7fef04a14e3f37e2be923d3c885c585d321aa52b lrnassar Fri Jun 12 14:33:05 2020 -0700 Removing hg19 from the MANE announcement at the request of EBI/NCBI refs #24787 diff --git src/hg/htdocs/goldenPath/newsarch.html src/hg/htdocs/goldenPath/newsarch.html index 72e8d38..728307d 100755 --- src/hg/htdocs/goldenPath/newsarch.html +++ src/hg/htdocs/goldenPath/newsarch.html @@ -939,54 +939,53 @@ <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> +<h2>Feb. 27, 2020 New NCBI RefSeq Select + MANE track for Human (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 +We are pleased to announce a new track, RefSeq Select+MANE, for the <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> +human assembly. 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" href="https://www.ncbi.nlm.nih.gov/refseq/MANE/">MANE project</a>, however, RefSeq Select transcripts that have a 100% identical match to a transcript in the Ensembl annotation are given the MANE Select designation. In this way, MANE Select is a subset of RefSeq Select. It should be noted, however, that there are cases where RefSeq Select transcripts are replaced when a different MANE Select transcript is chosen. Once the MANE project is complete, RefSeq Select and MANE Select for human should be nearly the same.</p> <p> In summary, this track provides a functional canonical gene set until the MANE set is complete. More information on this track and data can be found in the <a target="_blank" -href="../../cgi-bin/hgTrackUi?db=hg19&c=chr1&g=refSeqComposite">track description page</a>, +href="../../cgi-bin/hgTrackUi?db=hg38&c=chr1&g=refSeqComposite">track description page</a>, NCBI's <a target="_blank" href="https://www.ncbi.nlm.nih.gov/refseq/refseq_select/">RefSeq Select page</a>, and the <a target="_blank" href="https://www.ncbi.nlm.nih.gov/refseq/MANE/">MANE page</a>.</p> <p> We would like to thank NCBI for releasing the RefSeq Select data, as well as the NCBI and Ensembl-GENCODE collaboration for MANE. We would also like to thank Max Haussler and Lou Nassar for the development and release of these tracks.</p> <a name="021120"></a> <h2>Feb. 11, 2020 New GENCODE gene tracks: Human V33 (hg19/hg38) - Mouse M24 (mm10)</h2> <p> We are pleased to announce new GENCODE Gene annotation tracks, which correspond to <a href="http://www.ensembl.info/2019/10/17/whats-coming-up-in-ensembl-release-99/" target="_blank">Ensembl 99</a>, for three assemblies: <a target="_blank" href="../../cgi-bin/hgTrackUi?db=hg19&c=chr21&g=wgEncodeGencodeV33lift37">hg19/GRCh37</a>,