I have already seen some answers to the problem of analyzing different hypervariable regions of the 16S rRNA gene. And most of them are focused on the use of deblur and q2-fragment-insertion plugins.
I performed a meta-analysis considering 10 different sets of primers applying the Closed-reference OTU picking method.
I understand that the advantage of using deblur and the q2-fragment-insertion plugin is that it allows to recover all diversity present in the samples and also obtain a better resolution.
But I have the following question from one of the reviewers of my article:
What is the rationale to use 97% OTU clustering (closed reference) but not exact sequence variance? Exact sequence variance likely can provide a better resolution on the diversity.
In my opinion, the closed reference method is robust but allows to describe the diversity of the microbial community. Do you currently consider the use of the closed reference method to perform a meta-analysis unjustifiable?
Thank you very much in advance!!