I am running MetaPhlAn3 on my dataset (from bowtie2 files) and I was hoping you could help me with something I don’t understand.
When I looked at the outputs for a given individual, I do not obtain the same number of microbial species for the different outputs.
For example I obtained 97 species in the “rel_ab_w_read_stats” file and 457 species for the “clade_profiles” file. Why could that be?
I thought this could be because of some filtering but I noticed that some species with high MetaPhlAn score in the “clade_profiles” file are not present in the “rel_ab_w_read_stats” file and on the opposit some species with a low score are present in this “rel_ab_w_read_stats” file.
If you have any explanation for that, I would appreciate it.
Thank you in advance for your answer,