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
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http://galaxyproject.org/wiki/Support
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