Hi all, I am analyzing two different sequencing runs that do not align to the same start/end when aligned to the silva database. So running them together using the mothur SOP is not working. I wanted to merge the OTU tables but that doesn’t seem to be feasable either.
Ive decided to just switch gears and analyze them separately and compare. If I do this, does that mean I cant run beta diversity metrics or pcoa etc because theyre seperate runs? Or is there a way to compare them in mothur? Im primarily interested in understanding the change in diversity between the two batches.