Hi Matt,

The quickest way to use new genomes with most tools, including Bowtie, is to use them as a custom reference genome. To do this, load the genome in fasta format into your history.


Then, on the tool form (for Bowtie, will vary slightly between tools), set:

        Will you select a reference genome from your history or use a   
        built-in index?: "Use one from the history"

The form will refresh, them set:

        Select the reference genome: "dataset_for_your_loaded_genome"

Best practice:
1 - double check that the format is strict fasta (all lines wrapped to same length, no extra lines or hidden characters, sequence entries are unique within file).
  2 - use the same genome dataset for all steps within an analysis
  3 - load using FTP and make certain load is complete
http://galaxyproject.org/wiki/Learn/Upload%20via%20FTP


Hopefully this helps!

Best,

Jen
Galaxy team

On 12/3/11 6:37 PM, Matthew Biggs wrote:
Hello Galaxy Team,

I am writing to request that the genome of /Sinorhizobium meliloti /1021
be added to the "Map with Bowtie for Illumina" tool. I am using the main
server http://main.g2.bx.psu.edu/ and my user name is mbiggs.

Please let me know if this email is received.

Thanks,
Matt Biggs


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