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 http://cufflinks.cbcb.umd.edu/igenomes.html and more information about iGenomes here ftp://ftp.illumina.com/README.txt The annotations will be updated next week and will also include BWA Index files. Regards 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 <kanwarjag@gmail.com> To: galaxy-user <galaxy-user@lists.bx.psu.edu> Subject: [galaxy-user] Question about formattung mouse (mm9) GTF Message-ID: <CAN_Q6i4JS3fJUx__Cbv_H6veScTR0C3k3dLa96LFBRvk3oEcCg@mail.gmail.com> 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. Thanks