##
# cytoBands
##
track cytoBandIdeo
longLabel Chromosome ideogram with cytogenetic bands
shortLabel cytoBandIdeo
bigDataUrl cytobands/cytoBandIdeo.bigBed
type bigBed

##
# map
## 
track gc5Base
shortLabel GC Percent
longLabel GC Percent in 5-Base Windows
group map
visibility hide
autoScale Off
maxHeightPixels 128:36:16
graphTypeDefault Bar
gridDefault OFF
windowingFunction Mean
color 0,0,0
altColor 128,128,128
viewLimits 30:70
type bigWig 0 100
bigDataUrl gc5Base/gc5Base.bigWig
html gc5Base

include validation.trackDb.txt

##
# varRep
##
track rmsk
shortLabel RepeatMasker
longLabel Repeating Elements by RepeatMasker
group varRep
visibility hide
itemRgb on
maxItems 1000000
maxWindowToDraw 100000000
type bigBed 9 +
bigDataUrl rmsk/rmsk.bigBed
priority 1

track simpleRepeat
shortLabel Simple Repeats
longLabel Simple Tandem Repeats by TRF
group varRep
visibility hide
type bigBed 4 +
bigDataUrl trf/trf.bigBed
priority 2

track compositeRepeats
shortLabel Composite Repeats
longLabel  Composite Repeats
group varRep
visibility hide
maxItems 1000000
maxWindowToDraw 100000000
type bigBed 4
bigDataUrl compositeRepeats/compositeRepeats.bigBed
priority 3


include sedefSegDups.track.txt



##
# cenTelo
##
track cenSatAnnotation
shortLabel CenSat Annotation
longLabel Centromeric Satellite Annotation
group cenTelo
visibility hide
itemRgb on
maxItems 100000
type bigBed 9 +
bigDataUrl cenSat/cenSatAnnotation.bigBed
priority 2

track newSatellitesMonomersArrays
shortLabel New Satellites
longLabel New Satellites Monomers Arrays
group cenTelo
visibility hide
itemRgb on
maxItems 100000
type bigBed 4
bigDataUrl newSatellitesMonomersArrays/newSatellitesMonomersArrays.bigBed
priority 3

include as_annotation.trackDb.txt

##
# genes
##
include CAT_V4/trackDb.txt

track uwLiftoff
compositeTrack off
visibility hide
shortLabel LiftOff Genes
longLabel  LiftOff Genes Annotations based on GENCODE (from UW)
type bigGenePred
group genes
priority 800

    track uwLiftoffAll
    parent uwLiftoff on
    bigDataUrl uwLiftoff/chm13_v1.1_plus38Y.all.bb
    shortLabel LiftOff Genes (All)
    longLabel LiftOff Genes - all annotations (from UW)
    type bigGenePred
    group genes
    labelFields name, name2
    defaultLabelFields name
    searchIndex name,name2

    track uwLiftoffOrf
    parent uwLiftoff on
    bigDataUrl uwLiftoff/chm13_v1.1_plus38Y.orf_only.bb
    shortLabel LiftOff Genes (ORFs)
    longLabel LiftOff Genes V1 - annotations with ORFs (from UW)
    type bigGenePred
    group genes
    labelFields name, name2
    defaultLabelFields name
    searchIndex name,name2


track gencodeBlat
shortLabel GENCODE BLAT
longLabel BLAT of GENCODE RNAs
html gencodeBlat.html
group genes
type bigPsl
priority 15
color 0,0,100
canPack on
visibility hide
baseColorDefault diffCodons
baseColorUseCds given
baseColorUseSequence lfExtra
indelDoubleInsert on
indelQueryInsert on
showDiffBasesAllScales .
showDiffBasesMaxZoom 10000.0
showCdsAllScales .
showCdsMaxZoom 10000.0
labelFields name,geneSym,geneId,geneType
defaultLabelFields geneSym
labelSeparator " "
bigDataUrl gencodeBlat/gencodeBlat.bigBlatPsl
searchIndex name,geneSym,geneId


##
# comparative genomics
##
include cactus.trackDb.txt
include synteny.trackDb.txt
include grch38PriLastz.trackDb.txt

track chm13_uncovered_byGRCh38
shortLabel GRCH38 non-syntenic
longLabel GRCh38 non-syntenic
group compGeno
visibility hide
type bigBed 3
bigDataUrl grch38NonSyntenic/chm13_v1.1_uncoveredByGRCh38WinnowmapAlignments.bigBed
priority 50


##
# Expression/transcription/rna
##
include proseq.trackDb.txt
include rnaseq.trackDB.txt

##
# regulation
##
track cpgIsland
shortLabel CpG Islands
longLabel CpG Islands (Islands < 300 Bases are Light Green)
group regulation
visibility hide
color 0,100,0
altColor 128,228,128
type bigBed 4 +
priority 4
bigDataUrl cpgIsland/t2t-chm13-v1.1.cpgIslandExt.bb