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
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!