humann v3.7
How to use humann to get the abundance table of kegg-module? Can someone help me out?
To quantify KEGG modules you can run HUMAnN normally, then use the regroup_table
script to convert your UniRef gene families into KO abundances. You can then provide these KO abundances as input to HUMAnN and specify a set of KEGG module definitions as your pathway database to quantify. This is not a file that KEGG provides for free (to my knowledge), but if you have a KEGG license you can download it. I’m attaching a very old version to illustrate the format - I would NOT recommend using this file for analysis.
old-kegg-module-definitions.tsv (30.6 KB)