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.Matthews@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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