Regroup - rename combinations


It is not very clear to me how the humann3 regroup and rename scripts can be used together.

Following the tutorial I used the uniref90_level4ec option in the regroup script along with the ec option in the rename script to see the enzyme commission categories. Perfect.

I also used the uniref90_pfam option along with the pfam option and this also looks ok.

But it is not clear to me what should I do to use the kegg option of the rename script for example. Could you explain how these two scripts work together for the other possibilities? Do the options in the two scripts work in a pairwise manner or you can combine them using different ways?

Thank you very much for your time

The regroup script will sum up UniRefs into other functional units, but described by short identifiers rather than longer, human-readable names (glosses). The rename function simply attaches the names/glosses to the identifiers. There are a few cases where the groups/names aren’t 1:1, and that might be the cause of the confusion here. The “KO” groups might be called something like “KEGG Orthologs” in the naming script to carefully distinguish them from other KEGG data?