## Colors for the 4 treatments: ## UNTR #color -70,70,70 #color 90,90,90 ## DEX #color -0,80,153 #color 30,40,200 ## MG #color -0,119,34 #color 10,130,0 ## MGDEX #color -119,40,153 #color 120,0,150 ## colors: 90,90,90 30,40,200 10,130,0 120,0,150 ################### ## Track composites ## ## Coverage bigWigs: track lin28covSet compositeTrack on shortLabel Kinyamu H3K4me3 Tracks longLabel Lin28 and IgG coverage type bigWig allButtonPair on centerLabelsDense on dragAndDrop on priority 20 alwaysZero on graphTypeDefault bar maxHeightPixels 100:24:8 smoothingWindow 2 transformFunc NONE windowingFunction maximum gridDefault on viewLimits 0:20 visibility full #################### ## Track definitions: ## track lin28 parent lin28covSet bigDataUrl lin28_bowtie.bw shortLabel Lin28 bowtie longLabel Lin28 bowtie reads type bigWig color 30,40,200 priority 312 alwaysZero on graphTypeDefault bar maxHeightPixels 100:24:8 smoothingWindow 8 transformFunc NONE windowingFunction maximum gridDefault on viewLimits 0:20 visibility hide ## K36 coverage track untrK36adjIgG parent k36set on bigDataUrl untrK36adjIgG-floor0.bw shortLabel untr-K36-adjIgG Signal longLabel Depth of untr-K36-adjIgG reads type bigWig color 90,90,90 priority 241 alwaysZero on graphTypeDefault bar maxHeightPixels 100:24:8 smoothingWindow 4 transformFunc NONE windowingFunction maximum gridDefault on viewLimits 0:20 visibility full track dexK36adjIgG parent k36set on bigDataUrl dexK36adjIgG-floor0.bw shortLabel dex-K36-adjIgG Signal longLabel Depth of dex-K36-adjIgG reads type bigWig color 30,40,200 priority 242 alwaysZero on graphTypeDefault bar maxHeightPixels 100:24:8 smoothingWindow 4 transformFunc NONE windowingFunction maximum gridDefault on viewLimits 0:20 visibility full track mgK36adjIgG parent k36set on bigDataUrl mgK36adjIgG-floor0.bw shortLabel mg-K36-adjIgG Signal longLabel Depth of mg-K36-adjIgG reads type bigWig color 10,130,0 priority 243 alwaysZero on graphTypeDefault bar maxHeightPixels 100:24:8 smoothingWindow 4 transformFunc NONE windowingFunction maximum gridDefault on viewLimits 0:20 visibility full track mgdexK36adjIgG parent k36set on bigDataUrl mgdexK36adjIgG-floor0.bw shortLabel mgdex-K36-adjIgG Signal longLabel Depth of mgdex-K36-adjIgG reads type bigWig color 120,0,150 priority 244 alwaysZero on graphTypeDefault bar maxHeightPixels 100:24:8 smoothingWindow 4 transformFunc NONE windowingFunction maximum gridDefault on viewLimits 0:20 visibility full ## K4 peaks track Peaks-K4-UNTR parent k4peakSet bigDataUrl K4_UNTR_SICER-island-FDR.bed.bb shortLabel K4-UNTR Peaks longLabel Enriched regions for K4 UNTR type bigBed color 90,90,90 visibility dense priority 421 track Peaks-K4-DEX parent k4peakSet bigDataUrl K4_DEX_SICER-island-FDR.bed.bb shortLabel K4-DEX Peaks longLabel Enriched regions for K4 DEX type bigBed color 30,40,200 visibility dense priority 422 track Peaks-K4-MG parent k4peakSet bigDataUrl K4_MG_SICER-island-FDR.bed.bb shortLabel K4-MG Peaks longLabel Enriched regions for K4 MG type bigBed color 10,130,0 visibility dense priority 423 track Peaks-K4-MGDEX parent k4peakSet bigDataUrl K4_MGDEX_SICER-island-FDR.bed.bb shortLabel K4-MGDEX Peaks longLabel Enriched regions for K4 MGDEX type bigBed color 120,0,150 visibility dense priority 424 ## K36 peaks track Peaks-K36-UNTR parent k36peakSet on bigDataUrl UNTRK36_2of3_peaks.bed.bb shortLabel K36-UNTR Peaks longLabel Enriched regions for K36 UNTR type bigBed color 90,90,90 visibility dense priority 131 track Peaks-K36-DEX parent k36peakSet on bigDataUrl DEXK36_2of3_peaks.bed.bb shortLabel K36-DEX Peaks longLabel Enriched regions for K36 DEX type bigBed color 30,40,200 visibility dense priority 132 track Peaks-K36-MG parent k36peakSet on bigDataUrl MGK36_2of3_peaks.bed.bb shortLabel K36-MG Peaks longLabel Enriched regions for K36 MG type bigBed color 10,130,0 visibility dense priority 133 track Peaks-K36-MGDEX parent k36peakSet on bigDataUrl MGDEXK36_2of3_peaks.bed.bb shortLabel K36-MGDEX Peaks longLabel Enriched regions for K36 MGDEX type bigBed color 120,0,150 visibility dense priority 134 ## New SICERv1.1 K4 peaks track Peaks-K4-UNTRv1.1 parent k4peakSetV1.1 on bigDataUrl K4-UNTR-W200-G400-SICERv1.1-FDR1E-25.bb shortLabel K4-UNTR-v1.1 peaks longLabel Enriched regions for K4 UNTR (SICER v1.1) type bigBed color 90,90,90 visibility dense priority 111 track Peaks-K4-DEXv1.1 parent k4peakSetV1.1 on bigDataUrl K4-DEX-W200-G400-SICERv1.1-FDR1E-25.bb shortLabel K4-DEX-v1.1 peaks longLabel Enriched regions for K4 DEX (SICER v1.1) type bigBed color 30,40,200 visibility dense priority 112 track Peaks-K4-MGv1.1 parent k4peakSetV1.1 on bigDataUrl K4-MG-W200-G400-SICERv1.1-FDR1E-25.bb shortLabel K4-MG-v1.1 peaks longLabel Enriched regions for K4 MG (SICER v1.1) type bigBed color 10,130,0 visibility dense priority 113 track Peaks-K4-MGDEXv1.1 parent k4peakSetV1.1 on bigDataUrl K4-MGDEX-W200-G400-SICERv1.1-FDR1E-25.bb shortLabel K4-MGDEX-v1.1 peaks longLabel Enriched regions for K4 MGDEX (SICER v1.1) type bigBed color 120,0,150 visibility dense priority 114 ########################## ## Track multiWig overlays: # K36 signal track k36multiWig container multiWig aggregate transparentOverlay shortLabel K36 Adjusted Signal longLabel K36 Adjusted Signal showSubtrackColorOnUi on type bigWig viewLimits 0:48 maxHeightPixels 100:48:8 alwaysZero on graphTypeDefault bar smoothingWindow 8 transformFunc NONE windowingFunction maximum visibility full track untrK36multiWig table untrK36adjIgG bigDataUrl untrK36adjIgG-floor0.bw type bigWig parent k36multiWig color 160,160,160 priority 141 track dexK36multiWig table dexK36adjIgG bigDataUrl dexK36adjIgG-floor0.bw type bigWig parent k36multiWig color 70,100,220 priority 142 track mgK36multiWig table mgK36adjIgG bigDataUrl mgK36adjIgG-floor0.bw type bigWig parent k36multiWig color 130,190,100 priority 143 track mgdexK36multiWig table mgdexK36adjIgG bigDataUrl mgdexK36adjIgG-floor0.bw type bigWig parent k36multiWig color 170,80,220 priority 144 # K4 signal track k4multiWig container multiWig aggregate transparentOverlay shortLabel K4 Adjusted Signal longLabel K4 Adjusted Signal showSubtrackColorOnUi on type bigWig viewLimits 0:48 maxHeightPixels 100:48:8 alwaysZero on graphTypeDefault bar smoothingWindow 8 transformFunc NONE windowingFunction maximum visibility full track untrK4multiWig bigDataUrl kinyamu-K4-UNTR-MCF7.bw type bigWig parent k4multiWig color 160,160,160 priority 121 track dexK4multiWig bigDataUrl kinyamu-K4-DEX-MCF7.bw type bigWig parent k4multiWig color 70,100,220 priority 122 track mgK4multiWig bigDataUrl kinyamu-K4-MG-MCF7.bw type bigWig parent k4multiWig color 130,190,100 priority 123 track mgdexK4multiWig bigDataUrl kinyamu-K4-MGDEX-MCF7.bw type bigWig parent k4multiWig color 170,80,220 priority 124 ######################### ## Nucleosome positioning ## ## Peak sets: track k4NPSpeakSet compositeTrack on shortLabel Nucleosome Positions NPS longLabel Composite of Nucleosome Positions Using NPS type bigBed allButtonPair on centerLabelsDense on dragAndDrop on priority 1420 ## Coverage sets: track k4NPScoverageSet compositeTrack on shortLabel Nucleosome Coverage NPS longLabel Composite of Nucleosome Coverages Using NPS type bigWig allButtonPair on centerLabelsDense on dragAndDrop on priority 1450 alwaysZero on graphTypeDefault bar maxHeightPixels 100:48:8 smoothingWindow 2 transformFunc NONE windowingFunction maximum gridDefault on viewLimits -10:100 ## K4 input data track K4-UNTR-NPS parent k4NPSpeakSet bigDataUrl ES141_NPS_20nov2012.bb shortLabel UNTR Nucleosome Predictions longLabel UNTR Nucleosome Predictions type bigBed color 90,90,90 visibility dense priority 1421 track K4-DEX-NPS parent k4NPSpeakSet bigDataUrl ES142_NPS_20nov2012.bb shortLabel DEX Nucleosome Predictions longLabel DEX Nucleosome Predictions type bigBed color 30,40,200 visibility dense priority 1422 track K4-MG-NPS parent k4NPSpeakSet bigDataUrl ES143_NPS_20nov2012.bb shortLabel MG Nucleosome Predictions longLabel MG Nucleosome Predictions type bigBed color 10,130,0 visibility dense priority 1423 track K4-MGDEX-NPS parent k4NPSpeakSet bigDataUrl ES144_NPS_20nov2012.bb shortLabel MGDEX Nucleosome Predictions longLabel MGDEX Nucleosome Predictions type bigBed color 10,130,0 color 120,0,150 color 10,130,0 color 120,0,150 visibility dense priority 1424 ## K4 combined inputs track K4-All4-NPS parent k4NPSpeakSet bigDataUrl ES14-1234_inputLanes_NPS_19nov2012.bb shortLabel Combined Input Nucleosome Predictions longLabel Combined Input Nucleosome Predictions type bigBed color 230,100,25 visibility dense priority 1427 ## K4 combined inputs, bigWig coverage file # ES14-1234_inputLanes_NPS_19nov2012.bw track K4-UNTR-NPS-coverage parent k4NPScoverageSet on bigDataUrl ES141_NPS_20nov2012.bw shortLabel K4-UNTR Input Nucleosome Coverage longLabel K4-UNTR Input Nucleosome Coverage type bigWig color 90,90,90 priority 1457 alwaysZero on graphTypeDefault bar maxHeightPixels 100:48:8 smoothingWindow 2 transformFunc NONE windowingFunction maximum gridDefault on viewLimits -10:50 visibility full # ES14-1234_inputLanes_NPS_19nov2012.bw track K4-DEX-NPS-coverage parent k4NPScoverageSet on bigDataUrl ES141_NPS_20nov2012.bw shortLabel K4-DEX Input Nucleosome Coverage longLabel K4-DEX Input Nucleosome Coverage type bigWig color 30,40,200 priority 1457 alwaysZero on graphTypeDefault bar maxHeightPixels 100:48:8 smoothingWindow 2 transformFunc NONE windowingFunction maximum gridDefault on viewLimits -10:50 visibility full # ES14-1234_inputLanes_NPS_19nov2012.bw track K4-MG-NPS-coverage parent k4NPScoverageSet on bigDataUrl ES141_NPS_20nov2012.bw shortLabel K4-MG Input Nucleosome Coverage longLabel K4-MG Input Nucleosome Coverage type bigWig color 10,130,0 priority 1457 alwaysZero on graphTypeDefault bar maxHeightPixels 100:48:8 smoothingWindow 2 transformFunc NONE windowingFunction maximum gridDefault on viewLimits -10:50 visibility full # ES14-1234_inputLanes_NPS_19nov2012.bw track K4-MGDEX-NPS-coverage parent k4NPScoverageSet on bigDataUrl ES141_NPS_20nov2012.bw shortLabel K4-MGDEX Input Nucleosome Coverage longLabel K4-MGDEX Input Nucleosome Coverage type bigWig color 120,0,150 priority 1457 alwaysZero on graphTypeDefault bar maxHeightPixels 100:48:8 smoothingWindow 2 transformFunc NONE windowingFunction maximum gridDefault on viewLimits -10:50 visibility full # ES14-1234_inputLanes_NPS_19nov2012.bw track K4-All4-NPS-coverage parent k4NPScoverageSet on bigDataUrl ES14-1234_inputLanes_NPS_19nov2012.bw shortLabel Combined Input Nucleosome Coverage longLabel Combined Input Nucleosome Coverage type bigWig color 230,100,25 priority 1457 alwaysZero on graphTypeDefault bar maxHeightPixels 100:48:8 smoothingWindow 2 transformFunc NONE windowingFunction maximum gridDefault on viewLimits -10:50 visibility full ## K36 colors #color 90,90,90 #color 30,40,200 #color 10,130,0 #color 120,0,150 track kinyamuRnaSeq compositeTrack on shortLabel Kinyamu RNA-seq longLabel Kinyamu RNA-seq coverage type bigWig allButtonPair on centerLabelsDense on dragAndDrop on priority 820 alwaysZero on graphTypeDefault bar maxHeightPixels 100:24:8 smoothingWindow 2 transformFunc NONE windowingFunction maximum gridDefault on viewLimits 0:200 visibility full ## RNA-seq coverage track RNAuntr parent kinyamuRnaSeq on bigDataUrl ES540.1.sickle_q20_l20.fastq.topHat2pe_hg18.bw shortLabel Untreated RNA-seq longLabel Untreated RNA-seq coverage type bigWig color 90,90,90 priority 821 alwaysZero on graphTypeDefault bar maxHeightPixels 100:24:8 smoothingWindow 2 transformFunc NONE windowingFunction maximum gridDefault on viewLimits 0:200 visibility full track RNAdex parent kinyamuRnaSeq on bigDataUrl ES541.1.sickle_q20_l20.fastq.topHat2pe_hg18.bw shortLabel Dex RNA-seq longLabel Dex RNA-seq coverage type bigWig color 30,40,200 priority 822 alwaysZero on graphTypeDefault bar maxHeightPixels 100:24:8 smoothingWindow 2 transformFunc NONE windowingFunction maximum gridDefault on viewLimits 0:200 visibility full track RNAmg parent kinyamuRnaSeq on bigDataUrl ES542.1.sickle_q20_l20.fastq.topHat2pe_hg18.bw shortLabel Mg132 RNA-seq longLabel Mg132 RNA-seq coverage type bigWig color 10,130,0 priority 823 alwaysZero on graphTypeDefault bar maxHeightPixels 100:24:8 smoothingWindow 2 transformFunc NONE windowingFunction maximum gridDefault on viewLimits 0:200 visibility full track RNAmgdex parent kinyamuRnaSeq on bigDataUrl ES543.1.sickle_q20_l20.fastq.topHat2pe_hg18.bw shortLabel MgDex RNA-seq longLabel MgDex RNA-seq coverage type bigWig color 120,0,150 priority 824 alwaysZero on graphTypeDefault bar maxHeightPixels 100:24:8 smoothingWindow 2 transformFunc NONE windowingFunction maximum gridDefault on viewLimits 0:200 visibility full # ES540.1.sickle_q20_l20.fastq.topHat2pe_hg18.bw # ES541.1.sickle_q20_l20.fastq.topHat2pe_hg18.bw # ES542.1.sickle_q20_l20.fastq.topHat2pe_hg18.bw # ES543.1.sickle_q20_l20.fastq.topHat2pe_hg18.bw ## K4 peaks track HOMER-K4-UNTR parent k4homerSet bigDataUrl K4-UNTR_histone-nfr_peaks.bb shortLabel K4-UNTR HOMER Peaks longLabel HOMER Peaks for K4 UNTR type bigBed color 90,90,90 visibility dense priority 481 track HOMER-K4-DEX parent k4homerSet bigDataUrl K4-DEX_histone-nfr_peaks.bb shortLabel K4-DEX HOMER Peaks longLabel HOMER Peaks for K4 DEX type bigBed color 30,40,200 visibility dense priority 482 track HOMER-K4-MG parent k4homerSet bigDataUrl K4-MG_histone-nfr_peaks.bb shortLabel K4-MG HOMER Peaks longLabel HOMER Peaks for K4 MG type bigBed color 10,130,0 visibility dense priority 483 track HOMER-K4-MGDEX parent k4homerSet bigDataUrl K4-MGDEX_histone-nfr_peaks.bb shortLabel K4-MGDEX HOMER Peaks longLabel HOMER Peaks for K4 MGDEX type bigBed color 120,0,150 visibility dense priority 484 ## colors: 90,90,90 30,40,200 10,130,0 120,0,150 ## END