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 Chautard, PhD
Ontario Institute for Cancer Research
MaRS Centre, South Tower
101 College Street, Suite 800
Toronto, Ontario, Canada M5G 0A3
> 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"
> 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).
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