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-zero... 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
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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
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Carl Schmidt Associate Professor Animal & Food Sciences University of Delaware Newark, DE 19716 051 Townsend Hall schmidtc@udel.edu <mailto:schmidtc@udel.edu> 302-831-1334
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