#################################### ## track set ## NG167_strandedCoverage track NG167strandedCov superTrack on show shortLabel NG167_strandedCoverage longLabel NG167_strandedCoverage priority 1000 # ################################## # # Overlay multiple stranded tracks track siBaf60a_mESC_stranded superTrack NG167strandedCov full container multiWig aggregate transparentOverlay shortLabel siBaf60a_mESC stranded coverage longLabel siBaf60a_mESC stranded coverage showSubtrackColorOnUi on type bigWig priority 1001 alwaysZero off graphTypeDefault bar maxHeightPixels 100:66:8 smoothingWindow 2 transformFunc NONE windowingFunction mean+whiskers gridDefault on autoScale on viewLimits -50:50 visibility full # ################################## track siBaf60a_mESC_pos parent siBaf60a_mESC_stranded bigDataUrl siBaf60a_mESC.pos.bw type bigWig color 92,46,84 priority 1002 # ################################## track siBaf60a_mESC_neg parent siBaf60a_mESC_stranded bigDataUrl siBaf60a_mESC.neg.bw type bigWig color 130,47,47 priority 1001 # ################################## # # Overlay multiple stranded tracks track siNT_mESC_stranded superTrack NG167strandedCov full container multiWig aggregate transparentOverlay shortLabel siNT_mESC stranded coverage longLabel siNT_mESC stranded coverage showSubtrackColorOnUi on type bigWig priority 1003 alwaysZero off graphTypeDefault bar maxHeightPixels 100:66:8 smoothingWindow 2 transformFunc NONE windowingFunction mean+whiskers gridDefault on autoScale on viewLimits -50:50 visibility full # ################################## track siNT_mESC_pos parent siNT_mESC_stranded bigDataUrl siNT_mESC.pos.bw type bigWig color 86,43,44 priority 1004 # ################################## track siNT_mESC_neg parent siNT_mESC_stranded bigDataUrl siNT_mESC.neg.bw type bigWig color 133,73,33 priority 1003 ## Beginning of track view track NS50093ArcherHoffman compositeTrack on shortLabel NS50093ArcherHoffman longLabel NS50093ArcherHoffman priority 900 visibility full type bed 3 configurable on subGroup1 view Views \ COV=Coverage \ PEAK=Peaks \ JUNC=Junctions subGroup2 Group1 Group1 \ Brg1=Brg1 \ Fip1=Fip1 \ Input=Input subGroup3 Group2 Group2 \ mESC=mESC dimensions dimX=Group1 dimY=Group2 sortOrder Group1=+ Group2=+ view=+ ## Views track coverage data track NS50093ArcherHoffmanView1 parent NS50093ArcherHoffman shortLabel Coverage view COV visibility full type bigWig allButtonPair on centerLabelsDense on dragAndDrop on alwaysZero on graphTypeDefault bar maxHeightPixels 100:60:8 smoothingWindow 2 transformFunc NONE windowingFunction mean+whiskers gridDefault on viewLimits 0:20 viewUi on ## Coverage track track Brg1_coverage parent NS50093ArcherHoffmanView1 on bigDataUrl Brg1_1.sickle.merged.bowtie2Pe_mm10.sorted.bw shortLabel Brg1_mESC coverage longLabel Brg1_mESC coverage type bigWig color 123,31,31 priority 902 alwaysZero on graphTypeDefault bar maxHeightPixels 100:60:8 smoothingWindow 2 transformFunc NONE windowingFunction mean+whiskers gridDefault on viewLimits 0:20 visibility hide subGroups Group1=Brg1 Group2=mESC view=COV ## Coverage track track Fip1_coverage parent NS50093ArcherHoffmanView1 on bigDataUrl Fip1_1.sickle.merged.bowtie2Pe_mm10.sorted.bw shortLabel Fip1_mESC coverage longLabel Fip1_mESC coverage type bigWig color 163,92,4 priority 904 alwaysZero on graphTypeDefault bar maxHeightPixels 100:60:8 smoothingWindow 2 transformFunc NONE windowingFunction mean+whiskers gridDefault on viewLimits 0:20 visibility hide subGroups Group1=Fip1 Group2=mESC view=COV ## Coverage track track Input_coverage parent NS50093ArcherHoffmanView1 on bigDataUrl Input_1.sickle.merged.bowtie2Pe_mm10.sorted.bw shortLabel Input_mESC coverage longLabel Input_mESC coverage type bigWig color 29,86,7 priority 906 alwaysZero on graphTypeDefault bar maxHeightPixels 100:60:8 smoothingWindow 2 transformFunc NONE windowingFunction mean+whiskers gridDefault on viewLimits 0:20 visibility hide subGroups Group1=Input Group2=mESC view=COV ## Views track for ChIPseq peaks track NS50093ArcherHoffmanView3 parent NS50093ArcherHoffman shortLabel Peaks view PEAK visibility pack type bigBed allButtonPair on centerLabelsDense on dragAndDrop on viewUi on # Peak track track brg1vsInput_Homer.Region.200.50_Fdr0.001_p0.0001_Foc0_Loc2000_Fc4_Min0 parent NS50093ArcherHoffmanView3 on bigDataUrl homerComparison_Brg1-Vs-Input.findPeaks_none-region.200.50_fdr0.001_p0.0001_foc0_loc2000_fc4_min0.sorted.bb shortLabel brg1vsInput_Homer.Region.200.50_Fdr0.001_p0.0001_Foc0_Loc2000_Fc4_Min0 peaks longLabel brg1vsInput_Homer.Region.200.50_Fdr0.001_p0.0001_Foc0_Loc2000_Fc4_Min0 peaks type bigBed visibility pack priority 908 color 123,31,31 subGroups Group1=Brg1 Group2=mESC view=PEAK # Peak track track fip1vsInput_Homer-100-100-Fdr0.001-p0.001-Foc0.1-Loc1000-Fc3 parent NS50093ArcherHoffmanView3 on bigDataUrl homerComparison_Fip1-Vs-Input-100-100-fdr0.001-p0.001-foc0.1-loc1000-fc3.sorted.bb shortLabel fip1vsInput_Homer-100-100-Fdr0.001-p0.001-Foc0.1-Loc1000-Fc3 peaks longLabel fip1vsInput_Homer-100-100-Fdr0.001-p0.001-Foc0.1-Loc1000-Fc3 peaks type bigBed visibility pack priority 910 color 163,92,4 subGroups Group1=Fip1 Group2=mESC view=PEAK # Peak track track fip1vsInput_Homer-100-100-Fdr0.001-p0.001-Foc0.1-Loc1000-Fc4 parent NS50093ArcherHoffmanView3 on bigDataUrl homerComparison_Fip1-Vs-Input-100-100-fdr0.001-p0.001-foc0.1-loc1000-fc4.sorted.bb shortLabel fip1vsInput_Homer-100-100-Fdr0.001-p0.001-Foc0.1-Loc1000-Fc4 peaks longLabel fip1vsInput_Homer-100-100-Fdr0.001-p0.001-Foc0.1-Loc1000-Fc4 peaks type bigBed visibility pack priority 912 color 163,92,4 subGroups Group1=Fip1 Group2=mESC view=PEAK # Peak track track fip1vsInput_Homer-200-200-Fdr0.001-p0.001-Foc0.1-Loc1000-Fc1 parent NS50093ArcherHoffmanView3 on bigDataUrl homerComparison_Fip1-Vs-Input-200-200-fdr0.001-p0.001-foc0.1-loc1000-fc1.sorted.bb shortLabel fip1vsInput_Homer-200-200-Fdr0.001-p0.001-Foc0.1-Loc1000-Fc1 peaks longLabel fip1vsInput_Homer-200-200-Fdr0.001-p0.001-Foc0.1-Loc1000-Fc1 peaks type bigBed visibility pack priority 914 color 163,92,4 subGroups Group1=Fip1 Group2=mESC view=PEAK # Peak track track fip1vsInput_Homer-200-200-Fdr0.001-p0.001-Foc0.1-Loc1000-Fc2 parent NS50093ArcherHoffmanView3 on bigDataUrl homerComparison_Fip1-Vs-Input-200-200-fdr0.001-p0.001-foc0.1-loc1000-fc2.sorted.bb shortLabel fip1vsInput_Homer-200-200-Fdr0.001-p0.001-Foc0.1-Loc1000-Fc2 peaks longLabel fip1vsInput_Homer-200-200-Fdr0.001-p0.001-Foc0.1-Loc1000-Fc2 peaks type bigBed visibility pack priority 916 color 163,92,4 subGroups Group1=Fip1 Group2=mESC view=PEAK # Peak track track fip1vsInput_Homer-200-250-Fdr0.001-p0.0001-Foc0.1-Loc2000-Fc4 parent NS50093ArcherHoffmanView3 on bigDataUrl homerComparison_Fip1-Vs-Input-200-250-fdr0.001-p0.0001-foc0.1-loc2000-fc4.sorted.bb shortLabel fip1vsInput_Homer-200-250-Fdr0.001-p0.0001-Foc0.1-Loc2000-Fc4 peaks longLabel fip1vsInput_Homer-200-250-Fdr0.001-p0.0001-Foc0.1-Loc2000-Fc4 peaks type bigBed visibility pack priority 918 color 163,92,4 subGroups Group1=Fip1 Group2=mESC view=PEAK # Peak track track fip1vsInput_Homer-200-50-Fdr0.001-p0.0001-Foc0-Loc2000-Fc4 parent NS50093ArcherHoffmanView3 on bigDataUrl homerComparison_Fip1-Vs-Input-200-50-fdr0.001-p0.0001-foc0-loc2000-fc4.sorted.bb shortLabel fip1vsInput_Homer-200-50-Fdr0.001-p0.0001-Foc0-Loc2000-Fc4 peaks longLabel fip1vsInput_Homer-200-50-Fdr0.001-p0.0001-Foc0-Loc2000-Fc4 peaks type bigBed visibility pack priority 920 color 163,92,4 subGroups Group1=Fip1 Group2=mESC view=PEAK # Peak track track fip1vsInputpeaks_Macs parent NS50093ArcherHoffmanView3 on bigDataUrl macsComparison_Fip1-Vs-InputPeaks.bb shortLabel fip1vsInputpeaks_Macs peaks longLabel fip1vsInputpeaks_Macs peaks type bigBed visibility pack priority 922 color 163,92,4 subGroups Group1=Fip1 Group2=mESC view=PEAK # Peak track track fip1vsInputsummits_Macs parent NS50093ArcherHoffmanView3 on bigDataUrl macsComparison_Fip1-Vs-InputSummits.bb shortLabel fip1vsInputsummits_Macs peaks longLabel fip1vsInputsummits_Macs peaks type bigBed visibility pack priority 924 color 163,92,4 subGroups Group1=Fip1 Group2=mESC view=PEAK ## Beginning of track view track hoffmanNG167siBaf60aRNAseq compositeTrack on shortLabel hoffman NG167 siBaf60a RNAseq longLabel hoffman NG167 siBaf60a RNAseq priority 1100 visibility full type bed 3 configurable on subGroup1 view Views \ COV=Coverage \ PEAK=Peaks \ JUNC=Junctions subGroup2 Group1 Group1 \ siBaf60a=siBaf60a \ siNT=siNT subGroup3 Group2 Group2 \ mESC=mESC dimensions dimX=Group1 dimY=Group2 sortOrder Group1=+ Group2=+ view=+ ## Views track coverage data track hoffmanNG167siBaf60aRNAseqView1 parent hoffmanNG167siBaf60aRNAseq shortLabel Coverage view COV visibility full type bigWig allButtonPair on centerLabelsDense on dragAndDrop on alwaysZero on graphTypeDefault bar maxHeightPixels 100:60:8 smoothingWindow 2 transformFunc NONE windowingFunction mean+whiskers gridDefault on viewLimits 0:20 viewUi on ## Coverage track track ES1330_coverage_v1 parent hoffmanNG167siBaf60aRNAseqView1 on bigDataUrl ES1330_1.sickle.merged.cutadapt.topHat2peStr_mm10.slop0.neg.bw shortLabel siBaf60a_mESC ES1330 coverage longLabel siBaf60a_mESC ES1330 coverage type bigWig color 123,31,31 priority 1102 alwaysZero on graphTypeDefault bar maxHeightPixels 100:60:8 smoothingWindow 2 transformFunc NONE windowingFunction mean+whiskers gridDefault on viewLimits 0:20 visibility hide subGroups Group1=siBaf60a Group2=mESC view=COV ## Coverage track track ES1330_coverage_v2 parent hoffmanNG167siBaf60aRNAseqView1 on bigDataUrl ES1330_1.sickle.merged.cutadapt.topHat2peStr_mm10.slop0.pos.bw shortLabel siBaf60a_mESC ES1330 coverage longLabel siBaf60a_mESC ES1330 coverage type bigWig color 123,31,31 priority 1104 alwaysZero on graphTypeDefault bar maxHeightPixels 100:60:8 smoothingWindow 2 transformFunc NONE windowingFunction mean+whiskers gridDefault on viewLimits 0:20 visibility hide subGroups Group1=siBaf60a Group2=mESC view=COV ## Coverage track track ES1331_coverage_v1 parent hoffmanNG167siBaf60aRNAseqView1 on bigDataUrl ES1331_1.sickle.merged.cutadapt.topHat2peStr_mm10.slop0.neg.bw shortLabel siBaf60a_mESC ES1331 coverage longLabel siBaf60a_mESC ES1331 coverage type bigWig color 123,31,31 priority 1106 alwaysZero on graphTypeDefault bar maxHeightPixels 100:60:8 smoothingWindow 2 transformFunc NONE windowingFunction mean+whiskers gridDefault on viewLimits 0:20 visibility hide subGroups Group1=siBaf60a Group2=mESC view=COV ## Coverage track track ES1331_coverage_v2 parent hoffmanNG167siBaf60aRNAseqView1 on bigDataUrl ES1331_1.sickle.merged.cutadapt.topHat2peStr_mm10.slop0.pos.bw shortLabel siBaf60a_mESC ES1331 coverage longLabel siBaf60a_mESC ES1331 coverage type bigWig color 123,31,31 priority 1108 alwaysZero on graphTypeDefault bar maxHeightPixels 100:60:8 smoothingWindow 2 transformFunc NONE windowingFunction mean+whiskers gridDefault on viewLimits 0:20 visibility hide subGroups Group1=siBaf60a Group2=mESC view=COV ## Coverage track track ES1332_coverage_v1 parent hoffmanNG167siBaf60aRNAseqView1 on bigDataUrl ES1332_1.sickle.merged.cutadapt.topHat2peStr_mm10.slop0.neg.bw shortLabel siBaf60a_mESC ES1332 coverage longLabel siBaf60a_mESC ES1332 coverage type bigWig color 123,31,31 priority 1110 alwaysZero on graphTypeDefault bar maxHeightPixels 100:60:8 smoothingWindow 2 transformFunc NONE windowingFunction mean+whiskers gridDefault on viewLimits 0:20 visibility hide subGroups Group1=siBaf60a Group2=mESC view=COV ## Coverage track track ES1332_coverage_v2 parent hoffmanNG167siBaf60aRNAseqView1 on bigDataUrl ES1332_1.sickle.merged.cutadapt.topHat2peStr_mm10.slop0.pos.bw shortLabel siBaf60a_mESC ES1332 coverage longLabel siBaf60a_mESC ES1332 coverage type bigWig color 123,31,31 priority 1112 alwaysZero on graphTypeDefault bar maxHeightPixels 100:60:8 smoothingWindow 2 transformFunc NONE windowingFunction mean+whiskers gridDefault on viewLimits 0:20 visibility hide subGroups Group1=siBaf60a Group2=mESC view=COV ## Coverage track track ES1327_coverage_v1 parent hoffmanNG167siBaf60aRNAseqView1 on bigDataUrl ES1327_1.sickle.merged.cutadapt.topHat2peStr_mm10.slop0.neg.bw shortLabel siNT_mESC ES1327 coverage longLabel siNT_mESC ES1327 coverage type bigWig color 141,102,0 priority 1114 alwaysZero on graphTypeDefault bar maxHeightPixels 100:60:8 smoothingWindow 2 transformFunc NONE windowingFunction mean+whiskers gridDefault on viewLimits 0:20 visibility hide subGroups Group1=siNT Group2=mESC view=COV ## Coverage track track ES1327_coverage_v2 parent hoffmanNG167siBaf60aRNAseqView1 on bigDataUrl ES1327_1.sickle.merged.cutadapt.topHat2peStr_mm10.slop0.pos.bw shortLabel siNT_mESC ES1327 coverage longLabel siNT_mESC ES1327 coverage type bigWig color 141,102,0 priority 1116 alwaysZero on graphTypeDefault bar maxHeightPixels 100:60:8 smoothingWindow 2 transformFunc NONE windowingFunction mean+whiskers gridDefault on viewLimits 0:20 visibility hide subGroups Group1=siNT Group2=mESC view=COV ## Coverage track track ES1328_coverage_v1 parent hoffmanNG167siBaf60aRNAseqView1 on bigDataUrl ES1328_1.sickle.merged.cutadapt.topHat2peStr_mm10.slop0.neg.bw shortLabel siNT_mESC ES1328 coverage longLabel siNT_mESC ES1328 coverage type bigWig color 141,102,0 priority 1118 alwaysZero on graphTypeDefault bar maxHeightPixels 100:60:8 smoothingWindow 2 transformFunc NONE windowingFunction mean+whiskers gridDefault on viewLimits 0:20 visibility hide subGroups Group1=siNT Group2=mESC view=COV ## Coverage track track ES1328_coverage_v2 parent hoffmanNG167siBaf60aRNAseqView1 on bigDataUrl ES1328_1.sickle.merged.cutadapt.topHat2peStr_mm10.slop0.pos.bw shortLabel siNT_mESC ES1328 coverage longLabel siNT_mESC ES1328 coverage type bigWig color 141,102,0 priority 1120 alwaysZero on graphTypeDefault bar maxHeightPixels 100:60:8 smoothingWindow 2 transformFunc NONE windowingFunction mean+whiskers gridDefault on viewLimits 0:20 visibility hide subGroups Group1=siNT Group2=mESC view=COV ## Coverage track track ES1329_coverage_v1 parent hoffmanNG167siBaf60aRNAseqView1 on bigDataUrl ES1329_1.sickle.merged.cutadapt.topHat2peStr_mm10.slop0.neg.bw shortLabel siNT_mESC ES1329 coverage longLabel siNT_mESC ES1329 coverage type bigWig color 141,102,0 priority 1122 alwaysZero on graphTypeDefault bar maxHeightPixels 100:60:8 smoothingWindow 2 transformFunc NONE windowingFunction mean+whiskers gridDefault on viewLimits 0:20 visibility hide subGroups Group1=siNT Group2=mESC view=COV ## Coverage track track ES1329_coverage_v2 parent hoffmanNG167siBaf60aRNAseqView1 on bigDataUrl ES1329_1.sickle.merged.cutadapt.topHat2peStr_mm10.slop0.pos.bw shortLabel siNT_mESC ES1329 coverage longLabel siNT_mESC ES1329 coverage type bigWig color 141,102,0 priority 1124 alwaysZero on graphTypeDefault bar maxHeightPixels 100:60:8 smoothingWindow 2 transformFunc NONE windowingFunction mean+whiskers gridDefault on viewLimits 0:20 visibility hide subGroups Group1=siNT Group2=mESC view=COV ## Views track for RNAseq, junctions data track hoffmanNG167siBaf60aRNAseqView2 parent hoffmanNG167siBaf60aRNAseq shortLabel RNAseq_junctions view JUNC visibility pack type bigBed 12 allButtonPair on centerLabelsDense on dragAndDrop on thickDrawItem on scoreFilter 20 scoreFilterLimits 1:1000 viewUi on # combined junctions track track ES1330_junctions parent hoffmanNG167siBaf60aRNAseqView2 on bigDataUrl ES1330_1.sickle.merged.cutadapt.topHat2peStr_mm10.sorted.junctions.bb shortLabel siBaf60a_mESC ES1330 junctions longLabel siBaf60a_mESC ES1330 junctions type bigBed 12 visibility pack priority 1126 scoreMin 10 scoreMax 100 color 123,31,31 subGroups Group1=siBaf60a Group2=mESC view=JUNC # combined junctions track track ES1331_junctions parent hoffmanNG167siBaf60aRNAseqView2 on bigDataUrl ES1331_1.sickle.merged.cutadapt.topHat2peStr_mm10.sorted.junctions.bb shortLabel siBaf60a_mESC ES1331 junctions longLabel siBaf60a_mESC ES1331 junctions type bigBed 12 visibility pack priority 1128 scoreMin 10 scoreMax 100 color 123,31,31 subGroups Group1=siBaf60a Group2=mESC view=JUNC # combined junctions track track ES1332_junctions parent hoffmanNG167siBaf60aRNAseqView2 on bigDataUrl ES1332_1.sickle.merged.cutadapt.topHat2peStr_mm10.sorted.junctions.bb shortLabel siBaf60a_mESC ES1332 junctions longLabel siBaf60a_mESC ES1332 junctions type bigBed 12 visibility pack priority 1130 scoreMin 10 scoreMax 100 color 123,31,31 subGroups Group1=siBaf60a Group2=mESC view=JUNC # combined junctions track track ES1327_junctions parent hoffmanNG167siBaf60aRNAseqView2 on bigDataUrl ES1327_1.sickle.merged.cutadapt.topHat2peStr_mm10.sorted.junctions.bb shortLabel siNT_mESC ES1327 junctions longLabel siNT_mESC ES1327 junctions type bigBed 12 visibility pack priority 1132 scoreMin 10 scoreMax 100 color 141,102,0 subGroups Group1=siNT Group2=mESC view=JUNC # combined junctions track track ES1328_junctions parent hoffmanNG167siBaf60aRNAseqView2 on bigDataUrl ES1328_1.sickle.merged.cutadapt.topHat2peStr_mm10.sorted.junctions.bb shortLabel siNT_mESC ES1328 junctions longLabel siNT_mESC ES1328 junctions type bigBed 12 visibility pack priority 1134 scoreMin 10 scoreMax 100 color 141,102,0 subGroups Group1=siNT Group2=mESC view=JUNC # combined junctions track track ES1329_junctions parent hoffmanNG167siBaf60aRNAseqView2 on bigDataUrl ES1329_1.sickle.merged.cutadapt.topHat2peStr_mm10.sorted.junctions.bb shortLabel siNT_mESC ES1329 junctions longLabel siNT_mESC ES1329 junctions type bigBed 12 visibility pack priority 1136 scoreMin 10 scoreMax 100 color 141,102,0 subGroups Group1=siNT Group2=mESC view=JUNC # combined junctions track track siBaf60a_mESC_junctions parent hoffmanNG167siBaf60aRNAseqView2 on bigDataUrl siBaf60a_mESC.TopHat2_mm10.combinedJunctions.named.bb shortLabel siBaf60a_mESC junctions longLabel siBaf60a_mESC junctions type bigBed 12 visibility pack priority 1138 scoreMin 10 scoreMax 100 color 123,31,31 subGroups Group1=siBaf60a Group2=mESC view=JUNC # combined junctions track track siNT_mESC_junctions parent hoffmanNG167siBaf60aRNAseqView2 on bigDataUrl siNT_mESC.TopHat2_mm10.combinedJunctions.named.bb shortLabel siNT_mESC junctions longLabel siNT_mESC junctions type bigBed 12 visibility pack priority 1140 scoreMin 10 scoreMax 100 color 141,102,0 subGroups Group1=siNT Group2=mESC view=JUNC ## Beginning of track view track APAsites compositeTrack on shortLabel APA Sites longLabel APA Sites priority 200 visibility pack type bed 3 configurable on subGroup1 view Views \ PEAK=Sites subGroup2 Group1 Group1 \ data7vs8=data7vs8 subGroup3 Group2 Group2 \ mESC=mESC dimensions dimX=Group1 dimY=Group2 sortOrder Group1=+ Group2=+ view=+ ## Views track for ChIPseq peaks track APAsitesView parent APAsites shortLabel Sites view PEAK visibility pack type bigBed allButtonPair on centerLabelsDense on dragAndDrop on viewUi on # Peak track track charlesAPAdata7vs8 parent APAsitesView on bigDataUrl charlesAPA_data7vs8_mm10_sites.bb shortLabel charles APA sites (data7vs8) longLabel charles APA sites (data7vs8) type bigBed visibility pack priority 208 color 123,31,31 subGroups Group1=data7vs8 Group2=mESC view=PEAK