Hello,

I ran RGI tool and obtained AMR gene count data using MAGs (not reads) as shown below:

rgi main -i sample1.fasta -o sample1 -a DIAMOND -n 24 --clean

First question is this count data that rgi main outputted normalized or absolute?

If it's absolute (I presume), then I want to normalize these counts with RPKM method.

Can someone please suggest, how can I do that?

Please clarify!