<p>You need to specify an error profile to do this. However, you can shift quality scores of an existing profiles to get 10% error, which is easier than defining a complete profile.</p>

<p>For example, Illumina HiSeq 1000 has the error rate of 0.1% and you want 100 time more errors, so you should shift down the quality scores by 20 by setting both <code>qShift</code> and <code>qShift2</code> to -20. The following code will simulate paired end reads with 10% error.</p>

<pre><code>art_illumina -ss HS10 -i reference.fa -qs -20 -qs2 -20 -sam -p -l 100 -f 20 -m 200 -s 10 -o output
</code></pre>

CC BY-SA 3.0
2017-08-29T00:01:24.383Z
2017-08-29T00:01:24.383Z
Mehrdad Bakhtiari
<p>I'd like to simulate 10% sequencing error using <code>art_illumina</code>. The simulator doesn't have a parameter that I can just give the 10%, but it has this:</p>

<pre><code>-qs  --qShift   the amount to shift every first-read quality score by
-qs2 --qShift2  the amount to shift every second-read quality score by
                NOTE: For -qs/-qs2 option, a positive number will shift up 
                quality scores (the max is 93) that reduce substitution sequencing 
                errors and a negative number will shift down quality scores that 
                increase sequencing errors. If shifting scores by x, the error
                rate will be 1/(10^(x/10)) of the default profile.
</code></pre>

<p>Heng Li's <code>wgsim</code> has an option for base error rate. Can I do the same for <code>art_illumina</code>?</p>

<p><strong>Q:</strong> Does the "error rate" in the description mean sequencing error? If I set both <code>qShift</code> and <code>qShift2</code> to 10, <code>1/(10^(x/10)) == 0.1, where x is 10</code>, does that mean 10 is the value I should give to the simulator?</p>

CC BY-SA 3.0
2017-07-05T08:44:16.343Z
"a positive number will shift up quality scores that reduce substitution sequencing errors" -- I suspect you want to do the opposite: "a negative number will shift down quality scores that increase sequencing errors"
gringer
<ngs><simulated-data>
How to simulate "base error rate" in art_illumina?
# How to simulate "base error rate" in art_illumina?

(Asked by: username_0 on 2017-07-05)

I'd like to simulate 10% sequencing error using art_illumina. The simulator doesn't have a parameter that I can just give the 10%, but it has this:
-qs  --qShift   the amount to shift every first-read quality score by
-qs2 --qShift2  the amount to shift every second-read quality score by
                NOTE: For -qs/-qs2 option, a positive number will shift up 
                quality scores (the max is 93) that reduce substitution sequencing 
                errors and a negative number will shift down quality scores that 
                increase sequencing errors. If shifting scores by x, the error
                rate will be 1/(10^(x/10)) of the default profile.

Heng Li's wgsim has an option for base error rate. Can I do the same for art_illumina?
Q: Does the "error rate" in the description mean sequencing error? If I set both qShift and qShift2 to 10, 1/(10^(x/10)) == 0.1, where x is 10, does that mean 10 is the value I should give to the simulator?

**Tags:** ngs, simulated-data
> **Comments:**
> **username_1**: "a positive number will shift up quality scores that reduce substitution sequencing errors" -- I suspect you want to do the opposite: "a negative number will shift down quality scores that increase sequencing errors"  

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## 1 answers

### Answer by username_2 on 2017-08-29. Score: 4 | Accepted answer

You need to specify an error profile to do this. However, you can shift quality scores of an existing profiles to get 10% error, which is easier than defining a complete profile.
For example, Illumina HiSeq 1000 has the error rate of 0.1% and you want 100 time more errors, so you should shift down the quality scores by 20 by setting both qShift and qShift2 to -20. The following code will simulate paired end reads with 10% error.
art_illumina -ss HS10 -i reference.fa -qs -20 -qs2 -20 -sam -p -l 100 -f 20 -m 200 -s 10 -o output


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