Filter Data Samples

Hi to all!!

I would like to get a feedback from you about which is the best way to get rid of some samples, once I got my Feature-Table and find out that some of them have a very low OTU counts with a previously selected p-depth. I have seen the Filtering Tutorial and I was thinking on approach the qiime feature-table filter-samples command, but I am not sure if there is a better way to do so.
Also I was wondering if there is specific command to establish a prevalence cut off at genera level in order to proceed with a more specific statistic analysis.

Thank you very much in advance for your help!!

Greetings,

Serena

Good morning Serena,

Yep, that’s the perfect command to use.

I’m not sure… the problem with setting a cutoff is that any method you select will be somewhat arbitrary. And you know reviewer 3 is going to demand a different arbitrary cutoff. :roll_eyes:

I guess when I do filtering, it’s because it’s needed by the stat test (can’t have zeros) or because there’s a biological reason (interested in anaerobic microbes). I would try the test will all the data, and then consider filtering if needed.

Colin

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Hi Colin,

thank you very much for your response!! Yes I guess I will first look at the data and find out the “best arbitrary method” to go ahead with downstream analysis. :sweat_smile:

Thank you!!

Serena

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