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deduplication with UMI

Open yupingz opened this issue 3 years ago • 3 comments

I could not find description about how deduplication is done for fastq with UMI. I found "fastp considers one read as duplicated only if its all base pairs are identical as another one." Is it the same for fastq with UMI? Thanks!

yupingz avatar Feb 01 '23 19:02 yupingz

Hi I was wondering the same thing. Are UMIs taken into account with the dedup?

annajbott avatar May 31 '23 12:05 annajbott

Yes, UMIs are taken into account. Dedup is performed before UMIs are removed.

sfchen avatar May 31 '23 12:05 sfchen

Brilliant thanks!

annajbott avatar May 31 '23 12:05 annajbott