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Old 04-15-2009, 09:31 AM   #2
jnfass
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Location: Davis, CA

Join Date: Aug 2008
Posts: 88
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It all depends!

Which text file are you referring to? Pileup? Dumped hits? If you specify how exactly you generated it, that will help others help you ...

Also, for the map and downstream steps (consensus, SNP calling), maq puts a read that maps equally well (and satisfies the specified cutoffs) to multiple locations in the reference, in one of those locations ... randomly. This may or may not suit your needs, but as far as I know, there's no way to change it. You should be able to determine which reads map multiple times (and thus exclude them in a second round of mapping) by parsing the dumped hits file .. specified in the '-H' option to the map/match command ...

Hope that helps
~Joe
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