comparing 2 treatment groups

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 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?

Thank you.

You need to merge the samples at the beginning of the pipeline so that you only get one shared file.