Tuesday, September 25, 2012

v11: search track by GEO accession, and bug fixes

Get source code from dropbox folder.

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.