differences with other normalization methods about microbecensus

[snayfach]

Hello - there are a number of reasons why the two might disagree, including that 16S are not single copied. How are the 16S copies estimated? If you are using reference mapping, then you could be missing some 16S. If you are using assembly, it is known that 16S is v. hard to assemble. If you are doing amplicon sequencing, then you can't compare vs the bulk metagenome.

[sapuizait]

good point, yes reference mapping. In the past (before switching to microbecensus) I would use the silva db as reference and estimate the counts of shotgun sequencing reads per sample. So yes i guess there is some loss (from the taxa missing) and the multiple copy gene that bias the results a lot!
Thanks a lot for your quick reply!