8549c7efab6dec1e1dcbde6546a5c145f3a4c3d4
mspeir
Tue May 6 14:32:17 2014 -0700
adding announcement about stacked wiggle feature, plus fixing some other little documentation things, refs #11630
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<!-- News Section ============================================- -->
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<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>
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<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> 5 May 2014 -
+ Introducing the new stacked overlay for multi-wiggle tracks</b></font>
+ <p>
+ We are excited to announce the release of the new stacked
+ overlay method for multi-wiggle tracks. This new stacked overlay
+ method displays each graph stacked on top of each other.
+ </p>
+ <img style="border: 2px solid black; margin-left:auto;
+ margin-right:auto; display: block;"
+ src="images/stackedMultiWig_screenshot.png"
+ alt="Stacked screenshot">
+ <p>
+ Navigate to the track settings for <A HREF="cgi-bin/hgTrackUi?db=hg19&g=wgEncodeRegMarkH3k27ac"
+ >H3K27Ac Mark</A> on the human hg19 assembly to view this new stacked
+ overlay method on a multi-wiggle track. On the track settings page,
+ from the "Overlay method" drop-down menu select "stacked". Make sure
+ that the display mode is not set to hide, and click submit.
+ </p>
+ <p>
+ Credit for the implementation and testing of this new feature goes to
+ Brian Raney and Matthew Speir.
+ </p>
+
+ <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>
-
<!-- staged for archive use. NOTE: condense header line from .... </b></font><p> to </b></font>:
+ <font face="courier" size="3"><b> 29 Apr 2014 -
+ 100-species Conservation track re-release</b>:</font>
+ 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>
+
+ <font face="courier" size="3"><b> 5 May 2014 -
+ Introducing the new stacked overlay for multi-wiggle tracks</b>:</font>
+ We are excited to announce the release of the new "stacked"
+ overlay method for multi-wiggle tracks.
+ <a href="goldenPath/newsarch.html#050614">Read more</a>
+ -->
+ <!-- start archives -->
<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>
-
- <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>
-
-
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