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is trimming for PE symmetrical #158

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aistBMRG opened this issue May 24, 2019 · 1 comment
Open

is trimming for PE symmetrical #158

aistBMRG opened this issue May 24, 2019 · 1 comment

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@aistBMRG
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Thank you very much or developing fastp -- it is fast and does all that is needed.

Small question. Would it be possible to clarify whether adapter trimming is symmetrical for PE reads? For example if an adapter is detected for read 1 but not for read 2, will read 2 be trimmed anyway based on the adapter position in read 1. Seems that tools such as Atropos follow such rule.

Thank you.

Dieter.
@sfchen
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sfchen commented May 31, 2019

I believe you raised a very good question.

For PE data, most reads would be trimmed symmetrically since the adaptors are detected by finding the overlapped regions.

But for some cases (rarely happen), if one read is detected with adapter and the other one is not, fastp only trimmed the one with adaptor found.

But I am considering to implement symmetrical trimming for this case, although it happens rarely.

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@aistBMRG @sfchen