The bioBakery help forum

Does lefse takes care of rare taxa or feature?

Hi… I have unstratified output 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 in any sample? I just want to know if there is any additional filtering step needed or not.