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annotate carpet-src-1/tools/CARPET/PeakPeaker.xml @ 0:cdd489d98766

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Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
author matces
date Tue, 07 Jun 2011 16:50:41 -0400
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cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
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1 <tool id="Find peaks" name="PeakPicker" version="1.0.0">
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2 <description>Finding Peaks in a GFF Nimblegen File</description>
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3 <command interpreter="perl">PeakPeaker2.pl --in $input --out $output --t $type --dist_peaks $dist_peaks --col3 $col3 --log $log --perc $perc --num $num --dist $dist --w $window --f_pv $output2</command>
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4 <inputs>
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5 <param format="tabular" name="input" type="data" label="Source file"/>
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6 <param name="col3" size="20" type="text" value="Analisys" label="Analisys name"/>
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7 <param name="type" type="select" label="Analysis type">
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8 <option value="p">p-value</option>
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9 <option value="s">score</option>
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10 </param>
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11 <param name="perc" size="4" type="text" value="0.95" label="percentile value"/>
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12 <param name="log" size="2" type="text" value="7" label="-log p-value cutoff"/>
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13 <param name="num" size="2" type="text" value="3" label="minimal number of probes"/>
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14 <param name="dist" size="4" type="text" value="100" label="max distance between two probes"/>
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15 <param name="dist_peaks" size="4" type="text" value="200" label="min distance between two peaks"/>
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16 <param name="window" size="4" type="text" value="500" label="window length"/>
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17 </inputs>
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18 <outputs>
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19 <data format="bed" name="output" />
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20 <data format="gff" name="output2" />
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21 </outputs>
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23
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24 <help>
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25 .. class:: infomark
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26
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27 **What it does**
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28
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29 This tool utilizes NimbleGen ratio files in gff format as INPUT FILE and provides a table of the computed peaks in the same gff format.
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31 --------
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32
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33 **Parameters:**
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34
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35 - **Analysis type:**
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36 - **p-value** analysis performs peaks determination based on p-value inference
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37 - **score** analysis performs peaks determination based on a scoring system
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38 - **Percentile value:** it is used to calculate the threshold rate based on dataset distribution to filter out background
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39 - **-log p-value cutoff:** (required only for p-value based analysis) cutoff integer to be used to identify a significant peak
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40 - **minimal # of probes:** minimal number of consecutive probes used to define a peak
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41 - **max distance 2 probes:** greatest nucleotide distance (bp) between two probes that allow to consider two probes as adjacent
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42 - **min distance 2 peaks:** minimum nucleotide distance (bp) required to consider two peaks as separate entities
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43 - **window length:** length in bp of the window used for statistical analysis
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44
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45 --------
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47
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48 **INPUT FILE**
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49
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50 Nimblegen gives you back a GFF file with the coordinates of each probe and the normalized signal value --> log2(Cy5/Cy3).
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51
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52 Click here_ to download a GFF file example.
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53
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54 .. _here: /static/example_file/GFF_file_norm.txt.zip
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55
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56 Example of Nimblegen GFF format::
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57
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58 chr19 Nimblegen tiling_array 100000 1000051 -1.2 + . probe_name
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59 chr19 Nimblegen tiling_array 100100 1000151 2.9 + . probe_name
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60
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61 .. class:: warningmark
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62
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63 The sixth column **must** contain the normalized log2(cy5/cy3) that Nimblegen gives you back after the experiment
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66 ---------
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67
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68 .. class:: infomark
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69
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70 **How does it work?**
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71
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72 **Two assumptions:**
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74
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75 - data are enriched for signal in the positive direction ("one-tailed")
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76 - a peak (or enriched region) is represented by multiple probes that are genomically located close to each other
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79 **Statistical approach: sliding window**
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81
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82 A window centered at each probe of the array moves probe by probe. In each window Chi squared is calculated
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85 .. image:: static/images/CARPET/chi_squared.png
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88 by building a contingency table for each probe, and a p-value is assigned
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91 .. image:: static/images/CARPET/centered.png
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94 **"-log2(p-value)"** is associated to each probe. This value takes in account the neighbouring probes effect.
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95 This approach dramatically decreases the background signal.
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98 .. image:: static/images/CARPET/background.png
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101 New values are considered to defined an enriched locus
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104 .. image:: static/images/CARPET/pvalue.png
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107 Moreover a score is calculated taking into account the length and the raw signal of the peak
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108
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109
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110 .. image:: static/images/CARPET/pvalue_score.png
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112
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113 Output is a gff file
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115
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116 .. image:: static/images/CARPET/table_pv.png
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118
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119 **NON Statistical approach: score**
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120
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122 Only the raw signal of each probe is considered. Only the regions with a number of consecutive probes above the defined threshold are selected
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125 .. image:: static/images/CARPET/score.png
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127
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128 Output is a GFF file
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131 .. image:: static/images/CARPET/table_score.png
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134 and a GFF file with the p-values associate to each probe
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135
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136 </help>
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137
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138 </tool>
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139