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 a lot
From: Jennifer Jackson [j...@bx.psu.edu <mailto:j...@bx.psu.edu>]
Sent: Tuesday, July 17, 2012 1:58 AM
To: Irene Bassano
Cc: firstname.lastname@example.org <mailto:email@example.com>
Subject: Re: [galaxy-user] cuffdiff
On 7/16/12 4:11 PM, Irene Bassano wrote:
> 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:
And the "Common uses" protocols on the Cufflinks web site plus their new
paper (also linked at this site, from side bar, as "Protocol"):
> Thanks a lot!
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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:
To manage your subscriptions to this and other Galaxy lists,
please use the interface at: