track hubCentral
compositeTrack on
shortLabel my hub
longLabel my hub
group comphub
subGroup1 view Track_Type Snake=Alignments  
subGroup2 orgs Organisms Anc0=Anc0 Pleuco=Pleuco mouse=mouse rn5=rn5 hg38=hg38
dragAndDrop subTracks
#allButtonPair on
dimensions dimensionX=view dimensionY=orgs
noInherit on
priority 0
centerLabelsDense on
visibility full
html ../documentation/hubCentral
type bigBed 3

	track hubCentralAlignments
	shortLabel Alignments
	view Alignments
	visibility full
	subTrack hubCentral

		track snakeAnc0
		longLabel Anc0
		shortLabel Anc0
		otherSpecies Anc0
		visibility full
		parent hubCentralAlignments
		showSnpWidth 2898
		priority 2
		bigDataUrl ../lod.txt
		type halSnake
		group snake
		subGroups view=Snake orgs=Anc0

		track snakemouse
		longLabel mouse
		shortLabel mouse
		otherSpecies mouse
		visibility full
		parent hubCentralAlignments
		showSnpWidth 2898
		priority 4
		bigDataUrl ../lod.txt
		type halSnake
		group snake
		subGroups view=Snake orgs=mouse

		track snakern5
		longLabel rn5
		shortLabel rn5
		otherSpecies rn5
		visibility full
		parent hubCentralAlignments
		showSnpWidth 2898
		priority 5
		bigDataUrl ../lod.txt
		type halSnake
		group snake
		subGroups view=Snake orgs=rn5

		track snakehg38
		longLabel hg38
		shortLabel hg38
		otherSpecies hg38
		visibility hide
		parent hubCentralAlignments off
		showSnpWidth 2898
		priority 6
		bigDataUrl ../lod.txt
		type halSnake
		group snake
		subGroups view=Snake orgs=hg38

track repeatMasker_
compositeTrack on
shortLabel RepeatMasker
longLabel Repeating Elements by RepeatMasker
group varRep
priority 149.1
visibility dense
type bed 3 .
noInherit on
html ../trackDescriptions/repeatMasker

    track repeatMaskerSINE_
    parent repeatMasker_
    shortLabel SINE
    longLabel SINE Repeating Elements by RepeatMasker
    priority 1
    spectrum on
    maxWindowToDraw 10000000
    colorByStrand 50,50,150 150,50,50
    type bigBed 6 +
    bigDataUrl RepeatMasker/peromyscus_assembly_scaffolds.rmsk.SINE.bb

    track repeatMaskerLINE_
    parent repeatMasker_
    shortLabel LINE
    longLabel LINE Repeating Elements by RepeatMasker
    priority 2
    spectrum on
    maxWindowToDraw 10000000
    colorByStrand 50,50,150 150,50,50
    type bigBed 6 +
    bigDataUrl RepeatMasker/peromyscus_assembly_scaffolds.rmsk.LINE.bb

    track repeatMaskerLTR_
    parent repeatMasker_
    shortLabel LTR
    longLabel LTR Repeating Elements by RepeatMasker
    priority 3
    spectrum on
    maxWindowToDraw 10000000
    colorByStrand 50,50,150 150,50,50
    type bigBed 6 +
    bigDataUrl RepeatMasker/peromyscus_assembly_scaffolds.rmsk.LTR.bb

    track repeatMaskerDNA_
    parent repeatMasker_
    shortLabel DNA
    longLabel DNA Repeating Elements by RepeatMasker
    priority 4
    spectrum on
    maxWindowToDraw 10000000
    colorByStrand 50,50,150 150,50,50
    type bigBed 6 +
    bigDataUrl RepeatMasker/peromyscus_assembly_scaffolds.rmsk.DNA.bb

    track repeatMaskerSimple_
    parent repeatMasker_
    shortLabel Simple
    longLabel Simple Repeating Elements by RepeatMasker
    priority 5
    spectrum on
    maxWindowToDraw 10000000
    colorByStrand 50,50,150 150,50,50
    type bigBed 6 +
    bigDataUrl RepeatMasker/peromyscus_assembly_scaffolds.rmsk.Simple.bb

    track repeatMaskerLowComplexity_
    parent repeatMasker_
    shortLabel Low Complexity
    longLabel Low Complexity Repeating Elements by RepeatMasker
    priority 6
    spectrum on
    maxWindowToDraw 10000000
    colorByStrand 50,50,150 150,50,50
    type bigBed 6 +
    bigDataUrl RepeatMasker/peromyscus_assembly_scaffolds.rmsk.Low_complexity.bb

    track repeatMaskerSatellite_
    parent repeatMasker_
    shortLabel Satellite
    longLabel Satellite Repeating Elements by RepeatMasker
    priority 7
    spectrum on
    maxWindowToDraw 10000000
    colorByStrand 50,50,150 150,50,50
    type bigBed 6 +
    bigDataUrl RepeatMasker/peromyscus_assembly_scaffolds.rmsk.Satellite.bb

    track repeatMaskerUnknown_
    parent repeatMasker_
    shortLabel RNA
    longLabel RNA Repeating Elements by RepeatMasker
    priority 8
    spectrum on
    maxWindowToDraw 10000000
    colorByStrand 50,50,150 150,50,50
    type bigBed 6 +
    bigDataUrl RepeatMasker/peromyscus_assembly_scaffolds.rmsk.Unknown.bb


track genes_
compositeTrack on
shortLabel Genes
longLabel Genes and Gene liftovers
group genes
priority 149.1
visibility dense
type bed 3 .
noInherit on
html ../trackDescriptions/genes

    track genesh38_
    parent genes_
    shortLabel h38
    longLabel human to P. leucopus
    priority 5
    spectrum on
    maxWindowToDraw 10000000
    colorByStrand 50,50,150 150,50,50
    type bigBed 12 +
    searchIndex name
    bigDataUrl Genes/h38_2_Pleuco_genes.bigBed

    track genesm38_
    parent genes_
    shortLabel m38
    longLabel mouse to P. leucopus
    priority 6
    spectrum on
    maxWindowToDraw 10000000
    colorByStrand 50,50,150 150,50,50
    type bigBed 12 +
    bigDataUrl Genes/m38_2_Pleuco_genes.bigBed

    track genesrn5_
    parent genes_
    shortLabel rn5
    longLabel rat to P. leucopus
    priority 7
    spectrum on
    maxWindowToDraw 10000000
    colorByStrand 50,50,150 150,50,50
    type bigBed 12 +
    bigDataUrl Genes/rn5_2_Pleuco_genes.bigBed

    track genesPleuco_
    parent genes_
    shortLabel Pleuco
    longLabel P. leucopus Augustus annotation
    priority 1
    spectrum on
    maxWindowToDraw 10000000
    colorByStrand 50,50,150 150,50,50
    type bigBed 12 +
    searchIndex name
    bigDataUrl Genes/Pleuco_genes.bigBed

    track genesh38Exonerate_
    parent genes_
    shortLabel h38Exonerate
    longLabel human proteins to P leucopus using exonerate
    priority 3
    spectrum on
    maxWindowToDraw 10000000
    colorByStrand 50,50,150 150,50,50
    type bigBed 12 +
    searchIndex name
    bigDataUrl Genes/exonerate.hum2Pleuc.bigBed
    searchTrix Genes/exonerate.hum2Pleuc.search.ix
    labelFields name2

    track genesmusExonerate_
    parent genes_
    shortLabel mouseExonerate
    longLabel mouse uniprot-AUP000000589 proteins to P leucopus using exonerate
    priority 4
    spectrum on
    maxWindowToDraw 10000000
    colorByStrand 50,50,150 150,50,50
    type bigBed 12 +
    searchIndex name
    bigDataUrl Genes/exonerate.mus2Pleuc.bigBed

    track genesPleucostraw_
    parent genes_
    shortLabel PleucoStrawberry
    longLabel P. leucopus gene predictions from RNAseq, hisat2, strawberry
    priority 2 
    spectrum on
    maxWindowToDraw 10000000
    colorByStrand 50,50,150 150,50,50
    type bigBed 12 +
    searchIndex name
    bigDataUrl Genes/Pleuc.strawberry.bigBed

    track Pero_0.1_gene_annotation_
    parent genes_
    shortLabel Pero_0.1
    longLabel P leucopus reference gene annotation from Genbank 0.1
    priority 3
    spectrum on
    maxWindowToDraw 10000000
    colorByStrand 50,50,150 150,50,50
    type bigBed 12 +
    searchIndex name
    bigDataUrl Genes/ref_Pero_0.1.bigBed
    searchTrix Genes/ref_Pero_0.1.search.ix
    labelFields name2


track alignability
bigDataUrl Pleuco.alignability.bw
shortLabel Alignability
longLabel Alignability from Progressive Cactus
type bigWig

track Variation
compositeTrack on
shortLabel Variation
longLabel SNPs, INDELs, CNVs in P. leucopus
priority 0
centerLabelsDense on
type vcfTabix
html ../documentation/hubCentral

	track CNVs
	parent Variation on
	priority 1
	bigDataUrl Variation/CNV.vcf.gz
	shortLabel exonic P. leucopus CNVs
	longLabel exonic CNVs identified in three high coverage samples
	visibility dense 
	type vcfTabix

	track High_SNPs
	parent Variation on
	priority 2
	bigDataUrl Variation/High_hE.vcf.gz
	shortLabel P. leucopus High Effect
	longLabel High Effect SNPs identified from human exonerate gene model
	visibility dense
	type vcfTabix

	track Moderate_SNPs
	parent Variation on
	priority 3
	bigDataUrl Variation/Moderate_hE.vcf.gz
	shortLabel P. leucopus Moderate Effect
	longLabel Moderate Effect SNPs identified from human exonerate gene model
	visibility dense
	type vcfTabix

	track Low_SNPs
	parent Variation on
	priority 4
	bigDataUrl Variation/Low_hE.vcf.gz
	shortLabel P. leucopus Low Effect
	longLabel Low Effect SNPs identified from human exonerate gene model
	visibility dense
	type vcfTabix


	track Other_SNPs
	parent Variation on
	priority 5
	bigDataUrl Variation/AllOthers_hE.vcf.gz
	shortLabel P. leucopus Other SNPs
	longLabel "Modifier" [/ All Other] SNPs identified from human exonerate gene model
	visibility dense
	type vcfTabix

track brain
bigDataUrl RNAseq/brain_20036.bw
shortLabel Brain
longLabel Brain_20036
type bigWig

track decidua
bigDataUrl RNAseq/decidua_20603.bw
shortLabel Decidua
longLabel Decidua_20603
type bigWig

track embryo
bigDataUrl RNAseq/embryo.bw
shortLabel Embryo
longLabel Embryo
type bigWig

track gravid_uterus
bigDataUrl RNAseq/gravid_uterus_20603.bw
shortLabel Gravid_uterus
longLabel Gravid_uterus_20603
type bigWig

track heart
bigDataUrl RNAseq/heart_20348.bw
shortLabel Heart
longLabel Heart_20348
type bigWig

track kidney
bigDataUrl RNAseq/kidney_20348.bw
shortLabel Kidney
longLabel Kidney_20348
type bigWig

track liver
bigDataUrl RNAseq/liver_20351.bw
shortLabel Liver
longLabel Liver_20351
type bigWig

track lung
bigDataUrl RNAseq/lung_20348.bw
shortLabel Lung
longLabel Lung_20348
type bigWig

track neonate4
bigDataUrl RNAseq/neonate4.bw
shortLabel Neonate4
longLabel Neonate4
type bigWig

track neonateC
bigDataUrl RNAseq/neonateC.bw
shortLabel NeonateC
longLabel NeonateC
type bigWig

track ovaries_uterus
bigDataUrl RNAseq/ovaries_uterus_19998.bw
shortLabel Ovary_uterus
longLabel Ovaries_uterus_19998
type bigWig

track spleen
bigDataUrl RNAseq/spleen_20348.bw
shortLabel Speen
longLabel Spleen_20348
type bigWig

track testes
bigDataUrl RNAseq/testes_20036.bw
shortLabel Testes
longLabel Testes_20036
type bigWig