Preparing data for taxonomic classification

[a_ghosh]

I have 16s data, I’m trying to find the taxonomic classification.
I’m not entirely sure on how to train the feature classifier - Right now, I’m using the tutorial as reference and using the 99 OTU database to extract reference reads with primers 27F and 338R to train the classifier.

Does the data have to be trimmed(using cutadapt) between the 2 primers (including the primers) or should the primers be left on when the classifier is used ?
If someone could walk me through this step, I’d be very grateful!
Thanks!

[timanix (Timur Yergaliyev)]

Hi!

1. When you are extracting reference sequences for classifier training, you provide primers set to extract the sequence between them, so you don’t have primer sequences there after extracting.
2. After importing your data into Qiime2 you should remove primers with cutadapt.

So you will classify trimmed reads