Bowtie1 has a handy parameter -m that suppresses all alignments if more than one hit is found.
But it seems that bowtie2 doesn't have an equivalent parameter. Instead, what it does is to report one alignment when there are mutli-hits, but this is not the strict definition of "unique" mapping.
Did I miss anything?
But it seems that bowtie2 doesn't have an equivalent parameter. Instead, what it does is to report one alignment when there are mutli-hits, but this is not the strict definition of "unique" mapping.
Did I miss anything?
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