Hi.
I have a question about selecting parameters for Dada2. I have read the previous questions about dada2 selection. From my understanding, I should check the interactive quality plot of demultiplexing result and choose a parameter when they started the collapse.
However, it looks like a human being's observation is needed. Is there a way to select dada2 parameters? so the parameters can be programmable?
JIhyoung
Hi @Jhlee,
That's a great question! While this would certainly be a cool idea that would save a lot of time, the time spent during 'human observation' is quite important. Each dataset/analysis is different and there isn't a hard and fast quality score or trim/trunc lengths that would be appropriate to apply in a systematic way. Trimming is often used to remove primers as well as any low-quality bases at the 5’ end, and truncation choice can often be complicated (i.e. balancing error trimming vs. quality decisions).
Hope this helps!
Cheers 
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