After generating the table containing nseqs, sobs, coverage, simpson, invsimpson and Chao1, after rarefying, I just have a question.
Does sobs represent the number of OTU’s observed for the given number of sequences rarefied, and if so what is Chao1 representing?
I know Chao1 represents community richness, but is this in terms of OTUs sampled and if so how is this different from sobs?
Is it the case that sobs represents the mean number of OTUs in the rarefied reads, and Chao1 represents the minimum estimated number of OTUs in the entire sample?
sobs is actual species observed. Chao1 is a richness estimator-I wouldn’t use it, it was designed for macro communities and doesn’t seem to work well for microbial communities.
Ok, but does Chao 1 report the estimated minimum number of OTU’s in the entire sample after rarefaction.single?
Yes it was designed to use the seq abundance curve to estimate total richness of the sample. Again I wouldn’t use it for microbial communities-and neither would much of the field of microbial ecologists. If you want to use it, you should read up on the method and be able to justify your use.