Is it possible to let the data2 denosie choose the best parameter for trim and trunc? Thanks


(Archie Lee) #1

Is it possible to let the data2 denosie choose the best parameter for the following options? Thanks.

–p-trim-left-f 7
–p-trim-left-r 7
–p-trunc-len-f 260
–p-trunc-len-r 200 \


(Nicholas Bokulich) #2

Hi @archie,
No — there is not currently a way to allow dada2 to automatically select the “best” parameters. That’s actually a fairly tricky and subjective question! Much does depend on user input, e.g., trimming is often used to remove primers as well as any low-quality bases at the 5’ end, and truncation choice can often be complex (e.g., balancing error trimming vs. quality decisions).

Cool idea though!


(Archie Lee) #3

Thank you so much for the replying.