Mercurial > repos > bgruening > deeptools_plot_fingerprint

annotate plotFingerprint.xml @ 32:9dccc8fbaec2 draft

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"planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit ac42d29c298c026aa0c53c9db2553087ebc86b97"
author bgruening
date Fri, 11 Feb 2022 10:12:00 +0000
parents 17241d18624d
children 08fa75511924
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
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27
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1 <tool id="deeptools_plot_fingerprint" name="plotFingerprint" version="@WRAPPER_VERSION@.0" profile="18.01">
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2 <description>plots profiles of BAM files; useful for assessing ChIP signal strength</description>
0
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3 <macros>
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4 <token name="@BINARY@">plotFingerprint</token>
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5 <import>deepTools_macros.xml</import>
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6 </macros>
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7 <expand macro="requirements" />
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8 <command>
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9 <![CDATA[
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10 @multiple_input_bams@
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11 @BINARY@
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12 @THREADS@
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13 --bamfiles #echo " ".join($files)
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14 --labels #echo " ".join($labels)
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15 --plotFile $outFileName
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16
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17 #if $output.showOutputSettings == "yes"
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18 --plotFileFormat $output.outFileFormat
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19 #if $output.saveRawCounts:
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20 --outRawCounts '$outFileRawCounts'
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21 #end if
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22 #if $output.saveQualityMetrics:
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23 --outQualityMetrics '$outFileQualityMetrics'
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24 #if $output.JSDsample:
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25 #if "'{}'".format($output.JSDsample.display_name) in $labels:
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26 #set JSDidx = $labels.index("'{}'".format($output.JSDsample.display_name))
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27 --JSDsample '${JSDidx}.bam'
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28 #end if
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29 #end if
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30 #end if
0
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31 #else
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32 --plotFileFormat 'png'
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33 #end if
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34
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35 #if str($region).strip() != '':
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36 --region '$region'
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37 #end if
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38
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39 #if $advancedOpt.showAdvancedOpt == "yes":
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40 --binSize '$advancedOpt.binSize'
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41 --numberOfSamples '$advancedOpt.numberOfSamples'
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42
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43 $advancedOpt.ignoreDuplicates
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44 $advancedOpt.skipZeros
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45
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46 #if $advancedOpt.plotTitle and str($advancedOpt.plotTitle.value) != "":
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47 --plotTitle '$advancedOpt.plotTitle'
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48 #end if
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49 @ADVANCED_OPTS_READ_PROCESSING@
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50 @blacklist@
0
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51 #end if
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52 ]]>
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53 </command>
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54
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55 <inputs>
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56 <expand macro="multiple_input_bams" MIN="1"/>
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57 <expand macro="custom_sample_labels" />
0
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58 <expand macro="region_limit_operation" />
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59
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60 <conditional name="advancedOpt">
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61 <param name="showAdvancedOpt" type="select" label="Show advanced options" >
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62 <option value="no" selected="true">no</option>
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63 <option value="yes">yes</option>
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64 </param>
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65 <when value="no" />
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66 <when value="yes">
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67 <param argument="--binSize" type="integer" value="500" min="1"
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68 label="Bin size in bases"
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69 help="Length in bases for a window used to sample the genome."/>
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70 <param argument="--numberOfSamples" type="integer" value="100000" min="1"
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71 label="Number of samples"
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72 help="Number of samples taken from the genome to compute the scaling factors."/>
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73 <expand macro="read_processing_options" />
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74 <expand macro="skipZeros" />
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75 <expand macro="plotTitle" />
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76 <expand macro="blacklist" />
0
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77 </when>
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78 </conditional>
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79
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80 <conditional name="output">
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81 <param name="showOutputSettings" type="select" label="Show advanced output settings">
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82 <option value="no" selected="true">no</option>
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83 <option value="yes">yes</option>
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84 </param>
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85 <when value="no" />
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86 <when value="yes">
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87 <expand macro="input_image_file_format" />
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88 <param name="saveRawCounts" type="boolean" label="Save the bin counts" help="(--outRawCounts)"/>
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89 <param name="saveQualityMetrics" type="boolean" label="Save quality metrics"
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90 help="The file will have one row per input BAM file and columns containing a variety of QC metrics. For the full description of all metrics and their interpretation, please see our online documentation: http://deeptools.readthedocs.io/en/latest/content/feature/plotFingerprint_QC_metrics.html. (--outQualityMetrics)"/>
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91 <param name="JSDsample" type="data" format="bam" optional="true"
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92 label="Jensen-Shannon distance reference sample"
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93 help="If output metrics should be saved, then use this sample as the reference for computing the Jensen-Shannon distance and CHANCE metrics of all other samples. Normally this is an input sample. If you don't specify this, then these metrics will not be computed. This is only applicable if quality metrics are being saved. (--JSDsample)" />
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94 </when>
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95 </conditional>
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96 </inputs>
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97 <outputs>
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98 <expand macro="output_image_file_format" />
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99 <data format="tabular" name="outFileRawCounts" label="${tool.name} on ${on_string}: bin counts">
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100 <filter>
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101 ((
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102 output['showOutputSettings'] == 'yes' and
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103 output['saveRawCounts'] is True
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104 ))
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105 </filter>
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106 </data>
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107 <data format="tabular" name="outFileQualityMetrics" label="${tool.name} on ${on_string}: quality metrics">
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108 <filter>
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109 ((
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110 output['showOutputSettings'] == 'yes' and
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111 output['saveQualityMetrics'] is True
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112 ))
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113 </filter>
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114 </data>
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115 </outputs>
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116 <tests>
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117 <test>
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118 <param name="bamfiles" value="bowtie2 test1.bam,bowtie2 test1.bam" ftype="bam" />
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119 <param name="showAdvancedOpt" value="no" />
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120 <param name="showOutputSettings" value="no" />
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121 <output name="outFileName" file="plotFingerprint_result1.png" ftype="png" compare="sim_size" />
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122 </test>
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123 <test>
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124 <param name="bamfiles" value="bowtie2 test1.bam,bowtie2 test1.bam" ftype="bam" />
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125 <param name="showAdvancedOpt" value="yes" />
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126 <param name="showOutputSettings" value="yes" />
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127 <param name="saveRawCounts" value="True" />
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128 <param name="saveQualityMetrics" value="True" />
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129 <param name="plotTitle" value="Test Fingerprint Plot" />
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130 <param name="JSDsample" value="bowtie2 test1.bam" ftype="bam" />
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131 <output name="outFileName" file="plotFingerprint_result2.png" ftype="png" compare="sim_size" />
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132 <output name="outFileRawCounts" file="plotFingerprint_result2.tabular" ftype="tabular" />
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133 <output name="outFileQualityMetrics" file="plotFingerprint_quality_metrics.tabular" ftype="tabular" />
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134 </test>
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135 </tests>
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136 <help>
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137 <![CDATA[
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138
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139
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140 What it does
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141 ------------
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142
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143 This tool is useful for assessing the strength of a ChIP (i.e. how clearly the enrichment signal can be separated from the background)
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144 and is based on a method described in Diaz et al. (2012) Stat Appl Genet Mol Biol 11(3).
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145
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146
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147 Output
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148 ------
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149
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150 The default output is a diagnostic plot (see below for an example and further down for some background information).
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151
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152 Optionally, you can obtain the table of raw values that were used to generate the plot.
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153
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154 .. image:: $PATH_TO_IMAGES/plotFingerprint_output.png
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155 :width: 600
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156 :height: 395
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157
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158
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159 Example plot
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160 -------------
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161
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162 What follows is the output of ``plotFingerprint`` with our test ChIP-Seq data sets, limiting the analysis to chromosome X. Single-end reads were extended to
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163 200 bp (advanced options).
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164
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165 .. image:: $PATH_TO_IMAGES/bamFP_galaxy_output.png
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166 :width: 600
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167 :height: 450
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168
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169 -----
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170
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171 Theoretical Background
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172 ----------------------
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173
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174 The tool first samples indexed BAM files and sums the per-base coverage of reads/fragments overlapping a window (bin) of the specified length.
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175 These values are then sorted according to their rank (the bin with the highest number of reads has the highest rank)
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176 and the cumulative sum plotted. An ideal input (control) with a uniform distribution of reads alignments
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177 and infinite sequencing depth will result in a diagonal line. A very specific and strong ChIP enrichment, on the other hand, would result in a large portion
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178 of reads accumulating in just a few bins and the resulting plot showing a steep rise toward the right-most edge. Such results are
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179 most commonly seen with transcription factors.
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180
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181
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182 .. image:: $PATH_TO_IMAGES/QC_fingerprint.png
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183 :width: 600
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184 :height: 294
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185
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186 -----
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187
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188 @REFERENCES@
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189 ]]>
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190 </help>
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191 <expand macro="citations" />
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192 </tool>