Hi @jwdebelius
no worries, I am totally pleased by your help and the forum in general as I am new to Metagenomics and soaking up information.
As how MetaPhlAn works (Mapping shotgun reads against a precomputed database of marker genes specific for a clade) it is not possible to get full read counts because it maps I) only against few markers and not whole genomes and II) each clade consists of varying number of marker genes. So multiplying a clade's relative abundance with the total number of reads of a sample's library will result in a biased output. However, the MetaPhlAn author also proposed your Idea of multiplying by a constant and then rounding to the closest integer to get "pseudo-counts".
I am just searching for alternative analysis approaches that work with relative abundance data as this would fit the original idea of MetaPhlAn better.
Best
Philipp