My workflow until now:
Find fragments of a marker gene in unassembled metagenomes > download and assemble metagenomes > recover the gene neighborhood / gene set of interest
Right now I have a rough estimate of how abundant these genes are by the 'depth' noted on the assembled contigs (I use MEGAHIT for assembly). I was wondering if there's a more thorough/proper way to do this. I would like to compare the abundance of specific genes between a) samples in the same study, and b) different studies. I imagine that the size of the individual metagenomes should be considered in both cases, but point b) might add additional difficulties such as different sequencing techniques. I would appreciate your insights.