alignment with bowtie

[maria_mari]

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??

[epi]

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