## Beginning of track view
track             farris12Dec2014
compositeTrack    on
shortLabel        Farris MiSeq 12Dec2014
longLabel         Farris MiSeq 12Dec2014
priority          2200
visibility        full
type              bed 3
configurable      on
subGroup1         view Views \
   COV=Coverage \
   PEAK=Peaks \
   JUNC=Junctions
subGroup2         Group1 Group1 \ 
    PosCtrl1ng=PosCtrl1ng \
    HippoRNA300pg=HippoRNA300pg \
    PosCtrl300pg=PosCtrl300pg
sortOrder         Group1=+  view=+
 
   ## Views track coverage data
   track             farris12Dec2014View1
   parent            farris12Dec2014
   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             MES6651ngPositiveControl_coverage
      parent            farris12Dec2014View1 on
      bigDataUrl        MES6651ngPositiveControl_1.sickle.merged.topHat2pe_mm10.bw
      shortLabel        PosCtrl1ng coverage
      longLabel         PosCtrl1ng coverage
      type              bigWig
      color             205,51,51
      priority          2202
      alwaysZero        on
      graphTypeDefault  bar
      maxHeightPixels   100:60:8
      smoothingWindow   2
      transformFunc     NONE
      windowingFunction mean+whiskers
      gridDefault       on
      viewLimits        0:20
      visibility        hide
      subGroups         Group1=PosCtrl1ng view=COV
 
      ## Coverage track
      track             MES665300pgHippoRNA_coverage
      parent            farris12Dec2014View1 on
      bigDataUrl        MES665300pgHippoRNA_1.sickle.merged.topHat2pe_mm10.bw
      shortLabel        HippoRNA300pg coverage
      longLabel         HippoRNA300pg coverage
      type              bigWig
      color             69,139,0
      priority          2204
      alwaysZero        on
      graphTypeDefault  bar
      maxHeightPixels   100:60:8
      smoothingWindow   2
      transformFunc     NONE
      windowingFunction mean+whiskers
      gridDefault       on
      viewLimits        0:20
      visibility        hide
      subGroups         Group1=HippoRNA300pg view=COV
 
      ## Coverage track
      track             MES665300pgPositiveControl_coverage
      parent            farris12Dec2014View1 on
      bigDataUrl        MES665300pgPositiveControl_1.sickle.merged.topHat2pe_mm10.bw
      shortLabel        PosCtrl300pg coverage
      longLabel         PosCtrl300pg coverage
      type              bigWig
      color             16,78,139
      priority          2206
      alwaysZero        on
      graphTypeDefault  bar
      maxHeightPixels   100:60:8
      smoothingWindow   2
      transformFunc     NONE
      windowingFunction mean+whiskers
      gridDefault       on
      viewLimits        0:20
      visibility        hide
      subGroups         Group1=PosCtrl300pg view=COV
 
   ## Views track for RNAseq, junctions data
   track             farris12Dec2014View2
   parent            farris12Dec2014
   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             MES6651ngPositiveControl_junctions
      parent            farris12Dec2014View2 on
      bigDataUrl        MES6651ngPositiveControl_1.sickle.merged.topHat2pe_mm10.sorted.junc.bb
      shortLabel        PosCtrl1ng junctions
      longLabel         PosCtrl1ng junctions
      type              bigBed 12
      visibility        pack
      priority          2208
      scoreMin          10
      scoreMax          100
      color             205,51,51
      subGroups         Group1=PosCtrl1ng view=JUNC
 
      # combined junctions track
      track             MES665300pgHippoRNA_junctions
      parent            farris12Dec2014View2 on
      bigDataUrl        MES665300pgHippoRNA_1.sickle.merged.topHat2pe_mm10.sorted.junc.bb
      shortLabel        HippoRNA300pg junctions
      longLabel         HippoRNA300pg junctions
      type              bigBed 12
      visibility        pack
      priority          2210
      scoreMin          10
      scoreMax          100
      color             69,139,0
      subGroups         Group1=HippoRNA300pg view=JUNC
 
      # combined junctions track
      track             MES665300pgPositiveControl_junctions
      parent            farris12Dec2014View2 on
      bigDataUrl        MES665300pgPositiveControl_1.sickle.merged.topHat2pe_mm10.sorted.junc.bb
      shortLabel        PosCtrl300pg junctions
      longLabel         PosCtrl300pg junctions
      type              bigBed 12
      visibility        pack
      priority          2212
      scoreMin          10
      scoreMax          100
      color             16,78,139
      subGroups         Group1=PosCtrl300pg view=JUNC