v12 minor release: S. pombe genome, bug fixes

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S. pombe genome

Version 12 code release supports the genome of Schizosaccharomyces pombe, the fission yeast. It is the first fungi species supported by WashU Genome Browser.


The S. pombe genome assembly was released on March 2012 and was downloaded from PomBase. You're welcome to suggest additional annotation/public experimental assay data sets to be added to this genome.

Procedures to prepare the S. pombe genome database can be viewed here.

Bug fix

A major bug that prevents session from been restored when it's about juxtaposition with custom bed track is now fixed.

An error that prevents from parsing URL parameters was fixed. You can now append session information to a URL in the format of:

http://epigenomegateway.wustl.edu/browser/?genome=[ASSEMBLY]&session=[SESSION]

Where [ASSEMBLY] is name of genome assembly (e.g. hg19), and [SESSION] is session ID. By composing such an URL you can easily share saved sessions with others.

Additionally, you can append status ID to the URL: &statusid=[STATID]

v11: search track by GEO accession, and bug fixes

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Version 11 code release provides new feather that allows you to search for tracks with a list of GEO accession numbers, and a few bug fixes.

Find track by GEO accession

Follow these steps to see this new feature in action.

Click this link to open up the Browser with human genome hg19 but no data:

http://epigenomegateway.wustl.edu/browser/?genome=hg19

At navigation bar click tab "Genome heatmap":

Inside the panel, click tab "Find by GEO":

Enter GEO accessions. You can use a list of them here, one accession per line:


GSM469970
GSM521901
GSM521895
GSM521897
GSM521909
GSM521913
GSM469968
GSM521889
GSM608165
GSM945297
GSM788085
GSM733692
GSM607494
GSM733776
GSM945228

This function only accepts Sample accessions (names start with GSM), but not Series (names start with GSE), or Platforms (names start with GPL).

Press button "Search", a short moment later the search results appear:

Tracks are listed in the table on the right. You can press the button "Display all" to have all of them displayed.

Otherwise, you can selectively display a few by clicking on the track labels, and the selected tracks will be added to a table in the toolbox panel. After you finish selection, press button there to add them.

And thank Rebecca Lowdon for suggesting this feature!

Bug fix

A bug associated with displaying bigwig tracks as "wreath tracks" for the Henge View is corrected.

A bug affecting the parsing of mismatching base pairs in the SAM track is fixed.

v10 minor update: bug fix and more scrolling options

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This code release fixed a bug associated with SAM track display. When displaying read alignment data during genomic juxtaposition mode, the track image appeared to be shifted due to the bug, now it's fixed.

Besides, you can now drag on any of the genome annotation tracks to scroll.

Try this link to open the browser and show the tracks as displayed in the screen shot below:

http://epigenomegateway.wustl.edu/browser/?genome=hg19&juxtapose=LTR&gftk=LTR,full&coordinate=chr1:1340000-1390000&custombam=stat1hela,http://vizhub.wustl.edu/hubSample/hg19/sam1.gz,thin

As illustrated in this example, genomic juxtaposition focuses the view on LTR elements and reveals that STAT1 ChIP-Seq reads bind one LTR copy, suggesting this LTR copy has something to do with STAT1's business in HeLa cells.

STAT1 ChIP-Seq data comes from this publication: Genome-wide profiles of STAT1 DNA association using chromatin immunoprecipitation and massively parallel sequencing