what is dada2 message mean

[kimshinseung (ss)]

Hello

I am running 250 samples, and I get the following message from dada2.

2. Learning Error Rates

"267211440 total bases in 1113381 reads from 5 samples will be used for learning the error rates"

What does this mean?

Does that mean poor sequencing quality?

Thank you.

[cherman2 (Chloe Herman)]

Hello @kimshinseung,
Getting this message when running dada2 is normal. Colin explains this really well in this post:

Does learning error rates step of DAD2 have to have all samples under study?

Got it! Ok, I think everything is fine. Dada2 uses the first x samples (sorted) to build up the n-reads values and train the error models. Because errors are similar on each run, this is the default and should work well. You are good to go Colin

what this message is saying is that dada2 is basically training your error models with 267211440 total bases in 1113381 reads from 5 samples.
As long as you are getting an the correct output files from dada2 then you are golden

Hope this helps!
Chloe