------------------------------ Message: 4 >Date: Mon, 26 Sep 2011 16:13:54 -0700 >From: shamsher jagat <[email protected]> >To: galaxy-user <[email protected]> >Subject: [galaxy-user] mm9 reference GTF file for Cuffcompare >Message-ID: > <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. >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 ------------------------------ ___________________________________________________________ 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/
