Help troubleshoot for improving denoising stats

[colinbrislawn (Colin J Brislawn)]

@Priyanka_Mishra

So no need to truncate forward read, only for reverse reads will set truncate 260 right?

Try it and see!

(I usually try five to ten truncation settings to see what works best. You are off to a great start, so keep going!)

@Priyanka_Mishra

V3-V4 region PCR amplified

Here is how to calculated if the reads will overlap after truncating:

Merging, Quality control and overlapping

Hello Armin, Thank you for posting this really great question along with the detailed screenshots. I think you are on the right track. denoised: 99,046, merged: 57 Yep, that's your problem. Let's fix it! Sure. The pair of Illumina reads sequence your amplicons from both ends, with some overlap in the middle. 250 bp amplicon |-------------------------| 150 bp read |---------------> 150 bp read <---------------| 50 bp overlap (correct!) ^^^^^ Here'…