## Beginning of track view track HepG2_ATAC compositeTrack on shortLabel HepG2_ATAC longLabel HepG2_ATAC priority 700 visibility full type bed 3 configurable on subGroup1 view Views \ COV=Coverage \ PEAK=Peaks \ subGroup2 Group1 Group1 \ NTC=NTC \ siBrg1=siBrg1 \ sortOrder Group1=+ view=+ ## Views track coverage data track HepG2_ATACview1 parent HepG2_ATAC shortLabel Coverage view COV visibility full type bigWig allButtonPair on centerLabelsDense on dragAndDrop on alwaysZero on graphTypeDefault bar maxHeightPixels 100:40:8 smoothingWindow 2 transformFunc NONE windowingFunction mean+whiskers gridDefault on viewLimits 0:20 viewUi on ## Coverage track track NTC_free parent HepG2_ATACview1 on bigDataUrl NTC.merged.free.bw shortLabel NTC Free longLabel NTC Free type bigWig color 16,100,100 priority 701 alwaysZero on graphTypeDefault bar maxHeightPixels 100:40:8 smoothingWindow 2 transformFunc NONE windowingFunction mean+whiskers gridDefault on viewLimits 0:20 visibility hide subGroups Group1=NTC view=COV ## Coverage track track NTC_nuc parent HepG2_ATACview1 on bigDataUrl NTC.merged.nuc.bw shortLabel NTC nuc longLabel NTC nuc type bigWig color 16,120,120 priority 702 alwaysZero on graphTypeDefault bar maxHeightPixels 100:40:8 smoothingWindow 2 transformFunc NONE windowingFunction mean+whiskers gridDefault on viewLimits 0:20 visibility hide subGroups Group1=NTC view=COV ## Coverage track track NTC_all parent HepG2_ATACview1 on bigDataUrl NTC.merged.dedupe.view.bw shortLabel NTC ATAC longLabel NTC ATAC type bigWig color 16,140,140 priority 703 alwaysZero on graphTypeDefault bar maxHeightPixels 100:40:8 smoothingWindow 2 transformFunc NONE windowingFunction mean+whiskers gridDefault on viewLimits 0:20 visibility hide subGroups Group1=NTC view=COV ## Coverage track track siBrg1_free parent HepG2_ATACview1 on bigDataUrl siBrg1.merged.free.bw shortLabel siBrg1 Free longLabel siBrg1 Free type bigWig color 100,100,16 priority 704 alwaysZero on graphTypeDefault bar maxHeightPixels 100:40:8 smoothingWindow 2 transformFunc NONE windowingFunction mean+whiskers gridDefault on viewLimits 0:20 visibility hide subGroups Group1=siBrg1 view=COV ## Coverage track track siBrg1_nuc parent HepG2_ATACview1 on bigDataUrl siBrg1.merged.nuc.bw shortLabel siBrg1 nuc longLabel siBrg1 nuc type bigWig color 120,120,16 priority 705 alwaysZero on graphTypeDefault bar maxHeightPixels 100:40:8 smoothingWindow 2 transformFunc NONE windowingFunction mean+whiskers gridDefault on viewLimits 0:20 visibility hide subGroups Group1=siBrg1 view=COV ## Coverage track track siBrg1_ATAC parent HepG2_ATACview1 on bigDataUrl siBrg1.merged.dedupe.view.bw shortLabel siBrg1 ATAC longLabel siBrg1 ATAC type bigWig color 140,140,16 priority 706 alwaysZero on graphTypeDefault bar maxHeightPixels 100:40:8 smoothingWindow 2 transformFunc NONE windowingFunction mean+whiskers gridDefault on viewLimits 0:20 visibility hide subGroups Group1=siBrg1 view=COV ## Beginning of track view track A1_2_ChIPseq_Dec2015 compositeTrack on shortLabel A1_2 Dec2015 longLabel Trotter A1_2 ChIPseq Dec2015 priority 1000 visibility full type bed 3 configurable on subGroup1 view Views \ COV=Coverage \ PEAK=Peaks \ subGroup2 Group1 Group1 \ EtOH=EtOH \ Dex=Dex \ sortOrder Group1=+ view=+ ## Views track coverage data track A1_2_ChIPseq_Dec2015view1 parent A1_2_ChIPseq_Dec2015 shortLabel Coverage view COV visibility full type bigWig allButtonPair on centerLabelsDense on dragAndDrop on alwaysZero on graphTypeDefault bar maxHeightPixels 100:40:8 smoothingWindow 2 transformFunc NONE windowingFunction mean+whiskers gridDefault on viewLimits 0:20 viewUi on ## Coverage track track Dex_Input parent A1_2_ChIPseq_Dec2015view1 on bigDataUrl Dex_Input.bw shortLabel Dex Input longLabel Dex Input type bigWig color 100,16,100 priority 1001 alwaysZero on graphTypeDefault bar maxHeightPixels 100:40:8 smoothingWindow 2 transformFunc NONE windowingFunction mean+whiskers gridDefault on viewLimits 0:20 visibility hide subGroups Group1=Dex view=COV ## Coverage track track Dex_Novus_Brg1 parent A1_2_ChIPseq_Dec2015view1 on bigDataUrl Dex_Nov.bw shortLabel Dex Novus_Brg1 longLabel Dex Novus_Brg1 type bigWig color 140,16,140 priority 1002 alwaysZero on graphTypeDefault bar maxHeightPixels 100:40:8 smoothingWindow 2 transformFunc NONE windowingFunction mean+whiskers gridDefault on viewLimits 0:20 visibility hide subGroups Group1=Dex view=COV ## Coverage track track Dex_Lab_Brg1 parent A1_2_ChIPseq_Dec2015view1 on bigDataUrl Dex_Lab.bw shortLabel Dex Lab_Brg1 longLabel Dex Lab_Brg1 type bigWig color 180,16,180 priority 1003 alwaysZero on graphTypeDefault bar maxHeightPixels 100:40:8 smoothingWindow 2 transformFunc NONE windowingFunction mean+whiskers gridDefault on viewLimits 0:20 visibility hide subGroups Group1=Dex view=COV ## Coverage track track Dex_GR parent A1_2_ChIPseq_Dec2015view1 on bigDataUrl Dex_GR.bw shortLabel Dex GR longLabel Dex GR type bigWig color 220,16,220 priority 1004 alwaysZero on graphTypeDefault bar maxHeightPixels 100:40:8 smoothingWindow 2 transformFunc NONE windowingFunction mean+whiskers gridDefault on viewLimits 0:20 visibility hide subGroups Group1=Dex view=COV ## Coverage track track EtOH_Input parent A1_2_ChIPseq_Dec2015view1 on bigDataUrl EtOH_Input.bw shortLabel EtOH Input longLabel EtOH Input type bigWig color 0,100,16 priority 1005 alwaysZero on graphTypeDefault bar maxHeightPixels 100:40:8 smoothingWindow 2 transformFunc NONE windowingFunction mean+whiskers gridDefault on viewLimits 0:20 visibility hide subGroups Group1=EtOH view=COV ## Coverage track track EtOH_Novus_Brg1 parent A1_2_ChIPseq_Dec2015view1 on bigDataUrl EtOH_Nov.bw shortLabel EtOH Novus_Brg1 longLabel EtOH Novus_Brg1 type bigWig color 0,120,16 priority 1006 alwaysZero on graphTypeDefault bar maxHeightPixels 100:40:8 smoothingWindow 2 transformFunc NONE windowingFunction mean+whiskers gridDefault on viewLimits 0:20 visibility hide subGroups Group1=EtOH view=COV ## Coverage track track EtOH_Lab_Brg1 parent A1_2_ChIPseq_Dec2015view1 on bigDataUrl EtOH_Lab.bw shortLabel EtOH Lab_Brg1 longLabel EtOH Lab_Brg1 type bigWig color 0,140,16 priority 1007 alwaysZero on graphTypeDefault bar maxHeightPixels 100:40:8 smoothingWindow 2 transformFunc NONE windowingFunction mean+whiskers gridDefault on viewLimits 0:20 visibility hide subGroups Group1=EtOH view=COV ## Coverage track track EtOH_GR parent A1_2_ChIPseq_Dec2015view1 on bigDataUrl EtOH_GR.bw shortLabel EtOH GR longLabel EtOH GR type bigWig color 0,160,16 priority 1008 alwaysZero on graphTypeDefault bar maxHeightPixels 100:40:8 smoothingWindow 2 transformFunc NONE windowingFunction mean+whiskers gridDefault on viewLimits 0:20 visibility hide subGroups Group1=EtOH view=COV ## Hoffman ChIPseq composite with subgroup views track JHchipSeqSet compositeTrack on shortLabel Hoffman ChIPseq longLabel Hoffman ChIPseq priority 1130 subGroup1 view Views \ COV=Coverage \ PEAK=Peaks subGroup2 antibody Antibody \ siBrg1=siBrg1 \ Control=Control subGroup3 content Data_Content \ REP=Replicates \ UNION=Union dimensions dimX=antibody dimY=content sortOrder antibody=+ content=+ view=+ type bed 3 configurable on ## Views track for ChIPseq, coverage data track JHchipSeqView1 parent JHchipSeqSet shortLabel Coverage view COV visibility full type bigWig allButtonPair on centerLabelsDense on dragAndDrop on alwaysZero on graphTypeDefault bar maxHeightPixels 100:40:8 smoothingWindow 2 transformFunc NONE windowingFunction maximum gridDefault on viewLimits 0:15 viewUi on visibility hide priority 1131 ## Brg1 ChIP lane track Brg1_MiSeq200 parent JHchipSeqView1 on bigDataUrl MES231_1.sanger.sickle.bowtieSe_hg19.sorted.slop200.bw shortLabel Brg1 ChIPseq +200bp longLabel Brg1 ChIPseq +200bp fragment length type bigWig color 255,112,0 priority 1134 alwaysZero on graphTypeDefault bar maxHeightPixels 100:44:8 smoothingWindow 2 transformFunc NONE windowingFunction maximum gridDefault on viewLimits 0:15 viewLimitsMax 0:100 visibility hide subGroups antibody=Brg1 content=REP view=COV ## PolII ChIP lane track PolII_MiSeq200 parent JHchipSeqView1 on bigDataUrl MES232_1.sanger.sickle.bowtieSe_hg19.sorted.slop200.bw shortLabel PolII ChIPseq +200bp longLabel PolII ChIPseq +200bp fragment length type bigWig color 37,113,53 priority 1135 alwaysZero on graphTypeDefault bar maxHeightPixels 100:44:8 smoothingWindow 2 transformFunc NONE windowingFunction maximum gridDefault on viewLimits 0:15 viewLimitsMax 0:100 visibility hide subGroups antibody=RNAPolII content=REP view=COV ## Input lane track Input_MiSeq200 parent JHchipSeqView1 on bigDataUrl MES230_1.sanger.sickle.bowtieSe_hg19.sorted.slop200.bw shortLabel ChIPseq Input +200bp longLabel ChIPseq Input +200bp fragment length type bigWig color 110,110,140 priority 1136 alwaysZero on graphTypeDefault bar maxHeightPixels 100:44:8 smoothingWindow 2 transformFunc NONE windowingFunction maximum gridDefault on viewLimits 0:15 viewLimitsMax 0:100 visibility hide subGroups antibody=Input content=REP view=COV ## ChIPseq data coverage tracks union ## Brg1 ChIP lane track Brg1_MiSeq200_dec2013 parent JHchipSeqView1 on bigDataUrl Brg1ChIP_s.sickle.merged.bowtieSe_hg19.sorted.slop200.bw shortLabel Brg1 ChIPseq union longLabel Brg1 ChIPseq union type bigWig color 255,112,0 priority 1141 alwaysZero on graphTypeDefault bar maxHeightPixels 100:44:8 smoothingWindow 2 transformFunc NONE windowingFunction maximum gridDefault on viewLimits 0:15 viewLimitsMax 0:100 visibility full subGroups antibody=Brg1 content=UNION view=COV ## PolII ChIP lane track PolII_MiSeq200_dec2013 parent JHchipSeqView1 on bigDataUrl PolIIChIP_s.sickle.merged.bowtieSe_hg19.sorted.slop200.bw shortLabel PolII ChIPseq union longLabel PolII ChIPseq union type bigWig color 37,113,53 priority 1142 alwaysZero on graphTypeDefault bar maxHeightPixels 100:44:8 smoothingWindow 2 transformFunc NONE windowingFunction maximum gridDefault on viewLimits 0:15 viewLimitsMax 0:100 visibility full subGroups antibody=RNAPolII content=UNION view=COV ## Input lane track Input_MiSeq200_dec2013 parent JHchipSeqView1 on bigDataUrl InputControl_s.sickle.merged.bowtieSe_hg19.sorted.slop200.bw shortLabel ChIPseq Input union longLabel ChIPseq Input union type bigWig color 110,110,140 priority 1144 alwaysZero on graphTypeDefault bar maxHeightPixels 100:44:8 smoothingWindow 2 transformFunc NONE windowingFunction maximum gridDefault on viewLimits 0:15 viewLimitsMax 0:100 visibility full subGroups antibody=Input content=UNION view=COV ## Views track for ChIPseq peaks track JHchipSeqView2 parent JHchipSeqSet shortLabel Peaks view PEAK visibility pack type bigBed allButtonPair on centerLabelsDense on dragAndDrop on thickDrawItem on viewUi on priority 1180 # Brg1 ChIPseq peaks from Miseq, fc4, P-value 0.001 track Brg1chip_1k150fc4e3 parent JHchipSeqView2 bigDataUrl homerComparison_Brg1ChIP_Vs_InputControl.findPeaks_histoneregion.150.1000_fdr0.001_foc0.9_loc2000_fc4_min0.sorted.bb shortLabel Brg1 vs Input P.001 longLabel Brg1 vs Input, 150 peak width, 1k region, 4-fold, 0.001 FDR, 0 min tags type bigBed color 255,112,0 visibility hide priority 1182 subGroups antibody=Brg1 content=REP view=PEAK # Brg1 ChIPseq peaks from Miseq - fc2, P-value 0.003 track Brg1chip_1k150fc2e3 parent JHchipSeqView2 bigDataUrl homerComparison_Brg1ChIP_Vs_InputControl.findPeaks_histoneregion.150.1000_fdr0.003_p0.003_foc0.9_loc2000_fc2_min0.sorted.bb shortLabel Brg1 vs Input P.003 longLabel Brg1 vs Input, 150 peak width, 1k region, 2-fold, 0.003 FDR, 0 min tags type bigBed color 255,112,0 visibility hide priority 1184 subGroups antibody=Brg1 content=REP view=PEAK # Brg1 ChIPseq peaks from Miseq, min 10 track Brg1chip_jan2014_min10 parent JHchipSeqView2 bigDataUrl homerComparison_Brg1ChIP_Vs_InputControl.findPeaks_none-region.300.900_fdr0.001_p0.0001_foc0_loc2000_fc4_min10.sorted.bb shortLabel Brg1 vs Input union min10 longLabel Brg1 vs Input union, 300 peak width, 900 region, 4-fold, 0.001 FDR, 10 min tags type bigBed color 255,112,0 visibility full priority 1186 subGroups antibody=Brg1 content=UNION view=PEAK # Brg1 ChIPseq peaks from Miseq, min 5 track Brg1chip_jan2014_min5 parent JHchipSeqView2 bigDataUrl homerComparison_Brg1ChIP_Vs_InputControl.findPeaks_none-region.300.900_fdr0.001_p0.0001_foc0_loc2000_fc4_min5.sorted.bb shortLabel Brg1 vs Input union min5 longLabel Brg1 vs Input union, 300 peak width, 900 region, 4-fold, 0.001 FDR, 5 min tags (FINAL) type bigBed color 255,112,0 visibility hide priority 1188 subGroups antibody=Brg1 content=UNION view=PEAK # RNA PolII ChIPseq on MiSeq vs Input control track pol2chip_1k150fc4e3 parent JHchipSeqView2 bigDataUrl homerComparison_PolIIChIP_Vs_InputControl.findPeaks_histoneregion.150.1000_fdr0.001_foc0.9_loc2000_fc4_min0.sorted.bb shortLabel PolII vs Input longLabel PolII vs Input, 150 peak width, 1k region, 4-fold, 0.001 FDR, 0 min tags type bigBed color 37,113,53 visibility hide priority 1192 subGroups antibody=RNAPolII content=REP view=PEAK # RNA PolII ChIPseq on MiSeq vs Input, min 10 track pol2chip_jan2014_min10 parent JHchipSeqView2 bigDataUrl homerComparison_PolIIChIP_Vs_InputControl.findPeaks_none-region.300.900_fdr0.001_p0.0001_foc0_loc2000_fc4_min10.sorted.bb shortLabel PolII vs Input union min10 longLabel PolII vs Input union, 300 peak width, 900 region, 4-fold, 0.001 FDR, 10 min tags type bigBed color 37,113,53 visibility full priority 1194 subGroups antibody=RNAPolII content=UNION view=PEAK # RNA PolII ChIPseq on MiSeq vs Input, min 5 track pol2chip_jan2014_min5 parent JHchipSeqView2 bigDataUrl homerComparison_PolIIChIP_Vs_InputControl.findPeaks_none-region.300.900_fdr0.001_p0.0001_foc0_loc2000_fc4_min5.sorted.bb shortLabel PolII vs Input union min5 longLabel PolII vs Input union, 300 peak width, 900 region, 4-fold, 0.001 FDR, 5 min tags (FINAL) type bigBed color 37,113,53 visibility hide priority 1196 subGroups antibody=RNAPolII content=UNION view=PEAK ## siBrg1 RNAseq composite with subgroup views track hoffmanRnaseqSiBrg1Set compositeTrack on shortLabel Hoffman siBrg1 RNAseq longLabel Hoffman siBrg1 RNAseq priority 830 visibility full subGroup1 view Views \ COV=Coverage \ JUNC=Junction subGroup2 treatment Treatment \ siBrg1=siBrg1 \ Control=Control subGroup3 content Data_Content \ REP=Replicates \ UNION=Union dimensions dimX=treatment dimY=content sortOrder treatment=+ content=+ view=+ type bed 3 configurable on ## Views track for siBrg1 RNAseq, coverage data track hoffmanRnaseqSiBrg1View1 parent hoffmanRnaseqSiBrg1Set shortLabel Coverage view COV visibility full type bigWig allButtonPair on centerLabelsDense on dragAndDrop on alwaysZero on graphTypeDefault bar maxHeightPixels 100:40:8 smoothingWindow 2 transformFunc NONE windowingFunction maximum gridDefault on viewLimits 0:200 viewUi on ## RNAseq data coverage tracks ## siBrg1 replicate 1 track siBrg1_r1 parent hoffmanRnaseqSiBrg1View1 on bigDataUrl ES638_merged.topHat2pe.bw shortLabel RNAseq siBrg1_r1 longLabel RNAseq siBrg1_r1 type bigWig color 176,32,36 priority 831 alwaysZero on graphTypeDefault bar maxHeightPixels 100:40:8 smoothingWindow 2 transformFunc NONE windowingFunction maximum gridDefault on viewLimits 0:200 visibility full subGroups treatment=siBrg1 content=REP view=COV ## siBrg1 replicate 2 track siBrg1_r2 parent hoffmanRnaseqSiBrg1View1 on bigDataUrl ES639_merged.topHat2pe.bw shortLabel RNAseq siBrg1_r2 longLabel RNAseq siBrg1_r2 type bigWig color 176,32,36 priority 832 alwaysZero on graphTypeDefault bar maxHeightPixels 100:40:8 smoothingWindow 2 transformFunc NONE windowingFunction maximum gridDefault on viewLimits 0:200 visibility full subGroups treatment=siBrg1 content=REP view=COV ## siBrg1 replicate 3 track siBrg1_r3 parent hoffmanRnaseqSiBrg1View1 on bigDataUrl ES640_merged.topHat2pe.bw shortLabel RNAseq siBrg1_r3 longLabel RNAseq siBrg1_r3 type bigWig color 176,32,36 priority 833 alwaysZero on graphTypeDefault bar maxHeightPixels 100:40:8 smoothingWindow 2 transformFunc NONE windowingFunction maximum gridDefault on viewLimits 0:200 visibility full subGroups treatment=siBrg1 content=REP view=COV ## Control replicate 1 track Control_r1 parent hoffmanRnaseqSiBrg1View1 on bigDataUrl ES641_merged.topHat2pe.bw shortLabel RNAseq Control_r1 longLabel RNAseq Control_r1 type bigWig color 110,110,140 priority 835 alwaysZero on graphTypeDefault bar maxHeightPixels 100:40:8 smoothingWindow 2 transformFunc NONE windowingFunction maximum gridDefault on viewLimits 0:200 visibility full subGroups treatment=Control content=REP view=COV ## Control replicate 2 track Control_r2 parent hoffmanRnaseqSiBrg1View1 on bigDataUrl ES642_merged.topHat2pe.bw shortLabel RNAseq Control_r2 longLabel RNAseq Control_r2 type bigWig color 110,110,140 priority 836 alwaysZero on graphTypeDefault bar maxHeightPixels 100:40:8 smoothingWindow 2 transformFunc NONE windowingFunction maximum gridDefault on viewLimits 0:200 visibility full subGroups treatment=Control content=REP view=COV ## Control replicate 3 track Control_r3 parent hoffmanRnaseqSiBrg1View1 on bigDataUrl ES643_merged.topHat2pe.bw shortLabel RNAseq Control_r3 longLabel RNAseq Control_r3 type bigWig color 110,110,140 priority 837 alwaysZero on graphTypeDefault bar maxHeightPixels 100:40:8 smoothingWindow 2 transformFunc NONE windowingFunction maximum gridDefault on viewLimits 0:200 visibility full subGroups treatment=Control content=REP view=COV # Union of coverages across replicates per sample group ## RNAseq data coverage track union ## siBrg1 union coverage track siBrg1_union parent hoffmanRnaseqSiBrg1View1 on bigDataUrl siBrg1_union.TopHat2pe.bw shortLabel RNAseq siBrg1 longLabel RNAseq siBrg1 type bigWig color 146,22,24 priority 830 alwaysZero on graphTypeDefault bar maxHeightPixels 100:40:8 smoothingWindow 2 transformFunc NONE windowingFunction maximum gridDefault on autoScale on viewLimits 0:200 visibility full subGroups treatment=siBrg1 content=UNION view=COV ## Control union coverage track Control_union parent hoffmanRnaseqSiBrg1View1 on bigDataUrl Control_union.TopHat2pe.bw shortLabel RNAseq Control longLabel RNAseq Control type bigWig color 90,90,110 priority 834 alwaysZero on graphTypeDefault bar maxHeightPixels 100:40:8 smoothingWindow 2 transformFunc NONE windowingFunction maximum gridDefault on autoScale on viewLimits 0:200 visibility full subGroups treatment=Control content=UNION view=COV ## Views track for siBrg1 RNAseq, junctions track hoffmanRnaseqSiBrg1View2 parent hoffmanRnaseqSiBrg1Set shortLabel RNAseq_junctions view JUNC visibility pack type bigBed 12 allButtonPair on centerLabelsDense on dragAndDrop on thickDrawItem on scoreFilter 10 scoreFilterLimits 1:1000 viewUi on # siBrg1_r1 junctions track siBrg1_r1_junc parent hoffmanRnaseqSiBrg1View2 bigDataUrl ES638_merged.junctions.bb shortLabel TopHat2 junctions siBrg1_r1 longLabel TopHat2 junctions siBrg1_r1 type bigBed 12 color 176,32,36 visibility pack priority 851 subGroups treatment=siBrg1 content=REP view=JUNC # siBrg1_r2 junctions track siBrg1_r2_junc parent hoffmanRnaseqSiBrg1View2 bigDataUrl ES639_merged.junctions.bb shortLabel TopHat2 junctions siBrg1_r2 longLabel TopHat2 junctions siBrg1_r2 type bigBed 12 color 176,32,36 visibility pack priority 852 subGroups treatment=siBrg1 content=REP view=JUNC # siBrg1_r3 junctions track siBrg1_r3_junc parent hoffmanRnaseqSiBrg1View2 bigDataUrl ES640_merged.junctions.bb shortLabel TopHat2 junctions siBrg1_r3 longLabel TopHat2 junctions siBrg1_r3 type bigBed 12 color 176,32,36 visibility pack priority 853 subGroups treatment=siBrg1 content=REP view=JUNC # Control_r1 junctions track Control_r1_junc parent hoffmanRnaseqSiBrg1View2 bigDataUrl ES641_merged.junctions.bb shortLabel TopHat2 junctions Control_r1 longLabel TopHat2 junctions Control_r1 type bigBed 12 color 110,110,140 visibility pack priority 855 subGroups treatment=Control content=REP view=JUNC # Control_r2 junctions track Control_r2_junc parent hoffmanRnaseqSiBrg1View2 bigDataUrl ES642_merged.junctions.bb shortLabel TopHat2 junctions Control_r2 longLabel TopHat2 junctions Control_r2 type bigBed 12 color 110,110,140 visibility pack priority 856 subGroups treatment=Control content=REP view=JUNC # Control_r3 junctions track Control_r3_junc parent hoffmanRnaseqSiBrg1View2 bigDataUrl ES643_merged.junctions.bb shortLabel TopHat2 junctions Control_r3 longLabel TopHat2 junctions Control_r3 type bigBed 12 color 110,110,140 visibility pack priority 857 subGroups treatment=Control content=REP view=JUNC # siBrg1 combined junctions # siBrg1_combined_junctions.bb track siBrg1_junc parent hoffmanRnaseqSiBrg1View2 on bigDataUrl siBrg1_combined_junctions.bed12sort.bb shortLabel TopHat2 junctions siBrg1 longLabel TopHat2 junctions siBrg1 type bigBed 12 visibility pack priority 850 spectrum on scoreMin 10 scoreMax 100 # color 73,11,12 color 150,0,0 # altColor 201,30,33 # scoreFilter 10 # scoreFilterLimits 1:1000 # thickDrawItem on subGroups treatment=siBrg1 content=UNION view=JUNC # Control combined junctions # Control_combined_junctions.bb track Control_junc parent hoffmanRnaseqSiBrg1View2 on bigDataUrl Control_combined_junctions.bed12sort.bb shortLabel TopHat2 junctions Control longLabel TopHat2 junctions Control type bigBed 12 visibility pack priority 854 spectrum on scoreMin 10 scoreMax 100 # color 45,45,55 color 100,100,100 # altColor 149,149,183 # scoreFilter 10 # scoreFilterLimits 1:1000 # thickDrawItem on subGroups treatment=Control content=UNION view=JUNC ## siBaf60a RNAseq composite with subgroup views track hoffmanRnaseqSiBaf60aSet compositeTrack on shortLabel Hoffman siBaf60a RNAseq longLabel Hoffman siBaf60a RNAseq priority 930 visibility full subGroup1 view Views \ COV=Coverage \ JUNC=Junction subGroup2 treatment Treatment \ siBaf60a=siBaf60a \ NTC=NTC subGroup3 content Data_Content \ REP=Replicates \ UNION=Union dimensions dimX=treatment dimY=content sortOrder treatment=+ content=+ view=+ type bed 3 configurable on ## Views track for siBaf60a RNAseq, coverage data track hoffmanRnaseqSiBaf60aView1 parent hoffmanRnaseqSiBaf60aSet shortLabel Coverage view COV visibility full type bigWig allButtonPair on centerLabelsDense on dragAndDrop on alwaysZero on graphTypeDefault bar maxHeightPixels 100:40:8 smoothingWindow 2 transformFunc NONE windowingFunction maximum gridDefault on viewLimits 0:200 viewUi on ## RNAseq data coverage tracks ## siBaf60a replicate 1 track siBaf60a_r1 parent hoffmanRnaseqSiBaf60aView1 on bigDataUrl Baf60aL1_1.sickle.merged.topHat2pe_hg19.bw shortLabel RNAseq siBaf60a_r1 longLabel RNAseq siBaf60a_r1 type bigWig color 80,140,160 priority 931 alwaysZero on graphTypeDefault bar maxHeightPixels 100:40:8 smoothingWindow 2 transformFunc NONE windowingFunction maximum gridDefault on viewLimits 0:200 visibility full subGroups treatment=siBaf60a content=REP view=COV ## siBaf60a replicate 2 track siBaf60a_r2 parent hoffmanRnaseqSiBaf60aView1 on bigDataUrl Baf60aL4_1.sickle.merged.topHat2pe_hg19.bw shortLabel RNAseq siBaf60a_r2 longLabel RNAseq siBaf60a_r2 type bigWig color 80,140,160 priority 932 alwaysZero on graphTypeDefault bar maxHeightPixels 100:40:8 smoothingWindow 2 transformFunc NONE windowingFunction maximum gridDefault on viewLimits 0:200 visibility full subGroups treatment=siBaf60a content=REP view=COV ## siBaf60a replicate 3 track siBaf60a_r3 parent hoffmanRnaseqSiBaf60aView1 on bigDataUrl Baf60aL8_1.sickle.merged.topHat2pe_hg19.bw shortLabel RNAseq siBaf60a_r3 longLabel RNAseq siBaf60a_r3 type bigWig color 80,140,160 priority 933 alwaysZero on graphTypeDefault bar maxHeightPixels 100:40:8 smoothingWindow 2 transformFunc NONE windowingFunction maximum gridDefault on viewLimits 0:200 visibility full subGroups treatment=siBaf60a content=REP view=COV ## Control replicate 1 track NTC_r1 parent hoffmanRnaseqSiBaf60aView1 on bigDataUrl NTCL2_1.sickle.merged.topHat2pe_hg19.bw shortLabel RNAseq NTC_r1 longLabel RNAseq NTC_r1 type bigWig color 160,145,160 priority 935 alwaysZero on graphTypeDefault bar maxHeightPixels 100:40:8 smoothingWindow 2 transformFunc NONE windowingFunction maximum gridDefault on viewLimits 0:200 visibility full subGroups treatment=NTC content=REP view=COV ## Control replicate 2 track NTC_r2 parent hoffmanRnaseqSiBaf60aView1 on bigDataUrl NTCL3_1.sickle.merged.topHat2pe_hg19.bw shortLabel RNAseq NTC_r2 longLabel RNAseq NTC_r2 type bigWig color 160,145,160 priority 936 alwaysZero on graphTypeDefault bar maxHeightPixels 100:40:8 smoothingWindow 2 transformFunc NONE windowingFunction maximum gridDefault on viewLimits 0:200 visibility full subGroups treatment=NTC content=REP view=COV ## Control replicate 3 track NTC_r3 parent hoffmanRnaseqSiBaf60aView1 on bigDataUrl NTCL5_1.sickle.merged.topHat2pe_hg19.bw shortLabel RNAseq NTC_r3 longLabel RNAseq NTC_r3 type bigWig color 160,145,160 priority 937 alwaysZero on graphTypeDefault bar maxHeightPixels 100:40:8 smoothingWindow 2 transformFunc NONE windowingFunction maximum gridDefault on viewLimits 0:200 visibility full subGroups treatment=NTC content=REP view=COV ## RNAseq data coverage track union ## siBaf60a union coverage track siBaf60a_union parent hoffmanRnaseqSiBaf60aView1 on bigDataUrl siBaf60a_union.topHat2pe_hg19.bw shortLabel RNAseq siBaf60a longLabel RNAseq siBaf60a type bigWig color 0,100,125 priority 930 alwaysZero on graphTypeDefault bar maxHeightPixels 100:40:8 smoothingWindow 2 transformFunc NONE windowingFunction maximum gridDefault on autoScale on viewLimits 0:200 visibility full subGroups treatment=siBaf60a content=UNION view=COV ## RNAseq data coverage track union ## NTC union coverage track NTC_union parent hoffmanRnaseqSiBaf60aView1 on bigDataUrl NTC_union.topHat2pe_hg19.bw shortLabel RNAseq NTC longLabel RNAseq NTC type bigWig color 118,95,118 priority 934 alwaysZero on graphTypeDefault bar maxHeightPixels 100:40:8 smoothingWindow 2 transformFunc NONE windowingFunction maximum gridDefault on autoScale on viewLimits 0:200 visibility full subGroups treatment=NTC content=UNION view=COV ## Views track for siBaf60a RNAseq, junctions track hoffmanRnaseqSiBaf60aView2 parent hoffmanRnaseqSiBaf60aSet shortLabel RNAseq_junctions_Baf60a view JUNC visibility pack type bigBed 12 + allButtonPair on centerLabelsDense on dragAndDrop on thickDrawItem on scoreFilter 10 scoreFilterLimits 1:1000 # spectrum on # scoreMax 100 # scoreMin 1 viewUi on # color 255,0,0 # altColor 201,30,33 # minGrayLevel 6 # siBaf60a_r1 junctions track siBaf60a_r1_junc parent hoffmanRnaseqSiBaf60aView2 bigDataUrl Baf60aL1_1.sickle.merged.topHat2pe_hg19.sorted.bb shortLabel TopHat2 junctions siBaf60a_r1 longLabel TopHat2 junctions siBaf60a_r1 type bigBed 12 + color 80,140,160 visibility pack priority 951 subGroups treatment=siBaf60a content=REP view=JUNC # siBaf60a_r2 junctions track siBaf60a_r2_junc parent hoffmanRnaseqSiBaf60aView2 bigDataUrl Baf60aL4_1.sickle.merged.topHat2pe_hg19.sorted.bb shortLabel TopHat2 junctions siBaf60a_r2 longLabel TopHat2 junctions siBaf60a_r2 type bigBed 12 + color 80,140,160 visibility pack priority 952 subGroups treatment=siBaf60a content=REP view=JUNC # siBaf60a_r3 junctions track siBaf60a_r3_junc parent hoffmanRnaseqSiBaf60aView2 bigDataUrl Baf60aL8_1.sickle.merged.topHat2pe_hg19.sorted.bb shortLabel TopHat2 junctions siBaf60a_r3 longLabel TopHat2 junctions siBaf60a_r3 type bigBed 12 + color 80,140,160 visibility pack priority 953 subGroups treatment=siBaf60a content=REP view=JUNC # NTC_r1 junctions track NTC_r1_junc parent hoffmanRnaseqSiBaf60aView2 bigDataUrl NTCL2_1.sickle.merged.topHat2pe_hg19.sorted.bb shortLabel TopHat2 junctions NTC_r1 longLabel TopHat2 junctions NTC_r1 type bigBed 12 + color 160,145,160 visibility pack priority 955 subGroups treatment=NTC content=REP view=JUNC # NTC_r2 junctions track NTC_r2_junc parent hoffmanRnaseqSiBaf60aView2 bigDataUrl NTCL3_1.sickle.merged.topHat2pe_hg19.sorted.bb shortLabel TopHat2 junctions NTC_r2 longLabel TopHat2 junctions NTC_r2 type bigBed 12 + color 160,145,160 visibility pack priority 956 subGroups treatment=NTC content=REP view=JUNC # NTC_r3 junctions track NTC_r3_junc parent hoffmanRnaseqSiBaf60aView2 bigDataUrl NTCL5_1.sickle.merged.topHat2pe_hg19.sorted.bb shortLabel TopHat2 junctions NTC_r3 longLabel TopHat2 junctions NTC_r3 type bigBed 12 + color 160,145,160 visibility pack priority 957 subGroups treatment=NTC content=REP view=JUNC # siBaf60a_combined_junctions.bb track siBaf60a_junc parent hoffmanRnaseqSiBaf60aView2 on bigDataUrl siBaf60a.TopHat2_hg19.combinedJunctions.bb shortLabel TopHat2 junctions siBaf60a longLabel TopHat2 junctions siBaf60a type bigBed 12 + visibility pack priority 950 bedNameLabel Junction_readCounts color 0,100,125 spectrum on scoreMin 10 scoreMax 100 thickDrawItem on subGroups treatment=siBaf60a content=UNION view=JUNC # NTC_combined_junctions.bb track NTC_junc parent hoffmanRnaseqSiBaf60aView2 on bigDataUrl NTC.TopHat2_hg19.combinedJunctions.bb shortLabel TopHat2 junctions NTC longLabel TopHat2 junctions NTC type bigBed 12 + visibility pack priority 954 bedNameLabel Junction_readCounts color 118,95,118 spectrum on scoreMin 10 scoreMax 100 thickDrawItem on subGroups treatment=NTC content=UNION view=JUNC ## Beginning of track view track hoffmanRnaPol compositeTrack on shortLabel Hoffman RNAPolII ChIPseq longLabel Hoffman RNAPolII ChIPseq priority 1200 visibility full type bed 3 configurable on subGroup1 view Views \ COV=Coverage \ PEAK=Peaks \ JUNC=Junctions subGroup2 Group1 Group1 \ Baf60a=Baf60a \ Brg1=Brg1 subGroup3 Group2 Group2 \ NTC=NTC \ siRNA=siRNA subGroup4 Group3 Group3 \ input=input \ polII=polII dimensions dimX=Group1 dimY=Group2 sortOrder Group1=+ Group2=+ Group3=+ view=+ ## Views track coverage data track hoffmanRnaPolView1 parent hoffmanRnaPol shortLabel Coverage view COV visibility full type bigWig allButtonPair on centerLabelsDense on dragAndDrop on alwaysZero on graphTypeDefault bar maxHeightPixels 100:40:8 smoothingWindow 2 transformFunc NONE windowingFunction mean+whiskers gridDefault on viewLimits 0:20 viewUi on ## Coverage track track ES886_coverage parent hoffmanRnaPolView1 on bigDataUrl ES886_s.sickle.merged.bowtieSe_hg19.sorted.bamCov-150-bin10-normalizeUsingRPKM-scale.bw shortLabel Baf60a_NTC_input coverage longLabel Baf60a_NTC_input coverage type bigWig color 126,192,238 priority 1202 alwaysZero on graphTypeDefault bar maxHeightPixels 100:40:8 smoothingWindow 2 transformFunc NONE windowingFunction mean+whiskers gridDefault on viewLimits 0:20 visibility hide subGroups Group1=Baf60a Group2=NTC Group3=input view=COV ## Coverage track track ES887_coverage parent hoffmanRnaPolView1 on bigDataUrl ES887_s.sickle.merged.bowtieSe_hg19.sorted.bamCov-150-bin10-normalizeUsingRPKM-scale.bw shortLabel Baf60a_NTC_polII coverage longLabel Baf60a_NTC_polII coverage type bigWig color 72,118,255 priority 1204 alwaysZero on graphTypeDefault bar maxHeightPixels 100:40:8 smoothingWindow 2 transformFunc NONE windowingFunction mean+whiskers gridDefault on viewLimits 0:20 visibility hide subGroups Group1=Baf60a Group2=NTC Group3=polII view=COV ## Coverage track track ES888_coverage parent hoffmanRnaPolView1 on bigDataUrl ES888_s.sickle.merged.bowtieSe_hg19.sorted.bamCov-150-bin10-normalizeUsingRPKM-scale.bw shortLabel Baf60a_siRNA_input coverage longLabel Baf60a_siRNA_input coverage type bigWig color 79,148,205 priority 1206 alwaysZero on graphTypeDefault bar maxHeightPixels 100:40:8 smoothingWindow 2 transformFunc NONE windowingFunction mean+whiskers gridDefault on viewLimits 0:20 visibility hide subGroups Group1=Baf60a Group2=siRNA Group3=input view=COV ## Coverage track track ES889_coverage parent hoffmanRnaPolView1 on bigDataUrl ES889_s.sickle.merged.bowtieSe_hg19.sorted.bamCov-150-bin10-normalizeUsingRPKM-scale.bw shortLabel Baf60a_siRNA_polII coverage longLabel Baf60a_siRNA_polII coverage type bigWig color 39,64,139 priority 1208 alwaysZero on graphTypeDefault bar maxHeightPixels 100:40:8 smoothingWindow 2 transformFunc NONE windowingFunction mean+whiskers gridDefault on viewLimits 0:20 visibility hide subGroups Group1=Baf60a Group2=siRNA Group3=polII view=COV ## Coverage track track ES890_coverage parent hoffmanRnaPolView1 on bigDataUrl ES890_s.sickle.merged.bowtieSe_hg19.sorted.bamCov-150-bin10-normalizeUsingRPKM-scale.bw shortLabel Brg1_NTC_input coverage longLabel Brg1_NTC_input coverage type bigWig color 255,160,122 priority 1210 alwaysZero on graphTypeDefault bar maxHeightPixels 100:40:8 smoothingWindow 2 transformFunc NONE windowingFunction mean+whiskers gridDefault on viewLimits 0:20 visibility hide subGroups Group1=Brg1 Group2=NTC Group3=input view=COV ## Coverage track track ES891_coverage parent hoffmanRnaPolView1 on bigDataUrl ES891_s.sickle.merged.bowtieSe_hg19.sorted.bamCov-150-bin10-normalizeUsingRPKM-scale.bw shortLabel Brg1_NTC_polII coverage longLabel Brg1_NTC_polII coverage type bigWig color 255,99,71 priority 1212 alwaysZero on graphTypeDefault bar maxHeightPixels 100:40:8 smoothingWindow 2 transformFunc NONE windowingFunction mean+whiskers gridDefault on viewLimits 0:20 visibility hide subGroups Group1=Brg1 Group2=NTC Group3=polII view=COV ## Coverage track track ES892_coverage parent hoffmanRnaPolView1 on bigDataUrl ES892_s.sickle.merged.bowtieSe_hg19.sorted.bamCov-150-bin10-normalizeUsingRPKM-scale.bw shortLabel Brg1_siRNA_input coverage longLabel Brg1_siRNA_input coverage type bigWig color 205,92,92 priority 1214 alwaysZero on graphTypeDefault bar maxHeightPixels 100:40:8 smoothingWindow 2 transformFunc NONE windowingFunction mean+whiskers gridDefault on viewLimits 0:20 visibility hide subGroups Group1=Brg1 Group2=siRNA Group3=input view=COV ## Coverage track track ES893_coverage parent hoffmanRnaPolView1 on bigDataUrl ES893_s.sickle.merged.bowtieSe_hg19.sorted.bamCov-150-bin10-normalizeUsingRPKM-scale.bw shortLabel Brg1_siRNA_polII coverage longLabel Brg1_siRNA_polII coverage type bigWig color 178,34,34 priority 1216 alwaysZero on graphTypeDefault bar maxHeightPixels 100:40:8 smoothingWindow 2 transformFunc NONE windowingFunction mean+whiskers gridDefault on viewLimits 0:20 visibility hide subGroups Group1=Brg1 Group2=siRNA Group3=polII view=COV