The bioBakery help forum

Cannot regroup into kegg pathway in Humann3

Hi communities,
I tried to regroup the pathway into kegg pathway by following command.

humann_regroup_table -i merged_path.tsv -o ./path_kegg.tsv -g uniref90_ko

However, there was only unintegrated pathway in the output file.
Even when I tried to regroup into go pathway, there was the same issue.

How can I regroup the pathways with other databases…?

Thanks,
MinJi

You can regroup from UniRefs (gene families) to KOs (broader gene families), which is what the -g uniref90_ko argument is asking for (but it would require a genefamilies.tsv input file rather than pathways). We don’t currently support regrouping pathways with the built-in mapping options, and it would be challenging to regroup from MetaCyc pathways to KEGG pathways. You would be better off computing KOs from your gene families and then trying to compute KEGG pathways based on the KOs you found.

Thank you so much for replying me.
Do you have any recommend packages or softwares for computing KEGG pathways easily…?
It seems difficult to compute KEGG pathways from gene families one by one.

Thank you,
MinJi