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 <[email protected]> wrote: > > From: Matteo Bovolenta <[email protected]> > Subject: [galaxy-user] Gene Name in Cufflink/compare/diff > To: [email protected] > 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 [email protected] > http://www.unife.it/medicina/geneticamedica > http://www.bio-nmd.eu > registered in ORPHANET > http://www.orpha.net > > NOTA DI RISERVATEZZA: ai sensi del D.Lgs. 196/2003 si precisa che le > informazioni contenute in questo messaggio e nei relativi allegati > sono riservate ed a uso esclusivo del destinatario. Qualora il > messaggio in parola Le fosse pervenuto per errore, La invitiamo ad > eliminarlo senza copiarlo, a non inoltrarlo a terzi e a non farne > alcun uso, dando gentilmente comunicazione all'indirizzo del mittente: > [email protected] Grazie. > > CONFIDENTIALITY NOTICE: this message together with its annexes may > contain confidential, proprietary or legally privileged information > and is intended only for the use of the addressee named above. No > confidentiality or privilege is waived or lost by any mistransmission. > If you are not the intended recipient of this message you are hereby > notified that you must not use, disseminate, copy it in any form or > take any action in reliance on it. If you have received this message > in error please delete it and any copies of it and kindly inform the > sender of this e-mail by [email protected] Thank you > > _______________________________________________ > galaxy-user mailing list > [email protected] > http://lists.bx.psu.edu/listinfo/galaxy-user > > _______________________________________________ > galaxy-user mailing list > [email protected] > http://lists.bx.psu.edu/listinfo/galaxy-user J.
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