In the cufflink site, they have annotation from ucsc,ncbi & ensemble. not sure which one to download and then load into galaxy?
thanks,
Tao

Sent from my iPhone

On Aug 30, 2011, at 5:52 PM, "vasu punj" <punjv@yahoo.com> wrote:

If using Ensembl make sure it is properly formatted.
Vasu

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

From: Peng, Tao <tpeng@fhcrc.org>
Subject: [galaxy-user] annotation file for cufflinks
To: "Jennifer Jackson" <jen@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-----

___________________________________________________________
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/