Subset anaysis: p-sampling-depth 0 for some samples

I’m trying to analyze the distribution of a specific phylum within my amplicon data as a subset.
Sadly some of my samples contain no, or a tiny amount of sequencetypes.

How can I include this data in my anaysis? If the “p-sampling-depth” is 0 for some samples?

I’m trying to analyze a speficic phylum within my dataset.
However, some samples only contain low or even 0 sequences.

qiime taxa filter-table
–i-table table.qza
–i-taxonomy taxonomy.qza
–p-include D_1__Proteobacteria
–o-filtered-table table-filterd.qza

At the end I got a table which is missing some of my samples (0 sequences).
How can I include these? To do a downstream analysis?

Hi @Christian_Boedeker,
What is the command that you wish to use after this? I may be able to suggest a workaround.

This filtering behavior is intended, I would say — there is usually no reason to hang on to samples that contain zero sequences.

You could also try filtering out taxa using filter-features as described here:

That might not drop samples with zero sequences.

Let us know if that helps!

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