Inferring relative gene abundance from short reads

Question

[SushiRoll]

Hi all!

I'm doing some metagenomics analysis (Short read) and would like to get the relative abundance of certain antibiotic resistance genes to total 16S. I was thinking on mapping the reads to a specific database and then mapping the reads against the 16S gene. Finally I was thinking on dividing reads_mapping_gene/reads_mapping_16S to get a relative abundance. Does that sound like a sensible approach? I feel there's something I'm not considering.

Thanks!!!