[galaxy-user] Names for genes in RNA-Seq analysis

[Jennifer Jackson]

Hello Olivier,

Are you using a reference gene annotation GTF file? This would be 
required to obtain gene symbols. If yes and this is still an issue, the 
two things to double check are:
  1) the chromosome names between the GTF file (most commonly the 
problem) and the reference genome and the SAM alignment file are all the 
same (exactly the same) and
  2) the 9th column of the GTF file contains valid gene_id (also 
commonly incorrect) and transcript_id attributes

If this and everything else in the FAQ appear to be in the correct 
format, it might be time to contact the tool authors for advice at 
tophat.cufflinks at gmail.com.

Best wishes for your project,

Jen
Galaxy team

On 10/20/11 6:12 AM, GANDRILLON OLIVIER wrote:
> Hello
>
> I am using Galaxy to analyse RNA-seq libraries made from chicken cells.
>
> I just groomed my sequences, passed them through TopHat and then Cufflinks.
>
> This worked well and in the end I get a list of genes and their
> respective FPKM values.
>
> My only problem is that the names of the genes do not appears in the
> listing, they are simply reference as "CUFF.1, CUFF.2, " etc…
>
> Could you please tell me how I could obtain gene names? (I went through
> the FAQ and could not get the answer).
>
> Sincerely
>
> Olivier
>
>
>
> -----
> New mail adress: olivier.gandrillon at univ-lyon1.fr
>
> Dr Olivier Gandrillon
> Centre de Génétique et de Physiologie Moléculaires et Cellulaires
> UMR CNRS 5534
> Université Claude Bernard Lyon I
> Bat Gregor Mendel (ex 741)
> 16, rue Raphaël Dubois
> 69622 Villeurbanne Cedex
> Phone : 04-72-44-81-90
> Fax : 04-72-43-26-85
> Web adress :
> Lab: http://cgphimc.univ-lyon1.fr/spip.php?rubrique33&lang=en
> Perso: http://www.cgmc.univ-lyon1.fr/Gandrillon/OG/OG1.html
>
> "Comment obtenait-il l'adhésion du peuple aux nouveaux mensonges qu'il
> inventait chaque jour? Précisément parce que c'était des mensonges et
> précisément parce qu'ils étaient une insulte à la perception. Le peuple
> était hypnotisé par l'aplomb, ce droit qu'il s'octroyait de contredire
> l'évidence. Les gens portaient un regard médusé sur un Goebbels
> déchaîné. Ils voyaient en transparence son souhait énorme de nier le
> nain boiteux"
>
> Tobie Nathan, in "Qui a tué Arlozoroff"
>
>
>
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-- 
Jennifer Jackson
http://usegalaxy.org
http://galaxyproject.org/wiki/Support