I have used same metaphlan output as input for lefse in two formats. In first case, extracted out all the OTUs upto species level like:
And, in second case, using only upto genus level from the same metaphlan profile output:
type clade_name k__Bacteria|p__Actinobacteria|c__Actinobacteria|o__Actinomycetales|f__Actinomycetaceae|g__Actinomyces
But, I found both gives different results. I found some genus in the second case that were not found from the first case and vice-versa. Why am I getting this differences in output? Can anyone please help?