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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