qiime diversity alpha command / sampling depth parameter

User Support
1

Dear Qiime developers,

I have followed the moving pictures tutorial to analyze my data. Besides i ran the command: qiime diversity alpha in order to obtain specific diversity index. For example:

qiime diversity alpha
--i-table table.antartida.qza
--p-metric simpson
--o-alpha-diversity Indices\ alfa/simpson
Saved SampleData[AlphaDiversity] to: Indices alfa/simpson.qza

In this point i realized that the command does not have a sampling depth parameter. Is this not necessary for a correct diversity interpretation? Should i assume that all sequences in each sample are used?

Thank you in advance. I appreciate your work and the time you spend helping us!

2

Hi @mi_metodo,

The alpha diversity comamnd assumes that you're giving it a rarified table. (This is true in Core Diversity Metrics, it's just hidden.) You can use the rarified table from your core diversity metrics; it should be in the diversity folder as rarefied_table.qza.

Best,
Justine

1 Like
3

Oh I understand. I have not noticed about rarefied table in the diversity folder. Thank you! Very clear your answer.

Best,
Guille

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4

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