Comments (1)
Sorry, I just read that as per the SAM format, the secondary bit is set only for the 2nd onwards alignment(s) and not the first one. The NH:i value on the other hand is set for all alignments. So more reads will be retained when filtering as per [1] than as per [2], and [1] is actually not the right way to filter for uniquely mapped reads.
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Related Issues (20)
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