<p>The previous paragraph in the tutorial provides a link to the paper.</p>
<blockquote>
<p>We’ll use standard filtering parameters: maxN=0 (DADA2 requires no Ns), truncQ=2, rm.phix=TRUE and maxEE=2. The maxEE parameter sets the maximum number of “expected errors” allowed in a read, which is <a href="https://academic.oup.com/bioinformatics/article/31/21/3476/194979" rel="nofollow noreferrer">a better filter than simply averaging quality scores.</a></p>
</blockquote>

CC BY-SA 4.0
2021-12-20T15:26:34.383Z
2021-12-20T15:26:34.383Z
bodington
<p>I have just started the QC steps from the dada2 pipeline, and have failed to find a detailed explanation of what the maxEE argument entails.</p>
<p>I have surfed many forums, as well as the details given by the creators of the package, but they are lacking in detail. All it says is that:</p>
<pre><code>After truncation, reads with higher than maxEE &quot;expected errors&quot; will be discarded. Expected 
errors are calculated from the nominal definition of the quality score: EE = sum(10^(-Q/10))
</code></pre>
<p>What is Q in this instance? Is it the Quality score obtained from the <code>plotQualityProfile</code> function?</p>
<p>In the tutorial, it states that:</p>
<pre><code>The standard filtering parameters are starting points, not set in stone. If you want to speed up 
downstream computation, consider tightening maxEE. If too few reads are passing the filter, 
consider relaxing maxEE, perhaps especially on the reverse reads (eg. MaxEE = c (2,5)), and 
reducing the truncLen to remove low quality tails. 
</code></pre>
<p>What is 2, and 5 in this instance? What does an expected error of 2, or 5, actually mean?</p>
<p>Thanks</p>

<r><microbiome><16rrna>
maxEE parameter from DADA2 package in R
# maxEE parameter from DADA2 package in R

(Asked by: username_0 on 2021-12-02)

I have just started the QC steps from the dada2 pipeline, and have failed to find a detailed explanation of what the maxEE argument entails.
I have surfed many forums, as well as the details given by the creators of the package, but they are lacking in detail. All it says is that:
After truncation, reads with higher than maxEE "expected errors" will be discarded. Expected 
errors are calculated from the nominal definition of the quality score: EE = sum(10^(-Q/10))

What is Q in this instance? Is it the Quality score obtained from the plotQualityProfile function?
In the tutorial, it states that:
The standard filtering parameters are starting points, not set in stone. If you want to speed up 
downstream computation, consider tightening maxEE. If too few reads are passing the filter, 
consider relaxing maxEE, perhaps especially on the reverse reads (eg. MaxEE = c (2,5)), and 
reducing the truncLen to remove low quality tails. 

What is 2, and 5 in this instance? What does an expected error of 2, or 5, actually mean?
Thanks

**Tags:** r, microbiome, 16rrna

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## 1 answers

### Answer by username_1 on 2021-12-20. Score: 1

The previous paragraph in the tutorial provides a link to the paper.

> We’ll use standard filtering parameters: maxN=0 (DADA2 requires no Ns), truncQ=2, rm.phix=TRUE and maxEE=2. The maxEE parameter sets the maximum number of “expected errors” allowed in a read, which is [a better filter than simply averaging quality scores.](https://academic.oup.com/bioinformatics/article/31/21/3476/194979)


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