Extract reference reads during Training classifier

[Alan_Chan (Alan)]

Hi,

I am following the Training feature classifiers with q2-feature-classifier, specifically the extract reference reads part. How do I decide --p-truc-len? I have paired-end sequences and during dada2 denoising I trimmed 17 from both F/R and truc 285 F and 220 R. Do those parameters play a role in deciding my --p-truc-len parameter? My ref sequences are coming from Silva 132 qiime release rep set 16S /97

[thermokarst (Matthew Ryan Dillon)]

Hey there @Alan_Chan - have you seen the notes in this section of the tutorial? You don’t need to extract reads if you don’t want to — and in some cases it might not even be worth doing.

Do those parameters play a role in deciding my --p-truc-len parameter?

Since you have paired-end reads, I would follow this recommendation (from the tutorial):

For classification of paired-end reads and untrimmed single-end reads, we recommend training a classifier on sequences that have been extracted at the appropriate primer sites, but are not trimmed.

So, for now I would suggest extracting the reads using your primers, but not worrying about specifying a trunc-len. Hope that helps!