I have a question regarding training the feature classifier for 16s data. I have never worked with a bacteria dataset and so I am confused on which files to use. I have downloaded the Silva_132 Qiime files, but there are a variety of files so I am unsure on which one to choose. I thought I would use the raw data or the rep-set (16s, given my data), but I am honestly unsure.
I did see that you guys have a pre-trained classifier, but if I use this, then I would be skipping the “Extract reference reads” step that is recommended. Do you have any advice for me?