There is one more required data point to consider in the GTF file, for full functionality. Specifically, it must also contain the gene_name attribute (in the 9th column), such as:

chr1 unknown exon 14362 14829 . - . gene_id "WASH7P"; gene_name "WASH7P"; transcript_id "NR_024540"; tss_id "TSS6960";


Thanks for using Galaxy!
Jen

On 10/25/11 5:21 PM, Jennifer Jackson wrote:
Hello Carl,

Your question is similar to Olivier's, even though the problem is
presenting in a different way. There is most likely a data mismatch
problem as explained in my earlier reply to this thread and this prior
mailing list question:
http://gmod.827538.n3.nabble.com/Cufflinks-reporting-FPKM-values-of-all-zeroes-0-tt3183517.html#a3183928


Best wishes for your project as well,

Jen
Galaxy team

On 10/20/11 7:32 AM, Carl Schmidt wrote:
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.gandril...@univ-lyon1.fr
<mailto: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
<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
schmi...@udel.edu <mailto:schmi...@udel.edu>
302-831-1334








___________________________________________________________
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at usegalaxy.org. Please keep all replies on the list by
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--
Jennifer Jackson
http://usegalaxy.org
http://galaxyproject.org/wiki/Support
___________________________________________________________
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