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Old 02-01-2012, 02:22 AM   #1
maria_mari
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Location: Germany

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Default alignment with bowtie

Hi

I want to map with bowtie, 2 misstmaches per read and descarding reads with more than 1 reportable alignment:

bowtie -a --best --strata -m 1 -v 2 -S -l 36 ~/indexes/mm9 file.fastq > file.sam

is it correct? and how about the options? are they resonable for an alignment??
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Old 02-01-2012, 01:19 PM   #2
epi
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Default

try several options and see

seed length -l is best used with -n, and not -v mode

I will remove best and strata if you are just interested in unique alignments to save some computing time
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