Hello,

On 7/16/12 10:50 PM, i b wrote:
ok, so if I have 3 different samples I would use 3 different groups and
add my samples as replicate within each group.


Yes, where each sample represents an individual condition.

or did you mean to create just one group and add all my 3 samples as 3
replicates within that only group?

No, would be incorrect. Only replicates from the same sample/condition should be in the same group. This is not appear to be the case for your data, given the additional information.

Thanks!

Jen
Galaxy team
thanks a lot
ngs-ib
________________________________________
From: Jennifer Jackson [j...@bx.psu.edu <mailto:j...@bx.psu.edu>]
Sent: Tuesday, July 17, 2012 1:58 AM
To: Irene Bassano
Cc: galaxy-user@lists.bx.psu.edu <mailto:galaxy-user@lists.bx.psu.edu>
Subject: Re: [galaxy-user] cuffdiff

Hello Irene,

On 7/16/12 4:11 PM, Irene Bassano wrote:
 > Hi,
 > just few questions about cuffdiff if anyone can answer:
 >
 > 1.how can I load more than two sam/bam files?Galaxy gives spaceonly
for two files

Change the tool form for the option "Perform replicate analysis:" to be
"Yes" (the default is "No"). Use two conditions (Groups).

 >
 > 2.what to use as input: cufflinks, cuffcompare or cuffmerge?

GTF output from any of these may be appropriate.

Please see the tutorial on Galaxy main at:
http://main.g2.bx.psu.edu/u/jeremy/p/galaxy-rna-seq-analysis-exercise
FAQ:
http://main.g2.bx.psu.edu/u/jeremy/p/transcriptome-analysis-faq

And the "Common uses" protocols on the Cufflinks web site plus their new
paper (also linked at this site, from side bar, as "Protocol"):
http://cufflinks.cbcb.umd.edu/tutorial.html

Best,

Jen
Galaxy team

 >
 >
 > Thanks a lot!
 >
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--
Jennifer Jackson
http://galaxyproject.org



--
Jennifer Jackson
http://galaxyproject.org


___________________________________________________________
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