hub GCA_004024885.1 genome assembly
shortLabel tamarin
longLabel tamarin/Saguinus imperator/GCA_004024885.1_SagImp_v1_BIUU genome assembly
useOneFile on
email hclawson@ucsc.edu
descriptionUrl html/GCA_004024885.1_SagImp_v1_BIUU.description.html

genome GCA_004024885.1
taxId 9491
groups groups.txt
description tamarin
twoBitPath GCA_004024885.1.2bit
twoBitBptUrl GCA_004024885.1.2bit.bpt
chromSizes GCA_004024885.1.chrom.sizes.txt
chromAliasBb GCA_004024885.1.chromAlias.bb
organism SagImp_v1_BIUU Jan. 2019
defaultPos PVHO010000001.1:341312-351312
scientificName Saguinus imperator
htmlPath html/GCA_004024885.1_SagImp_v1_BIUU.description.html
blat dynablat-01.soe.ucsc.edu 4040 dynamic GCA/004/024/885/GCA_004024885.1
transBlat dynablat-01.soe.ucsc.edu 4040 dynamic GCA/004/024/885/GCA_004024885.1
isPcr dynablat-01.soe.ucsc.edu 4040 dynamic GCA/004/024/885/GCA_004024885.1
liftOver.GCA_011100555.2 liftOver/GCA_004024885.1ToGCA_011100555.2.over.chain.gz

track assembly
longLabel Assembly
shortLabel Assembly
visibility hide
colorByStrand 150,100,30 230,170,40
color 150,100,30
altColor 230,170,40
bigDataUrl bbi/GCA_004024885.1_SagImp_v1_BIUU.assembly.bb
type bigBed 6
html html/GCA_004024885.1_SagImp_v1_BIUU.assembly
searchIndex name
url https://www.ncbi.nlm.nih.gov/nuccore/$$
urlLabel NCBI Nucleotide database:
group map

track gap
longLabel AGP gap
shortLabel Gap (AGP defined)
visibility hide
color 0,0,0
bigDataUrl bbi/GCA_004024885.1_SagImp_v1_BIUU.gap.bb
type bigBed 4
group map
html html/GCA_004024885.1_SagImp_v1_BIUU.gap

track cytoBandIdeo
shortLabel Chromosome Band (Ideogram)
longLabel Ideogram for Orientation
group map
visibility dense
type bigBed 4 +
bigDataUrl bbi/GCA_004024885.1_SagImp_v1_BIUU.cytoBand.bb

track gc5Base
shortLabel GC Percent
longLabel GC Percent in 5-Base Windows
group map
visibility dense
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 bbi/GCA_004024885.1_SagImp_v1_BIUU.gc5Base.bw
html html/GCA_004024885.1_SagImp_v1_BIUU.gc5Base

track tanDups
shortLabel Tandem Dups
longLabel Paired identical sequences
compositeTrack on
visibility hide
type bigBed 12
group map
html html/GCA_004024885.1_SagImp_v1_BIUU.tanDups

    track gapOverlap
    parent tanDups on
    shortLabel Gap Overlaps
    longLabel Paired exactly identical sequence on each side of a gap
    bigDataUrl bbi/GCA_004024885.1_SagImp_v1_BIUU.gapOverlap.bb
    type bigBed 12

track repeatMasker
shortLabel RepeatMasker
longLabel RepeatMasker Repetitive Elements
type bigRmsk 9 +
visibility pack
group varRep
bigDataUrl bbi/GCA_004024885.1_SagImp_v1_BIUU.rmsk.bb
maxWindowToDraw 5000000
html html/GCA_004024885.1_SagImp_v1_BIUU.repeatMasker

track simpleRepeat
shortLabel Simple Repeats
longLabel Simple Tandem Repeats by TRF
group varRep
visibility dense
type bigBed 4 +
bigDataUrl bbi/GCA_004024885.1_SagImp_v1_BIUU.simpleRepeat.bb
html html/GCA_004024885.1_SagImp_v1_BIUU.simpleRepeat

track cpgIslands
compositeTrack on
shortLabel CpG Islands
longLabel CpG Islands (Islands < 300 Bases are Light Green)
group regulation
visibility dense
type bigBed 4 +
html html/GCA_004024885.1_SagImp_v1_BIUU.cpgIslands

    track cpgIslandExt
    parent cpgIslands off
    shortLabel CpG Islands
    longLabel CpG Islands (Islands < 300 Bases are Light Green)
    type bigBed 4 +
    priority 1
    bigDataUrl bbi/GCA_004024885.1_SagImp_v1_BIUU.cpgIslandExt.bb

    track cpgIslandExtUnmasked
    parent cpgIslands on
    shortLabel Unmasked CpG
    longLabel CpG Islands on All Sequence (Islands < 300 Bases are Light Green)
    type bigBed 4 +
    priority 2
    bigDataUrl bbi/GCA_004024885.1_SagImp_v1_BIUU.cpgIslandExtUnmasked.bb

track windowMasker
shortLabel WM + SDust
longLabel Genomic Intervals Masked by WindowMasker + SDust
group varRep
visibility dense
type bigBed 3
bigDataUrl bbi/GCA_004024885.1_SagImp_v1_BIUU.windowMasker.bb
html html/GCA_004024885.1_SagImp_v1_BIUU.windowMasker

track allGaps
shortLabel All Gaps
longLabel All gaps of unknown nucleotides (N's), including AGP annotated gaps
group map
visibility hide
type bigBed 3
bigDataUrl bbi/GCA_004024885.1_SagImp_v1_BIUU.allGaps.bb
html html/GCA_004024885.1_SagImp_v1_BIUU.allGaps

track augustus
shortLabel Augustus
longLabel Augustus Gene Predictions
group genes
visibility pack
color 180,0,0
type bigGenePred
bigDataUrl bbi/GCA_004024885.1_SagImp_v1_BIUU.augustus.bb
html html/GCA_004024885.1_SagImp_v1_BIUU.augustus

track xenoRefGene
shortLabel RefSeq mRNAs
longLabel RefSeq mRNAs mapped to this assembly
group rna
visibility pack
color 180,0,0
type bigGenePred
bigDataUrl bbi/GCA_004024885.1_SagImp_v1_BIUU.xenoRefGene.bb
url https://www.ncbi.nlm.nih.gov/nuccore/$$
urlLabel NCBI Nucleotide database:
labelFields name,geneName,geneName2
defaultLabelFields geneName
searchIndex name
searchTrix ixIxx/GCA_004024885.1_SagImp_v1_BIUU.xenoRefGene.ix
html html/GCA_004024885.1_SagImp_v1_BIUU.xenoRefGene

##############################################################################
# GCA_011100555.2 - tamarin - Saguinus imperator - taxId: 9491
##############################################################################
track chainNetGCA_011100555.2
compositeTrack on
shortLabel tamarin Chain/Net
longLabel tamarin (2019-01-15), Chain and Net Alignments
subGroup1 view Views chain=Chain net=Net
dragAndDrop subTracks
visibility hide
group compGeno
priority 100.1
color 0,0,0
altColor 100,50,0
type bed 3
sortOrder view=+
otherDb GCA_011100555.2
html html/GCA_004024885.1_SagImp_v1_BIUU.chainNet

    track chainNetGCA_011100555.2Viewchain
    shortLabel Chain
    view chain
    visibility pack
    parent chainNetGCA_011100555.2
    spectrum on

        track chainGCA_011100555.2
        parent chainNetGCA_011100555.2Viewchain
        subGroups view=chain
        shortLabel tamarin Chain
        longLabel tamarin (2019-01-15) Chained Alignments
        type bigChain GCA_011100555.2
        bigDataUrl bbi/GCA_004024885.1_SagImp_v1_BIUU.chainGCA_011100555.2.bb
        linkDataUrl bbi/GCA_004024885.1_SagImp_v1_BIUU.chainGCA_011100555.2Link.bb
        priority 1

        track chainSynGCA_011100555.2
        parent chainNetGCA_011100555.2Viewchain
        subGroups view=chain
        shortLabel tamarin synChain
        longLabel tamarin (2019-01-15) Syntenic Chained Alignments
        type bigChain GCA_011100555.2
        bigDataUrl bbi/GCA_004024885.1_SagImp_v1_BIUU.chainSynGCA_011100555.2.bb
        linkDataUrl bbi/GCA_004024885.1_SagImp_v1_BIUU.chainSynGCA_011100555.2Link.bb
        priority 2

        track chainLiftOverGCA_011100555.2
        parent chainNetGCA_011100555.2Viewchain
        subGroups view=chain
        shortLabel tamarin loChain
        longLabel tamarin (2019-01-15) Lift Over Chained Alignments
        type bigChain GCA_011100555.2
        bigDataUrl bbi/GCA_004024885.1_SagImp_v1_BIUU.chainLiftOverGCA_011100555.2.bb
        linkDataUrl bbi/GCA_004024885.1_SagImp_v1_BIUU.chainLiftOverGCA_011100555.2Link.bb
        priority 3

    track mafNetGCA_011100555.2Viewnet
    shortLabel Net
    view net
    visibility full
    parent chainNetGCA_011100555.2

        track netGCA_011100555.2
        parent mafNetGCA_011100555.2Viewnet
        subGroups view=net
        shortLabel tamarin net
        longLabel tamarin (2019-01-15) Net Alignment
        type bigMaf
        bigDataUrl bbi/GCA_004024885.1_SagImp_v1_BIUU.GCA_011100555.2.net.bb
        summary bbi/GCA_004024885.1_SagImp_v1_BIUU.GCA_011100555.2.net.summary.bb
        speciesOrder GCA_011100555.2
        priority 4

track HLTOGAannotvHg38v1
bigDataUrl bbi/HLTOGAannotVsHg38v1.bb
shortLabel TOGA vs. hg38
longLabel TOGA annotations using human/hg38 as reference
group genes
visibility pack
itemRgb on
type bigBed 12
searchIndex name
searchTrix  ixIxx/HLTOGAannotVsHg38v1.ix
html html/TOGAannotation