Thanks Jeremy,
The issue mentioned by Slim is also related to the same issue as of Matteo. In 
the end out put files either dont have geneIDS or has multiple enteries of 
particular gene. Any suggestion?

--- On Mon, 1/24/11, Slim Sassi <> wrote:

From: Slim Sassi <>
Subject: [galaxy-user] NGS RNA-seq
Date: Monday, January 24, 2011, 7:47 AM

I have followed the steps described by Jeremy in his exercise 
( to 
analyze RNA-seq data and all of the steps seemed to go ok except that at the 
end the gene IDs were missing, so for example the file CDS diff file had 
nothing in it. All the steps seemed to be executed correctly with proper 
mapping to various places in the mouse genome.
Please help



Slim O. Sassi, PhD
Research Fellow
Center for Computational and Integrative Biology, Massachusetts General Hospital
Department of Genetics, Harvard Medical School
185 Cambridge Street
CCIB- CPZN 7-7228 Simches Research Center
Boston MA 02114
Phone: (617) 726-5971
Fax: (617) 643-3328

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