4d1cbe4059ce40d0de6f2904d507fa913d6b05aa Merge parents e4ad034 1f9979f dschmelt Thu Aug 19 10:49:28 2021 -0700 Fixing merge conflixt No RM diff --cc src/hg/htdocs/goldenPath/newsarch.html index 6a868eb,8651e6a..d476582 --- src/hg/htdocs/goldenPath/newsarch.html +++ src/hg/htdocs/goldenPath/newsarch.html @@@ -40,44 -40,133 +40,133 @@@ <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> <!-- ============= 2021 archived news ============= --> <a name="2021"></a> + <a name="080421"></a> + <h2>Aug. 04, 2021 Addition of GRCm38 patch 6 sequences to mm10</h2> + <p> + We are pleased to announce the addition of GRCm38 patch release 6 to the mm10 assembly. mm10 has + been updated with patches since its release in 2012. The GRC patch releases do not change any + previously existing sequences; they simply add new sequences for fix patches or alternate haplotypes + that correspond to specific regions of the main chromosome sequences. For most users, the patches + are unlikely to make a difference and may complicate the analysis as they introduce more + duplication.</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/mm10/bigZips/latest/" + target="_blank">/latest</a>, + <a href="https://hgdownload.soe.ucsc.edu/goldenPath/mm10/bigZips/initial/" + target="_blank">/initial</a>, and + <a href="https://hgdownload.soe.ucsc.edu/goldenPath/mm10/bigZips/p6/" target="_blank">/p6</a> + download directories on the downloads server. With the addition of new sequences to mm10, we can + expect to see BLAT return more matches to the genome.</p> + + <ul> + <li> + The <b>initial/</b> subdirectory contains files for the initial release of GRCm38, which has 66 + sequences, no original alternate sequences, and no fix sequences. It is the same as the + parent download directory. This is probably the best genome file for aligners and most analysis + tasks, a version called "analysisSet" for the human genome. + </li> + <li> + The <b>p6/</b> subdirectory contains files for GRCm38.p6 (patch release 6). It has 239 sequences + including alternate and fix sequences. Note that these patches include + "strain-specific" sequences. You may want to check with the authors of your aligner if + the software can recognize these sequences. + </li> + <li> + The <b>latest/</b> symbolic link points to the subdirectory for the most recent patch version. + </li> + </ul> + + <p> + We would like to thank the <a href="https://www.ncbi.nlm.nih.gov/grc" target="_blank">Genome + Research Consortium</a> for creating the patches for mm10. We would also like to thank Galt Barber + and Jairo Navarro at UCSC for implementing and testing the latest patch to the mm10 genome.</p> + + <a name="080221"></a> + <h2>Aug. 02, 2021 New Genome Browser: X. tropicalis, xenTro10 (<em>Xenopus tropicalis</em>)</h2> + <p> + A genome browser is now available for the <em>Xenopus tropicalis</em> assembly released in Nov. 2019 by the + <a href="https://www.berkeley.edu/" target="_blank"> University of California, Berkeley</a> (UCB_Xtro_10.0). + <h3>About the assembly:</h3> + <ul> + <li><b>UCSC Genome Browser assembly ID:</b> <a href="../../cgi-bin/hgGateway?db=xenTro10" + target="_blank">xenTro10</a></li> + <li><b>Sequencing/Assembly provider ID:</b> <a href="https://www.berkeley.edu/"> + University of California, Berkeley</a></li> + <li><b>Assembly date:</b> Nov. 2019</li> + <li><B>Accession ID:</B> GCF_000004195.4</li> + <li><B>NCBI Genome ID:</B> <A HREF='https://www.ncbi.nlm.nih.gov/genome/80' + TARGET='_blank'>80</A> (<em>Xenopus tropicalis</em>)</li> + <li><B>NCBI Assembly ID:</B> <A HREF='https://www.ncbi.nlm.nih.gov/assembly/5323661' + TARGET='_blank'>5323661</A></li> + <li><B>NCBI BioProject ID:</B> <A HREF='https://www.ncbi.nlm.nih.gov/bioproject/577946' + TARGET='_blank'>577946</A></li> + <li><B>NCBI BioSample ID:</B> <A HREF='https://www.ncbi.nlm.nih.gov/biosample/SAMN13041969' + TARGET='_blank'>SAMN16261960</A></li> + <li><b>Scaffold count: </b>167</li> + <li><b>Total size: </b>1,451,301,209</li> + <li><a href="../goldenPath/credits.html#xentro_credits" + target="_blank" >Acknowledgments</a></li> + </ul> + <h3>Data and Downloads:</h3> + <ul> + <li><a href="../goldenPath/credits.html#xentro_use" + target="_blank" >Data use conditions and restrictions</a></li> + <li><a href="../goldenPath/help/ftp.html" + target="_blank" >Rsync</a> and + <a href="ftp://hgdownload.soe.ucsc.edu/goldenPath/xenTro10/" + target="_blank" >FTP</a></li> + <li><a href="http://hgdownload.soe.ucsc.edu/downloads.html#xentro" + target="_blank" >Downloads page</a></li> + </ul> + </p> + <p> + We would like to thank the University of California, Berkeley for creating this new X. tropicalis assembly. + We would also like to thank Hiram Clawson, Lou Nassar, and Gerardo Perez for the development and release of + the xenTro10 genome browser. + </p> + <a name="072021"></a> <h2>July 20, 2021 Updated GENCODE tracks released for hg38, hg19, and mm39</h2> <p> We have updated our GENCODE gene datasets to the latest releases; v38 for human (hg38 & hg19) and v27 for the mouse genome assembly (mm39). These new annotation data were released by GENCODE in May 2021 and correspond to the Ensembl Genes 104 dataset. </p> <p> These tracks can be found in our All GENCODE super-track folder, with subset tracks and abundant filter options. This super-track contains many previous versions of the GENCODE genes for easy comparison. From the -<a href="https://www.gencodegenes.org/human/stats.html"> +<a target="_blank" href="https://www.gencodegenes.org/human/stats.html"> GENCODE stats page</a>, this updated dataset has approximately 60.6k genes and 237k transcripts on the human hg38 assembly.</p> <p> For more information or to visualize the data, you can visit the following track description pages:</p> <ul> <li><a href="../../cgi-bin/hgTrackUi?db=hg38&g=wgEncodeGencodeV38"> All GENCODE v38 for hg38</a></li> <li><a href="../../cgi-bin/hgTrackUi?db=hg19&g=wgEncodeGencodeV38lift37"> GENCODE lifted Annotations V38lift37 for hg19</a></li> <li><a href="../../cgi-bin/hgTrackUi?db=mm39&g=wgEncodeGencodeVM27"> All GENCODE annotations VM27 for mm39</a></li> </ul>