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.
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.
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.
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.
