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Date: Mon, 26 Sep 2011 16:13:54 -0700 From: shamsher jagat <kanwarjag@gmail.com> To: galaxy-user <galaxy-user@lists.bx.psu.edu> Subject: [galaxy-user] mm9 reference GTF file for Cuffcompare Message-ID: <CAN_Q6i72ALsjHKgbQNRFo=kTywAB24BwAtJsEE-1NPa3z64DKA@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. Thanks

------------------------------ 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 http://cufflinks.cbcb.umd.edu/igenomes.html and more information about iGenomes here ftp://ftp.illumina.com/README.txt The annotations are few months old but we will have a full update in 2 weeks that will also include BWA Index files. Regards Jean Lozach Manager, Bioinformatics Illumina, Inc. 9885 Towne Centre Drive San Diego, CA 92121 ------------------------------