Hi Olivier, Did you try to run Cuffcompare (part of Cufflinks) on your results? According to the Cufflinks manual (http://cufflinks.cbcb.umd.edu/manual.html ):
>Cufflinks includes a program that you can use to help analyze the transfrags you assemble. The program cuffcompare helps you: > - Compare your assembled transcripts to a reference annotation > [...] In the Galaxy version of Cuffcompare, I think that you can provide a reference annotation file using "Use Reference Annotation:", which will be compared to your results with Cufflinks. It makes an "union" of the transcripts obtained with Cufflinks with the annotation file (both in *.gtf format). You can then obtain a transcript identifier for those already annotated. It also provides a class code for the transcripts, which can inform about a potential isoform for example. Hope this helps. Emilie -- Emilie Chautard, PhD Postdoctoral Fellow Ontario Institute for Cancer Research MaRS Centre, South Tower 101 College Street, Suite 800 Toronto, Ontario, Canada M5G 0A3 Tel: 416-673-8518 Toll-free: 1-866-678-6427 www.oicr.on.ca > Message: 7 > Date: Thu, 20 Oct 2011 15:12:45 +0200 > From: GANDRILLON OLIVIER <olivier.gandril...@univ-lyon1.fr> > To: "galaxy-u...@bx.psu.edu" <galaxy-u...@bx.psu.edu> > Subject: [galaxy-user] Names for genes in RNA-Seq analysis > Message-ID: <cac5eaed.8e99%olivier.gandril...@univ-lyon1.fr> > Content-Type: text/plain; charset="windows-1252" > > 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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