Message: 4
>Date: Mon, 26 Sep 2011 16:13:54 -0700
>From: shamsher jagat <kanwar...@gmail.com>
>To: galaxy-user <galaxy-user@lists.bx.psu.edu>
>Subject: [galaxy-user] mm9 reference GTF file for Cuffcompare
>       <CAN_Q6i72ALsjHKgbQNRFo=ktywab24bwatjsee-1npa3z64...@mail.gmail.com>
>Content-Type: text/plain; charset="iso-8859-1"
>I wonder if some has mouse genome GTF file compatible with Tophat/
>Cuffcompare. The contig names on  Ensembel and that of Tophat GTF file are
>not same.


Illumina provides a ftp site where you can download all the files you need to 
use TopHat and Cufflinks: Bowtie index and gtf files are present for about 20 
species. For most species, we do covered different data sources (mainly NCBI, 
Ensembl and UCSC) as well as different builds.

This resource is called iGenomes.

You can find all the links here
and more information about iGenomes here

The annotations are few months old but we will have a full update in 2 weeks 
that will also include BWA Index files.


Jean Lozach
Manager, Bioinformatics
Illumina, Inc.
9885 Towne Centre Drive
San Diego, CA 92121

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