I have two set of data, one sequenced on Illumina V3-V4 and another on V4 (515F/806R) primers. I used q2-fragment-insertion to produce an insertion-tree.qza to combine both sets.
I want to train feature classifier with q2-feature-classifier. Is it correct if I trained the classifier on V3-V4 primers? I am assuming both the primers have an overlap at V4 region? Otherwise how should i train the feature classifier?
Another question is, I read in the forum (Reads processing with different primers) that q2-fragment-insertion isn’t recommended for regions that have overlap. Could you please elaborate? Because i suppose my set of data has an overlapping V4 region, so i shouldn’t use fragment insertion?