track chain_cs10
bigDataUrl bbi/cs10.bigChain.bb
linkDataUrl bbi/cs10.bigLink.bb
shortLabel cs10 chain
longLabel cs10 aligned to JL_Father
type bigChain
visibility pack
group compGeno
priority 7

track rbest_cs10
bigDataUrl bbi/cs10.rbestChain.bb
linkDataUrl bbi/cs10.rbestLink.bb
shortLabel cs10 rbest
longLabel cs10 reciprocal-best chains to JL_Father
type bigChain
visibility hide
group compGeno
priority 9

track JL_Father_cs10genes
bigDataUrl bbi/cs10.genes.bb
shortLabel Genes from cs10
longLabel cs10 RefSeq gene models lifted onto JL_Father through the cs10 chain (not its own annotation)
type bigBed 12
visibility pack
group genes

track cytoBandIdeo
bigDataUrl bbi/JL_Father.cytoBand.bb
shortLabel Chromosome Band (Ideogram)
longLabel Ideogram for Orientation
type bigBed 4 +
visibility dense
group map

track JL_Father_gc
bigDataUrl bbi/JL_Father.gc.bw
shortLabel GC Percent
longLabel GC percent of JL_Father over non-N bases
type bigWig 0 100
viewLimits 25:55
autoScale off
windowingFunction mean
graphTypeDefault bar
maxHeightPixels 128:36:16
color 0,0,0
altColor 128,128,128
visibility dense
group map

track repeats
superTrack on show
shortLabel Repeats
longLabel Repeat annotation and masking for JL_Father
group varRep

track JL_Father_maskunion
parent repeats
bigDataUrl bbi/JL_Father.maskunion.bb
shortLabel Aligner mask
longLabel Union of our four maskers: the soft-masking every panel alignment ran on
type bigBed 3
visibility dense
group varRep
priority 2

track JL_Father_dustmasker
parent repeats
bigDataUrl bbi/JL_Father.dustmasker.bb
shortLabel dustmasker
longLabel dustmasker (low-complexity), WF-B
type bigBed 3
visibility hide
group varRep

track JL_Father_windowmasker
parent repeats
bigDataUrl bbi/JL_Father.windowmasker.bb
shortLabel WindowMasker
longLabel WindowMasker (over-represented k-mers), WF-B
type bigBed 3
visibility hide
group varRep

track JL_Father_tantan
parent repeats
bigDataUrl bbi/JL_Father.tantan.bb
shortLabel tantan
longLabel tantan (tandem repeats), WF-B
type bigBed 3
visibility hide
group varRep

track JL_Father_fastan
parent repeats
bigDataUrl bbi/JL_Father.fastan.bb
shortLabel FasTAN
longLabel FasTAN (satellite and long tandem arrays), WF-B
type bigBed 3
visibility hide
group varRep