## 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