root/galaxy-central/tools/metag_tools/blat_coverage_report.xml @ 2

リビジョン 2, 2.9 KB (コミッタ: hatakeyama, 14 年 前)

import galaxy-central
行番号 
1<tool id="generate_coverage_report" name="Polymorphism of the Reads">
2        <description>the percentage of reads supporting each nucleotide at each location</description>
3        <command interpreter="python">blat_coverage_report.py $input1 $output1</command>
4        <inputs>       
5                <param name="input1" type="data" format="tabular" label="Alignment result"/>
6        </inputs>
7        <outputs>
8                <data name="output1" format="tabular"/>
9        </outputs>
10        <tests>
11                <test>
12                <param name="input1" value="blat_coverage_report_test1.txt" ftype="tabular" />
13                <output name="output1" file="blat_coverage_report_test1.out" />
14                </test>
15        </tests>
16        <help>
17
18.. class:: warningmark
19
20**IMPORTANT**. Only works for BLAT **standard** or **pslx** output formats (hint: to output pslx format, add **-out=pslx** in the command).
21
22-----
23       
24**What it does**
25 
26 The tool will generate a table of 6 columns as following:
27 
28- 1st column: chromosome id.
29
30- 2nd column: chromosome location.
31
32- 3rd column: the nucleotide from reference genome at the chromosome location (2nd column).
33
34- 4th column: total coverage of the reads (number of reads that were mapped to the chromosome location).
35
36- 5th column: percentage of reads that support nucleotide **A** at this location.
37
38- 6th column: percentage of reads that support nucleotide **T** at this location.
39
40- 7th column: percentage of reads that support nucleotide **C** at this location.
41
42- 8th column: percentage of reads that support nucleotide **G** at this location.
43 
44 
45-----
46
47**Example**
48
49- The BLAT pslx results look like the following (tab separated with sequence at the end)::
50
51        30      0       0       0       0       0       0       0       +       seq0    30      0       30      chr     4639675 4549207 4549237 1       30,     0,      4549207,        cggacagcgccgccaccaacaaagccacca, cggacagcgccgccaccaacaaagccacca,
52        30      0       0       0       0       0       0       0       +       seq1    30      0       30      chr     4639675 614777  614807  1       30,     0,      614777,         aaaacaccggatgctccggcgctggcagat, aaaacaccggatgctccggcgctggcagat,
53        28      1       0       0       0       0       0       0       +       seq2    30      0       29      chr     4639675 3289283 3289312 1       29,     0,      3289283,        tttgcttttagtacaccggattcagaacc,  tttgctttcagtacaccggattcagaacc,
54        30      0       0       0       0       0       0       0       +       seq4    30      0       30      chr     4639675 2665584 2665614 1       30,     0,      2665584,        cacgctacgtgcgcccccgcccagaaggcg, cacgctacgtgcgcccccgcccagaaggcg,
55
56        The 14th column is the chromosome id, and the 16th and 17th columns shows the reads were mapped to chromosome start and end locations. 
57
58- The report showed overall coverage of reads on each chromosome location (partial result)::
59 
60   +-------+----------+------+------+--------+------+--------+------+
61   | title | location | ref. | cov. |   A    |  T   |   C    |  G   |
62   +-------+----------+------+------+--------+------+--------+------+   
63   |   chr |   614777 |  A   |  1   | A(100) | T(0) |   C(0) | G(0) |
64   |   chr |   614778 |  A   |  1   | A(100) | T(0) |   C(0) | G(0) |
65   |   chr |   614779 |  A   |  1   | A(100) | T(0) |   C(0) | G(0) |
66   +-------+----------+------+------+--------+------+--------+------+   
67       
68-----
69
70**Reference**
71 
72 **BLAT**: Kent, W James, BLAT--the BLAST-like alignment tool. (2002) Genome Research:12(4) 656-664.
73       
74        </help>
75</tool>
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