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Old 12-16-2010, 12:26 AM   #2
xinwu
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Location: Beijing

Join Date: Jul 2010
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Quote:
Originally Posted by khb View Post
I'm new in next generation sequencing, and I use Bowtie for the first time. Is there someone that know how to get only the sequences that only have one match? I tried this command.
bowtie hg19 -q input.fastq -m 1 --best --strata --all -S bowtie_out. I also tried without the --all command but both gave equal numbers of hits.
Thanks
IMO, all option only means all valid alignments ACCORDING TO YOUR CRITERIA. Since you set m option with 1, all option does nothing here. If you set m with 3, and without all option, reads with 2 alignments will only report one (k is 1 by default) alignment, if with all option, all alignments will be reported (2 alignments in this case).

Last edited by xinwu; 12-16-2010 at 12:33 AM.
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