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1 <tool id="cshl_fastx_nucleotides_distribution" name="Nucleotides Distribution">
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2 <description>chart</description>
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3 <command>fastx_nucleotide_distribution_graph.sh -t '$input.name' -i $input -o $output</command>
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4
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5 <inputs>
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6 <param format="txt" name="input" type="data" label="Statistics Text File (output of 'FASTX Statistics' tool)" />
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7 </inputs>
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8
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9 <outputs>
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10 <data format="png" name="output" metadata_source="input" />
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11 </outputs>
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12 <help>
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13
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14 **What it does**
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15
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16 Creates a stacked-histogram graph for the nucleotide distribution in the Solexa library.
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17
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18 .. class:: infomark
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19
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20 **TIP:** Use the **FASTQ Statistics** tool to generate the report file needed for this tool.
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21
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22 -----
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23
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24 **Output Examples**
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25
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26
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27
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28 The following chart clearly shows the barcode used at the 5'-end of the library: **GATCT**
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29
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30 .. image:: ./static/fastx_icons/fastq_nucleotides_distribution_1.png
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31
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32
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33
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34
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35
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36
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37
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38 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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39
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40 .. image:: ./static/fastx_icons/fastq_nucleotides_distribution_2.png
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41
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42
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43
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44
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45
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46
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47
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48
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49 The following chart shows a growing number of unknown (N) nucleotides towards later cycles (which might indicate a sequencing problem):
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50
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51 .. image:: ./static/fastx_icons/fastq_nucleotides_distribution_3.png
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52
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53
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54
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55
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56
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57
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58
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59
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60 But most of the time, the chart will look rather random:
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61
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62 .. image:: ./static/fastx_icons/fastq_nucleotides_distribution_4.png
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63
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64 </help>
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65 </tool>
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66 <!-- FASTQ-Nucleotides-Distribution is part of the FASTX-toolkit, by A.Gordon (gordon@cshl.edu) -->
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