Extracting ITS fungal reads

[Mantella86 (Martyn)]

Hi Everyone, what are your thoughts on using the qiime feature-classifier extract-reads
Extracting the primers.

Is this a must or can you go straight to the train classifier after the DADA2 step?

qiime feature-classifier fit-classifier-naive-bayes \
--i-reference-reads unite-ver8-seqs_99_04.02.2020.qza \
--i-reference-taxonomy unite-ver8-taxonomy_99_04.02.2020.qza \
--o-classifier unite-ver8-99-classifier-04.02.2020.qza

Hope my question makes sense.

Best wishes

[colinbrislawn (Colin J Brislawn)]

Hello again Martyn,

@Mantella86

Hi Everyone, what are your thoughts on using the qiime feature-classifier extract-reads

It's probably a good idea, that way the classifier is trained on the same region of the gene as your amplicons.

Here's another good idea, which you may have thought of already:
Use the RESCRIPt plugin to streamline this whole process, or try our a pre-trained classified that's already made by the Qiime2 team!

[Nicholas_Bokulich]

Hi @Mantella86 ,
Just to build on @colinbrislawn 's advice, we have a specific note about this on the classifier training tutorial here:
https://docs.qiime2.org/2021.4/tutorials/feature-classifier/#classification-of-fungal-its-sequences

I recommend training UNITE classifiers on the full reference sequences.

Good luck!