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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
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
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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
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