Merged Reads fastq files from DADA2

Hi all, hoping somebody can help me with this.

Is there a way to get the fastq files for the merged reads that are joined after running DADA2? I followed the moving pictures tutorial. I’d like to take these joined reads and look at their quality on a different platform.
From what I can tell, DADA2 merges the reads when it is denoising them, but I can’t figure out a way to export them after the fact.

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Hi @Anthony_DeSana! Welcome to the QIIME 2 forum!

The merged ASVs are the --o-representative-sequences Artifact, returned by dada2 denoise-paired. You can work with that FeatureData[Sequence] in many subsequent steps, and if you want to generate a table of the ASV sequences, run the following command:

https://docs.qiime2.org/2020.6/plugins/available/feature-table/tabulate-seqs/

All of this is covered in more detail in the Moving Pictures tutorial:

https://docs.qiime2.org/2020.6/tutorials/moving-pictures/

Have fun! :qiime2:

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