view fastx_nucleotides_distribution.xml @ 2:9353010b95df draft

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<tool id="cshl_fastx_nucleotides_distribution" version="1.0.0" name="Draw nucleotides distribution chart">
	<description></description>
    <requirements>
        <requirement type="package" version="0.0.13">fastx_toolkit</requirement>
    </requirements>
	<command>fastx_nucleotide_distribution_graph.sh -t '$input.name' -i $input -o $output</command>
	
	<inputs>
		<param format="txt" name="input" type="data" label="Statistics Text File" help="output of 'FASTX Statistics' tool" />
	</inputs>
	
	<outputs>
		<data format="png" name="output" metadata_source="input" />
	</outputs>
<help>

**What it does**

Creates a stacked-histogram graph for the nucleotide distribution in the Solexa library.

.. class:: infomark

**TIP:** Use the **FASTQ Statistics** tool to generate the report file needed for this tool.

-----

**Output Examples**

The following chart clearly shows the barcode used at the 5'-end of the library: **GATCT**

.. image:: fastq_nucleotides_distribution_1.png
 
In the following chart, one can almost 'read' the most abundant sequence by looking at the dominant values: **TGATA TCGTA TTGAT GACTG AA...**

.. image:: fastq_nucleotides_distribution_2.png

The following chart shows a growing number of unknown (N) nucleotides towards later cycles (which might indicate a sequencing problem):

.. image:: fastq_nucleotides_distribution_3.png

But most of the time, the chart will look rather random:

.. image:: fastq_nucleotides_distribution_4.png

------

This tool is based on `FASTX-toolkit`__ by Assaf Gordon.

 .. __: http://hannonlab.cshl.edu/fastx_toolkit/

</help>
<!-- FASTQ-Nucleotides-Distribution is part of the FASTX-toolkit, by A.Gordon ([e-mail]) -->
</tool>