Hello Matt, I am not sure what you mean by an annotated genome, would you be able to send more details? Meanwhile, I can let you know that the tools that use a reference genome (custom or native) all expect a fasta formatted input and use the data directly or create indexes from the data. Any DNA (and sometime RNA) nucleotide fasta file can be used and whether using something other than a complete genome makes sense scientifically is up to the user to determine. Thanks! Jen Galaxy team On 12/5/11 6:59 PM, Matthew Biggs wrote:

Hello Jennifer,

Thanks for your prompt reply. I had one other question about using a custom reference genome. Is it possible to use an annotated genome as the reference for a Bowtie alignment? Using a genome in fasta format is only so helpful.

Thanks, Matt Biggs

On Mon, Dec 5, 2011 at 8:24 AM, Jennifer Jackson <jen@bx.psu.edu <mailto:jen@bx.psu.edu>> wrote:

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 <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

_____________________________________________________________ The Galaxy User list should be used for the discussion of Galaxy analysis and other features on the public server at usegalaxy.org <http://usegalaxy.org>. Please keep all replies on the list by using "reply all" in your mail client. For discussion of local Galaxy instances and the Galaxy source code, please use the Galaxy Development list:

http://lists.bx.psu.edu/__listinfo/galaxy-dev <http://lists.bx.psu.edu/listinfo/galaxy-dev>

To manage your subscriptions to this and other Galaxy lists, please use the interface at:

http://lists.bx.psu.edu/

-- Jennifer Jackson http://usegalaxy.org http://galaxyproject.org/wiki/__Support <http://galaxyproject.org/wiki/Support>

-- Jennifer Jackson http://usegalaxy.org http://galaxyproject.org/wiki/Support