Filter Data Samples

#1

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

#2

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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#3

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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