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