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?
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.eduSubject: 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-exerciseFAQ:
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.htmlBest,
Jen
Galaxy
team
>
>
> Thanks a lot!
>
>
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--
Jennifer
Jackson
http://galaxyproject.org