q2-clawback summarize-Qiita-metadata-category-and-contexts

[iordanis (H20)]

Good evening everyone, I have some questions about using the q2-clawback plugin

Based on the tutorial we use the command

qiime clawback summarize-Qiita-metadata-category-and-contexts
--p-category empo_3
--o-visualization available_empo3.qzv

Question a) It is not clear to me why we are using this command?
b) In the parameter --p-category ---> besides empo3.gza, can we use it for human stool?
c) In the qzv generated what do we select and with what criterion for downstream analysis?

I am sorry for the many questions. And thanks a lot to the whole team for helping all users.

[Nicholas_Bokulich]

Hello @iordanis ,

Please see the q2-clawback tutorial, which answers these questions (and if not there, then the clawback reference, which is linked in the tutorial:

Using q2-clawback to assemble taxonomic weights

Note: This guide assumes you have installed QIIME 2 using one of the procedures in the install documents. This tutorial extends the q2-feature-classifier tutorial to show how you can improve taxonomic classification accuracy by assembling ecologically informed taxonomic weights for your samples using q2-clawback. This approach is described in this article: https://doi.org/10.1038/s41467-019-12669-6 We will retrain the naive Bayes classifier from the q2-feature-classifier to classify the ski…

I also recommend looking closely at the earth microbiome project ontologies to see what the different EMPO 3 types are.

Good luck!

[iordanis (H20)]

Hello @Nicholas_Bokulich

Thank you very much for the information and for the response.