Alpha diversity

[zeineldn (Mohamed zeineldin)]

Hello,

How could I get the alpha diversity for the individual samples?

After running the code i just found the significance between the group.

Thanks,
MZ

[jairideout (Jai Ram Rideout)]

Hi @zeineldn! You can export the per-sample alpha diversity values from the QIIME 2 Artifact (i.e. .qza file) that’s created by either qiime diversity alpha, qiime diversity core-metrics, or qiime diversity core-metrics-phylogenetic, depending on which command you ran to compute alpha diversity.

Check out the exporting tutorial for examples. The tutorial shows how to export a feature table and phylogenetic tree, but the general form of the export command will be the same for your alpha diversity .qza file. For example:

qiime tools export <your-alpha-diversity-file>.qza --output-dir exported-alpha-diversity

There will be a file in the exported-alpha-diversity/ directory called alpha-diversity.tsv, which is a TSV file containing the alpha diversity values per sample.