I want to get metabolic pathways from kegg output, especially kegg pathways, but didn’t find a good way to do so. I tried:
humann_renorm_table -i test_genefamilies.tsv -u relab -p -o test.ra.tsv
humann_regroup_table -i test.ra.tsv -o test.tsv -g uniref90_go -e 6
humann_rename_table -i test.tsv -o test.ko.tsv -n kegg-pathway
But 0 of ~2900 entries were renamed. Same result if I change “kegg-pathway” to “metacyc-pwy”. But if I use “humann_rename_table -i test.tsv -o test.ko.tsv -n kegg-orthology”, 86.15% were renamed. I was wondering if I did anything wrong in choosing the database for use? How can I get pathway results? I really appreciate your help!