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Trimming Multiple Copies of same adapter. #233

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PaulAONeill opened this issue Jan 17, 2020 · 2 comments
Open

Trimming Multiple Copies of same adapter. #233

PaulAONeill opened this issue Jan 17, 2020 · 2 comments

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@PaulAONeill
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Hello,

I found a problem sample which has multiple copies of a single adaptor in the same read.
fastp identifies the adaptor correctly AGATCGGAAGAGCACACGTCTGAACTCCAGTCA

and removed it from the sequence
AGATCGGAAGAGCACACGAGATCGGAAGAGCACACGTCTGAACTCCAGTCA

leaving
AGATCGGAAGAGCACACG

I can't see a parameter to remove adapters multiple times - could you please advise.

Thanks
@y9c
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y9c commented Feb 3, 2021

use the -n parameter in cutadapt...

Seems that fastp is not under maintenance now.

@sfchen
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sfchen commented Feb 3, 2021

use the -n parameter in cutadapt...

Seems that fastp is not under maintenance now.

No, I was too busy on anti-COVID19 activities. But I am still maintaining fastp

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@y9c @PaulAONeill @sfchen