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N wildcards should not be counted when computing the error rate #360

marcelm opened this issue Feb 26, 2019 · 0 comments


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commented Feb 26, 2019

In a match of an adapter containing N wildcards against the read, the wildcards should not contribute to the length. For example, if adapter CCNCCC is matched to CCTCAC then the error rate should be computed as 1/5=0.2 because there is one mismatch in five non-N bases.

Otherwise, adapter sequences such as ACGTN{20} have an unexpectedly high number of allowed errors.

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