I asked something similar before and thought I had solved the issue, but I have not. I have taken over a protocol that used cutadapt to trim the primers prior to running in mothur - this is the cutadapt code
#!/bin/bash
for read1 in *_1.fastq.gz;
do
cutadapt -g CCTACGGGAGGCAGCAG --untrimmed-output=untrimmed_$read1 $read1 > trimmed_$read1;
cutadapt -g ATTACCGCGGCTGCTGG --untrimmed-output=untrimmed_${read1%*_1.fastq.gz}_2.fastq.gz ${read1%*_1.fastq.gz}_2.fastq.gz > trimmed_${read1%*_1.fastq.gz}_2.fastq.gz;
done
I was advised to use trim.seqs in mothur instead because this wasn’t really working well. So my question is what kind of format does my oligos file need to be?
should it be
primer CCTACGGGAGGCAGCAG ATTACCGCGGCTGCTGG
or
forward CCTACGGGAGGCAGCAG
reverse ATTACCGCGGCTGCTGG