Filter-features without removing samples with zero counts from the output for posterior taxa-plots

[Vilma_Perez (Vilma Pérez)]

Hi everybody

I had to create a new topic with my question because the last topic with similar characteristics was closed ("Feature-table filter-features keep samples for heatmap"). After I filter my samples from features with less than 2 counts the script that I used removes automatically samples with zero counts. However, for the taxa plot, I need these samples to show the differences between different extraction methods used in my experiments. From the previous topic, @Nicholas_Bokulich generated a request to update this function and have the option to choose whether the samples with zero counts were removed or not (`filter-features` should not drop empty samples by default · Issue #184 · qiime2/q2-feature-table · GitHub). I would like to know if that was implemented or not because I have look and I don't seem to find anything like this. Is there any other function that would allow this?.

This is the script I am using:

qiime feature-table filter-features
--i-table samples.qza
--p-min-frequency 2
--o-filtered-table samples_2FreqFilter.qza

Thank you!

Cheers

[Nicholas_Bokulich]

Hi @Vilma_Perez,
That issue remains open and up for grabs. This is not yet implemented in q2-feature-table.

For the time being, the only other solution would be to export these data to plot outside of QIIME 2.

Good luck!