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comparison tools/fastx_toolkit/fastx_quality_statistics.xml @ 0:9071e359b9a3

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author xuebing
date Fri, 09 Mar 2012 19:37:19 -0500
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1 <tool id="cshl_fastx_quality_statistics" name="Compute quality statistics">
2 <description></description>
3 <requirements><requirement type="package">fastx_toolkit</requirement></requirements>
4 <command>zcat -f $input | fastx_quality_stats -o $output -Q 33</command>
5
6 <inputs>
7 <param format="fastqsanger" name="input" type="data" label="Library to analyse" />
8 </inputs>
9
10 <tests>
11 <test>
12 <param name="input" value="fastq_stats1.fastq" ftype="fastqsanger"/>
13 <output name="output" file="fastq_stats1.out" />
14 </test>
15 </tests>
16
17 <outputs>
18 <data format="txt" name="output" metadata_source="input" />
19 </outputs>
20
21 <help>
22
23 **What it does**
24
25 Creates quality statistics report for the given Solexa/FASTQ library.
26
27 .. class:: infomark
28
29 **TIP:** This statistics report can be used as input for **Quality Score** and **Nucleotides Distribution** tools.
30
31 -----
32
33 **The output file will contain the following fields:**
34
35 * column = column number (1 to 36 for a 36-cycles read Solexa file)
36 * count = number of bases found in this column.
37 * min = Lowest quality score value found in this column.
38 * max = Highest quality score value found in this column.
39 * sum = Sum of quality score values for this column.
40 * mean = Mean quality score value for this column.
41 * Q1 = 1st quartile quality score.
42 * med = Median quality score.
43 * Q3 = 3rd quartile quality score.
44 * IQR = Inter-Quartile range (Q3-Q1).
45 * lW = 'Left-Whisker' value (for boxplotting).
46 * rW = 'Right-Whisker' value (for boxplotting).
47 * A_Count = Count of 'A' nucleotides found in this column.
48 * C_Count = Count of 'C' nucleotides found in this column.
49 * G_Count = Count of 'G' nucleotides found in this column.
50 * T_Count = Count of 'T' nucleotides found in this column.
51 * N_Count = Count of 'N' nucleotides found in this column.
52
53
54 For example::
55
56 1 6362991 -4 40 250734117 39.41 40 40 40 0 40 40 1396976 1329101 678730 2958184 0
57 2 6362991 -5 40 250531036 39.37 40 40 40 0 40 40 1786786 1055766 1738025 1782414 0
58 3 6362991 -5 40 248722469 39.09 40 40 40 0 40 40 2296384 984875 1443989 1637743 0
59 4 6362991 -4 40 248214827 39.01 40 40 40 0 40 40 2536861 1167423 1248968 1409739 0
60 36 6362991 -5 40 117158566 18.41 7 15 30 23 -5 40 4074444 1402980 63287 822035 245
61
62 ------
63
64 This tool is based on `FASTX-toolkit`__ by Assaf Gordon.
65
66 .. __: http://hannonlab.cshl.edu/fastx_toolkit/
67
68 </help>
69 </tool>
70 <!-- FASTQ-Statistics is part of the FASTX-toolkit, by A.Gordon (gordon@cshl.edu) -->