Hi all, i have run 2 separate runs on mothur and obtained 2 make.shared files for my 2 treatment groups (control and patients).
Do i use the merge.files command to obtain a merged.shared output and proceed on with the merge.group command?
I’ve actually tried the above commands and it didn work. Just wondering does the merging of 2 separate runs have to be done at an earlier stage?
Will the observed OTU overlapped and be not unique anymore?