I am new in Qiime2, I have some questions about analysing microbial diversity.
- OTU methods in QIIME2
What are the outputs of the commands ‘chao1’ and ‘observed_otus’ (see screenshoot below). My understanding is that ‘chao1’ considers not only observed otus, but also non-observed rare species, while ‘observed_otus’ only considers observed otus. In this case, results from ‘chao1’ should be always bigger or equivalent to those from ‘observed_otus’. Further, if I removed singletons before using these two commands, the results from both should be the same, according to the chao1 formula. Am I correct?
In my analysis, after removing singletones, ‘chao1’ showed higher results than ‘observed_otus’. How can I interpret?
- ASV methods in QIIME2
In this method, singletons were removed by default. Then the results from ‘chao1’ and ‘observed_otus’ were the same. This is as expected if my understandings above were correct. If incorrect, how to interpret this.