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
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
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:
Did you try to run Cuffcompare (part of Cufflinks) on your results?
According to the Cufflinks manual
>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
Date: Thu, 20 Oct 2011 15:12:45 +0200
From: GANDRILLON OLIVIER <olivier.gandrillon(a)univ-lyon1.fr
To: "galaxy-user(a)bx.psu.edu <mailto:email@example.com>"
Subject: [galaxy-user] Names for genes in RNA-Seq analysis
Content-Type: text/plain; charset="windows-1252"
I am using Galaxy to analyse RNA-seq libraries made from chicken
I just groomed my sequences, passed them through TopHat and then
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).
The Galaxy User list should be used for the discussion of
Galaxy analysis and other features on the public server
. 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:
To manage your subscriptions to this and other Galaxy lists,
please use the interface at: