName; if (miniNameLabel != null) { miniNameLabel.setText(MiniAnnotationsLayerPanel.shortenedName(layerName)); miniNameLabel.setToolTipText(layerName); } } public void setLayerNameAndField(String layerName) { setLayerNameAndOtherField(layerName); if (nameTextField != null) { nameTextField.setText(layerName); } } public Feature2DHandler getFeatureHandler() { return annotationLayer.getFeatureHandler(); } public boolean getIsTransparent() { return getFeatureHandler().getIsTransparent(); } public void setIsTransparent(boolean isTransparent) { getFeatureHandler().setIsTransparent(isTransparent); } public boolean getIsEnlarged() { return getFeatureHandler().getIsEnlarged(); } public void setIsEnlarged(boolean isEnlarged) { getFeatureHandler().setIsEnlarged(isEnlarged); } public FeatureRenderer.PlottingOption getPlottingStyle() { return plottingStyle; } public void setPlottingStyle(FeatureRenderer.PlottingOption plottingStyle) { this.plottingStyle = plottingStyle; for (PlottingStyleButton button : plottingStyleButtons) { button.setCurrentState(plottingStyle); } } public void exportAnnotations() { new SaveAnnotationsDialog(getAnnotationLayer(), getLayerName()); } private boolean getImportAnnotationsEnabled() { return importAnnotationsEnabled; } public void setImportAnnotationsEnabled(boolean status) { importAnnotationsEnabled = status; if (importAnnotationsButton != null) { importAnnotationsButton.setEnabled(importAnnotationsEnabled); } } public void loadLoopList(String path, ChromosomeHandler chromosomeHandler) { Feature2DHandler.resultContainer result = getFeatureHandler().setLoopList(path, chromosomeHandler); if (result.n > 0) { setExportAbility(true); if (result.color != null) { setDefaultColor(result.color); } } } public Feature2DList getAllVisibleLoops() { return getFeatureHandler().getAllVisibleLoops(); } public void setExportAbility(boolean allowed) { canExport = allowed; if (exportButton != null) { exportButton.setEnabled(true); } if (censorButton != null) { censorButton.setEnabled(true); } } public void setExportButton(JButton exportButton) { this.exportButton = exportButton; } public void setCensorButton(JButton censorButton) { this.censorButton = censorButton; } public boolean getExportCapability() { return canExport; } public void setUndoAbility(boolean allowed) { canUndo = allowed; if (undoButton != null) { undoButton.setEnabled(true); } } public void setUndoButton(JButton undoButton) { this.undoButton = undoButton; } public boolean getUndoCapability() { return canUndo; } public boolean isActiveLayer(SuperAdapter superAdapter) { return annotationLayer.getId() == superAdapter.getActiveLayerHandler().getAnnotationLayer().getId(); } public void setActiveLayerButtonStatus(boolean status) { for (JToggleButton button : activeLayerButtons) { button.setSelected(status); button.revalidate(); } } public void setActiveLayerButton(JToggleButton activeLayerButton) { activeLayerButtons.add(activeLayerButton); } public int getNumberOfFeatures() { return annotationLayer.getNumberOfFeatures(); } public void setColorOfAllAnnotations(Color color) { setDefaultColor(color); annotationLayer.setColorOfAllAnnotations(color); } public Color getDefaultColor() { return defaultColor; } private void setDefaultColor(Color defaultColor) { this.defaultColor = defaultColor; if (colorChooserPanels.size() > 0) { for (ColorChooserPanel colorChooserPanel : colorChooserPanels) colorChooserPanel.setSelectedColor(defaultColor); } } public void setDeleteLayerButtonStatus(boolean status) { if (deleteLayerButton != null) { deleteLayerButton.setEnabled(status); deleteLayerButton.revalidate(); } } public void setDeleteLayerButton(JButton deleteLayerButton) { this.deleteLayerButton = deleteLayerButton; } public boolean getIsSparse() { return annotationLayer.getIsSparse(); } public void setIsSparse(boolean isSparse) { annotationLayer.setIsSparse(isSparse); } public FeatureRenderer.LineStyle getLineStyle() { return this.lineStyle; } public void setLineStyle(FeatureRenderer.LineStyle lineStyle) { this.lineStyle = lineStyle; } public void duplicateDetailsFrom(AnnotationLayerHandler handlerOriginal) { featureType = handlerOriginal.featureType; System.out.println("...p..."); setLayerNameAndField("Copy of " + handlerOriginal.getLayerName()); setLayerVisibility(handlerOriginal.getLayerVisibility()); setDefaultColor(handlerOriginal.getDefaultColor()); setIsTransparent(handlerOriginal.getIsTransparent()); setIsEnlarged(handlerOriginal.getIsEnlarged()); setPlottingStyle(handlerOriginal.getPlottingStyle()); Feature2DList origLists = handlerOriginal.getAnnotationLayer().getFeatureList(); annotationLayer.createMergedLoopLists(origLists.deepCopy()); setImportAnnotationsEnabled(handlerOriginal.getImportAnnotationsEnabled()); setExportAbility(handlerOriginal.getExportCapability()); setIsSparse(handlerOriginal.getIsSparse()); } public void mergeDetailsFrom(Collection originalHandlers) { StringBuilder cleanedTitle = new StringBuilder(); List allLists = new ArrayList<>(); for (AnnotationLayerHandler originalHandler : originalHandlers) { featureType = originalHandler.featureType; allLists.add(originalHandler.getAnnotationLayer().getFeatureList()); cleanedTitle.append("-").append(originalHandler.getLayerName().toLowerCase().replaceAll("layer", "").replaceAll("\\s", "")); setLayerVisibility(originalHandler.getLayerVisibility()); setColorOfAllAnnotations(originalHandler.getDefaultColor()); importAnnotationsEnabled |= originalHandler.getImportAnnotationsEnabled(); canExport |= originalHandler.getExportCapability(); } annotationLayer.createMergedLoopLists(allLists); setExportAbility(canExport); setLayerNameAndField("Merger" + cleanedTitle); } public void togglePlottingStyle() { try { plottingStyleButtons.get(0).doClick(); } catch (Exception e) { setPlottingStyle(FeatureRenderer.getNextState(getPlottingStyle())); } } public void setPlottingStyleButton(PlottingStyleButton plottingStyleButton) { plottingStyleButtons.add(plottingStyleButton); } public void setColorChooserPanel(ColorChooserPanel colorChooserPanel) { colorChooserPanels.add(colorChooserPanel); } public void setNameTextField(JTextField nameTextField) { this.nameTextField = nameTextField; } public void setMiniNameLabelField(JLabel miniNameLabel) { this.miniNameLabel = miniNameLabel; } public void setProperties(AnnotationLayer scaffoldLayer, String name, Color color) { setAnnotationLayer(scaffoldLayer); setLayerNameAndField(name); setColorOfAllAnnotations(color); } public List convertToFeaturePairs(AnnotationLayerHandler handler, List loops, MatrixZoomData zd, double binOriginX, double binOriginY, double scaleFactor) { return annotationLayer.getFeatureHandler().convertFeaturesToFeaturePairs(handler, loops, zd, binOriginX, binOriginY, scaleFactor); } } ================================================ FILE: src/juicebox/track/feature/CustomAnnotationRTree2DHandler.java ================================================ /* * The MIT License (MIT) * * Copyright (c) 2011-2020 Broad Institute, Aiden Lab, Rice University, Baylor College of Medicine * * Permission is hereby granted, free of charge, to any person obtaining a copy * of this software and associated documentation files (the "Software"), to deal * in the Software without restriction, including without limitation the rights * to use, copy, modify, merge, publish, distribute, sublicense, and/or sell * copies of the Software, and to permit persons to whom the Software is * furnished to do so, subject to the following conditions: * * The above copyright notice and this permission notice shall be included in * all copies or substantial portions of the Software. * * THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR * IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, * FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE * AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER * LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, * OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN * THE SOFTWARE. */ package juicebox.track.feature; import juicebox.mapcolorui.Feature2DHandler; import java.io.File; import java.io.PrintWriter; import java.util.ArrayList; import java.util.List; /** * Created by muhammadsaadshamim on 11/2/16. */ class CustomAnnotationRTree2DHandler extends Feature2DHandler { public CustomAnnotationRTree2DHandler(Feature2DList inputList) { clearLists(); setLoopList(inputList); } public void add(int chr1Idx, int chr2Idx, Feature2D feature) { loopList.add(chr1Idx, chr2Idx, feature); // TODO can be optimized further i.e. no need to remake entire rtree, just add necessary nodes remakeRTree(); } public int getNumberOfFeatures() { return loopList.getNumTotalFeatures(); } public void addAttributeFieldToAll(String key, String aNull) { loopList.addDefaultAttribute(key, aNull); } /** * Export feature list to given file path * * @param outputFile */ public void autoSaveNew(PrintWriter outputFile, Feature2D feature) { loopList.autoSaveNew(outputFile, feature); } /** * Export feature list to given file path * * @param outputFile */ public void autoSaveAll(PrintWriter outputFile) { loopList.autoSaveAll(outputFile); } public boolean checkAndRemoveFeature(int idx1, int idx2, Feature2D feature2D) { boolean somethingWasDeleted = loopList.checkAndRemoveFeature(idx1, idx2, feature2D); if (somethingWasDeleted) remakeRTree(); // TODO can be optimized further i.e. no need to remake entire rtree, just delete necessary nodes return somethingWasDeleted; } public Feature2DList getOverlap(Feature2DList inputList) { Feature2DList overlapFeature2DList = new Feature2DList(); overlapFeature2DList.add(loopList.getOverlap(inputList)); return overlapFeature2DList; } public Feature2D extractSingleFeature() { //noinspection LoopStatementThatDoesntLoop return loopList.extractSingleFeature(); } public List get(int chrIdx1, int chrIdx2) { return new ArrayList<>(loopList.get(chrIdx1, chrIdx2)); } public boolean exportFeatureList(File file, boolean b, Feature2DList.ListFormat na) { Feature2DList mergedList = new Feature2DList(); mergedList.add(loopList); return mergedList.exportFeatureList(file, b, na); } } ================================================ FILE: src/juicebox/track/feature/Feature2D.java ================================================ /* * The MIT License (MIT) * * Copyright (c) 2011-2021 Broad Institute, Aiden Lab, Rice University, Baylor College of Medicine * * Permission is hereby granted, free of charge, to any person obtaining a copy * of this software and associated documentation files (the "Software"), to deal * in the Software without restriction, including without limitation the rights * to use, copy, modify, merge, publish, distribute, sublicense, and/or sell * copies of the Software, and to permit persons to whom the Software is * furnished to do so, subject to the following conditions: * * The above copyright notice and this permission notice shall be included in * all copies or substantial portions of the Software. * * THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR * IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, * FITNESS FOR A PARTICULAR PURPOSE AND NON-INFRINGEMENT. IN NO EVENT SHALL THE * AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER * LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, * OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN * THE SOFTWARE. */ package juicebox.track.feature; import juicebox.HiCGlobals; import juicebox.assembly.AssemblyHeatmapHandler; import juicebox.assembly.Scaffold; import juicebox.data.ChromosomeHandler; import juicebox.data.anchor.MotifAnchor; import juicebox.tools.utils.juicer.arrowhead.ArrowheadScore; import juicebox.tools.utils.juicer.hiccups.HiCCUPSUtils; import java.awt.*; import java.text.DecimalFormat; import java.text.NumberFormat; import java.util.List; import java.util.*; /** * @author jrobinso, mshamim, mhoeger *

* reflection only used for plotting, should not be used by CLTs */ public class Feature2D implements Comparable { static final String genericHeader = "#chr1\tx1\tx2\tchr2\ty1\ty2\tname\tscore\tstrand1\tstrand2\tcolor"; private static final String genericLegacyHeader = "#chr1\tx1\tx2\tchr2\ty1\ty2\tcolor"; private static final String BEDPE_SPACER = "\t.\t.\t.\t."; private static final String[] categories = new String[]{"observed", "coordinate", "enriched", "expected", "fdr"}; public static int tolerance = 0; public static boolean allowHiCCUPSOrdering = false; final FeatureType featureType; final Map attributes; final String chr1; final String chr2; private final NumberFormat formatter = NumberFormat.getInstance(); final long start1; final long start2; long end1; long end2; private boolean isSelected = false; private Feature2D reflection = null; private Color color, translucentColor; public Feature2D(FeatureType featureType, String chr1, long start1, long end1, String chr2, long start2, long end2, Color c, Map attributes) { this.featureType = featureType; this.chr1 = chr1; this.start1 = start1; this.end1 = end1; this.chr2 = chr2; this.start2 = start2; this.end2 = end2; this.color = (c == null ? Color.black : c); setTranslucentColor(); this.attributes = attributes; } public static String getDefaultOutputFileHeader() { if (HiCGlobals.isLegacyOutputPrintingEnabled) { return genericLegacyHeader; } else { return genericHeader; } } public FeatureType getFeatureType() { return this.featureType; } private String getFeatureName() { if (featureType == FeatureType.PEAK) { return "Peak"; } if (featureType == FeatureType.DOMAIN) { return "Contact Domain"; } return "Feature"; } public String getChr1() { return chr1; } public String getChr2() { return chr2; } public long getStart1() { return start1; } public long getStart2() { return start2; } public long getEnd1() { return end1; } public void setEnd1(int end1) { this.end1 = end1; if (reflection != null) reflection.end2 = end1; } public long getEnd2() { return end2; } public void setEnd2(int end2) { this.end2 = end2; if (reflection != null) reflection.end1 = end2; } public long getWidth1() { return end1 - start1; } public long getWidth2() { return end2 - start2; } public long getMidPt1() { return midPoint(start1, end1); } public long getMidPt2() { return midPoint(start2, end2); } private long midPoint(long start, long end) { return (long) (start + (end - start) / 2.0); } public Color getColor() { if (isSelected) { return Color.DARK_GRAY; } else { return color; } } public void setColor(Color color) { this.color = color; if (reflection != null) reflection.color = color; setTranslucentColor(); } public Color getTranslucentColor() { if (isSelected) { return Color.DARK_GRAY; } else { return translucentColor; } } private void setTranslucentColor() { translucentColor = new Color(color.getRed(), color.getGreen(), color.getBlue(), 50); if (reflection != null) reflection.translucentColor = translucentColor; } public String tooltipText() { String scaledStart1 = formatter.format(start1 * HiCGlobals.hicMapScale + 1); String scaledStart2 = formatter.format(start2 * HiCGlobals.hicMapScale + 1); String scaledEnd1 = formatter.format(end1 * HiCGlobals.hicMapScale); String scaledEnd2 = formatter.format(end2 * HiCGlobals.hicMapScale); if (getFeatureType() == FeatureType.SCAFFOLD) { Scaffold scaffold = AssemblyHeatmapHandler.getSuperAdapter().getAssemblyStateTracker().getAssemblyHandler().getScaffoldFromFeature(this); scaledStart1 = formatter.format(scaffold.getCurrentStart() + 1); scaledStart2 = formatter.format(scaffold.getCurrentStart() + 1); scaledEnd1 = formatter.format(scaffold.getCurrentEnd()); scaledEnd2 = formatter.format(scaffold.getCurrentEnd()); } StringBuilder txt = new StringBuilder(); txt.append(""); txt.append(getFeatureName()); txt.append("
"); txt.append(""); txt.append(chr1).append(":").append(scaledStart1); if ((end1 - start1) > 1) { txt.append("-").append(scaledEnd1); } txt.append("
"); txt.append(""); txt.append(chr2).append(":").append(scaledStart2); if ((end2 - start2) > 1) { txt.append("-").append(scaledEnd2); } txt.append(""); DecimalFormat df = new DecimalFormat("#.##"); if (HiCGlobals.allowSpacingBetweenFeatureText) { // organize attributes into categories. +1 is for the leftover category if no keywords present ArrayList>> sortedFeatureAttributes = new ArrayList<>(); for (int i = 0; i < categories.length + 1; i++) { sortedFeatureAttributes.add(new ArrayList<>()); } // sorting the entries, also filtering out f1-f5 flags for (Map.Entry entry : attributes.entrySet()) { String tmpKey = entry.getKey(); boolean categoryHasBeenAssigned = false; for (int i = 0; i < categories.length; i++) { if (tmpKey.contains(categories[i])) { sortedFeatureAttributes.get(i).add(entry); categoryHasBeenAssigned = true; break; } } if (!categoryHasBeenAssigned) { sortedFeatureAttributes.get(categories.length).add(entry); } } // append to tooltip text, but now each category is spaced apart for (ArrayList> attributeCategory : sortedFeatureAttributes) { if (attributeCategory.isEmpty()) continue; //sort attributes before printing Comparator> cmp = new Comparator>() { @Override public int compare(Map.Entry o1, Map.Entry o2) { return o1.getKey().compareToIgnoreCase(o2.getKey()); } }; attributeCategory.sort(cmp); for (Map.Entry entry : attributeCategory) { String tmpKey = entry.getKey(); txt.append("
"); txt.append(""); txt.append(tmpKey); txt.append(" = "); try { txt.append(df.format(Double.valueOf(entry.getValue()))); } catch (Exception e) { txt.append(entry.getValue()); // for text i.e. non-decimals } txt.append(""); txt.append(""); } txt.append("
"); // the extra spacing between categories } } else { // simple text dump for plotting, no spacing or rearranging by category for (Map.Entry entry : attributes.entrySet()) { String tmpKey = entry.getKey(); if (!(tmpKey.equals("f1") || tmpKey.equals("f2") || tmpKey.equals("f3") || tmpKey.equals("f4") || tmpKey.equals("f5"))) { txt.append("
"); txt.append(""); txt.append(tmpKey); txt.append(" = "); //System.out.println(entry.getValue()); try { txt.append(df.format(Double.valueOf(entry.getValue()))); } catch (Exception e) { txt.append(entry.getValue()); } txt.append(""); txt.append(""); } } } return txt.toString(); } public String getOutputFileHeader() { StringBuilder output = new StringBuilder(getDefaultOutputFileHeader()); ArrayList keys = new ArrayList<>(attributes.keySet()); Collections.sort(keys); for (String key : keys) { output.append("\t").append(key); } return output.toString(); } private String simpleString() { return chr1 + "\t" + start1 + "\t" + end1 + "\t" + chr2 + "\t" + start2 + "\t" + end2; } private String justColorString() { return "\t" + color.getRed() + "," + color.getGreen() + "," + color.getBlue(); } public String simpleStringWithColor() { if (HiCGlobals.isLegacyOutputPrintingEnabled) { return simpleString() + justColorString(); } else if (this.containsAttributeKey("score")) { return simpleString() + "\t.\t" + this.attributes.get("score") + "\t.\t." + justColorString(); } else { return simpleString() + BEDPE_SPACER + justColorString(); } } @Override public String toString() { StringBuilder output = new StringBuilder(simpleStringWithColor()); ArrayList keys = new ArrayList<>(attributes.keySet()); Collections.sort(keys); for (String key : keys) { output.append("\t").append(attributes.get(key)); } return output.toString(); } public ArrayList getAttributeKeys() { ArrayList keys = new ArrayList<>(attributes.keySet()); Collections.sort(keys); return keys; } public String getAttribute(String key) { return attributes.get(key); } public void setAttribute(String key, String newVal) { attributes.put(key, newVal); // attribute directly shared between reflections if (reflection != null) reflection.attributes.put(key, newVal); } public float getFloatAttribute(String key) { return Float.parseFloat(attributes.get(key)); } public void addIntAttribute(String key, int value) { attributes.put(key, "" + value); } public void addFloatAttribute(String key, Float value) { attributes.put(key, "" + value); } public void addStringAttribute(String key, String value) { attributes.put(key, value); } /** * @param otherFeature * @return */ public boolean overlapsWith(Feature2D otherFeature) { float window1 = (otherFeature.getEnd1() - otherFeature.getStart1()) / 2; float window2 = (otherFeature.getEnd2() - otherFeature.getStart2()) / 2; long midOther1 = otherFeature.getMidPt1(); long midOther2 = otherFeature.getMidPt2(); return midOther1 >= (this.start1 - window1) && midOther1 <= (this.end1 + window1) && midOther2 >= (this.start2 - window2) && midOther2 <= (this.end2 + window2); } @Override public int compareTo(Feature2D o) { // highest observed point ordering needed for hiccups sorting if (allowHiCCUPSOrdering && attributes.containsKey(HiCCUPSUtils.OBSERVED) && o.attributes.containsKey(HiCCUPSUtils.OBSERVED)) { float val = Float.parseFloat(getAttribute(HiCCUPSUtils.OBSERVED)) - Float.parseFloat(o.getAttribute(HiCCUPSUtils.OBSERVED)); if (val > 0) return 1; if (val < 0) return -1; } long[] comparisons = new long[]{chr1.compareTo(o.chr1), chr2.compareTo(o.chr2), start1 - o.start1, start2 - o.start2, end1 - o.end1, end2 - o.end2}; for (long i : comparisons) { if (i != 0) if (i > 0) { return 1; } else { return -1; } } return 0; } public boolean isOnDiagonal() { return chr1.equals(chr2) && start1 == start2 && end1 == end2; } public Feature2D reflectionAcrossDiagonal() { if (reflection == null) { reflection = new Feature2D(featureType, chr2, start2, end2, chr1, start1, end1, color, attributes); reflection.reflection = this; } return reflection; } public boolean isInLowerLeft() { return chr1.equals(chr2) && start2 > start1; } public boolean isInUpperRight() { return chr1.equals(chr2) && start2 < start1; } public boolean doesNotContainAttributeKey(String attribute) { return !attributes.containsKey(attribute); } public boolean containsAttributeValue(String attribute) { return attributes.containsValue(attribute); } public boolean containsAttributeKey(String attribute) { return attributes.containsKey(attribute); } public String getLocationKey() { return start1 + "_" + start2; } public ArrowheadScore toArrowheadScore() { long[] indices = new long[]{start1, end1, start2, end2}; return new ArrowheadScore(indices); } @Override public boolean equals(Object obj) { if (obj == null) { return false; } if (getClass() != obj.getClass()) { return false; } if (this == obj) { return true; } final Feature2D other = (Feature2D) obj; if (chr1.equals(other.chr1)) { if (chr2.equals(other.chr2)) { if (Math.abs(start1 - other.start1) <= tolerance) { if (Math.abs(start2 - other.start2) <= tolerance) { if (Math.abs(end1 - other.end1) <= tolerance) { return Math.abs(end2 - other.end2) <= tolerance; } } } } } return false; } @Override public int hashCode() { return Objects.hash(chr1, end1, start1, chr2, end2, start2); } public void clearAttributes() { attributes.clear(); } public List getAnchors(boolean onlyUninitializedFeatures, ChromosomeHandler handler) { List originalFeatures = new ArrayList<>(); originalFeatures.add(this); List anchors = new ArrayList<>(); if (isOnDiagonal()) { // loops should not be on diagonal // anchors.add(new MotifAnchor(chr1, start1, end1, originalFeatures, originalFeatures)); } else { List emptyList = new ArrayList<>(); anchors.add(new MotifAnchor(chr1, start1, end1, originalFeatures, emptyList)); anchors.add(new MotifAnchor(chr2, start2, end2, emptyList, originalFeatures)); } return anchors; } public Feature2D deepCopy() { Map attrClone = new HashMap<>(); for (String key : attributes.keySet()) { attrClone.put(key, attributes.get(key)); } return new Feature2D(featureType, chr1, start1, end1, chr2, start2, end2, color, attrClone); } public void setSetIsSelectedColorUpdate(boolean setIsSelectedColorUpdate) { isSelected = setIsSelectedColorUpdate; } public Feature2DWithMotif toFeature2DWithMotif() { return new Feature2DWithMotif(featureType, chr1, start1, end1, chr2, start2, end2, color, attributes); } public boolean containsPoint(float x, float y) { return start1 <= x && x <= end1 && start2 <= y && y <= end2; } public boolean containsPoint(Point point) { return containsPoint(point.x, point.y); } public enum FeatureType { NONE, PEAK, DOMAIN, GENERIC, SCAFFOLD, SUPERSCAFFOLD, SELECTED_GROUP } } ================================================ FILE: src/juicebox/track/feature/Feature2DGuiContainer.java ================================================ /* * The MIT License (MIT) * * Copyright (c) 2011-2021 Broad Institute, Aiden Lab, Rice University, Baylor College of Medicine * * Permission is hereby granted, free of charge, to any person obtaining a copy * of this software and associated documentation files (the "Software"), to deal * in the Software without restriction, including without limitation the rights * to use, copy, modify, merge, publish, distribute, sublicense, and/or sell * copies of the Software, and to permit persons to whom the Software is * furnished to do so, subject to the following conditions: * * The above copyright notice and this permission notice shall be included in * all copies or substantial portions of the Software. * * THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR * IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, * FITNESS FOR A PARTICULAR PURPOSE AND NON-INFRINGEMENT. IN NO EVENT SHALL THE * AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER * LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, * OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN * THE SOFTWARE. */ package juicebox.track.feature; import java.awt.*; /** * Created by nathanielmusial on 6/26/17. */ public class Feature2DGuiContainer { private final Rectangle rectangle; private final Feature2D feature2D; private final AnnotationLayerHandler annotationLayerHandler; public Feature2DGuiContainer(Rectangle rectangle, Feature2D feature2D, AnnotationLayerHandler annotationLayerHandler) { this.rectangle = rectangle; this.feature2D = feature2D; this.annotationLayerHandler = annotationLayerHandler; } public Rectangle getRectangle() { return rectangle; } public Feature2D getFeature2D() { return feature2D; } public AnnotationLayerHandler getAnnotationLayerHandler() { return annotationLayerHandler; } } ================================================ FILE: src/juicebox/track/feature/Feature2DList.java ================================================ /* * The MIT License (MIT) * * Copyright (c) 2011-2021 Broad Institute, Aiden Lab, Rice University, Baylor College of Medicine * * Permission is hereby granted, free of charge, to any person obtaining a copy * of this software and associated documentation files (the "Software"), to deal * in the Software without restriction, including without limitation the rights * to use, copy, modify, merge, publish, distribute, sublicense, and/or sell * copies of the Software, and to permit persons to whom the Software is * furnished to do so, subject to the following conditions: * * The above copyright notice and this permission notice shall be included in * all copies or substantial portions of the Software. * * THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR * IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, * FITNESS FOR A PARTICULAR PURPOSE AND NON-INFRINGEMENT. IN NO EVENT SHALL THE * AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER * LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, * OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN * THE SOFTWARE. */ package juicebox.track.feature; import juicebox.HiCGlobals; import juicebox.data.HiCFileTools; import juicebox.data.basics.Chromosome; import java.awt.*; import java.io.File; import java.io.PrintWriter; import java.util.List; import java.util.*; import java.util.concurrent.ExecutorService; import java.util.concurrent.Executors; /** * List of two-dimensional features. Hashtable for each chromosome for quick viewing. * Visibility depends on user selection. * * @author Neva Durand, Muhammad Shamim, Marie Hoeger *

* TODO cleanup code and eliminate this class * It should become GenomeWideList * Helper functions should be relocated to Feature2DTools */ public class Feature2DList { /** * List of 2D features stored by chromosome */ private final Map> featureList = new HashMap<>(); private Map defaultAttributes = new HashMap<>(); public void parallelizedProcessLists(FeatureFunction featureFunction) { List keys = new ArrayList<>(featureList.keySet()); Collections.sort(keys); ExecutorService executor = Executors.newFixedThreadPool(keys.size()); for (String key : keys) { Runnable worker = new Runnable() { @Override public void run() { featureFunction.process(key, featureList.get(key)); } }; executor.execute(worker); } executor.shutdown(); while (!executor.isTerminated()) { } } /** * pass interface implementing a filter for features * * @param filter */ public synchronized void filterLists(FeatureFilter filter) { List keys = new ArrayList<>(featureList.keySet()); Collections.sort(keys); for (String key : keys) { featureList.put(key, filter.filter(key, featureList.get(key))); } } public Feature2DList() { } public Feature2DList(Feature2DList list) { add(list); defaultAttributes.putAll(list.defaultAttributes); } /** * Helper method to get the key, lowest ordinal chromosome first * * @param chr1Idx First chromosome index * @param chr2Idx Second chromosome index * @return key */ public static String getKey(int chr1Idx, int chr2Idx) { int c1; int c2; if (chr1Idx < chr2Idx) { c1 = chr1Idx; c2 = chr2Idx; } else { c1 = chr2Idx; c2 = chr1Idx; } return "" + c1 + "_" + c2; } /** * Helper method to get the key given chromosomes * * @param chr1 First chromosome * @param chr2 Second chromosome * @return key */ public static String getKey(Chromosome chr1, Chromosome chr2) { return getKey(chr1.getIndex(), chr2.getIndex()); } /** * values from list A that are common to list B within tolerance * * @param listA * @param listB * @return */ public static Feature2DList getIntersection(final Feature2DList listA, Feature2DList listB) { Feature2DList commonFeatures = new Feature2DList(listB); commonFeatures.filterLists(new FeatureFilter() { @Override public List filter(String chr, List feature2DList) { List commonVals = new ArrayList<>(); if (listA.containsKey(chr)) { List listAFeatures = listA.getFeatureList(chr); for (Feature2D feature : listAFeatures) { if (feature2DList.contains(feature)) { commonVals.add(feature); } } } return commonVals; } }); commonFeatures.removeDuplicates(); return commonFeatures; } // Iterate through new features and see if there is any overlap // TODO: implement this more efficiently, maybe rtree private synchronized static void addAllUnique(List inputFeatures, List existingFeatures) { for (Feature2D inputFeature : inputFeatures) { // Compare input with existing points if (!Feature2DTools.doesOverlap(inputFeature, existingFeatures)) { existingFeatures.add(inputFeature); } } } /** * Returns list of features on this chromosome pair * * @param chr1Idx First chromosome index * @param chr2Idx Second chromosome index * @return List of 2D features at that point */ public List get(int chr1Idx, int chr2Idx) { String key = getKey(chr1Idx, chr2Idx); if (!featureList.containsKey(key)) { List features = new ArrayList<>(); featureList.put(key, features); } return featureList.get(key); } /** * Returns list of features on this chromosome pair * Warning, this should be used carefully, assumes proper key nomenclature is used * should only be used when comparing equivalent lists * * @return List of 2D features for given key */ public List get(String key) { if (!featureList.containsKey(key)) { List features = new ArrayList<>(); featureList.put(key, features); } return featureList.get(key); } /** * Adds feature to appropriate chromosome pair list; key stored so that first chromosome always less than second * * @param chr1Idx First chromosome index * @param chr2Idx Second chromosome index * @param feature feature to add */ public synchronized void add(int chr1Idx, int chr2Idx, Feature2D feature) { String key = getKey(chr1Idx, chr2Idx); addByKey(key, feature); } /** * Adds feature to appropriate chromosome pair list; key stored so that first chromosome always less than second * * @param key chromosomal pair key * @param feature to add */ public synchronized void addByKey(String key, Feature2D feature) { feature = updateAttributeForFeature(feature); if (featureList.containsKey(key)) { featureList.get(key).add(feature);//could be an issue } else { List loops = new ArrayList<>(); loops.add(feature); featureList.put(key, loops); } } /** * Adds features to appropriate chromosome pair list; key stored so that first chromosome always less than second * * @param key chromosomal pair key * @param features to add */ public synchronized void addByKey(String key, List features) { features = updateAttributes(features); if (featureList.containsKey(key)) { featureList.get(key).addAll(features); } else { List loops = new ArrayList<>(features); featureList.put(key, loops); } } private synchronized Feature2D updateAttributeForFeature(Feature2D feature) { if (defaultAttributes != null) { if (feature.getAttributeKeys() == null) { for (String attribute : defaultAttributes.keySet()) { feature.addStringAttribute(attribute, defaultAttributes.get(attribute)); System.out.println("Added:1 " + attribute); //TODO find out why this doesn't work } } else { List featureKeys = feature.getAttributeKeys(); for (String customKey : defaultAttributes.keySet()) { if (!featureKeys.contains(customKey)) { feature.addStringAttribute(customKey, defaultAttributes.get(customKey)); } } } } return feature; } private synchronized List updateAttributes(List features) { processLists(new FeatureFunction() { @Override public void process(String chr, List feature2DList) { for (Feature2D feature : feature2DList) { updateAttributeForFeature(feature); } } }); return features; } private synchronized void putFeature(String key, List loops) { featureList.put(key, loops); } /** * Export feature list to given file path * * @param outputFile * @return true if successful */ public boolean exportFeatureList(File outputFile, boolean formattedOutput, ListFormat listFormat) { if (featureList != null && featureList.size() > 0) { final PrintWriter outputFilePrintWriter = HiCFileTools.openWriter(outputFile); if (exportFeatureList(outputFilePrintWriter, formattedOutput, listFormat)) { System.out.println(getNumTotalFeatures() + " features written to file: " + outputFile.getAbsolutePath()); } else { System.err.println("Error features not written to file: " + outputFile.getAbsolutePath()); } return true; } return false; } /** * Export feature list to given file path * * @param outputFilePrintWriter */ private boolean exportFeatureList(final PrintWriter outputFilePrintWriter, final boolean formattedOutput, final ListFormat listFormat) { if (featureList != null && featureList.size() > 0) { Feature2D featureZero = extractSingleFeature(); if (featureZero != null) { if (formattedOutput) { StringBuilder header = new StringBuilder(Feature2D.genericHeader); final ArrayList outputKeys = new ArrayList<>(); if (listFormat == ListFormat.ENRICHED) { outputKeys.addAll(Arrays.asList("observed", "expectedBL", "expectedDonut", "expectedH", "expectedV", "binBL", "binDonut", "binH", "binV", "fdrBL", "fdrDonut", "fdrH", "fdrV")); } else if (listFormat == ListFormat.FINAL) { outputKeys.addAll(Arrays.asList("observed", "expectedBL", "expectedDonut", "expectedH", "expectedV", "fdrBL", "fdrDonut", "fdrH", "fdrV", "numCollapsed", "centroid1", "centroid2", "radius")); } else if (listFormat == ListFormat.LOCALIZED) { if (featureZero.attributes.containsKey("motif_start_1") && featureZero.attributes.containsKey("expectedBL")) { outputKeys.addAll(Arrays.asList("observed", "expectedBL", "expectedDonut", "expectedH", "expectedV", "fdrBL", "fdrDonut", "fdrH", "fdrV", "numCollapsed", "centroid1", "centroid2", "radius", "motif_start_1", "motif_end_1", "sequence_1", "orientation_1", "uniqueness_1", "motif_start_2", "motif_end_2", "sequence_2", "orientation_2", "uniqueness_2", "highRes_start_1", "highRes_end_1", "highRes_start_2", "highRes_end_2", "upstream_start_1", "upstream_end_1", "downstream_start_2", "downstream_end_2", "localX", "localY", "localObserved", "localPval", "localZscore", "localPeakID")); } else if (featureZero.attributes.containsKey("motif_start_1")) { outputKeys.addAll(Arrays.asList("motif_start_1", "motif_end_1", "sequence_1", "orientation_1", "uniqueness_1", "motif_start_2", "motif_end_2", "sequence_2", "orientation_2", "uniqueness_2", "highRes_start_1", "highRes_end_1", "highRes_start_2", "highRes_end_2", "upstream_start_1", "upstream_end_1", "downstream_start_2", "downstream_end_2", "localX", "localY", "localObserved", "localPval", "localZscore", "localPeakID")); } else if (featureZero.attributes.containsKey("expectedBL")){ outputKeys.addAll(Arrays.asList("observed", "expectedBL", "expectedDonut", "expectedH", "expectedV", "fdrBL", "fdrDonut", "fdrH", "fdrV", "numCollapsed", "centroid1", "centroid2", "radius", "highRes_start_1", "highRes_end_1", "highRes_start_2", "highRes_end_2", "upstream_start_1", "upstream_end_1", "downstream_start_2", "downstream_end_2", "localX", "localY", "localObserved", "localPval", "localZscore", "localPeakID")); } else { outputKeys.addAll(Arrays.asList("highRes_start_1", "highRes_end_1", "highRes_start_2", "highRes_end_2", "upstream_start_1", "upstream_end_1", "downstream_start_2", "downstream_end_2", "localX", "localY", "localObserved", "localPval", "localZscore", "localPeakID")); } }else if (listFormat == ListFormat.ARROWHEAD) { outputKeys.addAll(Arrays.asList("score", "uVarScore", "lVarScore", "upSign", "loSign")); } for (String key : outputKeys) { header.append("\t").append(key); } outputFilePrintWriter.println(header); outputFilePrintWriter.println("# juicer_tools version " + HiCGlobals.versionNum); processLists(new FeatureFunction() { @Override public void process(String chr, List feature2DList) { for (Feature2D feature : feature2DList) { StringBuilder output = new StringBuilder(feature.simpleStringWithColor()); for (String key : outputKeys) { output.append("\t").append(feature.attributes.get(key)); } outputFilePrintWriter.println(output); } } }); } else { outputFilePrintWriter.println(featureZero.getOutputFileHeader()); processLists(new FeatureFunction() { @Override public void process(String chr, List feature2DList) { Collections.sort(feature2DList); for (Feature2D feature : feature2DList) { outputFilePrintWriter.println(feature); } } }); } } outputFilePrintWriter.close(); return true; } return false; } /** * Export feature list to given file path * * @param outputFile */ public void autoSaveNew(PrintWriter outputFile, Feature2D feature) { if (featureList != null && featureList.size() > 0) { outputFile.println(feature); } } /** * Export feature list to given file path * * @param outputFile */ public void autoSaveAll(PrintWriter outputFile) { if (featureList != null && featureList.size() > 0) { for (String key : featureList.keySet()) { for (Feature2D feature : featureList.get(key)) { outputFile.println(feature); } } } } /** * Get first feature found * * @return feature */ public Feature2D extractSingleFeature() { for (List features : featureList.values()) { //noinspection LoopStatementThatDoesntLoop for (Feature2D feature : features) { return feature; } } return null; } /* * Set color for the features * @param color */ public void setColor(final Color color) { processLists(new FeatureFunction() { @Override public void process(String chr, List feature2DList) { for (Feature2D feature : feature2DList) { feature.setColor(color); } } }); } /** * Adds features to appropriate chromosome pair list; * key stored so that first chromosome always less than second * * @param inputList * @return */ public synchronized void add(Feature2DList inputList) { Set inputKeySet = inputList.getKeySet(); for (String inputKey : inputKeySet) { List inputFeatures = inputList.getFeatureList(inputKey); if (featureList.containsKey(inputKey)) { featureList.get(inputKey).addAll(inputFeatures); } else { List features = new ArrayList<>(inputFeatures); putFeature(inputKey, features); } } } /** * Adds features to appropriate chromosome pair list if same * or similar point not already in list; * key stored so that first chromosome always less than second * * @param inputList * @return */ public synchronized void addUnique(Feature2DList inputList) { Set inputKeySet = inputList.getKeySet(); for (String inputKey : inputKeySet) { List inputFeatures = inputList.getFeatureList(inputKey); if (featureList.containsKey(inputKey)) { //features.addAll(inputFeatures); addAllUnique(inputFeatures, featureList.get(inputKey)); } else { List features = new ArrayList<>(inputFeatures); // featureList.put(inputKey, features); putFeature(inputKey, features); } } } public Feature2DList getOverlap(Feature2DList inputList) { Feature2DList output = new Feature2DList(); Set inputKeySet = inputList.getKeySet(); for (String inputKey : inputKeySet) { List inputFeatures = inputList.getFeatureList(inputKey); // there are features in both lists if (featureList.containsKey(inputKey)) { for (Feature2D myFeature : featureList.get(inputKey)) { if (Feature2DTools.doesOverlap(myFeature, inputFeatures)) { output.addByKey(inputKey, myFeature); } } } } return output; } public synchronized void setDefaultAttributes(Map defaultAttributes) { this.defaultAttributes = defaultAttributes; } public synchronized void addDefaultAttribute(String attribute, String value) { defaultAttributes.put(attribute, value); addAttributeFieldToAll(attribute, value); } public synchronized void addAttributeFieldToAll(final String newAttributeName, final String newAttributeValue) { processLists(new FeatureFunction() { @Override public void process(String chr, List feature2DList) { for (Feature2D feature : feature2DList) { if (feature.doesNotContainAttributeKey(newAttributeName)) feature.addStringAttribute(newAttributeName, newAttributeValue); } } }); } /** * Simple removal of exact duplicates (memory address) * TODO more detailed filtering by size/position/etc? NOTE that this is used by HiCCUPS */ public void removeDuplicates() { filterLists(new FeatureFilter() { @Override public List filter(String chr, List feature2DList) { return new ArrayList<>(new HashSet<>(feature2DList)); } }); } /** * Get all keys (chromosome pairs) for hashmap * * @return keySet */ private Set getKeySet() { return featureList.keySet(); } /** * Get feature list corresponding to key (chromosome pair) * * @param key * @return */ List getFeatureList(String key) { return featureList.get(key); } public enum ListFormat {ENRICHED, FINAL, LOCALIZED, ARROWHEAD, NA} /** * pass interface implementing a process for all features * * @param function */ public synchronized void processLists(FeatureFunction function) { List keys = new ArrayList<>(featureList.keySet()); Collections.sort(keys); for (String key : keys) { function.process(key, featureList.get(key)); } } /** * @return true if features available for this region (key = "chr1_chr2") */ public boolean containsKey(String key) { return featureList.containsKey(key); } public int getIndex(Chromosome chrX, Chromosome chrY, Feature2D feature2D) { final String key = Feature2DList.getKey(chrX, chrY); //this.convertFeaturesToContigs(key); List contigs = this.get(key); for (int i = 0; i < contigs.size(); i++) { Feature2D currentContig = contigs.get(i); if (currentContig.equals(feature2D)) { return i; } } return -1; // return -1 if input feature2D object is not present for the specified chromosomes } public int getNumTotalFeatures() { int total = 0; for (List chrList : featureList.values()) { total += chrList.size(); } return total; } public synchronized boolean checkAndRemoveFeature(int idx1, int idx2, Feature2D feature) { boolean somethingWasDeleted = false; String key = getKey(idx1, idx2); if (featureList.containsKey(key)) { try { somethingWasDeleted = featureList.get(key).remove(feature); } catch (Exception e) { System.err.println("Error encountered removing feature"); } if (featureList.get(key).size() == 0) featureList.remove(key); } return somethingWasDeleted; } public Feature2D searchForFeature(final int c1, final int start1, final int end1, final int c2, final int start2, final int end2) { final Feature2D[] feature = new Feature2D[1]; processLists(new FeatureFunction() { @Override public void process(String chr, List feature2DList) { for (Feature2D f : feature2DList) { if (f.getChr1().contains("" + c1) && f.getChr2().contains("" + c2) && f.start1 == start1 && f.start2 == start2 && f.end1 == end1 && f.end2 == end2) { feature[0] = f; break; } } } }); return feature[0]; } public void clearAllAttributes() { processLists(new FeatureFunction() { @Override public void process(String chr, List feature2DList) { for (Feature2D feature : feature2DList) { feature.clearAttributes(); } } }); } public Feature2DList deepCopy() { Feature2DList clone = new Feature2DList(); for (String key : featureList.keySet()) { List cloneList = new ArrayList<>(); for (Feature2D f : featureList.get(key)) { cloneList.add(f.deepCopy()); } clone.featureList.put(key, cloneList); } return clone; } public String printChromosomeRegionKeys() { StringBuilder features = new StringBuilder(); for (List feature2DS : featureList.values()) { for (Feature2D feature2D : feature2DS) { features.append(feature2D.getLocationKey()).append(", "); } } return features.toString(); } } ================================================ FILE: src/juicebox/track/feature/Feature2DParser.java ================================================ /* * The MIT License (MIT) * * Copyright (c) 2011-2021 Broad Institute, Aiden Lab, Rice University, Baylor College of Medicine * * Permission is hereby granted, free of charge, to any person obtaining a copy * of this software and associated documentation files (the "Software"), to deal * in the Software without restriction, including without limitation the rights * to use, copy, modify, merge, publish, distribute, sublicense, and/or sell * copies of the Software, and to permit persons to whom the Software is * furnished to do so, subject to the following conditions: * * The above copyright notice and this permission notice shall be included in * all copies or substantial portions of the Software. * * THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR * IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, * FITNESS FOR A PARTICULAR PURPOSE AND NON-INFRINGEMENT. IN NO EVENT SHALL THE * AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER * LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, * OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN * THE SOFTWARE. */ package juicebox.track.feature; import juicebox.HiCGlobals; import juicebox.MainWindow; import juicebox.data.ChromosomeHandler; import juicebox.data.HiCFileTools; import juicebox.data.basics.Chromosome; import juicebox.tools.utils.juicer.arrowhead.ArrowheadScoreList; import juicebox.tools.utils.juicer.arrowhead.HighScore; import org.broad.igv.Globals; import org.broad.igv.ui.color.ColorUtilities; import org.broad.igv.util.ParsingUtils; import javax.swing.*; import java.awt.*; import java.io.BufferedReader; import java.io.IOException; import java.io.InputStreamReader; import java.util.HashMap; import java.util.LinkedHashMap; import java.util.List; import java.util.Map; /** * Created by muhammadsaadshamim on 6/1/15. */ public class Feature2DParser { public static Feature2DList loadFeatures(String path, String genomeID, boolean loadAttributes, FeatureFilter featureFilter, boolean useFeature2DWithMotif) { return loadFeatures(path, HiCFileTools.loadChromosomes(genomeID), loadAttributes, featureFilter, useFeature2DWithMotif); } public static Feature2DList loadFeatures(String path, ChromosomeHandler handler, boolean loadAttributes, FeatureFilter featureFilter, final boolean useFeature2DWithMotif) { Feature2DList newList; String lowerCaseEnding = path.toLowerCase(); if (lowerCaseEnding.endsWith(".bedpe")) { newList = parseGeneralFile(path, handler, loadAttributes, featureFilter, new SpecificParser() { @Override void parseAndAddToList(String path, String[] headers, String[] tokens, int lineNum, boolean loadAttributes, String nextLine, ChromosomeHandler handler, Feature2DList newList, Feature2D.FeatureType featureType) throws IOException { parseBEDPEAndAddToList(path, headers, tokens, lineNum, loadAttributes, nextLine, handler, newList, featureType, useFeature2DWithMotif); } }); } else if (lowerCaseEnding.endsWith(".px")) { newList = parseGeneralFile(path, handler, loadAttributes, featureFilter, new SpecificParser() { @Override void parseAndAddToList(String path, String[] headers, String[] tokens, int lineNum, boolean loadAttributes, String nextLine, ChromosomeHandler handler, Feature2DList newList, Feature2D.FeatureType featureType) throws IOException { parsePxLoopsAndAddToList(path, headers, tokens, lineNum, loadAttributes, nextLine, handler, newList, featureType); } }); } else if (lowerCaseEnding.endsWith(".px2")) { newList = parseGeneralFile(path, handler, loadAttributes, featureFilter, new SpecificParser() { @Override void parseAndAddToList(String path, String[] headers, String[] tokens, int lineNum, boolean loadAttributes, String nextLine, ChromosomeHandler handler, Feature2DList newList, Feature2D.FeatureType featureType) throws IOException { parseDomainsAndAddToList(path, headers, tokens, lineNum, loadAttributes, nextLine, handler, newList, featureType); } }); } else { newList = parseGeneralFile(path, handler, loadAttributes, featureFilter, new SpecificParser() { @Override void parseAndAddToList(String path, String[] headers, String[] tokens, int lineNum, boolean loadAttributes, String nextLine, ChromosomeHandler handler, Feature2DList newList, Feature2D.FeatureType featureType) throws IOException { parseLegacyLoopsAndAddToList(path, headers, tokens, lineNum, loadAttributes, nextLine, handler, newList, featureType, useFeature2DWithMotif); } }); } newList.removeDuplicates(); return newList; } private static Feature2D.FeatureType parseTitleForFeatureType(String path) { if (path.contains("block") || path.contains("domain")) { return Feature2D.FeatureType.DOMAIN; } else if (path.contains("peak") || path.contains("loop")) { return Feature2D.FeatureType.PEAK; } else { return Feature2D.FeatureType.GENERIC; } } public static Feature2DList parseHighScoreList(int chrIndex, String chrName, int resolution, List binnedScores) { Feature2DList feature2DList = new Feature2DList(); for (HighScore score : binnedScores) { feature2DList.add(chrIndex, chrIndex, score.toFeature2D(chrName, resolution)); } return feature2DList; } public static Feature2DList parseArrowheadScoreList(int chrIndex, String chrName, ArrowheadScoreList scoreList) { Feature2DList feature2DList = new Feature2DList(); feature2DList.add(scoreList.toFeature2DList(chrIndex, chrName)); return feature2DList; } private static Feature2DList parseGeneralFile(String path, ChromosomeHandler handler, boolean loadAttributes, FeatureFilter featureFilter, SpecificParser parser) { Feature2DList newList = new Feature2DList(); try { //BufferedReader br = ParsingUtils.openBufferedReader(path); BufferedReader br = new BufferedReader(new InputStreamReader(ParsingUtils.openInputStream(path)), HiCGlobals.bufferSize); String nextLine; // header nextLine = br.readLine(); String[] headers = getHeaders(nextLine); Feature2D.FeatureType featureType = parseTitleForFeatureType(path); int lineNum = 1; while ((nextLine = br.readLine()) != null) { lineNum++; if (nextLine.startsWith("#")) continue; String[] tokens = Globals.tabPattern.split(nextLine); if (tokens.length > headers.length) { String text = "Improperly formatted file: \nLine " + lineNum + " has " + tokens.length + " entries" + " while header has " + headers.length; System.err.println(text); if (HiCGlobals.guiIsCurrentlyActive) { JOptionPane.showMessageDialog(MainWindow.getInstance(), text, "Error", JOptionPane.ERROR_MESSAGE); } throw new IOException(text); } parser.parseAndAddToList(path, headers, tokens, lineNum, loadAttributes, nextLine, handler, newList, featureType); } br.close(); } catch (Exception ec) { if (HiCGlobals.guiIsCurrentlyActive) { ec.printStackTrace(); } else { System.err.println("File " + path + " could not be parsed"); } } if (featureFilter != null) newList.filterLists(featureFilter); return newList; } /** * Backwards compatibility with original loops list * @param line Header token, usually not converted but old ones will be * @return Appropriate header */ private static String[] getHeaders(String line) { String[] tmpHeaders = Globals.tabPattern.split(line.replaceAll("#", "").trim()); String[] headers = new String[tmpHeaders.length]; Map translator = new HashMap<>(); translator.put("o", "observed"); translator.put("e_bl", "expectedBL"); translator.put("e_donut", "expectedDonut"); translator.put("e_h", "expectedH"); translator.put("e_v", "expectedV"); translator.put("fdr_bl", "fdrBL"); translator.put("fdr_donut", "fdrDonut"); translator.put("fdr_h", "fdrH"); translator.put("fdr_v", "fdrV"); translator.put("num_collapsed", "numCollapsed"); for (int i = 0; i < tmpHeaders.length; i++) { if (translator.containsKey(tmpHeaders[i])) { headers[i] = translator.get(tmpHeaders[i]); } else { headers[i] = tmpHeaders[i]; } } return headers; } private static abstract class SpecificParser { private static final int errorLimit = 100; private static int errorCount = 0; SpecificParser() { errorCount = 0; } private static Map parseAttributes(boolean loadAttributes, int attCol, String[] headers, String[] tokens) { Map attrs = new LinkedHashMap<>(); if (loadAttributes && tokens.length > attCol) { for (int i = attCol; i < tokens.length; i++) { attrs.put(headers[i], tokens[i]); } } return attrs; } private static void addToList(String chr1Name, String chr2Name, ChromosomeHandler handler, String nextLine, Feature2DList newList, boolean useFeature2DWithMotif, Feature2D.FeatureType featureType, int start1, int end1, int start2, int end2, Color c, Map attrs) { Chromosome chr1 = handler.getChromosomeFromName(chr1Name); Chromosome chr2 = handler.getChromosomeFromName(chr2Name); if (chr1 == null || chr2 == null) { handleError(nextLine); return; } // Convention is chr1 is lowest "index". Swap if necessary if (useFeature2DWithMotif) { if (chr1.getIndex() <= chr2.getIndex()) { newList.add(chr1.getIndex(), chr2.getIndex(), new Feature2DWithMotif(featureType, chr1Name, start1, end1, chr2Name, start2, end2, c, attrs)); } else { newList.add(chr2.getIndex(), chr1.getIndex(), new Feature2DWithMotif(featureType, chr2Name, start2, end2, chr1Name, start1, end1, c, attrs)); } } else { if (chr1.getIndex() <= chr2.getIndex()) { newList.add(chr1.getIndex(), chr2.getIndex(), new Feature2D(featureType, chr1Name, start1, end1, chr2Name, start2, end2, c, attrs)); } else { newList.add(chr2.getIndex(), chr1.getIndex(), new Feature2D(featureType, chr2Name, start2, end2, chr1Name, start1, end1, c, attrs)); } } } private static void addToList(String chrAName, Feature2D feature, ChromosomeHandler handler, String nextLine, Feature2DList newList) { Chromosome chrA = handler.getChromosomeFromName(chrAName); if (chrA == null) { handleError(nextLine); return; } newList.add(chrA.getIndex(), chrA.getIndex(), feature); } private static void handleError(String nextLine) { if (HiCGlobals.printVerboseComments) { if (errorCount < errorLimit) { System.err.println("Skipping line: " + nextLine); } else if (errorCount == errorLimit) { System.err.println("Maximum error count exceeded. Further errors will not be logged"); } } errorCount++; } abstract void parseAndAddToList(String path, String[] headers, String[] tokens, int lineNum, boolean loadAttributes, String nextLine, ChromosomeHandler handler, Feature2DList newList, Feature2D.FeatureType featureType) throws IOException; void parseDomainsAndAddToList(String path, String[] headers, String[] tokens, int lineNum, boolean loadAttributes, String nextLine, ChromosomeHandler handler, Feature2DList newList, Feature2D.FeatureType featureType) throws IOException { if (tokens.length < 3) return; String chrAName; int startA, endA; try { chrAName = tokens[0]; startA = Integer.parseInt(tokens[1]); endA = Integer.parseInt(tokens[2]); } catch (Exception e) { String text = "Line " + lineNum + " improperly formatted in
" + path + "
Line format should start with: CHR1 X1 X2"; System.err.println(text); if (HiCGlobals.guiIsCurrentlyActive) JOptionPane.showMessageDialog(MainWindow.getInstance(), text, "Error", JOptionPane.ERROR_MESSAGE); throw new IOException(text); } Color c = Color.black; Map attrs = parseAttributes(loadAttributes, 3, headers, tokens); Feature2D feature = new Feature2D(featureType, chrAName, startA, endA, chrAName, startA, endA, c, attrs); addToList(chrAName, feature, handler, nextLine, newList); } void parseBEDPEAndAddToList(String path, String[] headers, String[] tokens, int lineNum, boolean loadAttributes, String nextLine, ChromosomeHandler handler, Feature2DList newList, Feature2D.FeatureType featureType, boolean useFeature2DWithMotif) throws IOException { // BEDPE format // chrom1 start1 end1 chrom2 start2 end2 name(opt) score(opt) strand1(opt) strand2(opt) ...(opt)... // we will check for color in 11th column if (tokens.length < 6) return; String chr1Name, chr2Name; int start1, end1, start2, end2; try { chr1Name = tokens[0]; start1 = Integer.parseInt(tokens[1]); end1 = Integer.parseInt(tokens[2]); chr2Name = tokens[3]; start2 = Integer.parseInt(tokens[4]); end2 = Integer.parseInt(tokens[5]); } catch (Exception e) { String text = "Line " + lineNum + " improperly formatted in \n" + path + "\nLine format should start with: CHR1 X1 X2 CHR2 Y1 Y2"; System.err.println(text); if (HiCGlobals.guiIsCurrentlyActive) JOptionPane.showMessageDialog(MainWindow.getInstance(), text, "Error", JOptionPane.ERROR_MESSAGE); throw new IOException(text); } Color c = tokens.length > 10 ? ColorUtilities.stringToColor(tokens[10].trim()) : Color.black; Map attrs = parseAttributes(loadAttributes, 11, headers, tokens); try { attrs.put("score", "" + Float.parseFloat(tokens[7])); } catch (Exception e) { //ignore } addToList(chr1Name, chr2Name, handler, nextLine, newList, useFeature2DWithMotif, featureType, start1, end1, start2, end2, c, attrs); } void parseLegacyLoopsAndAddToList(String path, String[] headers, String[] tokens, int lineNum, boolean loadAttributes, String nextLine, ChromosomeHandler handler, Feature2DList newList, Feature2D.FeatureType featureType, boolean useFeature2DWithMotif) throws IOException { if (tokens.length < 6) return; String chr1Name, chr2Name; int start1, end1, start2, end2; try { chr1Name = tokens[0]; start1 = Integer.parseInt(tokens[1]); end1 = Integer.parseInt(tokens[2]); chr2Name = tokens[3]; start2 = Integer.parseInt(tokens[4]); end2 = Integer.parseInt(tokens[5]); } catch (Exception e) { String text = "Line " + lineNum + " improperly formatted in
" + path + "
Line format should start with: CHR1 X1 X2 CHR2 Y1 Y2"; System.err.println(text); if (HiCGlobals.guiIsCurrentlyActive) JOptionPane.showMessageDialog(MainWindow.getInstance(), text, "Error", JOptionPane.ERROR_MESSAGE); throw new IOException(text); } Color c = tokens.length > 6 ? ColorUtilities.stringToColor(tokens[6].trim()) : Color.black; Map attrs = parseAttributes(loadAttributes, 7, headers, tokens); addToList(chr1Name, chr2Name, handler, nextLine, newList, useFeature2DWithMotif, featureType, start1, end1, start2, end2, c, attrs); } void parsePxLoopsAndAddToList(String path, String[] headers, String[] tokens, int lineNum, boolean loadAttributes, String nextLine, ChromosomeHandler handler, Feature2DList newList, Feature2D.FeatureType featureType) throws IOException { // this was the prelim output used for old hiccups debugging if (tokens.length < 4) return; String chr1Name, chr2Name; int start1, end1, start2, end2; try { chr1Name = tokens[0]; start1 = Integer.parseInt(tokens[1]); end1 = start1 + 5000; chr2Name = tokens[2]; start2 = Integer.parseInt(tokens[3]); end2 = start2 + 5000; } catch (Exception e) { String text = "Line " + lineNum + " improperly formatted in
" + path + "
Line format should start with: CHR1 X1 CHR2 Y1"; System.err.println(text); if (HiCGlobals.guiIsCurrentlyActive) JOptionPane.showMessageDialog(MainWindow.getInstance(), text, "Error", JOptionPane.ERROR_MESSAGE); throw new IOException(text); } Color c = tokens.length > 4 ? ColorUtilities.stringToColor(tokens[4].trim()) : Color.black; Map attrs = parseAttributes(loadAttributes, 5, headers, tokens); addToList(chr1Name, chr2Name, handler, nextLine, newList, false, featureType, start1, end1, start2, end2, c, attrs); } } } ================================================ FILE: src/juicebox/track/feature/Feature2DTools.java ================================================ /* * The MIT License (MIT) * * Copyright (c) 2011-2020 Broad Institute, Aiden Lab, Rice University, Baylor College of Medicine * * Permission is hereby granted, free of charge, to any person obtaining a copy * of this software and associated documentation files (the "Software"), to deal * in the Software without restriction, including without limitation the rights * to use, copy, modify, merge, publish, distribute, sublicense, and/or sell * copies of the Software, and to permit persons to whom the Software is * furnished to do so, subject to the following conditions: * * The above copyright notice and this permission notice shall be included in * all copies or substantial portions of the Software. * * THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR * IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, * FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE * AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER * LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, * OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN * THE SOFTWARE. */ package juicebox.track.feature; import juicebox.HiCGlobals; import juicebox.tools.clt.juicer.CompareLists; import juicebox.tools.utils.juicer.hiccups.HiCCUPSUtils; import java.util.HashSet; import java.util.List; import java.util.Set; /** * Created by muhammadsaadshamim on 10/27/15. */ public class Feature2DTools { public static Feature2DList extractPeaksNearCentroids(final Feature2DList featureList, final Feature2DList centroids, final String errorMessage) { final Feature2DList peaks = new Feature2DList(); centroids.processLists(new FeatureFunction() { @Override public void process(String chr, List feature2DList) { if (featureList.containsKey(chr)) { final Set keys = new HashSet<>(); for (Feature2D f : feature2DList) { keys.add(f.getLocationKey()); } for (Feature2D f : featureList.getFeatureList(chr)) { if (keys.contains(f.getLocationKey())) { peaks.addByKey(chr, f); } } } else if (HiCGlobals.printVerboseComments) { System.err.println(chr + " key not found for centroids. Tag:NearCentroid-" + errorMessage + "Invalid set of centroids must have been calculated"); } } }); return peaks; } public static Feature2DList extractPeaksNotNearCentroids(final Feature2DList featureList, final Feature2DList centroids) { final Feature2DList peaks = new Feature2DList(); featureList.processLists(new FeatureFunction() { @Override public void process(String chr, List feature2DList) { if (centroids.containsKey(chr)) { // there are centroids for this chr i.e. need to check if loops should be added // get upper left corner location value final Set keys = new HashSet<>(); for (Feature2D f : centroids.getFeatureList(chr)) { keys.add(f.getLocationKey()); } // add pixels not already the centroid for (Feature2D f : feature2DList) { if (!keys.contains(f.getLocationKey())) { peaks.addByKey(chr, f); } } } else { // no centroids for chr i.e. all of these loops should be added peaks.addByKey(chr, feature2DList); } } }); return peaks; } /** * Calculate FDR values for all peaks * * @param fdrLogBL * @param fdrLogDonut * @param fdrLogH * @param fdrLogV */ public static void calculateFDR(Feature2DList features, final float[][] fdrLogBL, final float[][] fdrLogDonut, final float[][] fdrLogH, final float[][] fdrLogV) { features.processLists(new FeatureFunction() { @Override public void process(String chr, List feature2DList) { for (Feature2D feature : feature2DList) { HiCCUPSUtils.calculateFDR(feature, fdrLogBL, fdrLogDonut, fdrLogH, fdrLogV); } } }); } public static Feature2DList extractReproducibleCentroids(final Feature2DList firstFeatureList, Feature2DList secondFeatureList, final int radius) { final Feature2DList centroids = new Feature2DList(); secondFeatureList.processLists(new FeatureFunction() { @Override public void process(String chr, List secondFeature2DList) { if (firstFeatureList.containsKey(chr)) { List base1FeatureList = firstFeatureList.getFeatureList(chr); for (Feature2D f2 : secondFeature2DList) { for (Feature2D f1 : base1FeatureList) { int dx = (int) (f1.getStart1() - f2.getStart1()); int dy = (int) (f1.getStart2() - f2.getStart2()); double d = HiCCUPSUtils.hypotenuse(dx, dy); if (d <= radius) { //f2.setAttribute(HiCCUPSUtils.centroidAttr, "" + d); centroids.addByKey(chr, f2); break; } } } } } }); return centroids; } public static Feature2DList extractReproducibleCentroids(final Feature2DList firstFeatureList, Feature2DList secondFeatureList, final int radius, final double fraction) { final Feature2DList centroids = new Feature2DList(); secondFeatureList.processLists(new FeatureFunction() { @Override public void process(String chr, List secondFeature2DList) { if (firstFeatureList.containsKey(chr)) { List base1FeatureList = firstFeatureList.getFeatureList(chr); for (Feature2D f2 : secondFeature2DList) { double lowestDistance = -1; //Feature2D overlap = null; for (Feature2D f1 : base1FeatureList) { int dx = (int) (f1.getStart1() - f2.getStart1()); int dy = (int) (f1.getStart2() - f2.getStart2()); double d = HiCCUPSUtils.hypotenuse(dx, dy); if (d < lowestDistance || lowestDistance == -1) { //overlap = f1; lowestDistance = d; } } if (lowestDistance != -1) { double f = lowestDistance / (f2.getStart2() - f2.getStart1()); if (lowestDistance <= radius && f <= fraction) { centroids.addByKey(chr, f2); } } } } } }); return centroids; } /** * @return peaks within radius of diagonal */ public static Feature2DList getPeaksNearDiagonal(Feature2DList feature2DList, final int radius) { final Feature2DList peaks = new Feature2DList(); feature2DList.processLists(new FeatureFunction() { @Override public void process(String chr, List feature2DList) { for (Feature2D f : feature2DList) { int dist = (int) Math.abs(f.getStart1() - f.getStart2()); if (dist < radius) { //f.setAttribute(HiCCUPSUtils.nearDiagAttr, "1"); peaks.addByKey(chr, f); } } } }); return peaks; } /** * @return peaks with observed values exceeding limit */ public static Feature2DList getStrongPeaks(Feature2DList feature2DList, final int limit) { final Feature2DList peaks = new Feature2DList(); feature2DList.processLists(new FeatureFunction() { @Override public void process(String chr, List feature2DList) { for (Feature2D f : feature2DList) { float obs = f.getFloatAttribute(HiCCUPSUtils.OBSERVED); if (obs > limit) { //f.setAttribute(HiCCUPSUtils.StrongAttr, "1"); peaks.addByKey(chr, f); } } } }); return peaks; } /** * @param listA * @param listB * @return feature list where duplicates/common features are removed and results are color coded */ public static Feature2DList compareLists(final Feature2DList listA, final Feature2DList listB, boolean colorCode) { Feature2DList featuresUniqueToA = new Feature2DList(listA); Feature2DList featuresUniqueToB = new Feature2DList(listB); featuresUniqueToA.filterLists(new FeatureFilter() { @Override public List filter(String chr, List feature2DList) { if (listB.containsKey(chr)) { feature2DList.removeAll(listB.getFeatureList(chr)); } return feature2DList; } }); featuresUniqueToB.filterLists(new FeatureFilter() { @Override public List filter(String chr, List feature2DList) { if (listA.containsKey(chr)) { feature2DList.removeAll(listA.getFeatureList(chr)); } return feature2DList; } }); if (colorCode) { // color code results featuresUniqueToA.setColor(CompareLists.AAA); featuresUniqueToB.setColor(CompareLists.BBB); // also add an attribute in addition to color coding featuresUniqueToA.addAttributeFieldToAll("parent_list", "A"); featuresUniqueToB.addAttributeFieldToAll("parent_list", "B"); } // combine into one list Feature2DList results = new Feature2DList(featuresUniqueToA); results.add(featuresUniqueToB); return results; } public static Feature2DList subtract(final Feature2DList listA, final Feature2DList listB) { Feature2DList result = new Feature2DList(listA); result.filterLists(new FeatureFilter() { @Override public List filter(String chr, List feature2DList) { if (listB.containsKey(chr)) { feature2DList.removeAll(listB.getFeatureList(chr)); } return feature2DList; } }); result.removeDuplicates(); return result; } public static boolean loopIsUpstreamOfDomain(Feature2D loop, Feature2D domain, int threshold) { return loop.getEnd1() < domain.getStart1() - threshold && loop.getEnd2() < domain.getStart2() - threshold; } public static boolean loopIsDownstreamOfDomain(Feature2D loop, Feature2D domain, int threshold) { return loop.getStart1() > domain.getEnd1() + threshold && loop.getStart2() > domain.getEnd2() + threshold; } public static boolean domainContainsLoopWithinExpandedTolerance(Feature2D loop, Feature2D domain, int threshold) { return domain.getStart1() - threshold <= loop.getMidPt1() && loop.getMidPt1() <= domain.getEnd1() + threshold && domain.getStart2() - threshold <= loop.getMidPt2() && loop.getMidPt2() <= domain.getEnd2() + threshold; } /** * Compares a feature against all other features in list * * @param feature * @param existingFeatures * @return */ public static boolean doesOverlap(Feature2D feature, List existingFeatures) { boolean repeat = false; for (Feature2D existingFeature : existingFeatures) { if (existingFeature.overlapsWith(feature)) { repeat = true; } } return repeat; } public static boolean isResolutionPresent(final Feature2DList feature2DList, final int resolution) { final boolean[] returnValue = new boolean[1]; returnValue[0] = false; feature2DList.processLists(new FeatureFunction() { @Override public void process(String chr, List feature2DList) { for (Feature2D feature : feature2DList) { if (feature.getWidth1() == resolution) { returnValue[0] = true; return; } } } }); return returnValue[0]; } } ================================================ FILE: src/juicebox/track/feature/Feature2DWithMotif.java ================================================ /* * The MIT License (MIT) * * Copyright (c) 2011-2021 Broad Institute, Aiden Lab, Rice University, Baylor College of Medicine * * Permission is hereby granted, free of charge, to any person obtaining a copy * of this software and associated documentation files (the "Software"), to deal * in the Software without restriction, including without limitation the rights * to use, copy, modify, merge, publish, distribute, sublicense, and/or sell * copies of the Software, and to permit persons to whom the Software is * furnished to do so, subject to the following conditions: * * The above copyright notice and this permission notice shall be included in * all copies or substantial portions of the Software. * * THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR * IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, * FITNESS FOR A PARTICULAR PURPOSE AND NON-INFRINGEMENT. IN NO EVENT SHALL THE * AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER * LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, * OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN * THE SOFTWARE. */ package juicebox.track.feature; import juicebox.data.ChromosomeHandler; import juicebox.data.anchor.MotifAnchor; import juicebox.tools.clt.juicer.CompareLists; import java.awt.*; import java.util.List; import java.util.*; /** * Created by muhammadsaadshamim on 11/4/15. */ public class Feature2DWithMotif extends Feature2D { public static boolean useSimpleOutput = false; public static boolean uniquenessCheckEnabled = true; public static boolean lenientEqualityEnabled = false; private static int negReceived = 0; private static int negWritten = 0; private static int posNull = 0; private static int posWritten = 0; private static int negNull = 0; private final String MFS1 = "motif_start_1"; private final String MFE1 = "motif_end_1"; private final String MFSEQ1 = "sequence_1"; private final String MFO1 = "orientation_1"; private final String MFU1 = "uniqueness_1"; private final String MFS2 = "motif_start_2"; private final String MFE2 = "motif_end_2"; private final String MFSEQ2 = "sequence_2"; private final String MFO2 = "orientation_2"; private final String MFU2 = "uniqueness_2"; private final String LEGACY_MFS1 = "motif_x1"; private final String LEGACY_MFE1 = "motif_x2"; private final String LEGACY_MFS2 = "motif_y1"; private final String LEGACY_MFE2 = "motif_y2"; // true = +, false = -, null = NA private boolean strand1, strand2; // true - unique, false = inferred, null = NA private boolean unique1, unique2; private String sequence1, sequence2; private long motifStart1, motifEnd1, motifStart2, motifEnd2; private double score1, score2; public Feature2DWithMotif(FeatureType featureType, String chr1, long start1, long end1, String chr2, long start2, long end2, Color c, Map attributes) { super(featureType, chr1, start1, end1, chr2, start2, end2, c, attributes); importAttributesForMotifInformation(); } public void updateMotifData(boolean strand, boolean unique, String sequence, long motifStart, long motifEnd, boolean dataBelongsToAnchor1, double score) { if (unique) { if (dataBelongsToAnchor1) { if (sequence1 == null || score > score1) {//unique this.strand1 = strand; this.unique1 = unique; this.sequence1 = sequence; this.motifStart1 = motifStart; this.motifEnd1 = motifEnd; this.score1 = score; }/* else if (!(sequence.equals(sequence1) && motifStart1 == motifStart)) {//check equivalence for dups; otherwise not unique sequence1 = "null"; }*/ } else { if (sequence2 == null || score > score2) {//unique negReceived++; this.sequence2 = sequence; this.strand2 = strand; this.unique2 = unique; this.motifStart2 = motifStart; this.motifEnd2 = motifEnd; this.score2 = score; }/* else if (!(sequence.equals(sequence2) && motifStart2 == motifStart)) {//check equivalence for dups; otherwise not unique sequence2 = "null"; }*/ } } else {//inferred if (dataBelongsToAnchor1 && strand) { if (sequence1 == null) { this.strand1 = strand; this.unique1 = unique; this.sequence1 = sequence; this.motifStart1 = motifStart; this.motifEnd1 = motifEnd; this.score1 = score; } else if (!(sequence.equals(sequence1) && motifStart1 == motifStart)) { sequence1 = "null"; } } else if (!dataBelongsToAnchor1 && !strand) { if (sequence2 == null) { this.strand2 = strand; this.unique2 = unique; this.sequence2 = sequence; this.motifStart2 = motifStart; this.motifEnd2 = motifEnd; this.score2 = score; } else if (!(sequence.equals(sequence2) && motifStart2 == motifStart)) { sequence2 = "null"; } } } } private void importAttributesForMotifInformation() { String sequence1 = getAttribute(MFSEQ1); if (sequence1 != null && !sequence1.equalsIgnoreCase("null") && !sequence1.equalsIgnoreCase("na")) { boolean strand1 = getAttribute(MFO1).contains("p") || getAttribute(MFO1).contains("+"); boolean unique1 = getAttribute(MFU1).contains("u"); int motifStart1 = -1, motifEnd1 = -1; try { motifStart1 = Integer.parseInt(getAttribute(MFS1)); motifEnd1 = Integer.parseInt(getAttribute(MFE1)); } catch (Exception e) { try { motifStart1 = Integer.parseInt(getAttribute(LEGACY_MFS1)); motifEnd1 = Integer.parseInt(getAttribute(LEGACY_MFE1)); } catch (Exception ee) { ee.printStackTrace(); } } /* attributes.remove(MFO1); attributes.remove(MFU1); attributes.remove(MFS1); attributes.remove(MFE1); attributes.remove(MFSEQ1); */ // done last so that all info must be complete first // incomplete motifs will exit via catch before this point this.strand1 = strand1; this.unique1 = unique1; this.sequence1 = sequence1; this.motifStart1 = motifStart1; this.motifEnd1 = motifEnd1; } String sequence2 = getAttribute(MFSEQ2); if (sequence2 != null && !sequence2.equalsIgnoreCase("null") && !sequence2.equalsIgnoreCase("na")) { boolean strand2 = getAttribute(MFO2).contains("p") || getAttribute(MFO2).contains("+"); boolean unique2 = getAttribute(MFU2).contains("u"); int motifStart2 = -1, motifEnd2 = -1; try { motifStart2 = Integer.parseInt(getAttribute(MFS2)); motifEnd2 = Integer.parseInt(getAttribute(MFE2)); } catch (Exception e) { try { motifStart2 = Integer.parseInt(getAttribute(LEGACY_MFS2)); motifEnd2 = Integer.parseInt(getAttribute(LEGACY_MFE2)); } catch (Exception ee) { ee.printStackTrace(); } } /* attributes.remove(MFO2); attributes.remove(MFU2); attributes.remove(MFSEQ2); attributes.remove(MFS2); attributes.remove(MFE2); */ // done last so that all info must be complete first // incomplete motifs will exit via catch before this point this.strand2 = strand2; this.unique2 = unique2; this.sequence2 = sequence2; this.motifStart2 = motifStart2; this.motifEnd2 = motifEnd2; } } @Override public String getOutputFileHeader() { String additionalAttributes = "\t" + MFS1 + "\t" + MFE1 + "\t" + MFSEQ1 + "\t" + MFO1 + "\t" + MFU1 + "\t" + MFS2 + "\t" + MFE2 + "\t" + MFSEQ2 + "\t" + MFO2 + "\t" + MFU2; if (useSimpleOutput) { if (attributes.containsKey(CompareLists.PARENT_ATTRIBUTE)) { return genericHeader + "\t" + CompareLists.PARENT_ATTRIBUTE + additionalAttributes; } else { return genericHeader + additionalAttributes; } } return super.getOutputFileHeader() + additionalAttributes; } @Override public String toString() { String output = super.toString(); if (useSimpleOutput) { output = simpleStringWithColor(); if (attributes.containsKey(CompareLists.PARENT_ATTRIBUTE)) { output += "\t" + attributes.get(CompareLists.PARENT_ATTRIBUTE); } } if (sequence1 == null) { posNull++; output += "\tNA\tNA\tNA\tNA\tNA"; } else if (sequence1.equals("null")) { posNull++; output += "\tna\tna\tna\tna\tna"; } else { posWritten++; String orientation = strand1 ? "+" : "-"; String uniqueness = unique1 ? "u" : "i"; output += "\t" + motifStart1 + "\t" + motifEnd1 + "\t" + sequence1 + "\t" + orientation + "\t" + uniqueness; } if (sequence2 == null) { negNull++; output += "\tNA\tNA\tNA\tNA\tNA"; } else if (sequence2.equals("null")) { negNull++; output += "\tna\tna\tna\tna\tna"; } else { negWritten++; String orientation = strand2 ? "+" : "-"; String uniqueness = unique2 ? "u" : "i"; output += "\t" + motifStart2 + "\t" + motifEnd2 + "\t" + sequence2 + "\t" + orientation + "\t" + uniqueness; } return output; } @Override public List getAnchors(boolean onlyUninitializedFeatures, ChromosomeHandler handler) { List originalFeatures = new ArrayList<>(); originalFeatures.add(this); List anchors = new ArrayList<>(); if (isOnDiagonal()) { // loops should not be on diagonal // anchors.add(new MotifAnchor(chr1, start1, end1, originalFeatures, originalFeatures)); } else { List emptyList = new ArrayList<>(); // always should be only uninitialized? if (onlyUninitializedFeatures) { if (sequence1 == null || sequence1.equals("null")) { sequence1 = null; anchors.add(new MotifAnchor(chr1, start1, end1, originalFeatures, emptyList)); } if (sequence2 == null || sequence2.equals("null")) { sequence2 = null; anchors.add(new MotifAnchor(chr2, start2, end2, emptyList, originalFeatures)); } } else { anchors.add(new MotifAnchor(chr1, start1, end1, originalFeatures, emptyList)); anchors.add(new MotifAnchor(chr2, start2, end2, emptyList, originalFeatures)); } } return anchors; } @Override public boolean equals(Object obj) { if (super.equals(obj)) { Feature2DWithMotif o = (Feature2DWithMotif) obj; try { if ((sequence1 == null && o.sequence1 == null) || sequence1.equals(o.sequence1)) { if ((sequence2 == null && o.sequence2 == null) || sequence2.equals(o.sequence2)) { if (unique1 == o.unique1 && unique2 == o.unique2) { if (strand1 == o.strand1 && strand2 == o.strand2) { return true; } } } } } catch (Exception ignored) { } if (lenientEqualityEnabled) { // assuming this is B, obj is reference boolean motifsAreEqual = true; // reference has more data if (o.sequence1 != null && sequence1 == null) { // only if reference also follows convergent rule if (o.strand1) { motifsAreEqual = false; } } if (o.sequence2 != null && sequence2 == null) { // only if reference also follows convergent rule if (!o.strand2) { motifsAreEqual = false; } } // actually different data if (o.sequence1 != null && sequence1 != null && !sequence1.equals(o.sequence1)) { // only if reference also follows convergent rule if (o.strand1) { motifsAreEqual = false; } } if (o.sequence2 != null && sequence2 != null && !sequence2.equals(o.sequence2)) { // only if reference also follows convergent rule if (!o.strand2) { motifsAreEqual = false; } } /* if(o.sequence1 != null && sequence1 != null && sequence1.equals(o.sequence1)){ if(unique1 != o.unique1){ motifsAreEqual = false; } } if(o.sequence2 != null && sequence2 != null && sequence2.equals(o.sequence2)){ if(unique2 != o.unique2){ motifsAreEqual = false; } } */ return motifsAreEqual; } } return false; } @Override public int hashCode() { return Objects.hash(super.hashCode(), sequence1, sequence2); } public int getConvergenceStatus() { // ++, +- (convergent), -+ (divergent), --, other (incomplete) if (sequence1 != null && sequence2 != null) { if (unique1 && unique2) { if (strand1) { if (strand2) { return 0; } else { return 1; } } else { if (strand2) { return 2; } else { return 3; } } } else { return 4; } } else { return 5; } } @Override public Feature2D deepCopy() { Map attrClone = new HashMap<>(); for (String key : attributes.keySet()) { attrClone.put(key, attributes.get(key)); } Feature2DWithMotif clone = new Feature2DWithMotif(featureType, getChr1(), start1, end1, getChr2(), start2, end2, getColor(), attrClone); clone.strand1 = strand1; clone.strand2 = strand2; clone.unique1 = unique1; clone.unique2 = unique2; clone.sequence1 = sequence1; clone.sequence2 = sequence2; clone.motifStart1 = motifStart1; clone.motifEnd1 = motifEnd1; clone.motifStart2 = motifStart2; clone.motifEnd2 = motifEnd2; clone.score1 = score1; clone.score2 = score2; return clone; } } ================================================ FILE: src/juicebox/track/feature/FeatureFilter.java ================================================ /* * The MIT License (MIT) * * Copyright (c) 2011-2020 Broad Institute, Aiden Lab, Rice University, Baylor College of Medicine * * Permission is hereby granted, free of charge, to any person obtaining a copy * of this software and associated documentation files (the "Software"), to deal * in the Software without restriction, including without limitation the rights * to use, copy, modify, merge, publish, distribute, sublicense, and/or sell * copies of the Software, and to permit persons to whom the Software is * furnished to do so, subject to the following conditions: * * The above copyright notice and this permission notice shall be included in * all copies or substantial portions of the Software. * * THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR * IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, * FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE * AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER * LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, * OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN * THE SOFTWARE. */ package juicebox.track.feature; import java.util.List; /** * Created by muhammadsaadshamim on 7/30/15. */ public interface FeatureFilter { List filter(String chr, List feature2DList); } ================================================ FILE: src/juicebox/track/feature/FeatureFunction.java ================================================ /* * The MIT License (MIT) * * Copyright (c) 2011-2020 Broad Institute, Aiden Lab, Rice University, Baylor College of Medicine * * Permission is hereby granted, free of charge, to any person obtaining a copy * of this software and associated documentation files (the "Software"), to deal * in the Software without restriction, including without limitation the rights * to use, copy, modify, merge, publish, distribute, sublicense, and/or sell * copies of the Software, and to permit persons to whom the Software is * furnished to do so, subject to the following conditions: * * The above copyright notice and this permission notice shall be included in * all copies or substantial portions of the Software. * * THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR * IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, * FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE * AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER * LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, * OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN * THE SOFTWARE. */ package juicebox.track.feature; import java.util.List; /** * Created by muhammadsaadshamim on 7/30/15. */ public interface FeatureFunction { void process(String chr, List feature2DList); } ================================================ FILE: src/juicebox/track/tracksMenu_GalGal5.xml ================================================ ================================================ FILE: src/juicebox/track/tracksMenu_hg19.xml ================================================ ================================================ FILE: src/juicebox/track/tracksMenu_hg38.xml ================================================ ================================================ FILE: src/juicebox/track/tracksMenu_mm10.xml ================================================ ================================================ FILE: src/juicebox/track/tracksMenu_mm9.xml ================================================ ================================================ FILE: src/juicebox/windowui/DisabledGlassPane.java ================================================ /* * The MIT License (MIT) * * Copyright (c) 2011-2021 Broad Institute, Aiden Lab, Rice University, Baylor College of Medicine * * Permission is hereby granted, free of charge, to any person obtaining a copy * of this software and associated documentation files (the "Software"), to deal * in the Software without restriction, including without limitation the rights * to use, copy, modify, merge, publish, distribute, sublicense, and/or sell * copies of the Software, and to permit persons to whom the Software is * furnished to do so, subject to the following conditions: * * The above copyright notice and this permission notice shall be included in * all copies or substantial portions of the Software. * * THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR * IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, * FITNESS FOR A PARTICULAR PURPOSE AND NON-INFRINGEMENT. IN NO EVENT SHALL THE * AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER * LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, * OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN * THE SOFTWARE. */ package juicebox.windowui; import juicebox.HiCGlobals; import javax.swing.*; import javax.swing.border.Border; import javax.swing.border.EmptyBorder; import java.awt.*; import java.awt.event.KeyEvent; import java.awt.event.KeyListener; import java.awt.event.MouseAdapter; import java.awt.event.MouseMotionAdapter; /* * @author Rob Camick November 7, 2008 * Simple implementation of a Glass Pane that will capture and ignore all * events as well paint the glass pane to give the frame a "disabled" look. * * The background color of the glass pane should use a color with an * alpha value to create the disabled look. */ public class DisabledGlassPane extends JComponent implements KeyListener { private static final long serialVersionUID = 9000039; private final JLabel message = new JLabel(); public DisabledGlassPane(int cursor) { super(); // Set glass pane properties setOpaque(false); setCursor(Cursor.getPredefinedCursor(cursor)); Color base = UIManager.getColor("inactiveCaptionBorder"); Color background = new Color(base.getRed(), base.getGreen(), base.getBlue(), 128); setBackground(background); setLayout(new GridBagLayout()); message.setFont(HiCGlobals.font(30, true)); // Add a message label to the glass pane add(message, new GridBagConstraints()); message.setOpaque(false); Border MESSAGE_BORDER = new EmptyBorder(20, 20, 20, 20); message.setBorder(MESSAGE_BORDER); // Disable Mouse, Key and Focus events for the glass pane addMouseListener(new MouseAdapter() { }); addMouseMotionListener(new MouseMotionAdapter() { }); addKeyListener(this); setFocusTraversalKeysEnabled(false); } /* * The component is transparent but we want to paint the background * to give it the disabled look. */ @Override protected void paintComponent(Graphics g) { g.setColor(getBackground()); g.fillRect(0, 0, getSize().width, getSize().height); } /* * The background color of the message label will be the same as the * background of the glass pane without the alpha value */ @Override public void setBackground(Color background) { super.setBackground(background); Color messageBackground = new Color(background.getRGB()); message.setBackground(messageBackground); } /* * Implement the KeyListener to consume events */ public void keyPressed(KeyEvent e) { e.consume(); } public void keyTyped(KeyEvent e) { } public void keyReleased(KeyEvent e) { e.consume(); } /* * Make the glass pane visible and change the cursor to the wait cursor * * A message can be displayed and it will be centered on the frame. */ public void activate(String text) { if (text != null && text.length() > 0) { message.setVisible(true); message.setText(text); message.setForeground(getForeground()); } else message.setVisible(false); setVisible(true); requestFocusInWindow(); } /* * Hide the glass pane and restore the cursor */ public void deactivate() { setVisible(false); } } ================================================ FILE: src/juicebox/windowui/DumpDialog.java ================================================ /* * The MIT License (MIT) * * Copyright (c) 2011-2021 Broad Institute, Aiden Lab, Rice University, Baylor College of Medicine * * Permission is hereby granted, free of charge, to any person obtaining a copy * of this software and associated documentation files (the "Software"), to deal * in the Software without restriction, including without limitation the rights * to use, copy, modify, merge, publish, distribute, sublicense, and/or sell * copies of the Software, and to permit persons to whom the Software is * furnished to do so, subject to the following conditions: * * The above copyright notice and this permission notice shall be included in * all copies or substantial portions of the Software. * * THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR * IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, * FITNESS FOR A PARTICULAR PURPOSE AND NON-INFRINGEMENT. IN NO EVENT SHALL THE * AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER * LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, * OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN * THE SOFTWARE. */ package juicebox.windowui; import juicebox.DirectoryManager; import juicebox.HiC; import juicebox.MainWindow; import juicebox.data.ExpectedValueFunction; import juicebox.data.MatrixZoomData; import juicebox.data.NormalizationVector; import javax.swing.*; import java.awt.*; import java.io.IOException; import java.io.PrintWriter; public class DumpDialog extends JFileChooser { private static final long serialVersionUID = 900009; private JComboBox box; /** * TODO I think a good amount of the code below is duplicated in the dumpGeneralVector method and should call that instead * * @param mainWindow * @param hic */ public DumpDialog(MainWindow mainWindow, HiC hic) { super(); int result = showSaveDialog(mainWindow); if (result == JFileChooser.APPROVE_OPTION) { MatrixZoomData zd; try { zd = hic.getZd(); } catch (Exception e) { JOptionPane.showMessageDialog(this, "ZoomData error while writing", "Error", JOptionPane.ERROR_MESSAGE); return; } try { if (box.getSelectedItem().equals("Matrix")) { ExpectedValueFunction df = null; MatrixType matrixType = hic.getDisplayOption(); if (MatrixType.isExpectedValueType(matrixType)) { df = hic.getDataset().getExpectedValues(zd.getZoom(), hic.getObsNormalizationType()); if (df == null) { JOptionPane.showMessageDialog(this, box.getSelectedItem() + " not available", "Error", JOptionPane.ERROR_MESSAGE); return; } } zd.dump(new PrintWriter(getSelectedFile()), null, hic.getObsNormalizationType(), matrixType, true, hic.getCurrentRegionWindowGenomicPositions(), df, false); } else if (box.getSelectedItem().equals("Norm vector")) { if (hic.getObsNormalizationType().equals(NormalizationHandler.NONE)) { JOptionPane.showMessageDialog(this, "Selected normalization is None, nothing to write", "Error", JOptionPane.ERROR_MESSAGE); } else { NormalizationVector nv = hic.getNormalizationVector(zd.getChr1Idx()); PrintWriter pw = new PrintWriter(getSelectedFile()); // print out vector for (double[] array : nv.getData().getValues()) { for (double element : array) { pw.println(element); } } pw.close(); } } else if (box.getSelectedItem().toString().contains("Expected")) { final ExpectedValueFunction df = hic.getDataset().getExpectedValues(zd.getZoom(), hic.getObsNormalizationType()); if (df == null) { JOptionPane.showMessageDialog(this, box.getSelectedItem() + " not available", "Error", JOptionPane.ERROR_MESSAGE); return; } if (box.getSelectedItem().equals("Expected vector")) { long length = df.getLength(); int c = zd.getChr1Idx(); PrintWriter pw = new PrintWriter(getSelectedFile()); for (long i = 0; i < length; i++) { pw.println((float) df.getExpectedValue(c, i)); } pw.flush(); } else { PrintWriter pw = new PrintWriter(getSelectedFile()); // print out vector for (double[] values : df.getExpectedValuesNoNormalization().getValues()) { for (double element : values) { pw.println(element); } } pw.close(); } } } catch (IOException error) { JOptionPane.showMessageDialog(this, "Error while writing:\n" + error, "Error", JOptionPane.ERROR_MESSAGE); } } } protected JDialog createDialog(Component component) throws HeadlessException { JDialog dialog = super.createDialog(component); JPanel panel1 = new JPanel(); JLabel label = new JLabel("Dump "); box = new JComboBox<>(new String[]{"Matrix", "Norm vector", "Expected vector", "Expected genome-wide vector"}); panel1.add(label); panel1.add(box); dialog.add(panel1, BorderLayout.NORTH); setCurrentDirectory(DirectoryManager.getHiCDirectory()); setDialogTitle("Choose location for dump of matrix or vector"); setFileSelectionMode(JFileChooser.FILES_ONLY); return dialog; } } ================================================ FILE: src/juicebox/windowui/EditFeatureAttributesDialog.java ================================================ /* * The MIT License (MIT) * * Copyright (c) 2011-2021 Broad Institute, Aiden Lab, Rice University, Baylor College of Medicine * * Permission is hereby granted, free of charge, to any person obtaining a copy * of this software and associated documentation files (the "Software"), to deal * in the Software without restriction, including without limitation the rights * to use, copy, modify, merge, publish, distribute, sublicense, and/or sell * copies of the Software, and to permit persons to whom the Software is * furnished to do so, subject to the following conditions: * * The above copyright notice and this permission notice shall be included in * all copies or substantial portions of the Software. * * THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR * IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, * FITNESS FOR A PARTICULAR PURPOSE AND NON-INFRINGEMENT. IN NO EVENT SHALL THE * AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER * LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, * OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN * THE SOFTWARE. */ package juicebox.windowui; /** * Created by Marie on 6/25/15. */ import juicebox.MainWindow; import juicebox.track.feature.AnnotationLayer; import juicebox.track.feature.Feature2D; import javax.swing.*; import java.awt.event.ActionEvent; import java.awt.event.ActionListener; import java.awt.event.WindowAdapter; import java.awt.event.WindowEvent; import java.beans.PropertyChangeEvent; import java.beans.PropertyChangeListener; import java.util.ArrayList; import java.util.HashMap; /* 1.4 example used by DialogDemo.java. */ public class EditFeatureAttributesDialog extends JDialog implements ActionListener, PropertyChangeListener { private static final long serialVersionUID = 9000040; private final String defaultNewAttributeName = ""; private final String defaultNewAttributeValue = ""; private final HashMap textFields; private final Feature2D feature; private final AnnotationLayer annotationsLayer; private final ArrayList attributeKeys; private final JCheckBox echoOption; private final JOptionPane optionPane; private final String btnString1 = "Enter"; private String typedText = null; /** * Creates the reusable dialog. */ public EditFeatureAttributesDialog(MainWindow mainWindow, Feature2D feature, AnnotationLayer annotationsLayer) { super(mainWindow); this.annotationsLayer = annotationsLayer; this.feature = feature; setTitle("Attribute Editor"); textFields = new HashMap<>(); attributeKeys = feature.getAttributeKeys(); Object[] array = new Object[2 * (attributeKeys.size() + 2)]; int count = 0; //Create an array of the text and components to be displayed. for (String key : attributeKeys) { //Register an event handler that puts the text into the option pane. JTextField textField = new JTextField(10); textField.setText(feature.getAttribute(key)); textField.addActionListener(this); textFields.put(key, textField); array[count++] = key + ":"; array[count++] = textField; } // Add panes to input new attribute attributeKeys.add("New Field Name"); JTextField textField = new JTextField(10); textField.setText(defaultNewAttributeName); textField.addActionListener(this); textFields.put("New Field Name", textField); JTextField textField2 = new JTextField(10); textField2.setText(defaultNewAttributeValue); textField2.addActionListener(this); textFields.put("New Field Value", textField2); echoOption = new JCheckBox("Set value as default for new attribute"); array[count++] = "Add Attribute:"; array[count++] = textField; array[count++] = textField2; array[count] = echoOption; String btnString2 = "Cancel"; Object[] options = {btnString1, btnString2}; //Create the JOptionPane. optionPane = new JOptionPane(array, JOptionPane.QUESTION_MESSAGE, JOptionPane.YES_NO_OPTION, null, options, options[0]); //Make this dialog display it. setContentPane(new JScrollPane(optionPane)); //Handle window closing correctly. setDefaultCloseOperation(DO_NOTHING_ON_CLOSE); addWindowListener(new WindowAdapter() { public void windowClosing(WindowEvent we) { /* * Instead of directly closing the window, * we're going to change the JOptionPane's * value property. */ optionPane.setValue(JOptionPane.CLOSED_OPTION); } }); //Register an event handler that reacts to option pane state changes. optionPane.addPropertyChangeListener(this); pack(); setLocationRelativeTo(null); setVisible(true); } /** * Returns null if the typed string was invalid; * otherwise, returns the string as the user entered it. */ public String getValidatedText() { return typedText; } /** * This method handles events for the text field. */ public void actionPerformed(ActionEvent e) { optionPane.setValue(btnString1); } /** * This method reacts to state changes in the option pane. */ public void propertyChange(PropertyChangeEvent e) { String prop = e.getPropertyName(); if (isVisible() && (e.getSource() == optionPane) && (JOptionPane.VALUE_PROPERTY.equals(prop) || JOptionPane.INPUT_VALUE_PROPERTY.equals(prop))) { Object value = optionPane.getValue(); if (value == JOptionPane.UNINITIALIZED_VALUE) { //ignore reset return; } optionPane.setValue( JOptionPane.UNINITIALIZED_VALUE); if (btnString1.equals(value)) { for (String key : attributeKeys) { typedText = textFields.get(key).getText(); if (typedText != null) { // New Attribute if (key.equals("New Field Name")) { String newAttributeText = textFields.get("New Field Value").getText(); // TODO meh - if add to all (echo), things after won't work. // If added new attribute with valid field if (!typedText.equals(defaultNewAttributeName) && typedText != null) { if (!newAttributeText.equals(defaultNewAttributeValue)) { if (echoOption.isSelected()) { annotationsLayer.addAllAttributeValues(typedText, newAttributeText); } else { annotationsLayer.addAllAttributeValues(typedText, "null"); //sets default to null feature.setAttribute(typedText, newAttributeText); } } } // Update old attribute } else { // If text changed in already existing attributes, change value if (!typedText.equals(feature.getAttribute(key))) { feature.setAttribute(key, typedText); } } } } } typedText = null; clearAndHide(); } } /** * This method clears the dialog and hides it. */ private void clearAndHide() { //textField.setText(null); setVisible(false); } } ================================================ FILE: src/juicebox/windowui/FileDropTargetListener.java ================================================ /* * The MIT License (MIT) * * Copyright (c) 2011-2020 Broad Institute, Aiden Lab, Rice University, Baylor College of Medicine * * Permission is hereby granted, free of charge, to any person obtaining a copy * of this software and associated documentation files (the "Software"), to deal * in the Software without restriction, including without limitation the rights * to use, copy, modify, merge, publish, distribute, sublicense, and/or sell * copies of the Software, and to permit persons to whom the Software is * furnished to do so, subject to the following conditions: * * The above copyright notice and this permission notice shall be included in * all copies or substantial portions of the Software. * * THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR * IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, * FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE * AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER * LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, * OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN * THE SOFTWARE. */ package juicebox.windowui; import juicebox.gui.SuperAdapter; import org.broad.igv.util.HttpUtils; import java.awt.datatransfer.DataFlavor; import java.awt.datatransfer.Transferable; import java.awt.dnd.*; import java.io.File; import java.util.ArrayList; import java.util.Collections; import java.util.List; /** * Listener for drag&drop actions */ public class FileDropTargetListener implements DropTargetListener { private final SuperAdapter superAdapter; public FileDropTargetListener(SuperAdapter superAdapter) { this.superAdapter = superAdapter; } public void dragEnter(DropTargetDragEvent event) { if (isDragNotAcceptable(event)) { event.rejectDrag(); } } public void dragExit(DropTargetEvent event) { } public void dragOver(DropTargetDragEvent event) { // you can provide visual feedback here } public void dropActionChanged(DropTargetDragEvent event) { if (isDragNotAcceptable(event)) { event.rejectDrag(); } } public void drop(DropTargetDropEvent event) { if (!isDropAcceptable(event)) { event.rejectDrop(); return; } event.acceptDrop(DnDConstants.ACTION_COPY); Transferable transferable = event.getTransferable(); try { @SuppressWarnings("unchecked") // Transferable when called with DataFlavor javaFileList is guaranteed to return a File List. java.util.List files = (java.util.List) transferable.getTransferData(DataFlavor.javaFileListFlavor); List paths = new ArrayList<>(); for (File f : files) { paths.add(f.getAbsolutePath()); } superAdapter.safeLoad(paths, false, files.get(0).getName()); } catch (Exception e) { String obj; try { obj = transferable.getTransferData(DataFlavor.stringFlavor).toString(); if (HttpUtils.isRemoteURL(obj)) { superAdapter.safeLoad(Collections.singletonList(obj), false, obj); } } catch (Exception e1) { e1.printStackTrace(); } } superAdapter.repaint(); event.dropComplete(true); } private boolean isDragNotAcceptable(DropTargetDragEvent event) { // Check the available data flavors here // Currently accepting all flavors return (event.getDropAction() & DnDConstants.ACTION_COPY_OR_MOVE) == 0; } private boolean isDropAcceptable(DropTargetDropEvent event) { // Check the available data flavors here // Currently accepting all flavors return (event.getDropAction() & DnDConstants.ACTION_COPY_OR_MOVE) != 0; } } ================================================ FILE: src/juicebox/windowui/GoToPanel.java ================================================ /* * The MIT License (MIT) * * Copyright (c) 2011-2021 Broad Institute, Aiden Lab, Rice University, Baylor College of Medicine * * Permission is hereby granted, free of charge, to any person obtaining a copy * of this software and associated documentation files (the "Software"), to deal * in the Software without restriction, including without limitation the rights * to use, copy, modify, merge, publish, distribute, sublicense, and/or sell * copies of the Software, and to permit persons to whom the Software is * furnished to do so, subject to the following conditions: * * The above copyright notice and this permission notice shall be included in * all copies or substantial portions of the Software. * * THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR * IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, * FITNESS FOR A PARTICULAR PURPOSE AND NON-INFRINGEMENT. IN NO EVENT SHALL THE * AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER * LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, * OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN * THE SOFTWARE. */ package juicebox.windowui; import com.jidesoft.swing.JideButton; import juicebox.HiC; import juicebox.HiCGlobals; import juicebox.assembly.Scaffold; import juicebox.data.ChromosomeHandler; import juicebox.data.GeneLocation; import juicebox.data.basics.Chromosome; import juicebox.gui.SuperAdapter; import juicebox.tools.utils.juicer.GeneTools; import juicebox.track.HiCTrack; import javax.swing.*; import javax.swing.border.LineBorder; import java.awt.*; import java.awt.event.ActionEvent; import java.awt.event.ActionListener; import java.awt.event.FocusEvent; import java.awt.event.FocusListener; import java.io.BufferedReader; import java.io.IOException; import java.util.ArrayList; import java.util.Collections; import java.util.List; import java.util.Map; /** * Created by nchernia on 4/2/15. */ public class GoToPanel extends JPanel implements ActionListener, FocusListener { private static final long serialVersionUID = 9000041; private static JideButton goButton; private static JTextField positionChrLeft; private static JTextField positionChrTop; private final HiC hic; private final SuperAdapter superAdapter; private String genomeID; private Map geneLocationHashMap = null; public GoToPanel(SuperAdapter superAdapter) { super(); this.hic = superAdapter.getHiC(); this.superAdapter = superAdapter; JLabel goLabel = new JLabel("Goto"); goLabel.setHorizontalAlignment(SwingConstants.CENTER); JPanel goLabelPanel = new JPanel(); goLabelPanel.setBackground(HiCGlobals.backgroundColor); goLabelPanel.setLayout(new BorderLayout()); goLabelPanel.add(goLabel, BorderLayout.CENTER); positionChrTop = initializeGoToTextField(); positionChrLeft = initializeGoToTextField(); JPanel goPositionPanel = new JPanel(); goPositionPanel.setLayout(new BorderLayout()); goPositionPanel.add(positionChrTop, BorderLayout.PAGE_START); goPositionPanel.add(positionChrLeft, BorderLayout.PAGE_END); goButton = new JideButton(); goButton.setEnabled(false); goButton.setIcon(new ImageIcon(getClass().getResource("/toolbarButtonGraphics/general/Refresh24.gif"))); goButton.addActionListener(this); JPanel goButtonPanel = new JPanel(); goButtonPanel.setBackground(HiCGlobals.diffGrayColor); goButtonPanel.setLayout(new BoxLayout(goButtonPanel, BoxLayout.X_AXIS)); goButtonPanel.add(goPositionPanel, BorderLayout.PAGE_START); goButtonPanel.add(goButton); setBackground(HiCGlobals.diffGrayColor); setBorder(LineBorder.createGrayLineBorder()); setLayout(new BorderLayout()); add(goLabelPanel, BorderLayout.PAGE_START); add(goButtonPanel); setMinimumSize(new Dimension(100, 70)); setPreferredSize(new Dimension(120, 70)); setMaximumSize(new Dimension(200, 70)); } private JTextField initializeGoToTextField() { JTextField textField = new JTextField(); textField.setFont(new Font("Arial", Font.ITALIC, 10)); textField.setEnabled(false); textField.addActionListener(this); textField.addFocusListener(this); return textField; } public void setEnabled(boolean enabled) { super.setEnabled(enabled); positionChrTop.setEnabled(enabled); positionChrLeft.setEnabled(enabled); goButton.setEnabled(enabled); } public void actionPerformed(ActionEvent event) { if (positionChrLeft.getText().isEmpty() && positionChrTop.getText().isEmpty()) { positionChrTop.setBackground(Color.yellow); positionChrLeft.setBackground(Color.yellow); } else if (positionChrLeft.getText().isEmpty()) { positionChrLeft.setText(positionChrTop.getText()); } else if (positionChrTop.getText().isEmpty()) { positionChrTop.setText(positionChrLeft.getText()); } parsePositionText(); } public void setPositionChrLeft(String newPositionDate) { positionChrLeft.setText(newPositionDate); } public void setPositionChrTop(String newPositionDate) { positionChrTop.setText(newPositionDate); } private void parsePositionText() { if (SuperAdapter.assemblyModeCurrentlyActive) { goToScaffoldName(positionChrLeft.getText(), positionChrTop.getText()); return; } //Expected format 1: :-: //Expected format 2: :: List resultLeft = parse(positionChrLeft); String[] leftChrTokens = resultLeft.get(0); String[] leftDashChrTokens = resultLeft.get(1); List resultTop = parse(positionChrTop); String[] topChrTokens = resultTop.get(0); String[] topDashChrTokens = resultTop.get(1); if (topChrTokens.length == 1 || leftChrTokens.length == 1) { parseGenePositionText(); return; } ChromosomeHandler handler = hic.getDataset().getChromosomeHandler(); Chromosome topChr = handler.getChromosomeFromName(topChrTokens[0]); if (topChr == null) { positionChrTop.setBackground(Color.yellow); System.err.println("Cannot find " + topChrTokens[0] + " in dataset's chromosome list"); return; } Chromosome leftChr = handler.getChromosomeFromName(leftChrTokens[0]); if (leftChr == null) { positionChrLeft.setBackground(Color.yellow); System.err.println("Cannot find " + leftChrTokens[0] + " in dataset's chromosome list"); return; } // chrPositions {start, end, outBin, estimatedOutBinSize} int[] topChrPositions; try { topChrPositions = extractParametersFromTokens(topChrTokens, topDashChrTokens, positionChrTop); } catch (Exception e) { return; } int[] leftChrPositions; try { leftChrPositions = extractParametersFromTokens(leftChrTokens, leftDashChrTokens, positionChrLeft); } catch (Exception e) { return; } //Read resolution: int outBinSize = 0; HiC.Unit resolutionUnits = HiC.Unit.BP; int estimatedOutBinSize = Math.max(topChrPositions[3], leftChrPositions[3]); if (topChrTokens.length > 3 || (topDashChrTokens.length == 1 && topChrTokens.length > 2)) { try { int[] resolutionParameters = extractResolutionParametersFromTokens(topChrTokens, topDashChrTokens, positionChrTop); outBinSize = resolutionParameters[0]; if (resolutionParameters[1] < 0) { resolutionUnits = HiC.Unit.FRAG; } } catch (Exception e) { return; } } else if (leftChrTokens.length > 3 || (leftDashChrTokens.length == 1 && leftChrTokens.length > 2)) { try { int[] resolutionParameters = extractResolutionParametersFromTokens(leftChrTokens, leftDashChrTokens, positionChrLeft); outBinSize = resolutionParameters[0]; if (resolutionParameters[1] < 0) { resolutionUnits = HiC.Unit.FRAG; } } catch (Exception e) { return; } } else if (estimatedOutBinSize > 0) { outBinSize = estimatedOutBinSize; } else if (hic.getZoom().getBinSize() != 0) { //no resolution specified, not at whole genome view outBinSize = hic.getZoom().getBinSize(); if (outBinSize != Integer.MIN_VALUE) { resolutionUnits = hic.getZoom().getUnit(); } } positionChrTop.setBackground(Color.white); positionChrLeft.setBackground(Color.white); if (outBinSize == Integer.MIN_VALUE) { outBinSize = 250000; // If bin size is not valid, set to max bin size } hic.setLocation(topChr.getName(), leftChr.getName(), resolutionUnits, outBinSize, Math.max(topChrPositions[2], 0), Math.max(leftChrPositions[2], 0), hic.getScaleFactor(), HiC.ZoomCallType.STANDARD, "Goto", true); } private List parse(JTextField textField) { String dashDelimiters = "\\s+|\\-\\s*"; String[] tmpChrTokens = textField.getText().split(":"); String[] chrTokens = new String[0]; String[] dashChrTokens = new String[0]; if (tmpChrTokens.length == 1) { chrTokens = tmpChrTokens; } else if (tmpChrTokens.length == 2) { dashChrTokens = textField.getText().substring(tmpChrTokens[0].length() + 1).split(dashDelimiters); chrTokens = new String[dashChrTokens.length + 1]; chrTokens[0] = tmpChrTokens[0]; for (int i = 0; i < dashChrTokens.length; i++) { chrTokens[i + 1] = dashChrTokens[i]; } } else if (tmpChrTokens.length == 3) { dashChrTokens = textField.getText().substring(tmpChrTokens[0].length() + 1, tmpChrTokens[0].length() + tmpChrTokens[1].length() + 1).split(dashDelimiters); chrTokens = new String[dashChrTokens.length + 2]; chrTokens[0] = tmpChrTokens[0]; int i; for (i = 0; i < dashChrTokens.length; i++) { chrTokens[i + 1] = dashChrTokens[i]; } System.out.println(i); chrTokens[i + 1] = tmpChrTokens[2]; } List result = new ArrayList<>(); result.add(chrTokens); result.add(dashChrTokens); return result; } private int[] extractResolutionParametersFromTokens(String[] chrTokens, String[] dashChrTokens, JTextField positionChr) { int outBinSize = 0; int resolutionUnits = 1;//BP try { if (dashChrTokens.length == 1) { outBinSize = cleanUpNumber(chrTokens[2]); } else if (chrTokens.length > 3) { outBinSize = cleanUpNumber(chrTokens[3]); } System.out.println("Out bin size " + outBinSize); } catch (Exception e) { positionChr.setBackground(Color.yellow); System.err.println("Invalid resolution " + chrTokens[3]); } return new int[]{outBinSize, resolutionUnits}; } private int[] extractParametersFromTokens(String[] chrTokens, String[] dashChrTokens, JTextField positionChr) throws IOException { //Read positions: int start = 0, end = 0, outBin = 0, estimatedOutBinSize = 0; if (chrTokens.length > 2 && dashChrTokens.length > 1) { //Make sure values are numerical: try { start = Math.min(cleanUpNumber(chrTokens[1]), cleanUpNumber(chrTokens[2])); end = Math.max(cleanUpNumber(chrTokens[1]), cleanUpNumber(chrTokens[2])); } catch (Exception e) { System.err.println("Cannot parse " + chrTokens[1] + " or " + chrTokens[2] + ". Expecting int"); positionChr.setBackground(Color.yellow); throw new IOException(); } outBin = start + ((end - start) / 2); int diff = end - start; estimatedOutBinSize = getEstimationOfAppropriateZoomLevel(diff); } else if (chrTokens.length > 1) { //Make sure values are numerical: try { outBin = cleanUpNumber(chrTokens[1]); } catch (Exception e) { System.err.println("Cannot parse " + chrTokens[1] + ". Expecting int"); positionChr.setBackground(Color.yellow); throw new IOException(); } } return new int[]{start, end, outBin, estimatedOutBinSize}; } // TODO this should get map keys from official list of resolutions, sort the list, then return appropriately private int getEstimationOfAppropriateZoomLevel(int diff0) { // divide because the width from x1 to x2 in chromosome should be significantly bigger then the resolution int diff = diff0 / 1000; for (HiCZoom zoom : hic.getDataset().getBpZooms()) { int res = zoom.getBinSize(); if (diff >= res) return res; } return 5000; } private int cleanUpNumber(String number) { return (int) (Long.parseLong(number.toLowerCase() .replaceAll(",", "") .replaceAll("m", "000000") .replaceAll("k", "000")) / HiCGlobals.hicMapScale); } private void parseGenePositionText() { String genomeID = hic.getDataset().getGenomeId(); // Currently only human and mouse, not worrying about small differences in location between genomes if (genomeID.equals("b37")) genomeID = "hg19"; //if (geneLocationHashMap == null || !genomeID.equals(this.genomeID)) { //don't understand the genomeID check if (geneLocationHashMap == null || this.genomeID == null) { initializeGeneHashMap(genomeID); } else { extractGeneLocation(); } } private void initializeGeneHashMap(String genomeID) { if (genomeID.equals("hg19") || genomeID.equals("hg38") || genomeID.equals("mm9") || genomeID.equals("mm10")) { final String gID = genomeID; Runnable runnable = new Runnable() { @Override public void run() { unsafeInitializeGeneHashMap(gID); } }; superAdapter.executeLongRunningTask(runnable, "Initialize Gene Hash Map"); } else { for (HiCTrack track : hic.getLoadedTracks()) { if (track.getName().contains("refGene")) { Runnable runnable = new Runnable() { @Override public void run() { unsafeInitializeGeneHashMap(track.getLocator().getPath()); } }; superAdapter.executeLongRunningTask(runnable, "Initialize Gene Hash Map"); } } } } private void unsafeInitializeGeneHashMap(String genomeID) { // Custom format parsed from ref Gene file. // Name1 Name2 chromosome position (where position is midpoint of transcription start and end) BufferedReader reader; try { reader = GeneTools.getStreamToGeneFile(genomeID); } catch (Exception error) { SuperAdapter.showMessageDialog("Failed to read gene database"); positionChrTop.setBackground(Color.yellow); geneLocationHashMap = null; return; } try { ChromosomeHandler handler = hic.getChromosomeHandler(); geneLocationHashMap = GeneTools.getLocationMap(reader, handler); } catch (Exception error) { SuperAdapter.showMessageDialog("Failed to parse gene database"); positionChrTop.setBackground(Color.yellow); geneLocationHashMap = null; } if (geneLocationHashMap != null) this.genomeID = genomeID; //why was this needed? extractGeneLocation(); } private void goToScaffoldName(String scafName1, String scafName2) { long location1 = -1; long location2 = -1; String chr1Name = ""; String chr2Name = ""; for (Scaffold scaffold : superAdapter.getAssemblyStateTracker().getAssemblyHandler().getListOfScaffolds()) { if (scaffold.name.equals(scafName1)) { chr1Name = scaffold.chrName; location1 = scaffold.getCurrentFeature2D().getMidPt1(); } if (scaffold.name.equals(scafName2)) { chr2Name = scaffold.chrName; location2 = scaffold.getCurrentFeature2D().getMidPt2(); } } try { hic.setLocation(chr1Name, chr2Name, HiC.Unit.BP, hic.getZd().getBinSize(), location1, location2, hic.getScaleFactor(), HiC.ZoomCallType.STANDARD, "Assembly Goto", true); superAdapter.setNormalizationDisplayState(); } catch (NullPointerException e) { System.err.println("Cannot recognize scaffold name"); } } private void extractGeneLocation() { GeneLocation location1 = geneLocationHashMap.get(positionChrTop.getText().trim().toLowerCase()); GeneLocation location2 = geneLocationHashMap.get(positionChrLeft.getText().trim().toLowerCase()); if (location1 == null) { positionChrTop.setBackground(Color.yellow); SuperAdapter.showMessageDialog("Gene location map doesn't contain " + positionChrTop.getText().trim()); return; } if (location2 == null) { positionChrLeft.setBackground(Color.yellow); SuperAdapter.showMessageDialog("Gene location map doesn't contain " + positionChrLeft.getText().trim()); return; } // Note that the global BP resolutions might not be what's stored in the file List zooms = hic.getDataset().getBpZooms(); List bpResolutions = new ArrayList<>(); for (HiCZoom zoom:zooms){ bpResolutions.add(zoom.getBinSize()); } int geneZoomResolution = hic.getZoom().getBinSize(); if (!bpResolutions.contains(geneZoomResolution)) { geneZoomResolution = Collections.min(bpResolutions); } hic.setLocation(location1.getChromosome().getName(), location2.getChromosome().getName(), HiC.Unit.BP, geneZoomResolution, location1.getCenterPosition(), location2.getCenterPosition(), hic.getScaleFactor(), HiC.ZoomCallType.STANDARD, "Gene Goto", true); superAdapter.setNormalizationDisplayState(); } public void focusGained(FocusEvent event) { if (event.getSource() == positionChrLeft) positionChrLeft.setBackground(Color.white); else if (event.getSource() == positionChrTop) positionChrTop.setBackground(Color.white); } public void focusLost(FocusEvent event) { } } ================================================ FILE: src/juicebox/windowui/HiCChromosomeFigPanel.java ================================================ /* * The MIT License (MIT) * * Copyright (c) 2011-2021 Broad Institute, Aiden Lab, Rice University, Baylor College of Medicine * * Permission is hereby granted, free of charge, to any person obtaining a copy * of this software and associated documentation files (the "Software"), to deal * in the Software without restriction, including without limitation the rights * to use, copy, modify, merge, publish, distribute, sublicense, and/or sell * copies of the Software, and to permit persons to whom the Software is * furnished to do so, subject to the following conditions: * * The above copyright notice and this permission notice shall be included in * all copies or substantial portions of the Software. * * THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR * IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, * FITNESS FOR A PARTICULAR PURPOSE AND NON-INFRINGEMENT. IN NO EVENT SHALL THE * AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER * LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, * OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN * THE SOFTWARE. */ package juicebox.windowui; import juicebox.Context; import juicebox.HiC; import juicebox.HiCGlobals; import juicebox.MainWindow; import juicebox.data.ChromosomeHandler; import juicebox.data.MatrixZoomData; import juicebox.data.basics.Chromosome; import juicebox.track.HiCGridAxis; import javax.swing.*; import java.awt.*; import java.awt.event.*; import java.awt.geom.AffineTransform; import java.awt.geom.Point2D; import java.awt.geom.RoundRectangle2D; /** * @author Jay Jung Hee Ryu * @since 5/26/16. */ // extends to JScrollPane or ScrollBar// // Load chromosome figure shape from GapSizes from tool. public class HiCChromosomeFigPanel extends JComponent { private static final long serialVersionUID = 9000042; private final Font spanFont = HiCGlobals.font(12, false); private final HiC hic; private Orientation orientation; private Context context; private Point lastPoint = null; private int chrFigStart = 0; private int chrFigEnd = 0; public HiCChromosomeFigPanel(final HiC hic) { this.hic = hic; if (HiCGlobals.isDarkulaModeEnabled) { setBackground(Color.BLACK); } else { setBackground(Color.WHITE); } addMouseListener(new MouseAdapter() { @Override public void mouseClicked(MouseEvent mouseEvent) { if (mouseEvent.getClickCount() >= 1) { if (isHorizontal()) { try { Point2D.Double scale = getHiCScale(HiCChromosomeFigPanel.this.getWidth(), HiCChromosomeFigPanel.this.getHeight()); hic.moveBy((int) ((mouseEvent.getX() - (chrFigStart + chrFigEnd) / 2) * scale.getX()), 0); } catch (Exception e) { System.err.println("Error when horizontal region clicked"); } } else { try { Point2D.Double scale = getHiCScale(HiCChromosomeFigPanel.this.getHeight(), HiCChromosomeFigPanel.this.getWidth()); hic.moveBy(0, (int) ((mouseEvent.getY() + (chrFigStart + chrFigEnd) / 2) * scale.getX())); } catch (Exception e) { System.err.println("Error when vertical region clicked"); } } } } @Override public void mousePressed(MouseEvent e) { if (isHorizontal()) { if (e.getX() >= chrFigStart && e.getX() <= chrFigEnd) { lastPoint = e.getPoint(); setCursor(MainWindow.fistCursor); } } else { if (e.getY() >= -chrFigStart && e.getY() <= -chrFigEnd) { lastPoint = e.getPoint(); setCursor(MainWindow.fistCursor); } } } @Override public void mouseReleased(MouseEvent e) { lastPoint = null; setCursor(Cursor.getDefaultCursor()); } }); addMouseMotionListener(new MouseMotionAdapter() { @Override public void mouseDragged(MouseEvent e) { if (lastPoint != null) { if (isHorizontal()) { Point2D.Double scale = getHiCScale(HiCChromosomeFigPanel.this.getWidth(), HiCChromosomeFigPanel.this.getHeight()); hic.moveBy(((int) ((e.getX() - lastPoint.x) * scale.getX())), 0); } else { Point2D.Double scale = getHiCScale(HiCChromosomeFigPanel.this.getHeight(), HiCChromosomeFigPanel.this.getWidth()); hic.moveBy(0, (int) ((e.getY() - lastPoint.y) * scale.getX())); } lastPoint = e.getPoint(); } } }); addMouseWheelListener(new MouseWheelListener() { @Override public void mouseWheelMoved(MouseWheelEvent e) { int scroll = (int) Math.round(e.getPreciseWheelRotation()); if (isHorizontal()) { hic.moveBy(scroll, 0); } else { hic.moveBy(0, scroll); } } }); //todo Chromosome change pop-up menu } private Point2D.Double getHiCScale(int width, int height) { try { return new Point2D.Double((double) hic.getZd().getXGridAxis().getBinCount() / width, (double) hic.getZd().getYGridAxis().getBinCount() / height); } catch (Exception e) { return null; } } public void setContext(Context frame, Orientation orientation) { this.context = frame; this.orientation = orientation; } @Override protected void paintComponent(Graphics g) { super.paintComponent(g); ((Graphics2D) g).setRenderingHint(RenderingHints.KEY_ANTIALIASING, RenderingHints.VALUE_ANTIALIAS_ON); Graphics2D g2D = (Graphics2D) g; try { hic.getZd(); } catch (Exception e) { return; } if (context == null) return; g.setColor(Color.black); AffineTransform t = g2D.getTransform(); if (orientation == Orientation.VERTICAL) { AffineTransform rotateTransform = new AffineTransform(); rotateTransform.quadrantRotate(-1); g2D.transform(rotateTransform); } // Clear panel drawChr(g2D); g2D.setTransform(t); } private void drawChr(Graphics2D g) { Chromosome chromosome = context.getChromosome(); if (chromosome == null || ChromosomeHandler.isAllByAll(chromosome)) return; MatrixZoomData zd; try { zd = hic.getZd(); } catch (Exception e) { return; } if (zd == null || zd.getXGridAxis() == null || zd.getYGridAxis() == null) return; HiCGridAxis axis = isHorizontal() ? zd.getXGridAxis() : zd.getYGridAxis(); int endPositionBin = (int) ((axis.getBinNumberForGenomicPosition(chromosome.getLength()) - (int) context.getBinOrigin()) * hic.getScaleFactor()); int w = isHorizontal() ? getWidth() : getHeight(); w = Math.min(w, endPositionBin); int h = isHorizontal() ? getHeight() : getWidth(); g.setFont(spanFont); //Draw Chromosome Figure drawRegion(g, w, h); //Draw Chromosome Name String rangeString = chromosome.getName(); if (hic.isVSTypeDisplay()) { if (isHorizontal()) { rangeString = rangeString + " (observed)"; } else { rangeString = rangeString + " (control)"; } } int strWidth = g.getFontMetrics().stringWidth(rangeString); int vPos = h / 2 + 3; int strPosition = -(w + strWidth) / 2; if (isHorizontal()) strPosition = (w - strWidth) / 2; Rectangle r = new Rectangle(strPosition, h / 4, strWidth, h / 2); g.setClip(r); g.setColor(Color.BLACK); g.drawString(rangeString, strPosition, vPos); } private long genomeLength() { return context.getChromosome().getLength(); } private void drawRegion(Graphics2D g, int w, int h) { Color chrContour = new Color(116, 173, 212); Color chrFillIn = new Color(163, 202, 187); Color chrInside = new Color(222, 222, 222); long genomeLength = genomeLength(); long[] genomePositions; try { genomePositions = hic.getCurrentRegionWindowGenomicPositions(); } catch (Exception e) { return; } float chrFigLength = w - 2; if (isHorizontal()) { chrFigStart = Math.round((chrFigLength * genomePositions[0]) / genomeLength + 1); chrFigEnd = genomePositions[1] > genomeLength ? w - 1 : Math.round(chrFigLength * genomePositions[1] / genomeLength) + 1; int chrFigRegion = chrFigEnd - chrFigStart; g.setColor(chrContour); g.drawRoundRect(1, h / 4, w - 2, h / 2, h / 2, h / 2); // Lines g.drawLine(chrFigStart, h / 2, chrFigStart, h / 4 - 3); g.drawLine(0, 0, 0, 3); g.drawLine(chrFigStart, h / 4 - 3, 0, 3); MatrixZoomData zd; try { zd = hic.getZd(); } catch (Exception e) { return; } HiCGridAxis axis = isHorizontal() ? zd.getXGridAxis() : zd.getYGridAxis(); long maxX = context.getChromosome().getLength(); long x = (long) (axis.getBinNumberForGenomicPosition(maxX) * hic.getScaleFactor()); int endbinNumber = (int) ((genomePositions[1] > maxX) ? x : w); g.drawLine(chrFigEnd, h / 2, chrFigEnd, h / 4 - 3); g.drawLine(endbinNumber - 1, 0, endbinNumber - 1, 3); g.drawLine(chrFigEnd, h / 4 - 3, endbinNumber - 1, 3); // Later implement shape to create a chromosome shape RoundRectangle2D chrFig = new RoundRectangle2D.Double(1, h / 4, w - 2, h / 2, h / 2, h / 2); g.setClip(chrFig); g.setColor(chrInside); g.fillRect(1, h / 4, w - 2, h / 2); // Chromosome region Rectangle region = new Rectangle(chrFigStart, 0, chrFigRegion, h); g.clip(region); g.setColor(chrFillIn); g.fillRect(chrFigStart, 0, chrFigRegion, h); } else { chrFigStart = -Math.round((chrFigLength * genomePositions[2]) / genomeLength) - 1; chrFigEnd = genomePositions[3] > genomeLength ? -w + 1 : -Math.round(chrFigLength * genomePositions[3] / genomeLength) - 1; int chrFigRegion = -chrFigEnd + chrFigStart; g.setColor(chrContour); g.drawRoundRect(-w + 1, h / 4, w - 2, h / 2, h / 2, h / 2); // lines g.setColor(chrContour); g.drawLine(chrFigStart, h / 2, chrFigStart, h / 4 - 3); g.drawLine(0, 0, 0, 3); g.drawLine(chrFigStart, h / 4 - 3, 0, 3); g.drawLine(chrFigEnd, h / 2, chrFigEnd, h / 4 - 3); g.drawLine(-w + 1, 0, -w + 1, 3); g.drawLine(chrFigEnd, h / 4 - 3, -w + 1, 3); // Later implement shape to create a chromosome shape RoundRectangle2D chrFig = new RoundRectangle2D.Double(-w + 1, h / 4, w - 2, h / 2, h / 2, h / 2); g.setClip(chrFig); g.setColor(chrInside); g.fillRect(-w + 1, h / 4, w - 2, h / 2); // Chromosome region Rectangle region = new Rectangle(chrFigEnd, 0, chrFigRegion, h); g.clip(region); g.setColor(chrFillIn); g.fillRect(chrFigEnd, 0, chrFigRegion, h); } } private boolean isHorizontal() { return orientation == Orientation.HORIZONTAL; } public enum Orientation {HORIZONTAL, VERTICAL} } ================================================ FILE: src/juicebox/windowui/HiCKeyDispatcher.java ================================================ /* * The MIT License (MIT) * * Copyright (c) 2011-2021 Broad Institute, Aiden Lab, Rice University, Baylor College of Medicine * * Permission is hereby granted, free of charge, to any person obtaining a copy * of this software and associated documentation files (the "Software"), to deal * in the Software without restriction, including without limitation the rights * to use, copy, modify, merge, publish, distribute, sublicense, and/or sell * copies of the Software, and to permit persons to whom the Software is * furnished to do so, subject to the following conditions: * * The above copyright notice and this permission notice shall be included in * all copies or substantial portions of the Software. * * THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR * IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, * FITNESS FOR A PARTICULAR PURPOSE AND NON-INFRINGEMENT. IN NO EVENT SHALL THE * AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER * LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, * OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN * THE SOFTWARE. */ package juicebox.windowui; import juicebox.HiC; import juicebox.HiCGlobals; import juicebox.data.HiCFileLoader; import juicebox.gui.SuperAdapter; import juicebox.tools.dev.Private; import juicebox.track.feature.AnnotationLayerHandler; import org.broad.igv.ui.util.MessageUtils; import javax.swing.*; import java.awt.*; import java.awt.event.KeyEvent; import java.util.ArrayList; import java.util.List; public class HiCKeyDispatcher implements KeyEventDispatcher { private final HiC hic; private final JComboBox displayOptionComboBox; private final SuperAdapter superAdapter; private final List handlersPreviouslyHidden = new ArrayList<>(); public HiCKeyDispatcher(SuperAdapter superAdapter, HiC hic, JComboBox displayOptionComboBox) { super(); this.hic = hic; this.superAdapter = superAdapter; this.displayOptionComboBox = displayOptionComboBox; } @Override public boolean dispatchKeyEvent(KeyEvent e) { if (e.getID() == KeyEvent.KEY_PRESSED && e.getKeyCode() == KeyEvent.VK_F1) { if (hic.getControlZd() != null) { MatrixType displayOption = (MatrixType) displayOptionComboBox.getSelectedItem(); if (displayOption == MatrixType.CONTROL) { displayOptionComboBox.setSelectedItem(MatrixType.OBSERVED); } else if (displayOption == MatrixType.OBSERVED) { displayOptionComboBox.setSelectedItem(MatrixType.CONTROL); } } return true; } else if (e.getID() == KeyEvent.KEY_PRESSED && e.getKeyCode() == KeyEvent.VK_F2) { if (handlersPreviouslyHidden.size() > 0) { for (AnnotationLayerHandler handler : handlersPreviouslyHidden) { handler.setLayerVisibility(true); } handlersPreviouslyHidden.clear(); } else { for (AnnotationLayerHandler handler : superAdapter.getAllLayers()) { if (handler.getLayerVisibility()) { handler.setLayerVisibility(false); handlersPreviouslyHidden.add(handler); } } } superAdapter.updateMiniAnnotationsLayerPanel(); superAdapter.updateMainLayersPanel(); superAdapter.repaint(); return true; } else if (e.getID() == KeyEvent.KEY_PRESSED && e.getKeyCode() == KeyEvent.VK_F3) { for (AnnotationLayerHandler handler : superAdapter.getAllLayers()) { if (handler.getLayerVisibility()) { handler.setIsEnlarged(!handler.getIsEnlarged()); } } superAdapter.repaint(); return true; } else if (e.getID() == KeyEvent.KEY_PRESSED && e.getKeyCode() == KeyEvent.VK_F4) { for (AnnotationLayerHandler handler : superAdapter.getAllLayers()) { if (handler.getLayerVisibility()) { handler.setIsTransparent(!handler.getIsTransparent()); } } superAdapter.repaint(); return true; } else if (e.getID() == KeyEvent.KEY_PRESSED && e.getKeyCode() == KeyEvent.VK_F5) { for (AnnotationLayerHandler handler : superAdapter.getAllLayers()) { if (handler.getLayerVisibility()) { handler.setIsSparse(!handler.getIsSparse()); } } superAdapter.repaint(); return true; } else if (e.getID() == KeyEvent.KEY_PRESSED && e.getKeyCode() == KeyEvent.VK_F6) { for (AnnotationLayerHandler handler : superAdapter.getAllLayers()) { if (handler.getLayerVisibility()) { handler.togglePlottingStyle(); } } superAdapter.repaint(); return true; } else if (e.getID() == KeyEvent.KEY_PRESSED && e.getKeyCode() == KeyEvent.VK_F7) { String newURL = MessageUtils.showInputDialog("Specify a new properties file", HiCGlobals.defaultPropertiesURL); if (newURL != null) { HiCFileLoader.changeJuiceboxPropertiesFile(newURL); } return true; } else if (e.getID() == KeyEvent.KEY_PRESSED && e.getKeyCode() == KeyEvent.VK_F8) { Private.launchMapSubsetGUI(superAdapter); return true; } else if (e.getID() == KeyEvent.KEY_PRESSED && e.getKeyCode() == KeyEvent.VK_F9) { superAdapter.togglePanelVisible(); return true; } else if (e.getID() == KeyEvent.KEY_PRESSED && (e.getKeyCode() == KeyEvent.VK_U) && ((e.getModifiers() & Toolkit.getDefaultToolkit().getMenuShortcutKeyMask()) != 0)) { if (SuperAdapter.assemblyModeCurrentlyActive && superAdapter.getAssemblyStateTracker().checkUndo()) { superAdapter.getAssemblyStateTracker().undo(); superAdapter.getHeatmapPanel().removeSelection(); superAdapter.refresh(); } return true; } else if (e.getID() == KeyEvent.KEY_PRESSED && e.getExtendedKeyCode() == KeyEvent.VK_R && ((e.getModifiers() & Toolkit.getDefaultToolkit().getMenuShortcutKeyMask()) != 0)) { if (SuperAdapter.assemblyModeCurrentlyActive && superAdapter.getAssemblyStateTracker().checkRedo()) { superAdapter.getAssemblyStateTracker().redo(); superAdapter.getHeatmapPanel().removeSelection(); superAdapter.refresh(); } return true; } else { return false; } } } ================================================ FILE: src/juicebox/windowui/HiCLayout.java ================================================ /* * The MIT License (MIT) * * Copyright (c) 2011-2021 Broad Institute, Aiden Lab, Rice University, Baylor College of Medicine * * Permission is hereby granted, free of charge, to any person obtaining a copy * of this software and associated documentation files (the "Software"), to deal * in the Software without restriction, including without limitation the rights * to use, copy, modify, merge, publish, distribute, sublicense, and/or sell * copies of the Software, and to permit persons to whom the Software is * furnished to do so, subject to the following conditions: * * The above copyright notice and this permission notice shall be included in * all copies or substantial portions of the Software. * * THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR * IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, * FITNESS FOR A PARTICULAR PURPOSE AND NON-INFRINGEMENT. IN NO EVENT SHALL THE * AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER * LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, * OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN * THE SOFTWARE. */ package juicebox.windowui; import java.awt.*; /** * Layout manager for HiC panels, based loosely on BorderLayout */ public class HiCLayout implements LayoutManager2 { public static final String NORTH_WEST = "Northwest"; private static final String NORTH = "North"; private static final String SOUTH = "South"; private static final String EAST = "East"; private static final String WEST = "West"; private static final String CENTER = "Center"; private final int hgap = 0; private final int vgap = 0; private Component north; private Component west; private Component east; private Component south; private Component center; private Component northwest; /** * Adds the specified component to the layout, using the specified * constraint object. For border layouts, the constraint must be * one of the following constants: NORTH, * SOUTH, EAST, * WEST, or CENTER. *

* Most applications do not call this method directly. This method * is called when a component is added to a container using the * Container.add method with the same argument types. * * @param comp the component to be added. * @param constraints an object that specifies how and where * the component is added to the layout. * @throws IllegalArgumentException if the constraint object is not * a string, or if it not one of the five specified * constants. * @see java.awt.Container#add(java.awt.Component, java.lang.Object) * @since JDK1.1 */ public void addLayoutComponent(Component comp, Object constraints) { synchronized (comp.getTreeLock()) { if ((constraints == null) || (constraints instanceof String)) { addLayoutComponent((String) constraints, comp); } else { throw new IllegalArgumentException("cannot add to layout: constraint must be a string (or null)"); } } } public void addLayoutComponent(String name, Component comp) { synchronized (comp.getTreeLock()) { /* Special case: treat null the same as "Center". */ if (name == null) { name = "Center"; } /* Assign the component to one of the known regions of the layout. */ if (name.equalsIgnoreCase(CENTER)) { center = comp; } else if (name.equalsIgnoreCase(NORTH)) { north = comp; } else if (name.equalsIgnoreCase(SOUTH)) { south = comp; } else if (name.equalsIgnoreCase(EAST)) { east = comp; } else if (name.equalsIgnoreCase(WEST)) { west = comp; } else if (name.equalsIgnoreCase(NORTH_WEST)) { northwest = comp; } else { throw new IllegalArgumentException("cannot add to layout: unknown constraint: " + name); } } } /** * Removes the specified component from this border layout. This * method is called when a container calls its remove or * removeAll methods. Most applications do not call this * method directly. * * @param comp the component to be removed. * @see java.awt.Container#remove(java.awt.Component) * @see java.awt.Container#removeAll() */ public void removeLayoutComponent(Component comp) { synchronized (comp.getTreeLock()) { if (comp == center) { center = null; } else if (comp == north) { north = null; } else if (comp == south) { south = null; } else if (comp == east) { east = null; } else if (comp == west) { west = null; } else if (comp == northwest) { northwest = null; } } } /** * Determines the minimum size of the target container * using this layout manager. *

* This method is called when a container calls its * getMinimumSize method. Most applications do not call * this method directly. * * @param target the container in which to do the layout. * @return the minimum dimensions needed to lay out the subcomponents * of the specified container. * @see java.awt.Container * @see java.awt.BorderLayout#preferredLayoutSize * @see java.awt.Container#getMinimumSize() */ public Dimension minimumLayoutSize(Container target) { synchronized (target.getTreeLock()) { Dimension dim = new Dimension(0, 0); boolean ltr = target.getComponentOrientation().isLeftToRight(); Component c; if ((c = getChild(EAST, ltr)) != null) { Dimension d = c.getMinimumSize(); dim.width += d.width + hgap; dim.height = Math.max(d.height, dim.height); } if ((c = getChild(WEST, ltr)) != null) { Dimension d = c.getMinimumSize(); dim.width += d.width + hgap; dim.height = Math.max(d.height, dim.height); } if ((c = getChild(CENTER, ltr)) != null) { Dimension d = c.getMinimumSize(); dim.width += d.width; dim.height = Math.max(d.height, dim.height); } if ((c = getChild(NORTH, ltr)) != null) { Dimension d = c.getMinimumSize(); dim.width = Math.max(d.width, dim.width); dim.height += d.height + vgap; } if ((c = getChild(SOUTH, ltr)) != null) { Dimension d = c.getMinimumSize(); dim.width = Math.max(d.width, dim.width); dim.height += d.height + vgap; } Insets insets = target.getInsets(); dim.width += insets.left + insets.right; dim.height += insets.top + insets.bottom; return dim; } } /** * Determines the preferred size of the target * container using this layout manager, based on the components * in the container. *

* Most applications do not call this method directly. This method * is called when a container calls its getPreferredSize * method. * * @param target the container in which to do the layout. * @return the preferred dimensions to lay out the subcomponents * of the specified container. * @see java.awt.Container * @see java.awt.BorderLayout#minimumLayoutSize * @see java.awt.Container#getPreferredSize() */ public Dimension preferredLayoutSize(Container target) { synchronized (target.getTreeLock()) { Dimension dim = new Dimension(0, 0); boolean ltr = target.getComponentOrientation().isLeftToRight(); Component c; if ((c = getChild(EAST, ltr)) != null) { Dimension d = c.getPreferredSize(); dim.width += d.width + hgap; dim.height = Math.max(d.height, dim.height); } if ((c = getChild(WEST, ltr)) != null) { Dimension d = c.getPreferredSize(); dim.width += d.width + hgap; dim.height = Math.max(d.height, dim.height); } if ((c = getChild(CENTER, ltr)) != null) { Dimension d = c.getPreferredSize(); dim.width += d.width; dim.height = Math.max(d.height, dim.height); } if ((c = getChild(NORTH, ltr)) != null) { Dimension d = c.getPreferredSize(); dim.width = Math.max(d.width, dim.width); dim.height += d.height + vgap; } if ((c = getChild(SOUTH, ltr)) != null) { Dimension d = c.getPreferredSize(); dim.width = Math.max(d.width, dim.width); dim.height += d.height + vgap; } Insets insets = target.getInsets(); dim.width += insets.left + insets.right; dim.height += insets.top + insets.bottom; return dim; } } /** * Returns the maximum dimensions for this layout given the components * in the specified target container. * * @param target the component which needs to be laid out * @see Container * @see #minimumLayoutSize * @see #preferredLayoutSize */ public Dimension maximumLayoutSize(Container target) { return new Dimension(Integer.MAX_VALUE, Integer.MAX_VALUE); } /** * Returns the alignment along the x axis. This specifies how * the component would like to be aligned relative to other * components. The value should be a number between 0 and 1 * where 0 represents alignment along the origin, 1 is aligned * the furthest away from the origin, 0.5 is centered, etc. */ public float getLayoutAlignmentX(Container parent) { return 0.5f; } /** * Returns the alignment along the y axis. This specifies how * the component would like to be aligned relative to other * components. The value should be a number between 0 and 1 * where 0 represents alignment along the origin, 1 is aligned * the furthest away from the origin, 0.5 is centered, etc. */ public float getLayoutAlignmentY(Container parent) { return 0.5f; } /** * Invalidates the layout, indicating that if the layout manager * has cached information it should be discarded. */ public void invalidateLayout(Container target) { } /** * Lays out the container argument using this border layout. *

* This method actually reshapes the components in the specified * container in order to satisfy the constraints of this * BorderLayout object. The NORTH * and SOUTH components, if any, are placed at * the top and bottom of the container, respectively. The * WEST and EAST components are * then placed on the left and right, respectively. Finally, * the CENTER object is placed in any remaining * space in the middle. *

* Most applications do not call this method directly. This method * is called when a container calls its doLayout method. * * @param target the container in which to do the layout. * @see java.awt.Container * @see java.awt.Container#doLayout() */ public void layoutContainer(Container target) { synchronized (target.getTreeLock()) { Insets insets = target.getInsets(); int top = insets.top; int bottom = target.getHeight() - insets.bottom; int left = insets.left; int right = target.getWidth() - insets.right; int dh = bottom - top; int dw = right - left; int dx = west == null ? 0 : west.getPreferredSize().width + hgap; int dy = north == null ? 0 : north.getPreferredSize().height + vgap; if (south != null) dy += south.getPreferredSize().height + vgap; // Center must be square //int centerDim = Math.min(dw - dx, dh - dy); int centerDimX = dw - dx; int centerDimY = dh - dy; if (north != null) { Dimension d = north.getPreferredSize(); north.setBounds(left + dx, top, centerDimX, d.height); if (northwest != null) { northwest.setBounds(left, top, dx, d.height); } top += d.height + vgap; } if (west != null) { Dimension d = west.getPreferredSize(); west.setBounds(left, top, d.width, centerDimY); } if (center != null) { center.setBounds(left + west.getWidth() + hgap, top, centerDimX, centerDimY); } if (east != null) { int xEast = left + west.getWidth() + hgap + centerDimX + hgap; int wEast = Math.max(0, dw - xEast); east.setBounds(xEast, top, wEast, centerDimY); } if (south != null) { top += centerDimY + vgap; int hSouth = Math.max(0, dh - top); south.setBounds(left, top, dw, hSouth); } } } /** * Get the component that corresponds to the given constraint location * * @param key The desired absolute position, * either NORTH, SOUTH, EAST, or WEST. * @param ltr Is the component line direction left-to-right? */ private Component getChild(String key, boolean ltr) { Component result = null; if (key.equalsIgnoreCase(NORTH)) { result = north; } else if (key.equalsIgnoreCase(SOUTH)) { result = south; } else if (key.equalsIgnoreCase(WEST)) { result = west; } else if (key.equalsIgnoreCase(EAST)) { result = east; } else if (key.equalsIgnoreCase(CENTER)) { result = center; } else if (key.equalsIgnoreCase(NORTH_WEST)) { result = northwest; } if (result != null && !result.isVisible()) { result = null; } return result; } /** * Returns a string representation of the state of this border layout. * * @return a string representation of this border layout. */ public String toString() { return getClass().getName() + "[hgap=" + hgap + ",vgap=" + vgap + "]"; } } ================================================ FILE: src/juicebox/windowui/HiCRulerPanel.java ================================================ /* * The MIT License (MIT) * * Copyright (c) 2011-2021 Broad Institute, Aiden Lab, Rice University, Baylor College of Medicine * * Permission is hereby granted, free of charge, to any person obtaining a copy * of this software and associated documentation files (the "Software"), to deal * in the Software without restriction, including without limitation the rights * to use, copy, modify, merge, publish, distribute, sublicense, and/or sell * copies of the Software, and to permit persons to whom the Software is * furnished to do so, subject to the following conditions: * * The above copyright notice and this permission notice shall be included in * all copies or substantial portions of the Software. * * THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR * IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, * FITNESS FOR A PARTICULAR PURPOSE AND NON-INFRINGEMENT. IN NO EVENT SHALL THE * AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER * LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, * OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN * THE SOFTWARE. */ package juicebox.windowui; import juicebox.Context; import juicebox.HiC; import juicebox.HiCGlobals; import juicebox.data.ChromosomeHandler; import juicebox.data.MatrixZoomData; import juicebox.data.basics.Chromosome; import juicebox.track.HiCGridAxis; import javax.swing.*; import java.awt.*; import java.awt.geom.AffineTransform; import java.math.RoundingMode; import java.text.DecimalFormat; import java.text.NumberFormat; /** * @author jrobinso */ public class HiCRulerPanel extends JPanel { private static final long serialVersionUID = 9000043; private static boolean showOnlyEndPts = false; private static boolean showChromosomeFigure = true; private final Font tickFont = HiCGlobals.font(9, false); private final Font spanFont = HiCGlobals.font(12, false); private final HiC hic; private Orientation orientation; private Context context; public HiCRulerPanel(HiC hic) { this.hic = hic; if (HiCGlobals.isDarkulaModeEnabled) { setBackground(Color.BLACK); } else { setBackground(Color.WHITE); } } private static String formatNumber(double position) { if (showOnlyEndPts) { //Export Version NumberFormat df = NumberFormat.getInstance(); df.setMinimumFractionDigits(2); df.setMaximumFractionDigits(2); df.setRoundingMode(RoundingMode.DOWN); //return f.valueToString(position); return df.format(position); } else { DecimalFormat formatter = new DecimalFormat(); return formatter.format((int) position); } } private static TickSpacing findSpacing(long maxValue, int width, boolean scaleInKB) { if (maxValue < 10) { return new TickSpacing(1, HiC.Unit.BP.toString(), 1); } int maxNumberOfTickMarks = (int) Math.ceil(width / 25); // How many zeroes? int nZeroes = (int) Math.log10(maxValue); String majorUnit = scaleInKB ? "KB" : HiC.Unit.BP.toString(); int unitMultiplier = 1; if (nZeroes > 9) { majorUnit = scaleInKB ? "TB" : "GB"; unitMultiplier = (int) 1e9; } if (nZeroes > 6) { majorUnit = scaleInKB ? "GB" : "MB"; unitMultiplier = (int) 1e6; } else if (nZeroes > 3) { majorUnit = scaleInKB ? "MB" : "KB"; unitMultiplier = 1000; } int decrementIter = nZeroes - 1; while (decrementIter > -1) { int latestIncrement = (int) Math.pow(10, nZeroes - decrementIter); int nMajorTicks = (int) Math.ceil(maxValue / latestIncrement); if (nMajorTicks < maxNumberOfTickMarks) { return new TickSpacing(latestIncrement, majorUnit, unitMultiplier); } latestIncrement = (int) Math.pow(10, nZeroes - decrementIter + 1) / 2; nMajorTicks = (int) Math.ceil(maxValue / latestIncrement); if (nMajorTicks < maxNumberOfTickMarks) { return new TickSpacing(latestIncrement, majorUnit, unitMultiplier); } decrementIter--; } int spacing = (int) (maxValue / maxNumberOfTickMarks) / 250 * 250; return new TickSpacing(spacing, majorUnit, unitMultiplier); } public static boolean getShowOnlyEndPts() { return showOnlyEndPts; } public static void setShowOnlyEndPts(boolean toggled) { showOnlyEndPts = toggled; } public static boolean getShowChromosomeFigure() { return showChromosomeFigure; } public static void setShowChromosomeFigure(boolean toggled) { showChromosomeFigure = toggled; } public void setContext(Context frame, Orientation orientation) { this.context = frame; this.orientation = orientation; } @Override protected void paintComponent(Graphics g) { super.paintComponent(g); ((Graphics2D) g).setRenderingHint(RenderingHints.KEY_ANTIALIASING, RenderingHints.VALUE_ANTIALIAS_ON); Graphics2D g2D = (Graphics2D) g; try { hic.getZd(); } catch (Exception e) { return; } if (context == null) return; g.setColor(Color.black); AffineTransform t = g2D.getTransform(); if (orientation == Orientation.VERTICAL) { AffineTransform rotateTransform = new AffineTransform(); rotateTransform.quadrantRotate(-1); g2D.transform(rotateTransform); } // Clear panel drawTicks(g2D); // TODO ms3 drawChr(g2D); g2D.setTransform(t); } private void drawChr(Graphics g) { int w = isHorizontal() ? getWidth() : getHeight(); int h = isHorizontal() ? getHeight() : getWidth(); g.setFont(spanFont); Chromosome chromosome = context.getChromosome(); if (chromosome != null) { if (!ChromosomeHandler.isAllByAll(chromosome)) { String rangeString = chromosome.getName(); int strWidth = g.getFontMetrics().stringWidth(rangeString); int strPosition = (w - strWidth) / 2; if (!isHorizontal()) strPosition = -strPosition; if (hic.isVSTypeDisplay()) { if (isHorizontal()) { rangeString = rangeString + " (control)"; } else { rangeString = rangeString + " (observed)"; } } int vPos = h - 35; if (!showChromosomeFigure) { g.drawString(rangeString, strPosition, vPos); } } } } private boolean isHorizontal() { return orientation == Orientation.HORIZONTAL; } private void drawTicks(Graphics g) { int w = isHorizontal() ? getWidth() : getHeight(); int h = isHorizontal() ? getHeight() : getWidth(); Color topTick = new Color(0, 0, 255); Color leftTick = new Color(0, 128, 0); if (w < 50 || hic.getScaleFactor() == 0) { return; } g.setFont(tickFont); Chromosome chromosome = context.getChromosome(); if (chromosome == null) return; MatrixZoomData zd; try { zd = hic.getZd(); } catch (Exception e) { return; } if (zd == null || zd.getXGridAxis() == null || zd.getYGridAxis() == null) return; if (ChromosomeHandler.isAllByAll(chromosome)) { Point cursorPoint = hic.getGWCursorPoint(); if (cursorPoint != null) { int x1 = 0; ChromosomeHandler handler = hic.getChromosomeHandler(); // Index 0 is whole genome int genomeCoord = 0; for (int i = 1; i < handler.size(); i++) { Color tColor = isHorizontal() ? topTick : leftTick; g.setColor(tColor); double binOrigin = context.getBinOrigin(); Chromosome c = handler.getChromosomeFromIndex(i); genomeCoord += (c.getLength() / 1000); int xBin = zd.getXGridAxis().getBinNumberForGenomicPosition(genomeCoord); int x2 = (int) ((xBin - binOrigin) * hic.getScaleFactor()); int x = (x1 + x2) / 2; int strWidth = g.getFontMetrics().stringWidth(c.getName()); if (isHorizontal()) { if (x1 < cursorPoint.x && cursorPoint.x < x2) { int strPosition = x - strWidth / 2; g.drawString(c.getName(), strPosition, h - 15); g.drawLine(x2, h - 10, x2, h - 2); g.drawLine(x1, h - 10, x1, h - 2); break; } } else { if (-x2 < -cursorPoint.y && -cursorPoint.y < -x1) { int strPosition = -x - strWidth / 2; g.drawString(c.getName(), strPosition, h - 15); g.drawLine(-x2, h - 10, -x2, h - 2); g.drawLine(-x1, h - 10, -x1, h - 2); break; } } x1 = x2; } } } else { HiCGridAxis axis = isHorizontal() ? zd.getXGridAxis() : zd.getYGridAxis(); int binRange = (int) (w / hic.getScaleFactor()); double binOrigin = context.getBinOrigin(); // <= by definition at left/top of panel long genomeOrigin = axis.getGenomicStart(binOrigin); long genomeEnd = axis.getGenomicEnd(binOrigin + binRange); long range = genomeEnd - genomeOrigin; TickSpacing ts = findSpacing(range, w, false); if (showOnlyEndPts) { // Hundredths decimal point long[] genomePositions = hic.getCurrentRegionWindowGenomicPositions(); double startPosition = isHorizontal() ? genomePositions[0] : genomePositions[2]; double endPosition = isHorizontal() ? genomePositions[1] : genomePositions[3]; int endPositionBin = (int) (axis.getBinNumberForGenomicPosition((int) (endPosition - startPosition)) * hic.getScaleFactor()); // actual strings to print and their widths String startPositionString = formatNumber(startPosition / ts.getUnitMultiplier()) + " " + ts.getMajorUnit(); String endPositionString = formatNumber(endPosition / ts.getUnitMultiplier()) + " " + ts.getMajorUnit(); int startPositionStringWidth = g.getFontMetrics().stringWidth(startPositionString); int endPositionStringWidth = g.getFontMetrics().stringWidth(endPositionString); //draw start int drawPositionStartString = isHorizontal() ? 0 : -startPositionStringWidth; g.drawString(startPositionString, drawPositionStartString, h - 15); g.drawLine(0, h - 10, 0, h - 2); //draw end if (!isHorizontal()) endPositionBin = -endPositionBin; int drawPositionEndString = isHorizontal() ? endPositionBin - endPositionStringWidth : endPositionBin; g.drawString(endPositionString, drawPositionEndString, h - 15); g.drawLine(endPositionBin, h - 10, endPositionBin, h - 2); } else { try { long maxX = context.getChromosome().getLength(); double spacing = ts.getMajorTick(); // Find starting point closest to the current origin int nTick = (int) (genomeOrigin / spacing) - 1; int genomePosition = (int) (nTick * spacing); int binNumber = axis.getBinNumberForGenomicPosition(genomePosition); int x = (int) ((binNumber - binOrigin) * hic.getScaleFactor()); while (genomePosition < maxX && x < w) { Color tColor = isHorizontal() ? topTick : leftTick; g.setColor(tColor); genomePosition = (int) (nTick * spacing); binNumber = axis.getBinNumberForGenomicPosition(genomePosition); x = (int) ((binNumber - binOrigin) * hic.getScaleFactor()); String chrPosition = formatNumber((double) genomePosition / ts.getUnitMultiplier() * HiCGlobals.hicMapScale) + " " + ts.getMajorUnit(); int strWidth = g.getFontMetrics().stringWidth(chrPosition); int strPosition = isHorizontal() ? x - strWidth / 2 : -x - strWidth / 2; // prevent cut off near origin if (isHorizontal()) { if (binNumber == 0 && strPosition <= 0 && strPosition >= -strWidth / 2) strPosition = 0; } else { if (binNumber == 0 && strPosition >= -strWidth && strPosition <= -strWidth / 2) strPosition = -strWidth; } // todo bug or expected behavior? // see chr1 of k562 mapq30 at fragment resolution // axis is drawing overlapping positions onto each other // traces to getFragmentNumberForGenomicPosition method //System.out.println(genomePosition+"_"+chrPosition+"_"+strPosition); if (nTick % 2 == 0) g.drawString(chrPosition, strPosition, h - 15); int xpos = isHorizontal() ? x : -x; g.drawLine(xpos, h - 10, xpos, h - 2); nTick++; } /* //for previously selected g.setColor(new Color(200,0,0)); for(Feature2D feature2D:hic.getSuperAdaptor().getPreviousTempSelectedGroup()){ //add tick marks for previously selected group int startCoordinate = axis.getBinNumberForGenomicPosition(feature2D.getStart1()); int endCoordinate = axis.getBinNumberForGenomicPosition(feature2D.getEnd1()); startCoordinate = (int) ((startCoordinate - binOrigin) * hic.getScaleFactor()); endCoordinate = (int) ((endCoordinate - binOrigin) * hic.getScaleFactor()); g.drawLine(startCoordinate,h-10,startCoordinate,h-2); g.setColor(new Color(200,100,50)); g.drawLine(endCoordinate,h-10,endCoordinate,h-2); } */ } catch (Exception ignored) { } } } } public enum Orientation {HORIZONTAL, VERTICAL} static class TickSpacing { private final double majorTick; private final double minorTick; private String majorUnit = ""; private int unitMultiplier = 1; TickSpacing(double majorTick, String majorUnit, int unitMultiplier) { this.majorTick = majorTick; this.minorTick = majorTick / 10.0; this.majorUnit = majorUnit; this.unitMultiplier = unitMultiplier; } double getMajorTick() { return majorTick; } public double getMinorTick() { return minorTick; } String getMajorUnit() { return majorUnit; } public void setMajorUnit(String majorUnit) { this.majorUnit = majorUnit; } int getUnitMultiplier() { return unitMultiplier; } public void setUnitMultiplier(int unitMultiplier) { this.unitMultiplier = unitMultiplier; } } // TODO -- possibly generalize? class ClickLink { final Rectangle region; final String value; final String tooltipText; ClickLink(Rectangle region, String value, String tooltipText) { this.region = region; this.value = value; this.tooltipText = tooltipText; } } } ================================================ FILE: src/juicebox/windowui/HiCZoom.java ================================================ /* * The MIT License (MIT) * * Copyright (c) 2011-2020 Broad Institute, Aiden Lab, Rice University, Baylor College of Medicine * * Permission is hereby granted, free of charge, to any person obtaining a copy * of this software and associated documentation files (the "Software"), to deal * in the Software without restriction, including without limitation the rights * to use, copy, modify, merge, publish, distribute, sublicense, and/or sell * copies of the Software, and to permit persons to whom the Software is * furnished to do so, subject to the following conditions: * * The above copyright notice and this permission notice shall be included in * all copies or substantial portions of the Software. * * THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR * IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, * FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE * AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER * LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, * OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN * THE SOFTWARE. */ package juicebox.windowui; import juicebox.HiC; import java.util.Objects; /** * @author jrobinso * Date: 12/17/12 * Time: 9:16 AM */ public class HiCZoom implements Comparable { private final HiC.Unit unit; private final Integer binSize; public HiCZoom(HiC.Unit unit, int binSize) { this.unit = unit; this.binSize = binSize; } @SuppressWarnings("MethodDoesntCallSuperMethod") public HiCZoom clone() { return new HiCZoom(unit, binSize); } public HiC.Unit getUnit() { return unit; } public int getBinSize() { return binSize; } public String getKey() { return unit.toString() + "_" + binSize; } public String toString() { return getKey(); } @Override public boolean equals(Object o) { if (this == o) return true; if (o instanceof HiCZoom) { HiCZoom hiCZoom = (HiCZoom) o; return (binSize.equals(hiCZoom.binSize)) && (unit == hiCZoom.unit); } return false; } @Override public int hashCode() { return Objects.hash(unit.hashCode(), binSize); } @Override public int compareTo(HiCZoom o) { return binSize.compareTo(o.binSize); } } ================================================ FILE: src/juicebox/windowui/JBTreeCellRenderer.java ================================================ /* * The MIT License (MIT) * * Copyright (c) 2011-2021 Broad Institute, Aiden Lab, Rice University, Baylor College of Medicine * * Permission is hereby granted, free of charge, to any person obtaining a copy * of this software and associated documentation files (the "Software"), to deal * in the Software without restriction, including without limitation the rights * to use, copy, modify, merge, publish, distribute, sublicense, and/or sell * copies of the Software, and to permit persons to whom the Software is * furnished to do so, subject to the following conditions: * * The above copyright notice and this permission notice shall be included in * all copies or substantial portions of the Software. * * THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR * IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, * FITNESS FOR A PARTICULAR PURPOSE AND NON-INFRINGEMENT. IN NO EVENT SHALL THE * AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER * LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, * OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN * THE SOFTWARE. */ package juicebox.windowui; import javax.swing.*; import javax.swing.tree.DefaultTreeCellRenderer; import java.awt.*; public class JBTreeCellRenderer extends DefaultTreeCellRenderer { private static final long serialVersionUID = 900008; private final String[] parts; private final String[] colors; public JBTreeCellRenderer(String[] parts, String[] colors) { this.parts = parts; this.colors = colors; } @Override public Component getTreeCellRendererComponent(JTree tree, Object value, boolean sel, boolean expanded, boolean leaf, int row, boolean hasFocus) { String text = value.toString(); for (int i = 0; i < Math.min(parts.length, colors.length); i++) { text = text.replaceAll(parts[i], "" + parts[i] + ""); } String html = "" + text + ""; return super.getTreeCellRendererComponent( tree, html, sel, expanded, leaf, row, hasFocus); } } ================================================ FILE: src/juicebox/windowui/JSplitButton.java ================================================ /* * The MIT License (MIT) * * Copyright (c) 2011-2021 Broad Institute, Aiden Lab, Rice University, Baylor College of Medicine * * Permission is hereby granted, free of charge, to any person obtaining a copy * of this software and associated documentation files (the "Software"), to deal * in the Software without restriction, including without limitation the rights * to use, copy, modify, merge, publish, distribute, sublicense, and/or sell * copies of the Software, and to permit persons to whom the Software is * furnished to do so, subject to the following conditions: * * The above copyright notice and this permission notice shall be included in * all copies or substantial portions of the Software. * * THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR * IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, * FITNESS FOR A PARTICULAR PURPOSE AND NON-INFRINGEMENT. IN NO EVENT SHALL THE * AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER * LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, * OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN * THE SOFTWARE. */ package juicebox.windowui; import javax.accessibility.Accessible; import javax.accessibility.AccessibleContext; import javax.accessibility.AccessibleRole; import javax.swing.*; import javax.swing.event.ChangeListener; import javax.swing.plaf.ButtonUI; import java.awt.*; import java.awt.event.*; import java.awt.image.BufferedImage; /** * A split button. The user can either click the text, which executes an * action, or click the icon, which opens a popup menu. * * @author eoogbe */ class JSplitButton extends AbstractButton implements Accessible { private static final long serialVersionUID = 900002; private static final String uiClassID = "ButtonUI"; private static final int DEFAULT_POPUP_ICON_LENGTH = 10; private static final String ALWAYS_SHOWS_POPUP_CHANGED_PROPERTY = "alwaysShowPopup"; private static final String SPLIT_GAP_CHANGED_PROPERTY = "splitGap"; private static final String POPUP_ICON_CHANGED_PROPERTY = "popupIcon"; private static final String DISABLED_POPUP_ICON_CHANGED_PROPERTY = "disabledPopupIcon"; private static final String DISABLED_SELECTED_POPUP_ICON_CHANGED_PROPERTY = "disabledSelectedPopupIcon"; private static final String PRESSED_POPUP_ICON_CHANGED_PROPERTY = "pressedPopupIcon"; private static final String ROLLOVER_POPUP_ICON_CHANGED_PROPERTY = "rolloverPopupIcon"; private static final String ROLLOVER_SELECTED_POPUP_ICON_CHANGED_PROPERTY = "rolloverSelectedPopupIcon"; private static final String SELECTED_POPUP_ICON_CHANGED_PROPERTY = "selectedPopupIcon"; private static final String MAIN_TEXT_CHANGED_PROPERTY = "mainText"; private final JButton mainButton; private final JButton popupButton; private PopupAction popupAction; private boolean alwaysShowPopup; private int splitGap = 5; /** * Creates a new JSplitButton with no set text. */ private JSplitButton() { this(""); } /** * Creates a new JSplitButton with initial text. * * @param text the text displayed on this JSplitButton */ public JSplitButton(String text) { mainButton = new JButton(text); popupButton = new JButton(createDefaultPopupIcon()); // popupButton.setPreferredSize(new Dimension((int)popupButton.getPreferredSize().getWidth()+10,(int)popupButton.getPreferredSize().getHeight())); setModel(new DefaultButtonModel()); mainButton.setBorder(BorderFactory.createEmptyBorder()); // popupButton.setBorder(BorderFactory.createEmptyBorder()); mainButton.setContentAreaFilled(false); mainButton.addActionListener(new ActionListener() { @Override public void actionPerformed(ActionEvent e) { doClick(); } }); mainButton.addMouseListener(new MouseAdapter() { @Override public void mouseEntered(MouseEvent e) { if (isRolloverEnabled()) model.setRollover(true); } @Override public void mouseExited(MouseEvent e) { model.setRollover(false); } }); setLayout(new BoxLayout(this, BoxLayout.LINE_AXIS)); resetComponents(); init(null, null); } /** * Creates a new JSplitButton with properties taken from the Action * supplied. * * @param action used to specify the properties of this JSplitButton */ public JSplitButton(Action action) { this(); setAction(action); } private Icon createDefaultPopupIcon() { Image image = new BufferedImage(DEFAULT_POPUP_ICON_LENGTH, DEFAULT_POPUP_ICON_LENGTH, BufferedImage.TYPE_INT_ARGB); Graphics g = image.getGraphics(); g.setColor(new Color(255, 255, 255, 0)); g.fillRect(0, 0, DEFAULT_POPUP_ICON_LENGTH, DEFAULT_POPUP_ICON_LENGTH); g.setColor(Color.BLACK); Polygon traingle = new Polygon( new int[]{0, DEFAULT_POPUP_ICON_LENGTH, DEFAULT_POPUP_ICON_LENGTH / 2, 0}, new int[]{0, 0, DEFAULT_POPUP_ICON_LENGTH, 0}, 4 ); g.fillPolygon(traingle); g.dispose(); return new ImageIcon(image); } private void resetComponents() { removeAll(); add(mainButton); add(Box.createRigidArea(new Dimension(splitGap, 0))); add(new JSeparator(VERTICAL)); add(Box.createRigidArea(new Dimension(splitGap, 0))); add(popupButton); revalidate(); } /** * Returns true if this JSplitButton shows the popup menu for every * click. * * @return true if this JSplitButton shows the popup menu for every * click * @see JSplitButton#setAlwaysShowPopup(boolean) */ public boolean isAlwaysShowPopup() { return alwaysShowPopup; } /** * Sets whether this JSplitButton shows the popup menu for every click. * * @param alwaysShowPopup true if this JSplitButton shows the popup menu * for every click * @see JSplitButton#isAlwaysShowPopup() */ public void setAlwaysShowPopup(boolean alwaysShowPopup) { boolean oldValue = this.alwaysShowPopup; this.alwaysShowPopup = alwaysShowPopup; firePropertyChange(ALWAYS_SHOWS_POPUP_CHANGED_PROPERTY, oldValue, alwaysShowPopup); if (popupAction != null && oldValue != alwaysShowPopup) { setComponentPopupMenu(popupAction.getPopupMenu()); } } /** * Returns the gap between the separator and the labels on each side * * @return the gap between the separator and the labels on each side * @see JSplitButton#setSplitGap(int) */ public int getSplitGap() { return splitGap; } /** * Sets the gap between the separator and the labels on each side. * * @param splitGap the gap set * @see JSplitButton#getSplitGap() */ public void setSplitGap(int splitGap) { int oldValue = this.splitGap; this.splitGap = splitGap; firePropertyChange(SPLIT_GAP_CHANGED_PROPERTY, oldValue, splitGap); if (oldValue != splitGap) { resetComponents(); } } /** * Returns the Icon used on the popup side. This Icon is also used as the * "pressed" and "disabled" Icon if they are not explicitly set. * * @return the popupIcon property * @see AbstractButton#getIcon() * @see JSplitButton#setPopupIcon(Icon) */ private Icon getPopupIcon() { return popupButton.getIcon(); } /** * Sets the Icon used on the popup side. If null, the Icon will be set to * a default value. This Icon is also used as the "pressed" and "disabled" * Icon if they are not explicitly set. * * @param icon the Icon set * @see AbstractButton#setIcon(Icon) * @see JSplitButton#getPopupIcon() */ public void setPopupIcon(Icon icon) { Icon oldValue = getPopupIcon(); if (icon == null) icon = createDefaultPopupIcon(); firePropertyChange(POPUP_ICON_CHANGED_PROPERTY, oldValue, icon); if (!oldValue.equals(icon)) { popupButton.setIcon(icon); } } /** * Returns the icon used on the popup side when this JSplitButton is * disabled. If no disabled icon has been set this will forward the call * to the look and feel to construct an appropriate disabled Icon. Some * look and feels might not render the disabled Icon, in which case they * will ignore this. * * @return the disabledPopupIcon property * @see AbstractButton#getDisabledIcon() * @see JSplitButton#setDisabledPopupIcon(Icon) */ private Icon getDisabledPopupIcon() { return popupButton.getDisabledIcon(); } /** * Sets the icon used on the popup side when this JSplitButton is * disabled. Some look and feels might not render the disabled Icon, in * which case they will ignore this. * * @param icon the icon set * @see AbstractButton#setDisabledIcon(Icon) * @see JSplitButton#getDisabledPopupIcon() */ public void setDisabledPopupIcon(Icon icon) { Icon oldValue = getDisabledPopupIcon(); firePropertyChange(DISABLED_POPUP_ICON_CHANGED_PROPERTY, oldValue, icon); if (!oldValue.equals(icon)) { popupButton.setDisabledIcon(icon); } } /** * Returns the icon used on the popup side when this JSplitButton is * disabled and selected. If no disabled selected Icon has been set, this * will forward the call to the LookAndFeel to construct an appropriate * disabled Icon from the selection icon if it has been set and to * getDisabledPopupIcon() otherwise. * * @return the disabledSelctedPopupIcon property * @see AbstractButton#getDisabledSelectedIcon() * @see JSplitButton#setDisabledSelectedPopupIcon(Icon) */ private Icon getDisabledSelectedPopupIcon() { return popupButton.getDisabledSelectedIcon(); } /** * Sets the icon used on the popup side when this JSplitButton is * disabled and selected. * * @param icon the icon set * @see AbstractButton#setDisabledSelectedIcon(Icon) * @see JSplitButton#getDisabledSelectedPopupIcon() */ public void setDisabledSelectedPopupIcon(Icon icon) { Icon oldValue = getDisabledSelectedPopupIcon(); firePropertyChange(DISABLED_SELECTED_POPUP_ICON_CHANGED_PROPERTY, oldValue, icon); if (!oldValue.equals(icon)) { popupButton.setDisabledSelectedIcon(icon); } } /** * Returns the icon used on the popup side when this JSpitButton is * pressed. * * @return the pressedPopupIcon property * @see AbstractButton#getPressedIcon() * @see JSplitButton#setPressedPopupIcon(Icon) */ private Icon getPressedPopupIcon() { return popupButton.getPressedIcon(); } /** * Sets the icon used on the popup side when this JSplitButton is pressed. * * @param icon the icon set * @see AbstractButton#setPressedIcon(Icon) * @see JSplitButton#getPressedPopupIcon() */ public void setPressedPopupIcon(Icon icon) { Icon oldValue = getPressedPopupIcon(); firePropertyChange(PRESSED_POPUP_ICON_CHANGED_PROPERTY, oldValue, icon); if (!oldValue.equals(icon)) { popupButton.setPressedIcon(icon); } } /** * Returns the rollover icon used on the popup side. * * @return the rolloverPopupIcon property * @see AbstractButton#getRolloverIcon() * @see JSplitButton#setRolloverPopupIcon(Icon) */ private Icon getRolloverPopupIcon() { return popupButton.getRolloverIcon(); } /** * Sets the rollover icon used on the popup side. * * @param icon the icon set * @see AbstractButton#setRolloverIcon(Icon) * @see JSplitButton#getRolloverPopupIcon() */ public void setRolloverPopupIcon(Icon icon) { Icon oldValue = getRolloverPopupIcon(); firePropertyChange(ROLLOVER_POPUP_ICON_CHANGED_PROPERTY, oldValue, icon); if (!oldValue.equals(icon)) { popupButton.setRolloverIcon(icon); } } /** * Returns the rollover selection icon used on the popup side. * * @return the rolloverSelectedPopupIcon property * @see AbstractButton#getRolloverSelectedIcon() * @see JSplitButton#setRolloverSelectedPopupIcon(Icon) */ private Icon getRolloverSelectedPopupIcon() { return popupButton.getRolloverSelectedIcon(); } /** * Sets the rollover selection icon used on the popup side. * * @param icon the icon set * @see AbstractButton#setRolloverSelectedIcon(Icon) * @see JSplitButton#getRolloverSelectedPopupIcon() */ public void setRolloverSelectedPopupIcon(Icon icon) { Icon oldValue = getRolloverSelectedPopupIcon(); firePropertyChange(ROLLOVER_SELECTED_POPUP_ICON_CHANGED_PROPERTY, oldValue, icon); if (!oldValue.equals(icon)) { popupButton.setRolloverSelectedIcon(icon); } } /** * Returns the selected icon used on the popup side. * * @return the selectedPopupIcon property * @see AbstractButton#getSelectedIcon() * @see JSplitButton#setSelectedPopupIcon(Icon) */ private Icon getSelectedPopupIcon() { return popupButton.getSelectedIcon(); } /** * Sets the selected icon used on the popup side. * * @param icon the icon set * @see AbstractButton#setSelectedIcon(Icon) * @see JSplitButton#getSelectedPopupIcon() */ public void setSelectedPopupIcon(Icon icon) { Icon oldValue = getSelectedPopupIcon(); firePropertyChange(SELECTED_POPUP_ICON_CHANGED_PROPERTY, oldValue, icon); if (!oldValue.equals(icon)) { popupButton.setSelectedIcon(icon); } } /** * Returns the text of the main part of this JSplitButton. Use this * method instead of {@link AbstractButton#getText()}. * * @return the text of the main part of this JSplitButton * @see AbstractButton#getText() * @see JSplitButton#setMainText(String) */ private String getMainText() { return mainButton.getText(); } /** * Sets the text of the main part of this JSplitButton. Use this method * instead of {@link AbstractButton#setText(String)}. * * @param text the text set */ public void setMainText(String text) { String oldValue = getMainText(); firePropertyChange(MAIN_TEXT_CHANGED_PROPERTY, oldValue, text); if (!oldValue.equals(text)) { mainButton.setText(text); } } /* (non-Javadoc) * @see javax.swing.AbstractButton#addActionListener(java.awt.event.ActionListener) */ @Override public void addActionListener(ActionListener listener) { mainButton.addActionListener(listener); super.addActionListener(listener); } /* (non-Javadoc) * @see javax.swing.AbstractButton#removeActionListener(java.awt.event.ActionListener) */ @Override public void removeActionListener(ActionListener listener) { mainButton.removeActionListener(listener); super.removeActionListener(listener); } /* (non-Javadoc) * @see javax.swing.AbstractButton#addChangeListener(javax.swing.event.ChangeListener) */ @Override public void addChangeListener(ChangeListener listener) { mainButton.addChangeListener(listener); super.addChangeListener(listener); } /* (non-Javadoc) * @see javax.swing.AbstractButton#removeChangeListener(javax.swing.event.ChangeListener) */ @Override public void removeChangeListener(ChangeListener listener) { mainButton.removeChangeListener(listener); super.removeChangeListener(listener); } /* (non-Javadoc) * @see javax.swing.AbstractButton#addItemListener(java.awt.event.ItemListener) */ @Override public void addItemListener(ItemListener listener) { mainButton.addItemListener(listener); super.addItemListener(listener); } /* (non-Javadoc) * @see javax.swing.AbstractButton#removeItemListener(java.awt.event.ItemListener) */ @Override public void removeItemListener(ItemListener listener) { mainButton.removeItemListener(listener); super.removeItemListener(listener); } /* (non-Javadoc) * @see javax.swing.AbstractButton#getAction() */ @Override public Action getAction() { return mainButton.getAction(); } /* (non-Javadoc) * @see javax.swing.AbstractButton#setAction(javax.swing.Action) */ @Override public void setAction(Action action) { Action oldValue = getAction(); firePropertyChange("action", oldValue, action); mainButton.setAction(action); } /* (non-Javadoc) * @see javax.swing.JComponent#getAccessibleContext() */ @Override public AccessibleContext getAccessibleContext() { if (accessibleContext == null) { accessibleContext = new AccessibleJSplitButton(); } return accessibleContext; } /* (non-Javadoc) * @see javax.swing.JComponent#getComponentPopupMenu() */ @Override public JPopupMenu getComponentPopupMenu() { return (popupAction == null) ? null : popupAction.getPopupMenu(); } /* (non-Javadoc) * @see javax.swing.JComponent#setComponentPopupMenu(javax.swing.JPopupMenu) */ @Override public void setComponentPopupMenu(JPopupMenu popupMenu) { if (popupAction != null) { super.removeActionListener(popupAction); mainButton.removeActionListener(popupAction); popupButton.removeActionListener(popupAction); popupAction = null; } if (popupMenu != null) { popupAction = new PopupAction(popupMenu); popupButton.addActionListener(popupAction); if (alwaysShowPopup) { super.addActionListener(popupAction); mainButton.addActionListener(popupAction); } } } /* (non-Javadoc) * @see javax.swing.JComponent#getPopupLocation(java.awt.event.MouseEvent) */ @Override public Point getPopupLocation(MouseEvent event) { return getPopupLocationRelativeTo(event.getComponent()); } /* (non-Javadoc) * @see javax.swing.AbstractButton#getSelectedObjects() */ @Override public Object[] getSelectedObjects() { Object[] result = new Object[1]; if (mainButton.isSelected()) { result[0] = mainButton; } else if (popupButton.isSelected()) { result[0] = popupButton; } else { return null; } return result; } /* (non-Javadoc) * @see javax.swing.AbstractButton#getMnemonic() */ @Override public int getMnemonic() { return mainButton.getMnemonic(); } /* (non-Javadoc) * @see javax.swing.AbstractButton#setMnemonic(int) */ @Override public void setMnemonic(int mnemonic) { int oldValue = getMnemonic(); firePropertyChange(MNEMONIC_CHANGED_PROPERTY, oldValue, mnemonic); mainButton.setMnemonic(mnemonic); } /* (non-Javadoc) * @see javax.swing.AbstractButton#getDisplayedMnemonicIndex() */ @Override public int getDisplayedMnemonicIndex() { return mainButton.getDisplayedMnemonicIndex(); } /* (non-Javadoc) * @see javax.swing.AbstractButton#setDisplayedMnemonicIndex(int) */ @Override public void setDisplayedMnemonicIndex(int index) throws IllegalArgumentException { int oldValue = getDisplayedMnemonicIndex(); mainButton.setDisplayedMnemonicIndex(index); firePropertyChange("displayedMnemonicIndex", oldValue, index); } /* (non-Javadoc) * @see javax.swing.AbstractButton#setHideActionText(boolean) */ @Override public void setHideActionText(boolean hideActionText) { mainButton.setHideActionText(hideActionText); super.setHideActionText(hideActionText); } /* (non-Javadoc) * @see javax.swing.JComponent#getUIClassID() */ @Override public String getUIClassID() { return uiClassID; } /* (non-Javadoc) * @see javax.swing.AbstractButton#updateUI() */ @Override public void updateUI() { setUI((ButtonUI) UIManager.getUI(this)); } private Point getPopupLocationRelativeTo(Component comp) { Insets insets = getInsets(); int height = getHeight(); if (comp == popupButton) { Insets mainButtonInsets = mainButton.getInsets(); int width = mainButton.getWidth(); return new Point(-splitGap - width - mainButtonInsets.left - mainButtonInsets.right - 30, height); } else { Insets mainButtonInsets = mainButton.getInsets(); int width = mainButton.getWidth() + mainButtonInsets.left + mainButtonInsets.right + splitGap; if (comp == this) width += insets.left; return new Point(width, height); } } private class AccessibleJSplitButton extends AccessibleAbstractButton { private static final long serialVersionUID = 900001; @Override public AccessibleRole getAccessibleRole() { return AccessibleRole.PUSH_BUTTON; } } private class PopupAction implements ActionListener { private final JPopupMenu popupMenu; PopupAction(JPopupMenu popupMenu) { this.popupMenu = popupMenu; } /* (non-Javadoc) * @see java.awt.event.ActionListener#actionPerformed( * java.awt.event.ActionEvent) */ @Override public void actionPerformed(ActionEvent e) { Component comp = (Component) e.getSource(); Point popupLocation = getPopupLocationRelativeTo(comp); popupMenu.show(comp, popupLocation.x, popupLocation.y); } JPopupMenu getPopupMenu() { return popupMenu; } } } ================================================ FILE: src/juicebox/windowui/LoadAssemblyAnnotationsDialog.java ================================================ /* * The MIT License (MIT) * * Copyright (c) 2011-2021 Broad Institute, Aiden Lab, Rice University, Baylor College of Medicine * * Permission is hereby granted, free of charge, to any person obtaining a copy * of this software and associated documentation files (the "Software"), to deal * in the Software without restriction, including without limitation the rights * to use, copy, modify, merge, publish, distribute, sublicense, and/or sell * copies of the Software, and to permit persons to whom the Software is * furnished to do so, subject to the following conditions: * * The above copyright notice and this permission notice shall be included in * all copies or substantial portions of the Software. * * THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR * IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, * FITNESS FOR A PARTICULAR PURPOSE AND NON-INFRINGEMENT. IN NO EVENT SHALL THE * AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER * LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, * OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN * THE SOFTWARE. */ package juicebox.windowui; import juicebox.DirectoryManager; import juicebox.HiC; import juicebox.HiCGlobals; import juicebox.MainWindow; import juicebox.assembly.AssemblyFileImporter; import juicebox.assembly.AssemblyStateTracker; import juicebox.assembly.PsfFileImporter; import juicebox.gui.SuperAdapter; import juicebox.mapcolorui.FeatureRenderer; import juicebox.track.feature.AnnotationLayer; import juicebox.track.feature.AnnotationLayerHandler; import juicebox.windowui.layers.LayersPanel; import juicebox.windowui.layers.Load2DAnnotationsDialog; import org.broad.igv.ui.util.FileDialogUtils; import org.broad.igv.util.ResourceLocator; import javax.swing.*; import javax.swing.event.TreeSelectionEvent; import javax.swing.event.TreeSelectionListener; import javax.swing.tree.*; import java.awt.*; import java.awt.event.*; import java.io.BufferedReader; import java.io.File; import java.io.InputStream; import java.io.InputStreamReader; import java.util.ArrayList; import java.util.Enumeration; import java.util.HashMap; import java.util.Map; /** * Created by nathanielmusial on 6/29/17. */ public class LoadAssemblyAnnotationsDialog extends JDialog implements TreeSelectionListener { private static final long serialVersionUID = 9000044; private static DefaultMutableTreeNode customAddedFeatures = null; private final String[] searchHighlightColors = {"#ff0000", "#00ff00", "#0000ff", "#ff00ff", "#00ffff", "#ff9900", "#ff66ff", "#ffff00"}; private final JTree tree; private final JButton openAssemblyButton; private final Map loadedAnnotationsMap = new HashMap<>(); private final ArrayList mostRecentPaths = new ArrayList<>(); private File openAnnotationPath = DirectoryManager.getUserDirectory(); public LoadAssemblyAnnotationsDialog(final SuperAdapter superAdapter) { super(superAdapter.getMainWindow(), "Select Assembly annotation file(s) to open"); final LayersPanel layersPanel = superAdapter.getLayersPanel(); //Create the nodes. final DefaultMutableTreeNode top = new DefaultMutableTreeNode(new ItemInfo("root", ""), true); createNodes(top, superAdapter.getHiC()); //Create a tree that allows one selection at a time. tree = new JTree(top); tree.getSelectionModel().setSelectionMode(TreeSelectionModel.DISCONTIGUOUS_TREE_SELECTION); //Listen for when the selection changes. tree.addTreeSelectionListener(this); tree.setRootVisible(false); tree.addMouseListener(new MouseAdapter() { @Override public void mousePressed(MouseEvent mouseEvent) { TreePath selPath = tree.getPathForLocation(mouseEvent.getX(), mouseEvent.getY()); if (selPath != null) { if (mouseEvent.getClickCount() == 2) { DefaultMutableTreeNode node = (DefaultMutableTreeNode) selPath.getLastPathComponent(); if (node != null && node.isLeaf()) { TreePath[] paths = new TreePath[1]; paths[0] = selPath; try { safeLoadAssemblyFiles(paths, layersPanel, superAdapter); } catch (Exception e) { SuperAdapter.showMessageDialog("Unable to load file\n" + e.getLocalizedMessage()); } LoadAssemblyAnnotationsDialog.this.setVisible(false); } } } } }); //Create the scroll pane and add the tree to it. final JScrollPane treeView = new JScrollPane(tree); treeView.setPreferredSize(new Dimension(400, 400)); JPanel centerPanel = new JPanel(new BorderLayout()); centerPanel.add(treeView, BorderLayout.CENTER); add(centerPanel, BorderLayout.CENTER); JPanel buttonPanel = new JPanel(); openAssemblyButton = new JButton("Open Assembly"); openAssemblyButton.setEnabled(false); openAssemblyButton.addActionListener(new ActionListener() { @Override public void actionPerformed(ActionEvent e) { mostRecentPaths.clear(); safeLoadAssemblyFiles(tree.getSelectionPaths(), layersPanel, superAdapter); LoadAssemblyAnnotationsDialog.this.setVisible(false); } }); setDefaultCloseOperation(JDialog.DO_NOTHING_ON_CLOSE); addWindowListener(new WindowAdapter() { @Override public void windowClosing(WindowEvent e) { closeWindow(); } }); JButton cancelButton = new JButton("Cancel"); cancelButton.addActionListener(new ActionListener() { @Override public void actionPerformed(ActionEvent e) { closeWindow(); } }); cancelButton.setPreferredSize(new Dimension((int) cancelButton.getPreferredSize().getWidth(), (int) openAssemblyButton.getPreferredSize().getHeight())); buttonPanel.add(openAssemblyButton); buttonPanel.add(cancelButton); add(buttonPanel, BorderLayout.SOUTH); Dimension minimumSize = new Dimension(700, 400); setMinimumSize(minimumSize); setLocation(100, 100); pack(); addLocalButtonActionPerformed(superAdapter); } public static TreePath getPath(TreeNode treeNode) { java.util.List nodes = new ArrayList<>(); if (treeNode != null) { nodes.add(treeNode); treeNode = treeNode.getParent(); while (treeNode != null) { nodes.add(0, treeNode); treeNode = treeNode.getParent(); } } return nodes.isEmpty() ? null : new TreePath(nodes.toArray()); } private void closeWindow() { customAddedFeatures.removeFromParent(); for (String path : mostRecentPaths) { customAddedFeatures.remove(loadedAnnotationsMap.get(path)); loadedAnnotationsMap.remove(path); } mostRecentPaths.clear(); loadedAnnotationsMap.remove(customAddedFeatures); LoadAssemblyAnnotationsDialog.this.setVisible(false); } private void addLocalButtonActionPerformed(final SuperAdapter superAdapter) { // Get the main window final MainWindow window = superAdapter.getMainWindow(); DefaultTreeModel model = (DefaultTreeModel) tree.getModel(); DefaultMutableTreeNode root = (DefaultMutableTreeNode) model.getRoot(); boolean localFilesAdded = false; File[] twoDfiles = FileDialogUtils.chooseMultiple("Choose 2D Annotation file", openAnnotationPath, null); if (twoDfiles != null && twoDfiles.length > 0) { for (File file : twoDfiles) { if (file == null || !file.exists()) continue; localFilesAdded = true; if (customAddedFeatures == null) { customAddedFeatures = new DefaultMutableTreeNode( new ItemInfo("Added Assembly Files", ""), true); root.add(customAddedFeatures); } String path = file.getAbsolutePath(); openAnnotationPath = new File(path); if (loadedAnnotationsMap.containsKey(path)) { if (HiCGlobals.guiIsCurrentlyActive) { int dialogResult = JOptionPane.showConfirmDialog(window, file.getName() + " is already loaded. Would you like to overwrite it?", "Warning", JOptionPane.YES_NO_OPTION); if (dialogResult == JOptionPane.YES_OPTION) { customAddedFeatures.remove(loadedAnnotationsMap.get(path)); loadedAnnotationsMap.remove(path); } else { continue; } } } DefaultMutableTreeNode treeNode = new DefaultMutableTreeNode( new ItemInfo(file.getName(), path), false); loadedAnnotationsMap.put(path, treeNode); customAddedFeatures.add(treeNode); mostRecentPaths.add(path); } model.reload(root); expandTree(); } LoadAssemblyAnnotationsDialog.this.setVisible(localFilesAdded); } private void expandTree() { TreeNode root = (TreeNode) tree.getModel().getRoot(); TreePath rootPath = new TreePath(root); TreeNode node = (TreeNode) rootPath.getLastPathComponent(); for (Enumeration e = node.children(); e.hasMoreElements(); ) { TreePath childPath = rootPath.pathByAddingChild(e.nextElement()); if (!tree.isExpanded(childPath)) { tree.expandPath(childPath); } } if (!tree.isExpanded(rootPath)) { tree.expandPath(rootPath); } } private void safeLoadAssemblyFiles(final TreePath[] paths, final LayersPanel layersPanel, final SuperAdapter superAdapter) { Runnable runnable = new Runnable() { @Override public void run() { unsafeLoadAssemblyFiles(paths, layersPanel, superAdapter); } }; superAdapter.executeLongRunningTask(runnable, "load 2d annotation files"); } private void unsafeLoadAssemblyFiles(TreePath[] paths, LayersPanel layersPanel, SuperAdapter superAdapter) { // two-file format // single-file format String assemblyPath = null; String psfPath = null; for (TreePath path : paths) { DefaultMutableTreeNode node = (DefaultMutableTreeNode) path.getLastPathComponent(); if (node != null && node.isLeaf()) { ItemInfo info = (ItemInfo) node.getUserObject(); if (info.itemURL.endsWith("assembly")) { assemblyPath = info.itemURL; SuperAdapter.setDatasetTitle(assemblyPath); } else if (info.itemURL.endsWith("psf")) { psfPath = info.itemURL; SuperAdapter.setDatasetTitle(psfPath); HiCGlobals.phasing = true; } else { JOptionPane.showMessageDialog(layersPanel, "Unable to load invalid file!", "Error Message", JOptionPane.ERROR_MESSAGE); return; } } } if (assemblyPath != null || psfPath != null) { try { if (superAdapter.getAssemblyStateTracker() != null) { superAdapter.getAssemblyStateTracker().resetState(); superAdapter.refresh(); } AssemblyFileImporter assemblyFileImporter = null; if (assemblyPath != null) { assemblyFileImporter = new AssemblyFileImporter(assemblyPath, false); } else { assemblyFileImporter = new PsfFileImporter(psfPath, false); } //temp layer to allow deleting of other layers layersPanel.createNewLayerAndAddItToPanels(superAdapter, null); if (superAdapter.getAssemblyLayerHandlers() != null) { for (AnnotationLayerHandler annotationLayerHandler : superAdapter.getAssemblyLayerHandlers()) superAdapter.removeLayer(annotationLayerHandler); } // System.out.println("before import "+System.currentTimeMillis()); assemblyFileImporter.importAssembly(); // System.out.println("out import "+System.currentTimeMillis()); // Rescale resolution slider labels superAdapter.getMainViewPanel().getResolutionSlider().reset(); // Rescale axis tick labels superAdapter.getMainViewPanel().getRulerPanelX().repaint(); superAdapter.getMainViewPanel().getRulerPanelY().repaint(); // read in scaffold data AnnotationLayer scaffoldLayer = new AnnotationLayer( assemblyFileImporter.getAssemblyScaffoldHandler().getScaffoldFeature2DHandler(), AnnotationLayer.LayerType.SCAFFOLD); AnnotationLayerHandler scaffoldLayerHandler = layersPanel.createNewLayerAndAddItToPanels(superAdapter, null); scaffoldLayerHandler.setProperties(scaffoldLayer, "Scaf", Color.green); // System.out.println("after scaf layer "+System.currentTimeMillis()); // read in superscaffold data AnnotationLayer superscaffoldLayer = new AnnotationLayer( assemblyFileImporter.getAssemblyScaffoldHandler().getSuperscaffoldFeature2DHandler(), AnnotationLayer.LayerType.SUPERSCAFFOLD); AnnotationLayerHandler superscaffoldLayerHandler = layersPanel.createNewLayerAndAddItToPanels(superAdapter, null); superscaffoldLayerHandler.setProperties(superscaffoldLayer, "Chr", Color.blue); // System.out.println("after superscaf layer "+System.currentTimeMillis()); AnnotationLayerHandler editLayerHandler = layersPanel.createNewLayerAndAddItToPanels(superAdapter, null); editLayerHandler.setColorOfAllAnnotations(Color.black); editLayerHandler.setLayerNameAndField("Edit"); editLayerHandler.setLineStyle(FeatureRenderer.LineStyle.DASHED); editLayerHandler.getAnnotationLayer().setLayerType(AnnotationLayer.LayerType.EDIT); AssemblyStateTracker assemblyStateTracker = new AssemblyStateTracker(assemblyFileImporter.getAssemblyScaffoldHandler(), superAdapter); superAdapter.setAssemblyStateTracker(assemblyStateTracker); //superAdapter.getLayersPanel().updateAssemblyAnnotationsPanel(superAdapter); superAdapter.getMainMenuBar().setEnableAssemblyMenuOptions(true); superAdapter.getMainMenuBar().enableAssemblyEditsOnImport(superAdapter); for (AnnotationLayerHandler annotationLayerHandler : superAdapter.getAllLayers()) { if (annotationLayerHandler.getAnnotationLayerType() != AnnotationLayer.LayerType.EDIT && annotationLayerHandler.getAnnotationLayer().getFeatureList().getNumTotalFeatures() == 0) superAdapter.removeLayer(annotationLayerHandler); superAdapter.setActiveLayerHandler(scaffoldLayerHandler); superAdapter.getLayersPanel().updateBothLayersPanels(superAdapter); } } catch (Exception ee) { // System.err.println("Could not load selected annotation: " + info.itemName + " - " + info.itemURL); // SuperAdapter.showMessageDialog("Could not load loop selection: " + ee.getMessage()); if (assemblyPath != null) customAddedFeatures.remove(loadedAnnotationsMap.get(assemblyPath)); } } else { System.err.println("Invalid files..."); } } private void expandToWantedNode(DefaultMutableTreeNode dNode) { if (dNode != null) { tree.setExpandsSelectedPaths(true); TreePath path = new TreePath(dNode.getPath()); tree.scrollPathToVisible(path); tree.setSelectionPath(path); } } private boolean createNodes(DefaultMutableTreeNode top, HiC hic) { // Add dataset-specific 2d annotations DefaultMutableTreeNode subParent = new DefaultMutableTreeNode(new ItemInfo("Dataset-specific 2D Features"), true); ResourceLocator[] locators = {hic.getDataset().getPeaks(), hic.getDataset().getBlocks(), hic.getDataset().getSuperLoops()}; String[] locatorName = {"Peaks", "Contact Domains", "ChrX Super Loops"}; boolean datasetSpecificFeatureAdded = false; for (int i = 0; i < 3; i++) { if (locators[i] != null) { DefaultMutableTreeNode treeNode = new DefaultMutableTreeNode(new ItemInfo(locatorName[i], locators[i].getURLPath()), false); subParent.add(treeNode); datasetSpecificFeatureAdded = true; } } if (datasetSpecificFeatureAdded) top.add(subParent); // allow specific dataset features to be top-level // load remaining features from file DefaultMutableTreeNode parent = new DefaultMutableTreeNode(new ItemInfo("Chromatin Features"), true); top.add(parent); InputStream is = Load2DAnnotationsDialog.class.getResourceAsStream("annotations2d.txt"); BufferedReader reader = new BufferedReader(new InputStreamReader(is), HiCGlobals.bufferSize); String nextLine; try { while ((nextLine = reader.readLine()) != null) { final String[] values = nextLine.split(";"); if (values.length != 1 && values.length != 2) { JOptionPane.showMessageDialog(this, "Improper features file", "Error", JOptionPane.ERROR_MESSAGE); return false; } if (values.length == 1) { subParent = new DefaultMutableTreeNode(new ItemInfo(values[0]), true); parent.add(subParent); //node = new DefaultMutableTreeNode(new ItemInfo(key, values[0], values[1])); } else { DefaultMutableTreeNode node = new DefaultMutableTreeNode(new ItemInfo(values[0], values[1]), false); subParent.add(node); } } } catch (Exception ignored) { } if (customAddedFeatures != null) { top.add(customAddedFeatures); } return true; } /** * Required by TreeSelectionListener interface. */ public void valueChanged(TreeSelectionEvent e) { DefaultMutableTreeNode node = (DefaultMutableTreeNode) tree.getLastSelectedPathComponent(); if (node == null) return; openAssemblyButton.setEnabled(node.isLeaf()); } private void collapseAll(JTree tree) { int row = tree.getRowCount() - 1; while (row >= 0) { tree.collapseRow(row); row--; } } private class ItemInfo { final String itemName; final String itemURL; ItemInfo(String itemName, String itemURL) { this.itemName = itemName.trim(); this.itemURL = itemURL.trim(); } ItemInfo(String itemName) { this.itemName = itemName; itemURL = null; } public String toString() { return itemName; } } } ================================================ FILE: src/juicebox/windowui/LoadDialog.java ================================================ /* * The MIT License (MIT) * * Copyright (c) 2011-2021 Broad Institute, Aiden Lab, Rice University, Baylor College of Medicine * * Permission is hereby granted, free of charge, to any person obtaining a copy * of this software and associated documentation files (the "Software"), to deal * in the Software without restriction, including without limitation the rights * to use, copy, modify, merge, publish, distribute, sublicense, and/or sell * copies of the Software, and to permit persons to whom the Software is * furnished to do so, subject to the following conditions: * * The above copyright notice and this permission notice shall be included in * all copies or substantial portions of the Software. * * THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR * IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, * FITNESS FOR A PARTICULAR PURPOSE AND NON-INFRINGEMENT. IN NO EVENT SHALL THE * AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER * LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, * OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN * THE SOFTWARE. */ package juicebox.windowui; import com.jidesoft.swing.JideBoxLayout; import juicebox.DirectoryManager; import juicebox.MainWindow; import juicebox.data.HiCFileLoader; import juicebox.gui.SuperAdapter; import org.jetbrains.annotations.Nullable; import javax.swing.*; import javax.swing.event.TreeSelectionEvent; import javax.swing.event.TreeSelectionListener; import javax.swing.tree.DefaultMutableTreeNode; import javax.swing.tree.TreeNode; import javax.swing.tree.TreePath; import javax.swing.tree.TreeSelectionModel; import java.awt.*; import java.awt.event.*; import java.io.File; import java.util.List; import java.util.*; public class LoadDialog extends JDialog implements TreeSelectionListener, ActionListener { private static final long serialVersionUID = 9000045; public static File LAST_LOADED_HIC_FILE_PATH = DirectoryManager.getUserDirectory(); private static boolean actionLock = false; private final boolean success; private final String[] searchHighlightColors = {"#ff0000", "#00ff00", "#0000ff", "#ff00ff", "#00ffff", "#ff9900", "#ff66ff", "#ffff00"}; private final SuperAdapter superAdapter; private JTree tree; private JSplitButton openButton; private JMenuItem openButton30; private JButton cancelButton; private JButton localButton; private JButton urlButton; private JTextField fTextField; private boolean control; public LoadDialog(MainWindow mainWindow, Properties properties, SuperAdapter superAdapter) { super(mainWindow, "Select file(s) to open"); this.superAdapter = superAdapter; //Create the nodes. final DefaultMutableTreeNode top = new DefaultMutableTreeNode(new ItemInfo("root", "root", "")); //System.out.println(properties); if (properties != null) { if (!createNodes(top, properties)) { dispose(); success = false; return; } //Create a tree that allows one selection at a time. tree = new JTree(top); tree.getSelectionModel().setSelectionMode(TreeSelectionModel.DISCONTIGUOUS_TREE_SELECTION); //Listen for when the selection changes. tree.addTreeSelectionListener(this); tree.setRootVisible(false); tree.addMouseListener(new MouseAdapter() { @Override public void mousePressed(MouseEvent mouseEvent) { TreePath selPath = tree.getPathForLocation(mouseEvent.getX(), mouseEvent.getY()); if (selPath != null) { if (mouseEvent.getClickCount() == 2) { DefaultMutableTreeNode node = (DefaultMutableTreeNode) selPath.getLastPathComponent(); if (node != null && node.isLeaf()) { TreePath[] paths = new TreePath[1]; paths[0] = selPath; loadFiles(paths, null); } } } } }); //Create the scroll pane and add the tree to it. JScrollPane treeView = new JScrollPane(tree); treeView.setPreferredSize(new Dimension(400, 400)); JPanel centerPanel = new JPanel(new BorderLayout()); centerPanel.add(treeView, BorderLayout.CENTER); add(centerPanel, BorderLayout.CENTER); } else { JLabel label = new JLabel("Can't find properties file; no online maps to load"); label.setHorizontalAlignment(JLabel.CENTER); JPanel panel = new JPanel(new BorderLayout()); panel.add(label, BorderLayout.CENTER); add(panel, BorderLayout.CENTER); } JPanel buttonPanel = new JPanel(); openButton = createMAPQ0Button("Open (MAPQ > 0)"); openButton.setEnabled(false); openButton30 = createMAPQ30Menu(openButton, "Open (MAPQ \u2265 30)"); localButton = new JButton("Local..."); localButton.addActionListener(this); localButton.setPreferredSize(new Dimension((int) localButton.getPreferredSize().getWidth(), (int) openButton.getPreferredSize().getHeight())); urlButton = new JButton("URL..."); urlButton.addActionListener(this); urlButton.setPreferredSize(new Dimension((int) urlButton.getPreferredSize().getWidth(), (int) openButton.getPreferredSize().getHeight())); cancelButton = new JButton("Cancel"); cancelButton.addActionListener(this); cancelButton.setPreferredSize(new Dimension((int) cancelButton.getPreferredSize().getWidth(), (int) openButton.getPreferredSize().getHeight())); buttonPanel.add(openButton); buttonPanel.add(localButton); buttonPanel.add(urlButton); buttonPanel.add(cancelButton); add(buttonPanel, BorderLayout.SOUTH); Dimension minimumSize = new Dimension(700, 400); setMinimumSize(minimumSize); setLocation(100, 100); pack(); success = true; final JLabel fLabel = new JLabel(); fTextField = new JTextField(); fLabel.setText("Filter:"); fTextField.setToolTipText("Case Sensitive Search"); fTextField.setPreferredSize(new Dimension((int) cancelButton.getPreferredSize().getWidth(), (int) openButton.getPreferredSize().getHeight())); buttonPanel.add(fLabel, JideBoxLayout.FIX); buttonPanel.add(fTextField, JideBoxLayout.VARY); //*********************SEARCH FILTER******************************* fTextField.addKeyListener(new KeyAdapter() { public void keyReleased(KeyEvent e) { collapseAll(tree); @SuppressWarnings("unchecked") Enumeration en = top.preorderEnumeration(); if (!fTextField.getText().isEmpty()) { String[] searchStrings = fTextField.getText().split(","); colorSearchStrings(searchStrings); //Coloring text that matches input while (en.hasMoreElements()) { TreeNode leaf = en.nextElement(); String str = leaf.toString(); for (String term : searchStrings) { if (str.contains(term)) { expandToWantedNode(leaf); break; } } } } } }); } @Nullable public static TreePath getTreePath(TreeNode treeNode) { List nodes = new ArrayList<>(); if (treeNode != null) { nodes.add(treeNode); treeNode = treeNode.getParent(); while (treeNode != null) { nodes.add(0, treeNode); treeNode = treeNode.getParent(); } } return nodes.isEmpty() ? null : new TreePath(nodes.toArray()); } private JSplitButton createMAPQ0Button(String buttonText) { JSplitButton button = new JSplitButton(buttonText); button.addActionListener(this); return button; } private JMenuItem createMAPQ30Menu(JSplitButton button, String button30Text) { JMenuItem button30 = new JMenuItem(button30Text); button30.addActionListener(this); button30.setEnabled(false); JPopupMenu popupMenu = new JPopupMenu("MAPQ ≥ 30 Menu"); popupMenu.add(button30); popupMenu.setEnabled(false); button.setComponentPopupMenu(popupMenu); return button30; } public static TreeNode[] getPathToRoot(TreeNode aNode, int depth) { TreeNode[] retNodes; if (aNode == null) { if (depth == 0) return null; else retNodes = new TreeNode[depth]; } else { depth++; retNodes = getPathToRoot(aNode.getParent(), depth); retNodes[retNodes.length - depth] = aNode; } return retNodes; } private void expandToWantedNode(TreeNode dNode) { if (dNode != null) { tree.setExpandsSelectedPaths(true); TreePath path = new TreePath(getPathToRoot(dNode, 0)); tree.scrollPathToVisible(path); tree.setSelectionPath(path); } } //Overriding in order to change text color private void colorSearchStrings(final String[] parts) { tree.setCellRenderer(new JBTreeCellRenderer(parts, searchHighlightColors)); } public void setControl(boolean control) { this.control = control; } public boolean getSuccess() { return success; } private boolean createNodes(DefaultMutableTreeNode top, Properties properties) { // Enumeration enumeration = top.breadthFirstEnumeration(); // TreeSet is sorted, so properties file is implemented in order TreeSet keys = new TreeSet<>(properties.stringPropertyNames()); HashMap hashMap = new HashMap<>(); hashMap.put(((ItemInfo) top.getUserObject()).uid, top); //HashMap tempHash = new HashMap(); //tempHash.put(((ItemInfo) top.getUserObject()).uid, top); for (String key : keys) { String value = properties.getProperty(key); DefaultMutableTreeNode node; final String[] values = value.split(","); if (values.length != 3 && values.length != 2) { JOptionPane.showMessageDialog(this, "Improperly formatted properties file; incorrect # of fields", "Error", JOptionPane.ERROR_MESSAGE); return true; } if (values.length == 2) { node = new DefaultMutableTreeNode(new ItemInfo(key, values[0], values[1])); } else { node = new DefaultMutableTreeNode(new ItemInfo(key, values[0], values[1], values[2])); } hashMap.put(key, node); } for (String key : keys) { DefaultMutableTreeNode node = hashMap.get(key); DefaultMutableTreeNode parent = hashMap.get(((ItemInfo) node.getUserObject()).parentKey); if (parent == null) { JOptionPane.showMessageDialog(this, "Improperly formatted properties file; unable to find parent menu " + ((ItemInfo) hashMap.get(key).getUserObject()).parentKey + " for " + key, "Error", JOptionPane.ERROR_MESSAGE); return false; } else { parent.add(node); } } return true; } /** * Required by TreeSelectionListener interface. */ public void valueChanged(TreeSelectionEvent e) { DefaultMutableTreeNode node = (DefaultMutableTreeNode) tree.getLastSelectedPathComponent(); if (node == null) return; if (node.isLeaf()) { openButton.setEnabled(true); // maternal paternal openButton30.setEnabled(!((ItemInfo) node.getUserObject()).itemName.contains("aternal")); } else { openButton.setEnabled(false); openButton30.setEnabled(false); } } public void actionPerformed(ActionEvent e) { if (!actionLock) { try { //use lock as double click protection. actionLock = true; if (e.getSource() == openButton) { loadFiles(tree.getSelectionPaths(), null); } else if (e.getSource() == openButton30) { loadFiles(tree.getSelectionPaths(), "30"); } else if (e.getSource() == localButton) { LAST_LOADED_HIC_FILE_PATH = HiCFileLoader.loadMenuItemActionPerformed(superAdapter, control, LAST_LOADED_HIC_FILE_PATH); setVisible(false); } else if (e.getSource() == urlButton) { HiCFileLoader.loadFromURLActionPerformed(superAdapter, control); setVisible(false); } else if (e.getSource() == cancelButton) { setVisible(false); dispose(); } } finally { actionLock = false; } } } private void loadFiles(TreePath[] paths, String ext) { ArrayList filesToLoad = new ArrayList<>(); StringBuilder title = new StringBuilder(); for (TreePath path : paths) { DefaultMutableTreeNode node = (DefaultMutableTreeNode) path.getLastPathComponent(); if (node != null && node.isLeaf()) { filesToLoad.add((ItemInfo) node.getUserObject()); title.append(path.toString().replace("[", "").replace("]", "").replace(",", "")); if (ext != null) title.append(" MAPQ \u2265 ").append(ext); } } setVisible(false); java.util.List urls = new ArrayList<>(); for (ItemInfo info : filesToLoad) { if (info.itemURL == null || !info.itemURL.endsWith(".hic")) { JOptionPane.showMessageDialog(this, info.itemName + " is not a hic file, or the path to the file is not specified."); continue; } String toadd = info.itemURL; if (ext != null) { toadd = toadd.replace(".hic", "_" + ext + ".hic"); } System.out.println("New URL: " + toadd); urls.add(toadd); } //code to add a recent file to the menu superAdapter.safeLoad(urls, control, title.toString()); } private void collapseAll(JTree tree) { int row = tree.getRowCount() - 1; while (row >= 0) { tree.collapseRow(row); row--; } } private class ItemInfo { final String uid; final String itemName; final String parentKey; String itemURL; ItemInfo(String uid, String parentKey, String itemName, String itemURL) { this.uid = uid; this.parentKey = parentKey; this.itemName = itemName.trim(); this.itemURL = itemURL.trim(); } ItemInfo(String uid, String parentKey, String itemName) { this.parentKey = parentKey; this.itemName = itemName; this.uid = uid; } public String toString() { return itemName; } } } ================================================ FILE: src/juicebox/windowui/LoadModifiedAssemblyAnnotationsDialog.java ================================================ /* * The MIT License (MIT) * * Copyright (c) 2011-2021 Broad Institute, Aiden Lab, Rice University, Baylor College of Medicine * * Permission is hereby granted, free of charge, to any person obtaining a copy * of this software and associated documentation files (the "Software"), to deal * in the Software without restriction, including without limitation the rights * to use, copy, modify, merge, publish, distribute, sublicense, and/or sell * copies of the Software, and to permit persons to whom the Software is * furnished to do so, subject to the following conditions: * * The above copyright notice and this permission notice shall be included in * all copies or substantial portions of the Software. * * THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR * IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, * FITNESS FOR A PARTICULAR PURPOSE AND NON-INFRINGEMENT. IN NO EVENT SHALL THE * AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER * LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, * OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN * THE SOFTWARE. */ package juicebox.windowui; import juicebox.DirectoryManager; import juicebox.HiC; import juicebox.HiCGlobals; import juicebox.MainWindow; import juicebox.assembly.AssemblyFileImporter; import juicebox.assembly.AssemblyScaffoldHandler; import juicebox.assembly.PsfFileImporter; import juicebox.gui.SuperAdapter; import juicebox.windowui.layers.LayersPanel; import juicebox.windowui.layers.Load2DAnnotationsDialog; import org.broad.igv.ui.util.FileDialogUtils; import org.broad.igv.util.ResourceLocator; import javax.swing.*; import javax.swing.event.TreeSelectionEvent; import javax.swing.event.TreeSelectionListener; import javax.swing.tree.*; import java.awt.*; import java.awt.event.*; import java.io.BufferedReader; import java.io.File; import java.io.InputStream; import java.io.InputStreamReader; import java.util.ArrayList; import java.util.Enumeration; import java.util.HashMap; import java.util.Map; /** * Created by nathanielmusial on 6/29/17. */ public class LoadModifiedAssemblyAnnotationsDialog extends JDialog implements TreeSelectionListener { private static final long serialVersionUID = 9000013; private static DefaultMutableTreeNode customAddedFeatures = null; private final String[] searchHighlightColors = {"#ff0000", "#00ff00", "#0000ff", "#ff00ff", "#00ffff", "#ff9900", "#ff66ff", "#ffff00"}; private final JTree tree; private final JButton openAssemblyButton; private final Map loadedAnnotationsMap = new HashMap<>(); private final ArrayList mostRecentPaths = new ArrayList<>(); private File openAnnotationPath = DirectoryManager.getUserDirectory(); public LoadModifiedAssemblyAnnotationsDialog(final SuperAdapter superAdapter) { super(superAdapter.getMainWindow(), "Select Modified Assembly annotation file(s) to open"); final LayersPanel layersPanel = superAdapter.getLayersPanel(); //Create the nodes. final DefaultMutableTreeNode top = new DefaultMutableTreeNode(new ItemInfo("root", ""), true); createNodes(top, superAdapter.getHiC()); //Create a tree that allows one selection at a time. tree = new JTree(top); tree.getSelectionModel().setSelectionMode(TreeSelectionModel.DISCONTIGUOUS_TREE_SELECTION); //Listen for when the selection changes. tree.addTreeSelectionListener(this); tree.setRootVisible(false); tree.addMouseListener(new MouseAdapter() { @Override public void mousePressed(MouseEvent mouseEvent) { TreePath selPath = tree.getPathForLocation(mouseEvent.getX(), mouseEvent.getY()); if (selPath != null) { if (mouseEvent.getClickCount() == 2) { DefaultMutableTreeNode node = (DefaultMutableTreeNode) selPath.getLastPathComponent(); if (node != null && node.isLeaf()) { TreePath[] paths = new TreePath[1]; paths[0] = selPath; try { safeLoadAssemblyFiles(paths, layersPanel, superAdapter); } catch (Exception e) { SuperAdapter.showMessageDialog("Unable to load file\n" + e.getLocalizedMessage()); } LoadModifiedAssemblyAnnotationsDialog.this.setVisible(false); } } } } }); //Create the scroll pane and add the tree to it. final JScrollPane treeView = new JScrollPane(tree); treeView.setPreferredSize(new Dimension(400, 400)); JPanel centerPanel = new JPanel(new BorderLayout()); centerPanel.add(treeView, BorderLayout.CENTER); add(centerPanel, BorderLayout.CENTER); JPanel buttonPanel = new JPanel(); openAssemblyButton = new JButton("Open Assembly"); openAssemblyButton.setEnabled(false); openAssemblyButton.addActionListener(new ActionListener() { @Override public void actionPerformed(ActionEvent e) { mostRecentPaths.clear(); safeLoadAssemblyFiles(tree.getSelectionPaths(), layersPanel, superAdapter); LoadModifiedAssemblyAnnotationsDialog.this.setVisible(false); } }); setDefaultCloseOperation(JDialog.DO_NOTHING_ON_CLOSE); addWindowListener(new WindowAdapter() { @Override public void windowClosing(WindowEvent e) { closeWindow(); } }); JButton cancelButton = new JButton("Cancel"); cancelButton.addActionListener(new ActionListener() { @Override public void actionPerformed(ActionEvent e) { closeWindow(); } }); cancelButton.setPreferredSize(new Dimension((int) cancelButton.getPreferredSize().getWidth(), (int) openAssemblyButton.getPreferredSize().getHeight())); buttonPanel.add(openAssemblyButton); buttonPanel.add(cancelButton); add(buttonPanel, BorderLayout.SOUTH); Dimension minimumSize = new Dimension(700, 400); setMinimumSize(minimumSize); setLocation(100, 100); pack(); addLocalButtonActionPerformed(superAdapter); } public static TreePath getPath(TreeNode treeNode) { java.util.List nodes = new ArrayList<>(); if (treeNode != null) { nodes.add(treeNode); treeNode = treeNode.getParent(); while (treeNode != null) { nodes.add(0, treeNode); treeNode = treeNode.getParent(); } } return nodes.isEmpty() ? null : new TreePath(nodes.toArray()); } private void closeWindow() { customAddedFeatures.removeFromParent(); for (String path : mostRecentPaths) { customAddedFeatures.remove(loadedAnnotationsMap.get(path)); loadedAnnotationsMap.remove(path); } mostRecentPaths.clear(); loadedAnnotationsMap.remove(customAddedFeatures); LoadModifiedAssemblyAnnotationsDialog.this.setVisible(false); } private void addLocalButtonActionPerformed(final SuperAdapter superAdapter) { // Get the main window final MainWindow window = superAdapter.getMainWindow(); DefaultTreeModel model = (DefaultTreeModel) tree.getModel(); DefaultMutableTreeNode root = (DefaultMutableTreeNode) model.getRoot(); boolean localFilesAdded = false; File[] twoDfiles = FileDialogUtils.chooseMultiple("Choose Assembly files", openAnnotationPath, null); if (twoDfiles != null && twoDfiles.length > 0) { for (File file : twoDfiles) { if (file == null || !file.exists()) continue; localFilesAdded = true; if (customAddedFeatures == null) { customAddedFeatures = new DefaultMutableTreeNode( new ItemInfo("Added Assembly Files", ""), true); root.add(customAddedFeatures); } String path = file.getAbsolutePath(); openAnnotationPath = new File(path); if (loadedAnnotationsMap.containsKey(path)) { if (HiCGlobals.guiIsCurrentlyActive) { int dialogResult = JOptionPane.showConfirmDialog(window, file.getName() + " is already loaded. Would you like to overwrite it?", "Warning", JOptionPane.YES_NO_OPTION); if (dialogResult == JOptionPane.YES_OPTION) { customAddedFeatures.remove(loadedAnnotationsMap.get(path)); loadedAnnotationsMap.remove(path); } else { continue; } } } DefaultMutableTreeNode treeNode = new DefaultMutableTreeNode( new ItemInfo(file.getName(), path), false); loadedAnnotationsMap.put(path, treeNode); customAddedFeatures.add(treeNode); mostRecentPaths.add(path); } model.reload(root); expandTree(); } LoadModifiedAssemblyAnnotationsDialog.this.setVisible(localFilesAdded); } private void expandTree() { TreeNode root = (TreeNode) tree.getModel().getRoot(); TreePath rootPath = new TreePath(root); TreeNode node = (TreeNode) rootPath.getLastPathComponent(); for (Enumeration e = node.children(); e.hasMoreElements(); ) { TreePath childPath = rootPath.pathByAddingChild(e.nextElement()); if (!tree.isExpanded(childPath)) { tree.expandPath(childPath); } } if (!tree.isExpanded(rootPath)) { tree.expandPath(rootPath); } } private void safeLoadAssemblyFiles(final TreePath[] paths, final LayersPanel layersPanel, final SuperAdapter superAdapter) { Runnable runnable = new Runnable() { @Override public void run() { unsafeLoadAssemblyFiles(paths, layersPanel, superAdapter); } }; superAdapter.executeLongRunningTask(runnable, "load 2d annotation files"); } private void unsafeLoadAssemblyFiles(TreePath[] paths, LayersPanel layersPanel, SuperAdapter superAdapter) { String psfPath = null; String assemblyPath = null; for (TreePath path : paths) { DefaultMutableTreeNode node = (DefaultMutableTreeNode) path.getLastPathComponent(); if (node != null && node.isLeaf()) { ItemInfo info = (ItemInfo) node.getUserObject(); if (info.itemURL.endsWith("assembly")) { assemblyPath = info.itemURL; } else if (info.itemURL.endsWith("psf")) { psfPath = info.itemURL; } else { JOptionPane.showMessageDialog(layersPanel, "Unable to load invalid file!", "Error Message", JOptionPane.ERROR_MESSAGE); return; } } } if ((psfPath != null) || assemblyPath != null) { // try { AssemblyFileImporter assemblyFileImporter = null; if (assemblyPath != null) { assemblyFileImporter = new AssemblyFileImporter(assemblyPath, true); } else assemblyFileImporter = new PsfFileImporter(psfPath, true); assemblyFileImporter.importAssembly(); AssemblyScaffoldHandler modifiedAssemblyScaffoldHandler = assemblyFileImporter.getAssemblyScaffoldHandler(); superAdapter.getAssemblyStateTracker().assemblyActionPerformed(modifiedAssemblyScaffoldHandler, true); superAdapter.unsafeClearAllMatrixZoomCache(); superAdapter.refresh(); // } catch (Exception ee) { // System.err.println("Could not load selected annotation: " + info.itemName + " - " + info.itemURL); // SuperAdapter.showMessageDialog("Could not load loop Modified Assembly: " + ee.getMessage()); // customAddedFeatures.remove(loadedAnnotationsMap.get(info.itemURL)); //Todo needs to be a warning when trying to add annotations from a different genomeloadedAnnotationsMap.remove(path); // } } else { System.err.println("Invalid files..."); } } private void expandToWantedNode(DefaultMutableTreeNode dNode) { if (dNode != null) { tree.setExpandsSelectedPaths(true); TreePath path = new TreePath(dNode.getPath()); tree.scrollPathToVisible(path); tree.setSelectionPath(path); } } private boolean createNodes(DefaultMutableTreeNode top, HiC hic) { // Add dataset-specific 2d annotations DefaultMutableTreeNode subParent = new DefaultMutableTreeNode(new ItemInfo("Dataset-specific 2D Features"), true); ResourceLocator[] locators = {hic.getDataset().getPeaks(), hic.getDataset().getBlocks(), hic.getDataset().getSuperLoops()}; String[] locatorName = {"Peaks", "Contact Domains", "ChrX Super Loops"}; boolean datasetSpecificFeatureAdded = false; for (int i = 0; i < 3; i++) { if (locators[i] != null) { DefaultMutableTreeNode treeNode = new DefaultMutableTreeNode(new ItemInfo(locatorName[i], locators[i].getURLPath()), false); subParent.add(treeNode); datasetSpecificFeatureAdded = true; } } if (datasetSpecificFeatureAdded) top.add(subParent); // allow specific dataset features to be top-level // load remaining features from file DefaultMutableTreeNode parent = new DefaultMutableTreeNode(new ItemInfo("Chromatin Features"), true); top.add(parent); InputStream is = Load2DAnnotationsDialog.class.getResourceAsStream("annotations2d.txt"); BufferedReader reader = new BufferedReader(new InputStreamReader(is), HiCGlobals.bufferSize); String nextLine; try { while ((nextLine = reader.readLine()) != null) { final String[] values = nextLine.split(";"); if (values.length != 1 && values.length != 2) { JOptionPane.showMessageDialog(this, "Improper features file", "Error", JOptionPane.ERROR_MESSAGE); return false; } if (values.length == 1) { subParent = new DefaultMutableTreeNode(new ItemInfo(values[0]), true); parent.add(subParent); //node = new DefaultMutableTreeNode(new ItemInfo(key, values[0], values[1])); } else { DefaultMutableTreeNode node = new DefaultMutableTreeNode(new ItemInfo(values[0], values[1]), false); subParent.add(node); } } } catch (Exception ignored) { } if (customAddedFeatures != null) { top.add(customAddedFeatures); } return true; } /** * Required by TreeSelectionListener interface. */ public void valueChanged(TreeSelectionEvent e) { DefaultMutableTreeNode node = (DefaultMutableTreeNode) tree.getLastSelectedPathComponent(); if (node == null) return; openAssemblyButton.setEnabled(node.isLeaf()); } private void collapseAll(JTree tree) { int row = tree.getRowCount() - 1; while (row >= 0) { tree.collapseRow(row); row--; } } private class ItemInfo { final String itemName; final String itemURL; ItemInfo(String itemName, String itemURL) { this.itemName = itemName.trim(); this.itemURL = itemURL.trim(); } ItemInfo(String itemName) { this.itemName = itemName; itemURL = null; } public String toString() { return itemName; } } } ================================================ FILE: src/juicebox/windowui/MatrixType.java ================================================ /* * The MIT License (MIT) * * Copyright (c) 2011-2022 Broad Institute, Aiden Lab, Rice University, Baylor College of Medicine * * Permission is hereby granted, free of charge, to any person obtaining a copy * of this software and associated documentation files (the "Software"), to deal * in the Software without restriction, including without limitation the rights * to use, copy, modify, merge, publish, distribute, sublicense, and/or sell * copies of the Software, and to permit persons to whom the Software is * furnished to do so, subject to the following conditions: * * The above copyright notice and this permission notice shall be included in * all copies or substantial portions of the Software. * * THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR * IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, * FITNESS FOR A PARTICULAR PURPOSE AND NON-INFRINGEMENT. IN NO EVENT SHALL THE * AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER * LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, * OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN * THE SOFTWARE. */ package juicebox.windowui; public enum MatrixType { OBSERVED("Observed"), EXPECTED("Expected"), OE("Observed/Expected"), OEV2("Log[Observed/Expected]"), OEP1("(Observed+1)/(Expected+1)"), OEP1V2("Log[(Observed+1)/(Expected+1)]"), OME("Observed-Expected"), PEARSON("Observed Pearson"), LOG("Log[Observed+1]"), LOGEO("Log[Observed+1]/Log[Expected+1]"), EXPLOGEO("e^(Log[Observed+1]/Log[Expected+1])"), NORM2("Observed Norm^2"), CONTROL("Control"), OECTRL("Control/ExpectedC"), OECTRLV2("Log[Control/ExpectedC]"), OECTRLP1("(Control+1)/(ExpectedC+1)"), OECTRLP1V2("Log[(Control+1)/(ExpectedC+1)]"), CME("Control-ExpectedC"), PEARSONCTRL("Control Pearson"), LOGC("Log[Control+1]"), LOGCEO("Log[Control+1]/Log[ExpectedC+1]"), EXPLOGCEO("e^(Log[Control+1]/Log[ExpectedC+1])"), NORM2CTRL("Control Norm^2"), RATIO("Observed/Control * (AvgC/AvgO)"), RATIOV2("Log[Observed/Control * (AvgC/AvgO)]"), RATIOP1("(Observed+1)/(Control+1) * (AvgC+1)/(AvgO+1)"), RATIOP1V2("Log[(Observed+1)/(Control+1) * (AvgC+1)/(AvgO+1)]"), RATIO0("Observed/Control * (ExpC0/Exp0)"), RATIO0V2("Log[Observed/Control * (ExpC0/Exp0)]"), RATIO0P1("(Observed+1)/(Control+1) * (ExpC0+1)/(Exp0+1)"), RATIO0P1V2("Log[(Observed+1)/(Control+1) * (ExpC0+1)/(Exp0+1)]"), VS("Observed vs Control"), OEVS("Observed/Expected vs Control/ExpectedC"), OEVSV2("Log[Observed/Expected] vs Log[Control/ExpectedC]"), OEVSP1("(Observed+1)/(Expected+1) vs (Control+1)/(ExpectedC+1)"), OEVSP1V2("Log[(Observed+1)/(Expected+1)] vs Log[(Control+1)/(ExpectedC+1)]"), OERATIO("(Observed/Expected) / (Control/ExpectedC)"), OERATIOV2("Log[(Observed/Expected) / (Control/ExpectedC)]"), OERATIOP1("((Observed+1)/(Expected+1)) / ((Control+1)/(ExpectedC+1))"), OERATIOP1V2("Log[((Observed+1)/(Expected+1)) / ((Control+1)/(ExpectedC+1))]"), OERATIOMINUS("(Observed/Expected) - (Control/ExpectedC)"), OERATIOMINUSP1("(Observed+1)/(Expected+1) - (Control+1)/(ExpectedC+1)"), OCMEVS("Observed-Expected vs Control-Expected"), PEARSONVS("Observed Pearson vs Control Pearson"), LOGVS("Log[Observed/AvgO+1] vs Log[Control/AvgC+1]"), LOGEOVS("Log[Observed+1]/Log[Expected+1] vs Log[Control+1]/Log[ExpectedC+1]"), LOGRATIO("Log[Observed/AvgO+1]/Log[Control/AvgC+1]"), LOGRATIOV2("Log[Log[Observed/AvgO+1]/Log[Control/AvgC+1]]"), LOGEORATIO("(Log[Observed+1]/Log[Expected+1]) / (Log[Control+1]/Log[ExpectedC+1])"), LOGEORATIOV2("Log[(Log[Observed+1]/Log[Expected+1]) / (Log[Control+1]/Log[ExpectedC+1])]"), DIFF("Observed-Control"), NORM("Norm"), EIGENVECTOR("Eigenvector"), NORM2OBSVSCTRL("Observed Norm^2 vs Control Norm^2"); private static final MatrixType[] enabledMatrixTypesNoControl = new MatrixType[]{OBSERVED, EXPECTED, OE, OEV2, PEARSON, LOG}; private static final MatrixType[] enabledMatrixTypesWithControl = new MatrixType[]{ OBSERVED, CONTROL, EXPECTED, VS, RATIO, RATIOV2, OE, OECTRL, OEVS, OEV2, OECTRLV2, OEVSV2, PEARSON, PEARSONCTRL, PEARSONVS, LOG, LOGC, LOGEOVS}; private static final MatrixType[] enabledMatrixTypesNoControlDev = new MatrixType[]{OBSERVED, EXPECTED, OE, OEV2, OEP1, OEP1V2, OME, PEARSON, LOG, LOGEO, EXPLOGEO}; private static final MatrixType[] enabledMatrixTypesWithControlDev = new MatrixType[]{ OBSERVED, EXPECTED, OE, OEV2, OEP1, OEP1V2, OME, PEARSON, LOG, LOGEO, CONTROL, OECTRL, OECTRLV2, OECTRLP1, OECTRLP1V2, CME, PEARSONCTRL, LOGC, LOGCEO, VS, RATIO, RATIOV2, RATIOP1, RATIOP1V2, RATIO0, RATIO0V2, RATIO0P1, RATIO0P1V2, OERATIO, OERATIOV2, OERATIOP1, OERATIOP1V2, OERATIOMINUS, OERATIOMINUSP1, OEVS, OEVSV2, OEVSP1, OEVSP1V2, OCMEVS, PEARSONVS, DIFF, LOGVS, LOGEOVS, LOGRATIO, LOGRATIOV2, LOGEORATIO, LOGEORATIOV2, EXPLOGEO, EXPLOGCEO }; private static boolean useAdvancedViews = false; private final String value; MatrixType(String value) { this.value = value; } public static MatrixType enumValueFromString(String text) { if (text != null) { for (MatrixType matrix : MatrixType.values()) { if (text.equalsIgnoreCase(matrix.value)) { return matrix; } } if (text.equalsIgnoreCase("oe")) { return OE; } } return null; } /** * @return true is the option is generally available all maps or resolutions */ public static boolean isObservedOrControl(MatrixType option) { return option == OBSERVED || option == CONTROL; } /** * @return true is the option can be manipulated by the color range slider */ public static boolean isColorScaleType(MatrixType option) { return !isPearsonType(option); } /** * @return true if the option should allowed in genome-wide view */ public static boolean isValidGenomeWideOption(MatrixType option) { return !option.toString().toLowerCase().contains("expected"); } /** * @return true if the option requires control map but not expected vector */ public static boolean isSimpleControlType(MatrixType option) { return option.toString().toLowerCase().contains("control") && !option.toString().toLowerCase().contains("expected"); } /** * @return true if the option involves comparison/divis (but not pearsons) */ public static boolean isOEColorScaleType(MatrixType option) { return option == OEV2 || option == OEP1V2 || option == RATIOV2 || option == RATIOP1V2 || option == RATIO0V2 || option == RATIO0P1V2 || option == OECTRLV2 || option == OECTRLP1V2 || option == OEVSV2 || option == OEVSP1V2 || option == OERATIOV2 || option == OERATIOP1V2 || option == LOGRATIOV2 || option == LOGEORATIOV2 || isSubtactType(option); } public static boolean isSubtactType(MatrixType option) { return option.toString().toLowerCase().contains("-"); } /** * @return true if the option only works for intrachromosomal, not interchromosomal (genomewide may still be allowed) */ public static boolean isOnlyIntrachromosomalType(MatrixType option) { return isPearsonType(option) || isVSTypeDisplay(option); } /** * @return true if the option requires the expected vector */ public static boolean isExpectedValueType(MatrixType option) { return option.toString().toLowerCase().contains("expected"); } /** * @return true if the option uses pearson's */ public static boolean isPearsonType(MatrixType option) { return option.toString().toLowerCase().contains("pearson"); } /** * @return true if the option is dumped (clt) as a vector */ public static boolean isDumpVectorType(MatrixType option) { return option == NORM || option == EXPECTED; } /** * @return true if the option is dumped (clt) as a matrix */ public static boolean isDumpMatrixType(MatrixType option) { return option == OE || option == OBSERVED; } public static boolean isVSTypeDisplay(MatrixType option) { return option.toString().toLowerCase().contains("vs"); } public static boolean isControlPearsonType(MatrixType option) { return option.toString().toLowerCase().contains("control") && option.toString().toLowerCase().contains("pearson"); } public static MatrixType[] getOptions(boolean withControl) { if (withControl) { if (useAdvancedViews) { return MatrixType.enabledMatrixTypesWithControlDev; } return MatrixType.enabledMatrixTypesWithControl; } else { if (useAdvancedViews) { return MatrixType.enabledMatrixTypesNoControlDev; } return MatrixType.enabledMatrixTypesNoControl; } } public static void toggleAdvancedViews() { useAdvancedViews = !useAdvancedViews; } public static boolean getAdvancedViewEnabled() { return useAdvancedViews; } public String toString() { return value; } } ================================================ FILE: src/juicebox/windowui/NormalizationHandler.java ================================================ /* * The MIT License (MIT) * * Copyright (c) 2011-2021 Broad Institute, Aiden Lab, Rice University, Baylor College of Medicine * * Permission is hereby granted, free of charge, to any person obtaining a copy * of this software and associated documentation files (the "Software"), to deal * in the Software without restriction, including without limitation the rights * to use, copy, modify, merge, publish, distribute, sublicense, and/or sell * copies of the Software, and to permit persons to whom the Software is * furnished to do so, subject to the following conditions: * * The above copyright notice and this permission notice shall be included in * all copies or substantial portions of the Software. * * THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR * IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, * FITNESS FOR A PARTICULAR PURPOSE AND NON-INFRINGEMENT. IN NO EVENT SHALL THE * AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER * LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, * OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN * THE SOFTWARE. */ package juicebox.windowui; import java.util.ArrayList; import java.util.List; public class NormalizationHandler { public static final String strNONE = "NONE"; public static final String strVC = "VC"; public static final String strVC_SQRT = "VC_SQRT"; public static final String strKR = "KR"; public static final String strGW_KR = "GW_KR"; public static final String strINTER_KR = "INTER_KR"; public static final String strGW_VC = "GW_VC"; // todo, should we add a GW_VC_SQRT? public static final String strINTER_VC = "INTER_VC"; public static final String strSCALE = "SCALE"; public static final String strGW_SCALE = "GW_SCALE"; public static final String strINTER_SCALE = "INTER_SCALE"; public static final NormalizationType NONE = new NormalizationType(strNONE, "None"); public static final NormalizationType VC = new NormalizationType(strVC, "Coverage"); public static final NormalizationType VC_SQRT = new NormalizationType(strVC_SQRT, "Coverage (Sqrt)"); public static final NormalizationType KR = new NormalizationType(strKR, "Balanced"); public static final NormalizationType GW_KR = new NormalizationType(strGW_KR, "Genome-wide balanced"); public static final NormalizationType INTER_KR = new NormalizationType(strINTER_KR, "Inter balanced"); public static final NormalizationType GW_VC = new NormalizationType(strGW_VC, "Genome-wide coverage"); public static final NormalizationType INTER_VC = new NormalizationType(strINTER_VC, "Inter coverage");//, public static final NormalizationType SCALE = new NormalizationType(strSCALE, "Balanced++"); public static final NormalizationType GW_SCALE = new NormalizationType(strGW_SCALE, "Genome-wide Balanced++"); public static final NormalizationType INTER_SCALE = new NormalizationType(strINTER_SCALE, "Inter Balanced++"); private final static List currentlyAvailableNorms = new ArrayList<>(); public NormalizationHandler() { currentlyAvailableNorms.add(NONE); currentlyAvailableNorms.add(KR); currentlyAvailableNorms.add(VC); currentlyAvailableNorms.add(VC_SQRT); currentlyAvailableNorms.add(GW_KR); currentlyAvailableNorms.add(GW_VC); currentlyAvailableNorms.add(INTER_KR); currentlyAvailableNorms.add(INTER_VC); currentlyAvailableNorms.add(SCALE); currentlyAvailableNorms.add(GW_SCALE); currentlyAvailableNorms.add(INTER_SCALE); } public static List getAllNormTypes() { return currentlyAvailableNorms; } public static boolean isGenomeWideNorm(NormalizationType norm) { return isGenomeWideNormIntra(norm) || isGenomeWideNormInter(norm); } public static NormalizationType[] getAllGWNormTypes(boolean isUseOnlyScalingDefaults) { if (isUseOnlyScalingDefaults) { return new NormalizationType[]{GW_SCALE}; } return new NormalizationType[]{GW_KR, GW_VC, GW_SCALE, INTER_KR, INTER_VC, INTER_SCALE}; } public static boolean isGenomeWideNormIntra(NormalizationType norm) { return norm.equals(GW_KR) || norm.equals(GW_VC) || norm.equals(GW_SCALE); } public static boolean isGenomeWideNormInter(NormalizationType norm) { return norm.equals(INTER_KR) || norm.equals(INTER_VC) || norm.equals(INTER_SCALE); } public static Integer getIdealResolutionLimit(NormalizationType normalizationType) { if (isGenomeWideNorm(normalizationType)) { return 25000; } else { return 0; } } public NormalizationType getNormTypeFromString(String text) { if (text != null && text.length() > 0) { for (NormalizationType norm : currentlyAvailableNorms) { if (text.equalsIgnoreCase(norm.getLabel()) || text.equalsIgnoreCase(norm.getDescription())) { return norm; } } } NormalizationType newNormType = new NormalizationType(text, text); currentlyAvailableNorms.add(newNormType); return newNormType; } public List getDefaultSetForHiCFileBuilding() { List normalizationTypes = new ArrayList<>(); normalizationTypes.add(VC); normalizationTypes.add(VC_SQRT); //normalizationTypes.add(KR); normalizationTypes.add(SCALE); normalizationTypes.add(INTER_SCALE); normalizationTypes.add(GW_SCALE); return normalizationTypes; } } ================================================ FILE: src/juicebox/windowui/NormalizationType.java ================================================ /* * The MIT License (MIT) * * Copyright (c) 2011-2021 Broad Institute, Aiden Lab, Rice University, Baylor College of Medicine * * Permission is hereby granted, free of charge, to any person obtaining a copy * of this software and associated documentation files (the "Software"), to deal * in the Software without restriction, including without limitation the rights * to use, copy, modify, merge, publish, distribute, sublicense, and/or sell * copies of the Software, and to permit persons to whom the Software is * furnished to do so, subject to the following conditions: * * The above copyright notice and this permission notice shall be included in * all copies or substantial portions of the Software. * * THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR * IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, * FITNESS FOR A PARTICULAR PURPOSE AND NON-INFRINGEMENT. IN NO EVENT SHALL THE * AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER * LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, * OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN * THE SOFTWARE. */ package juicebox.windowui; import java.util.Objects; /** * @author jrobinso Date: 8/31/13 9:47 PM */ public class NormalizationType { //LOADED("Loaded"); private final String label; private final String description; public NormalizationType(String label, String description) { this.label = label.toUpperCase(); String description2 = description; if (label.endsWith("SCALE")) { description2 = description2.replaceAll("Fast scaling", "Balanced++"); description2 = description2.replaceAll("fast scaling", "Balanced++"); } this.description = description2; } public String getLabel() { return label; } public String getDescription() { return description; } @Override public String toString() { return label; } @Override public boolean equals(Object obj) { if (this == obj) { return true; } else if (obj instanceof NormalizationType) { NormalizationType norm2 = (NormalizationType) obj; return label.equals(norm2.getLabel()); } return false; } @Override public int hashCode() { return Objects.hash(label.hashCode(), description.hashCode()); } public boolean usesKR() { return label.contains("KR"); } public boolean usesVC() { return label.contains("VC"); } public boolean usesSCALE() { return label.contains("SCALE"); } public boolean isNONE() { return label.equals("NONE"); } } ================================================ FILE: src/juicebox/windowui/QCDialog.java ================================================ /* * The MIT License (MIT) * * Copyright (c) 2011-2021 Broad Institute, Aiden Lab, Rice University, Baylor College of Medicine * * Permission is hereby granted, free of charge, to any person obtaining a copy * of this software and associated documentation files (the "Software"), to deal * in the Software without restriction, including without limitation the rights * to use, copy, modify, merge, publish, distribute, sublicense, and/or sell * copies of the Software, and to permit persons to whom the Software is * furnished to do so, subject to the following conditions: * * The above copyright notice and this permission notice shall be included in * all copies or substantial portions of the Software. * * THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR * IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, * FITNESS FOR A PARTICULAR PURPOSE AND NON-INFRINGEMENT. IN NO EVENT SHALL THE * AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER * LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, * OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN * THE SOFTWARE. */ package juicebox.windowui; import juicebox.HiC; import juicebox.HiCGlobals; import juicebox.MainWindow; import juicebox.data.Dataset; import juicebox.data.ExpectedValueFunction; import org.jfree.chart.ChartFactory; import org.jfree.chart.ChartPanel; import org.jfree.chart.JFreeChart; import org.jfree.chart.axis.LogarithmicAxis; import org.jfree.chart.axis.NumberAxis; import org.jfree.chart.plot.PlotOrientation; import org.jfree.chart.plot.XYPlot; import org.jfree.data.xy.XYSeries; import org.jfree.data.xy.XYSeriesCollection; import javax.swing.*; import javax.swing.text.html.HTMLEditorKit; import javax.swing.text.html.StyleSheet; import java.awt.*; import java.util.NoSuchElementException; import java.util.Scanner; public class QCDialog extends JDialog { private static final long serialVersionUID = 9000012; private static final long[] logXAxis = {10, 12, 15, 19, 23, 28, 35, 43, 53, 66, 81, 100, 123, 152, 187, 231, 285, 351, 433, 534, 658, 811, 1000, 1233, 1520, 1874, 2310, 2848, 3511, 4329, 5337, 6579, 8111, 10000, 12328, 15199, 18738, 23101, 28480, 35112, 43288, 53367, 65793, 81113, 100000, 123285, 151991, 187382, 231013, 284804, 351119, 432876, 533670, 657933, 811131, 1000000, 1232847, 1519911, 1873817, 2310130, 2848036, 3511192, 4328761, 5336699, 6579332, 8111308, 10000000, 12328467, 15199111, 18738174, 23101297, 28480359, 35111917, 43287613, 53366992, 65793322, 81113083, 100000000, 123284674, 151991108, 187381742, 231012970, 284803587, 351119173, 432876128, 533669923, 657933225, 811130831, 1000000000, 1232846739, 1519911083, 1873817423, 2310129700L, 2848035868L, 3511191734L, 4328761281L, 5336699231L, 6579332247L, 8111308308L, 10000000000L}; public QCDialog(MainWindow mainWindow, HiC hic, String title, boolean isControl) { super(mainWindow); Dataset dataset = hic.getDataset(); if (isControl) { dataset = hic.getControlDataset(); } String text = dataset.getStatistics(); String textDescription = null; String textStatistics = null; String graphs = dataset.getGraphs(); JTextPane description = null; JTabbedPane tabbedPane = new JTabbedPane(); HTMLEditorKit kit = new HTMLEditorKit(); StyleSheet styleSheet = kit.getStyleSheet(); styleSheet.addRule("table { border-collapse: collapse;}"); styleSheet.addRule("body {font-family: Sans-Serif; font-size: 12;}"); styleSheet.addRule("td { padding: 2px; }"); styleSheet.addRule("th {border-bottom: 1px solid #000; text-align: left; background-color: #D8D8D8; font-weight: normal;}"); if (text != null) { int split = text.indexOf("

Sequencing
Sequenced Reads:" + value + "
Alignment (% Sequenced Reads)
Normal Paired:"; if (statsMap.containsKey(" Regular")) newStats += statsMap.get(" Regular"); else newStats += statsMap.get(" Normal Paired"); newStats += "
Chimeric Paired:"; if (statsMap.containsKey(" Normal chimeric")) newStats += statsMap.get(" Normal chimeric"); else newStats += statsMap.get(" Chimeric Paired"); newStats += "
Chimeric Ambiguous:"; if (statsMap.containsKey(" Abnormal chimeric")) newStats += statsMap.get(" Abnormal chimeric"); else newStats += statsMap.get(" Chimeric Ambiguous"); newStats += "
Unmapped:" + statsMap.get(" Unmapped") + "
Duplication and Complexity (% Sequenced Reads)
Alignable (Normal+Chimeric Paired):"; if (statsMap.containsKey(" Total alignable reads")) newStats += statsMap.get(" Total alignable reads"); else newStats += statsMap.get("Alignable (Normal+Chimeric Paired)"); newStats += "
Unique Reads:" + value; if (sequenced != -1) { newStats += " (" + decimalFormat.format(unique / (float) sequenced) + ")"; } newStats += "
Unique Reads:" + value + "
PCR Duplicates:" + value; int num; try { num = numberFormat.parse(value.trim()).intValue(); } catch (ParseException error) { num = -1; } if (sequenced != -1) { newStats += " (" + decimalFormat.format(num / (float) sequenced) + ")"; } newStats += "
PCR Duplicates:" + statsMap.get("PCR Duplicates") + "
Optical Duplicates:
Optical Duplicates:" + statsMap.get("Optical Duplicates") + "
Library Complexity Estimate:"; if (statsMap.containsKey("Library complexity (new)")) newStats += statsMap.get("Library complexity (new)"); else newStats += statsMap.get("Library Complexity Estimate"); newStats += "
Analysis of Unique Reads (% Sequenced Reads / % Unique Reads)
Intra-fragment Reads:" + value; int num; try { num = numberFormat.parse(value.trim()).intValue(); } catch (ParseException error) { num = -1; } if (sequenced != -1 && num != -1 && unique != -1) { newStats += " (" + decimalFormat.format(num / (float) sequenced) + " / " + decimalFormat.format(num / (float) unique) + ")"; } newStats += "
Below MAPQ Threshold:" + value.trim(); int num; try { num = numberFormat.parse(value).intValue(); } catch (ParseException error) { num = -1; } if (sequenced != -1 && num != -1 && unique != -1) { newStats += " (" + decimalFormat.format(num / (float) sequenced) + " / " + decimalFormat.format(num / (float) unique) + ")"; } newStats += "
Below MAPQ Threshold:" + statsMap.get("Below MAPQ Threshold") + "
Hi-C Contacts:" + value.trim(); int num; try { num = numberFormat.parse(value).intValue(); } catch (ParseException error) { num = -1; } if (sequenced != -1 && num != -1 && unique != -1) { newStats += " (" + decimalFormat.format(num / (float) sequenced) + " / " + decimalFormat.format(num / (float) unique) + ")"; } newStats += "
Hi-C Contacts:" + statsMap.get("Hi-C Contacts") + "
  Ligation Motif Present:" + value.substring(0, value.indexOf('(')); int num; try { num = numberFormat.parse(value.trim()).intValue(); } catch (ParseException error) { num = -1; } if (sequenced != -1 && num != -1 && unique != -1) { newStats += " (" + decimalFormat.format(num / (float) sequenced) + " / " + decimalFormat.format(num / (float) unique) + ")"; } newStats += "
  3' Bias (Long Range):" + num2 + "% - " + num1 + "%
  3' Bias (Long Range):" + statsMap.get(" 3' Bias (Long Range)") + "
  Pair Type % (L-I-O-R):" + num1 + "% - " + num2 + "% - " + num3 + "% - " + num4 + "%
  Pair Type % (L-I-O-R):" + statsMap.get(" Pair Type %(L-I-O-R)") + "
Analysis of Hi-C Contacts (% Sequenced Reads / % Unique Reads)
Inter-chromosomal:" + value.substring(0, value.indexOf('(')); int num; try { num = numberFormat.parse(value.trim()).intValue(); } catch (ParseException error) { num = -1; } if (sequenced != -1 && num != -1 && unique != -1) { newStats += " (" + decimalFormat.format(num / (float) sequenced) + " / " + decimalFormat.format(num / (float) unique) + ")"; } newStats += "
Inter-chromosomal:" + statsMap.get("Inter-chromosomal") + "
Intra-chromosomal:" + value.substring(0, value.indexOf('(')); int num; try { num = numberFormat.parse(value.trim()).intValue(); } catch (ParseException error) { num = -1; } if (sequenced != -1 && num != -1 && unique != -1) { newStats += " (" + decimalFormat.format(num / (float) sequenced) + " / " + decimalFormat.format(num / (float) unique) + ")"; } newStats += "
Intra-chromosomal:" + statsMap.get("Intra-chromosomal") + "
  Short Range (<20Kb):" + value.substring(0, value.indexOf('(')); int num; try { num = numberFormat.parse(value.trim()).intValue(); } catch (ParseException error) { num = -1; } if (sequenced != -1 && num != -1 && unique != -1) { newStats += " (" + decimalFormat.format(num / (float) sequenced) + " / " + decimalFormat.format(num / (float) unique) + ")"; } newStats += "
  Short Range (<20Kb):" + statsMap.get("Short Range (<20Kb)") + "
  Long Range (>20Kb):" + value.substring(0, value.indexOf('(')); int num; try { num = numberFormat.parse(value.trim()).intValue(); } catch (ParseException error) { num = -1; } if (sequenced != -1 && num != -1 && unique != -1) { newStats += " (" + decimalFormat.format(num / (float) sequenced) + " / " + decimalFormat.format(num / (float) unique) + ")"; } newStats += "
  Long Range (>20Kb):" + statsMap.get("Long Range (>20Kb)") + "
") + 8; textDescription = text.substring(0, split); textStatistics = text.substring(split); description = new JTextPane(); description.setPreferredSize(new Dimension(400,400)); description.setEditable(false); description.setContentType("text/html"); description.setEditorKit(kit); description.setText(textDescription); JScrollPane pane1 = new JScrollPane(description); tabbedPane.addTab("About Library", pane1); JTextPane textPane = new JTextPane(); textPane.setEditable(false); textPane.setContentType("text/html"); textPane.setEditorKit(kit); textPane.setText(textStatistics); JScrollPane pane = new JScrollPane(textPane); tabbedPane.addTab("Statistics", pane); } boolean success = true; if (graphs != null) { long[] A = new long[2000]; long sumA = 0; long[] mapq1 = new long[201]; long[] mapq2 = new long[201]; long[] mapq3 = new long[201]; long[] intraCount = new long[100]; final XYSeries intra = new XYSeries("Intra Count"); final XYSeries leftRead = new XYSeries("Left"); final XYSeries rightRead = new XYSeries("Right"); final XYSeries innerRead = new XYSeries("Inner"); final XYSeries outerRead = new XYSeries("Outer"); final XYSeries allMapq = new XYSeries("All MapQ"); final XYSeries intraMapq = new XYSeries("Intra MapQ"); final XYSeries interMapq = new XYSeries("Inter MapQ"); Scanner scanner = new Scanner(graphs); try { while (!scanner.next().equals("[")) ; for (int idx = 0; idx < 2000; idx++) { A[idx] = scanner.nextLong(); sumA += A[idx]; } while (!scanner.next().equals("[")) ; for (int idx = 0; idx < 201; idx++) { mapq1[idx] = scanner.nextInt(); mapq2[idx] = scanner.nextInt(); mapq3[idx] = scanner.nextInt(); } for (int idx = 199; idx >= 0; idx--) { mapq1[idx] = mapq1[idx] + mapq1[idx + 1]; mapq2[idx] = mapq2[idx] + mapq2[idx + 1]; mapq3[idx] = mapq3[idx] + mapq3[idx + 1]; allMapq.add(idx, mapq1[idx]); intraMapq.add(idx, mapq2[idx]); interMapq.add(idx, mapq3[idx]); } while (!scanner.next().equals("[")) ; for (int idx = 0; idx < 100; idx++) { int tmp = scanner.nextInt(); if (tmp != 0) innerRead.add(logXAxis[idx], tmp); intraCount[idx] = tmp; tmp = scanner.nextInt(); if (tmp != 0) outerRead.add(logXAxis[idx], tmp); intraCount[idx] += tmp; tmp = scanner.nextInt(); if (tmp != 0) rightRead.add(logXAxis[idx], tmp); intraCount[idx] += tmp; tmp = scanner.nextInt(); if (tmp != 0) leftRead.add(logXAxis[idx], tmp); intraCount[idx] += tmp; if (idx > 0) intraCount[idx] += intraCount[idx - 1]; if (intraCount[idx] != 0) intra.add(logXAxis[idx], intraCount[idx]); } } catch (NoSuchElementException exception) { JOptionPane.showMessageDialog(getParent(), "Graphing file improperly formatted", "Error", JOptionPane.ERROR_MESSAGE); success = false; } if (success) { final XYSeriesCollection readTypeCollection = new XYSeriesCollection(); readTypeCollection.addSeries(innerRead); readTypeCollection.addSeries(outerRead); readTypeCollection.addSeries(leftRead); readTypeCollection.addSeries(rightRead); final JFreeChart readTypeChart = ChartFactory.createXYLineChart( "Types of reads vs distance", // chart title "Distance (log)", // domain axis label "Binned Reads (log)", // range axis label readTypeCollection, // data PlotOrientation.VERTICAL, true, // include legend true, false ); final XYPlot readTypePlot = readTypeChart.getXYPlot(); readTypePlot.setDomainAxis(new LogarithmicAxis("Distance (log)")); readTypePlot.setRangeAxis(new LogarithmicAxis("Binned Reads (log)")); Color backgroundColor = HiCGlobals.isDarkulaModeEnabled ? Color.BLACK : Color.WHITE; readTypePlot.setBackgroundPaint(backgroundColor); readTypePlot.setRangeGridlinePaint(Color.lightGray); readTypePlot.setDomainGridlinePaint(Color.lightGray); readTypeChart.setBackgroundPaint(backgroundColor); readTypePlot.setOutlinePaint(Color.DARK_GRAY); final ChartPanel chartPanel = new ChartPanel(readTypeChart); final XYSeriesCollection reCollection = new XYSeriesCollection(); final XYSeries reDistance = new XYSeries("Distance"); for (int i = 0; i < A.length; i++) { if (A[i] != 0) reDistance.add(i, A[i] / (float) sumA); } reCollection.addSeries(reDistance); final JFreeChart reChart = ChartFactory.createXYLineChart( "Distance from closest restriction enzyme site", // chart title "Distance (bp)", // domain axis label "Fraction of Reads (log)", // range axis label reCollection, // data PlotOrientation.VERTICAL, true, // include legend true, false ); final XYPlot rePlot = reChart.getXYPlot(); rePlot.setDomainAxis(new NumberAxis("Distance (bp)")); rePlot.setRangeAxis(new LogarithmicAxis("Fraction of Reads (log)")); rePlot.setBackgroundPaint(backgroundColor); rePlot.setRangeGridlinePaint(Color.lightGray); rePlot.setDomainGridlinePaint(Color.lightGray); reChart.setBackgroundPaint(backgroundColor); rePlot.setOutlinePaint(Color.darkGray); final ChartPanel chartPanel2 = new ChartPanel(reChart); final XYSeriesCollection intraCollection = new XYSeriesCollection(); intraCollection.addSeries(intra); final JFreeChart intraChart = ChartFactory.createXYLineChart( "Intra reads vs distance", // chart title "Distance (log)", // domain axis label "Cumulative Sum of Binned Reads (log)", // range axis label intraCollection, // data PlotOrientation.VERTICAL, true, // include legend true, false ); final XYPlot intraPlot = intraChart.getXYPlot(); intraPlot.setDomainAxis(new LogarithmicAxis("Distance (log)")); intraPlot.setRangeAxis(new NumberAxis("Cumulative Sum of Binned Reads (log)")); intraPlot.setBackgroundPaint(backgroundColor); intraPlot.setRangeGridlinePaint(Color.lightGray); intraPlot.setDomainGridlinePaint(Color.lightGray); intraChart.setBackgroundPaint(backgroundColor); intraPlot.setOutlinePaint(Color.darkGray); final ChartPanel chartPanel3 = new ChartPanel(intraChart); final XYSeriesCollection mapqCollection = new XYSeriesCollection(); mapqCollection.addSeries(allMapq); mapqCollection.addSeries(intraMapq); mapqCollection.addSeries(interMapq); final JFreeChart mapqChart = ChartFactory.createXYLineChart( "MapQ Threshold Count", // chart title "MapQ threshold", // domain axis label "Count", // range axis label mapqCollection, // data PlotOrientation.VERTICAL, true, // include legend true, // include tooltips false ); final XYPlot mapqPlot = mapqChart.getXYPlot(); mapqPlot.setBackgroundPaint(backgroundColor); mapqPlot.setRangeGridlinePaint(Color.lightGray); mapqPlot.setDomainGridlinePaint(Color.lightGray); mapqChart.setBackgroundPaint(backgroundColor); mapqPlot.setOutlinePaint(Color.darkGray); final ChartPanel chartPanel4 = new ChartPanel(mapqChart); tabbedPane.addTab("Pair Type", chartPanel); tabbedPane.addTab("Restriction", chartPanel2); tabbedPane.addTab("Intra vs Distance", chartPanel3); tabbedPane.addTab("MapQ", chartPanel4); } } final ExpectedValueFunction df; if (isControl) { df = dataset.getExpectedValues(hic.getZoom(), hic.getControlNormalizationType()); } else { df = dataset.getExpectedValues(hic.getZoom(), hic.getObsNormalizationType()); } if (df != null) { double[] expected = df.getExpectedValuesNoNormalization().getValues().get(0); final XYSeriesCollection collection = new XYSeriesCollection(); final XYSeries expectedValues = new XYSeries("Expected"); for (int i = 0; i < expected.length; i++) { if (expected[i] > 0) expectedValues.add(i + 1, expected[i]); } collection.addSeries(expectedValues); String title1 = "Expected at " + hic.getZoom() + " norm " + hic.getObsNormalizationType(); final JFreeChart readTypeChart = ChartFactory.createXYLineChart( title1, // chart title "Distance between reads (log)", // domain axis label "Genome-wide expected (log)", // range axis label collection, // data PlotOrientation.VERTICAL, false, // include legend true, false ); final XYPlot readTypePlot = readTypeChart.getXYPlot(); readTypePlot.setDomainAxis(new LogarithmicAxis("Distance between reads (log)")); readTypePlot.setRangeAxis(new LogarithmicAxis("Genome-wide expected (log)")); Color backgroundColor = HiCGlobals.isDarkulaModeEnabled ? Color.BLACK : Color.WHITE; readTypePlot.setBackgroundPaint(backgroundColor); readTypePlot.setRangeGridlinePaint(Color.lightGray); readTypePlot.setDomainGridlinePaint(Color.lightGray); readTypeChart.setBackgroundPaint(backgroundColor); readTypePlot.setOutlinePaint(Color.darkGray); final ChartPanel chartPanel5 = new ChartPanel(readTypeChart); tabbedPane.addTab("Expected", chartPanel5); } if (text == null && graphs == null) { JOptionPane.showMessageDialog(this, "Sorry, no metrics are available for this dataset", "Error", JOptionPane.ERROR_MESSAGE); setVisible(false); dispose(); } else { getContentPane().add(tabbedPane); pack(); setModal(false); setLocation(100, 100); setTitle(title); setVisible(true); } } } ================================================ FILE: src/juicebox/windowui/RecentMenu.java ================================================ /* * The MIT License (MIT) * * Copyright (c) 2011-2021 Broad Institute, Aiden Lab, Rice University, Baylor College of Medicine * * Permission is hereby granted, free of charge, to any person obtaining a copy * of this software and associated documentation files (the "Software"), to deal * in the Software without restriction, including without limitation the rights * to use, copy, modify, merge, publish, distribute, sublicense, and/or sell * copies of the Software, and to permit persons to whom the Software is * furnished to do so, subject to the following conditions: * * The above copyright notice and this permission notice shall be included in * all copies or substantial portions of the Software. * * THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR * IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, * FITNESS FOR A PARTICULAR PURPOSE AND NON-INFRINGEMENT. IN NO EVENT SHALL THE * AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER * LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, * OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN * THE SOFTWARE. */ package juicebox.windowui; import juicebox.DirectoryManager; import juicebox.HiCGlobals; import juicebox.data.HiCFileTools; import juicebox.state.XMLFileWriter; import org.broad.igv.Globals; import org.w3c.dom.Document; import org.w3c.dom.Element; import org.w3c.dom.NodeList; import org.xml.sax.SAXException; import javax.swing.*; import javax.xml.parsers.DocumentBuilder; import javax.xml.parsers.DocumentBuilderFactory; import javax.xml.parsers.ParserConfigurationException; import java.awt.event.ActionEvent; import java.awt.event.ActionListener; import java.io.BufferedWriter; import java.io.File; import java.io.FileWriter; import java.io.IOException; import java.util.ArrayList; import java.util.Arrays; import java.util.List; import java.util.prefs.Preferences; /** * @author Ido Machol, Muhammad S Shamim, Neva Durand */ public abstract class RecentMenu extends JMenu { private static final long serialVersionUID = 9000046; private static final int maxLengthEntryName = 100; private final int m_maxItems; private final String m_entry; private final Preferences prefs = Preferences.userNodeForPackage(Globals.class); private final File JuiceboxStatesXML = new File(DirectoryManager.getHiCDirectory(), "JuiceboxStatesXML.txt"); private final HiCGlobals.menuType myType; private List m_items = new ArrayList<>(); public static final String delimiter = "@@"; public RecentMenu(String name, int count, String prefEntry, HiCGlobals.menuType type) { super(name); this.m_maxItems = count; this.m_entry = prefEntry; this.myType = type; String[] recentEntries = new String[count]; Arrays.fill(recentEntries, ""); boolean addedItem = false; // load recent positions from properties for (int i = this.m_maxItems - 1; i >= 0; i--) { String val = prefs.get(this.m_entry + i, ""); if (!val.equals("")) { addEntry(val, false); addedItem = true; } } if (!addedItem) { this.setEnabled(false); } } /** * Add "Clear" menu item to bottom of this list */ private void addClearItem() { //---- Clear Recent ---- JMenuItem clearMapList = new JMenuItem(); clearMapList.setText("Clear "); clearMapList.addActionListener(new ActionListener() { public void actionPerformed(ActionEvent e) { //Clear all items from preferences: for (int i = 0; i < m_maxItems; i++) { prefs.remove(m_entry + i); } //clear the existing items removeAll(); m_items = new ArrayList<>(); setEnabled(false); //Clean state data: if (myType == HiCGlobals.menuType.STATE) { try { BufferedWriter bWriter = new BufferedWriter(new FileWriter(HiCGlobals.stateFile, false)); BufferedWriter buffWriter = new BufferedWriter(new FileWriter(JuiceboxStatesXML, false)); HiCGlobals.savedStatesList.clear(); XMLFileWriter.overwriteXMLFile(); buffWriter.close(); bWriter.close(); } catch (IOException ex) { ex.printStackTrace(); } } } }); addSeparator(); add(clearMapList); } public static String[] encodeSafeDelimeterSplit(String path) { String pathProtected = path.replaceAll("@@Download", "@PROTECT@"); pathProtected = pathProtected.replaceAll("@@download", "@PROTECT@"); String[] splitString = pathProtected.split(RecentMenu.delimiter); for (int i = 0; i < splitString.length; i++) { splitString[i] = splitString[i].replaceAll("@PROTECT@", "@@download"); } return splitString; } /** * Add new recent entry, update file and menu * * @param savedEntryOriginal Name and Value of entry. * @param updateFile also save to file, Constructor call with false - no need to re-write. */ public void addEntry(String savedEntryOriginal, boolean updateFile) { //clear the existing items this.removeAll(); m_items.remove(savedEntryOriginal); m_items.add(0, savedEntryOriginal); //Chop last item if list is over size: if (this.m_items.size() > this.m_maxItems) { this.m_items.remove(this.m_items.size() - 1); } //add items back to the menu for (String m_item : this.m_items) { String[] temp = encodeSafeDelimeterSplit(m_item); if (!temp[0].equals("")) { String truncatedName = HiCFileTools.getTruncatedText(temp[0], maxLengthEntryName); JMenuItem menuItem = new JMenuItem(truncatedName); menuItem.setVisible(true); menuItem.setToolTipText(temp[0]); menuItem.setActionCommand(m_item); //menuItem.setActionMap(); menuItem.addActionListener(new ActionListener() { public void actionPerformed(ActionEvent actionEvent) { onSelectPosition(actionEvent.getActionCommand()); } }); this.add(menuItem); } } //update the file if (updateFile) { try { //todo: null in savedEntryOriginal will cause an exception... for (int i = 0; i < this.m_maxItems; i++) { if (i < this.m_items.size()) { prefs.put(this.m_entry + i, this.m_items.get(i)); } else { prefs.remove(this.m_entry + i); } } } catch (Exception x) { x.printStackTrace(); } } addClearItem(); //Enable saved states restore, if not already enabled: if (!this.isEnabled()) { this.setEnabled(true); } } /** * Abstract event, fires when recent map is selected. * * @param mapPath The file that was selected. */ protected abstract void onSelectPosition(String mapPath); //TODO--- Update recent menu when HiC states are imported public void updateNamesFromImport(String importedFile) { Document doc; DocumentBuilderFactory dbf = DocumentBuilderFactory.newInstance(); for (int c = 0; c < m_maxItems; c++) { prefs.remove(m_entry + c); } //clear the existing items removeAll(); m_items = new ArrayList<>(); //import names to previous states menu try { DocumentBuilder documentBuilder = dbf.newDocumentBuilder(); doc = documentBuilder.parse(importedFile); Element element = doc.getDocumentElement(); NodeList nodeList = element.getElementsByTagName("STATE"); for (int i = 0; i < nodeList.getLength(); i++) { String importedMapPath = nodeList.item(i).getAttributes().getNamedItem("SelectedPath").getNodeValue(); m_items.add(importedMapPath); } if (this.m_items.size() > this.m_maxItems) { this.m_items.remove(this.m_items.size() - 1); } for (String m_item : this.m_items) { if (!m_item.equals("")) { JMenuItem menuItem = new JMenuItem(m_item); menuItem.setVisible(true); menuItem.setToolTipText(m_item); menuItem.setActionCommand(m_item); //menuItem.setActionMap(); menuItem.addActionListener(new ActionListener() { public void actionPerformed(ActionEvent actionEvent) { onSelectPosition(actionEvent.getActionCommand()); } }); //menuItem.addMouseListener(new MouseListener() ); this.add(menuItem); } } for (int i = 0; i < this.m_maxItems; i++) { if (i < this.m_items.size()) { prefs.put(this.m_entry + i, this.m_items.get(i)); } else { prefs.remove(this.m_entry + i); } } addClearItem(); } catch (ParserConfigurationException | IOException | SAXException pce) { pce.printStackTrace(); } } public String checkForDuplicateNames(String savedNameOriginal) { //check for saved states String savedName = savedNameOriginal; boolean suitableNameNotFound = true; while (suitableNameNotFound) { suitableNameNotFound = false; boolean repFound = false; for (String item : m_items) { if (item.equals(savedName)) { repFound = true; break; } } if (repFound) { suitableNameNotFound = true; int option = JOptionPane.showConfirmDialog(null, "State name: \n" + savedName + "\n" + "already exists. Do you want to overwrite it?", "Confirm", JOptionPane.YES_NO_OPTION); if (option == JOptionPane.YES_OPTION) { return savedName; } if (option == JOptionPane.NO_OPTION) { savedName = JOptionPane.showInputDialog(null, "Please enter new name for state."); return savedName; } if (option == JOptionPane.CLOSED_OPTION) { savedName = ""; return savedName; } } } return savedName; } } ================================================ FILE: src/juicebox/windowui/SaveAssemblyDialog.java ================================================ /* * The MIT License (MIT) * * Copyright (c) 2011-2021 Broad Institute, Aiden Lab, Rice University, Baylor College of Medicine * * Permission is hereby granted, free of charge, to any person obtaining a copy * of this software and associated documentation files (the "Software"), to deal * in the Software without restriction, including without limitation the rights * to use, copy, modify, merge, publish, distribute, sublicense, and/or sell * copies of the Software, and to permit persons to whom the Software is * furnished to do so, subject to the following conditions: * * The above copyright notice and this permission notice shall be included in * all copies or substantial portions of the Software. * * THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR * IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, * FITNESS FOR A PARTICULAR PURPOSE AND NON-INFRINGEMENT. IN NO EVENT SHALL THE * AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER * LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, * OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN * THE SOFTWARE. */ package juicebox.windowui; import juicebox.DirectoryManager; import juicebox.HiCGlobals; import juicebox.MainWindow; import juicebox.assembly.AssemblyFileExporter; import juicebox.assembly.AssemblyScaffoldHandler; import juicebox.assembly.PsfFileExporter; import juicebox.gui.SuperAdapter; import javax.swing.*; import java.io.File; /** * Created by nathanielmusial on 6/30/17. */ public class SaveAssemblyDialog extends JFileChooser { private static final long serialVersionUID = 9000011; private final AssemblyScaffoldHandler assemblyScaffoldHandler; private final String mapName; public SaveAssemblyDialog(AssemblyScaffoldHandler assemblyScaffoldHandler, String mapName) { super(); this.mapName = mapName; this.assemblyScaffoldHandler = assemblyScaffoldHandler; menuOptions(); } // todo see SaveAnnotationsDialog // todo add file extension filter private void menuOptions() { setSelectedFile(new File(mapName + ".review")); if (HiCGlobals.guiIsCurrentlyActive) { int actionDialog = showSaveDialog(MainWindow.getInstance()); if (actionDialog == JFileChooser.APPROVE_OPTION) { File file = getSelectedFile(); String outputPath = file.getAbsolutePath(); if (file.exists()) { actionDialog = JOptionPane.showConfirmDialog(MainWindow.getInstance(), "Replace existing file?"); if (actionDialog == JOptionPane.NO_OPTION || actionDialog == JOptionPane.CANCEL_OPTION) return; } if (HiCGlobals.phasing) { PsfFileExporter psfFileExporter = new PsfFileExporter(assemblyScaffoldHandler, outputPath); psfFileExporter.exportPsfFile(); } else { AssemblyFileExporter assemblyFileExporter = new AssemblyFileExporter(assemblyScaffoldHandler, outputPath); assemblyFileExporter.exportAssemblyFile(); } String autoSaveFileName = DirectoryManager.getHiCDirectory() + "/" + (SuperAdapter.getDatasetTitle().split(".+?/(?=[^/]+$)")[1]).split("\\.(?=[^\\.]+$)")[0] + ".review.autosave.assembly"; File autoSaveFile = new File(autoSaveFileName); autoSaveFile.delete(); } } } } ================================================ FILE: src/juicebox/windowui/SaveImageDialog.java ================================================ /* * The MIT License (MIT) * * Copyright (c) 2011-2021 Broad Institute, Aiden Lab, Rice University, Baylor College of Medicine * * Permission is hereby granted, free of charge, to any person obtaining a copy * of this software and associated documentation files (the "Software"), to deal * in the Software without restriction, including without limitation the rights * to use, copy, modify, merge, publish, distribute, sublicense, and/or sell * copies of the Software, and to permit persons to whom the Software is * furnished to do so, subject to the following conditions: * * The above copyright notice and this permission notice shall be included in * all copies or substantial portions of the Software. * * THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR * IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, * FITNESS FOR A PARTICULAR PURPOSE AND NON-INFRINGEMENT. IN NO EVENT SHALL THE * AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER * LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, * OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN * THE SOFTWARE. */ package juicebox.windowui; import de.erichseifert.vectorgraphics2d.PDFGraphics2D; import de.erichseifert.vectorgraphics2d.ProcessingPipeline; import de.erichseifert.vectorgraphics2d.SVGGraphics2D; import juicebox.HiC; import juicebox.HiCGlobals; import juicebox.MainWindow; import javax.swing.*; import java.awt.*; import java.io.File; import java.io.FileOutputStream; import java.io.IOException; import java.text.SimpleDateFormat; import java.util.Date; public class SaveImageDialog extends JFileChooser { private static final long serialVersionUID = 9000014; private JTextField width; private JTextField height; public SaveImageDialog(String saveImagePath, final HiC hic, final MainWindow mainWindow, final JPanel hiCPanel, final String extension) { super(); if (saveImagePath != null) { setSelectedFile(new File(saveImagePath)); } else { String timeStamp = new SimpleDateFormat("yyyy.MM.dd.HH.mm.ss").format(new Date()); setSelectedFile(new File(timeStamp + ".HiCImage" + extension)); } if (HiCGlobals.guiIsCurrentlyActive) { int actionDialog = showSaveDialog(mainWindow); if (actionDialog == JFileChooser.APPROVE_OPTION) { File selectedFile = getSelectedFile(); final File outputFile; if (selectedFile.getPath().endsWith(".svg") || selectedFile.getPath().endsWith(".SVG") || selectedFile.getPath().endsWith(".pdf") || selectedFile.getPath().endsWith(".PDF")) { outputFile = selectedFile; } else { outputFile = new File(selectedFile + extension); } //saveImagePath = file.getPath(); if (outputFile.exists()) { actionDialog = JOptionPane.showConfirmDialog(MainWindow.getInstance(), "Replace existing file?"); if (actionDialog == JOptionPane.NO_OPTION || actionDialog == JOptionPane.CANCEL_OPTION) return; } mainWindow.executeLongRunningTask(new Runnable() { @Override public void run() { try { int w = Integer.parseInt(width.getText()); int h = Integer.parseInt(height.getText()); if (HiCGlobals.printVerboseComments) System.out.println("Exporting another figure"); if (outputFile.getPath().endsWith(".svg") || outputFile.getPath().endsWith(".SVG")) { exportAsSVG(outputFile, mainWindow, hic, hiCPanel, w, h); } else { exportAsPDF(outputFile, mainWindow, hic, hiCPanel, w, h); } } catch (NumberFormatException error) { JOptionPane.showMessageDialog(mainWindow, "Width and Height must be integers", "Error", JOptionPane.ERROR_MESSAGE); } } }, "Exporting Figure", "Exporting..."); } } } protected JDialog createDialog(Component parent) { JDialog myDialog = super.createDialog(parent); JLabel wLabel = new JLabel("Width"); JLabel hLabel = new JLabel("Height"); width = new JTextField("" + MainWindow.getInstance().getWidth()); width.setColumns(6); height = new JTextField("" + MainWindow.getInstance().getHeight()); height.setColumns(6); JPanel panel = new JPanel(); panel.add(wLabel); panel.add(width); panel.add(hLabel); panel.add(height); myDialog.add(panel, BorderLayout.NORTH); return myDialog; } private void exportAsPDF(File file, MainWindow mainWindow, HiC hic, final JPanel hiCPanel, final int w, final int h) { try { PDFGraphics2D g = new PDFGraphics2D(0, 0, w, h); plotDataOnGraphics(g, mainWindow, w, h, hic, hiCPanel); writeGraphicsToFile(g, file); } catch (Exception e) { System.err.println("Export PDF failed " + e); } } private void exportAsSVG(File file, MainWindow mainWindow, HiC hic, final JPanel hiCPanel, final int w, final int h) { try { SVGGraphics2D g = new SVGGraphics2D(0, 0, w, h); plotDataOnGraphics(g, mainWindow, w, h, hic, hiCPanel); writeGraphicsToFile(g, file); } catch (Exception e) { System.err.println("Export SVG failed " + e); } } private void writeGraphicsToFile(ProcessingPipeline g, File file) throws IOException { try (FileOutputStream fileOutputStream = new FileOutputStream(file)) { fileOutputStream.write(g.getBytes()); } } private void plotDataOnGraphics(Graphics g, final MainWindow mainWindow, final int w, final int h, final HiC hic, final JPanel hiCPanel) { // Print the panel on created graphics. if (w == mainWindow.getWidth() && h == mainWindow.getHeight()) { hiCPanel.printAll(g); } else { JDialog waitDialog = new JDialog(); JPanel panel1 = new JPanel(); panel1.add(new JLabel(" Creating and saving " + w + " by " + h + " image ")); //panel1.setPreferredSize(new Dimension(250,50)); waitDialog.add(panel1); waitDialog.setTitle("Please wait..."); waitDialog.pack(); waitDialog.setDefaultCloseOperation(JFrame.DO_NOTHING_ON_CLOSE); waitDialog.setLocation(100, 100); waitDialog.setVisible(true); mainWindow.setVisible(false); Dimension minSize = mainWindow.getMinimumSize(); Dimension prefSize = mainWindow.getPreferredSize(); hic.centerBP(0, 0); mainWindow.setMinimumSize(new Dimension(w, h)); mainWindow.setPreferredSize(new Dimension(w, h)); mainWindow.pack(); mainWindow.setState(Frame.ICONIFIED); mainWindow.setState(Frame.NORMAL); mainWindow.setVisible(true); mainWindow.setVisible(false); final Runnable painter = new Runnable() { public void run() { hiCPanel.paintImmediately(0, 0, w, h); } }; Thread thread = new Thread(painter) { public void run() { try { SwingUtilities.invokeAndWait(painter); } catch (Exception e) { e.printStackTrace(); } } }; thread.start(); hiCPanel.printAll(g); mainWindow.setPreferredSize(prefSize); mainWindow.setMinimumSize(minSize); mainWindow.setSize(new Dimension(w, h)); waitDialog.setVisible(false); waitDialog.dispose(); mainWindow.setVisible(true); } } } ================================================ FILE: src/juicebox/windowui/layers/LayerPanelButtons.java ================================================ /* * The MIT License (MIT) * * Copyright (c) 2011-2020 Broad Institute, Aiden Lab, Rice University, Baylor College of Medicine * * Permission is hereby granted, free of charge, to any person obtaining a copy * of this software and associated documentation files (the "Software"), to deal * in the Software without restriction, including without limitation the rights * to use, copy, modify, merge, publish, distribute, sublicense, and/or sell * copies of the Software, and to permit persons to whom the Software is * furnished to do so, subject to the following conditions: * * The above copyright notice and this permission notice shall be included in * all copies or substantial portions of the Software. * * THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR * IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, * FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE * AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER * LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, * OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN * THE SOFTWARE. */ package juicebox.windowui.layers; import juicebox.gui.SuperAdapter; import juicebox.mapcolorui.FeatureRenderer; import juicebox.track.feature.AnnotationLayerHandler; import org.broad.igv.ui.color.ColorChooserPanel; import javax.imageio.ImageIO; import javax.swing.*; import java.awt.*; import java.awt.event.ActionEvent; import java.awt.event.ActionListener; import java.awt.image.BufferedImage; import java.io.IOException; class LayerPanelButtons { public static final int miniButtonSize = 30; public static ColorChooserPanel createColorChooserButton(final SuperAdapter superAdapter, final AnnotationLayerHandler handler) { final ColorChooserPanel colorChooserPanel = new ColorChooserPanel(); colorChooserPanel.setSelectedColor(handler.getDefaultColor()); colorChooserPanel.addActionListener(new ActionListener() { @Override public void actionPerformed(ActionEvent e) { Color c = colorChooserPanel.getSelectedColor(); if (c != null) { handler.setColorOfAllAnnotations(c); superAdapter.repaint(); } } }); colorChooserPanel.setToolTipText("Re-color all annotations in this layer"); handler.setColorChooserPanel(colorChooserPanel); return colorChooserPanel; } public static JButton createCensorButton(final LayersPanel lp, final SuperAdapter superAdapter, final AnnotationLayerHandler handler) throws IOException { final JButton censorButton = createIconButton(lp, "/images/layer/hiclogo.png"); censorButton.addActionListener(new ActionListener() { @Override public void actionPerformed(ActionEvent e) { superAdapter.createCustomChromosomeMap(handler.getAnnotationLayer().getFeatureList(), handler.getLayerName()); } }); handler.setCensorButton(censorButton); censorButton.setEnabled(handler.getExportCapability()); censorButton.setToolTipText("Create sub-map (custom chromosome) from this layer"); return censorButton; } public static JToggleButton createVisibleButton(final Object lp, final SuperAdapter superAdapter, final AnnotationLayerHandler handler) throws IOException { final JToggleButton toggleVisibleButton = createToggleIconButton(lp, "/images/layer/eye_clicked_green.png", "/images/layer/eye_clicked.png", handler.getLayerVisibility()); toggleVisibleButton.addActionListener(new ActionListener() { @Override public void actionPerformed(ActionEvent e) { handler.setLayerVisibility(toggleVisibleButton.isSelected()); if (lp instanceof LayersPanel) { superAdapter.updateMiniAnnotationsLayerPanel(); } else if (lp instanceof MiniAnnotationsLayerPanel) { superAdapter.updateMainLayersPanel(); } superAdapter.repaint(); } }); toggleVisibleButton.setToolTipText("Toggle visibility of this layer"); return toggleVisibleButton; } /** * toggle transparency for this layer */ public static JToggleButton createTransparencyButton(final LayersPanel lp, final SuperAdapter superAdapter, final AnnotationLayerHandler handler) throws IOException { final JToggleButton toggleTransparentButton = createToggleIconButton(lp, "/images/layer/trans_clicked_green.png", "/images/layer/trans_clicked.png", handler.getIsTransparent()); toggleTransparentButton.addActionListener(new ActionListener() { @Override public void actionPerformed(ActionEvent e) { handler.setIsTransparent(toggleTransparentButton.isSelected()); superAdapter.repaint(); } }); toggleTransparentButton.setToolTipText("Toggle transparency of this layer"); return toggleTransparentButton; } /** * Sparse (/subset) plotting for 2d annotations */ public static JToggleButton createToggleSparseButton(final LayersPanel lp, final SuperAdapter superAdapter, final AnnotationLayerHandler handler) throws IOException { final JToggleButton toggleSparseButton = createToggleIconButton(lp, "/images/layer/sparse.png", "/images/layer/sparse.png", handler.getIsSparse()); toggleSparseButton.addActionListener(new ActionListener() { @Override public void actionPerformed(ActionEvent e) { handler.setIsSparse(toggleSparseButton.isSelected()); superAdapter.repaint(); } }); toggleSparseButton.setToolTipText("Plot a limited number of 2D annotations in this layer at a time " + "(speed up plotting when there are many annotations)."); return toggleSparseButton; } public static JButton createCopyButton(final LayersPanel lp, final SuperAdapter superAdapter, final AnnotationLayerHandler handler) throws IOException { JButton copyButton = createIconButton(lp, "/images/layer/copy.png"); copyButton.addActionListener(new ActionListener() { @Override public void actionPerformed(ActionEvent e) { //AnnotationLayerHandler handlerDup = lp.createNewLayerAndAddItToPanels(superAdapter, handler); } }); copyButton.setToolTipText("Duplicate this layer"); return copyButton; } public static JButton createMoveDownButton(final LayersPanel layersPanel, final SuperAdapter superAdapter, final JPanel layerBoxGUI, final JPanel parentPanel, final AnnotationLayerHandler handler) throws IOException { JButton downButton = createIconButton(layersPanel, "/images/layer/down.png"); downButton.addActionListener(new ActionListener() { @Override public void actionPerformed(ActionEvent e) { layerBoxGUI.remove(parentPanel); int index = superAdapter.moveDownIndex(handler); layerBoxGUI.add(parentPanel, index); layerBoxGUI.revalidate(); layerBoxGUI.repaint(); superAdapter.updateMiniAnnotationsLayerPanel(); superAdapter.repaint(); } }); downButton.setToolTipText("Move this layer down (drawing order)"); return downButton; } public static JButton createMoveUpButton(final LayersPanel layersPanel, final SuperAdapter superAdapter, final JPanel layerBoxGUI, final JPanel parentPanel, final AnnotationLayerHandler handler) throws IOException { JButton upButton = createIconButton(layersPanel, "/images/layer/up.png"); upButton.addActionListener(new ActionListener() { @Override public void actionPerformed(ActionEvent e) { layerBoxGUI.remove(parentPanel); int index = superAdapter.moveUpIndex(handler); layerBoxGUI.add(parentPanel, index); layerBoxGUI.revalidate(); layerBoxGUI.repaint(); superAdapter.updateMiniAnnotationsLayerPanel(); superAdapter.repaint(); } }); upButton.setToolTipText("Move this layer up (drawing order)"); return upButton; } public static JButton createDeleteButton(final LayersPanel layersPanel, final SuperAdapter superAdapter, final JPanel layerBoxGUI, final JPanel parentPanel, final AnnotationLayerHandler handler) throws IOException { JButton deleteButton = createIconButton(layersPanel, "/images/layer/trash.png"); deleteButton.addActionListener(new ActionListener() { @Override public void actionPerformed(ActionEvent e) { if (superAdapter.deleteCustomAnnotationDialog(handler.getLayerName()) == JOptionPane.YES_OPTION) { layerBoxGUI.remove(parentPanel); superAdapter.removeLayer(handler); layerBoxGUI.revalidate(); layerBoxGUI.repaint(); superAdapter.updateMiniAnnotationsLayerPanel(); superAdapter.repaint(); } } }); handler.setDeleteLayerButton(deleteButton); deleteButton.setToolTipText("Delete this layer"); return deleteButton; } /** * toggle whether the features will be enlarged for this layer */ public static JToggleButton createToggleEnlargeButton(final LayersPanel lp, final SuperAdapter superAdapter, final AnnotationLayerHandler handler) throws IOException { final JToggleButton toggleEnlargeButton = createToggleIconButton(lp, "/images/layer/enlarge_clicked_down.png", "/images/layer/enlarge_clicked_up.png", handler.getIsEnlarged()); toggleEnlargeButton.addActionListener(new ActionListener() { @Override public void actionPerformed(ActionEvent e) { handler.setIsEnlarged(toggleEnlargeButton.isSelected()); superAdapter.repaint(); } }); toggleEnlargeButton.setToolTipText("Enlarge features in this layer"); return toggleEnlargeButton; } /** * toggle plotting styles; setup and action done in helper function */ public static JButton createTogglePlottingStyleButton(final SuperAdapter superAdapter, final AnnotationLayerHandler handler) throws IOException { PlottingStyleButton togglePlottingStyleButton = createTogglePlottingStyleIconButton(handler, superAdapter); togglePlottingStyleButton.setToolTipText("Change partial plotting style in this layer"); handler.setPlottingStyleButton(togglePlottingStyleButton); return togglePlottingStyleButton; } /** * export annotations in layer to new file */ public static JButton createExportButton(final LayersPanel layersPanel, final AnnotationLayerHandler handler) throws IOException { final JButton exportLayerButton = createIconButton(layersPanel, "/images/layer/export_icon_green.png"); exportLayerButton.addActionListener(new ActionListener() { @Override public void actionPerformed(ActionEvent e) { handler.exportAnnotations(); } }); handler.setExportButton(exportLayerButton); exportLayerButton.setEnabled(handler.getExportCapability()); exportLayerButton.setToolTipText("Export annotations from this layer"); return exportLayerButton; } /** * undo last annotation in layer */ public static JButton createUndoButton(final LayersPanel lp, final SuperAdapter superAdapter, final AnnotationLayerHandler handler) throws IOException { final JButton undoButton = createIconButton(lp, "/images/layer/undo.png"); undoButton.addActionListener(new ActionListener() { @Override public void actionPerformed(ActionEvent e) { handler.undo(undoButton); superAdapter.repaint(); } }); handler.setUndoButton(undoButton); undoButton.setEnabled(handler.getUndoCapability()); undoButton.setToolTipText("Undo last new feature in this layer"); return undoButton; } /** * clear annotations in this layer */ public static JButton createEraseButton(final LayersPanel lp, final SuperAdapter superAdapter, final AnnotationLayerHandler handler) throws IOException { JButton clearButton = createIconButton(lp, "/images/layer/erase.png"); clearButton.addActionListener(new ActionListener() { @Override public void actionPerformed(ActionEvent e) { if (superAdapter.clearCustomAnnotationDialog() == JOptionPane.YES_OPTION) { //TODO: do something with the saving... just update temp? handler.clearAnnotations(); handler.setExportAbility(false); superAdapter.repaint(); handler.setExportAbility(false); handler.setUndoAbility(false); } } }); clearButton.setToolTipText("Clear all annotations in this layer"); return clearButton; } /** * button to set active layer */ public static JToggleButton createWritingButton(final Object lp, final SuperAdapter superAdapter, final AnnotationLayerHandler handler) throws IOException { final JToggleButton writeButton = createToggleIconButton(lp, "/images/layer/pencil.png", "/images/layer/pencil_gray.png", handler.isActiveLayer(superAdapter)); handler.setActiveLayerButton(writeButton); writeButton.addActionListener(new ActionListener() { @Override public void actionPerformed(ActionEvent e) { superAdapter.setActiveLayerHandler(handler); superAdapter.updateMiniAnnotationsLayerPanel(); superAdapter.updateMainLayersPanel(); superAdapter.repaint(); } }); writeButton.setToolTipText("Enable drawing of annotations to this layer; Hold down shift key, then click and drag on map"); return writeButton; } /** * triple state toggle button for plotting styles */ private static PlottingStyleButton createTogglePlottingStyleIconButton(final AnnotationLayerHandler handler, final SuperAdapter superAdapter) throws IOException { final PlottingStyleButton triStateButton = new PlottingStyleButton(); triStateButton.setPreferredSize(new Dimension(miniButtonSize, miniButtonSize)); triStateButton.setBorderPainted(false); triStateButton.addActionListener(new ActionListener() { @Override public void actionPerformed(ActionEvent e) { FeatureRenderer.PlottingOption currentState = FeatureRenderer.getNextState(handler.getPlottingStyle()); handler.setPlottingStyle(currentState); superAdapter.repaint(); } }); triStateButton.setCurrentState(handler.getPlottingStyle()); return triStateButton; } private static JButton createIconButton(Object ls, String url) throws IOException { BufferedImage imageActive = ImageIO.read(ls.getClass().getResource(url)); ImageIcon iconActive = new ImageIcon(imageActive); // image when button is inactive/transitioning (lighter shade/color) ImageIcon iconTransition = new ImageIcon(translucentImage(imageActive, 0.6f)); ImageIcon iconInactive = new ImageIcon(translucentImage(imageActive, 0.2f)); JButton button = new JButton(iconActive); button.setRolloverIcon(iconTransition); button.setPressedIcon(iconInactive); button.setBorderPainted(false); button.setPreferredSize(new Dimension(miniButtonSize, miniButtonSize)); return button; } /** * @return toggle button which changes icon transparency when clicked * @throws IOException */ private static JToggleButton createToggleIconButton(Object lp, String url1, String url2, boolean activatedStatus) throws IOException { // image when button is active/selected (is the darkest shade/color) //BufferedImage imageActive = ImageIO.read(getClass().getResource(url1)); ImageIcon iconActive = new ImageIcon(ImageIO.read(lp.getClass().getResource(url1))); // image when button is inactive/transitioning (lighter shade/color) ImageIcon iconTransitionDown = new ImageIcon(translucentImage(ImageIO.read(lp.getClass().getResource(url2)), 0.6f)); ImageIcon iconTransitionUp = new ImageIcon(translucentImage(ImageIO.read(lp.getClass().getResource(url1)), 0.6f)); ImageIcon iconInactive = new ImageIcon(translucentImage(ImageIO.read(lp.getClass().getResource(url2)), 0.2f)); ImageIcon iconDisabled = new ImageIcon(translucentImage(ImageIO.read(lp.getClass().getResource(url2)), 0.1f)); JToggleButton toggleButton = new JToggleButton(iconInactive); toggleButton.setRolloverIcon(iconTransitionDown); toggleButton.setPressedIcon(iconDisabled); toggleButton.setSelectedIcon(iconActive); toggleButton.setRolloverSelectedIcon(iconTransitionUp); toggleButton.setDisabledIcon(iconDisabled); toggleButton.setDisabledSelectedIcon(iconDisabled); toggleButton.setBorderPainted(false); toggleButton.setSelected(activatedStatus); toggleButton.setPreferredSize(new Dimension(miniButtonSize, miniButtonSize)); return toggleButton; } /** * @param originalImage * @param alpha * @return original image with transparency alpha */ public static Image translucentImage(BufferedImage originalImage, float alpha) { int width = originalImage.getWidth(), height = originalImage.getHeight(); BufferedImage newImage = new BufferedImage(width, height, BufferedImage.TYPE_INT_ARGB); Graphics2D g = newImage.createGraphics(); g.setComposite(AlphaComposite.getInstance(AlphaComposite.SRC_OVER, alpha)); g.drawImage(originalImage, 0, 0, width, height, null); g.dispose(); return newImage; } } ================================================ FILE: src/juicebox/windowui/layers/LayersPanel.java ================================================ /* * The MIT License (MIT) * * Copyright (c) 2011-2021 Broad Institute, Aiden Lab, Rice University, Baylor College of Medicine * * Permission is hereby granted, free of charge, to any person obtaining a copy * of this software and associated documentation files (the "Software"), to deal * in the Software without restriction, including without limitation the rights * to use, copy, modify, merge, publish, distribute, sublicense, and/or sell * copies of the Software, and to permit persons to whom the Software is * furnished to do so, subject to the following conditions: * * The above copyright notice and this permission notice shall be included in * all copies or substantial portions of the Software. * * THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR * IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, * FITNESS FOR A PARTICULAR PURPOSE AND NON-INFRINGEMENT. IN NO EVENT SHALL THE * AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER * LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, * OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN * THE SOFTWARE. */ package juicebox.windowui.layers; import juicebox.HiC; import juicebox.HiCGlobals; import juicebox.gui.SuperAdapter; import juicebox.track.*; import juicebox.track.feature.AnnotationLayerHandler; import juicebox.windowui.DisabledGlassPane; import org.broad.igv.ui.color.ColorChooserPanel; import javax.swing.*; import javax.swing.border.Border; import javax.swing.event.DocumentEvent; import javax.swing.event.DocumentListener; import java.awt.*; import java.awt.event.ActionEvent; import java.awt.event.ActionListener; import java.awt.event.WindowEvent; import java.awt.event.WindowListener; import java.io.IOException; import java.util.ArrayList; import java.util.List; /** * Created by muhammadsaadshamim on 8/4/16. */ public class LayersPanel extends JDialog { private static final long serialVersionUID = 9000047; public static final DisabledGlassPane disabledGlassPane = new DisabledGlassPane(Cursor.WAIT_CURSOR); private static LoadAction trackLoadAction; private static LoadEncodeAction encodeAction; private static Load2DAnnotationsDialog load2DAnnotationsDialog; private final JPanel layers2DPanel; // private JPanel assemblyAnnotationsPanel; private final JPanel layerBoxGUI2DAnnotations = new JPanel(new GridLayout(0, 1)); private final JTabbedPane tabbedPane; final JPanel layerBox1DGUI = new JPanel(); final JPanel annotations1DPanel; public LayersPanel(final SuperAdapter superAdapter) { super(superAdapter.getMainWindow(), "Annotations Layer Panel"); rootPane.setGlassPane(disabledGlassPane); Border padding = BorderFactory.createEmptyBorder(20, 20, 5, 20); annotations1DPanel = generate1DAnnotationsLayerSelectionPanel(superAdapter); if (annotations1DPanel != null) annotations1DPanel.setBorder(padding); layers2DPanel = generate2DAnnotationsLayerSelectionPanel(superAdapter); if (layers2DPanel != null) layers2DPanel.setBorder(padding); // assemblyAnnotationsPanel = generateAssemblyAnnotationsPanel(superAdapter); // if (assemblyAnnotationsPanel != null) assemblyAnnotationsPanel.setBorder(padding); tabbedPane = new JTabbedPane(); tabbedPane.addTab("1D Annotations", null, annotations1DPanel, "Manage 1D Annotations"); //tabbedPane.setMnemonicAt(1, KeyEvent.VK_2); tabbedPane.addTab("2D Annotations", null, layers2DPanel, "Manage 2D Annotations"); //tabbedPane.setMnemonicAt(0, KeyEvent.VK_1); // tabbedPane.addTab("Assembly Annotations", null, assemblyAnnotationsPanel, // "Manage Assembly Annotations"); setSize(1000, 700); add(tabbedPane); //setVisible(true); this.addWindowListener(new WindowListener() { public void windowActivated(WindowEvent e) { } public void windowClosed(WindowEvent e) { } public void windowClosing(WindowEvent e) { superAdapter.setLayersPanelGUIControllersSelected(false); } public void windowDeactivated(WindowEvent e) { } public void windowDeiconified(WindowEvent e) { } public void windowIconified(WindowEvent e) { } public void windowOpened(WindowEvent e) { } }); } public LoadEncodeAction getEncodeAction() { return encodeAction; } private JPanel generate1DAnnotationsLayerSelectionPanel(final SuperAdapter superAdapter) { layerBox1DGUI.setLayout(new GridLayout(0, 1)); JScrollPane scrollPane = new JScrollPane(layerBox1DGUI, JScrollPane.VERTICAL_SCROLLBAR_AS_NEEDED, JScrollPane.HORIZONTAL_SCROLLBAR_NEVER); JPanel buttonPanel = new JPanel(new GridLayout(1, 0)); JButton loadBasicButton = new JButton("Load Basic Annotations..."); buttonPanel.add(loadBasicButton); JButton addLocalButton = new JButton("Add Local..."); buttonPanel.add(addLocalButton); JButton loadEncodeButton = new JButton("Load ENCODE Tracks..."); buttonPanel.add(loadEncodeButton); JButton loadFromURLButton = new JButton("Load from URL..."); buttonPanel.add(loadFromURLButton); JButton refreshButton = new JButton("Refresh View"); buttonPanel.add(refreshButton); final JPanel pane = new JPanel(new BorderLayout()); pane.add(scrollPane, BorderLayout.CENTER); pane.add(buttonPanel, BorderLayout.PAGE_END); Dimension dim = pane.getPreferredSize(); dim.setSize(dim.getWidth(), dim.getHeight() * 4); pane.setPreferredSize(dim); final Runnable repaint1DLayersPanel = new Runnable() { @Override public void run() { redraw1DLayerPanels(superAdapter); } }; repaint1DLayersPanel.run(); trackLoadAction = new LoadAction("Load Basic Annotations...", superAdapter.getMainWindow(), superAdapter.getHiC(), repaint1DLayersPanel); loadBasicButton.addActionListener(new ActionListener() { @Override public void actionPerformed(ActionEvent e) { trackLoadAction.actionPerformed(e); } }); addLocalButton.addActionListener(new ActionListener() { @Override public void actionPerformed(ActionEvent e) { HiC hiC = superAdapter.getHiC(); if (hiC.getResourceTree() == null) { ResourceTree resourceTree = new ResourceTree(superAdapter.getHiC(), null); hiC.setResourceTree(resourceTree); } boolean loadSuccessful = superAdapter.getHiC().getResourceTree().addLocalButtonActionPerformed(superAdapter); if (loadSuccessful) { trackLoadAction.actionPerformed(e); } } }); encodeAction = new LoadEncodeAction("Load ENCODE Tracks...", superAdapter.getMainWindow(), superAdapter.getHiC(), repaint1DLayersPanel); loadEncodeButton.addActionListener(new ActionListener() { @Override public void actionPerformed(ActionEvent e) { encodeAction.actionPerformed(e); } }); loadFromURLButton.addActionListener(new ActionListener() { @Override public void actionPerformed(ActionEvent e) { superAdapter.safeLoadFromURLActionPerformed(repaint1DLayersPanel); } }); refreshButton.addActionListener(new ActionListener() { @Override public void actionPerformed(ActionEvent e) { superAdapter.refresh(); redraw1DLayerPanels(superAdapter); } }); return pane; } public void redraw1DLayerPanels(SuperAdapter superAdapter) { layerBox1DGUI.removeAll(); for (HiCTrack track : superAdapter.getHiC().getLoadedTracks()) { if (track != null) { layerBox1DGUI.add(new TrackConfigPanel(superAdapter, track)); } } layerBox1DGUI.revalidate(); layerBox1DGUI.repaint(); if (annotations1DPanel != null) { annotations1DPanel.revalidate(); annotations1DPanel.repaint(); } } /** * @param superAdapter * @return */ private JPanel generate2DAnnotationsLayerSelectionPanel(final SuperAdapter superAdapter) { int i = 0; for (AnnotationLayerHandler handler : superAdapter.getAllLayers()) { try { JPanel panel = createLayerPanel(handler, superAdapter, layerBoxGUI2DAnnotations); //layerPanels.add(panel); layerBoxGUI2DAnnotations.add(panel, 0); } catch (IOException e) { System.err.println("Unable to generate layer panel " + (i - 1)); //e.printStackTrace(); } } final JScrollPane scrollPane = new JScrollPane(layerBoxGUI2DAnnotations, JScrollPane.VERTICAL_SCROLLBAR_AS_NEEDED, JScrollPane.HORIZONTAL_SCROLLBAR_NEVER); JButton refreshButton = new JButton("Refresh View"); refreshButton.addActionListener(new ActionListener() { @Override public void actionPerformed(ActionEvent e) { superAdapter.updateMainLayersPanel(); superAdapter.updateMiniAnnotationsLayerPanel(); superAdapter.refresh(); } }); JButton importButton = new JButton("Load Loops/Domains..."); JButton addLocalButton = new JButton("Add Local..."); JButton newLayerButton = new JButton("Add New Layer"); JButton mergeButton = new JButton("Merge Visible Layers"); JPanel buttonPanel = new JPanel(new GridLayout(1, 0)); buttonPanel.add(importButton); buttonPanel.add(addLocalButton); buttonPanel.add(newLayerButton); buttonPanel.add(mergeButton); buttonPanel.add(refreshButton); final JPanel pane = new JPanel(new BorderLayout()); pane.add(scrollPane, BorderLayout.CENTER); pane.add(buttonPanel, BorderLayout.PAGE_END); Dimension dim = pane.getPreferredSize(); dim.setSize(dim.getWidth(), dim.getHeight() * 4); pane.setPreferredSize(dim); /* import 2d annotations into layer */ importButton.addActionListener(new ActionListener() { @Override public void actionPerformed(ActionEvent e) { if (load2DAnnotationsDialog == null) { load2DAnnotationsDialog = new Load2DAnnotationsDialog(LayersPanel.this, superAdapter); } load2DAnnotationsDialog.setVisible(true); } }); importButton.setToolTipText("Import annotations into new layer"); addLocalButton.addActionListener(new ActionListener() { @Override public void actionPerformed(ActionEvent e) { if (load2DAnnotationsDialog == null) { load2DAnnotationsDialog = new Load2DAnnotationsDialog(LayersPanel.this, superAdapter); } load2DAnnotationsDialog.addLocalButtonActionPerformed(LayersPanel.this); } }); newLayerButton.addActionListener(new ActionListener() { @Override public void actionPerformed(ActionEvent e) { createNewLayerAndAddItToPanels(superAdapter, null); } }); mergeButton.addActionListener(new ActionListener() { @Override public void actionPerformed(ActionEvent e) { merge2DAnnotationsAction(superAdapter); } }); superAdapter.updateLayerDeleteStatus(); return pane; } private JScrollPane generateLayers2DScrollPane(SuperAdapter superAdapter) { final JPanel layerBoxGUI = new JPanel(); //layerBoxGUI.setLayout(new BoxLayout(layerBoxGUI, BoxLayout.PAGE_AXIS)); layerBoxGUI.setLayout(new GridLayout(0, 1)); //initialize here int i = 0; for (AnnotationLayerHandler handler : superAdapter.getAllLayers()) { try { JPanel panel = createLayerPanel(handler, superAdapter, layerBoxGUI); //layerPanels.add(panel); layerBoxGUI.add(panel, 0); } catch (IOException e) { System.err.println("Unable to generate layer panel " + (i - 1)); //e.printStackTrace(); } } return new JScrollPane(layerBoxGUI, JScrollPane.VERTICAL_SCROLLBAR_AS_NEEDED, JScrollPane.HORIZONTAL_SCROLLBAR_NEVER); } public AnnotationLayerHandler createNewLayerAndAddItToPanels(SuperAdapter superAdapter, AnnotationLayerHandler sourceHandler) { AnnotationLayerHandler handler = superAdapter.createNewLayer(null); if (sourceHandler != null) handler.duplicateDetailsFrom(sourceHandler); try { JPanel panel = createLayerPanel(handler, superAdapter, layerBoxGUI2DAnnotations); layerBoxGUI2DAnnotations.add(panel, 0); layerBoxGUI2DAnnotations.revalidate(); layerBoxGUI2DAnnotations.repaint(); superAdapter.setActiveLayerHandler(handler); superAdapter.updateLayerDeleteStatus(); superAdapter.updateMiniAnnotationsLayerPanel(); superAdapter.updateMainLayersPanel(); } catch (Exception ee) { System.err.println("Unable to add new layer to GUI"); } return handler; } private void merge2DAnnotationsAction(SuperAdapter superAdapter) { List visibleLayers = new ArrayList<>(); for (AnnotationLayerHandler handler : superAdapter.getAllLayers()) { if (handler.getLayerVisibility()) { visibleLayers.add(handler); } } AnnotationLayerHandler mergedHandler = superAdapter.createNewLayer(null); mergedHandler.mergeDetailsFrom(visibleLayers); try { JPanel panel = createLayerPanel(mergedHandler, superAdapter, layerBoxGUI2DAnnotations); layerBoxGUI2DAnnotations.add(panel, 0); for (AnnotationLayerHandler handler : visibleLayers) { int index = superAdapter.removeLayer(handler); if (index > -1) { layerBoxGUI2DAnnotations.remove(index); } } layerBoxGUI2DAnnotations.revalidate(); layerBoxGUI2DAnnotations.repaint(); superAdapter.setActiveLayerHandler(mergedHandler); superAdapter.updateLayerDeleteStatus(); } catch (Exception ee) { System.err.println("Unable to add merged layer to GUI"); ee.printStackTrace(); } } /** * @param handler * @param superAdapter * @param layerBoxGUI * @return * @throws IOException */ private JPanel createLayerPanel(final AnnotationLayerHandler handler, final SuperAdapter superAdapter, final JPanel layerBoxGUI) throws IOException { final JPanel parentPanel = new JPanel(); parentPanel.setLayout(new FlowLayout()); /* layer name */ final JTextField nameField = new JTextField(handler.getLayerName(), 10); nameField.getDocument().addDocumentListener(anyTextChangeListener(handler, nameField)); nameField.setToolTipText("Change the name for this layer: " + nameField.getText()); nameField.setMaximumSize(new Dimension(100, 30)); handler.setNameTextField(nameField); /* show/hide annotations for this layer */ JToggleButton toggleVisibleButton = LayerPanelButtons.createVisibleButton(this, superAdapter, handler); JToggleButton toggleTransparentButton = LayerPanelButtons.createTransparencyButton(this, superAdapter, handler); JToggleButton toggleSparseButton = LayerPanelButtons.createToggleSparseButton(this, superAdapter, handler); JToggleButton toggleEnlargeButton = LayerPanelButtons.createToggleEnlargeButton(this, superAdapter, handler); JButton togglePlottingStyleButton = LayerPanelButtons.createTogglePlottingStyleButton(superAdapter, handler); JButton exportLayerButton = LayerPanelButtons.createExportButton(this, handler); JButton undoButton = LayerPanelButtons.createUndoButton(this, superAdapter, handler); ColorChooserPanel colorChooserPanel = LayerPanelButtons.createColorChooserButton(superAdapter, handler); JButton clearButton = LayerPanelButtons.createEraseButton(this, superAdapter, handler); JToggleButton writeButton = LayerPanelButtons.createWritingButton(this, superAdapter, handler); JButton deleteButton = LayerPanelButtons.createDeleteButton(this, superAdapter, layerBoxGUI, parentPanel, handler); JButton upButton = LayerPanelButtons.createMoveUpButton(this, superAdapter, layerBoxGUI, parentPanel, handler); JButton downButton = LayerPanelButtons.createMoveDownButton(this, superAdapter, layerBoxGUI, parentPanel, handler); JButton copyButton = LayerPanelButtons.createCopyButton(this, superAdapter, handler); parentPanel.add(nameField); Component[] allComponents = new Component[]{writeButton, toggleVisibleButton, colorChooserPanel, toggleTransparentButton, toggleEnlargeButton, togglePlottingStyleButton, toggleSparseButton, undoButton, clearButton, exportLayerButton, copyButton, upButton, downButton, deleteButton}; if (HiCGlobals.isDevCustomChromosomesAllowedPublic) { JButton censorButton = LayerPanelButtons.createCensorButton(this, superAdapter, handler); allComponents = new Component[]{writeButton, toggleVisibleButton, colorChooserPanel, toggleTransparentButton, toggleEnlargeButton, togglePlottingStyleButton, toggleSparseButton, undoButton, clearButton, censorButton, exportLayerButton, copyButton, upButton, downButton, deleteButton}; } for (Component component : allComponents) { if (component instanceof AbstractButton) { component.setMaximumSize(new Dimension(LayerPanelButtons.miniButtonSize, LayerPanelButtons.miniButtonSize)); } parentPanel.add(component); } return parentPanel; } private DocumentListener anyTextChangeListener(final AnnotationLayerHandler handler, final JTextField nameField) { return new DocumentListener() { @Override public void insertUpdate(DocumentEvent e) { handler.setLayerNameAndOtherField(nameField.getText()); nameField.setToolTipText("Change the name for this layer: " + nameField.getText()); } @Override public void removeUpdate(DocumentEvent e) { handler.setLayerNameAndOtherField(nameField.getText()); nameField.setToolTipText("Change the name for this layer: " + nameField.getText()); } @Override public void changedUpdate(DocumentEvent e) { handler.setLayerNameAndOtherField(nameField.getText()); nameField.setToolTipText("Change the name for this layer: " + nameField.getText()); } }; } public void updateLayers2DPanel(SuperAdapter superAdapter) { layers2DPanel.remove(0); layers2DPanel.add(generateLayers2DScrollPane(superAdapter), BorderLayout.CENTER, 0); tabbedPane.updateUI(); tabbedPane.repaint(); tabbedPane.revalidate(); } public void updateBothLayersPanels(SuperAdapter superAdapter) { superAdapter.updateMiniAnnotationsLayerPanel(); superAdapter.updateMainLayersPanel(); } public LoadAction getTrackLoadAction() { return trackLoadAction; } } ================================================ FILE: src/juicebox/windowui/layers/Load2DAnnotationsDialog.java ================================================ /* * The MIT License (MIT) * * Copyright (c) 2011-2021 Broad Institute, Aiden Lab, Rice University, Baylor College of Medicine * * Permission is hereby granted, free of charge, to any person obtaining a copy * of this software and associated documentation files (the "Software"), to deal * in the Software without restriction, including without limitation the rights * to use, copy, modify, merge, publish, distribute, sublicense, and/or sell * copies of the Software, and to permit persons to whom the Software is * furnished to do so, subject to the following conditions: * * The above copyright notice and this permission notice shall be included in * all copies or substantial portions of the Software. * * THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR * IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, * FITNESS FOR A PARTICULAR PURPOSE AND NON-INFRINGEMENT. IN NO EVENT SHALL THE * AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER * LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, * OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN * THE SOFTWARE. */ package juicebox.windowui.layers; import com.jidesoft.swing.JideBoxLayout; import juicebox.DirectoryManager; import juicebox.HiC; import juicebox.HiCGlobals; import juicebox.MainWindow; import juicebox.data.ChromosomeHandler; import juicebox.data.HiCFileTools; import juicebox.gui.SuperAdapter; import juicebox.track.feature.AnnotationLayerHandler; import juicebox.windowui.JBTreeCellRenderer; import juicebox.windowui.LoadDialog; import org.broad.igv.ui.util.FileDialogUtils; import org.broad.igv.util.ResourceLocator; import javax.swing.*; import javax.swing.event.TreeSelectionEvent; import javax.swing.event.TreeSelectionListener; import javax.swing.tree.*; import java.awt.*; import java.awt.event.*; import java.io.BufferedReader; import java.io.File; import java.io.InputStream; import java.io.InputStreamReader; import java.util.Enumeration; import java.util.HashMap; import java.util.Map; public class Load2DAnnotationsDialog extends JDialog implements TreeSelectionListener { private static final long serialVersionUID = 9000048; private static DefaultMutableTreeNode customAddedFeatures = null; private final String[] searchHighlightColors = {"#ff0000", "#00ff00", "#0000ff", "#ff00ff", "#00ffff", "#ff9900", "#ff66ff", "#ffff00"}; private final JTree tree; private final JButton openButton; private final JTextField fTextField; private final Map loadedAnnotationsMap = new HashMap<>(); private File openAnnotationPath = DirectoryManager.getUserDirectory(); public Load2DAnnotationsDialog(final LayersPanel layersPanel, final SuperAdapter superAdapter) { super(layersPanel, "Select 2D annotation file(s) to open"); setModal(true); final ChromosomeHandler chromosomeHandler = superAdapter.getHiC().getChromosomeHandler(); final MainWindow window = superAdapter.getMainWindow(); //Create the nodes. final DefaultMutableTreeNode top = new DefaultMutableTreeNode(new ItemInfo("root", ""), true); createNodes(top, superAdapter.getHiC()); //Create a tree that allows one selection at a time. tree = new JTree(top); tree.getSelectionModel().setSelectionMode(TreeSelectionModel.DISCONTIGUOUS_TREE_SELECTION); //Listen for when the selection changes. tree.addTreeSelectionListener(this); tree.setRootVisible(false); tree.addMouseListener(new MouseAdapter() { @Override public void mousePressed(MouseEvent mouseEvent) { TreePath selPath = tree.getPathForLocation(mouseEvent.getX(), mouseEvent.getY()); if (selPath != null) { if (mouseEvent.getClickCount() == 2) { DefaultMutableTreeNode node = (DefaultMutableTreeNode) selPath.getLastPathComponent(); if (node != null && node.isLeaf()) { TreePath[] paths = new TreePath[1]; paths[0] = selPath; try { safeLoadAnnotationFiles(paths, layersPanel, superAdapter, chromosomeHandler); } catch (Exception e) { SuperAdapter.showMessageDialog("Unable to load file\n" + e.getLocalizedMessage()); } Load2DAnnotationsDialog.this.setVisible(false); } } } } }); //Create the scroll pane and add the tree to it. final JScrollPane treeView = new JScrollPane(tree); treeView.setPreferredSize(new Dimension(400, 400)); JPanel centerPanel = new JPanel(new BorderLayout()); centerPanel.add(treeView, BorderLayout.CENTER); add(centerPanel, BorderLayout.CENTER); JPanel buttonPanel = new JPanel(); openButton = new JButton("Open"); openButton.setEnabled(false); openButton.addActionListener(new ActionListener() { @Override public void actionPerformed(ActionEvent e) { safeLoadAnnotationFiles(tree.getSelectionPaths(), layersPanel, superAdapter, chromosomeHandler); Load2DAnnotationsDialog.this.setVisible(false); } }); JButton urlButton = new JButton("URL..."); urlButton.addActionListener(new ActionListener() { @Override public void actionPerformed(ActionEvent e) { String url = JOptionPane.showInputDialog("Enter URL: "); if (url != null && url.length() > 0) { if (HiCFileTools.isDropboxURL(url)) { url = HiCFileTools.cleanUpDropboxURL(url); } url = url.trim(); if (customAddedFeatures == null) { customAddedFeatures = new DefaultMutableTreeNode( new ItemInfo("Added 2D Features", ""), true); top.add(customAddedFeatures); } if (loadedAnnotationsMap.containsKey(url)) { if (HiCGlobals.guiIsCurrentlyActive) { int dialogResult = JOptionPane.showConfirmDialog(window, "File is already loaded. Would you like to overwrite it?", "Warning", JOptionPane.YES_NO_OPTION); if (dialogResult == JOptionPane.YES_OPTION) { customAddedFeatures.remove(loadedAnnotationsMap.get(url)); loadedAnnotationsMap.remove(url); } else { return; } } } DefaultMutableTreeNode treeNode = new DefaultMutableTreeNode( new ItemInfo(url, url), false); loadedAnnotationsMap.put(url, treeNode); customAddedFeatures.add(treeNode); expandTree(); tree.updateUI(); } } }); urlButton.setPreferredSize(new Dimension((int) urlButton.getPreferredSize().getWidth(), (int) openButton.getPreferredSize().getHeight())); //setVisible(false); JButton cancelButton = new JButton("Cancel"); cancelButton.addActionListener(new ActionListener() { @Override public void actionPerformed(ActionEvent e) { Load2DAnnotationsDialog.this.setVisible(false); } }); cancelButton.setPreferredSize(new Dimension((int) cancelButton.getPreferredSize().getWidth(), (int) openButton.getPreferredSize().getHeight())); buttonPanel.add(openButton); buttonPanel.add(urlButton); buttonPanel.add(cancelButton); add(buttonPanel, BorderLayout.SOUTH); Dimension minimumSize = new Dimension(700, 400); setMinimumSize(minimumSize); setLocation(100, 100); pack(); final JLabel fLabel = new JLabel(); fTextField = new JTextField(); fLabel.setText("Filter:"); fTextField.setToolTipText("Case Sensitive Search"); fTextField.setPreferredSize(new Dimension((int) cancelButton.getPreferredSize().getWidth(), (int) openButton.getPreferredSize().getHeight())); buttonPanel.add(fLabel, JideBoxLayout.FIX); buttonPanel.add(fTextField, JideBoxLayout.VARY); //*********************SEARCH FILTER******************************* fTextField.addKeyListener(new KeyAdapter() { public void keyReleased(KeyEvent e) { collapseAll(tree); @SuppressWarnings("unchecked") Enumeration en = top.preorderEnumeration(); if (!fTextField.getText().isEmpty()) { String[] searchStrings = fTextField.getText().split(","); colorSearchStrings(searchStrings); //Coloring text that matches input while (en.hasMoreElements()) { TreeNode leaf = en.nextElement(); String str = leaf.toString(); for (String term : searchStrings) { if (str.contains(term)) { expandToWantedNode(leaf); break; } } } } } }); } public void addLocalButtonActionPerformed(final Component parentComponent) { // Get the main window DefaultTreeModel model = (DefaultTreeModel) tree.getModel(); DefaultMutableTreeNode root = (DefaultMutableTreeNode) model.getRoot(); boolean localFilesAdded = false; File[] twoDfiles = FileDialogUtils.chooseMultiple("Choose 2D Annotation file", openAnnotationPath, null); if (twoDfiles != null && twoDfiles.length > 0) { for (File file : twoDfiles) { if (file == null || !file.exists()) continue; localFilesAdded = true; if (customAddedFeatures == null) { customAddedFeatures = new DefaultMutableTreeNode( new ItemInfo("Added 2D Features", ""), true); root.add(customAddedFeatures); } String path = file.getAbsolutePath(); openAnnotationPath = new File(path); if (loadedAnnotationsMap.containsKey(path)) { if (HiCGlobals.guiIsCurrentlyActive) { int dialogResult = JOptionPane.showConfirmDialog(parentComponent, file.getName() + " is already loaded. Would you like to overwrite it?", "Warning", JOptionPane.YES_NO_OPTION); if (dialogResult == JOptionPane.YES_OPTION) { customAddedFeatures.remove(loadedAnnotationsMap.get(path)); loadedAnnotationsMap.remove(path); } else { continue; } } } DefaultMutableTreeNode treeNode = new DefaultMutableTreeNode( new ItemInfo(file.getName(), path), false); loadedAnnotationsMap.put(path, treeNode); customAddedFeatures.add(treeNode); } model.reload(root); expandTree(); } Load2DAnnotationsDialog.this.setVisible(localFilesAdded); } private void expandTree() { TreeNode root = (TreeNode) tree.getModel().getRoot(); TreePath rootPath = new TreePath(root); TreeNode node = (TreeNode) rootPath.getLastPathComponent(); for (Enumeration e = node.children(); e.hasMoreElements(); ) { TreePath childPath = rootPath.pathByAddingChild(e.nextElement()); if (!tree.isExpanded(childPath)) { tree.expandPath(childPath); } } if (!tree.isExpanded(rootPath)) { tree.expandPath(rootPath); } } private void safeLoadAnnotationFiles(final TreePath[] paths, final LayersPanel layersPanel, final SuperAdapter superAdapter, final ChromosomeHandler chromosomeHandler) { Runnable runnable = new Runnable() { @Override public void run() { unsafeLoadAnnotationFiles(paths, layersPanel, superAdapter, chromosomeHandler); } }; superAdapter.executeLongRunningTask(runnable, "load 2d annotation files"); } private void unsafeLoadAnnotationFiles(TreePath[] paths, LayersPanel layersPanel, SuperAdapter superAdapter, ChromosomeHandler chromosomeHandler) { for (TreePath path : paths) { DefaultMutableTreeNode node = (DefaultMutableTreeNode) path.getLastPathComponent(); if (node != null && node.isLeaf()) { ItemInfo info = (ItemInfo) node.getUserObject(); try { AnnotationLayerHandler handler = layersPanel.createNewLayerAndAddItToPanels(superAdapter, null); handler.setLayerNameAndField(info.itemName); handler.loadLoopList(info.itemURL, chromosomeHandler); } catch (Exception ee) { System.err.println("Could not load selected annotation: " + info.itemName + " - " + info.itemURL); SuperAdapter.showMessageDialog("Could not load loop selection: the loop list in" + info.itemName + "does not correspond to the genome"); customAddedFeatures.remove(loadedAnnotationsMap.get(info.itemURL)); //Todo needs to be a warning when trying to add annotations from a different genome loadedAnnotationsMap.remove(path); } } } } private void expandToWantedNode(TreeNode dNode) { if (dNode != null) { tree.setExpandsSelectedPaths(true); TreePath path = new TreePath(LoadDialog.getPathToRoot(dNode, 0)); tree.scrollPathToVisible(path); tree.setSelectionPath(path); } } //Overriding in order to change text color private void colorSearchStrings(final String[] parts) { tree.setCellRenderer(new JBTreeCellRenderer(parts, searchHighlightColors)); } private boolean createNodes(DefaultMutableTreeNode top, HiC hic) { // Add dataset-specific 2d annotations DefaultMutableTreeNode subParent = new DefaultMutableTreeNode(new ItemInfo("Dataset-specific 2D Features"), true); ResourceLocator[] locators = {hic.getDataset().getPeaks(), hic.getDataset().getBlocks(), hic.getDataset().getSuperLoops()}; String[] locatorName = {"Peaks", "Contact Domains", "ChrX Super Loops"}; boolean datasetSpecificFeatureAdded = false; for (int i = 0; i < 3; i++) { if (locators[i] != null) { DefaultMutableTreeNode treeNode = new DefaultMutableTreeNode(new ItemInfo(locatorName[i], locators[i].getURLPath()), false); subParent.add(treeNode); datasetSpecificFeatureAdded = true; } } if (datasetSpecificFeatureAdded) top.add(subParent); // allow specific dataset features to be top-level // load remaining features from file DefaultMutableTreeNode parent = new DefaultMutableTreeNode(new ItemInfo("Chromatin Features"), true); top.add(parent); InputStream is = Load2DAnnotationsDialog.class.getResourceAsStream("annotations2d.txt"); BufferedReader reader = new BufferedReader(new InputStreamReader(is), HiCGlobals.bufferSize); String nextLine; try { while ((nextLine = reader.readLine()) != null) { final String[] values = nextLine.split(";"); if (values.length != 1 && values.length != 2) { JOptionPane.showMessageDialog(this, "Improper features file", "Error", JOptionPane.ERROR_MESSAGE); return false; } if (values.length == 1) { subParent = new DefaultMutableTreeNode(new ItemInfo(values[0]), true); parent.add(subParent); //node = new DefaultMutableTreeNode(new ItemInfo(key, values[0], values[1])); } else { DefaultMutableTreeNode node = new DefaultMutableTreeNode(new ItemInfo(values[0], values[1]), false); subParent.add(node); } } } catch (Exception ignored) { } if (customAddedFeatures != null) { top.add(customAddedFeatures); } return true; } /** * Required by TreeSelectionListener interface. */ public void valueChanged(TreeSelectionEvent e) { DefaultMutableTreeNode node = (DefaultMutableTreeNode) tree.getLastSelectedPathComponent(); if (node == null) return; openButton.setEnabled(node.isLeaf()); } private void collapseAll(JTree tree) { int row = tree.getRowCount() - 1; while (row >= 0) { tree.collapseRow(row); row--; } } private class ItemInfo { final String itemName; final String itemURL; ItemInfo(String itemName, String itemURL) { this.itemName = itemName.trim(); this.itemURL = itemURL.trim(); } ItemInfo(String itemName) { this.itemName = itemName; itemURL = null; } public String toString() { return itemName; } } } ================================================ FILE: src/juicebox/windowui/layers/MiniAnnotationsLayerPanel.java ================================================ /* * The MIT License (MIT) * * Copyright (c) 2011-2021 Broad Institute, Aiden Lab, Rice University, Baylor College of Medicine * * Permission is hereby granted, free of charge, to any person obtaining a copy * of this software and associated documentation files (the "Software"), to deal * in the Software without restriction, including without limitation the rights * to use, copy, modify, merge, publish, distribute, sublicense, and/or sell * copies of the Software, and to permit persons to whom the Software is * furnished to do so, subject to the following conditions: * * The above copyright notice and this permission notice shall be included in * all copies or substantial portions of the Software. * * THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR * IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, * FITNESS FOR A PARTICULAR PURPOSE AND NON-INFRINGEMENT. IN NO EVENT SHALL THE * AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER * LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, * OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN * THE SOFTWARE. */ package juicebox.windowui.layers; import juicebox.gui.SuperAdapter; import juicebox.track.feature.AnnotationLayerHandler; import org.broad.igv.ui.color.ColorChooserPanel; import javax.swing.*; import java.awt.*; import java.io.IOException; /** * Created by ranganmostofa on 8/16/17. */ public class MiniAnnotationsLayerPanel extends JPanel { private static final long serialVersionUID = 9000049; private static final int MAX_NUM_LETTERS = 8; private final int miniButtonSize = 22; private final int maximumVisibleLayers = 5; private final int indivRowSize; private final int width, maxHeight; private int dynamicHeight; public MiniAnnotationsLayerPanel(SuperAdapter superAdapter, int width, int height) { this.width = width; this.maxHeight = height; indivRowSize = height / maximumVisibleLayers; //getRootPane().setGlassPane(disabledGlassPane); setMaximumSize(new Dimension(width, maxHeight)); setLayout(new GridLayout(0, 1)); setRows(superAdapter); } /** * Return a string with a maximum length. * If there are more characters, then string ends with an ellipsis ("..."). * * @param text * @return shortened text */ public static String shortenedName(final String text) { // The letters [iIl1] are slim enough to only count as half a character. double length = MAX_NUM_LETTERS + Math.ceil(text.replaceAll("[^iIl]", "").length() / 2.0d); if (text.length() > length) { return text.substring(0, MAX_NUM_LETTERS - 3) + "..."; } return text; } private void setRows(SuperAdapter superAdapter) { dynamicHeight = Math.min(superAdapter.getAllLayers().size(), maximumVisibleLayers) * indivRowSize; setMaximumSize(new Dimension(width, dynamicHeight)); setPreferredSize(new Dimension(width, dynamicHeight)); setMinimumSize(new Dimension(width, dynamicHeight)); JPanel jj = new JPanel(); jj.setMaximumSize(new Dimension(width, maxHeight)); jj.setLayout(new GridLayout(0, 1)); for (AnnotationLayerHandler handler : superAdapter.getAllLayers()) { try { JPanel panel = createMiniLayerPanel(handler, superAdapter); jj.add(panel, 0); } catch (IOException e) { System.err.println("Unable to generate layer panel " + handler); } } JScrollPane scrollPane = new JScrollPane(jj, JScrollPane.VERTICAL_SCROLLBAR_AS_NEEDED, JScrollPane.HORIZONTAL_SCROLLBAR_NEVER); scrollPane.setMaximumSize(new Dimension(width, dynamicHeight)); scrollPane.setPreferredSize(new Dimension(width, dynamicHeight)); scrollPane.setMinimumSize(new Dimension(width, dynamicHeight)); add(scrollPane); } private JPanel createMiniLayerPanel(final AnnotationLayerHandler handler, final SuperAdapter superAdapter) throws IOException { final JPanel parentPanel = new JPanel(); parentPanel.setLayout(new GridLayout(1, 0)); parentPanel.setSize(new Dimension(width, 10)); /* layer name */ JLabel nameField = new JLabel(shortenedName(handler.getLayerName())); handler.setMiniNameLabelField(nameField); nameField.setToolTipText(handler.getLayerName()); parentPanel.add(nameField); /* show/hide annotations for this layer */ JToggleButton toggleVisibleButton = LayerPanelButtons.createVisibleButton(this, superAdapter, handler); toggleVisibleButton.setMaximumSize(new Dimension(miniButtonSize, miniButtonSize)); parentPanel.add(toggleVisibleButton); ColorChooserPanel colorChooserPanel = LayerPanelButtons.createColorChooserButton(superAdapter, handler); colorChooserPanel.setMaximumSize(new Dimension(miniButtonSize, miniButtonSize)); parentPanel.add(colorChooserPanel); JButton togglePlottingStyleButton = LayerPanelButtons.createTogglePlottingStyleButton(superAdapter, handler); togglePlottingStyleButton.setMaximumSize(new Dimension(miniButtonSize, miniButtonSize)); parentPanel.add(togglePlottingStyleButton); JToggleButton writeButton = LayerPanelButtons.createWritingButton(this, superAdapter, handler); writeButton.setMaximumSize(new Dimension(miniButtonSize, miniButtonSize)); parentPanel.add(writeButton); return parentPanel; } public int getDynamicHeight() { return this.dynamicHeight; } public void updateRows(SuperAdapter superAdapter) { removeAll(); setRows(superAdapter); } } ================================================ FILE: src/juicebox/windowui/layers/PlottingStyleButton.java ================================================ /* * The MIT License (MIT) * * Copyright (c) 2011-2021 Broad Institute, Aiden Lab, Rice University, Baylor College of Medicine * * Permission is hereby granted, free of charge, to any person obtaining a copy * of this software and associated documentation files (the "Software"), to deal * in the Software without restriction, including without limitation the rights * to use, copy, modify, merge, publish, distribute, sublicense, and/or sell * copies of the Software, and to permit persons to whom the Software is * furnished to do so, subject to the following conditions: * * The above copyright notice and this permission notice shall be included in * all copies or substantial portions of the Software. * * THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR * IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, * FITNESS FOR A PARTICULAR PURPOSE AND NON-INFRINGEMENT. IN NO EVENT SHALL THE * AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER * LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, * OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN * THE SOFTWARE. */ package juicebox.windowui.layers; import juicebox.mapcolorui.FeatureRenderer; import javax.imageio.ImageIO; import javax.swing.*; import java.awt.image.BufferedImage; import java.io.IOException; public class PlottingStyleButton extends JButton { private static final long serialVersionUID = 9000050; private final ImageIcon iconActive1, iconTransition1, iconInactive1, iconActive2, iconTransition2, iconInactive2, iconActive3, iconTransition3, iconInactive3; public PlottingStyleButton() throws IOException { super(); // full String url1 = "/images/layer/full_clicked.png"; BufferedImage imageActive1 = ImageIO.read(getClass().getResource(url1)); iconActive1 = new ImageIcon(imageActive1); iconTransition1 = new ImageIcon(LayerPanelButtons.translucentImage(imageActive1, 0.6f)); iconInactive1 = new ImageIcon(LayerPanelButtons.translucentImage(imageActive1, 0.2f)); // ll String url2 = "/images/layer/ll_clicked.png"; BufferedImage imageActive2 = ImageIO.read(getClass().getResource(url2)); iconActive2 = new ImageIcon(imageActive2); iconTransition2 = new ImageIcon(LayerPanelButtons.translucentImage(imageActive2, 0.6f)); iconInactive2 = new ImageIcon(LayerPanelButtons.translucentImage(imageActive2, 0.2f)); // ur String url3 = "/images/layer/ur_clicked.png"; BufferedImage imageActive3 = ImageIO.read(getClass().getResource(url3)); iconActive3 = new ImageIcon(imageActive3); iconTransition3 = new ImageIcon(LayerPanelButtons.translucentImage(imageActive3, 0.6f)); iconInactive3 = new ImageIcon(LayerPanelButtons.translucentImage(imageActive3, 0.2f)); } public void setCurrentState(FeatureRenderer.PlottingOption state) { if (state == FeatureRenderer.PlottingOption.ONLY_LOWER_LEFT) { setIcon(iconActive2); setRolloverIcon(iconTransition3); setPressedIcon(iconActive3); setDisabledIcon(iconInactive2); } else if (state == FeatureRenderer.PlottingOption.ONLY_UPPER_RIGHT) { setIcon(iconActive3); setRolloverIcon(iconTransition1); setPressedIcon(iconActive1); setDisabledIcon(iconInactive3); } else if (state == FeatureRenderer.PlottingOption.EVERYTHING) { setIcon(iconActive1); setRolloverIcon(iconTransition2); setPressedIcon(iconActive2); setDisabledIcon(iconInactive1); } } } ================================================ FILE: src/juicebox/windowui/layers/SaveAnnotationsDialog.java ================================================ /* * The MIT License (MIT) * * Copyright (c) 2011-2021 Broad Institute, Aiden Lab, Rice University, Baylor College of Medicine * * Permission is hereby granted, free of charge, to any person obtaining a copy * of this software and associated documentation files (the "Software"), to deal * in the Software without restriction, including without limitation the rights * to use, copy, modify, merge, publish, distribute, sublicense, and/or sell * copies of the Software, and to permit persons to whom the Software is * furnished to do so, subject to the following conditions: * * The above copyright notice and this permission notice shall be included in * all copies or substantial portions of the Software. * * THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR * IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, * FITNESS FOR A PARTICULAR PURPOSE AND NON-INFRINGEMENT. IN NO EVENT SHALL THE * AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER * LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, * OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN * THE SOFTWARE. */ package juicebox.windowui.layers; import juicebox.HiCGlobals; import juicebox.MainWindow; import juicebox.track.feature.AnnotationLayer; import juicebox.track.feature.Feature2DList; import javax.swing.*; import javax.swing.filechooser.FileNameExtensionFilter; import java.io.File; import java.text.SimpleDateFormat; import java.util.Date; /** * Created by Marie on 6/5/15. */ public class SaveAnnotationsDialog extends JFileChooser { private static final long serialVersionUID = 9000010; private final AnnotationLayer annotations; private final Feature2DList otherList = null; private String mapName = ""; public SaveAnnotationsDialog(AnnotationLayer annotationsLayer, String mapName) { super(); this.annotations = annotationsLayer; this.mapName = mapName; menuOptions(); } private void menuOptions() { String timeStamp = new SimpleDateFormat("yyyy.MM.dd-HH.mm").format(new Date()); setSelectedFile(new File(mapName + "-" + timeStamp + ".bedpe")); //setCurrentDirectory(new File(System.getProperty("user.dir"))); FileNameExtensionFilter filter = new FileNameExtensionFilter( "BEDPE Files", "bedpe", "txt", "text"); setFileFilter(filter); if (HiCGlobals.guiIsCurrentlyActive) { int actionDialog = showSaveDialog(MainWindow.getInstance()); if (actionDialog == JFileChooser.APPROVE_OPTION) { File file = getSelectedFile(); String outputPath = file.getAbsolutePath(); if (file.exists()) { actionDialog = JOptionPane.showConfirmDialog(MainWindow.getInstance(), "Replace existing file?"); if (actionDialog == JOptionPane.NO_OPTION || actionDialog == JOptionPane.CANCEL_OPTION) return; } if (otherList == null) { if (!annotations.exportAnnotations(outputPath)) { JOptionPane.showMessageDialog(MainWindow.getInstance(), "No annotations to output", "Error", JOptionPane.ERROR_MESSAGE); } } else { if (!annotations.exportOverlap(otherList, outputPath)) { JOptionPane.showMessageDialog(MainWindow.getInstance(), "Unable to export annotations", "Error", JOptionPane.ERROR_MESSAGE); } } } } } } ================================================ FILE: src/juicebox/windowui/layers/UnsavedAnnotationWarning.java ================================================ /* * The MIT License (MIT) * * Copyright (c) 2011-2021 Broad Institute, Aiden Lab, Rice University, Baylor College of Medicine * * Permission is hereby granted, free of charge, to any person obtaining a copy * of this software and associated documentation files (the "Software"), to deal * in the Software without restriction, including without limitation the rights * to use, copy, modify, merge, publish, distribute, sublicense, and/or sell * copies of the Software, and to permit persons to whom the Software is * furnished to do so, subject to the following conditions: * * The above copyright notice and this permission notice shall be included in * all copies or substantial portions of the Software. * * THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR * IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, * FITNESS FOR A PARTICULAR PURPOSE AND NON-INFRINGEMENT. IN NO EVENT SHALL THE * AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER * LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, * OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN * THE SOFTWARE. */ package juicebox.windowui.layers; import juicebox.DirectoryManager; import juicebox.HiCGlobals; import juicebox.gui.SuperAdapter; import javax.swing.*; import java.io.File; /** * Created by Marie on 12/21/15. */ public class UnsavedAnnotationWarning { private final SuperAdapter superAdapter; public UnsavedAnnotationWarning(SuperAdapter adapter) { this.superAdapter = adapter; } public boolean checkAndDelete(boolean isCurrentSession) { if (superAdapter.unsavedEditsExist()) { return initPopup(isCurrentSession); } // There were no unsaved annotations, proceed return true; } private boolean initPopup(boolean isCurrentSession) { // Check for unsaved annotations JDialog.setDefaultLookAndFeelDecorated(true); //Custom button text Object[] options = {"Save Annotations", "Discard Annotations"}; String sessionTime = isCurrentSession ? "this" : "a previous"; int response = JOptionPane.showOptionDialog(null, "There are unsaved hand annotations from " + sessionTime + " session.\n" + "Would you like save them before you continue?", "Confirm", JOptionPane.YES_NO_OPTION, JOptionPane.QUESTION_MESSAGE, null, //do not use a custom Icon options, //the titles of buttons options[0]); //default button title if (response == JOptionPane.NO_OPTION) { System.out.println("Deleting annotations"); if (isCurrentSession) { superAdapter.getActiveLayerHandler().clearAnnotations(); } removeAllOldAnnotationFiles(); return true; } if (response == JOptionPane.CANCEL_OPTION || response == JOptionPane.CLOSED_OPTION) { System.out.println("Cancel"); return false; } if (response == JOptionPane.YES_OPTION) { String prefix = moveOldAnnotationFiles(); SuperAdapter.showMessageDialog("Files have been saved with prefix: " + prefix + "*\nin " + DirectoryManager.getHiCDirectory()); return true; } return false; } /** * simple deletion based on assumption of limited possible files * temp fix * todo something more sophisticated */ private void removeAllOldAnnotationFiles() { for (int i = 0; i < 10; i++) { File temp = new File(DirectoryManager.getHiCDirectory(), HiCGlobals.BACKUP_FILE_STEM + i + ".bedpe"); if (temp.exists()) { temp.delete(); } } } private String moveOldAnnotationFiles() { String timeStamp = System.nanoTime() + "_annotations_"; for (int i = 0; i < 10; i++) { File temp = new File(DirectoryManager.getHiCDirectory(), HiCGlobals.BACKUP_FILE_STEM + i + ".bedpe"); if (temp.exists()) { temp.renameTo(new File(DirectoryManager.getHiCDirectory(), timeStamp + i + ".bedpe")); } } return timeStamp; } } ================================================ FILE: src/juicebox/windowui/layers/annotations2d.txt ================================================ Loop Calls 4DN Dekker H1 hESC rep2 loops;https://hicfiles.s3.amazonaws.com/external/dekker/4dn/h1hesc_rep2_loops.txt 4DN Dekker H1 hffc6 rep1 loops;https://hicfiles.s3.amazonaws.com/external/dekker/4dn/hffc6_rep1_loops.txt Eagen et al. | bioRxiv 2017| Kc167 combined loops;https://hicfiles.s3.amazonaws.com/external/eagen/GSE89112_Kc167combined_loops.txt Mumbach Rubin Flynn et al. | Nature Methods 2016 | GM12878 cohesin combined loops;https://hicfiles.s3.amazonaws.com/external/mumbach/GSE80820_HiChIP_GM_cohesin_peaks.txt Mumbach Rubin Flynn et al. | Nature Methods 2016 | mESC oct4 combined loops;https://hicfiles.s3.amazonaws.com/external/mumbach/GSE80820_HiChIP_mES_Oct4_peaks.txt Mumbach Rubin Flynn et al. | Nature Methods 2016 | mESC cohesin combined loops;https://hicfiles.s3.amazonaws.com/external/mumbach/GSE80820_HiChIP_mES_cohesin_all_peaks.txt Darrow & Huntley et al. | PNAS 2016 | Patski combined loops;https://hicfiles.s3.amazonaws.com/hiseq/patski/DarrowHuntley-2015/combined_loops.txt Darrow & Huntley et al. | PNAS 2016 | Rhesus HIC020 loops;https://hicfiles.s3.amazonaws.com/hiseq/rhesus/DarrowHuntley-2015/HIC020_loops.txt Darrow & Huntley et al. | PNAS 2016 | RPE1 control combined loops;https://hicfiles.s3.amazonaws.com/hiseq/rpe1/DarrowHuntley-2015/WT-combined_loops.txt Darrow & Huntley et al. | PNAS 2016 | RPE1 delXa HIC001 loops;https://hicfiles.s3.amazonaws.com/hiseq/rpe1/DarrowHuntley-2015/del-Xa-combined_loops.txt Darrow & Huntley et al. | PNAS 2016 | RPE1 delXi combined loops;https://hicfiles.s3.amazonaws.com/hiseq/rpe1/DarrowHuntley-2015/del-Xi-combined_loops.txt Tang Luo Li et al. | Cell 2015 | GM12878 ChIA-PET loops;https://hicfiles.s3.amazonaws.com/external/tang/gm12878_loops.txt GM12878 in situ Hi-C (Rao and Huntley et al., Cell, 2014);https://hicfiles.s3.amazonaws.com/hiseq/gm12878/in-situ/combined_peaks.txt IMR90 in situ Hi-C (Rao and Huntley et al., Cell, 2014);https://hicfiles.s3.amazonaws.com/hiseq/imr90/in-situ/combined_peaks.txt HMEC in situ Hi-C (Rao and Huntley et al., Cell, 2014);https://hicfiles.s3.amazonaws.com/hiseq/hmec/in-situ/combined_peaks.txt NHEK in situ Hi-C (Rao and Huntley et al., Cell, 2014);https://hicfiles.s3.amazonaws.com/hiseq/nhek/in-situ/combined_peaks.txt K562 in situ Hi-C (Rao and Huntley et al., Cell, 2014);https://hicfiles.s3.amazonaws.com/hiseq/k562/in-situ/combined_peaks.txt KBM7 in situ Hi-C (Rao and Huntley et al., Cell, 2014);https://hicfiles.s3.amazonaws.com/hiseq/kbm7/in-situ/combined_peaks.txt HUVEC in situ Hi-C (Rao and Huntley et al., Cell, 2014);https://hicfiles.s3.amazonaws.com/hiseq/huvec/in-situ/combined_peaks.txt HeLa in situ Hi-C (Rao and Huntley et al., Cell, 2014);https://hicfiles.s3.amazonaws.com/hiseq/hela/in-situ/combined_peaks.txt CH12-LX in situ Hi-C (Rao and Huntley et al., Cell, 2014);https://hicfiles.s3.amazonaws.com/hiseq/ch12-lx-b-lymphoblasts/in-situ/combined_peaks.txt Hap1 in situ Hi-C (Sanborn and Rao et al., PNAS, 2015);https://hicfiles.s3.amazonaws.com/hiseq/hap1/in-situ/combined_peaks.txt ENCODE 5C GM12878 (Sanyal et al., Nature, 2012);https://hicfiles.s3.amazonaws.com/external/ENCODE-5C-GM12878.txt ENCODE 5C HeLa (Sanyal et al., Nature, 2012);https://hicfiles.s3.amazonaws.com/external/ENCODE-5C-HeLa.txt ENCODE 5C K562 (Sanyal et al., Nature, 2012);https://hicfiles.s3.amazonaws.com/external/ENCODE-5C-K562.txt Jin et al. Hi-C IMR90 (Nature, 2013);https://hicfiles.s3.amazonaws.com/external/JinRenAllLoops.txt Li et al. ChIA-PET/PolII K562 (Cell, 2012);https://hicfiles.s3.amazonaws.com/external/LiRuanK562.txt Li et al. ChIA-PET/CTCF K562 (Cell, 2012);https://hicfiles.s3.amazonaws.com/external/LiRuanK562CTCF.txt Domains 4DN Dekker H1 hESC rep1 domains;https://hicfiles.s3.amazonaws.com/external/dekker/4dn/h1hesc_rep1_domains.txt 4DN Dekker H1 hESC rep2 domains;https://hicfiles.s3.amazonaws.com/external/dekker/4dn/h1hesc_rep2_domains.txt 4DN Dekker H1 hffc6 rep1 domains;https://hicfiles.s3.amazonaws.com/external/dekker/4dn/hffc6_rep1_domains.txt Eagen et al. | bioRxiv 2017 | Kc167 combined domains;https://hicfiles.s3.amazonaws.com/external/eagen/GSE89112_Kc167combined_domains.txt Darrow & Huntley et al. | PNAS 2016 | RPE1 delXi combined domains;https://hicfiles.s3.amazonaws.com/hiseq/rpe1/DarrowHuntley-2015/del-Xi-combined_domains.txt Darrow & Huntley et al. | PNAS 2016 | RPE1 delXa HIC001 domains;https://hicfiles.s3.amazonaws.com/hiseq/rpe1/DarrowHuntley-2015/del-Xa-combined_domains.txt Darrow & Huntley et al. | PNAS 2016 | RPE1 control combined domains;https://hicfiles.s3.amazonaws.com/hiseq/rpe1/DarrowHuntley-2015/WT-combined_domains.txt Darrow & Huntley et al. | PNAS 2016 | Rhesus HIC020 domains;https://hicfiles.s3.amazonaws.com/hiseq/rhesus/DarrowHuntley-2015/HIC020_domains.txt Darrow & Huntley et al. | PNAS 2016 | Patski combined domains;https://hicfiles.s3.amazonaws.com/hiseq/patski/DarrowHuntley-2015/combined_domains.txt Sanborn & Rao et al. | PNAS 2015 | Hap1 domains;https://hicfiles.s3.amazonaws.com/hiseq/hap1/in-situ/combined_blocks.txt GM12878 in situ Hi-C (Rao and Huntley et al., Cell, 2014);https://hicfiles.s3.amazonaws.com/hiseq/gm12878/in-situ/combined_blocks.txt IMR90 in situ Hi-C (Rao and Huntley et al., Cell, 2014);https://hicfiles.s3.amazonaws.com/hiseq/imr90/in-situ/combined_blocks.txt HMEC in situ Hi-C (Rao and Huntley et al., Cell, 2014);https://hicfiles.s3.amazonaws.com/hiseq/hmec/in-situ/combined_blocks.txt NHEK in situ Hi-C (Rao and Huntley et al., Cell, 2014);https://hicfiles.s3.amazonaws.com/hiseq/nhek/in-situ/combined_blocks.txt K562 in situ Hi-C (Rao and Huntley et al., Cell, 2014);https://hicfiles.s3.amazonaws.com/hiseq/k562/in-situ/combined_blocks.txt KBM7 in situ Hi-C (Rao and Huntley et al., Cell, 2014);https://hicfiles.s3.amazonaws.com/hiseq/kbm7/in-situ/combined_blocks.txt HUVEC in situ Hi-C (Rao and Huntley et al., Cell, 2014);https://hicfiles.s3.amazonaws.com/hiseq/huvec/in-situ/combined_blocks.txt HeLa in situ Hi-C (Rao and Huntley et al., Cell, 2014);https://hicfiles.s3.amazonaws.com/hiseq/hela/in-situ/combined_blocks.txt CH12-LX in situ Hi-C (Rao and Huntley et al., Cell, 2014);https://hicfiles.s3.amazonaws.com/hiseq/ch12-lx-b-lymphoblasts/in-situ/combined_blocks.txt Hap1 in situ Hi-C (Sanborn and Rao et al., PNAS, 2015);https://hicfiles.s3.amazonaws.com/hiseq/hap1/in-situ/combined_blocks.txt Jin et al. Hi-C IMR90 TADs (Nature, 2013);https://hicfiles.s3.amazonaws.com/external/TADS_IMR90_hg19_looplist.txt Dixon et al. | Nature 2012 | IMR90 HindIII domains;https://hicfiles.s3.amazonaws.com/external/dixon/imr90-hindiii_blocks.txt ================================================ FILE: src/org/tc33/jheatchart/HeatChart.java ================================================ /* * The MIT License (MIT) * * Copyright (c) 2011-2021 Broad Institute, Aiden Lab, Rice University, Baylor College of Medicine * * Permission is hereby granted, free of charge, to any person obtaining a copy * of this software and associated documentation files (the "Software"), to deal * in the Software without restriction, including without limitation the rights * to use, copy, modify, merge, publish, distribute, sublicense, and/or sell * copies of the Software, and to permit persons to whom the Software is * furnished to do so, subject to the following conditions: * * The above copyright notice and this permission notice shall be included in * all copies or substantial portions of the Software. * * THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR * IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, * FITNESS FOR A PARTICULAR PURPOSE AND NON-INFRINGEMENT. IN NO EVENT SHALL THE * AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER * LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, * OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN * THE SOFTWARE. */ package org.tc33.jheatchart; import juicebox.HiCGlobals; import javax.imageio.IIOImage; import javax.imageio.ImageIO; import javax.imageio.ImageWriteParam; import javax.imageio.ImageWriter; import javax.imageio.stream.FileImageOutputStream; import java.awt.*; import java.awt.geom.AffineTransform; import java.awt.image.BufferedImage; import java.io.File; import java.io.IOException; import java.util.Iterator; /** * * From https://github.com/tc33/jheatchart * Tom Castle * * The HeatChart class describes a chart which can display * 3-dimensions of values - x,y and z, where x and y are the usual 2-dimensional * axis and z is portrayed by colour intensity. Heat charts are sometimes known * as heat maps. *

*

* Use of this chart would typically involve 3 steps: *

    *
  1. Construction of a new instance, providing the necessary z-values.
    2. *
  2. Configure the visual settings.
    3. *
  3. A call to either getChartImage() or saveToFile(String).
    4. *
*

*

Instantiation

*

* Construction of a new HeatChart instance is through its one * constructor which takes a 2-dimensional array of doubles which * should contain the z-values for the chart. Consider this array to be * the grid of values which will instead be represented as colours in the chart. *

*

* Setting of the x-values and y-values which are displayed along the * appropriate axis is optional, and by default will simply display the values * 0 to n-1, where n is the number of rows or columns. Otherwise, the x/y axis * values can be set with the setXValues and setYValues * methods. Both methods are overridden with two forms: *

*

Object axis values

*

*

* The simplest way to set the axis values is to use the methods which take an * array of Object[]. This array must have the same length as the number of * columns for setXValues and same as the number of rows for setYValues. The * string representation of the objects will then be used as the axis values. *

*

Offset and Interval

*

*

* This is convenient way of defining numerical values along the axis. One of * the two methods takes an interval and an offset for either the * x or y axis. These parameters supply the necessary information to describe * the values based upon the z-value indexes. The quantity of x-values and * y-values is already known from the lengths of the z-values array dimensions. * Then the offset parameters indicate what the first value will be, with the * intervals providing the increment from one column or row to the next. *

*

* Consider an example: * 

 * double[][] zValues = new double[][]{
 *        {1.2, 1.3, 1.5},
 *        {1.0, 1.1, 1.6},
 *        {0.7, 0.9, 1.3}
 * };
 * 

 * double xOffset = 1.0;
 * double yOffset = 0.0;
 * double xInterval = 1.0;
 * double yInterval = 2.0;
 * 

 * chart.setXValues(xOffset, xInterval);
 * chart.setYValues(yOffset, yInterval);
 *
*

*

In this example, the z-values range from 0.7 to 1.6. The x-values range * from the xOffset value 1.0 to 4.0, which is calculated as the number of x-values * multiplied by the xInterval, shifted by the xOffset of 1.0. The y-values are * calculated in the same way to give a range of values from 0.0 to 6.0. *

*

Configuration

*

* This step is optional. By default the heat chart will be generated without a * title or labels on the axis, and the colouring of the heat map will be in * grayscale. A large range of configuration options are available to customise * the chart. All customisations are available through simple accessor methods. * See the javadoc of each of the methods for more information. *

*

Output

*

* The generated heat chart can be obtained in two forms, using the following * methods: *

    *
  • getChartImage() - The chart will be returned as a * BufferedImage object that can be used in any number of ways, * most notably it can be inserted into a Swing component, for use in a GUI * application.
    • *
  • saveToFile(File) - The chart will be saved to the file * system at the file location specified as a parameter. The image format that * the image will be saved in is derived from the extension of the file name.
    • *
*

* Note: The chart image will not actually be created until * either saveToFile(File) or getChartImage() are called, and will be * regenerated on each successive call. */ public class HeatChart { /** * A basic logarithmic scale value of 0.3. */ public static final double SCALE_LOGARITHMIC = 0.3; /** * A basic exponential scale value of 3.0. */ public static final double SCALE_EXPONENTIAL = 3; /** * The linear scale value of 1.0. */ private static final double SCALE_LINEAR = 1.0; // x, y, z data values. private double[][] zValues; private Object[] xValues; private Object[] yValues; private boolean xValuesHorizontal; private boolean yValuesHorizontal; // General chart settings. private Dimension cellSize; private Dimension chartSize; private int margin; private Color backgroundColour; // Title settings. private String title; private Font titleFont; private Color titleColour; private Dimension titleSize; private int titleAscent; // Axis settings. private int axisThickness; private Color axisColour; private Font axisLabelsFont; private Color axisLabelColour; private String xAxisLabel; private String yAxisLabel; private Color axisValuesColour; private Font axisValuesFont; // The font size will be considered the maximum font size - it may be smaller if needed to fit in. private int xAxisValuesFrequency; private int yAxisValuesFrequency; private boolean showXAxisValues; private boolean showYAxisValues; // Generated axis properties. private int xAxisValuesHeight; private int xAxisValuesWidthMax; private int yAxisValuesHeight; private int yAxisValuesAscent; private int yAxisValuesWidthMax; private Dimension xAxisLabelSize; private int xAxisLabelDescent; private Dimension yAxisLabelSize; private int yAxisLabelAscent; // Heat map colour settings. private Color highValueColour; private Color lowValueColour; // How many RGB steps there are between the high and low colours. private int colourValueDistance; private double lowValue; private double highValue; // Key co-ordinate positions. private Point heatMapTL; private Point heatMapBR; private Point heatMapC; // Heat map dimensions. private Dimension heatMapSize; // Control variable for mapping z-values to colours. private double colourScale; /** * Constructs a heatmap for the given z-values against x/y-values that by * default will be the values 0 to n-1, where n is the number of columns or * rows. * * @param zValues the z-values, where each element is a row of z-values * in the resultant heat chart. */ public HeatChart(double[][] zValues) { this(zValues, min(zValues), max(zValues)); } /** * Constructs a heatmap for the given z-values against x/y-values that by * default will be the values 0 to n-1, where n is the number of columns or * rows. * * @param zValues the z-values, where each element is a row of z-values * in the resultant heat chart. * @param low the minimum possible value, which may or may not appear in the * z-values. * @param high the maximum possible value, which may or may not appear in * the z-values. */ private HeatChart(double[][] zValues, double low, double high) { this.zValues = zValues; this.lowValue = low; this.highValue = high; // Default x/y-value settings. setXValues(0, 1); setYValues(0, 1); // Default chart settings. this.cellSize = new Dimension(20, 20); this.margin = 20; this.backgroundColour = Color.WHITE; // Default title settings. this.title = null; this.titleFont = HiCGlobals.font(16, true); this.titleColour = Color.BLACK; // Default axis settings. this.xAxisLabel = null; this.yAxisLabel = null; this.axisThickness = 2; this.axisColour = Color.BLACK; this.axisLabelsFont = HiCGlobals.font(12, false); this.axisLabelColour = Color.BLACK; this.axisValuesColour = Color.BLACK; this.axisValuesFont = HiCGlobals.font(10, false); this.xAxisValuesFrequency = 1; this.xAxisValuesHeight = 0; this.xValuesHorizontal = false; this.showXAxisValues = true; this.showYAxisValues = true; this.yAxisValuesFrequency = 1; this.yAxisValuesHeight = 0; this.yValuesHorizontal = true; // Default heatmap settings. this.highValueColour = Color.BLACK; this.lowValueColour = Color.WHITE; this.colourScale = SCALE_LINEAR; updateColourDistance(); } /** * Finds and returns the maximum value in a 2-dimensional array of doubles. * * @return the largest value in the array. */ private static double max(double[][] values) { double max = 0; for (double[] value : values) { for (double aValue : value) { max = Math.max(aValue, max); } } return max; } /** * Finds and returns the minimum value in a 2-dimensional array of doubles. * * @return the smallest value in the array. */ private static double min(double[][] values) { double min = Double.MAX_VALUE; for (double[] value : values) { for (double aValue : value) { min = Math.min(aValue, min); } } return min; } /** * Returns the low value. This is the value at which the low value colour * will be applied. * * @return the low value. */ public double getLowValue() { return lowValue; } /** * Returns the high value. This is the value at which the high value colour * will be applied. * * @return the high value. */ public double getHighValue() { return highValue; } /** * Returns a permissive integer range of data values by rounding up the high value, * and rounding down the low value, before calculating the range. * * @return the permissive int range of data values. */ public int getPermissiveIntRange() { return (int) (Math.ceil(highValue) - Math.floor(lowValue)); } /** * Returns the range of data values. This is the difference between the hig value * and low value. * * @return the range of data values. */ public double getDataRange() { return highValue - lowValue; } /** * Returns the 2-dimensional array of z-values currently in use. Each * element is a double array which represents one row of the heat map, or * all the z-values for one y-value. * * @return an array of the z-values in current use, that is, those values * which will define the colour of each cell in the resultant heat map. */ public double[][] getZValues() { return zValues; } /** * Replaces the z-values array. See the * {@link #setZValues(double[][], double, double)} method for an example of * z-values. The smallest and largest values in the array are used as the * minimum and maximum values respectively. * * @param zValues the array to replace the current array with. The number * of elements in each inner array must be identical. */ public void setZValues(double[][] zValues) { setZValues(zValues, min(zValues), max(zValues)); } /** * Replaces the z-values array. The number of elements should match the * number of y-values, with each element containing a double array with * an equal number of elements that matches the number of x-values. Use this * method where the minimum and maximum values possible are not contained * within the dataset. *

*

Example

*

* 

     * new double[][]{
     *   {1.0,1.2,1.4},
     *   {1.2,1.3,1.5},
     *   {0.9,1.3,1.2},
     *   {0.8,1.6,1.1}
     * };
     *
*

* The above zValues array is equivalent to: *

* * * * * * * * * * * * * * * * * * * * * * * * * * *
y
1.01.21.4
1.21.31.5
0.91.31.2
0.81.61.1
x
* * @param zValues the array to replace the current array with. The number * of elements in each inner array must be identical. * @param low the minimum possible value, which may or may not appear in the * z-values. * @param high the maximum possible value, which may or may not appear in * the z-values. */ private void setZValues(double[][] zValues, double low, double high) { this.zValues = zValues; this.lowValue = low; this.highValue = high; } /** * Sets the x-values which are plotted along the x-axis. The x-values are * calculated based upon the indexes of the z-values array: *

* 

     * x-value = x-offset + (column-index * x-interval)
     *
*

*

The x-interval defines the gap between each x-value and the x-offset * is applied to each value to offset them all from zero. *

*

Alternatively the x-values can be set more directly with the * setXValues(Object[]) method. * * @param xOffset an offset value to be applied to the index of each z-value * element. * @param xInterval an interval that will separate each x-value item. */ public void setXValues(double xOffset, double xInterval) { // Update the x-values according to the offset and interval. xValues = new Object[zValues[0].length]; for (int i = 0; i < zValues[0].length; i++) { xValues[i] = xOffset + (i * xInterval); } } /** * Sets the y-values which are plotted along the y-axis. The y-values are * calculated based upon the indexes of the z-values array: *

* 

     * y-value = y-offset + (column-index * y-interval)
     *
*

*

The y-interval defines the gap between each y-value and the y-offset * is applied to each value to offset them all from zero. *

*

Alternatively the y-values can be set more directly with the * setYValues(Object[]) method. * * @param yOffset an offset value to be applied to the index of each z-value * element. * @param yInterval an interval that will separate each y-value item. */ public void setYValues(double yOffset, double yInterval) { // Update the y-values according to the offset and interval. yValues = new Object[zValues.length]; for (int i = 0; i < zValues.length; i++) { yValues[i] = yOffset + (i * yInterval); } } /** * Returns the x-values which are currently set to display along the x-axis. * The array that is returned is either that which was explicitly set with * setXValues(Object[]) or that was generated from the offset * and interval that were given to setXValues(double, double), * in which case the object type of each element will be Double. * * @return an array of the values that are to be displayed along the x-axis. */ public Object[] getXValues() { return xValues; } /** * Sets the x-values which are plotted along the x-axis. The given x-values * array must be the same length as the z-values array has columns. Each * of the x-values elements will be displayed according to their toString * representation. * * @param xValues an array of elements to be displayed as values along the * x-axis. */ public void setXValues(Object[] xValues) { this.xValues = xValues; } /** * Returns the y-values which are currently set to display along the y-axis. * The array that is returned is either that which was explicitly set with * setYValues(Object[]) or that was generated from the offset * and interval that were given to setYValues(double, double), * in which case the object type of each element will be Double. * * @return an array of the values that are to be displayed along the y-axis. */ public Object[] getYValues() { return yValues; } /** * Sets the y-values which are plotted along the y-axis. The given y-values * array must be the same length as the z-values array has columns. Each * of the y-values elements will be displayed according to their toString * representation. * * @param yValues an array of elements to be displayed as values along the * y-axis. */ public void setYValues(Object[] yValues) { this.yValues = yValues; } /** * Returns whether the text of the values along the x-axis are to be drawn * horizontally left-to-right, or vertically top-to-bottom. * * @return true if the x-values will be drawn horizontally, false if they * will be drawn vertically. */ public boolean isXValuesHorizontal() { return xValuesHorizontal; } /** * Sets whether the text of the values along the x-axis should be drawn * horizontally left-to-right, or vertically top-to-bottom. * * @param xValuesHorizontal true if x-values should be drawn horizontally, * false if they should be drawn vertically. */ public void setXValuesHorizontal(boolean xValuesHorizontal) { this.xValuesHorizontal = xValuesHorizontal; } /** * Returns whether the text of the values along the y-axis are to be drawn * horizontally left-to-right, or vertically top-to-bottom. * * @return true if the y-values will be drawn horizontally, false if they * will be drawn vertically. */ public boolean isYValuesHorizontal() { return yValuesHorizontal; } /** * Sets whether the text of the values along the y-axis should be drawn * horizontally left-to-right, or vertically top-to-bottom. * * @param yValuesHorizontal true if y-values should be drawn horizontally, * false if they should be drawn vertically. */ public void setYValuesHorizontal(boolean yValuesHorizontal) { this.yValuesHorizontal = yValuesHorizontal; } /** * Returns the width of each individual data cell that constitutes a value * in the x,y,z space. * * @return the width of each cell. * @deprecated As of release 0.6, replaced by {@link #getCellSize} */ @Deprecated public int getCellWidth() { return cellSize.width; } /** * Sets the width of each individual cell that constitutes a value in x,y,z * data space. By setting the cell width, any previously set chart width * will be overwritten with a value calculated based upon this value and the * number of cells in there are along the x-axis. * * @param cellWidth the new width to use for each individual data cell. * @deprecated As of release 0.6, replaced by {@link #setCellSize(Dimension)} */ @Deprecated public void setCellWidth(int cellWidth) { setCellSize(new Dimension(cellWidth, cellSize.height)); } /** * Returns the height of each individual data cell that constitutes a value * in the x,y,z space. * * @return the height of each cell. * @deprecated As of release 0.6, replaced by {@link #getCellSize()} */ @Deprecated public int getCellHeight() { return cellSize.height; } /** * Sets the height of each individual cell that constitutes a value in x,y,z * data space. By setting the cell height, any previously set chart height * will be overwritten with a value calculated based upon this value and the * number of cells in there are along the y-axis. * * @param cellHeight the new height to use for each individual data cell. * @deprecated As of release 0.6, replaced by {@link #setCellSize(Dimension)} */ @Deprecated public void setCellHeight(int cellHeight) { setCellSize(new Dimension(cellSize.width, cellHeight)); } /** * Returns the size of each individual data cell that constitutes a value in * the x,y,z space. * * @return the size of each individual data cell. * @since 0.6 */ public Dimension getCellSize() { return cellSize; } /** * Sets the size of each individual cell that constitutes a value in x,y,z * data space. By setting the cell size, any previously set chart size will * be overwritten with a value calculated based upon this value and the * number of cells along each axis. * * @param cellSize the new size to use for each individual data cell. * @since 0.6 */ private void setCellSize(Dimension cellSize) { this.cellSize = cellSize; } /** * Returns the width of the chart in pixels as calculated according to the * cell dimensions, chart margin and other size settings. * * @return the width in pixels of the chart image to be generated. * @deprecated As of release 0.6, replaced by {@link #getChartSize()} */ @Deprecated public int getChartWidth() { return chartSize.width; } /** * Returns the height of the chart in pixels as calculated according to the * cell dimensions, chart margin and other size settings. * * @return the height in pixels of the chart image to be generated. * @deprecated As of release 0.6, replaced by {@link #getChartSize()} */ @Deprecated public int getChartHeight() { return chartSize.height; } /** * Returns the size of the chart in pixels as calculated according to the * cell dimensions, chart margin and other size settings. * * @return the size in pixels of the chart image to be generated. * @since 0.6 */ public Dimension getChartSize() { return chartSize; } /** * Returns the String that will be used as the title of any successive * calls to generate a chart. * * @return the title of the chart. */ public String getTitle() { return title; } /** * Sets the String that will be used as the title of any successive * calls to generate a chart. The title will be displayed centralised * horizontally at the top of any generated charts. *

*

* If the title is set to null then no title will be displayed. *

*

* Defaults to null. * * @param title the chart title to set. */ public void setTitle(String title) { this.title = title; } /** * Returns the String that will be displayed as a description of the * x-axis in any generated charts. * * @return the display label describing the x-axis. */ public String getXAxisLabel() { return xAxisLabel; } /** * Sets the String that will be displayed as a description of the * x-axis in any generated charts. The label will be displayed * horizontally central of the x-axis bar. *

*

* If the xAxisLabel is set to null then no label will be * displayed. *

*

* Defaults to null. * * @param xAxisLabel the label to be displayed describing the x-axis. */ public void setXAxisLabel(String xAxisLabel) { this.xAxisLabel = xAxisLabel; } /** * Returns the String that will be displayed as a description of the * y-axis in any generated charts. * * @return the display label describing the y-axis. */ public String getYAxisLabel() { return yAxisLabel; } /** * Sets the String that will be displayed as a description of the * y-axis in any generated charts. The label will be displayed * horizontally central of the y-axis bar. *

*

* If the yAxisLabel is set to null then no label will be * displayed. *

*

* Defaults to null. * * @param yAxisLabel the label to be displayed describing the y-axis. */ public void setYAxisLabel(String yAxisLabel) { this.yAxisLabel = yAxisLabel; } /** * Returns the width of the margin in pixels to be left as empty space * around the heat map element. * * @return the size of the margin to be left blank around the edge of the * chart. */ public int getChartMargin() { return margin; } /** * Sets the width of the margin in pixels to be left as empty space around * the heat map element. If a title is set then half the margin will be * directly above the title and half directly below it. Where axis labels * are set then the axis labels may sit partially in the margin. *

*

* Defaults to 20 pixels. * * @param margin the new margin to be left as blank space around the heat * map. */ public void setChartMargin(int margin) { this.margin = margin; } /** * Returns an object that represents the colour to be used as the * background for the whole chart. * * @return the colour to be used to fill the chart background. */ public Color getBackgroundColour() { return backgroundColour; } /** * Sets the colour to be used on the background of the chart. A transparent * background can be set by setting a background colour with an alpha value. * The transparency will only be effective when the image is saved as a png * or gif. *

*

* Defaults to Color.WHITE. * * @param backgroundColour the new colour to be set as the background fill. */ public void setBackgroundColour(Color backgroundColour) { if (backgroundColour == null) { backgroundColour = Color.WHITE; } this.backgroundColour = backgroundColour; } /** * Returns the Font that describes the visual style of the * title. * * @return the Font that will be used to render the title. */ public Font getTitleFont() { return titleFont; } /** * Sets a new Font to be used in rendering the chart's title * String. *

*

* Defaults to Sans-Serif, BOLD, 16 pixels. * * @param titleFont the Font that should be used when rendering the chart * title. */ public void setTitleFont(Font titleFont) { this.titleFont = titleFont; } /** * Returns the Color that represents the colour the title text * should be painted in. * * @return the currently set colour to be used in painting the chart title. */ public Color getTitleColour() { return titleColour; } /** * Sets the Color that describes the colour to be used for the * chart title String. *

*

* Defaults to Color.BLACK. * * @param titleColour the colour to paint the chart's title String. */ public void setTitleColour(Color titleColour) { this.titleColour = titleColour; } /** * Returns the width of the axis bars in pixels. Both axis bars have the * same thickness. * * @return the thickness of the axis bars in pixels. */ public int getAxisThickness() { return axisThickness; } /** * Sets the width of the axis bars in pixels. Both axis bars use the same * thickness. *

*

* Defaults to 2 pixels. * * @param axisThickness the thickness to use for the axis bars in any newly * generated charts. */ public void setAxisThickness(int axisThickness) { this.axisThickness = axisThickness; } /** * Returns the colour that is set to be used for the axis bars. Both axis * bars use the same colour. * * @return the colour in use for the axis bars. */ public Color getAxisColour() { return axisColour; } /** * Sets the colour to be used on the axis bars. Both axis bars use the same * colour. *

*

* Defaults to Color.BLACK. * * @param axisColour the colour to be set for use on the axis bars. */ public void setAxisColour(Color axisColour) { this.axisColour = axisColour; } /** * Returns the font that describes the visual style of the labels of the * axis. Both axis' labels use the same font. * * @return the font used to define the visual style of the axis labels. */ public Font getAxisLabelsFont() { return axisLabelsFont; } /** * Sets the font that describes the visual style of the axis labels. Both * axis' labels use the same font. *

*

* Defaults to Sans-Serif, PLAIN, 12 pixels. * * @param axisLabelsFont the font to be used to define the visual style of * the axis labels. */ public void setAxisLabelsFont(Font axisLabelsFont) { this.axisLabelsFont = axisLabelsFont; } /** * Returns the current colour of the axis labels. Both labels use the same * colour. * * @return the colour of the axis label text. */ public Color getAxisLabelColour() { return axisLabelColour; } /** * Sets the colour of the text displayed as axis labels. Both labels use * the same colour. *

*

* Defaults to Color.BLACK. * * @param axisLabelColour the colour to use for the axis label text. */ public void setAxisLabelColour(Color axisLabelColour) { this.axisLabelColour = axisLabelColour; } /** * Returns the font which describes the visual style of the axis values. * The axis values are those values displayed alongside the axis bars at * regular intervals. Both axis use the same font. * * @return the font in use for the axis values. */ public Font getAxisValuesFont() { return axisValuesFont; } /** * Sets the font which describes the visual style of the axis values. The * axis values are those values displayed alongside the axis bars at * regular intervals. Both axis use the same font. *

*

* Defaults to Sans-Serif, PLAIN, 10 pixels. * * @param axisValuesFont the font that should be used for the axis values. */ public void setAxisValuesFont(Font axisValuesFont) { this.axisValuesFont = axisValuesFont; } /** * Returns the colour of the axis values as they will be painted along the * axis bars. Both axis use the same colour. * * @return the colour of the values displayed along the axis bars. */ public Color getAxisValuesColour() { return axisValuesColour; } /** * Sets the colour to be used for the axis values as they will be painted * along the axis bars. Both axis use the same colour. *

*

* Defaults to Color.BLACK. * * @param axisValuesColour the new colour to be used for the axis bar values. */ public void setAxisValuesColour(Color axisValuesColour) { this.axisValuesColour = axisValuesColour; } /** * Returns the frequency of the values displayed along the x-axis. The * frequency is how many columns in the x-dimension have their value * displayed. A frequency of 2 would mean every other column has a value * shown and a frequency of 3 would mean every third column would be given a * value. * * @return the frequency of the values displayed against columns. */ public int getXAxisValuesFrequency() { return xAxisValuesFrequency; } /** * Sets the frequency of the values displayed along the x-axis. The * frequency is how many columns in the x-dimension have their value * displayed. A frequency of 2 would mean every other column has a value and * a frequency of 3 would mean every third column would be given a value. *

*

* Defaults to 1. Every column is given a value. * * @param axisValuesFrequency the frequency of the values displayed against * columns, where 1 is every column and 2 is every other column. */ public void setXAxisValuesFrequency(int axisValuesFrequency) { this.xAxisValuesFrequency = axisValuesFrequency; } /** * Returns the frequency of the values displayed along the y-axis. The * frequency is how many rows in the y-dimension have their value displayed. * A frequency of 2 would mean every other row has a value and a frequency * of 3 would mean every third row would be given a value. * * @return the frequency of the values displayed against rows. */ public int getYAxisValuesFrequency() { return yAxisValuesFrequency; } /** * Sets the frequency of the values displayed along the y-axis. The * frequency is how many rows in the y-dimension have their value displayed. * A frequency of 2 would mean every other row has a value and a frequency * of 3 would mean every third row would be given a value. *

*

* Defaults to 1. Every row is given a value. * * @param axisValuesFrequency the frequency of the values displayed against * rows, where 1 is every row and 2 is every other row. */ public void setYAxisValuesFrequency(int axisValuesFrequency) { yAxisValuesFrequency = axisValuesFrequency; } /** * Returns whether axis values are to be shown at all for the x-axis. *

*

* If axis values are not shown then more space is allocated to the heat * map. * * @return true if the x-axis values will be displayed, false otherwise. */ public boolean isShowXAxisValues() { //TODO Could get rid of these flags and use a frequency of -1 to signal no values. return showXAxisValues; } /** * Sets whether axis values are to be shown at all for the x-axis. *

*

* If axis values are not shown then more space is allocated to the heat * map. *

*

* Defaults to true. * * @param showXAxisValues true if x-axis values should be displayed, false * if they should be hidden. */ public void setShowXAxisValues(boolean showXAxisValues) { this.showXAxisValues = showXAxisValues; } /** * Returns whether axis values are to be shown at all for the y-axis. *

*

* If axis values are not shown then more space is allocated to the heat * map. * * @return true if the y-axis values will be displayed, false otherwise. */ public boolean isShowYAxisValues() { return showYAxisValues; } /** * Sets whether axis values are to be shown at all for the y-axis. *

*

* If axis values are not shown then more space is allocated to the heat * map. *

*

* Defaults to true. * * @param showYAxisValues true if y-axis values should be displayed, false * if they should be hidden. */ public void setShowYAxisValues(boolean showYAxisValues) { this.showYAxisValues = showYAxisValues; } /** * Returns the colour that is currently to be displayed for the heat map * cells with the highest z-value in the dataset. *

*

* The full colour range will go through each RGB step between the high * value colour and the low value colour. * * @return the colour in use for cells of the highest z-value. */ public Color getHighValueColour() { return highValueColour; } /** * Sets the colour to be used to fill cells of the heat map with the * highest z-values in the dataset. *

*

* The full colour range will go through each RGB step between the high * value colour and the low value colour. *

*

* Defaults to Color.BLACK. * * @param highValueColour the colour to use for cells of the highest * z-value. */ public void setHighValueColour(Color highValueColour) { this.highValueColour = highValueColour; updateColourDistance(); } /** * Returns the colour that is currently to be displayed for the heat map * cells with the lowest z-value in the dataset. *

*

* The full colour range will go through each RGB step between the high * value colour and the low value colour. * * @return the colour in use for cells of the lowest z-value. */ public Color getLowValueColour() { return lowValueColour; } /** * Sets the colour to be used to fill cells of the heat map with the * lowest z-values in the dataset. *

*

* The full colour range will go through each RGB step between the high * value colour and the low value colour. *

*

* Defaults to Color.WHITE. * * @param lowValueColour the colour to use for cells of the lowest * z-value. */ public void setLowValueColour(Color lowValueColour) { this.lowValueColour = lowValueColour; updateColourDistance(); } /** * Returns the scale that is currently in use to map z-value to colour. A * value of 1.0 will give a linear scale, which will * spread the distribution of colours evenly amoungst the full range of * represented z-values. A value of greater than 1.0 will give an * exponential scale that will produce greater emphasis * for the separation between higher values and a value between 0.0 and 1.0 * will provide a logarithmic scale, with greater * separation of low values. * * @return the scale factor that is being used to map from z-value to colour. */ public double getColourScale() { return colourScale; } /** * Sets the scale that is currently in use to map z-value to colour. A * value of 1.0 will give a linear scale, which will * spread the distribution of colours evenly amoungst the full range of * represented z-values. A value of greater than 1.0 will give an * exponential scale that will produce greater emphasis * for the separation between higher values and a value between 0.0 and 1.0 * will provide a logarithmic scale, with greater * separation of low values. Values of 0.0 or less are illegal. *

*

* Defaults to a linear scale value of 1.0. * * @param colourScale the scale that should be used to map from z-value to * colour. */ public void setColourScale(double colourScale) { this.colourScale = colourScale; } /* * Calculate and update the field for the distance between the low colour * and high colour. The distance is the number of steps between one colour * and the other using an RGB coding with 0-255 values for each of red, * green and blue. So the maximum colour distance is 255 + 255 + 255. */ private void updateColourDistance() { int r1 = lowValueColour.getRed(); int g1 = lowValueColour.getGreen(); int b1 = lowValueColour.getBlue(); int r2 = highValueColour.getRed(); int g2 = highValueColour.getGreen(); int b2 = highValueColour.getBlue(); colourValueDistance = Math.abs(r1 - r2); colourValueDistance += Math.abs(g1 - g2); colourValueDistance += Math.abs(b1 - b2); } /** * Generates a new chart Image based upon the currently held * settings and then attempts to save that image to disk, to the location * provided as a File parameter. The image type of the saved file will * equal the extension of the filename provided, so it is essential that a * suitable extension be included on the file name. *

*

* All supported ImageIO file types are supported, including * PNG, JPG and GIF. *

*

* No chart will be generated until this or the related * getChartImage() method are called. All successive calls * will result in the generation of a new chart image, no caching is used. * * @param outputFile the file location that the generated image file should * be written to. The File must have a suitable filename, with an extension * of a valid image format (as supported by ImageIO). * @throws IOException if the output file's filename has no extension or * if there the file is unable to written to. Reasons for this include a * non-existant file location (check with the File exists() method on the * parent directory), or the permissions of the write location may be * incorrect. */ public void saveToFile(File outputFile) throws IOException { String filename = outputFile.getName(); int extPoint = filename.lastIndexOf('.'); if (extPoint < 0) { throw new IOException("Illegal filename, no extension used."); } // Determine the extension of the filename. String ext = filename.substring(extPoint + 1); // Handle jpg without transparency. if (ext.equalsIgnoreCase("jpg") || ext.equalsIgnoreCase("jpeg")) { BufferedImage chart = (BufferedImage) getChartImage(false); // Save our graphic. saveGraphicJpeg(chart, outputFile, 1.0f); } else { BufferedImage chart = (BufferedImage) getChartImage(true); ImageIO.write(chart, ext, outputFile); } } private void saveGraphicJpeg(BufferedImage chart, File outputFile, float quality) throws IOException { // Setup correct compression for jpeg. Iterator iter = ImageIO.getImageWritersByFormatName("jpeg"); ImageWriter writer = iter.next(); ImageWriteParam iwp = writer.getDefaultWriteParam(); iwp.setCompressionMode(ImageWriteParam.MODE_EXPLICIT); iwp.setCompressionQuality(quality); // Output the image. FileImageOutputStream output = new FileImageOutputStream(outputFile); writer.setOutput(output); IIOImage image = new IIOImage(chart, null, null); writer.write(null, image, iwp); writer.dispose(); } /** * Generates and returns a new chart Image configured * according to this object's currently held settings. The given parameter * determines whether transparency should be enabled for the generated * image. *

*

* No chart will be generated until this or the related * saveToFile(File) method are called. All successive calls * will result in the generation of a new chart image, no caching is used. * * @param alpha whether to enable transparency. * @return A newly generated chart Image. The returned image * is a BufferedImage. */ private Image getChartImage(boolean alpha) { // Calculate all unknown dimensions. measureComponents(); updateCoordinates(); // Determine image type based upon whether require alpha or not. // Using BufferedImage.TYPE_INT_ARGB seems to break on jpg. int imageType = (alpha ? BufferedImage.TYPE_4BYTE_ABGR : BufferedImage.TYPE_3BYTE_BGR); // Create our chart image which we will eventually draw everything on. BufferedImage chartImage = new BufferedImage(chartSize.width, chartSize.height, imageType); Graphics2D chartGraphics = chartImage.createGraphics(); // Use anti-aliasing where ever possible. chartGraphics.setRenderingHint(RenderingHints.KEY_ANTIALIASING, RenderingHints.VALUE_ANTIALIAS_ON); // Set the background. chartGraphics.setColor(backgroundColour); chartGraphics.fillRect(0, 0, chartSize.width, chartSize.height); // Draw the title. drawTitle(chartGraphics); // Draw the heatmap image. drawHeatMap(chartGraphics, zValues); // Draw the axis labels. TODO MSS - redo drawing axes drawXLabel(chartGraphics); drawYLabel(chartGraphics); // Draw the axis bars. drawAxisBars(chartGraphics); // Draw axis values. drawXValues(chartGraphics); drawYValues(chartGraphics); return chartImage; } /** * Generates and returns a new chart Image configured * according to this object's currently held settings. By default the image * is generated with no transparency. *

*

* No chart will be generated until this or the related * saveToFile(File) method are called. All successive calls * will result in the generation of a new chart image, no caching is used. * * @return A newly generated chart Image. The returned image * is a BufferedImage. */ public Image getChartImage() { return getChartImage(false); } /* * Calculates all unknown component dimensions. */ private void measureComponents() { //TODO This would be a good place to check that all settings have sensible values or throw illegal state exception. //TODO Put this somewhere so it only gets created once. BufferedImage chartImage = new BufferedImage(1, 1, BufferedImage.TYPE_INT_ARGB); Graphics2D tempGraphics = chartImage.createGraphics(); // Calculate title dimensions. if (title != null) { tempGraphics.setFont(titleFont); FontMetrics metrics = tempGraphics.getFontMetrics(); titleSize = new Dimension(metrics.stringWidth(title), metrics.getHeight()); titleAscent = metrics.getAscent(); } else { titleSize = new Dimension(0, 0); } // Calculate x-axis label dimensions. if (xAxisLabel != null) { tempGraphics.setFont(axisLabelsFont); FontMetrics metrics = tempGraphics.getFontMetrics(); xAxisLabelSize = new Dimension(metrics.stringWidth(xAxisLabel), metrics.getHeight()); xAxisLabelDescent = metrics.getDescent(); } else { xAxisLabelSize = new Dimension(0, 0); } // Calculate y-axis label dimensions. if (yAxisLabel != null) { tempGraphics.setFont(axisLabelsFont); FontMetrics metrics = tempGraphics.getFontMetrics(); yAxisLabelSize = new Dimension(metrics.stringWidth(yAxisLabel), metrics.getHeight()); yAxisLabelAscent = metrics.getAscent(); } else { yAxisLabelSize = new Dimension(0, 0); } // Calculate x-axis value dimensions. if (showXAxisValues) { tempGraphics.setFont(axisValuesFont); FontMetrics metrics = tempGraphics.getFontMetrics(); xAxisValuesHeight = metrics.getHeight(); xAxisValuesWidthMax = 0; for (Object o : xValues) { int w = metrics.stringWidth(o.toString()); if (w > xAxisValuesWidthMax) { xAxisValuesWidthMax = w; } } } else { xAxisValuesHeight = 0; } // Calculate y-axis value dimensions. if (showYAxisValues) { tempGraphics.setFont(axisValuesFont); FontMetrics metrics = tempGraphics.getFontMetrics(); yAxisValuesHeight = metrics.getHeight(); yAxisValuesAscent = metrics.getAscent(); yAxisValuesWidthMax = 0; for (Object o : yValues) { int w = metrics.stringWidth(o.toString()); if (w > yAxisValuesWidthMax) { yAxisValuesWidthMax = w; } } } else { yAxisValuesHeight = 0; } // Calculate heatmap dimensions. int heatMapWidth = (zValues[0].length * cellSize.width); int heatMapHeight = (zValues.length * cellSize.height); heatMapSize = new Dimension(heatMapWidth, heatMapHeight); int yValuesHorizontalSize; if (yValuesHorizontal) { yValuesHorizontalSize = yAxisValuesWidthMax; } else { yValuesHorizontalSize = yAxisValuesHeight; } int xValuesVerticalSize; if (xValuesHorizontal) { xValuesVerticalSize = xAxisValuesHeight; } else { xValuesVerticalSize = xAxisValuesWidthMax; } // Calculate chart dimensions. int chartWidth = heatMapWidth + (2 * margin) + yAxisLabelSize.height + yValuesHorizontalSize + axisThickness; int chartHeight = heatMapHeight + (2 * margin) + xAxisLabelSize.height + xValuesVerticalSize + titleSize.height + axisThickness; chartSize = new Dimension(chartWidth, chartHeight); } /* * Calculates the co-ordinates of some key positions. */ private void updateCoordinates() { // Top-left of heat map. int x = margin + axisThickness + yAxisLabelSize.height; x += (yValuesHorizontal ? yAxisValuesWidthMax : yAxisValuesHeight); int y = titleSize.height + margin; heatMapTL = new Point(x, y); // Top-right of heat map. x = heatMapTL.x + heatMapSize.width; y = heatMapTL.y + heatMapSize.height; heatMapBR = new Point(x, y); // Centre of heat map. x = heatMapTL.x + (heatMapSize.width / 2); y = heatMapTL.y + (heatMapSize.height / 2); heatMapC = new Point(x, y); } /* * Draws the title String on the chart if title is not null. */ private void drawTitle(Graphics2D chartGraphics) { if (title != null) { // Strings are drawn from the baseline position of the leftmost char. int yTitle = (margin / 2) + titleAscent; int xTitle = (chartSize.width / 2) - (titleSize.width / 2); chartGraphics.setFont(titleFont); chartGraphics.setColor(titleColour); chartGraphics.drawString(title, xTitle, yTitle); } } /* * Creates the actual heatmap element as an image, that can then be drawn * onto a chart. */ private void drawHeatMap(Graphics2D chartGraphics, double[][] data) { // Calculate the available size for the heatmap. int noYCells = data.length; int noXCells = data[0].length; //double dataMin = min(data); //double dataMax = max(data); BufferedImage heatMapImage = new BufferedImage(heatMapSize.width, heatMapSize.height, BufferedImage.TYPE_INT_ARGB); Graphics2D heatMapGraphics = heatMapImage.createGraphics(); for (int x = 0; x < noXCells; x++) { for (int y = 0; y < noYCells; y++) { // Set colour depending on zValues. heatMapGraphics.setColor(getCellColour(data[y][x], lowValue, highValue)); int cellX = x * cellSize.width; int cellY = y * cellSize.height; heatMapGraphics.fillRect(cellX, cellY, cellSize.width, cellSize.height); } } // Draw the heat map onto the chart. chartGraphics.drawImage(heatMapImage, heatMapTL.x, heatMapTL.y, heatMapSize.width, heatMapSize.height, null); } /* * Draws the x-axis label string if it is not null. */ private void drawXLabel(Graphics2D chartGraphics) { if (xAxisLabel != null) { // Strings are drawn from the baseline position of the leftmost char. int yPosXAxisLabel = chartSize.height - (margin / 2) - xAxisLabelDescent; //TODO This will need to be updated if the y-axis values/label can be moved to the right. int xPosXAxisLabel = heatMapC.x - (xAxisLabelSize.width / 2); chartGraphics.setFont(axisLabelsFont); chartGraphics.setColor(axisLabelColour); chartGraphics.drawString(xAxisLabel, xPosXAxisLabel, yPosXAxisLabel); } } /* * Draws the y-axis label string if it is not null. */ private void drawYLabel(Graphics2D chartGraphics) { if (yAxisLabel != null) { // Strings are drawn from the baseline position of the leftmost char. int yPosYAxisLabel = heatMapC.y + (yAxisLabelSize.width / 2); int xPosYAxisLabel = (margin / 2) + yAxisLabelAscent; chartGraphics.setFont(axisLabelsFont); chartGraphics.setColor(axisLabelColour); // Create 270 degree rotated transform. AffineTransform transform = chartGraphics.getTransform(); AffineTransform originalTransform = (AffineTransform) transform.clone(); transform.rotate(Math.toRadians(270), xPosYAxisLabel, yPosYAxisLabel); chartGraphics.setTransform(transform); // Draw string. chartGraphics.drawString(yAxisLabel, xPosYAxisLabel, yPosYAxisLabel); // Revert to original transform before rotation. chartGraphics.setTransform(originalTransform); } } /* * Draws the bars of the x-axis and y-axis. */ private void drawAxisBars(Graphics2D chartGraphics) { if (axisThickness > 0) { chartGraphics.setColor(axisColour); // Draw x-axis. int x = heatMapTL.x - axisThickness; int y = heatMapBR.y; int width = heatMapSize.width + axisThickness; int height = axisThickness; chartGraphics.fillRect(x, y, width, height); // Draw y-axis. x = heatMapTL.x - axisThickness; y = heatMapTL.y; width = axisThickness; height = heatMapSize.height; chartGraphics.fillRect(x, y, width, height); } } /* * Draws the x-values onto the x-axis if showXAxisValues is set to true. */ private void drawXValues(Graphics2D chartGraphics) { if (!showXAxisValues) { return; } chartGraphics.setColor(axisValuesColour); for (int i = 0; i < xValues.length; i++) { if (i % xAxisValuesFrequency != 0) { continue; } String xValueStr = xValues[i].toString(); chartGraphics.setFont(axisValuesFont); FontMetrics metrics = chartGraphics.getFontMetrics(); int valueWidth = metrics.stringWidth(xValueStr); if (xValuesHorizontal) { // Draw the value with whatever font is now set. int valueXPos = (i * cellSize.width) + ((cellSize.width / 2) - (valueWidth / 2)); valueXPos += heatMapTL.x; int valueYPos = heatMapBR.y + metrics.getAscent() + 1; chartGraphics.drawString(xValueStr, valueXPos, valueYPos); } else { int valueXPos = heatMapTL.x + (i * cellSize.width) + ((cellSize.width / 2) + (xAxisValuesHeight / 2)); int valueYPos = heatMapBR.y + axisThickness + valueWidth; // Create 270 degree rotated transform. AffineTransform transform = chartGraphics.getTransform(); AffineTransform originalTransform = (AffineTransform) transform.clone(); transform.rotate(Math.toRadians(270), valueXPos, valueYPos); chartGraphics.setTransform(transform); // Draw the string. chartGraphics.drawString(xValueStr, valueXPos, valueYPos); // Revert to original transform before rotation. chartGraphics.setTransform(originalTransform); } } } /* * Draws the y-values onto the y-axis if showYAxisValues is set to true. */ private void drawYValues(Graphics2D chartGraphics) { if (!showYAxisValues) { return; } chartGraphics.setColor(axisValuesColour); for (int i = 0; i < yValues.length; i++) { if (i % yAxisValuesFrequency != 0) { continue; } String yValueStr = yValues[i].toString(); chartGraphics.setFont(axisValuesFont); FontMetrics metrics = chartGraphics.getFontMetrics(); int valueWidth = metrics.stringWidth(yValueStr); if (yValuesHorizontal) { // Draw the value with whatever font is now set. int valueXPos = margin + yAxisLabelSize.height + (yAxisValuesWidthMax - valueWidth); int valueYPos = heatMapTL.y + (i * cellSize.height) + (cellSize.height / 2) + (yAxisValuesAscent / 2); chartGraphics.drawString(yValueStr, valueXPos, valueYPos); } else { int valueXPos = margin + yAxisLabelSize.height + yAxisValuesAscent; int valueYPos = heatMapTL.y + (i * cellSize.height) + (cellSize.height / 2) + (valueWidth / 2); // Create 270 degree rotated transform. AffineTransform transform = chartGraphics.getTransform(); AffineTransform originalTransform = (AffineTransform) transform.clone(); transform.rotate(Math.toRadians(270), valueXPos, valueYPos); chartGraphics.setTransform(transform); // Draw the string. chartGraphics.drawString(yValueStr, valueXPos, valueYPos); // Revert to original transform before rotation. chartGraphics.setTransform(originalTransform); } } } /* * Determines what colour a heat map cell should be based upon the cell * values. */ private Color getCellColour(double data, double min, double max) { double range = max - min; double position = data - min; // What proportion of the way through the possible values is that. double percentPosition = position / range; // Which colour group does that put us in. int colourPosition = getColourPosition(percentPosition); int r = lowValueColour.getRed(); int g = lowValueColour.getGreen(); int b = lowValueColour.getBlue(); // Make n shifts of the colour, where n is the colourPosition. for (int i = 0; i < colourPosition; i++) { int rDistance = r - highValueColour.getRed(); int gDistance = g - highValueColour.getGreen(); int bDistance = b - highValueColour.getBlue(); if ((Math.abs(rDistance) >= Math.abs(gDistance)) && (Math.abs(rDistance) >= Math.abs(bDistance))) { // Red must be the largest. r = changeColourValue(r, rDistance); } else if (Math.abs(gDistance) >= Math.abs(bDistance)) { // Green must be the largest. g = changeColourValue(g, gDistance); } else { // Blue must be the largest. b = changeColourValue(b, bDistance); } } return new Color(r, g, b); } /* * Returns how many colour shifts are required from the lowValueColour to * get to the correct colour position. The result will be different * depending on the colour scale used: LINEAR, LOGARITHMIC, EXPONENTIAL. */ private int getColourPosition(double percentPosition) { return (int) Math.round(colourValueDistance * Math.pow(percentPosition, colourScale)); } private int changeColourValue(int colourValue, int colourDistance) { if (colourDistance < 0) { return colourValue + 1; } else if (colourDistance > 0) { return colourValue - 1; } else { // This shouldn't actually happen here. return colourValue; } } /** * Returns the top left corner of the heat map * for use when drawing over the image * * @return the coordinates for the top left corner of the heat map */ public Point getHeatMapTL() { return heatMapTL; } /** * Returns the bottom right corner of the heat map * for use when drawing over the image * * @return the coordinates for the bottom right corner of the heat map */ public Point getHeatMapBR() { return heatMapBR; } /** * Returns the center of the heat map * for use when drawing over the image * * @return the coordinates for the center of the heat map */ public Point getHeatMapC() { return heatMapC; } /** * Returns the top right corner of the heat map * for use when drawing over the image * * @return the coordinates for the top right corner of the heat map */ public Point getHeatMapTR() { return new Point(heatMapBR.x, heatMapTL.y); } /** * Returns the bottom left corner of the heat map * for use when drawing over the image * * @return the coordinates for the bottom left corner of the heat map */ public Point getHeatMapBL() { return new Point(heatMapTL.x, heatMapBR.y); } } ================================================ FILE: src/org/tc33/jheatchart/LICENSE.MD ================================================ This file includes a copy of both: GNU GENERAL PUBLIC LICENSE GNU LESSER GENERAL PUBLIC LICENSE ---------------------------------------------------------------------- GNU GENERAL PUBLIC LICENSE Version 3, 29 June 2007 Copyright (C) 2007 Free Software Foundation, Inc. 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The hypothetical commands `show w' and `show c' should show the appropriate parts of the General Public License. Of course, your program's commands might be different; for a GUI interface, you would use an "about box". You should also get your employer (if you work as a programmer) or school, if any, to sign a "copyright disclaimer" for the program, if necessary. For more information on this, and how to apply and follow the GNU GPL, see . The GNU General Public License does not permit incorporating your program into proprietary programs. If your program is a subroutine library, you may consider it more useful to permit linking proprietary applications with the library. If this is what you want to do, use the GNU Lesser General Public License instead of this License. But first, please read . GNU LESSER GENERAL PUBLIC LICENSE Version 3, 29 June 2007 Copyright (C) 2007 Free Software Foundation, Inc. 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Each version is given a distinguishing version number. If the Library as you received it specifies that a certain numbered version of the GNU Lesser General Public License "or any later version" applies to it, you have the option of following the terms and conditions either of that published version or of any later version published by the Free Software Foundation. If the Library as you received it does not specify a version number of the GNU Lesser General Public License, you may choose any version of the GNU Lesser General Public License ever published by the Free Software Foundation. If the Library as you received it specifies that a proxy can decide whether future versions of the GNU Lesser General Public License shall apply, that proxy's public statement of acceptance of any version is permanent authorization for you to choose that version for the Library. ================================================ FILE: src/org/tc33/jheatchart/README.MD ================================================ Note The APA heatmap plotting module in Juicebox Tools uses a modified version of JHeatChart developed by Tom Castle. JHeatChart is open source under an LGPL license. The main heatmap plotting of the standard Juicebox GUI does not use JHeatChart. JHeatChart - https://github.com/tc33/jheatchart - MSS ******************************************************************************* JHeatChart v.0.6 Tom Castle: www.tc33.org ******************************************************************************* | | | JHeatChart is made available under a GPL license, for full details of the | | license see the included LICENSE text file. | | | |-----------------------------------------------------------------------------| For the latest version of JHeatChart and any tutorials and examples that exist, see the JHeatChart project pages at http://www.tc33.org. Contents of release: jheatchart-0.6 | jheatchart-0.6.jar - the library. Put this anywhere on your class path. | src - directory containing all the java source. | ... | javadoc - directory containing the javadoc for this release. | ... | README - this file. | LICENSE - details of the GPL license this software is covered by. Usage: Simply put the jheatchart jar file on your class path and then you are free to create instances of HeatChart. Example code: // Create some dummy data. double[][] data = new double[][]{{3,2,3,4,5,6}, {2,3,4,5,6,7}, {3,4,5,6,7,6}, {4,5,6,7,6,5}}; // Create our heat chart using our data. HeatChart chart = new HeatChart(data); // Customise the chart. chart.setTitle("This is my chart title"); chart.setXAxisLabel("X Axis"); chart.setYAxisLabel("Y Axis"); // Output the chart to a file. chart.saveToFile(new File("my-chart.png")); ================================================ FILE: src/resources/manifests/juicebox_jar/META-INF/MANIFEST.MF ================================================ Manifest-Version: 1.0 Main-Class: juicebox.MainWindow ================================================ FILE: src/resources/manifests/juicer_tools_jar/META-INF/MANIFEST.MF ================================================ Manifest-Version: 1.0 Main-Class: juicebox.tools.HiCTools