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N wildcards in adapter should never incur a mismatch #453

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marcelm opened this issue Apr 15, 2020 · 0 comments
Closed

N wildcards in adapter should never incur a mismatch #453

marcelm opened this issue Apr 15, 2020 · 0 comments

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@marcelm
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marcelm commented Apr 15, 2020

Currently, an adapter such as -g ^NNACGT will match a read that starts with NTACGT with one mismatch since the first N in the read is counted as a mismatch.

The is unexpected. Instead, all N wildcards in an adapter sequence should match whatever character is in the read at the corresponding position. (Unless --no-match-adapter-wildcards/-N has been used.)

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