alpha-rarefaction.qzv (382.7 KB)
Ive attached my alpha-rarefaction cure. I am struggling to set sampling depth for alpha diversity. How to do I interpret this curve?
Kindly help me with this
Hi @steffi,
See this tutorial for more information on using alpha-rarefaction.
Your curve looks a little unusual — diversity levels off but then jumps up again around 14k sequences. Do not be alarmed — these curves are built from averaging multiple samples at each depth, and samples that do not have enough sequences at a specific depth are ignored. So the sudden increase is likely just because the number of samples that have 14k+ sequences drops dramatically (and the second plot showing sample counts confirms this). The samples that do have higher sequence counts just happen to also have higher diversity.
So interpret these as you usually would — choose a rarefaction depth where the curves begin to level off (the first time!).
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