Hi Nicholas,
Additional question.
I decided to run the trunc/trim as 6/299 for forward reads and 6/290 for the reverse reads and after looking at table.qzv, I noticed that I have terribly low frequencies.( See below)
I am running 2 other parameters to see if maybe I needed to trim more, to remove added noise (currently running), but for the meantime I wanted to ask if you had any idea of what this could mean.
Note: I did read another post where it states that for ITS data, after DADA2 I would run filter-table-feature-filter (is this correct) and would this be okay to do with my samples? Link here (ITS) and here (using filter table-feature-filter on low frequency table.qzv)
Based on this information, could you tell me what is the best step for me to take and or refer me to another link?
