Mapping to KEGG pathways in PICRUSt2

[Laura Bennett]

Hi all, 

I am new to PICRUST. Have a missed something? In PICRUSt, you could previously map KO abundances to KEGG pathways.

However in PICRUSt2, while you can find KO and E.C. number abundances per sample, you can only map E.C. to metacyc pathways and no longer map KOs to KEGG pathways?

Am I missing something/ doing something wrong?

Thanks

Laura

[Gavin Douglas]

Hi Laura,

Yes that's correct there is no mapping to KEGG pathways by default. This is because the KEGG database is closed-source now and I do not have access to the latest mapping files to share. You can certainly plug in whatever mapping file you want though, which I would be happy to help with if you have one in-hand.

Best,

Gavin

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[Laura Bennett]

Hi Gavin, 

Thanks for the reply, of course this makes sense!

If we had our own mapping file that mapped KEGG pathways to KEGG orthologs (MAP),  then run_minpath.py would work like this:

run_minpath.py  -i predicted_metagenome.tsv -o minpath_out -m MAP  --intermediate minpath_working --no_regroup 

I.e. we want to map KO to KEGG pathways using our MAP file, but to skip the re-grouping step to reactions that is required for E.C. numbers.

Am I correct?  regroup is only required in the case of EC numbers? 

Thanks again, 

Laura

[Gavin Douglas]

Hi Laura,

Yes that’s correct! If you run into any issues I’m happy to help.

Best,

Gavin

[Laura Bennett]

Thanks Gavin!

I will let you know if I have any problems. Appreciate the help. 

Best wishes

Laura