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
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?
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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