question about the --p-trunc-q function

[Mantella86 (Martyn)]

Hi all, i see the default for the --p-trunc-q function for denoising paired send sequences is 2 but can you use higher than this such as 10 or 20?

best wishes

[lizgehret]

Hi @Mantella86,

That is a great question! You can absolutely use a higher number, depending on the quality score you'd like to utilize for this parameter. This is set to a small number as the default because reads will be truncated at the first instance of a quality score less than or equal to this value. One thing to keep in mind is that if the resulting read is then shorter than trunc-len, it will be discarded.

Cheers,
Liz

[Mantella86 (Martyn)]

Thank you for clarifying Liz. I am analysing the ITS from fungi which is very variable so i have not trimmed and filtering based on quality alone.

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?

Best wishes.

[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