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?

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?



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