track chain_cs10
bigDataUrl bbi/cs10.bigChain.bb
linkDataUrl bbi/cs10.bigLink.bb
shortLabel cs10 chain
longLabel cs10 aligned to SKFBa
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 SKFBa
type bigChain
visibility hide
group compGeno
priority 9

track SKFBa_genes
bigDataUrl bbi/SKFBa.anno.bb
shortLabel Gene models
longLabel Gene models published with SKFBa (Salk pangenome, primary high-confidence)
searchIndex name
type bigBed 12 +
visibility pack
group genes
priority 2

track SKFBa_cs10genes
bigDataUrl bbi/cs10.genes.bb
shortLabel Genes from cs10
longLabel cs10 RefSeq gene models lifted onto SKFBa through the cs10 chain (not its own annotation)
type bigBed 12
visibility hide
group genes

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

track SKFBa_gap
bigDataUrl bbi/SKFBa.gap.bb
shortLabel Gaps
longLabel Assembly gaps (runs of N) in SKFBa
type bigBed 3
color 0,0,0
visibility dense
group map

track SKFBa_gc
bigDataUrl bbi/SKFBa.gc.bw
shortLabel GC Percent
longLabel GC percent of SKFBa 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 SKFBa_cannabinoid
bigDataUrl bbi/SKFBa.cannabinoid.bb
shortLabel Cannabinoid synthases
longLabel Full-length THCAS (red), CBDAS (blue) and CBCAS (green) copies (Salk pangenome)
type bigBed 9
itemRgb on
visibility pack
group genes
priority 30

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

track SKFBa_rmsk
parent repeats
bigDataUrl bbi/SKFBa.rmsk.bb
shortLabel RepeatMasker
longLabel RepeatMasker run published with SKFBa (Salk pangenome); colored by repeat class
itemRgb on
type bigBed 9 +
visibility dense
group varRep
priority 1

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

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

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

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