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view fastx_toolkit-0.0.6/galaxy/tools/fastx_toolkit/fastx_nucleotides_distribution.xml @ 3:997f5136985f draft default tip
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author | xilinxu |
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date | Thu, 14 Aug 2014 04:52:17 -0400 |
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<tool id="cshl_fastx_nucleotides_distribution" name="Nucleotides Distribution"> <description>chart</description> <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 (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:: ./static/fastx_icons/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:: ./static/fastx_icons/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:: ./static/fastx_icons/fastq_nucleotides_distribution_3.png But most of the time, the chart will look rather random: .. image:: ./static/fastx_icons/fastq_nucleotides_distribution_4.png </help> </tool> <!-- FASTQ-Nucleotides-Distribution is part of the FASTX-toolkit, by A.Gordon (gordon@cshl.edu) -->