Hi Roberta,

Here is a link to the documentation for replicate handling for the 'NGS: RNA Analysis' tool Cuffdiff:

Other related areas of the documentation are:

Also see (under 'RNA-seq analysis tools'):

Good luck with your project!

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:

I managed to make it work. Thank you for your help.

Jennifer Jackson
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