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Old 10-09-2012, 07:52 PM   #5
fubar
Crusty old bioinformatician
 
Location: Melbourne, Australia

Join Date: Oct 2010
Posts: 8
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Quote:
Originally Posted by 2004rs View Post
Another newbie question - is this capability integrated into Galaxy?
The answer depends on exactly what you mean by "into Galaxy"
1. No, not on the public Galaxy instances run by the Galaxy Team.
2. Yes, if you have your own Galaxy. There's at least one suitable tool I seem to remember seeing in the main Toolshed - but it required Matlab (!) for some strange reason... OTOH, you can find a version that uses pysam (warning: work in progress!) at https://bitbucket.org/fubar/rgalaxy/...ics/bams2mx.py and https://bitbucket.org/fubar/rgalaxy/...cs/bams2mx.xml if you're game to try it. There's a bunch of other downstream tools in that repo that can use the resulting count matrixes including edgeR, DESeq and further downstream, GSEA and SPIA wrappers too. Enjoy but remember, YMMV.
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