dada2 trim and trunc values determination after paired end demultiplex

I’m confused in choosing values of trim and trunc in dada2 according to what?
my primer length is 50 nucleotide but when i looked at my sequence samples the first nucleotide repeates in forward sequence about (10-13) and reverse about 6 nucleotides.
I used trim value f and r 13 and used trunc lens f and r 300 according to quality plot which give me median of sequencd sample for reverse and forward reads 301 and 300 nts respectively is that value is true or not ?

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I’m sorry, @hasnaa, but I don’t understand what you are trying to ask here.

If you’re looking for general information on how to choose DADA2 parameters, the preprint explains how the algorithm works. This has helped me understand how to choose parameters, by showing me what they do. There have also been dozens of detailed discussions of how to select DADA2 trim and trunc parameters on this forum. This “best-of” includes a lovely visual aid, and the search :mag: feature will help you find others.

If that’s not what you’re looking for, please clarify your question.

Chris :rabbit:


still confused about my data how I know the best place to trim and trunc lens value
I used this value is that true --p-trim-left-f 17 --p-trim-left-r 21 --p-trunc-len-f 300 --p-trunc-len-r 300 according my data or not?

@hasnaa, I shared some resources in my post above that will help you answer that question. Please take some time to read them and try to understand them.

If there are specific things you don’t understand, I’d be happy to work with you on figuring them out. Feel free to post followup questions related to DADA2 parameters here.


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hi, Chris
the post you mentioned (best of) solved my problem thanks alot for your help.