Salmon in metagenomics mode (--meta) yield gene per million reads or per sample?

[JSSaini]

Hello, I am quantifying the abundance of genes in metagenomics data using paired-end reads (R1 and R2). I used --meta flag according to the salmon manual and provided R1 and R2 of each sample. However, what would be the unit of gene abundance quantification? Is it "gene per million" (GPM) reads? or Gene per million for each sample?

And also, what normalization method is used, especially for the quantification of gene abundance in metagenomics data?

Thank you for your prompt help.

Kind regards, Jaspreet

[JSSaini]

@rob-p I would be grateful if you could take a minute to read this. I will appreciate your response. Thank you.