ok, so if I have 3 different samples I would use 3 different goups and add my samples as replicate within each group.
 
or did you mean to create just one group and add all my 3 samples as 3 replicates within that only group?
 
thanks a lot
ngs-ib
________________________________________
From: Jennifer Jackson [jen@bx.psu.edu]
Sent: Tuesday, July 17, 2012 1:58 AM
To: Irene Bassano
Cc: 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