# Low feature counts after DADA2

**URL:** https://forum.qiime2.org/t/low-feature-counts-after-dada2/16266
**Category:** User Support
**Tags:** dada2
**Created:** [August 27, 2020, 6:04am UTC](https://forum.qiime2.org/t/low-feature-counts-after-dada2/16266 "2020-08-27T06:04:47Z")
**Posts on this page:** 1
**Showing post:** 5

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### Author: ![Joselyn\_Chicas](https://forum.qiime2.org/user_avatar/forum.qiime2.org/joselyn_chicas/32/8883_2.png) [@Joselyn\_Chicas](https://forum.qiime2.org/u/Joselyn_Chicas)
#### Post date: [August 30, 2020, 3:12am UTC](https://forum.qiime2.org/t/low-feature-counts-after-dada2/16266/5 "2020-08-30T03:12:22Z")

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Hi @llenzi  
Thanks so much for your reply.  
We sent our samples to a third party lab but they reported that sample quality was good and PCR cycles were 30-35 cycles  
I followed your suggestion and I tried try the ‘–p-discard-untrimmed’ option.  
qiime cutadapt trim-paired   
--i-demultiplexed-sequences demux-paired-end.qza   
--p-front-f CCTACGGGNGGCWGCAG   
--p-front-r GACTACHVGGGTATCTAATCC   
--p-discard-untrimmed   
--o-trimmed-sequences trim-paired-demux.qza   
--verbose

 ![image](https://forum-qiime2-org.s3.dualstack.us-west-2.amazonaws.com/original/2X/f/f0f1151f896d4d922e10bfb8d4fa86bc368c2eb5.jpeg)  
Now I was able to get all the sequences 280 bp long. So after that I tried different parameters but I was just able to improve my percentage of input non-chimeric (~31%).  
qiime dada2 denoise-paired   
--i-demultiplexed-seqs trim-paired-demux.qza   
--p-trim-left-f 60   
--p-trim-left-r 37   
--p-trunc-len-f 278   
--p-trunc-len-r 204   
--p-max-ee-f 5   
--p-max-ee-r 5   
--o-table table-maxee.qza   
--o-representative-sequences rep-seqs-maxee.qza   
--o-denoising-stats denoising-stats-maxee.qza   
--verbose  
 ![image](https://forum-qiime2-org.s3.dualstack.us-west-2.amazonaws.com/original/2X/5/52872bc436c74a70227052ac4df79373c8abc271.png)

However, I have a few questions:

1. After cutadapt step, my sequences are 280bp long, Does this mean I have to calculate a different trunc limit that the one I used before (truncating length should not go over 116 bp)?
2. Do you have any suggestion about truncation and trimming parameters?

With the sample, I am not sure if it is the most representative sample, however I have a limited service units I can use to run my data so unfortunately I don't have other choice than try several times with only a few samples before running my whole data set.

Thanks so much,

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