Use Classifier for trimmed v regions

[Nicholas_Bokulich]

Hi @iordanis ,

@iordanis

So here is question, on classifier step after I trim off the primers can i use a pretraining classifier with out primers?
or build my own classifier with out primers? For example using the GenBank with RESCRIPt. Or other database.

Yes, definitely. Training a region-specific classifier is even shown in the RESCRIPt tutorial on the forum, e.g., here (shown with SILVA, but you can do the same with an NCBI classifier following get-data-ncbi):

Processing, filtering, and evaluating the SILVA database (and other reference sequence data) with RESCRIPt

Please consider this tutorial a living document, which may change based upon community feedback and ongoing plugin development. RESCRIPt RESCRIPt (REference Sequence annotation and CuRatIon Pipeline) is a python package and QIIME 2 plugin for formatting, managing, and manipulating sequence reference databases. This package was designed for compiling, manipulating, and evaluating sequence reference databases from SILVA, NCBI, Greengenes, GTDB, and other sources, and for constru…

@iordanis

And something more i read from many post that, combine datasets from different v region suggests the fragment-insertion step. can anyone explain me after that step which database we use? because we have multi v regions.

It sounds like you may be looking for q2-sidle, depending on the V regions that you have. But if you have a bunch of sequences from different V regions mixed in a single file you could technically also use a full-length 16S classifier to taxonomically classify all of these.

Good luck!