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-indels
–p-times 1
–p-overlap 3
–p-match-read-wildcards
–p-match-adapter-wildcards
–o-trimmed-sequences trimmed-seqs-darte.qza
–output-dir /mnt/home/choiji22/jin_test/darte_file \
–cmd-config PATH
–verbose
–quiet
–help \
anybody has the same problems?