Hi @Nicholas_Bokulich thank you for your response.
Regarding the Q2-ITSxpress plugin, this tutorial does not have the ITS extraction step. Apologies for my naivety as I am a newbie but is it necessary or is the trimming of the primers in this tutorial sufficient?
Thank you.
Hi @emmlemore .
The q2-itsxpress tutorial does have an ITS extraction step with the qiime itsxpress trim-pair-output-unmerged command. This tutorial does not.
They are two steps to achieve similar goals. ITSxpress trims to the ITS domain, removing the adjacent rRNA gene domains. But the primers are usually situated quite close to the ITS with only a bit of the rRNA gene domain present, so the difference is usually minimal. So which method you choose depends on your primer set and experimental goals, but both are valid options.
Good luck!