Hello Candace,
Hopefully you have already discovered this, but genomes can be loaded
(usually using FTP) into a history and used as a custom genome with many
tools. The genomes are loaded in fasta format and indexes are generated
by the tools themselves. Most tools that use a reference genome include
an option to use a custom reference genome (including Tophat and the
other Tuxedo tools).
Sorry for the delay in reply. Next time, for a data or tool use
question, the galaxy-u...@bx.psu.edu mailing list would probably be a
better choice (lower volume and reserved for usage topics).
http://galaxyproject.org/wiki/Support#Public_mailing_list_Q_.26_A_discussions
http://galaxyproject.org/wiki/Mailing%20Lists
Best wishes for your project,
Jen
Galaxy team
On 9/22/11 7:00 AM, Candace Seeve wrote:
I'd like to map RNA-Seq data from two different bacterial species to
their genomes. How do I go about getting a custom index added to the
galaxy server? One of the genomes is not yet published so is it possible
to keep the indexes private?
Thanks,
Candace
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Jennifer Jackson
http://usegalaxy.org
http://galaxyproject.org/wiki/Support
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