Miseq paired-end data with no barcodes

Hi @ksn! Yes, you’ll want to demultiplex the sequences, which will also remove the barcodes during the process. Check out the q2-cutadapt Community Tutorial for details. The tutorial’s example data are single-end sequences, so the commands you’ll use will differ slightly. Check out this forum post for details about how to modify the tutorial commands for paired-end data (you can ignore the first steps describing UBAM files, since your data are already in FASTQ format).