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57 lines
1.5 KiB
XML
57 lines
1.5 KiB
XML
<tool id="cshl_fastq_quality_boxplot" name="Draw quality score boxplot">
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<description></description>
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<requirements><requirement type="package">fastx_toolkit</requirement></requirements>
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<command>fastq_quality_boxplot_graph.sh -t '$input.name' -i $input -o $output</command>
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<inputs>
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<param format="txt" name="input" type="data" label="Statistics report file" help="output of 'FASTQ Statistics' tool" />
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</inputs>
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<outputs>
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<data format="png" name="output" metadata_source="input" />
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</outputs>
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<help>
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**What it does**
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Creates a boxplot graph for the quality scores in the library.
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.. class:: infomark
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**TIP:** Use the **FASTQ Statistics** tool to generate the report file needed for this tool.
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-----
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**Output Examples**
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* Black horizontal lines are medians
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* Rectangular red boxes show the Inter-quartile Range (IQR) (top value is Q3, bottom value is Q1)
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* Whiskers show outlier at max. 1.5*IQR
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An excellent quality library (median quality is 40 for almost all 36 cycles):
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.. image:: ./static/fastx_icons/fastq_quality_boxplot_1.png
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A relatively good quality library (median quality degrades towards later cycles):
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.. image:: ./static/fastx_icons/fastq_quality_boxplot_2.png
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A low quality library (median drops quickly):
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.. image:: ./static/fastx_icons/fastq_quality_boxplot_3.png
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------
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This tool is based on `FASTX-toolkit`__ by Assaf Gordon.
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.. __: http://hannonlab.cshl.edu/fastx_toolkit/
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</help>
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</tool>
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<!-- FASTQ-Quality-Boxplot is part of the FASTX-toolkit, by A.Gordon (gordon@cshl.edu) -->
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