Hello,
I am using HUMAnN v4 and managed to generate a table of KOs corresponding to my data. I have been trying to group them into modules. Providing the module definitions in a structured way i.e. following the module definitions using logical structures doesn’t work with the humann_regroup_table script. I used the -c option to provide this custom file.
For example: M00000 (K03518+K03519+K03520) does not group my KOs despite all three KOs being detected in all my samples
On a related note, can pathway/module abundances be computed after the main humann run using the logic in the humann v1 paper? I see only the main humann script has an option to provide alternative pathway definitions
To the first question, it might be that your whitespace is off. See the attached set of KEGG module definitions for guidance. These are quite old now, but I have used them internally on HUMAnN 2 and 3 (and the syntax should be the same with HUMAnN 4).
To the second question: Yes, you can start HUMAnN from a genefamilies.tsv file as --input and it will compute reaction and pathway abundance without having to redo all the search steps starting from sequencing reads.
old-kegg-module-definitions.tsv (30.6 KB)