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
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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