I have two metagenomes and did assembly reads to contigs, and also mapped reads back to contigs. I need to know the difference in abundance of sequences could be assigned to particular genomes and the functional capacities of species in two metagenomes.
The point is the contigs can have different number of reads re-mapped.
My question is how can I normalize the sequencing depth of two data to see the difference between them? For example, data1: 5 contigs -> species A data2: 3 contigs -> species B => species A could be more than species B in data1
data1: 5 contigs (number of reads re-covered are 5,10,30,5,50) -> species A data2: 3 contigs (number of reads re-covered are 60,30,40) -> species B => it could be species B are more abundant than species A in data 2
Any one can help or suggest? Thanks in advance.