# DADA2 denoising filtering/merging step removing 60-70% of reads

**URL:** https://forum.qiime2.org/t/dada2-denoising-filtering-merging-step-removing-60-70-of-reads/33070
**Category:** User Support
**Created:** [April 30, 2025, 11:41am UTC](https://forum.qiime2.org/t/dada2-denoising-filtering-merging-step-removing-60-70-of-reads/33070 "2025-04-30T11:41:28Z")
**Posts on this page:** 1
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### Author: ![timanix](https://forum.qiime2.org/user_avatar/forum.qiime2.org/timanix/32/17879_2.png) [@timanix](https://forum.qiime2.org/u/timanix)
#### Post date: [April 30, 2025, 12:17pm UTC](https://forum.qiime2.org/t/dada2-denoising-filtering-merging-step-removing-60-70-of-reads/33070/2 "2025-04-30T12:17:37Z")

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Hello!  
First of all, thank you for providing all the details and structuring your post. It saves a lot of time!

Based on your qzv files, your samples collected most of the issues that could decrease the number of output sequences:

- filtering (low scores)
- chimeras
- merging

Considering that you already removed the primers and discarded sequences without them, I can suggest:

- using 260 and 230 trunc. values for F and R reads
- decreasing minimum overlap to 6
- increasing max\_ee values for F and R
- setting --p-min-fold-parent-over-abundance to, for example, 8 ([not more than 16](https://forum.qiime2.org/t/dada2-low-non-chimeric-read-counts-after-denoising-step-p-min-fold-parent-over-abundance/32625/2))

and see how it affects your stats.

Best,

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