get rid of redundant reads in BOWTIE2
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6.1 years ago
andynkili ▴ 10

Is it possible to get every reads that match several loci  on the reference (using the read mappers bowtie2)?

i've looked for any options allowing to do so, but i'm only aware of the --al option, saving all the reads that machted the reference sequence. The ultimate goal is to keep only the reads that have a unique position (match) in the reference sequence, i.e the reads that can be trusted regarding their position.

alignment read mapping bowtie2 sequencing NGS • 1.3k views
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