Hi @Mehrbod_Estaki,
I ran this command:
qiime cutadapt trim-paired --i-demultiplexed-sequences demux-paired-end.qza --p-cores 2 --p-front-f CYGCGGTAATTCCAGCTC --p-front-r AYGGTATCTRATCRTCTTYG --p-discard-untrimmed --p-no-indels --o-trimmed-sequences reads_trimmed.qza
And I obtained this output:
reads-trimmed-summary.qzv (344.6 KB)
I mean there were very few samples from which the primers were removed, so I think that the primers were removed by the sequencing center. I am awaiting for them to confirm this.
This is the summary of the DADA2 stats:
dada2-table-summary.qzv (422.6 KB)
Cheers,
Pablo