04e474318652ef6cb769df351301c2fc26ec50bf luvina Fri Jan 8 08:40:43 2016 -0800 added snp144 announcement diff --git src/hg/htdocs/indexNews.html src/hg/htdocs/indexNews.html index ee1c3f5..055b782 100755 --- src/hg/htdocs/indexNews.html +++ src/hg/htdocs/indexNews.html @@ -1,163 +1,155 @@ <!-- News Section ============================================- --> <TABLE style="background-color:#888888; width: 100%; border-width: 0px; border-spacing: 0px; padding: 0px"> <TR><TD> <TABLE style="background-color:#fffee8; width: 100%; border-width: 0px; border-spacing: 0px; padding: 0px"> <TR><TD> <TABLE style="background-color:#D9E4F8; background-image: url('images/hr.gif'); width: 100%; border: 0px"> <TR><TD> <!--cheap trick to get background on row to be continuous--> <TABLE CELLPADDING=0 CELLSPACING=0 WIDTH="100%"> <TR><TD ALIGN="left"> <font size="4"><a name="TOC"></a><b> News</b></font><a href="http://www.twitter.com/GenomeBrowser" target="_blank"><img src="http://twitter-badges.s3.amazonaws.com/t_small-a.png" title="Follow @GenomeBrowser on Twitter" alt="Follow @GenomeBrowser on Twitter" style="vertical-align:text-bottom; margin-left: 15px;"></a> <a title="Genome Browser Facebook page" href="http://www.facebook.com/ucscGenomeBrowser" target="_blank"><img src="/images/FB-f-Logo__blue_22.jpg" style="vertical-align:text-bottom; margin-left: 15px;" alt="Genome Browser Facebook page"></a> <a href="https://plus.google.com/107643636314131661344" rel="publisher"></a> </TD> <TD ALIGN="right"><A HREF="goldenPath/newsarch.html"><IMG SRC="images/news.jpg" ALT="" ALIGN="right" BORDER=0></A> </TD></TR></TABLE> </TD></TR></TABLE> <TABLE style="background-color:#fffee8; width: 100%; padding: 0px"> <TR><TH HEIGHT=3></TH></TR> <TR><TD WIDTH=10></TD> <TD> <P> To receive announcements of new genome assembly releases, new software features, updates and training seminars by email, subscribe to the <A HREF="http://groups.google.com/a/soe.ucsc.edu/group/genome-announce?hl=en" TARGET=_blank>genome-announce</A> mailing list. Please see our <a href="http://genome.ucsc.edu/blog" target=_blank>blog</a> for posts about Genome Browser tools, features, projects and more. </p> <!-- start news --> <hr> <p> - <font color="#006666" size="4"><b> - Happy Holidays from the UCSC Genome Browser! —</b></font> - Here's a <A - HREF="../cgi-bin/hgTracks?db=hg38&hgct_customText=http://hgwdev.cse.ucsc.edu/~brianlee/customTracks/testBigGenePred/testFun/customTrackLines">card</A> - for you! + <font color="#006666" size="4"><b> 08 January 2016 - + dbSNP 144 Available for hg19 and hg39</b></font> + <p> + We are pleased to announce the release of four tracks derived + from NCBI <a href="http://www.ncbi.nlm.nih.gov/SNP/"> + dbSNP</a> Build 144 data, available on the two most + recent human assemblies GRCh37/hg19 and GRCh38/hg38. + </p> + <p> + There are four SNP tracks available as part of this release. + One is a track containing all mappings of reference SNPs + to the human assembly, labeled "All SNPs (144)". + The other three tracks are subsets of this track + and show interesting and easily defined subsets of dbSNP: + </p> + + <ul> + <li>Common SNPs (144): uniquely mapped variants that appear + in at least 1% of the population or are 100% non-reference</li> + <li>Flagged SNPs (144): uniquely mapped variants, excluding + Common SNPs, that have been flagged by dbSNP as + "clinically associated"</li> + <li>Mult. SNPs (144): variants that have been mapped to more + than one genomic location</li> + </ul> + <p> + By default, only the Common SNPs (144) are visible; + other tracks must be made visible using the track controls. + You will find the other SNPs (144) tracks on both + of GRCh37/hg19 and GRCh38/hg38 browsers in the "Variation" group. + </p> + <p> + The tracks were produced at UCSC by Angie Hinrichs and + Luvina Guruvadoo. We'd like to thank the dbSNP group at + NCBI for providing access to these data. + </p> <hr> + <p> <font color="#006666" size="4"><b> 21 December 2015 - Two New Assemblies Now Available in the Genome Browser</b></font> <p> A Genome Browser is now available for the frog (<em>Xenopus tropicalis</em>) assembly released September 2012 by the <a href="http://genome.jgi.doe.gov/" target="_blank">US DOE Joint Genome Institute (JGI-PGF)</a> (JGI v7.0, UCSC version xenTro7). For more information and statistics about this assembly, see the NCBI assembly record for <a href="http://www.ncbi.nlm.nih.gov/assembly/515038" target="_blank"> Xtropicalis_v7</a>. There are 7,728 scaffolds with a total size of 1,437,530,879 bases. </p> <p> Bulk downloads of the sequence and annotation data may be obtained from the Genome Browser <a href="ftp://hgdownload.soe.ucsc.edu/goldenPath/xenTro7/">FTP server</a> or the <a href="http://hgdownload.soe.ucsc.edu/downloads.html#xentro">Downloads</a> page. Please observe the <a href="goldenPath/credits.html#xentro_use">conditions for use</a> when accessing and using these data sets. The annotation tracks for this browser were generated by UCSC and collaborators woldwide. See the <a href="goldenPath/credits.html#xentro_credits">Credits</a> page for a detailed list of the organizations and individuals who contributed to this release. </p> --- <p> A Genome Browser is now available for the cat (<em>Felis catus</em>) assembly released November 2014 by the International Cat Genome Sequencing Consortium (ICGSC version Felis_catus_8.0, UCSC version felCat8). For more information and statistics about this assembly, see the NCBI assembly record for <a href="http://www.ncbi.nlm.nih.gov/assembly/1373248" target="_blank"> Felis_catus_8.0</a>. There are 267,625 scaffolds with a total size of 2,641,342,258 bases. </p> <p> Bulk downloads of the sequence and annotation data may be obtained from the Genome Browser <a href="ftp://hgdownload.soe.ucsc.edu/goldenPath/felCat8/">FTP server</a> or the <a href="http://hgdownload.soe.ucsc.edu/downloads.html#cat">Downloads</a> page. Please observe the <a href="goldenPath/credits.html#cat_use">conditions for use</a> when accessing and using these data sets. The annotation tracks for this browser were generated by UCSC and collaborators woldwide. See the <a href="goldenPath/credits.html#cat_credits">Credits</a> page for a detailed list of the organizations and individuals who contributed to this release. </p> <hr> - <p> - <font color="#006666" size="4"><b>16 December 2015 — - Output from Related Tables Now Available in the Data Integrator</b></font> - <p> - In the UCSC Genome Browser database, detailed information on the annotations for many tracks - is stored in extra tables. This information can include things such as identifiers - in other databases, transcript status, or other descriptive information. You can now obtain - data from these related tables in your output from the - <a href="cgi-bin/hgIntegrator">Data Integrator</a>. - </p> + <!-- start archives --> +<!--staged for future release + + - <p> - To add related tables to your Data Integrator output, first, select and add at least one - track to your data sources. Then, scroll down to the "Output Options" section and click the - <button type="button">Choose fields</button> button. - Lastly, at the bottom of the section for each selected track, you will see a drop-down menu - labeled "Related tables" which allows you to select and add various tables to your output. - <p><img style="border: 1px solid black; display: block;" - src="images/hgIntegratorRelatedTablesAnnouncement.png"> - <p> - For more information about using the Data Integrator, please see the - <a href="goldenPath/help/hgIntegratorHelp.html">User Guide</a>. - </p> - <p> - Thank you to Angie Hinrichs and Matthew Speir for their work on this feature. - </p> - <hr> - <!-- start archives --> -<!--staged for future release <p> <font color="#006666" size="4"><b> 21 December 2015 - Two New Assemblies Now Available in the Genome Browser</b></font> <p> Genome Browsers are now available for the frog (<em>Xenopus tropicalis</em>) and cat (<i>Felis catus</i>) assemblies. <a href="goldenPath/newsarch.html#122115">Read more</a>. </p> +--> <p> <font color="#006666" size="4"><b>16 December 2015 — Output from Related Tables Now Available in the Data Integrator</b>: </font> You can now obtain data from these related tables in your output from the <a href="cgi-bin/hgIntegaror">Data Integrator</a>. <a href="goldenPath/newsarch.html#121615">Read more</a>. </p> ---> - <p> - <font color="#006666" size="4"><b>9 December 2015 — - Data from 1000 Genomes Project Phase 3 Now Available</b>: </font> - We have made data from Phase 3 of the - <a href="http://www.1000genomes.org/" target="_blank">1000 Genomes Project</a> - available for the hg19 version of the human assembly. - <a href="goldenPath/newsarch.html#120915">Read more</a>. - </p> - <p> - <font color="#006666" size="4"><b>25 November 2015 — - New "View - In External Tools" Menu Sends Data to Prediction Websites!</b></font> - Do you often get the current sequence with "View - DNA" just to copy - and paste it into another website? With the new menu "View - In External Tools" - you can now send the current region to remote tools with two clicks. - <a href="goldenPath/newsarch.html#112515">Read more</a>. - </p> </TD><TD WIDTH=15> </TD></TR></TABLE> <BR></TD></TR></TABLE> </TD></TR></TABLE>