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 <j...@bx.psu.edu
<mailto:j...@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


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



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