Roberta, I'm traveling right now so I'm forwarding your message to our
help list. Thanks.

---------- Forwarded message ----------
From: Roberta Galletti <>
Date: Tue, Sep 11, 2012 at 5:19 AM
Subject: Re: Galaxy: RNA-seq analysis problems
To: James Taylor <>

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.

Roberta Galletti, PhD
Laboratoire de Reproduction et Développement des Plantes
Ecole Normale Supérieure de Lyon, UMR 5667
46, allée d'Italie
69364 LYON cedex 07

e-mail 1:
e-mail 2:
Skype contact: roberta1977
...A lab is just another place to play....
 From 'Dancing naked in the mind field'
Kary B. Mullis, Nobel Prize in Chemistry 1993.

The Galaxy User list should be used for the discussion of
Galaxy analysis and other features on the public server
at  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:

Reply via email to