Hi Roberta,
Here is a link to the documentation for replicate handling for the 'NGS:
RNA Analysis' tool Cuffdiff:
http://cufflinks.cbcb.umd.edu/howitworks.html#reps
Other related areas of the documentation are:
http://cufflinks.cbcb.umd.edu/faq.html#cuffdiff
http://cufflinks.cbcb.umd.edu/howitworks.html#hdif
Also see (under 'RNA-seq analysis tools'):
http://wiki.g2.bx.psu.edu/Support#Interpreting_scientific_results
Good luck with your project!
Jen
Galaxy team
On 9/11/12 7:45 AM, James Taylor wrote:
Roberta, I'm traveling right now so I'm forwarding your message to our
help list. Thanks.
---------- Forwarded message ----------
From: Roberta Galletti <roberta.galle...@ens-lyon.fr>
Date: Tue, Sep 11, 2012 at 5:19 AM
Subject: Re: Galaxy: RNA-seq analysis problems
To: James Taylor <ja...@jamestaylor.org>
Hello James,
sorry to bother you again, but I've one more question for you. I know
that most existing methodologies to analyze RNA-seq data, have a
strong dependency on sequencing depth for their differential
expression calls and that this results might have a considerable
number of false positives. Unfortunately, 1 out of 3 biological
replicates of a set of my samples have a much bigger seq depth with
respect to the other two samples. Do the programs in the Galaxy NGS:
RNA Analysis section take into account this problem and normalize it?
Thank you in advance for you help,
Roberta Galletti.
On 6/11/2012 5:36 PM, James Taylor wrote:
Glad to hear it! Thanks!
On Jun 8, 2012, at 9:37 AM, Roberta Galletti wrote:
James,
I managed to make it work. Thank you for your help.
Roberta.
--
Jennifer Jackson
http://galaxyproject.org
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