I am working with an illumina Miseq paired end amplicon dataset using dada2. I recently completed a similar project using Qiime1 and felt confident in what I was doing. I’m a little confused with when to merge the paired end reads in the dada2 pipeline. Is this a step I should do before dada2 (using PEAR etc.) or do I do it after dada2? I see there are two dada2 options for paired and single reads and I’m not sure if this is referring to paired end sequencing or referring to the sequences already being paired.
Hi @Stream_biofilm! You’ll want to import your unjoined paired-end sequences and use q2-dada2 to denoise them. dada2 will join the reads for you during denoising. It’s recommended that you avoid joining your reads prior to running DADA2. See these forum topics for more details: