Normalization of RGI counts #126
Description
Hello!
I am using RGI to characterize antimicrobial resistance genes from shotgun metagenomic data generated from complex food matrices.
Could you suggest what is the best downstream normalization of ARG reads counts?
As scaling factor is it recommended using the total number of reads after host genome removal (non-host reads only) or are there some other specific normalization strategy for comparing AMR abundance across samples in food?
Thank you