Dear Qiime2 Team,
I have a question based on fungal ITS2 300bp paired-end MiSeq reads. Due to the variable region of ITS2, is it advisable to trim primer sequences using cutadapt (python-package) before merging your reads?
For a Miseq run paired-end 300bp, I understood, that you can end up sequencing into your reverse primer and vice-versa and that can influence your merging with DADA2. That would for example happen if you don’t want to truncate the reads to achieve an overlap when you have a quality drop in the end of your R2 reads. Do you think implementing cutadapt into Qiime2 is therefore a good idea?