Hello Sarah,

We can add this genome to the list to be indexed for Bowtie.

Meanwhile, quickest way to work with small genomes immediately is as a custom genome. Simply load the genome into your history in fasta format and start using it with tools, including Bowtie. Just set these options to get started:

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

  Select the reference genome: <pick the dataset containing genome>


http://wiki.g2.bx.psu.edu/Support#Custom_reference_genome
http://wiki.g2.bx.psu.edu/Learn/CustomGenomes

Thanks!

Jen
Galaxy team

On 8/21/12 12:21 PM, Sarah Marcus wrote:
Dear All,
I was wondering if it would be possible to add Mycobacterium
tuberculosis H37Rv as a reference genome to the list of built-in indexes
in the Map with Bowtie for Illumina (version 1.1.2) tool.
Thank you,
Sarah
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