Rarefy metagenomic adatasets for taxonomic profiling using MetaPhlAn3

Question

[serene.s]

Hi community I wanted to rarefy my metagenomic datasets before profiling them for the taxonomy using metaphlan3. I am not able to find any methods. Also can anyone please explain why is it a good idea to rarefy the datasets before doing the taxonomic assignments using Metaphlan3? How would it affect the results? I have datasets that range from 1GB to 39 GB size and in the terms of DNA yield range from 1.2 Mbasepairs to 10.3 MBasepairs.

Thanks in Advance Saraswati

[andres.firrincieli]

why is it a good idea to rarefy the datasets before doing the taxonomic assignments using Metaphlan3? How would it affect the results?

It depends on the kind of analysis: link