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- After quality control and denoising I didn’t get a good result. I think the problem is in “merging”. I also did quality control and denoising for a total different 16S dataset and again the problem was with the merging step and consequently I didn’t get enough non-chimeric data.
The codes that I have used and also the photo are the following:
qiime2 dada2 denoise-paired
2- Can anyone explain the concept of merging and how does that work, please? It is not that clear for me.
3- How to know how much overlapping do we have?
P.S: I do not want to remove any reverse reads. I want to keep them.