extract classifier trimming question?

Hi, I have a question regarding the trimming on extract classifier command:

qiime feature-classifier extract-reads \
--i-sequences gg-13-8.99_otus.qza \
--p-trunc-len 350 \
--o-reads gg-13-8.99.ref.seqs.qza

Is the trunc length the same as the initial number of base pairs or read lengths?

I hope the question makes sense.

best wishes

Hi @Mantella86 ,

The the extract reads action is searching the query sequences (regardless of their length) and extracting the region flanked by your forward and reverse primers. It then truncates that read based on the trunc-len parameter you set.
For example if your query sequences are full 1500 bp 16S region, and you extract the V3-V4 region with your given primers, you will first end up with reads that are ~440bp (give or take a bit) and then they will be truncated at the 350th position so all of the your final reads will be 350 nt in length. Hope that clarifies it a bit.

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