Mapping metatranscriptomics rRNA reads to MAG 16S rRNA genes

Question

[dark.lord]

Hi all,

I have 3 MAGs and I would like to map the metatranscriptomic rRNA reads to the 16S of these 3 MAGs to see whether there is a differential expression - basically a differential expression analyses on 16S instead of functional genes. The procedure I was thinking of involve either kallisto or bbmap + samtools and featureCounts. I was wondering however how to present the results - is there such a thing as rRNA-TPM, and does it make conceptually sense? Also, I would be happy if you could redirect/address to some papers which reported this kind of analyses.

Best

S