Creating a PCOA with different sequence batches


Is it possible to generate a PCOA analysis with two different count tables? I have two sequence runs that were sequenced in different sequencing centers and each used a different primer sets - sequence batch A used a V3-V5 region amplicon while sequence batch B used a V4 only region amplicon. I used different coordinates for each when running pcr.seqs and screen-seqs commands for each. Is there a way to join the files after that to create a otu table that uses both -batch A and batch B sequences to later be used to generate a unique analysis?

Thank you!

You’d really be best off analyzing the data separately. This is what I’ve done when these types of situations arise.