Question on path_abun_unstrat

[Chao-Jui Chang]

Dear PICRUSt2 team

I have a simple question on the understanding of the output files of the PICRUST2. 

The PICRUST2 provides the 5 output data/files.

EC_predicted_and_nsti

KO_predicted_and_nsti

EC_metagenome_out

KO_metagenome_out

pathways_out

As far as I understand in the Fig. 1a of the original paper

the EC_metagenome_out comes from the EC_predicted_and_nsti and ASV abundance

and 

the  KO_metagenome_out comes from the KO_predicted_and_nsti and ASV abundance

but how about pathways_out

it seems it was completed by the tool- MinPath

but I'm not sure if it is built by the KO result or the EC result

the description of the MinPath on GitHub (https://github.com/mgtools/MinPath)

written that KEGG and MetaCyc pathways included in Minpath were updated as of May 10, 2021.

Since the pathway ID in path_abun_unstrat looks like from, thus I assume this result comes from EC_metagenome_out

Can you help me to clarify it?

Sincerely,
Chao-Jui

[Robyn Wright]

Hi there,

Yes, the pathway abundance file is calculated from the EC numbers. You can see some more information on the wiki page here, but the mapping file has been taken from HUMANn2 and the approach used also follows their methods. You can also see some more information in the FAQ.

Robyn

[Chao-Jui Chang]

Hi  Robyn

Thank you for your clarification and information

I have a further question: can we use KO numbers to calculate pathway abundance in PICRUSt2?

best, 

Chao-Jui

roby...@gmail.com 在 2024年11月8日 星期五晚上8:59:17 [UTC+8] 的信中寫道：

[Robyn Wright]

That's not currently an option with the default files, but I believe that if you made a mapping file then you could probably use the pathway_pipeline.py script with this file instead. You can see the options for this script here.

I can't remember who I have mentioned it to now, but I am currently working on an update to the database used by PICRUSt2. I will see if I am able to map from KO's to pathways. 

Robyn