In MetaPhlan there is an optional section to select “Ignore_eukaryotes” - if this is selected, is this just not displaying what the results for eukaryotes are? Or is it actually filtering out host reads from the microbial reads? Thanks
Hi @bethp
The tool is not filtering or changing your original data files. It is just annotating what is input. So, using that option is telling the tool to ignore any annotation that might be present (as a primary or sub hit) for that excluded group.
If this doesn’t help, please explain a bit more. Thanks!