I have been using mothur for many years now, and have always used Metastats to assess shifts in relative abundance using the outputted q-values. I have a couple of questions:
Firstly, in the more recent versions of mothur, the q-values are no longer outputted. Out of curiosity - why is this the case?
Secondly, in the age of analysing unique sequences, how can multiple corrections be applied and justified? It gets to the point where highly significant P-values have a q-value of 1, due to the sheer number of comparisons (in my case, over 10000 OTUs). I wonder whether focussing on the core microbiome is a good solution?