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/>
___________________________________________________________
The Galaxy User list should be used for the discussion of
Galaxy analysis and other features on the public server
at usegalaxy.org. Please keep all replies on the list by
using "reply all" in your mail client. For discussion of
local Galaxy instances and the Galaxy source code, please
use the Galaxy Development list:
http://lists.bx.psu.edu/listinfo/galaxy-dev
To manage your subscriptions to this and other Galaxy lists,
please use the interface at:
http://lists.bx.psu.edu/
--
Jennifer Jackson
http://galaxyproject.org
___________________________________________________________
The Galaxy User list should be used for the discussion of
Galaxy analysis and other features on the public server
at usegalaxy.org. Please keep all replies on the list by
using "reply all" in your mail client. For discussion of
local Galaxy instances and the Galaxy source code, please
use the Galaxy Development list:
http://lists.bx.psu.edu/listinfo/galaxy-dev
To manage your subscriptions to this and other Galaxy lists,
please use the interface at:
http://lists.bx.psu.edu/
