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-...@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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