Entering edit mode
5 months ago
microorganism_001
▴
30
For processing our 16s data two primer sequences were being used for amplification. I want to remove those two sequences with fastp. Could you tell anyone how it is possible?
forward primer - CCTACGGGNGGCWGCAG
^ ^
reverse primer - GACTACHVGGGTATCTAATCC
^^
My command is the following I was writing a script with BASH. Could anyone help me to rectify it? Thanks in advance.
fastp \
-i ${first} \
-I ${second} \
-F 5 \
-T 30 \
-n 1 \
-x \
--adapter_sequence=CCTACGGG[ACGT]GGC[AT]GCAG \
--adapter_sequence_r2=GACTAC[ACT][ACG]GGGTATCTAATCC \
-o ${first}_trimmed.fastq \
-O ${second}_trimmed.fastq
Apparently
cutadapt
will support IUPAC characters. May want to look at that as an option.