Picrust2 pathway abundance output: IDs translated into actual pathway names

Library Plugin Support
1

Dear QIIME2 team,
I would like to know if there is a way of translating pathway and KEGG orthologs IDs into the actual pathway and gene names. Here you have examples of multiple IDs pathways:
PWY-1269
PWY-1361
POLYISOPRENSYN-PWY
PPGPPMET-PWY
PRPP-PWY
...

Thank you for your constant support and help,

Daniela

2

Hi @Daniela_Vargas, I moved this question over to "Community Plugin Support" - maybe @gmdouglas can comment on this question?

2 Likes
3

Hey @Daniela_Vargas,

You can get the pathway descriptions with PICRUSt2, but not with the QIIME 2 plugin. You can checkout this part of the tutorial to see how to add descriptions to the PICRUSt2 pathway output file: PICRUSt2 Tutorial (v2.3.0 beta) · picrust/picrust2 Wiki · GitHub

Note that those are MetaCyc pathway ids rather than KEGG pathway ids by the way.

You might run into issues running the add_description.py script on the BIOM file straight from QIIME 2, but if so you can also see the mapping file of pathway ids to pathway names in this file within the PICRUSt2 github repo: picrust2/default_files/description_mapfiles/metacyc_pathways_info.txt.gz

Hopefully that helps!

Best,

Gavin

3 Likes
4

Thanks @gmdouglas!
I found it! Thank you also for the clarification about the MetaCyc pathway ids rather than KEGG pathway ids.
I really appreciate your help!
Best!
Daniela

1 Like