KEGG categories L2 and L3

[Lina Maria]

Hi Gavin,

I used q2-picrust2 for getting the table and then moved to picrust2 for getting the names of each of the pathways. Now, I want to get the KEGG pathways at levels 2 and 3 but I am not sure how to do it. Could you help me, please?

Thank you so much

Lina M

[Gavin Douglas]

Hi there,

There is a rough R script you can use for doing that analysis, you can see it discussed here: https://github.com/gavinmdouglas/picrust2_manuscript/issues/2#issuecomment-1138633679

There is also a discussion there about how to change the code to change what levels are collapsed to.

Cheers,

Gavin

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[Lina Marìa Martìnez]

Hi Gavin,

Thank you for your response.  Following the links and reaching the FAQ, you say that you prefer to use the pathway-level inference implemented in picrust2.  I was checking this step but it says that a stratified table in "contributional" format breaking down how the ASVs contribute to gene family abundances in each sample is required. Q2-picrust2 doesn't provide that table. Is there a way to be able to use this method using the table from the plugin in qiime2? 

Thank you for your help

Lina M

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[Gavin Douglas]

Hi Lina,

No unfortunately you would need to use the standalone version to get a stratified table.

Cheers,

Gavin

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[Lina Marìa Martìnez]

Hi Gavin,

Thanks for your reply and help. In that case, I will use the standalone version.

Lina M

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