TPM or RPKM for Metagenomic Contig Abundance

Question

[joshua.kirsch]

I'd like to calculate the differential abundance of a group of contigs in my assembly and compare the relative mapping of these contigs between samples. Previous papers have used RPKM to calculate summed for values for groups of genes or contigs (eg how many reads mapped to ARGs). In other words, they calculated per-gene or per-contig RPKM values and then summed these in samples and compared these summed values between samples. From my understanding, RPKM has flaws and the RNA-Seq field recommends TPM instead. For this application, what do you folks suggest?

[Ram]

All of RPKM, FPKM and TPM are relative measure that can be used to compare transcript expression levels within samples. Stricly speaking, none of them are valid for cross-sample comparison.

[SergFly]

The question then arises. How do metagenomic samples compare?