# DADA2 -- denoise

**URL:** https://forum.qiime2.org/t/dada2-denoise/33767
**Category:** General Discussion
**Tags:** dada2
**Created:** [November 6, 2025, 5:57pm UTC](https://forum.qiime2.org/t/dada2-denoise/33767 "2025-11-06T17:57:24Z")
**Posts on this page:** 3
**Page:** 1

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### Author: ![karitorikin](https://forum.qiime2.org/user_avatar/forum.qiime2.org/karitorikin/32/21255_2.png) [@karitorikin](https://forum.qiime2.org/u/karitorikin)
#### Post date: [November 6, 2025, 5:57pm UTC](https://forum.qiime2.org/t/dada2-denoise/33767/1 "2025-11-06T17:57:24Z")

</div>

hi, below you can find my demux.qzv showing the read quality before DADA2 denoising, I cannot adjust my truncation values properly. I am replicating one of the studies done before and I know the OTU count that they had, yet mine results after all is almost half of it.

How can I adjust my parameters ?  
I set this previously.

```css
TRUNC_F=250 TRUNC_R=230 , qiime dada2 denoise-paired \\
--i-demultiplexed-seqs demux.qza \\
--p-trim-left-f 0 \\
--p-trim-left-r 0 \\
--p-trunc-len-f ${TRUNC_F} \\
--p-trunc-len-r ${TRUNC_R} \\
--o-table table.qza \\
--o-representative-sequences rep-seqs.qza \\
--o-denoising-stats denoising-stats.qza \\
--p-n-threads ${CPUS_PER_TASK} --verbose

```

[demux.qzv](https://forum.qiime2.org/uploads/short-url/dtZkPZ6jqPK1xFsyzzcflF89bcA.qzv) (312.7 KB)

 ![Screenshot 2025-11-06 at 17.42.56](https://forum-qiime2-org.s3.dualstack.us-west-2.amazonaws.com/original/3X/3/d/3dda7c90f1c7281cfb0b9f7b0b7fcb34be99c807.png)

 ![Screenshot 2025-11-06 at 17.43.03](https://forum-qiime2-org.s3.dualstack.us-west-2.amazonaws.com/original/3X/7/0/7078770d7137120d86925b62a34e09285b15aff1.png)

 ![Screenshot 2025-11-06 at 17.43.09](https://forum-qiime2-org.s3.dualstack.us-west-2.amazonaws.com/original/3X/6/1/61273c31e0e4474732d125576349c8158931e16d.png)

 ![Screenshot 2025-11-06 at 17.43.19](https://forum-qiime2-org.s3.dualstack.us-west-2.amazonaws.com/original/3X/a/c/aca18ec597a6d1ab54db323638287ee640e5c559.png)

 ![Screenshot 2025-11-06 at 17.43.24](https://forum-qiime2-org.s3.dualstack.us-west-2.amazonaws.com/original/3X/2/5/25300fa1a17355b00069fd0614dd2496d4f0b37b.png)

---

<div class="post-metadata">

### 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 6, 2025, 10:48pm UTC](https://forum.qiime2.org/t/dada2-denoise/33767/2 "2025-11-06T22:48:10Z")

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Hello @karitorikin,

Welcome to the forums! :qiime2:

When working with a new data source, I often run DADA2 several (3-10) times, looking for the best settings to get reads to join.

> [@karitorikin](#):
>
> I set this previously.
> 
> ```auto
> TRUNC_F=250 TRUNC_R=230
> 
> ```

Great!

Next, I would try  
f240,r230  
f240,r220  
f230,r220  
f230,r210

Have you made the `denoising-stats.qzv` file and opened it? You can see the percent of reads that merge inside that file!

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<div class="post-metadata">

### Author: ![karitorikin](https://forum.qiime2.org/user_avatar/forum.qiime2.org/karitorikin/32/21255_2.png) [@karitorikin](https://forum.qiime2.org/u/karitorikin)
#### Post date: [November 7, 2025, 7:13am UTC](https://forum.qiime2.org/t/dada2-denoise/33767/3 "2025-11-07T07:13:55Z")

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Yes, I checked the denoising-stats every time after running. Thank you for your help, I guess I’ll do the same !! 🫡