Answers.Body: <p>It'd be rare to run into Illumina encoded quality scores any more, I doubt there are machines running that still produce those. Everything produced at the moment uses Sanger encoded (phred + 33) scores.</p>
  
  <p>There is no optimum value for <code>-q</code> and <code>-l</code>, though reasonable values would typically be &lt;=5 for <code>-q</code> and ~5 for <code>-l</code>.</p>
  
Answers.ContentLicense: CC BY-SA 4.0
Answers.CreationDate: 2018-07-15T07:17:40.340Z
Answers.LastActivityDate: 2018-07-15T07:17:40.340Z
Answers.UserDisplayName: Devon Ryan
Body: <p>I am using <a href="https://github.com/najoshi/sickle" rel="nofollow noreferrer">sickle</a> package from bioconda to trim my reads from the Illumina Miseq.</p>
  <p>When I tried following code, it failed to run</p>
  <pre><code>sickle pe -t illumina -f file1   -r file2  -o output1  -p output2  -s combined_output -q 27 -l 25  
  </code></pre>
  <p>When I replaced <strong>illumina</strong> with <strong>sanger</strong>, it works. But my reads are from the illumina. Could anyone clarify if using this option is acceptable ? Also, what is the optimum value of -q and -l</p>
  <hr />
  <p>Sickle examines quality and length quality thresholds via a sliding window. This assesses whether to trim the 3'-end of reads, for example removing a sudden drop in quality. It can also assess whether the quality of the 5' end is sufficiently high for trimming.</p>
  
Tags: <ngs><covid-19><trimming><virus>
Title: Using sickle for quality trimming
ThreadText: # Using sickle for quality trimming
  
  (Asked by: username_0 on 2018-07-15)
  
  I am using [sickle](https://github.com/najoshi/sickle) package from bioconda to trim my reads from the Illumina Miseq.
  
  When I tried following code, it failed to run
  
  ```
  sickle pe -t illumina -f file1   -r file2  -o output1  -p output2  -s combined_output -q 27 -l 25  
  
  ```
  
  When I replaced **illumina** with **sanger**, it works. But my reads are from the illumina. Could anyone clarify if using this option is acceptable ? Also, what is the optimum value of -q and -l
  
  ---
  
  Sickle examines quality and length quality thresholds via a sliding window. This assesses whether to trim the 3'-end of reads, for example removing a sudden drop in quality. It can also assess whether the quality of the 5' end is sufficiently high for trimming.
  
  **Tags:** ngs, covid-19, trimming, virus
  
  
  ---
  
  ## 1 answers
  
  ### Answer by username_1 on 2018-07-15. Score: 2 | Accepted answer
  
  It'd be rare to run into Illumina encoded quality scores any more, I doubt there are machines running that still produce those. Everything produced at the moment uses Sanger encoded (phred + 33) scores.
  
  There is no optimum value for `-q` and `-l`, though reasonable values would typically be <=5 for `-q` and ~5 for `-l`.
  
  
  ---
  
  