Hello Alicia,
There are two tools in the main Galaxy Tool Shed (http://toolshed.g2.bx.psu.edu/) that would likely be helpful. Read the input requirements for each to decide which is a better fit. Search for 'deseq' to find them:
deseq_and_sam2counts deseq_hts
To use these tools, a local or cloud instance will be needed. Help to get started is in these wikis: http://usegalaxy.org/cloud http://getgalaxy.org http://wiki.g2.bx.psu.edu/Tool%20Shed
The best list to use for local/cloud support is the galaxy-dev@bx.psu.edu. http://wiki.g2.bx.psu.edu/Support#Mailing_Lists
Also sure to subscribe to the galaxy-announce mailing list and follow the Distribution News Briefs to stay updated: http://wiki.g2.bx.psu.edu/News
Best,
Jen Galaxy team
On 10/5/12 8:40 AM, Alicia R. Pérez-Porro wrote:
Hi all,
I'm about to start doing gene expression analysis but i don't have a reference genome. I got my sequences from Illumina and i did my assemblies with CLC bio. I was planning to use DESeq for the analysis but for that i need my gene expression count values. There is any tool in Galaxy that i can use for that?
Thanks, Alicia.
––
Alicia R. Pérez-Porro PhD student
Giribet lab Department of Organismic and Evolutionary Biology MCZ labs Harvard University 26 Oxford St, Cambridge MA 02138 phone: +1 617-496-5308 fax: +1 617-495-5667 www.oeb.harvard.edu/faculty/giribet/ http://www.oeb.harvard.edu/faculty/giribet/
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