Hi I have down-loaded UCSC HG19 annotation files from Cufflinks; Should I just 
load genes.GTF file (about 100 MB) to galaxy for cufflink analysis?

Thanks,


tao


-----Original Message-----
From: vasu punj [mailto:pu...@yahoo.com]
Sent: Tue 8/30/2011 5:52 PM
To: Jennifer Jackson; galaxy-user; Peng, Tao
Subject: Re: [galaxy-user] annotation file for cufflinks
 
If using Ensembl make sure it is properly formatted.
Vasu

--- On Tue, 8/30/11, Peng, Tao <tp...@fhcrc.org> wrote:


From: Peng, Tao <tp...@fhcrc.org>
Subject: [galaxy-user] annotation file for cufflinks
To: "Jennifer Jackson" <j...@bx.psu.edu>, "galaxy-user" 
<galaxy-user@lists.bx.psu.edu>
Date: Tuesday, August 30, 2011, 1:52 PM



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


-----Inline Attachment Follows-----


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