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/mm10/mouseDevTimecourse.html src/hg/makeDb/trackDb/mouse/mm10/mouseDevTimecourse.html index 665db07a543..b6e1cac45ee 100644 --- src/hg/makeDb/trackDb/mouse/mm10/mouseDevTimecourse.html +++ src/hg/makeDb/trackDb/mouse/mm10/mouseDevTimecourse.html @@ -1,83 +1,83 @@ <h2>Description</h2> <p> This track set displays bulk RNA-seq gene expression data from a mouse developmental time course, covering 17 tissues across up to 8 time points (embryonic days 10.5 through 16.5 and postnatal day 0). Expression values (FPKM and TPM) were generated by RSEM from alignments to the mm10 reference genome using either GENCODE M4 or M21 annotations. Raw per-base RNA-seq signal (bigWig) tracks are also available for the same samples.</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> -<p>The five sub tracks are:</p> +<p>The five subtracks, in the order they appear in the track list, are:</p> <ul> + <li><b>Timecourse M21 TPM</b> – TPM values using GENCODE M21 + annotations, shown by default</li> + <li><b>Timecourse M21 FPKM</b> – FPKM values using GENCODE M21 + annotations</li> <li><b>Timecourse M4 TPM</b> – TPM values using GENCODE M4 annotations</li> <li><b>Timecourse M4 FPKM</b> – FPKM values using GENCODE M4 annotations</li> - <li><b>Timecourse M21 TPM</b> – TPM values using GENCODE M21 - annotations</li> - <li><b>Timecourse M21 FPKM</b> – FPKM values using GENCODE M21 - annotations</li> <li><b>Timecourse Signal</b> – RNA-seq signal (bigWig) tracks for unique and all aligned reads</li> </ul> <!--#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 and quantified at the gene level using RSEM. For each annotation set (GENCODE M4 and M21), the FPKM or 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), and the bed file was converted into a bigBarChart bigBed file.</p> <p> 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/mm10.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/mm10/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 files underlying this track can be downloaded from <a href="https://hgdownload.soe.ucsc.edu/gbdb/mm10/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"-->