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comparison fastx_nucleotides_distribution.xml @ 0:bcc5424a4a3c

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author devteam
date Wed, 25 Sep 2013 11:14:24 -0400
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1 <tool id="cshl_fastx_nucleotides_distribution" version="1.0.0" name="Draw nucleotides distribution chart">
2 <description></description>
3 <requirements>
4 <requirement type="package" version="0.0.13">fastx_toolkit</requirement>
5 </requirements>
6 <command>fastx_nucleotide_distribution_graph.sh -t '$input.name' -i $input -o $output</command>
7
8 <inputs>
9 <param format="txt" version="1.0.0" name="input" type="data" label="Statistics Text File" help="output of 'FASTX Statistics' tool" />
10 </inputs>
11
12 <outputs>
13 <data format="png" version="1.0.0" name="output" metadata_source="input" />
14 </outputs>
15 <help>
16
17 **What it does**
18
19 Creates a stacked-histogram graph for the nucleotide distribution in the Solexa library.
20
21 .. class:: infomark
22
23 **TIP:** Use the **FASTQ Statistics** tool to generate the report file needed for this tool.
24
25 -----
26
27 **Output Examples**
28
29 The following chart clearly shows the barcode used at the 5'-end of the library: **GATCT**
30
31 .. image:: ${static_path}/fastx_icons/fastq_nucleotides_distribution_1.png
32
33 In the following chart, one can almost 'read' the most abundant sequence by looking at the dominant values: **TGATA TCGTA TTGAT GACTG AA...**
34
35 .. image:: ${static_path}/fastx_icons/fastq_nucleotides_distribution_2.png
36
37 The following chart shows a growing number of unknown (N) nucleotides towards later cycles (which might indicate a sequencing problem):
38
39 .. image:: ${static_path}/fastx_icons/fastq_nucleotides_distribution_3.png
40
41 But most of the time, the chart will look rather random:
42
43 .. image:: ${static_path}/fastx_icons/fastq_nucleotides_distribution_4.png
44
45 ------
46
47 This tool is based on `FASTX-toolkit`__ by Assaf Gordon.
48
49 .. __: http://hannonlab.cshl.edu/fastx_toolkit/
50
51 </help>
52 <!-- FASTQ-Nucleotides-Distribution is part of the FASTX-toolkit, by A.Gordon (gordon@cshl.edu) -->
53 </tool>