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Old 12-16-2010, 12:12 AM   #1
khb
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Location: Oslo

Join Date: Dec 2010
Posts: 15
Default Bowtie parameters

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
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