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 <ssassi@CCIB.MGH.HARVARD.EDU> wrote: From: Slim Sassi <ssassi@CCIB.MGH.HARVARD.EDU> Subject: [galaxy-user] NGS RNA-seq To: galaxy-user@bx.psu.edu Date: Monday, January 24, 2011, 7:47 AM Hello, I have followed the steps described by Jeremy in his exercise (http://main.g2.bx.psu.edu/u/jeremy/p/galaxy-rna-seq-analysis-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 Thanks Slim 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 ssassi@ccib.mgh.harvard.edu The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail. _______________________________________________ galaxy-user mailing list galaxy-user@lists.bx.psu.edu http://lists.bx.psu.edu/listinfo/galaxy-user