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