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!
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>
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,
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.
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: