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Old 01-05-2011, 02:11 AM   #1
Location: India

Join Date: Nov 2010
Posts: 17
Default Bowtie mapping with more mismatches

We have 50bp reads and want to map with bowtie with 6mm. However it seems that only 3 mm are allowed at max. I have tried to look on net and many people suggested to use -e option..I am not sure what would be the best parameters to map SOLiD 50bp reads with 6mm ? Can anyone help on this?
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