Best place/way to merge read sets after dada2

We have at least 2, but likely more, datasets that are conglomeration of runs that have different read lengths. I have to process them separately with dada2 to maximize each dataset when running dada2-denoise-paired. What would be your recommendation for merging? Ideally, I would like to merge them immediately after the denoising so that I don’t have to mess with processing both datasets separately, but wasn’t sure the best way to concatenate that won’t introduce some variable that leads to issues downstream.


Hi @John,

That should work, assuming that each run has the same forward and reverse primers (and are all paired-end). So you should be able to just directly merge your feature tables with feature-table merge.

If you don’t have the same primers for every paired-end run, then you need to analyze things separately because your sequences would not be directly comparable.

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