How to normalize gene abundance from metagenomic data?

Question

[v.berriosfarias]

hello this is the first time that I have to perform a gene abundance profile along several number of samples using genes with different sizes:

I have been following a tutorial: https://metagenomics-workshop.readthedocs.io/en/latest/annotation/quantification.html

and a necessary step for gene abundance profiling is to normalize the gene abundance counts. On that tutorial TPM (transcripts per million reads) is suggested. given that the TPM calculation is designed for transcriptomics/metatranscriptomics I want to know if TPM calculation from metagenomic read counts is a correct way of normalization:

Basically I mapped the paired end metagenomic reads agains their contigs, searched for the gene loci and built a bam file from where I want to perform the gene abundance calculation.

I think that Deseq R package is the best thing to do here ahead of gene abundance normalization. what do you thing?

[Asaf]

Did you sequence DNA (metagenomics) or RNA (metatranscriptomics)? How different from each other your samples are? Different donors or the same donor?