Answers.Body: <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>
  
Answers.ContentLicense: CC BY-SA 3.0
Answers.CreationDate: 2017-08-29T00:01:24.383Z
Answers.LastActivityDate: 2017-08-29T00:01:24.383Z
Answers.UserDisplayName: Mehrdad Bakhtiari
Body: <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>
  
Comments.ContentLicense: CC BY-SA 3.0
Comments.CreationDate: 2017-07-05T08:44:16.343Z
Comments.Text: "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"
Comments.UserDisplayName: gringer
Tags: <ngs><simulated-data>
Title: How to simulate "base error rate" in art_illumina?
ThreadText: # 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"  
  
  ---
  
  ## 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
  
  ```
  
  
  ---
  
  