Can you tell me how to chose (the best way) the sampling depth for Alpha and Beta Diversity for my sample below:
| RAG-1 | 199285 |
|---|---|
| NOV-2017-5044 | 133732 |
| RAG-3 | 132876 |
| RAG-2 | 123372 |
| OCT-2017-5036 | 104454 |
| MAY-2017-5016 | 97564 |
| RAG-4 | 55881 |
| MAY-2017-5015 | 12297 |
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Hi @dasqiime22,
I moved this question to its own topic as it was no longer relevant to the original thread. This helps us keep the forum organized and others can easily search their questions and topics.
The question you are asking is a great one with no real right answer, there are recommendations and guidelines on how to pick these and I’ve highlighted my own thoughts on the matter previously.
In your case, you can simply choose 12297 since that is the lowest # that will you to retain all your samples and that is generally considered a pretty good depth coverage for most communities.
Note that there are methods in qiime2 (i.e. DECIPHER, ANCOM, gneiss, q2-breakaway) that don’t require rarefying your reads, so those are all certainly worth exploring too.
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