RE: Rarefying and taxonomy

Hi Justine!

Hope you are doing well!

I have a question or want to confirm that the .csv taxonomy table that is obtained from the taxa bar plot analysis is not rarefied. I want to use that table for further analysis and it needs to be rarefied. I know that for diversity core-metrics-phylogenetic and diversity alpha-rarefaction you have to rarefied first. But for the taxonomic analysis there is no parameter to rarefy. I just want to confirm that that's case and I am not misunderstanding this step.
I would appreciate your response!

Thanks and best regards!

The table that you can obtain from taxabarplot is not rarefied(unless you used rarefied table as input). You can use it and rarefy it externally.
If you want to perform it in Qiime2, you can collapse your feature table at desired taxonomy level and then rarefy it. After it you can use it in Qiime2 or export as a biom file and then convert it to tsv format.

Hello @timanix,

Thanks so much for the response. Super helpful. I will follow those steps.

Best regards!

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