## Dr. Kevin Trotter MiSeq ChIPseq data
track             trotterJune2014Set
compositeTrack    on
shortLabel        Trotter Brg1/GR ChIPseq June 2014
longLabel         Trotter Brg1/GR ChIPseq June 2014
priority          1030
visibility        full
subGroup1         view Views \
            COV=Coverage \
            PEAK=Peaks
subGroup2         treatment Treatment \
            EtOH=EtOH \
            Dex=Dex
subGroup3         transfection Transfection \
            Brg1=Brg1 \
            None=None
subGroup4         antibody Signal \
            Input=Input \
            Brg1=Brg1 \
            GR=GR
dimensions        dimX=treatment dimY=antibody
sortOrder         antibody=+ treatment=- transfection=+ view=+
type              bed 3
configurable      on

   ## Views track for June2014 ChIPseq, coverage data
   track             trotterJune2014View1
   parent            trotterJune2014Set
   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        0:20
   viewUi            on

      ## ChIPseq data coverage tracks
      ## GR-EtOHBrg1
      track             GR-EtOHBrg1June2014
      parent            trotterJune2014View1 on
      bigDataUrl        MES524GREtOHBRG1_s.sickle.merged.bowtieSe_hg19.sorted.slop150.bw
      shortLabel        GR+EtOH+Brg1
      longLabel         ChIPseq GR+EtOH+Brg1 (Trotter)
      type              bigWig
      color             0,92,81
      priority          1031
      alwaysZero        on
      graphTypeDefault  bar
      maxHeightPixels   100:40:8
      smoothingWindow   2
      transformFunc     NONE
      windowingFunction maximum
      gridDefault       on
      viewLimits        0:20
      visibility        hide
      subGroups         antibody=GR treatment=EtOH transfection=Brg1 view=COV

      ## GR-DexBrg1
      track             GR-DexBrg1June2014
      parent            trotterJune2014View1 on
      bigDataUrl        MES525GRDexBRG1_s.sickle.merged.bowtieSe_hg19.sorted.slop150.bw
      shortLabel        GR+Dex+Brg1
      longLabel         ChIPseq GR+Dex+Brg1 (Trotter)
      type              bigWig
      color             0,61,54
      priority          1032
      alwaysZero        on
      graphTypeDefault  bar
      maxHeightPixels   100:40:8
      smoothingWindow   2
      transformFunc     NONE
      windowingFunction maximum
      gridDefault       on
      viewLimits        0:20
      visibility        hide
      subGroups         antibody=GR treatment=Dex transfection=Brg1 view=COV

      ## Input-EtOH
      track             InputEtOHJune2014
      parent            trotterJune2014View1 on
      bigDataUrl        MES511InputEtOH_s.sickle.merged.bowtieSe_hg19.sorted.slop150.bw
      shortLabel        Input+EtOH
      longLabel         ChIPseq Input+EtOH (Trotter)
      type              bigWig
      color             170,136,170
      priority          1033
      alwaysZero        on
      graphTypeDefault  bar
      maxHeightPixels   100:40:8
      smoothingWindow   2
      transformFunc     NONE
      windowingFunction maximum
      gridDefault       on
      viewLimits        0:20
      visibility        hide
      subGroups         antibody=Input treatment=EtOH transfection=None view=COV

      ## Input-Dex
      track             InputDexJune2014
      parent            trotterJune2014View1 on
      bigDataUrl        MES512InputDex_s.sickle.merged.bowtieSe_hg19.sorted.slop150.bw
      shortLabel        Input+Dex
      longLabel         ChIPseq Input+Dex (Trotter)
      type              bigWig
      color             113,91,113
      priority          1034
      alwaysZero        on
      graphTypeDefault  bar
      maxHeightPixels   100:40:8
      smoothingWindow   2
      transformFunc     NONE
      windowingFunction maximum
      gridDefault       on
      viewLimits        0:20
      visibility        hide
      subGroups         antibody=Input treatment=Dex transfection=None view=COV

      ## Brg1-EtOH
      track             Brg1-EtOHJune2014
      parent            trotterJune2014View1 on
      bigDataUrl        MES514BRG1EtOH_s.sickle.merged.bowtieSe_hg19.sorted.slop150.bw
      shortLabel        Brg1+EtOH
      longLabel         ChIPseq Brg1+EtOH (Trotter)
      type              bigWig
      color             188,47,47
      priority          1038
      alwaysZero        on
      graphTypeDefault  bar
      maxHeightPixels   100:40:8
      smoothingWindow   2
      transformFunc     NONE
      windowingFunction maximum
      gridDefault       on
      viewLimits        0:20
      visibility        hide
      subGroups         antibody=Brg1 treatment=EtOH transfection=Brg1 view=COV

      ## Brg1-DexBrg1
      track             Brg1-DexBrg1June2014
      parent            trotterJune2014View1 on
      bigDataUrl        MES515BRG1Dex_s.sickle.merged.bowtieSe_hg19.sorted.slop150.bw
      shortLabel        Brg1+Dex
      longLabel         ChIPseq Brg1+Dex (Trotter)
      type              bigWig
      color             125,31,31
      priority          1039
      alwaysZero        on
      graphTypeDefault  bar
      maxHeightPixels   100:40:8
      smoothingWindow   2
      transformFunc     NONE
      windowingFunction maximum
      gridDefault       on
      viewLimits        0:20
      visibility        hide
      subGroups         antibody=Brg1 treatment=Dex transfection=Brg1 view=COV

## Color chart
#  .            . red green blue
## Greys
#  1       grey62 170   136  170
#  2      dimgrey 113    91  113
## Reds
#  3       brown3 188    47   47
#  4       brown4 125    31   31
## Yellows
#  5   darkorange 255   134   18
#  6      orange4 170    89   12
## Greens
#  7 springgreen4   0    92   81
#  8       grey15   0    61   54
## Blues
#  9  dodgerblue3  22    94  201
# 10  dodgerblue4  15    63  134