how to rarefy data?

lca123 · February 11, 2020, 6:40pm

Hey there,
Does
qiime diversity alpha --i-table table.qza --p-metric shannon --o-alpha-diversity out.qza

rarefy data?

Leo

lca123 · February 11, 2020, 5:26pm

Hey there,
I know there is other commad for alpha rarefaction, but my question is whether the above command also somehow rarefy the data, as we don’t input a “rarefy” option.

Stephanieorch · February 11, 2020, 5:44pm

Hi Leo,

This command cannot rarefy data.

If you are ever curious about the possibilities of commands what you can always do is add --help at the end of the command to see all of the possible inputs.

Best,
Stephanie