Apply Sampling Depth Parameter to weighted_normalized_unifrac

[Florian_Hoffmann]

Hi everyone,

I have generated the beta-diversity core metrics results in my jupyter notebook using a particular sampling depth (–p-sampling-depth 676). However, this command does not produce the Weighted Normalized UniFrac (weighted_normalized_unifrac_distance_matrix.qza) file. Therefore, I had to generate this one separately using this code:

!qiime diversity beta-phylogenetic
–i-table deblur/table.qza
–i-phylogeny phylogeny/rooted_tree.qza
–p-metric weighted_normalized_unifrac
–o-distance-matrix core-metrics-results/weighted_normalized_unifrac_distance_matrix.qza

As far as I know, I cannot add a sampling depth parameter.

I would like to know if there is a different command/approach that allows me to add a sampling depth parameter into this analysis.
I need this parameter to exclude some lower read samples.

Many thanks in advance!

Florian

[jwdebelius (Justine Debelius)]

Hi @Florian_Hoffmann,

Welcome to the forum!

Core metrics does a normalization step and produces a rarefied table (located in core-metrics-results/rarefied_table.qza). My recommendation would be to use that table in your normalized UniFrac command.

You may also want to try filtering your samples to exclude those with a low sequencing depth (I like the data filtering tutorial).

Best,
Justine

[Florian_Hoffmann]

Thank you so much @jwdebelius! Using the rarefied table worked!

Florian