alignment with bowtie

maria_mari · 02-01-2012, 02:22 AM

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 · 02-01-2012, 01:19 PM

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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02-01-2012, 02:22 AM	#1
maria_mari Member Location: Germany Join Date: Jan 2012 Posts: 17	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??

02-01-2012, 01:19 PM	#2
epi Member Location: USA Join Date: Jan 2012 Posts: 38	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