Mercurial > repos > bgruening > diffbind

annotate diffbind.xml @ 29:3aa2c26cc990 draft

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diffbind commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
author iuc
date Tue, 31 Aug 2021 08:02:07 +0000
parents f567dc4145ac
children 6b235ac52faf
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f567dc4145ac "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diffbind commit 77828512472bf9815bdda725a58a2321f7803661"
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1 <tool id="diffbind" name="DiffBind" version="2.10.0+galaxy0">
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2 <description> differential binding analysis of ChIP-Seq peak data</description>
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3 <xrefs>
3aa2c26cc990 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diffbind commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
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4 <xref type="bio.tools">diffbind</xref>
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5 </xrefs>
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6 <requirements>
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7 <requirement type="package" version="2.10.0">bioconductor-diffbind</requirement>
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8 <requirement type="package" version="3.5.1">r-base</requirement>
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9 <requirement type="package" version="1.20.3">r-getopt</requirement>
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10 <requirement type="package" version="0.2.20">r-rjson</requirement>
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11 </requirements>
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12 <stdio>
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13 <regex match="Execution halted"
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14 source="both"
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15 level="fatal"
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16 description="Execution halted." />
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17 <regex match="Input-Error 01"
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18 source="both"
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19 level="fatal"
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20 description="Error in your input parameters: Make sure you only apply factors to selected samples." />
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21 <regex match="Error in"
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22 source="both"
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23 level="fatal"
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24 description="An undefined error occured, please check your input carefully and contact your administrator." />
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25 </stdio>
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26 <version_command><![CDATA[
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27 echo $(R --version | grep version | grep -v GNU)", DiffBind version" $(R --vanilla --slave -e "library(DiffBind); cat(sessionInfo()\$otherPkgs\$DiffBind\$Version)" 2> /dev/null | grep -v -i "WARNING: ")", rjson version" $(R --vanilla --slave -e "library(rjson); cat(sessionInfo()\$otherPkgs\$rjson\$Version)" 2> /dev/null | grep -v -i "WARNING: ")
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28 ]]></version_command>
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29 <command><![CDATA[
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30 #import re
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31 #import json
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33 ## Adapted from DESeq2 wrapper
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34 #set $temp_factor_names = list()
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35 #set $temp_factor = list()
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36
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37 #for $g in $rep_group:
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39 #set $peak_files = list()
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40 #set $bam_files = list()
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41 #set $bam_controls = list()
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43 #for $file in $g.peaks:
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44 #set $file_name = str($g.groupName) + "-" + re.sub('[^\w\-]', '_', str($file.element_identifier)) + "-peaks.bed"
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45 ln -s '${file}' '${file_name}' &&
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46 $peak_files.append($file_name)
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47 #end for
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49 #for $bam in $g.bamreads:
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50 #set $bam_name = re.sub('[^\w\-]', '_', str($bam.element_identifier))
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51 #set $bam_file = $bam_name + "-bamreads.bam"
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52 #set $bam_index = $bam_name + "-bamreads.bai"
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53 ln -s '${bam}' '${bam_file}' &&
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54 ln -s '${bam.metadata.bam_index}' '${bam_index}' &&
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55 $bam_files.append($bam_file)
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56 #end for
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58 $temp_factor.append( {str($g.groupName): $peak_files} )
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59 $temp_factor.append( {str($g.groupName): $bam_files} )
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61 #if str( $g.bamcontrol ) != 'None':
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62 #for $ctrl in $g.bamcontrol:
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63 #set $ctrl_name = re.sub('[^\w\-]', '_', str($ctrl.element_identifier))
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64 #set $ctrl_file = $ctrl_name + "-bamcontrol.bam"
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65 #set ctrl_index = $ctrl_name + "-bamcontrol.bai"
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66 #if $ctrl_file not in json.dumps($temp_factor):
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67 ln -s '${ctrl}' '${ctrl_file}' &&
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68 ln -s '${ctrl.metadata.bam_index}' '${ctrl_index}' &&
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69 #end if
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70 $bam_controls.append($ctrl_file)
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71 #end for
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72 $temp_factor.append( {str($g.groupName): $bam_controls} )
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73 #end if
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74
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75 #end for
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76
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77 $temp_factor.reverse()
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78 $temp_factor_names.append(["Condition", $temp_factor])
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79
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80
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81 Rscript '$__tool_directory__/diffbind.R'
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82
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83 -i '#echo json.dumps(temp_factor_names)#'
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84 -o '$outfile'
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85 -t $th
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86 -f $out.format
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87 -p '$plots'
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88
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89 #if $scorecol:
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90 -n "$scorecol"
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91 #end if
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92 #if $lowerbetter:
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93 -l "$lowerbetter"
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94 #end if
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95 #if $summits:
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96 -s "$summits"
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97 #end if
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98
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99 #if $out.binding_matrix:
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100 -b
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101 #end if
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102
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103 #if $out.rdata:
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104 -r
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105 #end if
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106
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107 #if $out.analysis_info:
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108 -a
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109 #end if
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110
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111 #if $out.rscript:
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112 && cp '$__tool_directory__/diffbind.R' '$rscript'
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113 #end if
22
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114 ]]>
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115 </command>
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116 <inputs>
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117 <repeat name="rep_group" title="Group" min="2" max="2" default="2">
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118 <param name="groupName" type="text" label="Name"
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119 help="Name for the Group that the peak and BAM files belong to e.g. Resistant/Responsive (two Groups must be specified for DiffBind). NOTE: Please only use letters, numbers or underscores.">
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120 <sanitizer>
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121 <valid initial="string.letters,string.digits"><add value="_" /></valid>
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122 </sanitizer>
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123 <validator type="empty_field" />
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124 </param>
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125 <param name="peaks" type="data" format="bed" multiple="true" label="Peak files" help="Result of your Peak calling experiment"/>
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126 <param name="bamreads" type="data" format="bam" multiple="true" label="Read BAM files" help="Specify the Read BAM files used in the Peak calling. The input order of the BAM files for the samples MUST match the input order of the peaks files."/>
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127 <param name="bamcontrol" type="data" format="bam" multiple="true" optional="True" label="Control BAM files" help="If specifying a control BAM file, all samples are required to specify one, see Help section below. The input order of the BAM files for the samples MUST match the input order of the peaks files."/>
22
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128 </repeat>
23
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129
24
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130 <param name="scorecol" type="integer" min="0" value="8" label="Score Column" help="Column in peak files that contains peak scores. Default: 8 (narrowPeak)">
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131 <sanitizer>
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132 <valid initial="string.digits"/>
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133 </sanitizer>
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134 </param>
23
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135 <param name="lowerbetter" type="boolean" truevalue="True" falsevalue="" checked="False" label="Lower score is better?" help="DiffBind by default assumes that a higher score indicates a better peak, for example narrowPeaks -log10pvalue. If this is not the case, for example if the score is a p-value or FDR, set this option to Yes. Default: No" />
24
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136 <param name="summits" type="integer" min="0" optional="True" label="Summits" help="Extend peaks Nbp up- and downstream of the summit. For punctate peaks it is advisable to extend (e.g. 250bp), see the DiffBind User Guide">
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137 <sanitizer>
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138 <valid initial="string.digits"/>
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139 </sanitizer>
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140 </param>
23
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141 <param name="th" type="float" value="0.05" min="0" max="1" label="FDR Threshold" help="Significance threshold; all sites with FDR less than or equal to this value will be included in the output. A value of 1 will output all binding sites. Default: 0.05"/>
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142
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143 <!-- Output Options -->
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144 <section name="out" expanded="false" title="Output Options">
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145 <param name="format" type="select" label="Output Format">
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146 <option value="interval" selected="True">Interval</option>
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147 <option value="bed">BED</option>
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148 <option value="tabular">Tabular (tab-separated)</option>
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149 </param>
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150 <param name="pdf" type="boolean" truevalue="True" falsevalue="" checked="False" label="Visualising the analysis results" help="output an additional PDF file" />
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151 <param name="binding_matrix" type="boolean" truevalue="True" falsevalue="" checked="False" label="Output binding affinity matrix?" help="Output a table of the binding scores" />
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152 <param name="rdata" type="boolean" truevalue="True" falsevalue="" checked="False" label="Output RData file?" help="Output all the data used by R to construct the plots and tables, can be loaded into R. Default: No"/>
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153 <param name="rscript" type="boolean" truevalue="True" falsevalue="False" checked="False" label="Output Rscript?" help="If this option is set to Yes, the Rscript used will be provided as a text file in the output. Default: No"/>
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154 <param name="analysis_info" type="boolean" truevalue="True" falsevalue="False" checked="False" label="Output analysis info?" help="If this option is set to Yes, information from the dba.count and dba.analyze commmands will be output in a text file. Default: No"/>
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155 </section>
22
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156 </inputs>
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157
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158 <outputs>
25
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159 <data name="outfile" format="interval" label="${tool.name} on ${on_string}: Differentially bound sites">
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160 <change_format>
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161 <when input="out.format" value="bed" format="bed" />
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162 <when input="out.format" value="tabular" format="tabular" />
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163 </change_format>
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164 </data>
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165 <data name="plots" format="pdf" label="${tool.name} on ${on_string}: Plots">
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166 <filter>out['pdf']</filter>
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167 </data>
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168 <data name="binding_matrix" format="tabular" from_work_dir="bmatrix.tab" label="${tool.name} on ${on_string}: Binding matrix">
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169 <filter>out['binding_matrix']</filter>
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170 </data>
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171 <data name="rdata" format="rdata" from_work_dir="DiffBind_analysis.RData" label="${tool.name} on ${on_string}: RData file">
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172 <filter>out['rdata']</filter>
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173 </data>
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174 <data name="rscript" format="txt" label="${tool.name} on ${on_string}: Rscript">
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175 <filter>out['rscript']</filter>
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176 </data>
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177 <data name="analysis_info" format="txt" from_work_dir="DiffBind_analysis_info.txt" label="${tool.name} on ${on_string}: Analysis info">
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178 <filter>out['analysis_info']</filter>
22
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179 </data>
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180 </outputs>
23
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181
22
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182 <tests>
25
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183 <!-- Ensure outputs work -->
23
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184 <test expect_num_outputs="6">
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185 <repeat name="rep_group">
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186 <param name="groupName" value="Resistant"/>
25
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187 <param name="peaks" ftype="bed" value="BT474_ER_1.bed.gz,BT474_ER_2.bed.gz"/>
23
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188 <param name="bamreads" ftype="bam" value="BT474_ER_1.bam,BT474_ER_2.bam" />
22
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189 </repeat>
23
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190 <repeat name="rep_group">
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191 <param name="groupName" value="Responsive"/>
25
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192 <param name="peaks" ftype="bed" value="MCF7_ER_1.bed.gz,MCF7_ER_2.bed.gz"/>
23
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193 <param name="bamreads" ftype="bam" value="MCF7_ER_1.bam,MCF7_ER_2.bam" />
22
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194 </repeat>
23
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195 <param name="scorecol" value="5" />
25
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196 <param name="format" value="interval"/>
22
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197 <param name="pdf" value="True" />
23
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198 <param name="binding_matrix" value="True" />
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199 <param name="rdata" value="True" />
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200 <param name="rscript" value="True"/>
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201 <param name="analysis_info" value="True"/>
25
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202 <output name="outfile" ftype="interval" value="out_diffbind.interval" />
23
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203 <output name="plots" value="out_plots.pdf" compare="sim_size" />
25
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204 <output name="binding_matrix" value="out_binding_matrix.tab" />
23
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205 <output name="rdata" value="DiffBind_analysis.RData" compare="sim_size"/>
25
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206 <output name="rscript">
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207 <assert_contents>
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208 <has_text text="write.table"/>
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209 </assert_contents>
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210 </output>
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211 <output name="analysis_info" compare="sim_size" >
23
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212 <assert_contents>
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213 <has_text text="SessionInfo"/>
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214 </assert_contents>
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215 </output>
22
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216 </test>
26
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217 <!-- Ensure control BAMs input works -->
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218 <test expect_num_outputs="1">
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219 <repeat name="rep_group">
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220 <param name="groupName" value="Resistant"/>
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221 <param name="peaks" ftype="bed" value="BT474_ER_1.bed.gz,BT474_ER_2.bed.gz"/>
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222 <param name="bamreads" ftype="bam" value="BT474_ER_1.bam,BT474_ER_2.bam" />
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223 <param name="bamcontrol" ftype="bam" value="input1.bam,input2.bam" />
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224 </repeat>
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225 <repeat name="rep_group">
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226 <param name="groupName" value="Responsive"/>
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227 <param name="peaks" ftype="bed" value="MCF7_ER_1.bed.gz,MCF7_ER_2.bed.gz"/>
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228 <param name="bamreads" ftype="bam" value="MCF7_ER_1.bam,MCF7_ER_2.bam" />
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229 <param name="bamcontrol" ftype="bam" value="input1.bam,input2.bam" />
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230 </repeat>
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231 <param name="scorecol" value="5" />
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232 <param name="format" value="interval"/>
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233 <output name="outfile" ftype="interval" value="out_diffbind_ctrl.interval" />
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234 </test>
25
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235 <!-- Ensure BED output works -->
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236 <test expect_num_outputs="1">
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237 <repeat name="rep_group">
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238 <param name="groupName" value="Resistant"/>
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239 <param name="peaks" ftype="bed" value="BT474_ER_1.bed.gz,BT474_ER_2.bed.gz"/>
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240 <param name="bamreads" ftype="bam" value="BT474_ER_1.bam,BT474_ER_2.bam" />
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241 </repeat>
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242 <repeat name="rep_group">
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243 <param name="groupName" value="Responsive"/>
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244 <param name="peaks" ftype="bed" value="MCF7_ER_1.bed.gz,MCF7_ER_2.bed.gz"/>
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245 <param name="bamreads" ftype="bam" value="MCF7_ER_1.bam,MCF7_ER_2.bam" />
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246 </repeat>
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247 <param name="scorecol" value="5" />
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248 <param name="format" value="bed"/>
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249 <output name="outfile" ftype="bed" value="out_diffbind.bed" />
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250 </test>
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251 <!-- Ensure tabular output works -->
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252 <test expect_num_outputs="1">
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253 <repeat name="rep_group">
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254 <param name="groupName" value="Resistant"/>
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255 <param name="peaks" ftype="bed" value="BT474_ER_1.bed.gz,BT474_ER_2.bed.gz"/>
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256 <param name="bamreads" ftype="bam" value="BT474_ER_1.bam,BT474_ER_2.bam" />
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257 </repeat>
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258 <repeat name="rep_group">
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259 <param name="groupName" value="Responsive"/>
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260 <param name="peaks" ftype="bed" value="MCF7_ER_1.bed.gz,MCF7_ER_2.bed.gz"/>
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261 <param name="bamreads" ftype="bam" value="MCF7_ER_1.bam,MCF7_ER_2.bam" />
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262 </repeat>
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263 <param name="scorecol" value="5" />
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264 <param name="format" value="tabular"/>
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265 <output name="outfile" ftype="tabular" file="out_diffbind.tab" />
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266 </test>
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267 </tests>
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268 <help><![CDATA[
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269
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270 .. class:: infomark
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271
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272 **What it does**
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273
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274 DiffBind_ is a `Bioconductor package`_ that provides functions for processing ChIP-Seq data enriched for genomic loci where specific
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275 protein/DNA binding occurs, including peak sets identified by ChIP-Seq peak callers and
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276 aligned sequence read datasets. It is designed to work with multiple peak sets simultaneously,
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277 representing different ChIP experiments (antibodies, transcription factor and/or histone
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278 marks, experimental conditions, replicates) as well as managing the results of multiple peak
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279 callers.
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280
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281 The primary emphasis of DiffBind is on identifying sites that are differentially bound
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282 between two sample groups. It includes functions to support the processing of peak sets,
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283 including overlapping and merging peak sets, counting sequencing reads overlapping intervals
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284 in peak sets, and identifying statistically significantly differentially bound sites based on
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285 evidence of binding affinity (measured by differences in read densities). To this end it uses
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286 statistical routines developed in an RNA-Seq context (primarily the Bioconductor packages
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287 edgeR and DESeq2). Additionally, the package builds on Rgraphics routines to provide a
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288 set of standardized plots to aid in binding analysis.
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289
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290 The `DiffBind User Guide`_ includes a brief overview of the processing flow, followed by four sections of
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291 examples: the first focusing on the core task of obtaining differentially bound sites based on
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292 affinity data, the second working through the main plotting routines, the third discussing the
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293 use of a blocking factor, and the fourth revisiting occupancy data (peak calls) in more detail,
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294 as well as comparing the results of an occupancy-based analysis with an affinity-based one.
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295 Finally, certain technical aspects of the how these analyses are accomplished are detailed.
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296
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297 **Note this DiffBind tool requires a minimum of four samples (two groups with two replicates each).**
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298
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299 -----
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300
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301 **Inputs**
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302
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303 DiffBind works primarily with peaksets, which are sets of genomic intervals representing
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304 candidate protein binding sites. Each interval consists of a chromosome, a start and end
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305 position, and usually a score of some type indicating confidence in, or strength of, the peak.
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306 Associated with each peakset are metadata relating to the experiment from which the peakset
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307 was derived. Additionally, files containing mapped sequencing reads (BAM files) need to
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308 be associated with each peakset (one for the ChIP data, and optionally another representing
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309 a control sample)
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310
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311 **Groups**
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312
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313 You have to specify the name of the Group and the peak and BAM files for the two Groups you want to compare (e.g Resistant and Responsive) in the tool form above.
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314
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315 Example:
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316
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317 ============= =============
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318 **Sample** **Group**
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319 ------------- -------------
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320 BT4741 Resistant
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321 BT4742 Resistant
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322 MCF71 Responsive
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323 MCF72 Responsive
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324 ============= =============
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325
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326
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327 **Peak files**
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328
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329 Result of your Peak calling experiment in bed format, one file for each sample is required. The peak caller, format and score column can be specified in the tool form above. The default settings expect narrowPeak bed format, which has the score in the 8th column (-log10pvalue), and can be output from MACS2.
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330
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331 Example:
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332
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333 ======= ======= ======= =============== ==============
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334 1 2 3 4 **5 (Score)**
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335 ======= ======= ======= =============== ==============
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336 chr18 215562 216063 peak_16037 56.11
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337 chr18 311530 312105 peak_16038 222.49
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338 chr18 356656 357315 peak_16039 92.06
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339 chr18 371110 372092 peak_16040 123.86
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340 chr18 395116 396464 peak_16041 1545.39
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341 chr18 399014 400382 peak_16042 1835.19
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342 chr18 499134 500200 peak_16043 748.32
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343 chr18 503518 504552 peak_16044 818.30
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344 chr18 531672 532274 peak_16045 159.30
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345 chr18 568326 569282 peak_16046 601.11
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346 ======= ======= ======= =============== ==============
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347
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348 * BAM file which contains the mapped sequencing reads associated with each peakset, one file for each sample is required.
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349 * Optional: Control BAM file representing a control dataset. If used, has to be specified for all samples. Note that the DiffBind authors say control reads are best utilized prior to running DiffBind, at the peak calling stage (e.g. with MACS2) and in blacklists, see this `Bioconductor post`_.
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350
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351 -----
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352
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353 **Outputs**
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354
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355 This tool outputs
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356
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357 * a table of differentially bound sites in Interval, BED or Tabular 0-based format
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358
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359 Optionally, under **Output Options** you can choose to output
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360
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361 * a PDF of plots (Heatmap, PCA, MA, Volcano, Boxplots)
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362 * a binding affinity matrix
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363 * the R script used by this tool
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364 * an RData file of the R objects generated
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365 * a text file with information on the analysis (number of Intervals, FriP scores, method used)
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366
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367 **Differentially Bound Sites**
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368
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369 The default output is Interval format, for information on Interval format see here_. Alternatively, you can choose to output BED or Tabular 0-based format as below. For an explanation of the 0-based and 1-based coordinate systems see this `Biostars post`_.
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370
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371 Example - **Interval format**:
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372
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373 ====== ====== ====== ======== ===== ====== ===========================================
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374 Chrom Start End Name Score Strand **Comment**
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375 ====== ====== ====== ======== ===== ====== ===========================================
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376 chr18 394599 396513 DiffBind 0 \. 1914|7.15|5.55|7.89|-2.35|7.06e-24|9.84e-21
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377 chr18 111566 112005 DiffBind 0 \. 439|5.71|6.53|3.63|2.89|1.27e-08|8.88e-06
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378 chr18 346463 347342 DiffBind 0 \. 879|5|5.77|3.24|2.52|6.51e-06|0.00303
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379 chr18 399013 400382 DiffBind 0 \. 1369|7.62|7|8.05|-1.04|1.04e-05|0.00364
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380 chr18 371109 372102 DiffBind 0 \. 993|4.63|3.07|5.36|-2.3|8.1e-05|0.0226
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381 ====== ====== ====== ======== ===== ====== ===========================================
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382
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383 Columns contain the following data:
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384
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385 * **Chrom**: Chromosome name
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386 * **Start**: Start position of site
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387 * **End**: End position of site
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388 * **Score**: 0
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389 * **Name**: DiffBind
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390 * **Strand**: Strand
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391 * **Comment**: The pipe ("|") separated values in this column correspond to:
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392
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393 * *width*: Length of site
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394 * *Conc*: Mean read concentration over all the samples (the default calculation uses log2 normalized ChIP read counts with control read counts subtracted)
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395 * *Conc_Group1*: Mean concentration over the first group (e.g. Responsive)
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396 * *Conc_Group2*: Mean concentration over second group (e.g. Resistant)
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397 * *Fold*: Fold shows the difference in mean concentrations between the two groups (e.g. Responsive - Resistant), with a positive value indicating increased binding affinity in the first group and a negative value indicating increased binding affinity in the second group.
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398 * *p.value*: P-value confidence measure for identifying these sites as differentially bound
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399 * *FDR*: a multiple testing corrected FDR p-value
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400
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401 Example - **BED format**:
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402
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403 ===== ====== ====== ======== ===== ======
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404 Chrom Start End Name Score Strand
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405 ===== ====== ====== ======== ===== ======
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406 chr18 394599 396513 DiffBind 0 \.
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407 chr18 111566 112005 DiffBind 0 \.
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408 chr18 346463 347342 DiffBind 0 \.
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409 chr18 399013 400382 DiffBind 0 \.
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410 chr18 371109 372102 DiffBind 0 \.
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411 ===== ====== ====== ======== ===== ======
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412
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413 Example - **Tabular format**:
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414
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415 ===== ====== ====== ======== ===== ====== ==== =============== ============== ===== ======== ========
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416 Chrom Start End Name Score Strand Conc Conc_Responsive Conc_Resistant Fold p.value FDR
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417 ===== ====== ====== ======== ===== ====== ==== =============== ============== ===== ======== ========
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418 chr18 394599 396513 DiffBind 0 \. 7.15 5.55 7.89 -2.35 7.06E-24 9.84E-21
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419 chr18 111566 112005 DiffBind 0 \. 5.71 6.53 3.63 2.89 1.27E-08 8.88E-06
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420 chr18 346463 347342 DiffBind 0 \. 5 5.77 3.24 2.52 6.51E-06 0.00303
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421 chr18 399013 400382 DiffBind 0 \. 7.62 7 8.05 -1.04 1.04E-05 0.00364
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422 chr18 371109 372102 DiffBind 0 \. 4.63 3.07 5.36 -2.3 8.10E-05 0.0226
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423 ===== ====== ====== ======== ===== ====== ==== =============== ============== ===== ======== ========
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425
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426 **Binding Affinity Matrix**
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427
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428 The final result of counting is a binding affinity matrix containing a (normalized) read count for each sample at every potential binding site. With this matrix, the samples can be re-clustered using affinity, rather than occupancy, data. The binding affinity matrix can be used for QC plotting as well as for subsequent
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429 differential analysis. Note that this output is a tabular 0-based format.
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430
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431 Example:
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diff changeset
432
24
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433 ===== ====== ====== ========= ========= ========== ==========
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iuc
parents: 24
diff changeset
434 Chrom Start End MCF7_ER_1 MCF7_ER_2 BT474_ER_1 BT474_ER_2
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iuc
parents: 23
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435 ===== ====== ====== ========= ========= ========== ==========
15bbd86c6c7b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diffbind commit 11f68fe2b872f5abc5b660adb10336b0955fa0ee
iuc
parents: 23
diff changeset
436 chr18 111567 112005 137.6152 59.87837 29.41393 19.95945
15bbd86c6c7b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diffbind commit 11f68fe2b872f5abc5b660adb10336b0955fa0ee
iuc
parents: 23
diff changeset
437 chr18 189223 189652 19.95945 12.60597 11.55547 23.11095
15bbd86c6c7b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diffbind commit 11f68fe2b872f5abc5b660adb10336b0955fa0ee
iuc
parents: 23
diff changeset
438 chr18 215232 216063 11.55547 15.75746 31.51493 72.48434
15bbd86c6c7b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diffbind commit 11f68fe2b872f5abc5b660adb10336b0955fa0ee
iuc
parents: 23
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439 chr18 311530 312172 17.85846 11.55547 54.62588 43.07040
15bbd86c6c7b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diffbind commit 11f68fe2b872f5abc5b660adb10336b0955fa0ee
iuc
parents: 23
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440 chr18 346464 347342 75.63583 40.96941 21.00995 16.80796
15bbd86c6c7b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diffbind commit 11f68fe2b872f5abc5b660adb10336b0955fa0ee
iuc
parents: 23
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441 chr18 356560 357362 11.55547 14.70696 57.77737 53.57538
15bbd86c6c7b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diffbind commit 11f68fe2b872f5abc5b660adb10336b0955fa0ee
iuc
parents: 23
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442 chr18 371110 372102 8.403982 9.454479 81.93882 82.98932
15bbd86c6c7b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diffbind commit 11f68fe2b872f5abc5b660adb10336b0955fa0ee
iuc
parents: 23
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443 chr18 394600 396513 56.72687 43.07040 510.5419 438.0575
15bbd86c6c7b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diffbind commit 11f68fe2b872f5abc5b660adb10336b0955fa0ee
iuc
parents: 23
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444 chr18 399014 400382 156.5241 117.6557 558.8648 496.8854
15bbd86c6c7b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diffbind commit 11f68fe2b872f5abc5b660adb10336b0955fa0ee
iuc
parents: 23
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445 chr18 498906 500200 767.9138 278.3819 196.4430 181.7361
15bbd86c6c7b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diffbind commit 11f68fe2b872f5abc5b660adb10336b0955fa0ee
iuc
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446 ===== ====== ====== ========= ========= ========== ==========
22
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447
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448 -----
22
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449
51f0f4df83c2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diffbind commit 9de99de5fb4c62f889814ea43b8800ce8d28eb83
iuc
parents:
diff changeset
450 **More Information**
51f0f4df83c2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diffbind commit 9de99de5fb4c62f889814ea43b8800ce8d28eb83
iuc
parents:
diff changeset
451
51f0f4df83c2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diffbind commit 9de99de5fb4c62f889814ea43b8800ce8d28eb83
iuc
parents:
diff changeset
452 Generally, processing data with DiffBind involves five phases:
51f0f4df83c2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diffbind commit 9de99de5fb4c62f889814ea43b8800ce8d28eb83
iuc
parents:
diff changeset
453
51f0f4df83c2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diffbind commit 9de99de5fb4c62f889814ea43b8800ce8d28eb83
iuc
parents:
diff changeset
454 #. Reading in peaksets
51f0f4df83c2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diffbind commit 9de99de5fb4c62f889814ea43b8800ce8d28eb83
iuc
parents:
diff changeset
455 #. Occupancy analysis
51f0f4df83c2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diffbind commit 9de99de5fb4c62f889814ea43b8800ce8d28eb83
iuc
parents:
diff changeset
456 #. Counting reads
51f0f4df83c2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diffbind commit 9de99de5fb4c62f889814ea43b8800ce8d28eb83
iuc
parents:
diff changeset
457 #. Differential binding affinity analysis
51f0f4df83c2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diffbind commit 9de99de5fb4c62f889814ea43b8800ce8d28eb83
iuc
parents:
diff changeset
458 #. Plotting and reporting
51f0f4df83c2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diffbind commit 9de99de5fb4c62f889814ea43b8800ce8d28eb83
iuc
parents:
diff changeset
459
51f0f4df83c2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diffbind commit 9de99de5fb4c62f889814ea43b8800ce8d28eb83
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parents:
diff changeset
460
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461 **Reading in peaksets**:
22
51f0f4df83c2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diffbind commit 9de99de5fb4c62f889814ea43b8800ce8d28eb83
iuc
parents:
diff changeset
462
51f0f4df83c2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diffbind commit 9de99de5fb4c62f889814ea43b8800ce8d28eb83
iuc
parents:
diff changeset
463 The first step is to read in a set of peaksets and associated
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parents: 22
diff changeset
464 metadata. Peaksets are derived either from ChIP-Seq peak callers, such as **MACS2**, or using some other criterion (e.g. genomic windows, or all the promoter regions
393393c58c35 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diffbind commit cc4c1c4131518b9cbf986a1f252767ff73ca938e
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parents: 22
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465 in a genome). A single experiment can have more than
22
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466 one associated peakset; e.g. if multiple peak callers are used for comparison purposes
51f0f4df83c2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diffbind commit 9de99de5fb4c62f889814ea43b8800ce8d28eb83
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parents:
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467 each sample would have more than one line in the sample sheet. Once the peaksets
51f0f4df83c2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diffbind commit 9de99de5fb4c62f889814ea43b8800ce8d28eb83
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diff changeset
468 are read in, a merging function finds all overlapping peaks and derives a single set of
51f0f4df83c2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diffbind commit 9de99de5fb4c62f889814ea43b8800ce8d28eb83
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parents:
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469 unique genomic intervals covering all the supplied peaks (a consensus peakset for the
51f0f4df83c2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diffbind commit 9de99de5fb4c62f889814ea43b8800ce8d28eb83
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470 experiment).
51f0f4df83c2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diffbind commit 9de99de5fb4c62f889814ea43b8800ce8d28eb83
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471
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472 **Occupancy analysis**:
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473
51f0f4df83c2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diffbind commit 9de99de5fb4c62f889814ea43b8800ce8d28eb83
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474 Peaksets, especially those generated by peak callers, provide
51f0f4df83c2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diffbind commit 9de99de5fb4c62f889814ea43b8800ce8d28eb83
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parents:
diff changeset
475 an insight into the potential occupancy of the protein being ChIPed for at specific
51f0f4df83c2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diffbind commit 9de99de5fb4c62f889814ea43b8800ce8d28eb83
iuc
parents:
diff changeset
476 genomic loci. After the peaksets have been loaded, it can be useful to perform some
51f0f4df83c2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diffbind commit 9de99de5fb4c62f889814ea43b8800ce8d28eb83
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parents:
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477 exploratory plotting to determine how these occupancy maps agree with each other,
51f0f4df83c2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diffbind commit 9de99de5fb4c62f889814ea43b8800ce8d28eb83
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478 e.g. between experimental replicates (re-doing the ChIP under the same conditions),
51f0f4df83c2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diffbind commit 9de99de5fb4c62f889814ea43b8800ce8d28eb83
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parents:
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479 between different peak callers on the same experiment, and within groups of samples
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parents:
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480 representing a common experimental condition. DiffBind provides functions to enable
51f0f4df83c2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diffbind commit 9de99de5fb4c62f889814ea43b8800ce8d28eb83
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481 overlaps to be examined, as well as functions to determine how well similar samples
51f0f4df83c2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diffbind commit 9de99de5fb4c62f889814ea43b8800ce8d28eb83
iuc
parents:
diff changeset
482 cluster together. Beyond quality control, the product of an occupancy analysis may be
51f0f4df83c2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diffbind commit 9de99de5fb4c62f889814ea43b8800ce8d28eb83
iuc
parents:
diff changeset
483 a consensus peakset, representing an overall set of candidate binding sites to be used
51f0f4df83c2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diffbind commit 9de99de5fb4c62f889814ea43b8800ce8d28eb83
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parents:
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484 in further analysis.
51f0f4df83c2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diffbind commit 9de99de5fb4c62f889814ea43b8800ce8d28eb83
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485
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486 **Counting reads**:
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diff changeset
487
51f0f4df83c2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diffbind commit 9de99de5fb4c62f889814ea43b8800ce8d28eb83
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parents:
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488 Once a consensus peakset has been derived, DiffBind can use the
51f0f4df83c2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diffbind commit 9de99de5fb4c62f889814ea43b8800ce8d28eb83
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parents:
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489 supplied sequence read files to count how many reads overlap each interval for each
51f0f4df83c2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diffbind commit 9de99de5fb4c62f889814ea43b8800ce8d28eb83
iuc
parents:
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490 unique sample. The peaks in the consensus peakset may be re-centered and trimmed
51f0f4df83c2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diffbind commit 9de99de5fb4c62f889814ea43b8800ce8d28eb83
iuc
parents:
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491 based on calculating their summits (point of greatest read overlap) in order to provide
51f0f4df83c2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diffbind commit 9de99de5fb4c62f889814ea43b8800ce8d28eb83
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492 more standardized peak intervals. The final result of counting is a binding affinity matrix
51f0f4df83c2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diffbind commit 9de99de5fb4c62f889814ea43b8800ce8d28eb83
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493 containing a (normalized) read count for each sample at every potential binding site.
51f0f4df83c2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diffbind commit 9de99de5fb4c62f889814ea43b8800ce8d28eb83
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494 With this matrix, the samples can be re-clustered using affinity, rather than occupancy,
51f0f4df83c2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diffbind commit 9de99de5fb4c62f889814ea43b8800ce8d28eb83
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495 data. The binding affinity matrix is used for QC plotting as well as for subsequent
51f0f4df83c2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diffbind commit 9de99de5fb4c62f889814ea43b8800ce8d28eb83
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496 differential analysis.
51f0f4df83c2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diffbind commit 9de99de5fb4c62f889814ea43b8800ce8d28eb83
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497
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498 **Differential binding affinity analysis**:
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diff changeset
499
51f0f4df83c2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diffbind commit 9de99de5fb4c62f889814ea43b8800ce8d28eb83
iuc
parents:
diff changeset
500 The core functionality of DiffBind is the
51f0f4df83c2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diffbind commit 9de99de5fb4c62f889814ea43b8800ce8d28eb83
iuc
parents:
diff changeset
501 differential binding affinity analysis, which enables binding sites to be identified that
51f0f4df83c2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diffbind commit 9de99de5fb4c62f889814ea43b8800ce8d28eb83
iuc
parents:
diff changeset
502 are statistically significantly differentially bound between sample groups. To accomplish
51f0f4df83c2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diffbind commit 9de99de5fb4c62f889814ea43b8800ce8d28eb83
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parents:
diff changeset
503 this, first a contrast (or contrasts) is established, dividing the samples into groups to
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504 be compared. Next the core analysis routines are executed, by default using DESeq2.
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505 This will assign a p-value and FDR to each candidate binding site indicating confidence
51f0f4df83c2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diffbind commit 9de99de5fb4c62f889814ea43b8800ce8d28eb83
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506 that they are differentially bound.
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507
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508 **Plotting and reporting**:
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diff changeset
509
51f0f4df83c2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diffbind commit 9de99de5fb4c62f889814ea43b8800ce8d28eb83
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parents:
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510 Once one or more contrasts have been run, DiffBind provides
51f0f4df83c2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diffbind commit 9de99de5fb4c62f889814ea43b8800ce8d28eb83
iuc
parents:
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511 a number of functions for reporting and plotting the results. MA plots give an
51f0f4df83c2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diffbind commit 9de99de5fb4c62f889814ea43b8800ce8d28eb83
iuc
parents:
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512 overview of the results of the analysis, while correlation heatmaps and PCA plots show
51f0f4df83c2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diffbind commit 9de99de5fb4c62f889814ea43b8800ce8d28eb83
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513 how the groups cluster based on differentially bound sites. Boxplots show the distribution
51f0f4df83c2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diffbind commit 9de99de5fb4c62f889814ea43b8800ce8d28eb83
iuc
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514 of reads within differentially bound sites corresponding to whether they gain or
51f0f4df83c2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diffbind commit 9de99de5fb4c62f889814ea43b8800ce8d28eb83
iuc
parents:
diff changeset
515 lose affinity between the two sample groups. A reporting mechanism enables differentially
51f0f4df83c2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diffbind commit 9de99de5fb4c62f889814ea43b8800ce8d28eb83
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516 bound sites to be extracted for further processing, such as annotation, motif, and
51f0f4df83c2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diffbind commit 9de99de5fb4c62f889814ea43b8800ce8d28eb83
iuc
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517 pathway analyses.
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518
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519 -----
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520
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521 **References**
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522
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523 DiffBind Authors: Rory Stark, Gordon Brown (2011)
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524 Wrapper authors: Bjoern Gruening, Pavankumar Videm
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525
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526 .. _DiffBind: https://bioconductor.org/packages/release/bioc/html/DiffBind.html
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527 .. _`Bioconductor package`: https://bioconductor.org/packages/release/bioc/html/DiffBind.html
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528 .. _`DiffBind User Guide`: https://bioconductor.org/packages/release/bioc/vignettes/DiffBind/inst/doc/DiffBind.pdf
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529 .. _`Bioconductor post`: https://support.bioconductor.org/p/69924/
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530 .. _here: https://galaxyproject.org/learn/datatypes/#interval
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531 .. _`Biostars post`: https://www.biostars.org/p/84686/
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532
22
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533 ]]>
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534 </help>
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535 <citations>
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536 <citation type="doi">doi:10.1038/nature10730</citation>
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537 </citations>
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538 </tool>