I want to filter otus and samples from my otu table such as Qiime1 did with ‘filter_otus_from_otu_table.py’ and ‘filter_samples_from_otu_table.py.’ Correct me if I’m wrong but I don’t think dada2 does this? If not, do I need to run ‘qiime feature-table filter-features’ and ‘qiime feature-table filter-samples’ before running ‘qiime dada2 denoise-paired?’
Hi @Alan_Chan,
Qiime2 can indeed do both those things. Check out the filtering tutorial here for examples of these and let us know if you have any additional questions.
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Sorry, let me ask a better question: In what order do I run dada2 denoise, filter out otus/samples, and rarefy?
Hi @Alan_Chan,
As long as these samples are all from the same run and have gone through the same amplicon preparation it doesn’t really matter whether you denoise first then filter the samples or filter then denoise. Filtering OTUs/features happens after DADA2 because at that point they aren’t denoised yet so we’re not sure about their identity yet.
As for rarefying, you would also do this after dada2 and after you’ve removed whatever samples/features you wanted from your final feature table. The point of rarefying is to ensure even sampling depth across all samples so if you were to rarefy then remove some features then you may end up with uneven sampling depth again across samples.
Hope that clarifies things a bit!
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