Question: 11. Question About Formatting Mouse (Mm9) Gtf (Shamsher Jagat) (Galaxy-User Digest, Vol 64, Issue 11)
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Lozach, Jean • 20 wrote:
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
To: galaxy-user <galaxy-user@lists.bx.psu.edu>
Subject: [galaxy-user] Question about formattung mouse (mm9) GTF
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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
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