Cutadapt for sequences with different primers

Hi, i tried to use cutadapt in qiime2 for the sequences with different primers. They are paired-end sequences. I tried to use the trim-paired, as my fastq files are already in demux-paired-end.qza; but really not sure what to fill in with these *** showing below… i have around 20 primer sets in all my sequences.
$ qiime cutadapt trim-spaired
–i-demultiplexed-sequences demux-paired-end-darte.qza
—-p-cores 1
–p-adapter-f ***
–p-front-f ***
–p-adapter-r ***
–p-front-r ***
–p-error-rate 0.1
–p-times 1
–p-overlap 3
–o-trimmed-sequences trimmed-seqs-darte.qza
–output-dir /mnt/home/choiji22/jin_test/darte_file \
–cmd-config PATH
–help \

anybody has the same problems?

Hi @mly! Have you had a chance to review the official cutadapt documentation? The q2-cutadapt plugin wraps the cutadapt tool, and exposes several of the cutadapt parameters, including the adapter and front parameters, which are explained in detail in those official docs. It is worth noting, QIIME 2 adds an -f and a -r for forward and reverse to the relevant parameter names, respectively. Let us know how it goes! :t_rex:

1 Like

This topic was automatically closed 31 days after the last reply. New replies are no longer allowed.