KEGG Orthogroups count output

Microbial community profiling HUMAnN
1

Hello,

I am using humann v3.9. Is there a straightforward way to generate KEGG orthogroup abundance in counts? I know the output is in non-integers because the gene family abundances are transformed into RPK’s to account for gene length. Instead, I would like to account for gene length by including gene length as an offset in my models. Are the raw count abundances available in one of the intermediate file outputs? Thank you for your help.

2

This is not an option in HUMAnN 1-3, but the newly released HUMAnN 4 allows you to report abundances in unadjusted counts if desired (I included a note about this in the release notes since it is a common request). If you run HUMAnN asking for counts, you can then regroup UniRef90s to KOs and the KOs will be in counts still.

3

Thank you for your help!