REgarding the full example workflow DADA2 about astrobiomike.github.io

[Cesar2112]

Thanks for the clarification Mike and your early answer.
I was missunderstanding the process and now is clearer.
You are right, both pipelines follows the same steps in the same order.

Cheers,
César

[AstrobioMike]

Hey there, César!

Thanks for the kind words :)

I'm not sure what part you are referring to being the opposite from the dada2 tutorial. That also infers the sequences on the forward and reverse reads separately (the dada() steps) prior to merging them (the mergePairs() step). First is the "Sample Inference" section, then next is the "Merge paired reads" section. Mine on Happy Belly goes the same way. Am i misunderstanding or maybe not seeing what you are saying is opposite?

As for why the ASV-inference happens prior to merging the pairs, it has to do with how dada2 works. dada2 utilizes the quality scores and error profiles of the reads, which can be very different between forward and reverse, and becomes artificial at the overlapping regions. I also remember this being unique about the dada2 approach. That's just my terminology-based remembrance of why it does things this way. If you want an actual, technical explanation, haha, I'd look at the initial dada2 paper and then maybe search the dada2 github issues and post a question there if you can't find anything :)