Very low percentage of merged reads in DADA2 with 16S V4, 2×150 bp paired-end sequencing

[SoilRotifer (Mike Robeson)]

Hi @Sergio

@Sergio

he expected V4 amplicon is approximately 250 bp, so theoretically I should have around 50 bp of overlap between R1 and R2:

150 + 150 − 250 ≈ 50 bp overlap

I'd still look into truncating your reads a little, given the amount of overlap you have. That is, there is going to be in increase in the chance of mismatches with longer overlap, even with high-quality data. See this thread.

I also had a similar case in which I also had to trim a little from the 5' end, with similar scores. I assume these might be from the new score/binning methods used? If so, hopefully some one else can provide recommendations / insight.

-Cheers!