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 should find in it the Ensembl mm9 GTF file compatible with TopHat 

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

The annotations will be updated next week and will also include BWA Index files.


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

Message: 11
Date: Wed, 12 Oct 2011 04:26:15 -0700
From: shamsher jagat <>
To: galaxy-user <>
Subject: [galaxy-user] Question about formattung mouse (mm9) GTF
Content-Type: text/plain; charset="iso-8859-1"

I have read in the mailing list that you have a workflow  which can modify
the human GTF file so that it will be compatible with Top Hat. Will it also
work with Ensembl mm9 GTF or there is a different work flow.

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