df8c8dcd64bc7d71f9711df629b6d0178d6fa26f max Tue Feb 25 13:33:12 2020 -0800 trying to reduce the confusion in docs between refseq select and MANE, refs #24787 diff --git src/hg/makeDb/trackDb/refSeqComposite.ra src/hg/makeDb/trackDb/refSeqComposite.ra index 134f5c1..55c0213 100644 --- src/hg/makeDb/trackDb/refSeqComposite.ra +++ src/hg/makeDb/trackDb/refSeqComposite.ra @@ -1,219 +1,209 @@ track refSeqComposite compositeTrack on shortLabel NCBI RefSeq longLabel RefSeq gene predictions from NCBI group genes visibility pack type genePred dragAndDrop subTracks noInherit on #subGroup1 view Views aNcbiRefSeq=NCBI_RefSeq zUcscRefSeq=UCSC_RefSeq allButtonPair on dataVersion /gbdb/$D/ncbiRefSeq/ncbiRefSeqVersion.txt priority 2 dbPrefixUrls hg="http://www.genenames.org/cgi-bin/gene_symbol_report?hgnc_id=$$" dm="http://flybase.org/reports/$$" ce="http://www.wormbase.org/db/gene/gene?name=$$" rn="https://rgd.mcw.edu/rgdweb/search/search.html?term=$$" sacCer="https://www.yeastgenome.org/locus/$$" danRer="https://zfin.org/$$" mm="http://www.informatics.jax.org/marker/$$" xenTro="https://www.xenbase.org/gene/showgene.do?method=display&geneId=$$" dbPrefixLabels hg="HGNC" dm="FlyBase" ce="WormBase" rn="RGD" sacCer="SGD" danRer="ZFIN" mm="MGI" xenTro="XenBase" pennantIcon Updated red ../goldenPath/newsarch.html#020720b "updated Feb. 7, 2020" track ncbiRefSeq parent refSeqComposite off color 12,12,120 shortLabel RefSeq All longLabel NCBI RefSeq genes, curated and predicted (NM_*, XM_*, NR_*, XR_*, NP_*, YP_*) idXref ncbiRefSeqLink mrnaAcc name baseColorUseCds given baseColorDefault genomicCodons priority 1 track ncbiRefSeqCurated color 12,12,120 parent refSeqComposite on shortLabel RefSeq Curated longLabel NCBI RefSeq genes, curated subset (NM_*, NR_*, NP_* or YP_*) idXref ncbiRefSeqLink mrnaAcc name baseColorUseCds given baseColorDefault genomicCodons priority 2 track ncbiRefSeqPredicted color 12,12,120 parent refSeqComposite off shortLabel RefSeq Predicted longLabel NCBI RefSeq genes, predicted subset (XM_* or XR_*) idXref ncbiRefSeqLink mrnaAcc name baseColorUseCds given baseColorDefault genomicCodons priority 3 track ncbiRefSeqOther color 32,32,32 parent refSeqComposite off shortLabel RefSeq Other longLabel NCBI RefSeq Other Annotations (not NM_*, NR_*, XM_*, XR_*, NP_* or YP_*) priority 4 searchIndex name searchTrix /gbdb/$D/ncbiRefSeq/ncbiRefSeqOther.ix bigDataUrl /gbdb/$D/ncbiRefSeq/ncbiRefSeqOther.bb type bigBed 12 + labelFields gene skipEmptyFields on urls GeneID="https://www.ncbi.nlm.nih.gov/gene/$$" MIM="https://www.ncbi.nlm.nih.gov/omim/612091" HGNC="http://www.genenames.org/cgi-bin/gene_symbol_report?hgnc_id=$$" FlyBase="http://flybase.org/reports/$$" WormBase="http://www.wormbase.org/db/gene/gene?name=$$" RGD="https://rgd.mcw.edu/rgdweb/search/search.html?term=$$" SGD="https://www.yeastgenome.org/locus/$$" miRBase="http://www.mirbase.org/cgi-bin/mirna_entry.pl?acc=$$" ZFIN="https://zfin.org/$$" MGI="http://www.informatics.jax.org/marker/$$" track ncbiRefSeqPsl priority 5 parent refSeqComposite off shortLabel RefSeq Alignments longLabel RefSeq Alignments of RNAs type psl indelDoubleInsert on indelQueryInsert on showDiffBasesAllScales . showDiffBasesMaxZoom 10000.0 showCdsMaxZoom 10000.0 showCdsAllScales . baseColorDefault diffCodons pslSequence no baseColorUseSequence extFile seqNcbiRefSeq extNcbiRefSeq baseColorUseCds table ncbiRefSeqCds idXref ncbiRefSeqLink mrnaAcc name color 0,0,0 pepTable ncbiRefSeqPepTable track ncbiRefSeqGenomicDiff parent refSeqComposite off priority 6 type bigBed 9 + skipEmptyFields on shortLabel RefSeq Diffs longLabel Differences between NCBI RefSeq Transcripts and the Reference Genome bigDataUrl /gbdb/$D/ncbiRefSeq/ncbiRefSeqGenomicDiff.bb itemRgb on - track ncbiRefSeqSelect + track refGene override parent refSeqComposite off + shortLabel UCSC RefSeq + longLabel UCSC annotations of RefSeq RNAs (NM_* and NR_*) + color 12,12,120 + type genePred refPep refMrna + idXref hgFixed.refLink mrnaAcc name + dataVersion priority 7 - type genePred - shortLabel RefSeq Select/MANE - longLabel NCBI RefSeq Select/MANE: One representative transcript per protein-coding gene - trackHandler ncbiRefSeq - idXref ncbiRefSeqLink mrnaAcc name - color 20,20,160 baseColorUseCds given baseColorDefault genomicCodons - track ncbiRefSeqHgmd + track ncbiRefSeqSelect parent refSeqComposite off - priority 7 + priority 8 type genePred - shortLabel RefSeq HGMD - longLabel NCBI RefSeq curated and annotated by HGMD, usually one per clinically relevant gene + shortLabel RefSeq Select+MANE + longLabel NCBI RefSeq Select+MANE subset: one representative transcript per protein-coding gene trackHandler ncbiRefSeq idXref ncbiRefSeqLink mrnaAcc name color 20,20,160 baseColorUseCds given baseColorDefault genomicCodons - track ncbiRefSeqMane + track ncbiRefSeqHgmd parent refSeqComposite off - priority 8 + priority 9 type genePred - shortLabel RefSeq MANE - longLabel RefSeq selected representative transcript for each gene, MANE 0.5 + shortLabel RefSeq HGMD + longLabel NCBI RefSeq HGMD subset: transcripts with clinical variants in HGMD trackHandler ncbiRefSeq - baseColorUseCds given - baseColorDefault genomicCodons - - track refGene override - parent refSeqComposite off - shortLabel UCSC RefSeq - longLabel UCSC annotations of RefSeq RNAs (NM_* and NR_*) - color 12,12,120 - type genePred refPep refMrna - idXref hgFixed.refLink mrnaAcc name - dataVersion - priority 9 + idXref ncbiRefSeqLink mrnaAcc name + color 20,20,160 baseColorUseCds given baseColorDefault genomicCodons searchName ncbiRefSeqCuratedName2 searchTable ncbiRefSeqCurated searchMethod prefix query select chrom, txStart,txEnd, name from %s where name2 like '%s%%' searchPriority 1.07200 searchName ncbiRefSeqPredictedName2 searchTable ncbiRefSeqPredicted searchMethod prefix query select chrom, txStart,txEnd, name from %s where name2 like '%s%%' searchPriority 1.07201 searchName ncbiRefSeqCuratedProtAcc searchTable ncbiRefSeqCurated searchType genePred searchMethod prefix xrefTable ncbiRefSeqLink xrefQuery select id,protAcc from %s where protAcc like '%s%%' termRegex [NY]P_[0-9]+(\.[0-9]+)? dontCheck XP_[0-9]+(\.[0-9]+)? searchPriority 2.07201 searchName ncbiRefSeqPredictedProtAcc searchTable ncbiRefSeqPredicted searchType genePred searchMethod prefix xrefTable ncbiRefSeqLink xrefQuery select id,protAcc from %s where protAcc like '%s%%' termRegex XP_[0-9]+(\.[0-9]+)? dontCheck [NY]P_[0-9]+(\.[0-9]+)? searchPriority 2.07203 searchName ncbiRefSeqCuratedProduct searchTable ncbiRefSeqCurated searchType genePred searchMethod fuzzy xrefTable ncbiRefSeqLink xrefQuery select id,product from %s where product like '%%%s%%' searchPriority 2.07201 searchName ncbiRefSeqPredictedProduct searchTable ncbiRefSeqPredicted searchType genePred searchMethod fuzzy xrefTable ncbiRefSeqLink xrefQuery select id,product from %s where product like '%%%s%%' searchPriority 2.07203 searchTable ncbiRefSeqCurated searchMethod exact searchType genePred semiShortCircuit 1 termRegex [NY][MRP]_[0-9]{6}[0-9]*\.[0-9]+ searchPriority 2.07202 searchName ncbiRefSeqCuratedNoVersion searchTable ncbiRefSeqCurated query select chrom,txStart,txEnd,name from %s where name like '%s.%%' semiShortCircuit 1 termRegex [NY][MRP]_[0-9]{6}[0-9]* dontCheck [NY][MRP]_[0-9]{6}[0-9]*\.[0-9]+ searchPriority 2.07202 searchTable ncbiRefSeqPredicted searchMethod exact searchType genePred semiShortCircuit 1 termRegex X[MR]_[0-9]{6}[0-9]*\.[0-9]+ searchPriority 2.07204 searchName ncbiRefSeqPredictedNoVersion searchTable ncbiRefSeqPredicted query select chrom,txStart,txEnd,name from %s where name like '%s.%%' semiShortCircuit 1 termRegex X[MR]_[0-9]{6}[0-9]* dontCheck X[MR]_[0-9]{6}[0-9]*\.[0-9]+ searchPriority 2.07204 searchTable ncbiRefSeqOther searchPriority 2.07207 searchType bigBed