track orfs
shortLabel Consensus Annotations
longLabel	Dfam/RepeatMasker Annotations 
group annotate
visibility dense
color 30,30,0
type bigBed 6
priority 2
bigDataUrl orfs.bb

track repNames
shortLabel Consensus Sequence
longLabel Repeat Browser Consensus
group annotate
visibility full
color 0,0,0
type bigBed 12 +
priority 1
bigDataUrl build.bb
searchIndex name
searchTrix repNames.ix
url	https://hgwdev.gi.ucsc.edu/~max/kznf/hg38reps/fig/hist/$$.png
urlLabel Length Distributions
urls rbName="https://hgwdev.gi.ucsc.edu/~max/kznf/hg38reps/fig/hist/$$.png" dfamName="https://dfam.org/browse?name_accession=$$" 
dataVersion hg38reps Version

track GENCODEv32_cds
shortLabel GENCODEv32 CDS
longLabel GENCODEv32 CDS exons
group annotate
visibility dense
color 0,100,0
type bigBed 8 +
priority 3
bigDataUrl gencode_cds.bb 
#url http://public.gi.ucsc.edu/~jferna10/rep/repeats2/html/$$.html
#urlLabel Link to Consensus Alignment

track GENCODEv32_ncRNA
shortLabel GENCODEv32 ncRNA
longLabel GENCODEv32 ncRNA exons
group annotate
visibility hide
color 0,100,100
type bigBed 8 +
priority 3
bigDataUrl gencode_ncRNA.bb
urls coords="https://genome.ucsc.edu/cgi-bin/hgTracks?db=hg38&position=$$"

track GENCODEv32_UTR
shortLabel GENCODEv32 UTRs
longLabel GENCODEv32 UTR exons
group annotate
visibility dense
color 0,100,0
type bigBed 8 +
priority 3
bigDataUrl gencode_utr.bb
#url http://public.gi.ucsc.edu/~jferna10/rep/repeats2/html/$$.html
#urlLabel Link to Consensus Alignment

track Tandem_Repeats
shortLabel Tandem Repeats
longLabel Tandem Repeats
group annotate
visibility dense
color 0,0,0
type bigBed 4 +
priority 4
bigDataUrl trf.bb

track Consensus_Alignments
shortLabel Self Alignments
longLabel Alignments of Other Repeat Browser Consensuses 
group annotate
visibility hide
color 0,0,0
type bigPsl
priority 5
bigDataUrl other_cons_aln.bb

track Mapping_Coverage
shortLabel Mapping Coverage (hg38)
longLabel Coverage Plot of All hg38 Instances to the Consensus 
group lift
visibility hide
color 0,0,0
type bigWig
priority 1
bigDataUrl liftOverCoverage.bw

track Mapping_Instances
shortLabel Instances Mappings (hg38)
longLabel Mappings of Random (500 or less) Genomic Instances to the Consensus 
group lift
visibility hide
color 0,0,0
type bigPsl
priority 1
bigDataUrl mappings_500.bb

include trackDb.schmittges2016.txt
include trackDb.imbeault2017.txt
include trackDb.primates.txt
include trackDb.tsankov2014.txt
include trackDb.theunissen2016.txt
include trackDb.uw_histone.txt
include trackDb.meta.txt
include trackDb.dnase.txt
include trackDb.encTFBSclustered.txt