68ea2e19f239f06bafd09853a0c1e4d4a991abc7 gperez2 Tue Jan 31 13:26:41 2023 -0800 Fixing GRC typo, refs #29964 diff --git src/hg/htdocs/goldenPath/newsarch.html src/hg/htdocs/goldenPath/newsarch.html index b94b8b6..cdb3215 100755 --- src/hg/htdocs/goldenPath/newsarch.html +++ src/hg/htdocs/goldenPath/newsarch.html @@ -84,31 +84,31 @@ sequences, 261 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>p14/</b> subdirectory contains files for GRCh38.p14 (patch release 14), which has 711 sequences, 351 alternate sequences, and 166 fix 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 hg38. We would also like to thank Galt Barber, +Reference Consortium</a> for creating the patches for hg38. We would also like to thank Galt Barber, Jairo Navarro, and Gerardo Perez at UCSC for implementing and testing the latest patch to the hg38 genome.</p> <a name="2022"></a> <a name="122022"></a> <h2>Dec 20, 2022 Multiz Alignment & Conservation (470 mammals) for hg38</h2> <p> A new <a href="/cgi-bin/hgTrackUi?db=hg38&g=cons470way" target="_blank">470-way Multiz Alignment & Conservation</a> track has been added to the human <a href="/cgi-bin/hgGateway?db=hg38" target="_blank">(GRCh38/hg38)</a> genome browser. The composite track displays multiple alignments (Multiz) and measurements of evolutionary conservation (phastCons and phyloP) for 470 mammals. </p> <h3>Tracks available:</h3> <ul> @@ -1892,31 +1892,31 @@ sequences, 261 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>p13/</b> subdirectory contains files for GRCh38.p13 (patch release 13). It has 640 sequences including alternate and fix 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 hg38. We would also like to thank Galt Barber, +Reference Consortium</a> for creating the patches for hg38. We would also like to thank Galt Barber, Jairo Navarro, and Gerardo Perez at UCSC for implementing and testing the latest patch to the hg38 genome.</p> <a name="092721"></a> <h2>Sep. 27, 2021 JASPAR tracks for human (hg19/hg38)</h2> <p> We are pleased to announce the release of the <a target="_blank" href="/cgi-bin/hgTrackUi?db=hg38&g=jaspar&position=default"> JASPAR Transcription Factors tracks</a> for human assemblies hg19/GRCh37 and hg38/GRCh38.</p> <p> These data represent genome-wide predicted binding sites for TF (transcription factor) binding profiles in the <a target="_blank" href="http://jaspar.genereg.net/about/"> JASPAR CORE collection</a>. This collection is an open-source database containing a curated, non-redundant set of binding profiles derived from published collections of experimentally defined transcription factor binding sites for eukaryotes.</a> @@ -2012,31 +2012,31 @@ 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 +Reference 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> @@ -5743,31 +5743,31 @@ 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 +We would like to thank the Genome Reference 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 (hg38)</h2> <p> 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 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