458125d8cf4fa7b339c5f3cad7eda29611ad8007 hiram Thu Apr 14 18:11:02 2022 -0700 this hub.txt does NOT belong in the source tree no redmine diff --git src/hg/makeDb/doc/chm13v2.0/hub.txt src/hg/makeDb/doc/chm13v2.0/hub.txt deleted file mode 100644 index b61a0a0..0000000 --- src/hg/makeDb/doc/chm13v2.0/hub.txt +++ /dev/null @@ -1,616 +0,0 @@ -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 CP068269.2:145458455-145495201 -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 from NCBI Genbank Sequences -shortLabel Assembly -visibility hide -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 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 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 hide -type bigBed 6 + -colorByStrand 50,50,150 150,50,50 -maxWindowToDraw 10000000 -spectrum on -html html/GCA_009914755.4_T2T-CHM13v2.0.repeatMasker - 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- 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 hide -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 -shortLabel CpG Islands -longLabel CpG Islands (Islands < 300 Bases are Light Green) -group regulation -visibility hide -type bigBed 4 + -html html/GCA_009914755.4_T2T-CHM13v2.0.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_009914755.4_T2T-CHM13v2.0.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_009914755.4_T2T-CHM13v2.0.cpgIslandExtUnmasked.bb - -track windowMasker -shortLabel WM + SDust -longLabel Genomic Intervals Masked by WindowMasker + SDust -group varRep -visibility hide -type bigBed 3 -bigDataUrl bbi/GCA_009914755.4_T2T-CHM13v2.0.windowMasker.bb -html html/GCA_009914755.4_T2T-CHM13v2.0.windowMasker - -track xenoRefGene -shortLabel RefSeq mRNAs -longLabel RefSeq mRNAs mapped to this assembly -group rna -visibility hide -color 180,0,0 -type bigGenePred -bigDataUrl bbi/GCA_009914755.4_T2T-CHM13v2.0.xenoRefGene.bb -labelFields name,geneName,geneName2 -searchIndex name -searchTrix ixIxx/GCA_009914755.4_T2T-CHM13v2.0.xenoRefGene.ix -html html/GCA_009914755.4_T2T-CHM13v2.0.xenoRefGene - 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priority 8 - - track chainHg19 - subTrack GCA_009914755.4_T2T-CHM13v2.0ChainNetViewchain off - subGroups view=chain species=s002 clade=c00 - shortLabel hg19 Chain - longLabel hg19 (Feb. 2009) Chained Alignments - type bigChain hg19 - bigDataUrl bbi/GCA_009914755.4_T2T-CHM13v2.0.chainHg19.bb - linkDataUrl bbi/GCA_009914755.4_T2T-CHM13v2.0.chainHg19Link.bb - otherDb hg19 - html html/GCA_009914755.4_T2T-CHM13v2.0.chainNet - priority 9 - - track chainSynHg19 - subTrack GCA_009914755.4_T2T-CHM13v2.0ChainNetViewchain off - subGroups view=chain species=s002 clade=c00 - shortLabel hg19 synChain - longLabel hg19 (Feb. 2009) Syntenic Chained Alignments - type bigChain hg19 - bigDataUrl bbi/GCA_009914755.4_T2T-CHM13v2.0.chainSynHg19.bb - linkDataUrl bbi/GCA_009914755.4_T2T-CHM13v2.0.chainSynHg19Link.bb - otherDb hg19 - html html/GCA_009914755.4_T2T-CHM13v2.0.chainNet - priority 10 - - track chainRBestHg19 - subTrack GCA_009914755.4_T2T-CHM13v2.0ChainNetViewchain off - subGroups view=chain species=s002 clade=c00 - 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summary bbi/GCA_009914755.4_T2T-CHM13v2.0.GCA_021950905.1.rbestNet.summary.bb - speciesOrder GCA_021950905.1 - html html/GCA_009914755.4_T2T-CHM13v2.0.chainNet - priority 3 - - track liftOverNetGCA_021950905.1 - parent GCA_009914755.4_T2T-CHM13v2.0MafNetViewnet - subGroups view=net species=s000 clade=c00 - shortLabel HG002 pat liftOverNet - longLabel HG002 pat GCA_021950905.1_HG002.pat.cur.20211005 (2022-02-04) Lift Over Net Alignment - type bigMaf - bigDataUrl bbi/GCA_009914755.4_T2T-CHM13v2.0.GCA_021950905.1.liftOverNet.bb - summary bbi/GCA_009914755.4_T2T-CHM13v2.0.GCA_021950905.1.liftOverNet.summary.bb - speciesOrder GCA_021950905.1 - html html/GCA_009914755.4_T2T-CHM13v2.0.chainNet - priority 4 - - track netGCA_021951015.1 - parent GCA_009914755.4_T2T-CHM13v2.0MafNetViewnet - subGroups view=net species=s001 clade=c00 - shortLabel HG002 mat Net - longLabel HG002 mat GCA_021951015.1_HG002.mat.cur.20211005 (2022-02-04) Net Alignment - type bigMaf - bigDataUrl bbi/GCA_009914755.4_T2T-CHM13v2.0.GCA_021951015.1.net.bb - summary bbi/GCA_009914755.4_T2T-CHM13v2.0.GCA_021951015.1.net.summary.bb - speciesOrder GCA_021951015.1 - html html/GCA_009914755.4_T2T-CHM13v2.0.chainNet - priority 5 - - track synNetGCA_021951015.1 - parent GCA_009914755.4_T2T-CHM13v2.0MafNetViewnet - subGroups view=net species=s001 clade=c00 - shortLabel HG002 mat synNet - longLabel HG002 mat GCA_021951015.1_HG002.mat.cur.20211005 (2022-02-04) Syntenic Net Alignment - type bigMaf - bigDataUrl bbi/GCA_009914755.4_T2T-CHM13v2.0.GCA_021951015.1.synNet.bb - summary bbi/GCA_009914755.4_T2T-CHM13v2.0.GCA_021951015.1.synNet.summary.bb - speciesOrder GCA_021951015.1 - html html/GCA_009914755.4_T2T-CHM13v2.0.chainNet - priority 6 - - track rbestNetGCA_021951015.1 - parent GCA_009914755.4_T2T-CHM13v2.0MafNetViewnet - subGroups view=net species=s001 clade=c00 - shortLabel HG002 mat rbestNet - longLabel HG002 mat GCA_021951015.1_HG002.mat.cur.20211005 (2022-02-04) Reciprocal Best Net Alignment - type bigMaf - bigDataUrl bbi/GCA_009914755.4_T2T-CHM13v2.0.GCA_021951015.1.rbestNet.bb - summary bbi/GCA_009914755.4_T2T-CHM13v2.0.GCA_021951015.1.rbestNet.summary.bb - speciesOrder GCA_021951015.1 - html html/GCA_009914755.4_T2T-CHM13v2.0.chainNet - priority 7 - - track liftOverNetGCA_021951015.1 - parent GCA_009914755.4_T2T-CHM13v2.0MafNetViewnet - subGroups view=net species=s001 clade=c00 - shortLabel HG002 mat liftOverNet - longLabel HG002 mat GCA_021951015.1_HG002.mat.cur.20211005 (2022-02-04) Lift Over Net Alignment - type bigMaf - bigDataUrl bbi/GCA_009914755.4_T2T-CHM13v2.0.GCA_021951015.1.liftOverNet.bb - summary bbi/GCA_009914755.4_T2T-CHM13v2.0.GCA_021951015.1.liftOverNet.summary.bb - speciesOrder GCA_021951015.1 - html html/GCA_009914755.4_T2T-CHM13v2.0.chainNet - priority 8 - - track netHg19 - parent GCA_009914755.4_T2T-CHM13v2.0MafNetViewnet - subGroups view=net species=s002 clade=c00 - shortLabel hg19 Net - longLabel hg19 (Feb. 2009) Net Alignment - type bigMaf - bigDataUrl bbi/GCA_009914755.4_T2T-CHM13v2.0.hg19.net.bb - summary bbi/GCA_009914755.4_T2T-CHM13v2.0.hg19.net.summary.bb - speciesOrder hg19 - html html/GCA_009914755.4_T2T-CHM13v2.0.chainNet - priority 9 - - track synNetHg19 - parent GCA_009914755.4_T2T-CHM13v2.0MafNetViewnet - subGroups view=net species=s002 clade=c00 - shortLabel hg19 synNet - longLabel hg19 (Feb. 2009) Syntenic Net Alignment - type bigMaf - bigDataUrl bbi/GCA_009914755.4_T2T-CHM13v2.0.hg19.synNet.bb - summary bbi/GCA_009914755.4_T2T-CHM13v2.0.hg19.synNet.summary.bb - speciesOrder hg19 - html html/GCA_009914755.4_T2T-CHM13v2.0.chainNet - priority 10 - - track rbestNetHg19 - parent GCA_009914755.4_T2T-CHM13v2.0MafNetViewnet - subGroups view=net species=s002 clade=c00 - shortLabel hg19 rbestNet - longLabel hg19 (Feb. 2009) Reciprocal Best Net Alignment - type bigMaf - bigDataUrl bbi/GCA_009914755.4_T2T-CHM13v2.0.hg19.rbestNet.bb - summary bbi/GCA_009914755.4_T2T-CHM13v2.0.hg19.rbestNet.summary.bb - speciesOrder hg19 - html html/GCA_009914755.4_T2T-CHM13v2.0.chainNet - priority 11 - - track liftOverNetHg19 - parent GCA_009914755.4_T2T-CHM13v2.0MafNetViewnet - subGroups view=net species=s002 clade=c00 - shortLabel hg19 liftOverNet - longLabel hg19 (Feb. 2009) Lift Over Net Alignment - type bigMaf - bigDataUrl bbi/GCA_009914755.4_T2T-CHM13v2.0.hg19.liftOverNet.bb - summary bbi/GCA_009914755.4_T2T-CHM13v2.0.hg19.liftOverNet.summary.bb - speciesOrder hg19 - html html/GCA_009914755.4_T2T-CHM13v2.0.chainNet - priority 12 - - track netHg38 - parent GCA_009914755.4_T2T-CHM13v2.0MafNetViewnet - subGroups view=net species=s003 clade=c00 - shortLabel hg38 Net - longLabel hg38 (Dec. 2013) Net Alignment - type bigMaf - bigDataUrl bbi/GCA_009914755.4_T2T-CHM13v2.0.hg38.net.bb - summary bbi/GCA_009914755.4_T2T-CHM13v2.0.hg38.net.summary.bb - speciesOrder hg38 - html html/GCA_009914755.4_T2T-CHM13v2.0.chainNet - priority 13 - - track synNetHg38 - parent GCA_009914755.4_T2T-CHM13v2.0MafNetViewnet - subGroups view=net species=s003 clade=c00 - shortLabel hg38 synNet - longLabel hg38 (Dec. 2013) Syntenic Net Alignment - type bigMaf - bigDataUrl bbi/GCA_009914755.4_T2T-CHM13v2.0.hg38.synNet.bb - summary bbi/GCA_009914755.4_T2T-CHM13v2.0.hg38.synNet.summary.bb - speciesOrder hg38 - html html/GCA_009914755.4_T2T-CHM13v2.0.chainNet - priority 14 - - track rbestNetHg38 - parent GCA_009914755.4_T2T-CHM13v2.0MafNetViewnet - subGroups view=net species=s003 clade=c00 - shortLabel hg38 rbestNet - longLabel hg38 (Dec. 2013) Reciprocal Best Net Alignment - type bigMaf - bigDataUrl bbi/GCA_009914755.4_T2T-CHM13v2.0.hg38.rbestNet.bb - summary bbi/GCA_009914755.4_T2T-CHM13v2.0.hg38.rbestNet.summary.bb - speciesOrder hg38 - html html/GCA_009914755.4_T2T-CHM13v2.0.chainNet - priority 15 - - track liftOverNetHg38 - parent GCA_009914755.4_T2T-CHM13v2.0MafNetViewnet - subGroups view=net species=s003 clade=c00 - shortLabel hg38 liftOverNet - longLabel hg38 (Dec. 2013) Lift Over Net Alignment - type bigMaf - bigDataUrl bbi/GCA_009914755.4_T2T-CHM13v2.0.hg38.liftOverNet.bb - summary bbi/GCA_009914755.4_T2T-CHM13v2.0.hg38.liftOverNet.summary.bb - speciesOrder hg38 - html html/GCA_009914755.4_T2T-CHM13v2.0.chainNet - priority 16 - -include GCA_009914755.4.userTrackDb.txt