92bf9b755b6bcaf3c69c3332f5e42ce53ec3555f jnavarr5 Tue Mar 17 16:55:38 2020 -0700 Announcing the chrMT patch, refs #24648 diff --git src/hg/htdocs/goldenPath/newsarch.html src/hg/htdocs/goldenPath/newsarch.html index 18696c9..41e6fd1 100755 --- src/hg/htdocs/goldenPath/newsarch.html +++ src/hg/htdocs/goldenPath/newsarch.html @@ -39,30 +39,59 @@ </div> <div class="col-sm-3"> <ul> <li><a href="#2005">2005 News</a></li> <li><a href="#2004">2004 News</a></li> <li><a href="#2003">2003 News</a></li> <li><a href="#2002">2002 News</a></li> <li><a href="#2001">2001 News</a></li> </ul> </div> </div> </div> <!-- ============= 2020 archived news ============= --> <a name="2020"></a> +<a name="031720"></a> +<h2>Mar. 17, 2020 New mitochondrial sequence for human (hg19)</h2> +<p> +We are pleased to announce the release of a patch to the hg19 assembly that will introduce a new +mitochondrial sequence, <a href="../../cgi-bin/hgTracks?db=hg19&position=chrMT:4277-5648" +target="_blank">chrMT</a>, to the assembly. We used GenBank sequence NC_001807 for chrM in hg19 and +earlier, but the sequence preferred by the community is the revised Cambridge Reference Sequence +(rCRS), <a href="https://www.ncbi.nlm.nih.gov/nuccore/251831106" target="_blank">NC_012920</a>. The +new chrMT is the rCRS, NC_012920. <a href="https://www.ncbi.nlm.nih.gov/grc/help/patches/" +target="_blank">Patch sequences</a> from +<a href="https://www.ncbi.nlm.nih.gov/assembly/GCA_000001405.14" target="_blank">GRCh37.p13</a> have +also been added to hg19.</p> +<p> +More information on how patch sequences are incorporated can be found on the +<a href="http://genome.ucsc.edu/blog/patches/" target="_blank">Patching up the Genome</a> blog post. +The blog post contains details about the new +<a href="https://hgdownload.soe.ucsc.edu/goldenPath/hg19/bigZips/latest/" +target="_blank">/latest</a> download directory on the downloads server. With the addition of new +sequences to hg19, we can expect to see BLAT return more matches to the genome.</p> +<p> +Also, with these patches, the hg19 genome is not optimal anymore for aligners. So we added an +"<a href="https://hgdownload.soe.ucsc.edu/goldenPath/hg19/bigZips/analysisSet/" +target="_blank">analysis set</a>" version of the hg19 genome fasta file to our +<a href="https://hgdownload.soe.ucsc.edu/goldenPath/hg19/bigZips/" target="_blank">bigZips</a> +directory, and indexes for BWA, Bowtie2, and Hisat2.</p> +<p> +We would like to thank the Genome Research Consortium for creating the patches to hg19. We would +also like to thank Angie Hinrichs and Jairo Navarro at UCSC for implementing and testing the latest +patch to hg19.</a> <a name="022720"></a> <h2>Feb. 27, 2020 New NCBI RefSeq Select + MANE track for Human (hg19/hg38)</h2> <p> We are pleased to announce a new track, RefSeq Select+MANE, for the <a target="_blank" href="../../cgi-bin/hgTrackUi?db=hg19&c=chr1&g=refSeqComposite">GRCh37/hg19</a> and <a target="_blank" href="../../cgi-bin/hgTrackUi?db=hg38&c=chr1&g=refSeqComposite">GRCh38/hg38</a> human assemblies. This track is a combination of NCBI transcripts with the <em>RefSeq Select</em> tag, as well as transcripts with the <em>MANE Select</em> tag. The result is a track with a single representative transcript for every protein-coding gene. The track can be found as part of the NCBI RefSeq composite track.</p> <p> <a target="_blank" href="https://www.ncbi.nlm.nih.gov/refseq/refseq_select/">RefSeq Select</a> transcripts are chosen by an NCBI pipeline to be representative of every protein-coding gene. As part of the <a target="_blank"