Hi

Should the --no-1mm-upfront parameter be used with bowtie2 to allow exactly 1 vs 2 mismatches? If so how to use it?

Should 1 as cutoff for MAPQ be used to discriminate the exactly 1 time aligned vs >1 time aligned reads?

Look forward to your reply,

Carol

Should the --no-1mm-upfront parameter be used with bowtie2 to allow exactly 1 vs 2 mismatches? If so how to use it?

Should 1 as cutoff for MAPQ be used to discriminate the exactly 1 time aligned vs >1 time aligned reads?

Look forward to your reply,

Carol

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