p-sampling-depth

[colinbrislawn (Colin J Brislawn)]

Hello CARMEN,

@DECARO

Hi, I am in a trouble to decide the --p-sampling-depth value.

You are not the only one. This is a common question because you are balancing keeping more samples and keeping more reads in each sample.

Mehrbod has a great discussion of this trade-off here:

Deep sequencing

Dear, Is there a minimal number of sequences (deep) for sample size for 16S sequencing for the robustness of the results? Can I find some papers that explain about this. Because I read good papers with few sequences and another with a lot of sequences per sample. Thanks for your attention.

The good news is that your minimum frequency is pretty good!

Minimum frequency 30,572.0

You should be able to use --p-sampling-depth 30500 and keep all your samples.