Greengenes 2 with 515F-926R primers

[raincx (Javiera)]

Hi Daniel! Thank you so much for this amazing work.

I have a question, which command do you recommand me to use with data obtained by DADA2 using V4-V5 primers 515FB-926R.

Kindly,
Javiera

[wasade (Daniel McDonald)]

Hi @raincx,

In Qiita (https://qiita.ucsd.edu), we developed and rely on Deblur so I have limited hands on experience with DADA2. We placed 90, 100, 125, and 150nt fwd read ASVs from 515F into Greengenes2, so I would anticipate reasonable overlap with your data assuming operating on the fwd read and the trim length matches -- the command for that is filter-features. If use of the reverse read is important for a specific question being asked, then the closed reference action with vsearch would be needed through the non-v4-16s action.

Best,
Daniel