I am very new to microbiome analysis. I have paired raw demultiplexed data from Novaseq 6000, as supplied by the company for my samples and I used FASTQ manifest protocol to import them to QIIME2. I am using version 2022.2,
However, the next step is denoising, and I want to use dada2, but I am confused as to how to use trim and trunc functions.
I used V3-V4 primers for amplification.
I am also uploading how the demux.qzv file is showing random 10000 sequences from all. PLease help.
Here are some videos from our most recent workshop(lecture tutorial) that I think will help explain the trim and trunc functions, the tutorial video uses the galaxy interface, but the parameters are the same regardless of which interface you are using. You will want to remove your primers(and any other non-biological sequences) before running DADA2, as it will filter out reads where these are found as chimeras, for more information on this see this documentation.
Generally, you may find that the Atacama Soils tutorial is helpful as it shows a complete analysis using paired-end data.