1e8a4303eb78516828c700131dfdeeea350f6c11 pauline Tue Apr 29 16:19:26 2014 -0700 Adding announcement about re-release of 100way data. refs #12405 #12260 diff --git src/hg/htdocs/indexNews.html src/hg/htdocs/indexNews.html index 6b104f2..0f40f71 100755 --- src/hg/htdocs/indexNews.html +++ src/hg/htdocs/indexNews.html @@ -1,128 +1,136 @@ <!-- News Section ============================================- --> <TABLE WIDTH="100%" BGCOLOR="#888888" BORDER="0" CELLSPACING="0" CELLPADDING="1"> <TR><TD> <TABLE BGCOLOR="#fffee8" WIDTH="100%" BORDER="0" CELLSPACING="0" CELLPADDING="0"> <TR><TD> <TABLE BGCOLOR="#D9E4F8" BACKGROUND="images/hr.gif" WIDTH="100%" BORDER=0> <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" alt="Follow GenomeBrowser on Twitter" style="vertical-align:text-bottom; margin-left: 15px;"></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 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.</P> <!-- start news --> <hr> <p> + <font face="courier" size="3"><b> 29 Apr 2014 - + 100-species Conservation track re-release</b></font> + <p> + We released the initial version of the 100-species Conservation track + for the hg19 human assembly in November 2013. Over the past few months, + we found a couple of inconsistencies and decided, for the integrity of + the data, that we should rerun the computation pipeline and re-release + the data. The fixes required minimal changes, and resulted in a more + precise data set. We published the new version of the hg19 100-species + Conservation track on 15 April 2014. + </p> + <p> + Here are more details about the two fixes that we made: + </p> + <p> + 1. We tracked down the cause of some unusual gaps in the alignments to a + bug in the multiz program used in our alignment pipeline. The Penn State + Bioinformatics Group provided us with a fixed version of multiz that we + used to rerun the pipeline. + </p> + <p> + 2. We inadvertently used the pre-release assembly for one of the species + in the 100-way alignment: the panda. We replaced this assembly with the + correct version and verified that the data sets for all other species + were correct before rerunning the pipeline. + </p> + <hr> + + <p> <font face="courier" size="3"><b> 18 April 2014 - New Motif Displays for Transcription Factor ChIP-seq Track and New Genome Segmentations from ENCODE</b></font> <p> The Browser's default displayed Transcription Factor ChIP-seq track is updating to the <a class="euro" href="http://genome.ucsc.edu/cgi-bin/hgTrackUi?db=hg19&g=wgEncodeRegTfbsClusteredV3">latest data release</a>, which has been enhanced with the display of Factorbook motifs. Within a cluster, a green highlight indicates the highest scoring site of a Factorbook-identified canonical motif for the corresponding factor. Upon clicking a transcription factor's cluster with a motif, the details page now displays the motif's sequence logo, alignment and underlying Positional Weight Matrix. Also, the track configuration page now enables the filtering of factors. </p> <p> The newly added <a class="euro" href="http://genome.ucsc.edu/cgi-bin/hgTrackUi?db=hg19&g=wgEncodeAwgSegmentation"> Genome Segmentations from ENCODE</a> tracks display multivariate genome-segmentation performed on <a target=ucscVocab href="http://genome.ucsc.edu/cgi-bin/hgEncodeVocab?term=GM12878,H1-hESC,K562,HeLa-S3,HepG2,HUVEC">six human cell types</a> (GM12878, K562, H1-hESC, HeLa-S3, HepG2, and HUVEC), integrating ChIP-seq data for <a target=ucscVocab href="http://genome.ucsc.edu/cgi-bin/hgEncodeVocab?term=CTCF,H3K4me1,H3K4me2,H3K4me3,H3K27ac,H3K9ac,H3K36me3,H4K20me1,H3K27me3,Pol2,Input"> eight chromatin marks, RNA Polymerase II, the CTCF transcription factor and input data</a>. In total, twenty-five states were used to segment the genome, and these states were then grouped and colored to highlight predicted functional elements. These Genome Segmentations are the same data as found in the Analysis Working Group Hub, but are now hosted natively in the Browser with enhanced filtering capability where desired segmented states can be selected using the 'Filter by Segment Type' control on the track configuration page. </p> <hr> - <p> - <font face="courier" size="3"><b>15 April 2014 - - New Minke Whale (balAcu1) Assembly Now Available in the Genome Browser</b></font> - <p> - A Genome Browser is now available for the minke whale (Balaenoptera acutorostrata scammoni) - assembly released October 2013 by the <A HREF="http://eng.kiost.ac/kordi_eng/main/" TARGET="_BLANK"> - Korea Ocean Research & Development Institute</A> (KORDI version BalAcu1.0, UCSC version balAcu1). - For more information and statistics about this assembly, see the NCBI assembly record for - <A HREF="http://www.ncbi.nlm.nih.gov/assembly/78761" TARGET="_BLANK">BalAcu1.0</A>. There are - 10,776 scaffolds with a total size of 2,431,687,698 bases. - </p> - - <p> - Bulk downloads of the sequence and annotation data may be obtained from the Genome Browser - <A HREF="ftp://hgdownload.cse.ucsc.edu/goldenPath/balAcu1/">FTP server</A> or the - <A HREF="http://hgdownload.cse.ucsc.edu/downloads.html#minke_whale">Downloads</A> page. Please - observe the <A HREF="goldenPath/credits.html#minke_whale_use">conditions for use</A> when accessing and - using these data sets. The annotation tracks for this browser were generated by UCSC and - collaborators worldwide. See the <A HREF="goldenPath/credits.html#minke_whale_credits">Credits</A> - page for a detailed list of the organizations and individuals who contributed to this release. - </p> - <hr> <!-- staged for archive use. NOTE: condense header line from .... </b></font><p> to </b></font>: <p> <font face="courier" size="3"><b>18 April 2014 - New Motif Displays and New Genome Segmentations from ENCODE</b></font>: The Browser's default displayed <a class="euro" href="http://genome.ucsc.edu/cgi-bin/hgTrackUi?db=hg19&g=wgEncodeRegTfbsClusteredV3">Transcription Factor ChIP-seq track</a> updated to the latest release, enhanced with the display of Factorbook motifs. And the Browser added <a class="euro" href="http://genome.ucsc.edu/cgi-bin/hgTrackUi?db=hg19&g=wgEncodeAwgSegmentation">Genome Segmentations from ENCODE</a> tracks, which segment the genome into twenty-five states that were then grouped and colored to highlight predicted functional elements. <a href="goldenPath/newsarch.html#041814">Read more</a>. </p> + <font face="courier" size="3"><b> 29 Apr 2014 - + 100-species Conservation track re-release</b></font> + <p> + We released the initial version of the 100-species Conservation track + for the hg19 human assembly in November 2013. Over the past few months, + we found a couple of inconsistencies and decided, for the integrity of + the data, that we should rerun the computation pipeline and re-release + the data. <a href="goldenPath/newsarch.html#042914">Read more</a> + + --> + <!-- start archives --> + <p> <font face="courier" size="3"><b>15 April 2014 - New Minke Whale (balAcu1) Assembly Now Available in the Genome Browser</b></font>: A Genome Browser is now available for the minke whale (Balaenoptera acutorostrata scammoni) assembly released October 2013 by the Korea Ocean Research & Development Institute. <a href="goldenPath/newsarch.html#041514">Read more</a>. </p> - --> - <!-- start archives --> <p> <font face="courier" size="3"><b>11 April 2014 - 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#041114">Read more</a>. </p> - <p> - <font face="courier" size="3"><b>06 March 2014 - - The new GRCh38 Human Genome Browser is here!</b></font>: - In the final days of 2013, the Genome Reference Consortium (GRC) - released the eagerly awaited GRCh38 human genome assembly, the - first major revision of the human genome in more than four years. - <a href="goldenPath/newsarch.html#030614">Read more</a>. - </p> - </TD><TD WIDTH=15> </TD></TR></TABLE> <BR></TD></TR></TABLE> </TD></TR></TABLE>