Hi Matteo and Vasu, There are different ways to refer to genes. Names that start with NM_ are termed 'accession numbers,' and they are a valid way to refer to genes. Matteo, what you may want is the canonical gene name (e.g. Xkr4). If so, you'll want to use a gene annotation/reference file from UCSC; when you are getting the file, you'll want to select the table with the word 'canonical' in it. E.g. for hg19/UCSC genes, there is a table called knownCanonical that provides the canonical gene names. Thanks, J. On Jan 24, 2011, at 9:38 AM, vasu punj wrote:
This is a knwon issue of GTF file from Ensembl
--- On Mon, 1/24/11, Matteo Bovolenta <bvlmtt@unife.it> wrote:
From: Matteo Bovolenta <bvlmtt@unife.it> Subject: [galaxy-user] Gene Name in Cufflink/compare/diff To: galaxy-user@bx.psu.edu Date: Monday, January 24, 2011, 5:05 AM
Hi all,
when I run a RNASeq analysis using tophat, cufflink, coffcompare and cuffdiff by aligning my data to the RefSeq genes I obtain tables from cufflink/compare/diff which does not include the gene name, but only the NM_. Does someone knows how I can obtain all the tables with the gene name?
Thank you all very much for the support,
Best Regards,
Matteo
-- Matteo Bovolenta, PhD Dipartimento di Medicina Sperimentale e Diagnostica Sezione di Genetica Medica Università di Ferrara Via Fossato di Mortara, 74 44100 Ferrara tel +39 0532 974449(office) tel +39 0532 974502 (lab) fax +39 0532 236157 email bvlmtt@unife.it http://www.unife.it/medicina/geneticamedica http://www.bio-nmd.eu registered in ORPHANET http://www.orpha.net
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J.