How can I determine what my maxEE should be when running DADA2? I've looked over this, and I don't think it says how you could find it in qiime2.
Would I be able to find it in my demux.qzv? Is there a command I can use to find maxEE or will I have to compute on my own? I've attached my demux.qzv in case it helps.
demux.qzv (290.6 KB)
Thanks in advance.
This is not a parameter you calculate but rather it is a parameter you choose when you are denoising with dada2. The maxEE represents the maximum number of expected errors you are allowing and by default this is set to 2 and you can change that to whatever you want. I don’t have any general guidelines as how you should choose this but unless something is going wrong with your denoising, it’s probably a safe bet just leaving it on its default. You can read a bit more on the topic on the dada2 tutorial as well.
--p-max-ee FLOAT Reads with number of expected errors higher
than this value will be discarded.
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