fastp error in adapter or primer trimming
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5 months ago

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
NGS fastp trimmomatic • 284 views
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Apparently cutadapt will support IUPAC characters. May want to look at that as an option.

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