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Old 09-22-2011, 07:05 AM   #3
Senior Member
Location: MA

Join Date: Oct 2010
Posts: 160

Hi Simon,

Thanks for the quick answer!
So if I want to do an alignment where there's no limit in the number of hits (-m has no limit) a read is reported (i.e., take each contig in the ref file as independent), should I take off the --best option? Or what do you recommend?
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