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

[Christian_Boedeker]

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?

[Christian_Boedeker]

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?

[Nicholas_Bokulich]

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:

Error while using metadata-based filtering

Hey there @MartinLubell! Hopefully we can help you out! Hidden away at the end of this section of the Filtering data tutorial is this little hint: If your filtering query is more complex than those supported through qiime taxa filter-table, you should use qiime feature-table filter-features. Sounds like you are a perfect candidate for this, since your query is becoming a bit complex now, and feature-table filter-features supports SQL-based queries, which are super powerful! So, let's rew…

That might not drop samples with zero sequences.

Let us know if that helps!