Hello Olivier, Emilie and the Galaxy community -

I have run into a similar problem with my RNA-seq analysis, in that I can run the analysis up to the point of Cufflinks producing a list of FPKM values for my genome of interest (in this case, Staphylococcus aureus strain Newman).  However, I cannot find a place to download a compatible .GTF file with the reference annotation.  Would you or anyone else in the community know of tool or database where .GTF files could be created from another input file (such as GFF3), or better yet, just downloaded?

As for possibilities with file conversion, most microbial genomes are available from NCBI in a variety of formats (but not GTF).  For S. aureus Newman, these files can be found at the following link:


Many thanks for your help!


Joe J. Harrison
Senior Fellow
Department of Microbiology
University of Washington
1705 NE Pacific Street, HSB J181
Seattle, WA USA 98195

On 10/20/2011 11:26 AM, Emilie Chautard wrote:
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 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

Message: 7
Date: Thu, 20 Oct 2011 15:12:45 +0200
From: GANDRILLON OLIVIER <olivier.gandrillon@univ-lyon1.fr>
To: "galaxy-user@bx.psu.edu" <galaxy-user@bx.psu.edu>
Subject: [galaxy-user] Names for genes in RNA-Seq analysis
Message-ID: <CAC5EAED.8E99%olivier.gandrillon@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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