Mercurial > repos > devteam > short_reads_figure_score
comparison short_reads_figure_score.xml @ 0:b52b9c7aabd9 draft default tip
Imported from capsule None
author | devteam |
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date | Mon, 19 May 2014 12:35:00 -0400 |
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-1:000000000000 | 0:b52b9c7aabd9 |
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1 <tool id="quality_score_distribution" name="Build base quality distribution" version="1.0.2"> | |
2 <description></description> | |
3 <requirements> | |
4 <requirement type="package" version="2.11.1">fontconfig</requirement> | |
5 <requirement type="package" version="1.0.3">rpy</requirement> | |
6 <requirement type="package" version="2.11.0">R</requirement> | |
7 </requirements> | |
8 <command interpreter="python">short_reads_figure_score.py $input1 $output1 </command> | |
9 <inputs> | |
10 <page> | |
11 <param name="input1" type="data" format="qualsolexa, qual454" label="Quality score file" help="No dataset? Read tip below"/> | |
12 </page> | |
13 </inputs> | |
14 | |
15 <outputs> | |
16 <data name="output1" format="png" /> | |
17 </outputs> | |
18 <tests> | |
19 <test> | |
20 <param name="input1" value="solexa.qual" ftype="qualsolexa" /> | |
21 <output name="output1" file="solexaScore.png" ftype="png" /> | |
22 </test> | |
23 <test> | |
24 <param name="input1" value="454.qual" ftype="qual454" /> | |
25 <output name="output1" file="454Score.png" ftype="png" /> | |
26 </test> | |
27 </tests> | |
28 <help> | |
29 | |
30 .. class:: warningmark | |
31 | |
32 To use this tool, your dataset needs to be in the *Quality Score* format. Click the pencil icon next to your dataset to set the datatype to *Quality Score* (see below for examples). | |
33 | |
34 ----- | |
35 | |
36 **What it does** | |
37 | |
38 This tool takes Quality Files generated by Roche (454), Illumina (Solexa), or ABI SOLiD machines and builds a graph showing score distribution like the one below. Such graph allows you to perform initial evaluation of data quality in a single pass. | |
39 | |
40 ----- | |
41 | |
42 **Examples of Quality Data** | |
43 | |
44 Roche (454) or ABI SOLiD data:: | |
45 | |
46 >seq1 | |
47 23 33 34 25 28 28 28 32 23 34 27 4 28 28 31 21 28 | |
48 | |
49 Illumina (Solexa) data:: | |
50 | |
51 -40 -40 40 -40 -40 -40 -40 40 | |
52 | |
53 ----- | |
54 | |
55 **Output example** | |
56 | |
57 Quality scores are summarized as boxplot (Roche 454 FLX data): | |
58 | |
59 .. image:: short_reads_boxplot.png | |
60 | |
61 where the **X-axis** is coordinate along the read and the **Y-axis** is quality score adjusted to comply with the Phred score metric. Units on the X-axis depend on whether your data comes from Roche (454) or Illumina (Solexa) and ABI SOLiD machines: | |
62 | |
63 - For Roche (454) X-axis (shown above) indicates **relative** position (in %) within reads as this technology produces reads of different lengths; | |
64 - For Illumina (Solexa) and ABI SOLiD X-axis shows **absolute** position in nucleotides within reads. | |
65 | |
66 Every box on the plot shows the following values:: | |
67 | |
68 o <---- Outliers | |
69 o | |
70 -+- <---- Upper Extreme Value that is no more | |
71 | than box length away from the box | |
72 | | |
73 +--+--+ <---- Upper Quartile | |
74 | | | |
75 +-----+ <---- Median | |
76 | | | |
77 +--+--+ <---- Lower Quartile | |
78 | | |
79 | | |
80 -+- <---- Lower Extreme Value that is no more | |
81 than box length away from the box | |
82 o <---- Outlier | |
83 | |
84 | |
85 | |
86 </help> | |
87 </tool> |