Hi William,

To be sure that we are talking about the same thing, you are trying to use a custom reference genome with Bowtie? As the target genome? If so, then what you want to load is a fasta file of the chromosomes/scaffolds/contigs that represent that species, for a particular genome build. This may come from a public source or from your own project, if you are assembling a genome. But regardless of source, the final product should be a fasta file, which you load into a history and label as fasta, and that is what Galaxy would accept as a valid custom reference genome input on tool forms.


If all of this sounds like what you are wanting to do, then I am not clear where the fastq data fits in. The query in a Bowtie job would be in fastq format, but no indexes are needed for a query. Indexes should never be datasets in a history.

Now, if you are doing something different, such setting up databases in a local install, then creating indexes would be part of that process, but the Galaxy UI is not the place to this. Instead, you will want to follow the procedure in this wiki: http://wiki.g2.bx.psu.edu/Admin/NGS%20Local%20Setup (in particular, see "Setting Up the Reference Genomes for NGS Tools")

All of that said, there are no specific blocks that would prevent you from using something other than a full reference genome as a target in a Bowtie run. I am fairly certain that almost any properly formatted fasta file could be used as long as the sequence identifiers were unique within the file. I've created and used small "dummy" fasta files as custom reference genomes with Bowtie myself without issues.

My apologies if your question is still not addressed. So if this does not clear things up, maybe it would help if you explained a bit more about what the final goal is? We want to make sure you are getting the correct help to resolve any outstanding issues,

Best,

Jen
Galaxy team

On 2/7/12 12:34 PM, William Light wrote:
Jennifer,

I am having some issues figuring out if I can use bowtie to take my
index (I have two that I want to upload) and generate one fasta file.
  When I use the bowtie-inspect command, the only thing I seem able to
generate is a list of the sequences used to make the index (which are
SOLiD sequences that I used to make the index) rather than one fasta
file that represents the seqeunce.  I have the fastq that I used to
generate the reference uploaded right now, and in poking around, it
seems that there is some issue with making the .ebwt files on a platform
other than the one that galaxy runs on.  Am I just missing the right
command line settings for making one fasta file?

  - Will Light
    Northwester University

On Mon, Feb 6, 2012 at 8:14 PM, Jennifer Jackson <j...@bx.psu.edu
<mailto:j...@bx.psu.edu>> wrote:

    Hello William,

    To use a custom reference genome, all you need to upload is the
    single fasta file for the genome. Galaxy will do the rest and create
    indexes as appropriate.

    Hopefully this helps!

    Thanks,
    Jen
    Galaxy team


    On 2/6/12 11:51 AM, William Light wrote:

        I recently tried to upload a custom made index for bowtie using
        Filezilla as my FTP source, but I got an error message, I think
        due to
        the autodetect for file type not recognizing this file type.  Is
        there
        something special that I should do to upload my six .ebwt files
        for my
        reference?



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