Tutorial "Moving pictures" | alpha rarefaction | the question about right palm jumping

Hello,

I'm wondering what is the correct answer for this "Question" in the moving pictures tutorial:

When grouping samples by “body-site” and viewing the alpha rarefaction plot for the “observed_features” metric, the line for the “right palm” samples appears to level out at about 40, but then jumps to about 140. What do you think is happening here? (Hint: be sure to look at both the top and bottom plots.)
QIIME 2 View

(I think there is an error about the numbers 40 and 135 when I look at the graph but the question still here.)

The number of sample begin at 9 and is bring down to 3 at about 900 of depth and in the same time the observed features rise up from 45 to 135 (which means the 6 other samples pull down the observed feature median when they can be here).
So I wonder what depth threshold we can use for the body-site analyse: 9 samples to increase the power of the statistical analysis or only 3 samples but with much depth. This choice can completely change the results.

As the 3 samples have more depths, maybe there are better in sequencing quality (DNA extraction...) than the 6 other so putting the 6 outside of the analyse is a good choice. Or maybe the 3 samples are just different in observed feature for other reason.
Can you help me for the interpretation please?

More broadly, in this tutorial why the alpha rarefaction plotting is not before the alpha and beta diversity? Because I think the alpha rarefaction plotting can help to choose the depth threshold, no?

Thank you for creating qiime2 and the support you provide :slight_smile:.
I already have multiple answers for my others questions (and quickly), this is really helpful. Thanks!

Jérémy Tournayre

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