I have been working with a HUMAnN3 dataset derieved from fecal samples with ca 21,000 pathways in it. In order to filter away some of these pathways I decided to only keep pathways with a pathcoverage “score” of above 0. This resulted in only 167 pathways remaining. I fail to believe that this is a reasonable number but I can not see anything wrong with my methodology. Have I missed something obvious here? Am I wrong in using the pathcoverage file in filtering?
Any help will be appreciated!