Calculating minimum frequency count

[Alan_Chan (Alan)]

Hi,

I want to filter my feature table at .001%. I understand there is currently not a way to filter based on percentages, instead only on counts. As such I would like to know if I can solve this by doing some math. If I take .001%(.00001) of my Total Frequency 4,861,050 from my Feature Table Summary (i.e., the result of running qiime feature-table summarize ), it would come out to 49. Is it appropriate to then use 49 as my --p-min-frequency in order to achieve a .001% filter?

Attached is my featsummarize.qzv (2.1 MB). Thanks in advance.

[Nicholas_Bokulich]

Hi @Alan_Chan,

@Alan_Chan

As such I would like to know if I can solve this by doing some math

Yes, that is correct — just use the total frequency to calculate what minimum frequency meets your threshold criterion. Your calculation looks correct.

Good luck!