# DADA2 denoise is removing more than 50% of the data
**URL:** https://forum.qiime2.org/t/dada2-denoise-is-removing-more-than-50-of-the-data/25569
**Category:** User Support
**Tags:** dada2, chimera
**Created:** [February 21, 2023, 10:27pm UTC](https://forum.qiime2.org/t/dada2-denoise-is-removing-more-than-50-of-the-data/25569 "2023-02-21T22:27:14Z")
**Posts on this page:** 6
**Page:** 1
### Author:  [@ankurnaqib](https://forum.qiime2.org/u/ankurnaqib)
#### Post date: [February 21, 2023, 10:27pm UTC](https://forum.qiime2.org/t/dada2-denoise-is-removing-more-than-50-of-the-data/25569/1 "2023-02-21T22:27:14Z")
Hi,
I am going through the usual QIIME2 pipeline and I noticed that DADA2 denoise is removing almost 50% of the data (as seen in the denoising\_stats.qzv file).
[denoising\_stats.qzv](https://forum.qiime2.org/uploads/short-url/7UsMPHocyxx7rynf5Nsmj753qm3.qzv) (1.2 MB)
I tried running the same data using a different tool and it does not end up removing the same amount of data as DADA2. I used cutadapt to remove primers prior to running DADA2, using the command:-
qiime cutadapt trim-single --i-demultiplexed-sequences demux\_seqs\_original.qza --p-cores 8 --p-minimum-length 350 --o-trimmed-sequences demux\_seqs.qza --p-adapter CCTACGGGAGGCAGCAG...ATTAGAWACCCBDGTAGTCC --p-discard-untrimmed
[demux\_seqs.qzv](https://forum.qiime2.org/uploads/short-url/7w6hUVjE0yrHUdLIqWut3I3IGj1.qzv) (296.7 KB)
The DADA2 command I use is:-
qiime dada2 denoise-single
--p-n-threads 200
--i-demultiplexed-seqs ./demux\_seqs.qza
--p-trunc-len 0
--output-dir DADA2\_denoising\_output
--verbose
&\> DADA2\_denoising.log
I have a few questions:-
1. Is it possible to know how specifically denoising is removing so many sequence reads from the samples? I dont see quality as a big issue as I am already removing low-quality data and primer sequences from the dataset.
2. Is it possible that all of the removed data is basically chimeras and they are just reported like this? I say this because within the denoising report, I don't see many chimeras being detected within the samples.
---
### Author:  [@colinbrislawn](https://forum.qiime2.org/u/colinbrislawn)
#### Post date: [February 23, 2023, 9:58pm UTC](https://forum.qiime2.org/t/dada2-denoise-is-removing-more-than-50-of-the-data/25569/2 "2023-02-23T21:58:23Z")
Good afternoon,
> [@ankurnaqib](#):
>
> - Is it possible to know how specifically denoising is removing so many sequence reads from the samples? I dont see quality as a big issue as I am already removing low-quality data and primer sequences from the dataset.
Yes! In newer version of Qiime2 and the q2-dada2 plugin, more detailed statistics are reported about this process. When you upgrade from 2021.11.0 to version [2022.11](https://docs.qiime2.org/2022.11/install/native/), as an example, the dada2 output will include percent reads removed due to joining and chimera filtering as separate columns, which should answer you question. 🔬
> [@ankurnaqib](#):
>
> 1. Is it possible that all of the removed data is basically chimeras and they are just reported like this? I say this because within the denoising report, I don't see many chimeras being detected within the samples.
That is possible! 🤔
I'm guessing something is wrong with read joining, but you will have to [update](https://docs.qiime2.org/2022.11/install/native/) and rerun DADA2 to find out!
---
### Author:  [@ankurnaqib](https://forum.qiime2.org/u/ankurnaqib)
#### Post date: [February 24, 2023, 9:54pm UTC](https://forum.qiime2.org/t/dada2-denoise-is-removing-more-than-50-of-the-data/25569/3 "2023-02-24T21:54:05Z")
Hi Colin,
Thank you for responding. I took your advice and updated my qiime to version 2022.11. It ran successfully and generated a log file. But I am not seeing any extra information like you mentioned. It shows the same columns it showed with the previous version. Is there a different place I got to look for the detailed statistics? Thank you for your help.
[denoising\_stats\_v2.qzv](https://forum.qiime2.org/uploads/short-url/aoIcHGdkRE862YWvzc5JOysS028.qzv) (1.2 MB)
[DADA2\_denoising\_v2.txt](https://forum.qiime2.org/uploads/short-url/nVmMoXo3456kncOGDU1rFKnoYZr.txt) (1.7 KB)
---
### Author:  [@colinbrislawn](https://forum.qiime2.org/u/colinbrislawn)
#### Post date: [February 25, 2023, 12:53am UTC](https://forum.qiime2.org/t/dada2-denoise-is-removing-more-than-50-of-the-data/25569/4 "2023-02-25T00:53:44Z")
Ah, I made a mistake.
`denoise_single` will not have columns for joining, as joining/merging only applies to paired-end reads.
This means that the majority of your read losses are in the main `dada()` error correction / removal step ([code here](https://github.com/qiime2/q2-dada2/blob/master/q2_dada2/assets/run_dada.R#L373-L378)), just like you found when running the older version of DADA2.
I'm not sure what's causing this, or why some samples are more affected than others.
Anyone got any ideas?
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### Author:  [@colinbrislawn](https://forum.qiime2.org/u/colinbrislawn)
#### Post date: [March 10, 2023, 4:19pm UTC](https://forum.qiime2.org/t/dada2-denoise-is-removing-more-than-50-of-the-data/25569/11 "2023-03-10T16:19:06Z")
Oh, I missed something really important!
> [@ankurnaqib](#):
>
> qiime dada2 denoise-single
This DADA2 pipeline is made for single end Illumina reads. But when I check the quality graph...
That looks like paired-end reads that had already been joined! 🙀
âš Using joined, paired-end reads with `dada2 denoise-single` breaks this pipeline.
The good news is that there is a good solution to this problem: import your reads before pairing, then use [qiime dada2 denoise-paired](https://docs.qiime2.org/2023.2/plugins/available/dada2/denoise-paired/).
---
### Author:  [@system](https://forum.qiime2.org/u/system)
#### Post date: [April 10, 2023, 11:35pm UTC](https://forum.qiime2.org/t/dada2-denoise-is-removing-more-than-50-of-the-data/25569/14 "2023-04-10T23:35:01Z")
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