d7106732e0f5642c0b28736e41587a4d17a64071 luvina Mon Jun 29 11:26:13 2015 -0700 added gencode genes announcement to homepage diff --git src/hg/htdocs/indexNews.html src/hg/htdocs/indexNews.html index 637c900..df586cf 100755 --- src/hg/htdocs/indexNews.html +++ src/hg/htdocs/indexNews.html @@ -24,116 +24,131 @@ <TABLE BGCOLOR="#fffee8" WIDTH="100%" CELLPADDING=0> <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 face="courier" size="3"><b>29 June 2015 - + GENCODE Genes Now the Default Gene Set on the Human (GRCh38/hg38) Assembly</b></font> + <p> + In a move towards standardizing on a common gene set within the bioinformatics + community, UCSC has made the decision to adopt the GENCODE set of gene models + as our default gene set on the human genome assembly. Today we have released + the GENCODE v22 comprehensive gene set as our default gene set on human + genome assembly GRCh38 (hg38), replacing the previous default UCSC Genes set + generated by UCSC. To facilitate this transition, the new gene set employs + the same familiar UCSC Genes schema, using nearly all the same table names + and fields that have appeared in earlier versions of the UCSC set. + </p> + <p> + By default, the browser displays only the transcripts tagged as "basic" by the + GENCODE Consortium. These may be found in the track labeled "GENCODE Basic" in + the Genes and Gene Predictions track group. However, all the transcripts in the + GENCODE comprehensive set are present in the tables, and may be viewed by + adjusting the track configuration settings for the All GENCODE super-track. + The most recent version of the UCSC-generated genes can still be accessed in + the track "Old UCSC Genes". + </p> + <p> + The new release has 195,178 total transcripts, compared with 104,178 in the + previous version. The total number of canonical genes has increased from + 48,424 to 49,534. Comparing the new gene set with the previous version: + </p> + <ul> + <li>9,459 transcripts did not change.</li> + <li>22,088 transcripts were not carried forward to the new version.</li> + <li>43,681 transcripts are "compatible" with those in the previous set, + meaning that the two transcripts show consistent splicing. In most cases, + the old and new transcripts differ in the lengths of their UTRs.</li> + <li>28,950 transcripts overlap with those in the previous set, but do not + show consistent splicing (i.e., they contain overlapping introns with + differing splice sites)</li> + </ul> + <p> + More details about the new GENCODE Basic track can be found on the + <a href="https://genome.ucsc.edu/cgi-bin/hgTrackUi?db=hg38&g=knownGene"> + GENCODE Basic track description page</a>. + </p> + <hr> + <hr> <p> <font face="courier" size="3"><b>26 June 2015 - New Bonobo (panPan1) Assembly Now Available in the Genome Browser</b></font> <p> We are pleased to announce the release of a Genome Browser for the May 2012 assembly of bonobo, <em>Pan paniscus</em> (Max-Planck Institute panpan1, UCSC version panPan1). The assembly was provided by the <a href="http://www.eva.mpg.de/" target="_blank">Max-Planck Institute for Evolutionary Anthropology</a>. There are 10,867 scaffolds with a total size of 2,869,190,071 bases. </p> <p> Bulk downloads of the sequence and annotation data are available via the Genome Browser <a href="ftp://hgdownload.cse.ucsc.edu/goldenPath/panPan1/">FTP server</a> or the <a href="http://hgdownload.cse.ucsc.edu/downloads.html#bonobo">Downloads</a> page. These data have <a href="goldenPath/credits.html#bonobo_credits">specific conditions for use</a>. The bonobo (panPan1) browser annotation tracks were generated by UCSC and collaborators worldwide. See the <a href="goldenPath/credits.html#bonobo_credits">Credits</a> page for a detailed list of the organizations and individuals who contributed to this release. </p> <hr> - <p> - <font face="courier" size="3"><b>12 June 2015 - - Data Integrator</b></font> - <p>Have you ever wished that the Table Browser could associate your custom track items - with some other track, while retaining the item names from both? We have released a - new tool that can do just that, and more: the Data Integrator. - </p> - - <p>Using the Data Integrator you can select up to five tracks, including custom tracks - and hub tracks, and output tab-separated text that contains all the fields from both - the first track and the overlapping items from the other track(s). If you need only - a subset of the fields from your selected tracks, the Data Integrator allows you to - choose which fields to include in the output. You can also query your current Genome - Browser position, search for positions of items such as genes, SNPs, etc. by name, - query over a set of up to 1000 positions, and even retrieve genome-wide data - (subject to data size). The Data Integrator output can be viewed in your web browser - window or downloaded to an optionally gzip-compressed file. Look for "Data Integrator" - in the Genome Browser Tools menu (top blue bar) if you'd like to try it out. - </p> - </p> - - <p>For more information about the Data Integrator's capabilities and usage, see the - user's guide: - <a href="http://genome.ucsc.edu/goldenPath/help/hgIntegratorHelp.html" - >http://genome.ucsc.edu/goldenPath/help/hgIntegratorHelp.html</a>. - As always, we welcome questions and feedback on our public mailing list: - <a href="mailto:genome@soe.ucsc.edu" - >genome@soe.ucsc.edu</a> - <!-- above address is genome at soe.ucsc.edu --> - </p> - - <p>Thanks to Angie Hinrichs and Matthew Speir for all of their work on this feature. - </p> - - <hr> <!-- start archives --> <!-- + <p> + <font face="courier" size="3"><b>29 June 2015 - + GENCODE Genes Now Default Gene Set on the Human (GRCh38/hg38) Assembly</b>: + </font> + In a move towards standardizing on a common gene set within the bioinformatics + community, UCSC has made the decision to adopt the GENCODE set of gene models + as our default gene set on the human genome assembly. + <a href="goldenPath/newsarch.html#062915">Read more</a>. + </p> + + <p> <font face="courier" size="3"><b>26 June 2015 - New Bonobo (panPan1) Assembly Now Available in the Genome Browser</b>: </font> We are pleased to announce the release of a Genome Browser for the May 2012 assembly of bonobo, <em>Pan paniscus</em> (Max-Planck Institute panpan1, UCSC version panPan1). <a href="goldenPath/newsarch.html#062615">Read more</a>. + </p> +--> <font face="courier" size="3"><b>12 June 2015 - Data Integrator</b>: </font> Have you ever wished that the Table Browser could associate your custom track items with some other track, while retaining the item names from both? We have released a new tool that can do just that, and more: the Data Integrator. <a href="goldenPath/newsarch.html#061215">Read more</a>. </p> ---> <p> <font face="courier" size="3"><b>28 May 2015 - New UCSC Genes Track Released for GRCm38/mm10</b>: </font> We're happy to announce the release of an updated UCSC Genes track for the GRCm38/mm10 mouse Genome Browser. <a href="goldenPath/newsarch.html#052815">Read more</a>. </p> - - <p> - <font face="courier" size="3"><b>15 May 2015 - - Work for Us! New Job Openings on the UCSC Genome Browser Project</b>: </font> - The UCSC Genome Browser project team is looking for two talented people to join our - engineering staff based in Santa Cruz, CA. - <a href="goldenPath/newsarch.html#051515">Read more</a>. - </p> </TD><TD WIDTH=15> </TD></TR></TABLE> <BR></TD></TR></TABLE> </TD></TR></TABLE>