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52 lines
1.7 KiB
XML
52 lines
1.7 KiB
XML
<tool id="cshl_fastx_nucleotides_distribution" name="Draw nucleotides distribution chart">
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<description></description>
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<requirements><requirement type="package">fastx_toolkit</requirement></requirements>
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<command>fastx_nucleotide_distribution_graph.sh -t '$input.name' -i $input -o $output</command>
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<inputs>
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<param format="txt" name="input" type="data" label="Statistics Text File" help="output of 'FASTX Statistics' tool" />
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</inputs>
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<outputs>
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<data format="png" name="output" metadata_source="input" />
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</outputs>
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<help>
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**What it does**
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Creates a stacked-histogram graph for the nucleotide distribution in the Solexa library.
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.. class:: infomark
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**TIP:** Use the **FASTQ Statistics** tool to generate the report file needed for this tool.
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-----
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**Output Examples**
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The following chart clearly shows the barcode used at the 5'-end of the library: **GATCT**
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.. image:: ./static/fastx_icons/fastq_nucleotides_distribution_1.png
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In the following chart, one can almost 'read' the most abundant sequence by looking at the dominant values: **TGATA TCGTA TTGAT GACTG AA...**
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.. image:: ./static/fastx_icons/fastq_nucleotides_distribution_2.png
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The following chart shows a growing number of unknown (N) nucleotides towards later cycles (which might indicate a sequencing problem):
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.. image:: ./static/fastx_icons/fastq_nucleotides_distribution_3.png
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But most of the time, the chart will look rather random:
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.. image:: ./static/fastx_icons/fastq_nucleotides_distribution_4.png
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------
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This tool is based on `FASTX-toolkit`__ by Assaf Gordon.
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.. __: http://hannonlab.cshl.edu/fastx_toolkit/
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</help>
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</tool>
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<!-- FASTQ-Nucleotides-Distribution is part of the FASTX-toolkit, by A.Gordon (gordon@cshl.edu) -->
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