This http://bioperl.org/pipermail/bioperl-l/2005-November/020109.html might help to convert gff to gtf.

From: galaxy-user-bounces@lists.bx.psu.edu [mailto:galaxy-user-bounces@lists.bx.psu.edu] On Behalf Of Gary Xie
Sent: Friday, September 23, 2011 4:41 PM
To: Peng, Tao
Cc: galaxy-user
Subject: Re: [galaxy-user] annotation file for cufflinks

I had a similar question, after i downloaded a bacterial ref genome GFF file and loaded it into Galaxy, the "use reference annotation" feature of Cufflinks kept telling it need to be the GTF file instead,

When I check the Cufflinks manual at http://cufflinks.cbcb.umd.edu/manual.html

It looks like both GFF and GTF should be ok.

Any insight?

Gary

On Aug 30, 2011, at 12:52 PM, Peng, Tao wrote:

Hi jen and galaxy users, when I try to use cufflinks in GALAXY and select "use reference annotation", I am NOT sure how to get the annotation file in GTF format for cufflinks.

I was trying to down-load the annotation file from Illumina donated package in Cufflink website, I am NOT sure this is the right way to go for?

Thanks,

tao

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