I am trying to compare two genetically different strains that I have
sequenced using SOLiD.  I was trying to ask where these two strains are
different, either in terms of deletions or polymorphisms, and one idea I
had was to use Bowtie to create an index from one of these strains and then
to map my reads for the other strain using this index.  Is this a
reasonable strategy?

 - Will Light
   Northwestern University
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