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Hello Joe,
Have you found a way to convert microbial genomes from one of the
formats available on Genbank to .GTF files? We are having similar
issues with sequenced Prochlorococcus genomes, as well as with
some of our own in-house bacterial genomes.
Thanks
Daniel
On 20/10/2011 21:17, Joe Harrison wrote:
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:
ftp://ftp.ncbi.nih.gov/genbank/genomes/Bacteria/Staphylococcus_aureus_Newman_uid18801
Many thanks for your help!
Joe
---
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
--
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 <[email protected]>
To: "[email protected]"
<[email protected]>
Subject: [galaxy-user] Names for genes in RNA-Seq analysis
Message-ID: <cac5eaed.8e99%[email protected]>
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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___________________________________________________________
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/
--
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
Daniel Sher, PhD
Department of Marine Biology
Leon H. Charney School of Marine Sciences
University of Haifa, Mt. Carmel 31905, Haifa, Israel
Office +972-4-8240731
Lab +972-4-8288961
email: [email protected]
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