562929f81d9d89531be4f778e221fe3a350a5f68 braney Fri Jan 10 12:33:44 2020 -0800 temporarily disable MGC track diff --git src/hg/makeDb/trackDb/trackDb.genbank.ra src/hg/makeDb/trackDb/trackDb.genbank.ra index b6a2129..54a9fc9 100644 --- src/hg/makeDb/trackDb/trackDb.genbank.ra +++ src/hg/makeDb/trackDb/trackDb.genbank.ra @@ -1,211 +1,211 @@ # # Genbank tracks # track refGene shortLabel RefSeq Genes longLabel RefSeq Genes group genes visibility dense color 12,12,120 type genePred refPep refMrna idXref hgFixed.refLink mrnaAcc name baseColorUseCds given priority 2 track mrna table all_mrna shortLabel $Organism mRNAs longLabel $Organism mRNAs from GenBank group rna visibility pack type psl . baseColorUseCds genbank baseColorUseSequence genbank baseColorDefault diffCodons showDiffBasesAllScales . indelDoubleInsert on indelQueryInsert on indelPolyA on priority 1 track tightMrna shortLabel Tight mRNAS longLabel Tightly Filtered $Organism mRNAs from GenBank group rna visibility hide spectrum on type psl . baseColorUseCds genbank baseColorUseSequence genbank baseColorDefault diffCodons showDiffBasesAllScales . indelDoubleInsert on indelQueryInsert on indelPolyA on track intronEst shortLabel Spliced ESTs longLabel $Organism ESTs That Have Been Spliced group rna visibility dense spectrum on intronGap 30 type psl est baseColorUseSequence genbank showDiffBasesAllScales . indelDoubleInsert on indelQueryInsert on maxItems 300 priority 2 track est table all_est shortLabel $Organism ESTs longLabel $Organism ESTs Including Unspliced group rna visibility hide spectrum on intronGap 30 type psl est baseColorUseSequence genbank indelDoubleInsert on indelQueryInsert on maxItems 300 track tightEst shortLabel Tight ESTs longLabel Tightly Filtered $Organism ESTs Including Unspliced group rna visibility hide spectrum on type psl est baseColorUseSequence genbank indelDoubleInsert on indelQueryInsert on track xenoMrna shortLabel Other mRNAs longLabel Non-$Organism mRNAs from GenBank group rna visibility hide spectrum on type psl xeno baseColorUseCds genbank baseColorUseSequence genbank showDiffBasesAllScales . indelDoubleInsert on indelQueryInsert on track xenoBestMrna shortLabel Other Best mRNAs longLabel Non-$Organism mRNAs from GenBank Best in Genome Alignments group rna visibility hide spectrum on type psl xeno baseColorUseCds genbank baseColorUseSequence genbank showDiffBasesAllScales . indelDoubleInsert on indelQueryInsert on track xenoEst shortLabel Other ESTs longLabel Non-$Organism ESTs from GenBank group rna visibility hide spectrum on type psl xeno baseColorUseSequence genbank indelDoubleInsert on indelQueryInsert on url https://www.ncbi.nlm.nih.gov/htbin-post/Entrez/query?form=4&db=n&term=$$ track xenoRefGene shortLabel Other RefSeq longLabel Non-$Organism RefSeq Genes group genes visibility dense color 12,12,120 type genePred xenoRefPep xenoRefMrna priority 3 -track mgcFullMrna -shortLabel MGC Genes -longLabel Mammalian Gene Collection Full ORF mRNAs -group genes -visibility hide -color 0,100,0 -type psl -baseColorDefault diffCodons -baseColorUseCds genbank -baseColorUseSequence genbank -indelDoubleInsert on -indelQueryInsert on -showDiffBasesAllScales . -showDiffBasesMaxZoom 10000.0 -showCdsAllScales . -showCdsMaxZoom 10000.0 +#track mgcFullMrna +#shortLabel MGC Genes +#longLabel Mammalian Gene Collection Full ORF mRNAs +#group genes +#visibility hide +#color 0,100,0 +#type psl +#baseColorDefault diffCodons +#baseColorUseCds genbank +#baseColorUseSequence genbank +#indelDoubleInsert on +#indelQueryInsert on +#showDiffBasesAllScales . +#showDiffBasesMaxZoom 10000.0 +#showCdsAllScales . +#showCdsMaxZoom 10000.0 searchName refGeneAcc searchTable refGene searchMethod exact searchType genePred semiShortCircuit 1 termRegex N(M|R)_[0-9]{6}[0-9]* searchPriority 9.5 searchName mrnaAcc searchTable all_mrna searchMethod prefix searchType mrnaAcc shortCircuit 1 semiShortCircuit 1 termRegex [a-z][a-z0-9][0-9]+ searchPriority 10 searchName refLink searchTable refGene searchType refGene searchPriority 2 grepIndex genbankGrep/refLink.mrnaAccProduct searchTable xenoRefGene searchType refGene searchPriority 2.1 grepIndex refLinkGrep/refLink.mrnaAccProduct searchName mrnaKeyword searchTable all_mrna searchType mrnaKeyword searchPriority 15 grepIndex genbankGrep searchTable mgcFullMrna searchType psl searchPriority 25 semiShortCircuit 1 # keep adjacent to MGC track orfeomeMrna shortLabel ORFeome Clones longLabel ORFeome Collaboration Gene Clones group genes visibility hide color 34,139,34 type psl baseColorDefault diffCodons baseColorUseCds genbank baseColorUseSequence genbank indelDoubleInsert on indelQueryInsert on showDiffBasesAllScales . showDiffBasesMaxZoom 10000.0 showCdsAllScales . showCdsMaxZoom 10000.0 searchTable orfeomeMrna searchType psl searchPriority 25 semiShortCircuit 1