question about the --p-trunc-q function

[lizgehret]

Hi @Mantella86,

@Mantella86

I tried --p-trunc-q 10 and --p-trunc-q 20 to see how they compared. I get lots of data from both but lose more sequences at --p-trunc-q 20. I am not sure which to use though. Would you say its safe to use either if there is enough data?

That is a great question! I'd like to refer you to this forum comment regarding when to utilize --p-trunc-q, and how that relates to the DADA2 pipeline. This should better inform your judgement on what to use for this parameter, if you should choose to move forward with using it!

Cheers,
Liz