b1cabf573dc930b78de2f4e5a369c68f7655d9ba hiram Mon Apr 11 15:36:26 2022 -0700 initial set of files for chm13v2.0 hub construction refs #29203 diff --git src/hg/makeDb/doc/chm13v2.0/hub.txt src/hg/makeDb/doc/chm13v2.0/hub.txt new file mode 100644 index 0000000..dd8f26c --- /dev/null +++ src/hg/makeDb/doc/chm13v2.0/hub.txt @@ -0,0 +1,618 @@ +hub GCA_009914755.4 genome assembly +shortLabel human T2T CHM13 v2.0 +longLabel human T2T CHM13 v2.0/Homo sapiens/GCA_009914755.4_T2T-CHM13v2.0 genome assembly +email hclawson@ucsc.edu +descriptionUrl html/GCA_009914755.4_T2T-CHM13v2.0.description.html +useOneFile on + +genome GCA_009914755.4 +taxId 9606 +groups groups.txt +description human T2T CHM13 v2.0 +twoBitPath GCA_009914755.4.2bit +twoBitBptUrl GCA_009914755.4.2bit.bpt +chromSizes GCA_009914755.4.chrom.sizes.txt +chromAlias GCA_009914755.4.chromAlias.txt +organism human T2T CHM13 v2.0 +defaultPos CP068269.2:145462284-145491793 +scientificName Homo sapiens +htmlPath html/GCA_009914755.4_T2T-CHM13v2.0.description.html +blat dynablat-01.soe.ucsc.edu 4040 dynamic GCA/009/914/755/GCA_009914755.4 +transBlat dynablat-01.soe.ucsc.edu 4040 dynamic GCA/009/914/755/GCA_009914755.4 +isPcr dynablat-01.soe.ucsc.edu 4040 dynamic GCA/009/914/755/GCA_009914755.4 +liftOver.GCA_021950905.1 liftOver/GCA_009914755.4ToGCA_021950905.1.over.chain.gz +liftOver.GCA_021951015.1 liftOver/GCA_009914755.4ToGCA_021951015.1.over.chain.gz +liftOver.hg19 liftOver/GCA_009914755.4ToHg19.over.chain.gz +liftOver.hg38 liftOver/GCA_009914755.4ToHg38.over.chain.gz + +track assembly +longLabel Assembly +shortLabel Assembly +visibility pack +colorByStrand 150,100,30 230,170,40 +color 150,100,30 +altColor 230,170,40 +bigDataUrl bbi/GCA_009914755.4_T2T-CHM13v2.0.assembly.bb +type bigBed 6 +html html/GCA_009914755.4_T2T-CHM13v2.0.assembly +searchIndex name +searchTrix ixIxx/GCA_009914755.4_T2T-CHM13v2.0.assembly.ix +url https://www.ncbi.nlm.nih.gov/nuccore/$$ +urlLabel NCBI Nucleotide database +group map + +track gc5Base +shortLabel GC Percent +longLabel GC Percent in 5-Base Windows +group map +visibility full +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_009914755.4_T2T-CHM13v2.0.gc5Base.bw +html html/GCA_009914755.4_T2T-CHM13v2.0.gc5Base + +track repeatMasker +compositeTrack on +shortLabel RepeatMasker +longLabel Repeating Elements by RepeatMasker +group varRep +visibility dense +type bigBed 6 + +colorByStrand 50,50,150 150,50,50 +maxWindowToDraw 10000000 +spectrum on +html html/GCA_009914755.4_T2T-CHM13v2.0.repeatMasker + + track repeatMaskerSINE + parent repeatMasker + shortLabel SINE + longLabel SINE Repeating Elements by RepeatMasker + type bigBed 6 + + priority 1 + bigDataUrl bbi/GCA_009914755.4_T2T-CHM13v2.0.rmsk.SINE.bb + + track repeatMaskerLINE + parent repeatMasker + shortLabel LINE + longLabel LINE Repeating Elements by RepeatMasker + type bigBed 6 + + priority 2 + bigDataUrl bbi/GCA_009914755.4_T2T-CHM13v2.0.rmsk.LINE.bb + + track repeatMaskerLTR + parent repeatMasker + shortLabel LTR + longLabel LTR Repeating Elements by RepeatMasker + type bigBed 6 + + priority 3 + bigDataUrl bbi/GCA_009914755.4_T2T-CHM13v2.0.rmsk.LTR.bb + + track repeatMaskerDNA + parent repeatMasker + shortLabel DNA + longLabel DNA Repeating Elements by RepeatMasker + type bigBed 6 + + priority 4 + bigDataUrl bbi/GCA_009914755.4_T2T-CHM13v2.0.rmsk.DNA.bb + + track repeatMaskerSimple + parent repeatMasker + shortLabel Simple + longLabel Simple Repeating Elements by RepeatMasker + type bigBed 6 + + priority 5 + bigDataUrl bbi/GCA_009914755.4_T2T-CHM13v2.0.rmsk.Simple.bb + + track repeatMaskerLowComplexity + parent repeatMasker + shortLabel Low Complexity + longLabel Low Complexity Repeating Elements by RepeatMasker + type bigBed 6 + + priority 6 + bigDataUrl bbi/GCA_009914755.4_T2T-CHM13v2.0.rmsk.Low_complexity.bb + + track repeatMaskerSatellite + parent repeatMasker + shortLabel Satellite + longLabel Satellite Repeating Elements by RepeatMasker + type bigBed 6 + + priority 7 + bigDataUrl bbi/GCA_009914755.4_T2T-CHM13v2.0.rmsk.Satellite.bb + + track repeatMaskerRNA + parent repeatMasker + shortLabel RNA + longLabel RNA Repeating Elements by RepeatMasker + type bigBed 6 + + priority 8 + bigDataUrl bbi/GCA_009914755.4_T2T-CHM13v2.0.rmsk.RNA.bb + + track repeatMaskerOther + parent repeatMasker + shortLabel Other + longLabel Other Repeating Elements by RepeatMasker + type bigBed 6 + + priority 9 + bigDataUrl bbi/GCA_009914755.4_T2T-CHM13v2.0.rmsk.Other.bb + +track simpleRepeat +shortLabel Simple Repeats +longLabel Simple Tandem Repeats by TRF +group varRep +visibility dense +type bigBed 4 + +bigDataUrl bbi/GCA_009914755.4_T2T-CHM13v2.0.simpleRepeat.bb +html html/GCA_009914755.4_T2T-CHM13v2.0.simpleRepeat + +track cpgIslands +compositeTrack on 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