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

[Carl Schmidt]

I am also using Galaxy to analyze RNA-seq libraries from chicken.
While the names of the genes appear in the Cufflinks output, the FPKM  
values are all zero.


On Oct 20, 2011, at 9:12 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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Carl Schmidt
Associate Professor
Animal & Food Sciences
University of Delaware
Newark, DE 19716
051 Townsend Hall
schmidtc at udel.edu
302-831-1334






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