78988553dd9b460c26f0b9f21f15a1aacfad9dab lrnassar Fri Aug 21 15:44:40 2026 -0700 Polish pass on the mouseDevTimecourse tracks after a Playwright QA sweep. refs #37001 Sentence-case the tissue names and the facet column titles, so the barChart facet filter reads "Tissue / Spleen" rather than "tissue / spleen" and the bigWig matrix reads "Spleen". Only the first character is upper-cased. Added sentenceCaseTissues.sh, which does the .facets and .categories files and is idempotent, since the hub still ships lower-case and this has to be replayed after any refetch. The count and color column names are deliberately left lower-case: barChartUi.c requires a field literally named "count" to load the file at all, and facetedTable.c keys its merge logic on "count", "color" and "val". Renaming the faceted columns means trackDb matches, so the stanzas now read barChartFacets Tissue,Timepoint. Set priority on the container children so the default-visible M21 TPM sorts first and the signal composite sorts last. The composite needs an explicit value; without one it inherits the superTrack's 0.6 and floats to the top. Fix the All reads view, which was inert. Every all-reads subtrack shipped parent off, so switching the view to full revealed nothing. The view's own visibility already gates drawing, so the subtrack state should not encode the view as well. The default image is unchanged at 78 unique-reads rep1 tracks, and switching the view to full now yields 156. This also makes the Rep 2 toggle symmetric across the two views. Rename the bigWig subGroup3 display label from Age to Timepoint, matching the barChart facet and the .facets column. The group name stays "age" because dimensions and sortOrder reference it by name. Add relatedTracks cross-links between the mm10 container and Tabula Muris. Not Tabula Muris Senis, which is not on the RR. Description pages: reorder the mm10 subtrack list to match the new display order, "sub tracks" to "subtracks", capitalise the colour legend tissue names, and correct the mm39 Il11ra2 note - the gene appears three times, two of them stacked at one position and sharing a details page, with the third 497 kb away. Makedocs record the casing step, its ordering constraint relative to the reorder and colour steps, and the count/color naming constraint. diff --git src/hg/makeDb/trackDb/relatedTracks.ra src/hg/makeDb/trackDb/relatedTracks.ra index fa99a6ab96b..0a242190bbd 100644 --- src/hg/makeDb/trackDb/relatedTracks.ra +++ src/hg/makeDb/trackDb/relatedTracks.ra @@ -94,30 +94,34 @@ hg19 >avada varaico The latest variants mined from published papers. The AVADA track is no longer updated. # mm39: mm39 knownGene knownGeneArchive View previous versions of GENCODE Genes mm39 knownGeneArchive knownGene View the latest GENCODE Genes version # mm10 ENCODE4 Regulation: mm10 encode4Reg encode3Reg The previous version of this track mm10 encode3Reg encode4Reg The newer version of this track mm10 ~encode4Reg cCREs Related ENCODE4 data mm10 ~mouseDevTimecourse encode3Reg Related ENCODE track mm10 ~mouseDevTimecourse encode4Reg Related ENCODE track +# mm10 mouse gene expression cross-links: +mm10 mouseDevTimecourse tabulaMuris Single-cell gene expression across adult mouse organs +mm10 tabulaMuris mouseDevTimecourse Bulk RNA-seq gene expression across mouse development + # hg38 long-read SV supertrack cross-links to other SV resources: hg38 longReadVariants gnomadStructuralVariants Short-read structural variants from gnomAD v4.1 hg38 gnomadStructuralVariants longReadVariants Long-read structural variants across multiple cohorts hg38 longReadVariants dbVarSv NCBI dbVar structural variants (short-read and long-read, germline and clinical) hg38 dbVarSv longReadVariants Long-read structural variants across multiple cohorts hg38 longReadVariants dgvPlus Database of Genomic Variants (DGV) structural variation catalog hg38 dgvPlus longReadVariants Long-read structural variants across multiple cohorts hg38 longReadVariants giabSv Genome in a Bottle high-confidence SV benchmark callsets hg38 giabSv longReadVariants Long-read structural variants across multiple cohorts hg38 longReadVariants mei Polymorphic Mobile Element Insertions (Alu, L1, SVA, HERVK, snRNA) from HGSVC3 long-read assemblies hg38 mei longReadVariants Long-read structural variants across multiple cohorts (parent SV callsets for the HGSVC3 MEI track) hs1 longReadVariants mei Polymorphic Mobile Element Insertions (Alu, L1, SVA, HERVK, snRNA) from HGSVC3 long-read assemblies hs1 mei longReadVariants Long-read structural variants across multiple cohorts (parent SV callsets for the HGSVC3 MEI track) # EVE cross-links: