fastp
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can fastp deal with random bases like cutadapt?
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 \
is this a common requirement? if yes, it can be implemented.
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.