Hi John,

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.


Best Wishes,
David.

__________________________________
Dr David A. Matthews

Senior Lecturer in Virology
Room E49
Department of Cellular and Molecular Medicine,
School of Medical Sciences
University Walk,
University of Bristol
Bristol.
BS8 1TD
U.K.

Tel. +44 117 3312058
Fax. +44 117 3312091

d.a.matth...@bristol.ac.uk






On 9 Jun 2011, at 15:18, John David Osborne wrote:

> Are there any tools in Galaxy to align short reads against multiple reference 
> sequences?
>  
> 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! :)
>  
>  -John
>  
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