LEFSE: Should I remove features with low relative abundance or lefse will take care of it?

Question

[deep771992chanda]

Hi… I have pathway abundance outputs from HUMAnN 3.0. I want to find out differentially abundant pathways between two groups. For that, I have removed those features (pathways) which are not present in at least 10% of the total samples. But, in addition, should I also need to remove those features which show relative abundance below a certain percentage (say, <0.01%) in any sample? I just want to know if there is any additional filtering step needed or not.

Thanks, DC7