mothur

What kind of .oligos file should I have for trim.seqs?

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

Either should work - give them a try and let us know if you have any issues

This topic was automatically closed 10 days after the last reply. New replies are no longer allowed.