Dear Carl After having solved a couple of other problems, I am now to the point where I can: 1.either get the FKPM and no names or 2. have the names and FKPM values to zero (or "OK" ?)
So I was wondering whether you had solved this FKPM value problem with chicken you had? Best Olivier Le 26/10/11 02:21, « Jennifer Jackson » <j...@bx.psu.edu> a écrit : >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-ze >roes-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, " etcŠ >>> >>> 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" >>> >>> ___________________________________________________________ >>> The Galaxy User list should be used for the discussion of >>> Galaxy analysis and other features on the public server >>> at usegalaxy.org. Please keep all replies on the list by >>> using "reply all" in your mail client. For discussion of >>> local Galaxy instances and the Galaxy source code, please >>> use the Galaxy Development list: >>> >>> http://lists.bx.psu.edu/listinfo/galaxy-dev >>> >>> To manage your subscriptions to this and other Galaxy lists, >>> please use the interface at: >>> >>> http://lists.bx.psu.edu/ >> >> 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 >> >> >> >> >> >> >> >> >> ___________________________________________________________ >> The Galaxy User list should be used for the discussion of >> Galaxy analysis and other features on the public server >> at usegalaxy.org. Please keep all replies on the list by >> using "reply all" in your mail client. For discussion of >> local Galaxy instances and the Galaxy source code, please >> use the Galaxy Development list: >> >> http://lists.bx.psu.edu/listinfo/galaxy-dev >> >> To manage your subscriptions to this and other Galaxy lists, >> please use the interface at: >> >> http://lists.bx.psu.edu/ > >-- >Jennifer Jackson >http://usegalaxy.org >http://galaxyproject.org/wiki/Support ___________________________________________________________ The Galaxy User list should be used for the discussion of Galaxy analysis and other features on the public server at usegalaxy.org. Please keep all replies on the list by using "reply all" in your mail client. For discussion of local Galaxy instances and the Galaxy source code, please use the Galaxy Development list: http://lists.bx.psu.edu/listinfo/galaxy-dev To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/
