e4e3a81fd04f0a799894b069d1977092d60f5bba jnavarr5 Thu Aug 7 15:43:08 2025 -0700 Updating the track description page. Moving the Methods section before the Data Access, restructuring the Display Conventions section, adding a link to the recount3 website... Removing .html from the html line in trackDb, refs #34886 diff --git src/hg/makeDb/trackDb/recount3.html src/hg/makeDb/trackDb/recount3.html index 481ad806789..a1b0ba6c578 100644 --- src/hg/makeDb/trackDb/recount3.html +++ src/hg/makeDb/trackDb/recount3.html @@ -1,81 +1,84 @@ <!DOCTYPE html> <html> <head> </head> <body> <h2>Description</h2> <p> -Recount3 is a comprehensive resource for re-analyzing RNA-seq data. It provides uniformly processed -RNA-seq data and associated metadata from a wide range of studies, enabling researchers to access -and analyze gene expression data in a consistent manner. Recount3 aggregates data from multiple -sources, including the Sequence Read Archive (SRA) and the Genotype-Tissue Expression (GTEx) project, -and reprocesses it using a standardized pipeline. This allows for cross-study comparisons and -meta-analyses, facilitating discoveries in genomics and transcriptomics. +<a href="https://rna.recount.bio/" target="_blank">Recount3</a> is a comprehensive resource for +re-analyzing RNA-seq data. It provides uniformly processed RNA-seq data and associated metadata +from a wide range of studies, enabling researchers to access and analyze gene expression data in a +consistent manner. Recount3 aggregates data from multiple sources, including the Sequence Read +Archive (SRA) and the Genotype-Tissue Expression (GTEx) project, and reprocesses it using a +standardized pipeline. This allows for cross-study comparisons and meta-analyses, facilitating +discoveries in genomics and transcriptomics. </p><p> These tracks display the recount3 intron data including split read counts. </p> <h2>Display Conventions</h2> <p> -Intron blocks are grayscale colored based on read support (darker tones indicate higher coverage). <br> -Split read counts and splice motifs are shown on mouseover. <br> +Intron blocks are grayscale colored based on read support (darker tones indicate higher coverage). By default only introns with a minimum read count of 10,000 are shown. This setting can be changed -on the track configuration page. <br> -The intron ends are color coded: +on the track configuration page. The SRA track is only visible when zoomed in within 10 million +bases because of its data density. +</p> +<p> +The intron ends are color-coded: <ul> <li><b><font color="#2E2585">Dark blue</font></b> GT donors and AG acceptors (CT and AC on the minus strand) </li> <li><b><font color="#5DA899">Teal</font></b> GC donors (GT on the minus strand) </li> <li><b><font color="#C26A77">Faded red</font></b> AT donors and AC acceptors (GT and GT on the minus strand) </li> +<li>Introns with non-standard ends do not have colored tags.</li> </ul> -Introns with non standard ends do not have colored tags. -<br> -The SRA track is only visible when zoomed in within 10 million bases because of its data density. +<p> +Split read counts and splice motifs are shown on mouseover. +</p> + +<h2>Methods</h2> +<p> +Junction files were converted to bed format. For grayscaling total read count was log10 +transformed and multiplied by 10 to get a score between 0 and 225, which can be found +in the bed score field. </p> <h2>Data Access</h2> The raw data can be explored interactively with the <a href="https://genome.ucsc.edu/cgi-bin/hgTables">Table Browser</a> or the <a href="https://genome.ucsc.edu/cgi-bin/hgIntegrator">Data Integrator</a>. For automated analysis, the data may be queried from our <a href="https://genome.ucsc.edu/goldenPath/help/api.html">REST API</a>.<br> Please refer to our <a href="https://groups.google.com/a/soe.ucsc.edu/forum/#!forum/genome">mailing list archives</a> for questions, or our <a href="https://genome.ucsc.edu/FAQ/FAQdownloads.html#downloads36">Data Access FAQ</a> for more information. <p> The original junction files can be found at <br> <a href="https://snaptron.cs.jhu.edu/data/gtexv2/junctions.bgz" target="_blank"> https://snaptron.cs.jhu.edu/data/gtexv2/junctions.bgz</a><br> <a href="https://snaptron.cs.jhu.edu/data/tcgav2/junctions.bgz" target="_blank"> https://snaptron.cs.jhu.edu/data/tcgav2/junctions.bgz</a><br> <a href="https://snaptron.cs.jhu.edu/data/srav3h/junctions.bgz" target="_blank"> https://snaptron.cs.jhu.edu/data/srav3h/junctions.bgz</a><br> <a href="https://snaptron.cs.jhu.edu/data/ccle/junctions.bgz" target="_blank"> https://snaptron.cs.jhu.edu/data/ccle/junctions.bgz</a><br> <a href="https://snaptron.cs.jhu.edu/data/srav1m/junctions.bgz" target="_blank"> https://snaptron.cs.jhu.edu/data/srav1m/junctions.bgz (mouse)</a><br> </p> -<h2>Methods</h2> -<p> -Junction files were converted to bed format. For grayscaling total read count was log10 -transformed and multiplied by 10 to get a score between 0 and 225, which can be found -in the bed score field. -</p> - <h2>References</h2> <p> Wilks C, Zheng SC, Chen FY, Charles R, Solomon B, Ling JP, Imada EL, Zhang D, Joseph L, Leek JT <em>et al</em>. <a href="https://genomebiology.biomedcentral.com/articles/10.1186/s13059-021-02533-6" target="_blank"> recount3: summaries and queries for large-scale RNA-seq expression and splicing</a>. <em>Genome Biol</em>. 2021 Nov 29;22(1):323. PMID: <a href="https://www.ncbi.nlm.nih.gov/pubmed/34844637" target="_blank">34844637</a>; PMC: <a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8628444/" target="_blank">PMC8628444</a> </p>