Probably the simplest thing for you to do would be to concatenate the two
genomes one after the other using the concatenate tool under "text
manipulation". This will generate a new organism with apparently two
chromosomes one from bacteria A and one from bacteria B. When you run tophat or
bowtie the sam file will indicate which "chromosome" (i.e. which bacteria) it
assigned the read to.
Hope this helps.
Dr David A. Matthews
Senior Lecturer in Virology
Department of Cellular and Molecular Medicine,
School of Medical Sciences
University of Bristol
Tel. +44 117 3312058
Fax. +44 117 3312091
On 9 Jun 2011, at 15:18, John David Osborne wrote:
> Are there any tools in Galaxy to align short reads against multiple reference
> I have a dozen microbial genomes sequenced for which there are 2 reference
> genomes already sequenced. We have tried aligning each of these individually
> against either of the reference genomes - some align better against the first
> reference genome, some align better against the second reference genome.
> Ideally though I would like to be able to align against both at the same
> time. Is this possible?
> I have found a tool called GenomeMapper and hints of 2 other tools in
> development that do something like this, but nothing for Galaxy yet.
> How do others proceed with this type of problem? Workflows appreciated! :)
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The Galaxy User list should be used for the discussion of
Galaxy analysis and other features on the public server
at 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:
To manage your subscriptions to this and other Galaxy lists,
please use the interface at: