p-sampling-depth

[DECARO (CARMEN)]

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

Metric	Sample
Number of samples	45
Number of features	2,146
Total frequency	3,318,807

Frequency per sample

	Frequency
Minimum frequency	30,572.0
1st quartile	55,012.0
Median frequency	70,415.0
3rd quartile	86,541.0
Maximum frequency	136,126.0
Mean frequency	73,751.26666666666

Frequency per feature

	Frequency
Minimum frequency	1.0
1st quartile	11.0
Median frequency	54.0
3rd quartile	264.75
Maximum frequency	402,868.0
Mean frequency	1,546.508387698043

How I to decide the --p-sampling-depth ?

thanks
Carmen

[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.

[DECARO (CARMEN)]

Hi, thanks for you suggestions, however I tried using --p-sampling- depth 30500 but without good results. How can I do?

[colinbrislawn (Colin J Brislawn)]

Tell me more!

How were these results bad? What were you hoping for based on your choice of threshold?

[DECARO (CARMEN)]

I sent the command :
qiime diversity core-metrics-phylogenetic
--i-phylogeny rooted-tree.qza
--i-table table.qza
--p-sampling-depth 30500
--m-metadata-file sample-metadata.tsv
--output-dir core-metrics-results
I have this results: "There were some problems with the command"

[lizgehret]

Hi @DECARO,

Check out the first error listed in your screenshot:

(1/18) Invalid value for '--output-dir': 'core-metrics-results' already exists, will not overwrite.

This directory already exists from your current location on your machine. You can either delete that existing directory, change the name of your '--output-dir' directory, or move to a different location on your machine to create another 'core-metrics-results' directory.

Cheers