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can fastp deal with random bases like cutadapt?

Open junjunlab opened this issue 6 months ago • 2 comments

Hi, I have added random bases in the adaptors, can fastp remove these random bases like cutadapt does(--match-read-wildcards -a NNNNNNNNNNAGATCGGAAGAGCACACGTC)?

This is related code for cutadapt:

cutadapt  -j 20 --match-read-wildcards \
	  	  -a NNNNNNNNNNAGATCGGAAGAGCACACGTC \
	  	  --quality-cutoff 20 \
	  	  -e 0.1 -O 6 \
	  	  -m 20 -M 35 \
	  	  --discard-untrimmed \

junjunlab avatar Jun 21 '25 10:06 junjunlab

is this a common requirement? if yes, it can be implemented.

sfchen avatar Jun 26 '25 23:06 sfchen

if your data is paired-end, the adapters will be trimmed, along with the random bases. if your data is single-end, the random bases will be kept.

I want to know why we have such random bases and why we should trim them? mostly random bases are used for unique identifiers, they should be kept or separated, not trimmed and discarded.

sfchen avatar Jun 26 '25 23:06 sfchen