5ac72ff7faebbfea5a4eb9a16815111d36304462 markd Fri Dec 12 02:01:42 2025 -0800 improved formating of recount3 track description diff --git src/hg/makeDb/trackDb/recount3.html src/hg/makeDb/trackDb/recount3.html index 22489068208..a979bf4a533 100644 --- src/hg/makeDb/trackDb/recount3.html +++ src/hg/makeDb/trackDb/recount3.html @@ -1,95 +1,103 @@ <!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. </p> <p> These tracks display the recount3 intron data, including split read counts and splice junction motifs. </p> <h2>Display Conventions</h2> <p> Intron items are colored based on splice junction motifs and read support (darker colors indicate higher coverage). Split read counts and splice motifs are shown on mouseover. By default, only introns with a minimum read count of 10,000 are shown. This setting can be changed on the track configuration page. </p> <p> The intron items are color-coded: <ul> <li><b><font color="#00bfff">Sky blue</font></b> GT donors and AG acceptors (CT and AC on the minus strand)</li> <li><b><font color="#00ced1">Turquoise</font></b> GC donors (GT on the minus strand)</li> <li><b><font color="#ff8c00">Orange</font></b> AT donors and AC acceptors (GT and GT on the minus strand)</li> <li><b><font color="#a9a9a9">Grey</font></b> Non-canonical junction motifs. These could be sequencing errors, polymorphisms, or very rare U12 introns.</li> </ul> </p> <p> Introns can be filtered by: <ul> <li><b>read count</b> - Number of split reads supporting the intron. The default is a minimum of 10,000 reads.</li> <li><b>intron size</b> - Length of the intron. The default is 30 to 100,000.</li> <li><b>splice junction motif</b> - The motif is specified in the form <em>GT/AG</em>, with canonical motifs being uppercase and unknown motifs being lowercase. The default is no filtering.</li> <li><b>strand</b> - Filter by positive strand ('+'), negative strand ('-'), and/or unknown strand ('.'). The default is no strand filtering ('all'). </li> </ul> </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> +The original junction files for human can be found at: +</p> +<ul> + <li> <a href="https://snaptron.cs.jhu.edu/data/gtexv2/junctions.bgz" target="_blank"> + https://snaptron.cs.jhu.edu/data/gtexv2/junctions.bgz</a> + <li> <a href="https://snaptron.cs.jhu.edu/data/tcgav2/junctions.bgz" target="_blank"> + https://snaptron.cs.jhu.edu/data/tcgav2/junctions.bgz</a> + <li> <a href="https://snaptron.cs.jhu.edu/data/srav3h/junctions.bgz" target="_blank"> + https://snaptron.cs.jhu.edu/data/srav3h/junctions.bgz</a> + <li> <a href="https://snaptron.cs.jhu.edu/data/ccle/junctions.bgz" target="_blank"> + https://snaptron.cs.jhu.edu/data/ccle/junctions.bgz</a> +</ul> +<p> +The mouse junction file is at: +</p> +<ul> + <li> <a href="https://snaptron.cs.jhu.edu/data/srav1m/junctions.bgz" target="_blank"> + https://snaptron.cs.jhu.edu/data/srav1m/junctions.bgz</a> +</ul> </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>