## TopHat2 junctions, merged across lanes per sample
track             TopHat2Junc
compositeTrack    on
shortLabel        TopHat2 merged junctions
longLabel         TopHat2 merged junctions
type              bigBed 12
allButtonPair     on
centerLabelsDense on
dragAndDrop       on
priority          580
visibility        dense

# siBrg1_r1 junctions
track             siBrg1_r1_junc
parent            TopHat2Junc
bigDataUrl        ES638_merged.junctions.bb
shortLabel        TopHat2 junctions siBrg1_r1
longLabel         TopHat2 junctions siBrg1_r1
type              bigBed 12
color             176,32,36
visibility        dense
priority          581

# siBrg1_r2 junctions
track             siBrg1_r2_junc
parent            TopHat2Junc
bigDataUrl        ES639_merged.junctions.bb
shortLabel        TopHat2 junctions siBrg1_r2
longLabel         TopHat2 junctions siBrg1_r2
type              bigBed 12
color             176,32,36
visibility        dense
priority          582

# siBrg1_r3 junctions
track             siBrg1_r3_junc
parent            TopHat2Junc
bigDataUrl        ES640_merged.junctions.bb
shortLabel        TopHat2 junctions siBrg1_r3
longLabel         TopHat2 junctions siBrg1_r3
type              bigBed 12
color             176,32,36
visibility        dense
priority          583

# Control_r1 junctions
track             Control_r1_junc
parent            TopHat2Junc
bigDataUrl        ES641_merged.junctions.bb
shortLabel        TopHat2 junctions Control_r1
longLabel         TopHat2 junctions Control_r1
type              bigBed 12
color             110,110,140
visibility        dense
priority          584

# Control_r2 junctions
track             Control_r2_junc
parent            TopHat2Junc
bigDataUrl        ES642_merged.junctions.bb
shortLabel        TopHat2 junctions Control_r2
longLabel         TopHat2 junctions Control_r2
type              bigBed 12
color             110,110,140
visibility        dense
priority          585

# Control_r3 junctions
track             Control_r3_junc
parent            TopHat2Junc
bigDataUrl        ES643_merged.junctions.bb
shortLabel        TopHat2 junctions Control_r3
longLabel         TopHat2 junctions Control_r3
type              bigBed 12
color             110,110,140
visibility        dense
priority          586

## TopHat2 junctions, merged across lanes per sample
track             TopHat2JuncComb
compositeTrack    on
shortLabel        TopHat2 combined junctions
longLabel         TopHat2 combined junctions
type              bigBed 12
allButtonPair     on
centerLabelsDense on
dragAndDrop       on
priority          570
visibility        pack
thickDrawItem     on

# siBrg1 combined junctions
# siBrg1_combined_junctions.bb
track             siBrg1_junc
parent            TopHat2JuncComb
bigDataUrl        siBrg1_combined_junctions.bed12sort.bb
shortLabel        TopHat2 junctions siBrg1
longLabel         TopHat2 junctions siBrg1
type              bigBed 12 .
visibility        pack
priority          575
spectrum          on
scoreMin          1
scoreMax          200
color             128,0,0
altColor          255,128,128
scoreFilterLimits 1:1000
scoreFilter       10
minGrayLevel      4

# Control combined junctions
# Control_combined_junctions.bb
track             Control_junc
parent            TopHat2JuncComb
bigDataUrl        Control_combined_junctions.bed12sort.bb
shortLabel        TopHat2 junctions Control
longLabel         TopHat2 junctions Control
type              bigBed 12 .
visibility        pack
priority          576
spectrum          on
scoreMin          0
scoreMax          200
color             0,0,128
altColor          128,128,255
scoreFilterLimits 1:1000
scoreFilter       10
minGrayLevel      4