23bea12e98867f3cd6b931d0537c68b57a2f0503 gperez2 Thu Jul 31 10:54:57 2025 -0700 Incorporating Lou's feedback to bedMethyl.html and announcing the bedMethyl/bigMethyl type, refs #36002 diff --git src/hg/htdocs/goldenPath/newsarch.html src/hg/htdocs/goldenPath/newsarch.html index 928e8102a3c..7bf6187c402 100755 --- src/hg/htdocs/goldenPath/newsarch.html +++ src/hg/htdocs/goldenPath/newsarch.html @@ -52,30 +52,64 @@ <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="2025"></a> +<a name="073125"></a> +<h2>July 31, 2025 New bedMethyl and bigMethyl track type</h2> +<p> +We are excited to announce support for a new track format for visualizing DNA +methylation data: +<a href="https://www.encodeproject.org/data-standards/wgbs/" target="_blank">bedMethyl</a>. +This format, and its binary-indexed counterpart, <b>bigMethyl</b>, is designed to +represent methylation calls from bisulfite sequencing or similar methods at single-base resolution +across the genome.</p> +<p> +The <a href="help/bedMethyl.html" target="_blank">bedMethyl</a> format extends the standard +<a href="/FAQ/FAQformat.html#format1" target="_blank">BED 9 format</a> to include additional fields +such as coverage, percent methylation, and the number of modified and canonical bases. When viewed +in the Genome Browser, hovering over or clicking an item reveals these additional details. Items are +color-coded from <b><font color="#0000FF">0%</font></b> methylated (blue) to +<b><font color="#FF0000">100%</font></b> (red). Methylation calls are shown separately for CpG sites +(<b>m</b>) and non-CpG (CHG/CHH) sites (<b>h</b>). +</p> +<p class="text-center"> +<img "1080" height="148" src="../../images/bedMethylEx.jpg"> +</p> +<p> +The <a href="help/bedMethyl.html#bigMethyl" target="_blank">bigMethyl</a> +format allows fast access to large methylation datasets and is ideal for displaying +these tracks at scale in the Genome Browser.</p> +<p> +For more information, see the +<a href="help/bedMethyl.html" target="_blank">bedMethyl and bigMethyl Track Format</a> help page. +</p> +<p> +We would like to thank Brian Joseph Raney, Max Haeussler, and Gerardo Perez for their work +developing and testing this track format.</p> + +</p> <a name="072325"></a> <h2>July 23, 2025 Bionano DLE-1 CTTAAG sites for human, hg38 and hg19</h2> <p> We are happy to announce the release of the Bionano DLE-1 track for human assemblies <a href="/cgi-bin/hgTrackUi?db=hg38&position=default&g=genotypeArrays" target="_blank">hg38</a> and <a href="/cgi-bin/hgTrackUi?db=hg19&position=default&g=genotypeArrays" target="_blank">hg19</a>. These tracks show the CTTAAG sites used by the <a href="https://www.bionano.com/" target="_blank">Bionano Optical Genome Mapping system</a>, an assay to detect structural variants. </p> <p> OGM (Optical Genome Mapping) begins with the isolation of ultra-high molecular weight (UHMW) DNA from blood, bone marrow aspirates, cultured cells (including chorionic villi and amniocytes), tissue, or tumor biopsies. A single enzymatic reaction places fluorescent labels throughout the genome at a specific sequence motif. The labeled DNA molecules are linearized in nanochannel