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comparison fastq_quality_boxplot.xml @ 0:78a7d28f2a15 draft

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author idot
date Wed, 10 Jul 2013 06:13:48 -0400
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1 <tool id="cshl_fastq_quality_boxplot" name="Draw quality score boxplot">
2 <description></description>
3
4 <command>fastq_quality_boxplot_graph.sh -t '$input.name' -i $input -o '$output'</command>
5
6 <inputs>
7 <param format="txt" name="input" type="data" label="Statistics report file" help="output of 'FASTQ Statistics' tool" />
8 </inputs>
9
10 <outputs>
11 <data format="png" name="output" metadata_source="input"
12 />
13 </outputs>
14 <help>
15
16 **What it does**
17
18 Creates a boxplot graph for the quality scores in the library.
19
20 .. class:: infomark
21
22 **TIP:** Use the **FASTQ Statistics** tool to generate the report file needed for this tool.
23
24 -----
25
26 **Output Examples**
27
28 * Black horizontal lines are medians
29 * Rectangular red boxes show the Inter-quartile Range (IQR) (top value is Q3, bottom value is Q1)
30 * Whiskers show outlier at max. 1.5*IQR
31
32
33 An excellent quality library (median quality is 40 for almost all 36 cycles):
34
35 .. image:: ../static/fastx_icons/fastq_quality_boxplot_1.png
36
37
38 A relatively good quality library (median quality degrades towards later cycles):
39
40 .. image:: ../static/fastx_icons/fastq_quality_boxplot_2.png
41
42 A low quality library (median drops quickly):
43
44 .. image:: ../static/fastx_icons/fastq_quality_boxplot_3.png
45
46 ------
47
48 This tool is based on `FASTX-toolkit`__ by Assaf Gordon.
49
50 .. __: http://hannonlab.cshl.edu/fastx_toolkit/
51
52 </help>
53 </tool>
54 <!-- FASTQ-Quality-Boxplot is part of the FASTX-toolkit, by A.Gordon (gordon@cshl.edu) -->