|
0
|
1 <tool id="cshl_fastx_nucleotides_distribution" name="Draw nucleotides distribution chart">
|
|
|
2 <description></description>
|
|
|
3 <command>fastx_nucleotide_distribution_graph.sh -t '$input.name' -i $input -o '$output'</command>
|
|
|
4
|
|
|
5 <inputs>
|
|
|
6 <param format="txt" name="input" type="data" label="Statistics Text File" help="output of 'FASTX Statistics' tool" />
|
|
|
7 </inputs>
|
|
|
8
|
|
|
9 <outputs>
|
|
|
10 <data format="png" name="output" metadata_source="input"
|
|
|
11 />
|
|
|
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) -->
|
