Hello everyone! I´m about to perform the taxonomic classification of my 16S PE sequence data. The primers used for sequencing the V3-V4 region of my data were 341-F and 805-R. In qiime2 there is a trained classifier that is made for the 515-806 region, and the other is the full-length (both from the Greengenes database). The question is, is it ok to use the 515-806 classifier despite not being the same length extension of my primers (341-805)? or should I use the "full-length" version?
I decided to use Greengenes despite not being so curated as Silva, because in a previous publication I used Greengenes with qiime1. However, if the Silva database is much better, I will use it.
But I don´t know what taxonomic assignment method is the best in my case.
Apart from that, I made the denoisng step with the DADA2 denoising step and ASV were created, I do not have OTUs. So, is the Greengenes database an adequate db for this?
Thank you for your suggestions!
I would recommend using the full-length version if you do not have a set of reference files specifically curated for your amplicon region. Some users on the forum might have have made these files for you, just look around.
Fortunately, we've made a plugin that will allow you to easily prepare your own SILVA classifier. Check out our awesome RESCRIPt plugin. You can follow the tutorial here to make your own classifier based on the 341-F and 805-R primers.