I have 2 series of 16s data, 1 sequenced with v3-v4 region, 2 sequenced with v4 region. now, I wanna run them together in mothur. How can I do that? does anyone experience that?
You can’t compare V3-V4 data to V4 data. They are separate datasets. The primers you use have different biases, you’ll have batch effects, etc. Your life will be much easier to redo everything with the V4 region.