e2ca170ffa028279df201ec24efe354cdf351401 gperez2 Thu Feb 5 13:46:39 2026 -0800 Releasing and announcing the recount3 track, refs #34886 diff --git src/hg/htdocs/goldenPath/newsarch.html src/hg/htdocs/goldenPath/newsarch.html index 15af2794149..d04ce7d48c6 100755 --- src/hg/htdocs/goldenPath/newsarch.html +++ src/hg/htdocs/goldenPath/newsarch.html @@ -52,30 +52,89 @@ <p>You can sign-up to get these announcements via our <a target=_blank href="https://groups.google.com/a/soe.ucsc.edu/g/genome-announce?hl=en">Genome-announce</a> email list. We send around one short announcement email every two weeks.</p> <p>Smaller software changes are not announced here. A summary of the three-weekly release changes can be found <a target=_blank href="https://genecats.gi.ucsc.edu/builds/versions.html">here</a>. For the full list of our daily code changes head to our <a href="https://github.com/ucscGenomeBrowser/kent/commits/master" target=_blank>GitHub page</a>. Lastly, see our <a href="credits.html" target="_blank"> credits page</a> for acknowledgments of the data we host.</p> <!-- ============= 2025 archived news ============= --> <a name="2026"></a> +<a name="020526"></a> +<h2>Feb. 05, 2026 New recount3 track for hg38 and mm10</h2> +<p> +We are happy to announce the release of the <a href="http://rna.recount.bio" + target="_blank">recount3</a> track for +<a href="/cgi-bin/hgTrackUi?db=hg38&position=default&g=recount3" target="_blank">hg38</a> and +<a href="/cgi-bin/hgTrackUi?db=mm10&position=default&g=recount3" target="_blank">mm10</a>. 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 +<a href="https://www.ncbi.nlm.nih.gov/sra/docs/" target="_blank">Sequence Read Archive (SRA)</a> +and the <a href="https://commonfund.nih.gov/GTEx" + target="_blank">Genotype-Tissue Expression (GTEx) project</a>, and reprocesses it using a +standardized pipeline. This allows for cross-study comparisons and meta-analyses, facilitating +discoveries in genomics and transcriptomics. +</p> +<p> +The tracks display recount3 intron data, including split read counts and splice junction motifs. +</p> +<div class="text-center"> +<img src="../../images/newsArchImages/recount3.png" width='80%'></a> +</div> + +<p> +For hg38, the tracks available are: +</p> +<ul> + <li>recount3 GTEx introns</li> + <li>recount3 TCGA introns</li> + <li>recount3 SRA introns</li> + <li>recount3 CCLE introns</li> +</ul> +<p> +For mm10: +</p> +<ul> + <li>recount3 SRA introns</li> +</ul> +<p> +Introns can be filtered by intron size, split read count, splice junction motif, and strand; intron +items are color-coded, with darker colors indicating higher coverage: +</p> +<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 and AG acceptors (CT and GC on the +minus strand)</li> + <li><b><font color="#ff8c00">Orange</font></b>: AT donors and AC acceptors (GT and AT 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> +We would like to thank the ReCount team for making this data available. We would also like to thank +Jeltje van Baren, Mark Diekhans, and Gerardo Perez for their efforts on this release. +</p> + + <a name="020326a"></a> <h2>Feb. 03, 2026 New "Visible Tracks" group feature</h2> <p> We are excited to announce a new improvement to the UCSC Genome Browser: the <b>Visible Tracks</b> group. The Genome Browser now includes a dynamic track group that automatically displays all currently visible tracks in one convenient location. This means you no longer need to hunt through multiple track categories to adjust tracks you've already turned on. </p> <div class="text-center"> <img src="/images/newsArchImages/visibleTracks.png" width='55%'> </div> <p> Previously, managing visible tracks required navigating back to their original categories — whether that was Genes and Gene Predictions, Conservation, Variation, or any other group. Now, all your active tracks appear together in the <b>Visible Tracks</b> group, making it faster and easier