Hello, Team Qiime2 forum, I have used 8 primers to amplify the sequences of bacterial genes and then pooled the data to generate amplicon sequencing data. I wanted to see the OUT/ASV clustering in the dataset. For the same, I have imported the data in qiime2 followed by denoising using DADA2. Crea…

Hi @Dhwani_Dholakia , sorry for the slow reply. @Keegan-Evans will be with you soon!

@Dhwani_Dholakia , Thanks for providing the details that you have about your analysis! I am wondering about the genes you are targeting in your study, it could just be that SILVA is not the correct database to use with your project. However given the extremely low rate of annotation that you ended …

@Keegan-Evans , How do we remove primer sequences, because here we have used 8 different primers. Usually, the cutadapt accepts one primer pair. Also, why does primer act as garbage? Its a part of natural sequence just like the next amplicon, that is amplified

@Dhwani_Dholakia , You can simply pass q2-cutadapt all of the primers that you want trimmed, for example: --p-adapter-f forward_adapter_1 forward_adapter_2 forward_adapter_3 They have to be removed before denoising with q2-dada2. This is to avoid any issues with DADA2's chimera removal tools. Sour…