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 <bvl...@unife.it> wrote:
> 
> From: Matteo Bovolenta <bvl...@unife.it>
> Subject: [galaxy-user] Gene Name in Cufflink/compare/diff
> To: galaxy-u...@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 bvl...@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.



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