I am trying to run the rarefaction curve in QIIME2. It works out very well. The question I am having is how to set the n in the --p-max-depth? Here is the summary information of my feature table:

Frequency per sample

Frequency
Minimum frequency 1,826.0
1st quartile 17,273.0
Median frequency 24,558.0
3rd quartile 35,431.0
Maximum frequency 221,055.0
Mean frequency 31,315.43828715365

Hi @Bing,
There isnâ€™t a simple answer to this as it depends a bit on your data. The approach that I typically take is to start by setting --p-max-depth to a value around the median frequency per sample. In your case, this could be 25,000 (Iâ€™m just rounding to the nearest thousand from the information you provided, but rounding isnâ€™t required). You may want to increase that value if the lines in the resulting rarefaction plot donâ€™t appear to be â€śleveling outâ€ť, or decrease that value if you seem to be losing many of your samples due to total frequencies being closer to your minimum sampling depth than your maximum sampling depth.

I added these guidelines to the new section on Alpha Rarefaction Plotting in the Moving Pictures tutorial (added in QIIME 2 2017.10). There is some other important information in that new section, including definitions of some of the terms Iâ€™m using in my answer here, so be sure to read that.