It would be nice if mothur provided a clean method of taking an average value across biological subsamples. For instance, I have 3 soil subsamples per plot, but want to describe the bacteria present on a per-plot basis. Presently, I’m going to R to average values across subsamples in a .shared file, but it would be nice to be able to do this within mothur. Also, there are some downstream compatibility things that would need to be thought through. E.g., downstream commands in mothur require integer values in a .shared file - - - but is rounding average values up to the next integer the best approach? For one thing, if you’ve rarefied earlier, rounding messes up the total read counts per sample.
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