<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>

CC BY-SA 4.0
2018-07-15T07:17:40.340Z
2018-07-15T07:17:40.340Z
Devon Ryan
<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>

<ngs><covid-19><trimming><virus>
Using sickle for quality trimming
# Using sickle for quality trimming

(Asked by: username_0 on 2018-07-15)

I am using 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

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## 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`.


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