Hello! I'm coming here to acquire wisdom in the arts of metagenomics. I have built a phyloseq object with an OTU table consisting in MAGs abundances per samples. The abundance estimation method I chose in this case is the coverM "counts" method, this is, reads mapped against a specific MAG without further considerations. So I have this discrete counts OTUs table. The first thing people only lab has recommended is to normalize this OTUs table with the DESEq2 implemented method. Another recommendation I have got is to divide the resulting normalized counts by the genome size of each MAG but I dont know if this is a correct second step of normalization.
So, is it acceptable to first normalize the reads counts with DESeq2 and then divide the counts by the genome sizes?
