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?
Yes --- there are a few posts on the forum that touch on this, so I won't go into any details here. If you have more specific questions about this, feel free to open up a new thread under the User Support category!
A q2-cutadapt is currently on our radar, as one option in the larger discussion of primer removal ! It would be really convenient if users were able to do this kind of thing within QIIME 2, and cutadapt certainly looks like a good candidate at the moment! Stay tuned!
