I noticed on Seqanswers there was a post inquiring about the potential
addition of DE-Seq (Anders & Huber) to the growing stack of tools
available in galaxy.
I for one would love to see this integrated.
I typically use it in combination with HT-Seq, a set of python scripts
also from Simon Anders. This simply has the functionality of
converting a SAM alignment to simple counts of reads per transcript
across the genome. Probably there are tools is Galaxy that do a
similar thing. In any case I think many people are using TopHat -> HT-
Seq -> DE-Seq for analysis of RNAseq data so it would be great if DE-
Seq were supported in Galaxy
My two cents..
Thanks for all your great work!
Institute for Genomic Biology
University of Illinois
1206 W. Gregory Drive MC-195
Urbana, IL 61801
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