Hopefully somebody can help me. I’m not totally new to mothur as I analyzed most of my single microbial communities with it. But now I want to compare these communities with each other in a multiple sample analyses, and I`m already failing to generate the make.shared.file.
I have three communities to compare (A-B-C). When I’m establishing the group file should I use the make.group command and the three single unique.fasta files for community A, B and C, and if yes, how should I generate the needed single list.file for the make.shared command? In case, that I 'm barking up the wrong tree, can anybody support me with I short tutorial which files I should use for generating the list and group file for multiple sample analyses?
Sorry to bother you with that, but I already spend a serious amount of time to find out myself.