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.
MetaPhlan2 does not support paired-end analysis so it would be better to run the analysis on each file and then merge the output to get the full picture of the data or if the paired-end information is not going to be used to run any further analysis such as assembly then it is better to avoid