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

track Punto_Rojo_cs10genes
bigDataUrl bbi/cs10.genes.bb
shortLabel Genes from cs10
longLabel cs10 RefSeq gene models lifted onto Punto_Rojo through the cs10 chain (not its own annotation)
type bigBed 12
visibility pack
group genes

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

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

track Punto_Rojo_gc
bigDataUrl bbi/Punto_Rojo.gc.bw
shortLabel GC Percent
longLabel GC percent of Punto_Rojo 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 Punto_Rojo
group varRep

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

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

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

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