b80137060da6eaa02e20272671b45db104f26691 lrnassar Mon Jan 22 15:36:56 2024 -0800 Fixing some small typos, no RM diff --git src/hg/htdocs/goldenPath/newsarch.html src/hg/htdocs/goldenPath/newsarch.html index a974558..76c4357 100755 --- src/hg/htdocs/goldenPath/newsarch.html +++ src/hg/htdocs/goldenPath/newsarch.html @@ -174,31 +174,31 @@ </ul></div> <div class="col-sm-4"> <ul> <li>Columbia Medellin</li> <li>Han SoChina</li> <li>Vietnam Kinh</li> <li>Punjabo Pakis</li> </ul></div> </div> </div> <p> The <a target="_blank>" href="/cgi-bin/hgTrackUi?db=hg38&c=chr6&g=consHprc90way">90-way Multiple Alignment track</a> contains multiple alignments of 90 human genomes generated by the Minigraph-Cactus pangenome pipeline, which creates pangenomes directly from whole-genome alignments. This method builds graphs containing all forms of genetic variation while allowing the use of current mapping and genotyping tools. The confirmation page sorts the Maternal and Paternal haplotypes by the same 14 subpopulations described above. </p> -<h3>Acknowledgements</h3> +<h3>Acknowledgments</h3> <p> We are always looking for feedback, if you would like to see other HPRC data, or the data presented differently, please contact us at <a href="mailto:genome@soe.ucsc.edu">genome@soe.ucsc.edu</a>. Likewise, if you find this data useful and see potential improvements, we would be interested in hearing from you. </p> <p> We would like to thank the Human Pangenome Reference Consortium for taking on this genomics challenge and providing these data. In particular, we would like to thank Benedict Paten, Heng Li and Glenn Hickey for their help in putting these Browser tracks together. From our team, we would like to thank Max Haeussler, Brian Raney, Mark Diekhans, Hiram Clawson, Gerardo Perez, Jairo Navarro, and Lou Nassar for their work in developing, testing, and releasing these tracks.</p> <!-- ============= 2023 archived news ============= --> @@ -2199,31 +2199,31 @@ target="_blank">https://hgdownload.soe.ucsc.edu/hubs/GCA/009/914/755/GCA_009914755.4/</a></p> <p> We also provide FASTA files there with two different sequence identifiers (the "chr1" format and Genbank accessions), gene annotations in GFF and other formats and assembly indexes with either Genbank or "chr1" sequence names for the aligners bwa-mem2, bowtie2, hisat2 and minimap2. Detailed download instructions can be found in the README and on our <a href="https://genome.ucsc.edu/cgi-bin/hgGateway?db=hub_3267197_GCA_009914755.4" target="_blank">assembly description page</a></p> <p> All liftOver files, including files to/from hg19/hg38 and CHM13 can also be found on our download server: <a href="https://hgdownload.gi.ucsc.edu/hubs/GCA/009/914/755/GCA_009914755.4/liftOver/" target="_blank">https://hgdownload.gi.ucsc.edu/hubs/GCA/009/914/755/GCA_009914755.4/liftOver/</a></p> -<h3>Acknowledgements</h3> +<h3>Acknowledgments</h3> <p> We would like to thank the <a href="https://sites.google.com/ucsc.edu/t2tworkinggroup" target="_blank">T2T Consortium</a> for this landmark accomplishment. We would like to extend an additional kudos to our fellow <a href="https://genomics.ucsc.edu/" target="_blank">UCSC Genomics Institute</a> members who are part of the consortium, Karen Miga, Benedict Paten, Kishwar Shafin, Mark Diekhans, and Miten Jain. Lastly, to the engineers and QA members of the Genome Browser for the rapid development and release of CHM13 data and features.</p> <a name="041122"></a> <h2>Apr. 11, 2022 CRISPR Targets for Cow (bosTau9) now available</h2> <p> We are happy to announce the release of the the <a href="/cgi-bin/hgTrackUi?db=bosTau9&c=chr6&g=crisprAllTargets">CRISPR Targets</a> track for the @@ -9753,31 +9753,31 @@ <li><a href="http://hgdownload.soe.ucsc.edu/hubs/gtexAnalysis/gtexAse.html" target="_blank"> GTEx Analysis Hub: Allele-Specific Expression</a> on <a href=" ../cgi-bin/hgTracks?db=hg38&hubUrl= http://hgdownload.soe.ucsc.edu/hubs/gtexAnalysis/gtexAnalysisHub.html" target="_blank">hg19</a> and <a href="../cgi-bin/hgTracks?db=hg38&hubUrl=http://hgdownload.soe.ucsc.edu/hubs/gtexAnalysis/gtexAnalysisHub.html" target="_blank">hg38</a>.</li> </ul> <p> Please see the related October 11, 2017 publication in <i>Nature</i>, "<a href="https://www.nature.com/nature/journal/v550/n7675/full/nature24277.html" target="_blank">Genetic effects on gene expression across human tissues</a>" for an in-depth article about these data.</p> <p> -Acknowledgements to UCSC Genome Browser engineer, Kate Rosenbloom, for creating these tracks. +Acknowledgments to UCSC Genome Browser engineer, Kate Rosenbloom, for creating these tracks. </p> <a name="092917"></a> <h2>Sep. 29, 2017 VAI tool can now output HGVS terms</h2> <p> The UCSC Genome Browser has <a href="help/query.html#HGVS" target="_blank">continued to expand</a> the support for Human Genome Variation Society (HGVS) nomenclature. We have recently enhanced our <a href="/cgi-bin/hgVai" target="_blank">Variant Annotation Integrator (VAI) tool</a> to allow output of HGVS terms from inputed variants when the gene prediction source is set to annotate on RefSeq genes.</p> <p> For a quick experience click the "Get results" button in this <a href="http://genome.ucsc.edu/cgi-bin/hgVai?hgS_doOtherUser=submit&hgS_otherUserName=brianlee&hgS_otherUserSessionName=hg38.exampleVAI" target="_blank">example session</a>. This session is loaded with an artifical input of variants on the human hg38 assembly with NCBI RefSeq Genes track (curated NM_*, NR_*, and YP_* subset)