791195a390b6bf8faf3194648e27b9fb208b9365 kuhn Thu May 19 14:52:17 2022 -0700 added explicit opening of evaSnp tracks to release announcement. Too late for most people, but I just sent the link to someone and wanted them to see the track open and obvious diff --git src/hg/htdocs/goldenPath/newsarch.html src/hg/htdocs/goldenPath/newsarch.html index 87d47c4..78a9e55 100755 --- src/hg/htdocs/goldenPath/newsarch.html +++ src/hg/htdocs/goldenPath/newsarch.html @@ -161,36 +161,36 @@ <a target="_blank" href="/cgi-bin/hgTrackUi?db=hg38&g=skinSoleBoldo&position=default">Skin Sole-Boldo</a> </li> </ul> <p> We hope that this combined format will facilitate research and comparison with the recently released <a href="#033122">Tabula Sapiens</a> expression tracks. We would like to thank Jim Kent, Brittney Wick, Jonathan Casper, and Jairo Navarro for their work in creating and releasing these tracks. </p> <a name="050322"></a> <h2>May 3, 2022 New GnomAD Mutation Constraint track on GRCh38/hg38</h2> <p> We have just released the <b>GnomAD Genomes Mutation Constraint</b> track on the human GRCh38/hg38 -genome assembly. This track's data is based on GnomAD v3.1.2 and shows +genome assembly. This track's data is based on gnomAD v3.1.2 and shows relative frequency of variation in one kilobase windows across the entire genome. This quantifies population occurrence of disruptive variation caused by purifying natural selection, similar to negative selection on loss-of-function (LoF) for genes, but -calculated for non-coding regions, too. View the complete set of GnomAD tracks and read more on the -<a href="/cgi-bin/hgTrackUi?db=hg38&g=gnomadVariants">GnomAD description page</a>. +calculated for non-coding regions, too. View the complete set of gnomAD tracks and read more on the +<a href="/cgi-bin/hgTrackUi?db=hg38&g=gnomadVariants">gnomAD description page</a>. <a name="050222"></a> <h2>May 2, 2022 New Track Hub bigBarChart display and selection features</h2> <p> We are pleased to announce new settings to support the display of bigBarChart data in Track Hubs. <a href="help/hgTrackHubHelp.html#Intro">Track Hubs</a> are web-accessible directories of genomic data that can be viewed on the UCSC Genome Browser. Track Hubs allow a lab to share and host all their genomic data (<a href="help/bam.html">BAMs</a>, <a href="help/vcf.html">VCFs</a>, etc.) via a single Genome Browser link. The <a href="help/barChart.html">bigBarChart</a> track format displays a bar graph of category-specific values over genomic regions and is useful for displaying gene expression across a spectrum of tissues or other datasets where it is desirable to compare a set of related variables over specific genomic regions.</p> <p> Two new settings <a href="help/trackDb/trackDbHub.html#barChartBarMinWidth">barChartBarMinWidth</a> and <a href="help/trackDb/trackDbHub.html#barChartBarMinPadding">barChartBarMinPadding</a> @@ -258,42 +258,46 @@ </p> <a name="042222"></a> <h2>Apr. 22, 2022 European Variant Archive (EVA) data now available on 16 assemblies</h2> <p> The <a href="https://www.ebi.ac.uk/eva/" target="_blank">European Variant Archive</a> has extensive data on variation across many different species and assemblies. We have updated our 16 most popular non-human genome assemblies with their latest data: <a href="https://www.ebi.ac.uk/eva/?RS-Release&releaseVersion=3" target="_blank">Release 3</a>. Adding more to this dataset, we processed the raw data to include two extra fields, describing variant class and amino acid change if present. You can read more about these datasets on the <a href="/cgi-bin/hgTrackUi?db=mm39&g=evaSnp">description page</a> of any of the listed organisms. UCSC is proud to support research into ever-increasing species diversity and variant display. Happy Earth Day!</p> <ul> -<li>Mouse (<a href="/cgi-bin/hgTracks?db=mm39">mm39</a>, <a href="/cgi-bin/hgTracks?db=mm10">mm10</a>) -<li>Zebrafish (<a href="/cgi-bin/hgTracks?db=danRer11">danRer11</a>, <a href="/cgi-bin/hgTracks?db=danRer10">danRer10</a>) -<li>Cow (<a href="/cgi-bin/hgTracks?db=bosTau9">bosTau9</a>) -<li>Fruit Fly (<a href="/cgi-bin/hgTracks?db=dm6">dm6</a>) -<li>Chicken (<a href="/cgi-bin/hgTracks?db=galGal6">galGal6</a>, <a href="/cgi-bin/hgTracks?db=galGal5">galGal5</a>) -<li>Pig (<a href="/cgi-bin/hgTracks?db=susScr11">susScr11</a>) -<li>Rat (<a href="/cgi-bin/hgTracks?db=rn7">rn7</a>, <a href="/cgi-bin/hgTracks?db=rn6">rn6</a>) -<li>Horse (<a href="/cgi-bin/hgTracks?db=equCab3">equCab3</a>) -<li>Rhesus (<a href="/cgi-bin/hgTracks?db=rheMac10">rheMac10</a>) -<li>Macaque (<a href="/cgi-bin/hgTracks?db=macFas5">macFas5</a>) -<li>Sheep (<a href="/cgi-bin/hgTracks?db=oviAri4">oviAri4</a>) -<li>Cat (<a href="/cgi-bin/hgTracks?db=felCat9">felCat9</a>) +<li>Mouse (<a href="/cgi-bin/hgTracks?db=mm39&evaSnp=pack">mm39</a>, + <a href="/cgi-bin/hgTracks?db=mm10&evaSnp=pack">mm10</a>) +<li>Zebrafish (<a href="/cgi-bin/hgTracks?db=danRer11&evaSnp=pack">danRer11</a>, + <a href="/cgi-bin/hgTracks?db=danRer10&evaSnp=pack">danRer10</a>) +<li>Cow (<a href="/cgi-bin/hgTracks?db=bosTau9&evaSnp=pack">bosTau9</a>) +<li>Fruit Fly (<a href="/cgi-bin/hgTracks?db=dm6&evaSnp=pack">dm6</a>) +<li>Chicken (<a href="/cgi-bin/hgTracks?db=galGal6&evaSnp=pack">galGal6</a>, + <a href="/cgi-bin/hgTracks?db=galGal5&evaSnp=pack">galGal5</a>) +<li>Pig (<a href="/cgi-bin/hgTracks?db=susScr11&evaSnp=pack">susScr11</a>) +<li>Rat (<a href="/cgi-bin/hgTracks?db=rn7&evaSnp=pack">rn7</a>, + <a href="/cgi-bin/hgTracks?db=rn6&evaSnp=pack">rn6</a>) +<li>Horse (<a href="/cgi-bin/hgTracks?db=equCab3&evaSnp=pack">equCab3</a>) +<li>Rhesus (<a href="/cgi-bin/hgTracks?db=rheMac10&evaSnp=pack">rheMac10</a>) +<li>Macaque (<a href="/cgi-bin/hgTracks?db=macFas5&evaSnp=pack">macFas5</a>) +<li>Sheep (<a href="/cgi-bin/hgTracks?db=oviAri4&evaSnp=pack">oviAri4</a>) +<li>Cat (<a href="/cgi-bin/hgTracks?db=felCat9&evaSnp=pack">felCat9</a>) </ul> <a name="041522"></a> <h2>Apr. 15, 2022 DECIPHER variants track for human (hg38)</h2> <p> We are pleased to announce the release of two DECIPHER variant tracks, <a href="/cgi-bin/hgTrackUi?db=hg38&c=chrX&g=decipher">DECIPHER CNVs</a> and <a href="/cgi-bin/hgTrackUi?db=hg38&c=chrX&g=decipherSnvs">DECIPHER SNVs</a>, available for human (GRCh38/hg38)</a>. The genomic locations of DECIPHER variants are labeled with the DECIPHER variant descriptions. <b>Mouseover</b> on items shows variant details, clinical interpretation, and associated conditions. Further information on each variant is displayed on the details page by a click onto any variant. </p> <p>