Hi there, 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! Chris Christopher Balakrishnan Institute for Genomic Biology University of Illinois 1206 W. Gregory Drive MC-195 Urbana, IL 61801 phone: 617-905-2910 http://myweb.ecu.edu/balakrishnanc
Hi Chris You may find DESeq at the Galaxy website http://galaxy.fml.mpg.de/ Le 14/06/2011 19:28, Christopher Balakrishnan a écrit :
Hi there,
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!
Chris Christopher Balakrishnan Institute for Genomic Biology University of Illinois 1206 W. Gregory Drive MC-195 Urbana, IL 61801 phone: 617-905-2910 http://myweb.ecu.edu/balakrishnanc
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participants (2)
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Christopher Balakrishnan -
Philippe Lefebvre