Need to trim primers but this will prevent merging sequences?

[SoilRotifer (Mike Robeson)]

@MicrobeManager

So how much wiggle room do I have? I don't know if I can remove the adapters with cutadapt or do much truncation in dada2 without hindering sample merging across the board. Some advice would be appreciated!

Removing the primers will not affect the overlap, as the primers are located on the 5' ends of the forward and reverse reads. It is the truncation of the 3' ends that is the important factor in determining how much overlap you require.

@MicrobeManager

assuming minimum 20 bp are needed for overlap, this leaves only 16 bp left to truncate across both reads.

Only 12 bp are required. You can see the default settings when typing qiime dada2 denoise-paired --help

To better determine how much overlap you'd need I refer you to the following thread:

Merging, Quality control and overlapping

Hello to everyone. I have some questions related to qiime2 and I would appreciate it if you can help me out please. First of all, I have to say that one part of my question is similar to an old post in qiime forum (problem with merging step in qiime2 with dada2) but since those explanations weren’t clear for me I will ask again. I try to give details as much as I can. I am analyzing the 16S data and I have 48 paired-end samples. The primers are: 16S-341F and 16S-805R. The questions are : 1-…

This is also a nice overview too:

Questions about V3–V4 primers for 16S rRNA amplicon sequencing, and calculating overlap

Hi there, I’ve got some questions about primers and about calculating overlap for paired-end reads. I hope I’m posting in an appropriate place. Sorry, if not. This is my first post. Background: We’ve done some 16S rRNA amplicon sequencing with primers that Illumina says are used to sequence the V3 and V4 variable regions of the 16S rRNA gene. The Illumina guide can be found here. Forward primer: 5’-TCGTCGGCAGCGTCAGATGTGTATAAGAGACAGCCTACGGGNGGCWGCAG-3’ Reverse primer: 5’-GTCTCGTGGGCTCGGAGA…

-Cheers!
-Mike