# Merging, Quality control and overlapping **URL:** https://forum.qiime2.org/t/merging-quality-control-and-overlapping/12618 **Category:** User Support **Tags:** best-of-the-forum **Created:** [November 25, 2019, 2:07pm UTC](https://forum.qiime2.org/t/merging-quality-control-and-overlapping/12618 "2019-11-25T14:07:50Z") **Posts on this page:** 1 **Showing post:** 2
### Author: ![colinbrislawn](https://forum.qiime2.org/user_avatar/forum.qiime2.org/colinbrislawn/32/6221_2.png) [@colinbrislawn](https://forum.qiime2.org/u/colinbrislawn) #### Post date: [November 25, 2019, 2:34pm UTC](https://forum.qiime2.org/t/merging-quality-control-and-overlapping/12618/2 "2019-11-25T14:34:55Z")
Hello Armin, Thank you for posting this really great question along with the detailed screenshots. I think you are on the right track. > [@ari\_sh70](#): > > I think the problem is in โ€œmergingโ€. > denoised: 99,046, merged: 57 ๐Ÿ™€ Yep, that's your problem. Let's fix it! * * * > [@ari\_sh70](#): > > 2- Can anyone explain the concept of merging and how does that work, please? It is not that clear for me. Sure. The pair of Illumina reads sequence your amplicons from both ends, with some overlap in the middle. ```auto 250 bp amplicon |-------------------------| 150 bp read |---------------> 150 bp read <---------------| 50 bp overlap (correct!) ^^^^^ ``` > [@ari\_sh70](#): > > 3- How to know how much overlapping do we have? Here's how I work it out: ```plaintext (forward read) + (reverse read) - (length of amplicon) = overlap 150 forward + 150 reverse - 250 amplicon = 50 overlap ``` This matches the diagram I showed above. For your data, here are the numbers I know so far: ```plaintext 216 forward + (218 - 2) reverse - (16S-341F and 16S-805R) amplicon = overlap 216 forward + 216 reverse - (805 - 341) amplicon = overlap 432 - 464 = overlap -32 = overlap ``` EDIT: So your overlap is _negative_, which means there is a 32 bp gap between your paired ends. ๐Ÿ™€ > [@ari\_sh70](#): > > P.S: I do not want to remove any reverse reads. I want to keep them. I agree! Let's me know if this helps answer your questions, then we can see how we can fix it! Colin --- _[View the full topic](https://forum.qiime2.org/t/merging-quality-control-and-overlapping/12618)._