dada2 paired / with vs without primer / merged huge loss

[SoilRotifer (Mike Robeson)]

Hi @JeremyTournayre,

You can check out this post, and the rest of the thread, for a very similar discussion:

Looking for help joining paired-end reads

Well... this was specifically in reference to my comment about using cutadapt. That is, if you run cutadapt to remove the primers, your sequences will be shorter. So you'd have to re-visualize them. Trimming the 5' ends will not have an effect on the merging process, specifically. It is the quality and overlap of the 3' ends that matter. As long as the quality is good, and there is enough over-lap to merge the reads, being "too long" or "too short" won't matter. Did you try the specific t…

-Mike