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.cuffli...@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.gandril...@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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___________________________________________________________
The Galaxy User list should be used for the discussion of
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