Question regarding KEGG mapping file.

[Terrance Colunga]

Hello,

I am currently analysing 16S data from human using PICRUSt2 algorithm.

I want to predict KEGG pathways abundances using KO abundance table, and I read FAQ and there are: 

"Nonetheless, you can infer KEGG pathways levels by using the last publicly available mapping of KEGG orthologs to pathways (which is from around 2011)"

 

I tried the command, and I successfully got pathway abundance table, but then I got the another mapping file from KEGG REST API, linking pathway to KO, which produces the completely different result.

Which result should I trust, from the default mapping file from 2011 or from the mapping file I generate from KEGG REST API?

Additionally, as KEGG REST API can be accessed from academic users, why do PICRUSt2 not use these mapping file?

Sincerely,

[Gavin Douglas]

Hi Terrance,

I haven’t tested any newer KEGG mapping files, but my understanding is that there have been numerous additions and changes to KOs and pathway definitions. I would expect the newer mapping file to have more information though - are you mainly finding very different pathways reported or are there different abundances being calculated for well-characterized pathways (e.g. Glycolysis)?

I don’t think that we are allowed to distribute the REST-API mapping files and I’m also unsure whether you’re allowed to publish with those mapping files without a subscription. I set the default pathway outputs to be MetaCyc pathways to avoid these possible issues. A lot of users have been asking for newer KEGG mapfiles though so I would be happy to distribute those if I am allowed.

Best,

Gavin

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