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Old 12-16-2010, 12:40 AM   #1
Location: Oslo

Join Date: Dec 2010
Posts: 15
Question Help with Bowtie, only unique alignments

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.
khb is offline   Reply With Quote
Old 12-16-2010, 01:35 AM   #2
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Location: Cambridge, UK

Join Date: May 2010
Posts: 311

I think the command you entered is the correct one to return only the reads that have only one valid match in the best error stratum (i.e. with the least number of mismatches). Reads that map at more than one location should be reported as unmapped.

-m 1 --all should be the same as -m 1 alone.

Do you find reads with multiple map positions from the output of the command you posted?

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