Hello to all! I would like to ask for some advice. I'm currently trying to analyze taxonomy of the metagenome from river floodplain, for what I downloaded SRA file from NCBI and converted it with fastq-dump and --split option to two fasta files (forward and reverse reads). Then I used Metaphlan2 for both fasta files separately. What I see in results - its % difference in taxonomic abundance between this 2 files. My question: should I merge this results in order to receive a full picture, or I shouldn't have split files with fastq-dump at the beginning? I will highly appreciate any help, as I'm a little bit confused how to proceed here.