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/mouse/mm39/developmentTimecourseM21mm39TPM.html src/hg/makeDb/trackDb/mouse/mm39/developmentTimecourseM21mm39TPM.html index b6a4d3bf0a8..3963e6dd381 100644 --- src/hg/makeDb/trackDb/mouse/mm39/developmentTimecourseM21mm39TPM.html +++ src/hg/makeDb/trackDb/mouse/mm39/developmentTimecourseM21mm39TPM.html @@ -1,81 +1,89 @@ <h2>Description</h2> <p> This track displays TPM (transcripts per million) gene expression values from a mouse developmental time course bulk RNA-seq experiment covering 17 tissues across up to 8 time points (embryonic days 10.5 through 16.5 and postnatal day 0). Values were generated by RSEM from alignments to the mm10 reference genome using the GENCODE M21 annotation set and -lifted over to the mm39 reference genome. Each bar in the chart represents one replicate from one tissue at one +lifted over to the mm39 reference genome. Each bar in the chart +represents one replicate from one tissue at one developmental time point.</p> <p> The data were produced as part of the <a href="https://www.encodeproject.org/" target="_blank">ENCODE</a> project at the <a href="http://woldlab.caltech.edu/" target="_blank">Wold Lab</a>, Caltech. Each tissue and time point has two biological replicates, each shown as its own bar. Bars can be filtered by tissue and time point using the track configuration controls.</p> <!--#insert file="../../mouseDevTimecourseDisplay.shared.html"--> <h2>Methods</h2> <p> RNA-seq reads were processed using the <a href="https://www.encodeproject.org/pipelines/ENCPL002LSE/" target="_blank">ENCODE long RNA-seq pipeline</a>. Reads were aligned to the mm10 genome using STAR (Dobin <em>et al</em>., 2013) and quantified at the gene level using RSEM (Li and Dewey, 2011) with the GENCODE M21 annotation set. The TPM column from the RSEM gene quantification files across all tissues and replicates was concatenated into a single matrix. This matrix was then converted into the UCSC <a href="/goldenPath/help/barChart.html#example6" target="_blank">faceted bigBarChart</a> format (bed, categories, and facet files). The bed file was converted to the mm39 genome using liftOver and then converted into a bigBarChart bigBed file.</p> <p> The mm39 annotations were lifted from mm10. Of the 55,536 genes in the mm10 GENCODE M21 data, 55,447 lifted successfully and 89 did not. Of those 89, 42 are on chr14 and 40 of those fall within chr14:3.2-26.3 Mb; about half carry -Gm or Rik names, indicating predicted rather than curated genes. One gene, -Il11ra2, appears twice because a copy on an unplaced mm10 scaffold lifts to -the same mm39 position as the primary-chromosome copy.</p> +Gm or Rik names, indicating predicted rather than curated genes. The +gene Il11ra2 appears three times. Two of those copies sit at the same +position, chr4:42,656,355-42,661,893, because a copy that is on an unplaced +scaffold in mm10 lifted onto the same place as the copy on the main +chromosome. Both carry the same expression values, and clicking either one +opens the same details page. The third copy is about 497 kb away, at +chr4:42,159,195-42,164,733.</p> <p> -The steps and <a href="https://github.com/ucscGenomeBrowser/kent/tree/master/src/hg/makeDb/scripts/mouseDevTimecourse" +The steps and <a +href="https://github.com/ucscGenomeBrowser/kent/tree/master/src/hg/makeDb/scripts/mouseDevTimecourse" target="_blank">scripts</a> used to build this track are documented in our -<a href="https://github.com/ucscGenomeBrowser/kent/blob/master/src/hg/makeDb/doc/mm39/mouseDevTimecourse.txt" +<a +href="https://github.com/ucscGenomeBrowser/kent/blob/master/src/hg/makeDb/doc/mm39/mouseDevTimecourse.txt" target="_blank">makedoc</a>, and the track configuration is in -<a href="https://github.com/ucscGenomeBrowser/kent/blob/master/src/hg/makeDb/trackDb/mouse/mm39/mouseDevTimecourse.ra" +<a +href="https://github.com/ucscGenomeBrowser/kent/blob/master/src/hg/makeDb/trackDb/mouse/mm39/mouseDevTimecourse.ra" target="_blank">mouseDevTimecourse.ra</a>.</p> <h2>Data Access</h2> <p> The data in this track can be explored interactively with the <a href="../cgi-bin/hgTables">Table Browser</a> or the <a href="../cgi-bin/hgIntegrator">Data Integrator</a>. For programmatic access, the track can be accessed using the Genome Browser's <a href="/goldenPath/help/api.html" target="_blank">REST API</a>.</p> <p> The bigBarChart bigBed file underlying this track can be downloaded from <a href="https://hgdownload.soe.ucsc.edu/gbdb/mm39/mouseDevTimecourse/" target="_blank">our download server</a>. Individual regions or the whole genome annotation can be obtained using our tool <tt>bigBedToBed</tt>, which can be compiled from the source code or downloaded as a precompiled binary for your system. Instructions for downloading source code and binaries can be found <a href="https://hgdownload.soe.ucsc.edu/downloads.html#utilities_downloads" target="_blank">here</a>.</p> <p>The original data files and experimental metadata are available from the <a href="https://www.encodeproject.org/publications/e0d01543-9965-4edb-933c-778a40575cd9/" target="_blank">ENCODE Portal</a>.</p> <p>Please refer to our <a href="../FAQ/FAQdownloads.html#download36" target="_blank">Data Access FAQ</a> for more information.</p> <!--#insert file="../../mouseDevTimecourseCreditsAndReferences.shared.html"-->