kegg pathway

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Elizabeth Aceves

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Jul 5, 2021, 5:28:21 PM7/5/21
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Hi !

I have been working with PICRUSt2 output, but I have a doubt. 
I know that i need a map of KEGG orthologs to KEGG pathways for running pathway_pipeline.py 
My question is: how can I get this map? 

Thanks.
Elizabeth

Gavin Douglas

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Jul 5, 2021, 6:56:28 PM7/5/21
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Hi there this FAQ post I think will answer your question: https://github.com/picrust/picrust2/wiki/Frequently-Asked-Questions#how-can-i-determine-kegg-pathway-abundances-from-the-predicted-ko-abundances

The map of KOs to pathways is part of hte PICRUSt2 source repo, so you can download that from https://github.com/picrust/picrust2/ to get the mapfile (the filepath is shown at the above FAQ).

You can download the latest mapping of KOs to pathways (that I am not able to distribute due to licensing restrictions) from the KEGG website’s API, as long as you’re doing non-commercial research.


Cheers,

Gavin


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Elizabeth Aceves

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Jul 5, 2021, 9:53:34 PM7/5/21
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It really helped me!
Thank you so much!

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