Can anyone tell me how to interpret/significance of the results produced by alpha rarefaction?
My graph is showing below.
Hi @dasqiime22,
These rarefaction plots aren’t used for any statistical testing but rather are meant to help you explore the alpha diversity of your community as a function of your sampling effort. You can read more about these plots here. On the X axis you are randomly sumsampling your reads and calculating the index of choice at that level on the Y axis. The ideal situation is where you see a plateau in all your samples/groups which you are seeing in your case. This vaguely tells us that at these sequencing depths captured the maximum diversity of the community and if we had more reads it is unlikely that we would capture a different relationship.
Some people use these plots to compare alpha diversity across groups but this is not the case for these q2 plots. You can use the alpha-diversity and alpha-phylogenetic plugins for statistical testing.
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