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merge_qual.html
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<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01//EN" "http://www.w3.org/TR/html4/strict.dtd">
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<title>
allpairs_global command
</title>
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<div>
<a href="https://drive5.com/usearch">
<img alt="USEARCH v12" src="usearch12_banner.jpg" style="position:absolute; top:40px; left:10px; padding:0px; border:0px;"/>
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<div class="ManText" style="left:20px; position: absolute; left:135px; width:695px; background-color:white; padding:10px">
<h1>
Quality filtering while merging (not recommended)
</h1>
<p class="ManText">
<strong>
See also
<br/>
</strong>
<a href="cmd_fastq_mergepairs.html">
fastq_mergepairs command
</a>
<br/>
<a href="merge_pair.html">
Introduction to paired read merging
</a>
</p>
<p class="ManText">
The fastq_mergepairs command supports
<a href="exp_errs.html">
quality filtering by expected errors
</a>
. The maximum number of expected errors is specified by the fastq_merge_maxee option, e.g.:
</p>
<p class="ManText">
<span class="ManText ManCode">
usearch -fastq_mergepairs SampleA_R1.fastq -fastqout merged.fq -fastq_merge_maxee 1.0
</span>
</p>
<p class="ManText">
The number of expected error is a floating-point number. Using 1.0 specifies that the merged read should have zero as the most probable number of errors according to its Q scores.
</p>
<p class="ManText">
<strong>
Not recommended for making an OTU table
<br/>
</strong>
If you are going to create an
<a href="otu_table.html">
OTU table
</a>
, you should perform quality filtering as a separate step using the
<a href="cmd_fastq_filter.html">
fastq_filter command
</a>
. This is because many reads with >1 expected errors will map successfully to an OTU so you will get better sensitivity by mapping all reads.
</p>
<p class="ManText">
Therefore, the best strategy is to perform
<a href="cmd_cluster_otus.html">
OTU clustering
</a>
or
<a href="cmd_unoise3.html">
denoising
</a>
(error-correction) with quality-filtered reads then create the OTU table (
<a href="cmd_otutab.html">
otutab command
</a>
) using
<em>
all
</em>
merged reads
<em>
before
</em>
quality filtering.
<br/>
</p>
</div>
</div>
</body>
</html>