I am attempting to perform meta-analysis, where all of the obtained studies examined V3-V4, but using different sets of primers. There are obvious problems with comparing different variable regions, but I’m not sure if these problems apply when using the same variable region with different primers. To my understanding these sequences too do not align at 3’ and as a result can cause same problems with defining unique sequences abundance (as described here ).
This leads me to the following question - should sequences from same region but generated with different primers be treated the same way as sequences from different regions, i.e. preferentially using q2-fragment-insertion or are there perhaps other, more appropriate methods (unfortunetely the obtained sequences are with primers already removed) to combine this kind of data?
Thank you for your help. I look forward to your response.