annotate diffbind.xml @ 18:f907216064f6 draft default tip

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diffbind commit fd148a124034b44d0d61db3eec32ff991d8c152c
author iuc
date Mon, 08 Jul 2024 18:31:51 +0000
parents 2605cbdaa7d8
children
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rev   line source
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1 <tool id="diffbind" name="DiffBind" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@">
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2 <description> differential binding analysis of ChIP-Seq peak data</description>
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3 <macros>
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4 <token name="@TOOL_VERSION@">3.12.0</token>
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5 <token name="@VERSION_SUFFIX@">0</token>
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6 <token name="@PROFILE@">22.05</token>
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7 </macros>
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8 <xrefs>
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9 <xref type="bio.tools">diffbind</xref>
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10 <xref type="bioconductor">diffbind</xref>
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11 </xrefs>
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12 <requirements>
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13 <requirement type="package" version="@TOOL_VERSION@">bioconductor-diffbind</requirement>
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14 <requirement type="package" version="1.20.4">r-getopt</requirement>
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15 <requirement type="package" version="4.0.16">bioconductor-edger</requirement>
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16 </requirements>
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17 <stdio>
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18 <regex match="Execution halted"
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19 source="both"
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20 level="fatal"
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21 description="Execution halted." />
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22 <regex match="Input-Error 01"
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23 source="both"
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24 level="fatal"
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25 description="Error in your input parameters: Make sure you only apply factors to selected samples." />
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26 <regex match="Error in"
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27 source="both"
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28 level="fatal"
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29 description="An undefined error occured, please check your input carefully and contact your administrator." />
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30 </stdio>
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31 <version_command><![CDATA[
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32 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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33 ]]></version_command>
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34 <command><![CDATA[
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35 #import re
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36 #import json
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37
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38 ## Adapted from DESeq2 wrapper
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39 #set $temp_factor_names = list()
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40 #set $temp_factor = list()
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41
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42 #for $g in $rep_group:
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43
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44 #set $peak_files = dict()
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45 #set $bam_files = dict()
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46 #set $bam_controls = dict()
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47
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48 #for $file in $g.peaks:
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49 #set $file_name = str($g.groupName) + "-" + re.sub('[^\w\-]', '_', str($file.element_identifier)) + "-peaks.bed"
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50 ln -s '${file}' '${file_name}' &&
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51 #set $peak_files[str($file.element_identifier)] = str($file_name)
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52 #end for
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53
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54 #for $bam in $g.bamreads:
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55 #set $bam_name = re.sub('[^\w\-]', '_', str($bam.element_identifier))
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56 #set $bam_file = $bam_name + "-bamreads.bam"
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57 #set $bam_index = $bam_name + "-bamreads.bai"
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58 ln -s '${bam}' '${bam_file}' &&
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59 ln -s '${bam.metadata.bam_index}' '${bam_index}' &&
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60 #set $bam_files[str($bam.element_identifier)] = str($bam_file)
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61 #end for
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62
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63 #if len($peak_files.keys()) != len($bam_files.keys())
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64 >&2 echo "Group $g.groupName: same number of Peak and Bam files needs to be given" && exit 1 &&
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65 #end if
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66 $temp_factor.append( {str($g.groupName): [f[1] for f in sorted($peak_files.items())]} )
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67 $temp_factor.append( {str($g.groupName): [f[1] for f in sorted($bam_files.items())]} )
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69 #if str( $g.bamcontrol ) != 'None':
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70 #for $ctrl in $g.bamcontrol:
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71 #set $ctrl_name = re.sub('[^\w\-]', '_', str($ctrl.element_identifier))
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72 #set $ctrl_file = $ctrl_name + "-bamcontrol.bam"
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73 #set $ctrl_index = $ctrl_name + "-bamcontrol.bai"
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74 #if $ctrl_file not in json.dumps($temp_factor):
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75 ln -s '${ctrl}' '${ctrl_file}' &&
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76 ln -s '${ctrl.metadata.bam_index}' '${ctrl_index}' &&
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77 #end if
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78 #set $bam_controls[str($ctrl.element_identifier)] = str($ctrl_file)
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79 #end for
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80 #if len($peak_files.keys()) != len($bam_files.keys())
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81 >&2 echo "Group $g.groupName: same number of Peak and Bam control files needs to be given" && exit 1 &&
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82 #end if
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83 $temp_factor.append( {str($g.groupName): [f[1] for f in sorted($bam_controls.items())]} )
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84 #end if
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85
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86 #end for
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87
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88 $temp_factor.reverse()
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89 $temp_factor_names.append(["Condition", $temp_factor])
11
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90
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91
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92 Rscript '$__tool_directory__/diffbind.R'
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93
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94 -i '#echo json.dumps(temp_factor_names)#'
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95 -o '$outfile'
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96 -m '$method'
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97 -t $th
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98 -f $out.format
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99 -p '$plots'
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100 -O $minoverlap
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101 #if $use_blacklist:
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102 -B
11
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103 #end if
18
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104 -n $scorecol
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105 #if $lowerbetter:
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106 -l "$lowerbetter"
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107 #end if
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108 #if $summits:
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109 -s "$summits"
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110 #end if
10
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111
11
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112 #if $out.binding_matrix:
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113 -b
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114 #end if
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115
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116 #if $out.rdata:
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117 -r
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118 #end if
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119
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120 #if $out.analysis_info:
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121 -a
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122 #end if
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123
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124 #if $out.rscript:
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125 && cp '$__tool_directory__/diffbind.R' '$rscript'
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126 #end if
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127 ]]>
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128 </command>
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129 <inputs>
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130 <repeat name="rep_group" title="Group" min="2" max="2" default="2">
11
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131 <param name="groupName" type="text" label="Name"
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132 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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133 <sanitizer>
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134 <valid initial="string.letters,string.digits"><add value="_" /></valid>
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135 </sanitizer>
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136 <validator type="empty_field" />
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137 </param>
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138 <param name="peaks" type="data" format="bed" multiple="true" label="Peak files" help="Result of your Peak calling experiment"/>
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139 <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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140 <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."/>
9
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141 </repeat>
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142 <param name="method" type="select" label="Underlying method by which to analyze differential binding affinity">
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143 <option value="DBA_DESEQ2" selected="True">DESeq2</option>
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144 <option value="DBA_EDGER">edgeR</option>
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145 </param>
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146 <param name="use_blacklist" type="boolean" truevalue="True" falsevalue="" checked="False" label="Filters peak intervals that overlap a blacklist from ENCODE" help="Works with human, mouse, worm and fly. Assembly version is determined from the BAM files." />
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147 <param name="minoverlap" type="integer" min="1" value="2" label="Only include peaks in at least this many peaksets in the main binding matrix">
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148 <sanitizer>
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149 <valid initial="string.digits"/>
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150 </sanitizer>
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151 </param>
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152 <param name="scorecol" type="integer" min="0" value="5" label="Score Column" help="Column in peak files that contains peak scores. Default: 5 (narrowPeak)">
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153 <sanitizer>
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154 <valid initial="string.digits"/>
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155 </sanitizer>
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156 </param>
11
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157 <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" />
12
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158 <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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159 <sanitizer>
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160 <valid initial="string.digits"/>
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161 </sanitizer>
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162 </param>
11
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163 <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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164
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165 <!-- Output Options -->
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166 <section name="out" expanded="false" title="Output Options">
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167 <param name="format" type="select" label="Output Format">
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168 <option value="interval" selected="True">Interval</option>
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169 <option value="bed">BED</option>
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170 <option value="tabular">Tabular (tab-separated)</option>
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171 </param>
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172 <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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173 <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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174 <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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175 <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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176 <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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177 </section>
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178 </inputs>
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179
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180 <outputs>
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181 <data name="outfile" format="interval" label="${tool.name} on ${on_string}: Differentially bound sites">
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182 <change_format>
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183 <when input="out.format" value="bed" format="bed" />
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184 <when input="out.format" value="tabular" format="tabular" />
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185 </change_format>
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186 </data>
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187 <data name="plots" format="pdf" label="${tool.name} on ${on_string}: Plots">
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188 <filter>out['pdf']</filter>
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189 </data>
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190 <data name="binding_matrix" format="tabular" from_work_dir="bmatrix.tab" label="${tool.name} on ${on_string}: Binding matrix">
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191 <filter>out['binding_matrix']</filter>
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192 </data>
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193 <data name="rdata" format="rdata" from_work_dir="DiffBind_analysis.RData" label="${tool.name} on ${on_string}: RData file">
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194 <filter>out['rdata']</filter>
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195 </data>
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196 <data name="rscript" format="txt" label="${tool.name} on ${on_string}: Rscript">
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197 <filter>out['rscript']</filter>
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198 </data>
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199 <data name="analysis_info" format="txt" from_work_dir="DiffBind_analysis_info.txt" label="${tool.name} on ${on_string}: Analysis info">
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200 <filter>out['analysis_info']</filter>
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201 </data>
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202 </outputs>
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203
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204 <tests>
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205 <!-- Ensure outputs work -->
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206 <test expect_num_outputs="6">
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207 <repeat name="rep_group">
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208 <param name="groupName" value="Resistant"/>
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209 <param name="peaks" ftype="bed" value="BT474_ER_1.bed.gz,BT474_ER_2.bed.gz"/>
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210 <param name="bamreads" ftype="bam" value="BT474_ER_1.bam,BT474_ER_2.bam" />
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211 </repeat>
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212 <repeat name="rep_group">
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213 <param name="groupName" value="Responsive"/>
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214 <param name="peaks" ftype="bed" value="MCF7_ER_1.bed.gz,MCF7_ER_2.bed.gz"/>
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215 <param name="bamreads" ftype="bam" value="MCF7_ER_1.bam,MCF7_ER_2.bam" />
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216 </repeat>
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217 <param name="scorecol" value="5" />
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218 <param name="format" value="interval"/>
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219 <param name="pdf" value="True" />
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220 <param name="binding_matrix" value="True" />
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221 <param name="rdata" value="True" />
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222 <param name="rscript" value="True"/>
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223 <param name="analysis_info" value="True"/>
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224 <output name="outfile" ftype="interval" value="out_diffbind.interval" />
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225 <output name="plots" value="out_plots.pdf" compare="sim_size" />
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226 <output name="binding_matrix" value="out_binding_matrix.tab" />
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227 <output name="rdata" value="DiffBind_analysis.RData" compare="sim_size"/>
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228 <output name="rscript">
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229 <assert_contents>
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230 <has_text text="write.table"/>
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231 </assert_contents>
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232 </output>
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233 <output name="analysis_info" compare="sim_size" >
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234 <assert_contents>
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235 <has_text text="SessionInfo"/>
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236 </assert_contents>
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237 </output>
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238 </test>
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239 <!-- Ensure EDGER works -->
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240 <test expect_num_outputs="3">
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241 <repeat name="rep_group">
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242 <param name="groupName" value="Resistant"/>
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243 <param name="peaks" ftype="bed" value="BT474_ER_1.bed.gz,BT474_ER_2.bed.gz"/>
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244 <param name="bamreads" ftype="bam" value="BT474_ER_1.bam,BT474_ER_2.bam" />
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245 </repeat>
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246 <repeat name="rep_group">
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247 <param name="groupName" value="Responsive"/>
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248 <param name="peaks" ftype="bed" value="MCF7_ER_1.bed.gz,MCF7_ER_2.bed.gz"/>
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249 <param name="bamreads" ftype="bam" value="MCF7_ER_1.bam,MCF7_ER_2.bam" />
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250 </repeat>
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251 <param name="scorecol" value="5" />
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252 <param name="method" value="DBA_EDGER" />
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253 <param name="format" value="interval"/>
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254 <param name="pdf" value="True" />
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255 <param name="binding_matrix" value="True" />
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256 <param name="rscript" value="False"/>
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257 <output name="outfile" ftype="interval" value="out_diffbind_edger.interval" />
f907216064f6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diffbind commit fd148a124034b44d0d61db3eec32ff991d8c152c
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258 <output name="plots" value="out_plots_edger.pdf" compare="sim_size" />
f907216064f6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diffbind commit fd148a124034b44d0d61db3eec32ff991d8c152c
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259 <output name="binding_matrix" value="out_binding_matrix_edger.tab" />
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260 </test>
14
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261 <!-- Ensure control BAMs input works -->
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262 <test expect_num_outputs="1">
c97a786e8fb5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diffbind commit 1fe103338548dd65731a5a0887be59745370debd
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263 <repeat name="rep_group">
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264 <param name="groupName" value="Resistant"/>
c97a786e8fb5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diffbind commit 1fe103338548dd65731a5a0887be59745370debd
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265 <param name="peaks" ftype="bed" value="BT474_ER_1.bed.gz,BT474_ER_2.bed.gz"/>
c97a786e8fb5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diffbind commit 1fe103338548dd65731a5a0887be59745370debd
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266 <param name="bamreads" ftype="bam" value="BT474_ER_1.bam,BT474_ER_2.bam" />
c97a786e8fb5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diffbind commit 1fe103338548dd65731a5a0887be59745370debd
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267 <param name="bamcontrol" ftype="bam" value="input1.bam,input2.bam" />
c97a786e8fb5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diffbind commit 1fe103338548dd65731a5a0887be59745370debd
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268 </repeat>
c97a786e8fb5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diffbind commit 1fe103338548dd65731a5a0887be59745370debd
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269 <repeat name="rep_group">
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270 <param name="groupName" value="Responsive"/>
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271 <param name="peaks" ftype="bed" value="MCF7_ER_1.bed.gz,MCF7_ER_2.bed.gz"/>
c97a786e8fb5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diffbind commit 1fe103338548dd65731a5a0887be59745370debd
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272 <param name="bamreads" ftype="bam" value="MCF7_ER_1.bam,MCF7_ER_2.bam" />
c97a786e8fb5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diffbind commit 1fe103338548dd65731a5a0887be59745370debd
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273 <param name="bamcontrol" ftype="bam" value="input1.bam,input2.bam" />
c97a786e8fb5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diffbind commit 1fe103338548dd65731a5a0887be59745370debd
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274 </repeat>
c97a786e8fb5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diffbind commit 1fe103338548dd65731a5a0887be59745370debd
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275 <param name="scorecol" value="5" />
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276 <param name="format" value="interval"/>
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277 <output name="outfile" ftype="interval" value="out_diffbind_ctrl.interval" />
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278 </test>
13
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279 <!-- Ensure BED output works -->
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280 <test expect_num_outputs="1">
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281 <repeat name="rep_group">
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282 <param name="groupName" value="Resistant"/>
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283 <param name="peaks" ftype="bed" value="BT474_ER_1.bed.gz,BT474_ER_2.bed.gz"/>
1de83981d43c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diffbind commit 13485bed6a57ec4a34cab4ec6bb8b36d219e3610
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284 <param name="bamreads" ftype="bam" value="BT474_ER_1.bam,BT474_ER_2.bam" />
1de83981d43c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diffbind commit 13485bed6a57ec4a34cab4ec6bb8b36d219e3610
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285 </repeat>
1de83981d43c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diffbind commit 13485bed6a57ec4a34cab4ec6bb8b36d219e3610
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286 <repeat name="rep_group">
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287 <param name="groupName" value="Responsive"/>
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288 <param name="peaks" ftype="bed" value="MCF7_ER_1.bed.gz,MCF7_ER_2.bed.gz"/>
1de83981d43c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diffbind commit 13485bed6a57ec4a34cab4ec6bb8b36d219e3610
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289 <param name="bamreads" ftype="bam" value="MCF7_ER_1.bam,MCF7_ER_2.bam" />
1de83981d43c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diffbind commit 13485bed6a57ec4a34cab4ec6bb8b36d219e3610
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290 </repeat>
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291 <param name="scorecol" value="5" />
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292 <param name="format" value="bed"/>
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293 <output name="outfile" ftype="bed" value="out_diffbind.bed" />
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294 </test>
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295 <!-- Ensure tabular output works -->
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296 <test expect_num_outputs="1">
1de83981d43c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diffbind commit 13485bed6a57ec4a34cab4ec6bb8b36d219e3610
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297 <repeat name="rep_group">
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298 <param name="groupName" value="Resistant"/>
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299 <param name="peaks" ftype="bed" value="BT474_ER_1.bed.gz,BT474_ER_2.bed.gz"/>
1de83981d43c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diffbind commit 13485bed6a57ec4a34cab4ec6bb8b36d219e3610
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300 <param name="bamreads" ftype="bam" value="BT474_ER_1.bam,BT474_ER_2.bam" />
1de83981d43c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diffbind commit 13485bed6a57ec4a34cab4ec6bb8b36d219e3610
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301 </repeat>
1de83981d43c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diffbind commit 13485bed6a57ec4a34cab4ec6bb8b36d219e3610
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302 <repeat name="rep_group">
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303 <param name="groupName" value="Responsive"/>
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304 <param name="peaks" ftype="bed" value="MCF7_ER_1.bed.gz,MCF7_ER_2.bed.gz"/>
1de83981d43c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diffbind commit 13485bed6a57ec4a34cab4ec6bb8b36d219e3610
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305 <param name="bamreads" ftype="bam" value="MCF7_ER_1.bam,MCF7_ER_2.bam" />
1de83981d43c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diffbind commit 13485bed6a57ec4a34cab4ec6bb8b36d219e3610
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306 </repeat>
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307 <param name="scorecol" value="5" />
1de83981d43c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diffbind commit 13485bed6a57ec4a34cab4ec6bb8b36d219e3610
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308 <param name="format" value="tabular"/>
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309 <output name="outfile" ftype="tabular" file="out_diffbind.tab" />
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310 </test>
18
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311 <!-- Ensure minoverlap works -->
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312 <test expect_num_outputs="1">
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313 <repeat name="rep_group">
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314 <param name="groupName" value="Resistant"/>
f907216064f6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diffbind commit fd148a124034b44d0d61db3eec32ff991d8c152c
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315 <param name="peaks" ftype="bed" value="BT474_ER_1.bed.gz,BT474_ER_2.bed.gz"/>
f907216064f6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diffbind commit fd148a124034b44d0d61db3eec32ff991d8c152c
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316 <param name="bamreads" ftype="bam" value="BT474_ER_1.bam,BT474_ER_2.bam" />
f907216064f6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diffbind commit fd148a124034b44d0d61db3eec32ff991d8c152c
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317 </repeat>
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318 <repeat name="rep_group">
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319 <param name="groupName" value="Responsive"/>
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320 <param name="peaks" ftype="bed" value="MCF7_ER_1.bed.gz,MCF7_ER_2.bed.gz"/>
f907216064f6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diffbind commit fd148a124034b44d0d61db3eec32ff991d8c152c
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321 <param name="bamreads" ftype="bam" value="MCF7_ER_1.bam,MCF7_ER_2.bam" />
f907216064f6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diffbind commit fd148a124034b44d0d61db3eec32ff991d8c152c
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322 </repeat>
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323 <param name="minoverlap" value="1" />
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324 <param name="scorecol" value="5" />
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325 <param name="format" value="tabular"/>
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326 <output name="outfile" ftype="tabular" file="out_diffbind_minoverlap1.tab" />
f907216064f6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diffbind commit fd148a124034b44d0d61db3eec32ff991d8c152c
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327 </test>
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328 <!-- Ensure blacklist filtering works -->
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329 <test expect_num_outputs="1">
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330 <repeat name="rep_group">
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331 <param name="groupName" value="Resistant"/>
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332 <param name="peaks" ftype="bed" value="BT474_ER_1.bed.gz,BT474_ER_2.bed.gz"/>
f907216064f6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diffbind commit fd148a124034b44d0d61db3eec32ff991d8c152c
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333 <param name="bamreads" ftype="bam" value="BT474_ER_1.bam,BT474_ER_2.bam" />
f907216064f6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diffbind commit fd148a124034b44d0d61db3eec32ff991d8c152c
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334 </repeat>
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335 <repeat name="rep_group">
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336 <param name="groupName" value="Responsive"/>
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337 <param name="peaks" ftype="bed" value="MCF7_ER_1.bed.gz,MCF7_ER_2.bed.gz"/>
f907216064f6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diffbind commit fd148a124034b44d0d61db3eec32ff991d8c152c
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338 <param name="bamreads" ftype="bam" value="MCF7_ER_1.bam,MCF7_ER_2.bam" />
f907216064f6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diffbind commit fd148a124034b44d0d61db3eec32ff991d8c152c
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339 </repeat>
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340 <param name="use_blacklist" value="True"/>
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341 <param name="scorecol" value="5" />
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342 <param name="format" value="tabular"/>
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343 <output name="outfile" ftype="tabular" file="out_diffbind_blacklist.tab" />
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344 </test>
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345 </tests>
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346 <help><![CDATA[
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347
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348 .. class:: infomark
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349
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350 **What it does**
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351
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352 DiffBind_ is a `Bioconductor package`_ that provides functions for processing ChIP-Seq data enriched for genomic loci where specific
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353 protein/DNA binding occurs, including peak sets identified by ChIP-Seq peak callers and
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354 aligned sequence read datasets. It is designed to work with multiple peak sets simultaneously,
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355 representing different ChIP experiments (antibodies, transcription factor and/or histone
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356 marks, experimental conditions, replicates) as well as managing the results of multiple peak
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357 callers.
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358
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359 The primary emphasis of DiffBind is on identifying sites that are differentially bound
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360 between two sample groups. It includes functions to support the processing of peak sets,
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361 including overlapping and merging peak sets, counting sequencing reads overlapping intervals
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362 in peak sets, and identifying statistically significantly differentially bound sites based on
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363 evidence of binding affinity (measured by differences in read densities). To this end it uses
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364 statistical routines developed in an RNA-Seq context (primarily the Bioconductor packages
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365 edgeR and DESeq2). Additionally, the package builds on Rgraphics routines to provide a
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366 set of standardized plots to aid in binding analysis.
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367
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368 The `DiffBind User Guide`_ includes a brief overview of the processing flow, followed by four sections of
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369 examples: the first focusing on the core task of obtaining differentially bound sites based on
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370 affinity data, the second working through the main plotting routines, the third discussing the
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371 use of a blocking factor, and the fourth revisiting occupancy data (peak calls) in more detail,
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372 as well as comparing the results of an occupancy-based analysis with an affinity-based one.
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373 Finally, certain technical aspects of the how these analyses are accomplished are detailed.
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374
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375 **Note this DiffBind tool requires a minimum of four samples (two groups with two replicates each).**
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376
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377 -----
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378
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379 **Inputs**
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380
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381 DiffBind works primarily with peaksets, which are sets of genomic intervals representing
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382 candidate protein binding sites. Each interval consists of a chromosome, a start and end
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383 position, and usually a score of some type indicating confidence in, or strength of, the peak.
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384 Associated with each peakset are metadata relating to the experiment from which the peakset
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385 was derived. Additionally, files containing mapped sequencing reads (BAM files) need to
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386 be associated with each peakset (one for the ChIP data, and optionally another representing
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387 a control sample)
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388
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389 Inputs for a group will be sorted by identifier before processing. For each group the corresponding
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390 sets of peak and BAM files need to be provided. Ideally this is accomplished by providing the data in
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391 collections.
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392
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393
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394 **Groups**
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395
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396 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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397
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398 Example:
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399
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400 ============= =============
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401 **Sample** **Group**
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402 ------------- -------------
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403 BT4741 Resistant
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404 BT4742 Resistant
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405 MCF71 Responsive
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406 MCF72 Responsive
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407 ============= =============
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408
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409
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410 **Peak files**
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411
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412 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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413
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414 Example:
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415
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416 ======= ======= ======= =============== ==============
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417 1 2 3 4 **5 (Score)**
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418 ======= ======= ======= =============== ==============
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419 chr18 215562 216063 peak_16037 56.11
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420 chr18 311530 312105 peak_16038 222.49
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421 chr18 356656 357315 peak_16039 92.06
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422 chr18 371110 372092 peak_16040 123.86
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423 chr18 395116 396464 peak_16041 1545.39
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424 chr18 399014 400382 peak_16042 1835.19
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425 chr18 499134 500200 peak_16043 748.32
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426 chr18 503518 504552 peak_16044 818.30
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427 chr18 531672 532274 peak_16045 159.30
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428 chr18 568326 569282 peak_16046 601.11
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429 ======= ======= ======= =============== ==============
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430
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431 * BAM file which contains the mapped sequencing reads associated with each peakset, one file for each sample is required.
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432 * 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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433
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434 -----
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435
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436 **Outputs**
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437
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438 This tool outputs
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439
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440 * a table of differentially bound sites in Interval, BED or Tabular 0-based format
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441
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442 Optionally, under **Output Options** you can choose to output
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443
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444 * a PDF of plots (Heatmap, PCA, MA, Volcano, Boxplots)
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445 * a binding affinity matrix
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446 * the R script used by this tool
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447 * an RData file of the R objects generated
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448 * a text file with information on the analysis (number of Intervals, FriP scores, method used)
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449
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450 **Differentially Bound Sites**
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451
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452 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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453
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454 Example - **Interval format**:
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455
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456 ====== ====== ====== ======== ===== ====== ===========================================
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457 Chrom Start End Name Score Strand **Comment**
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458 ====== ====== ====== ======== ===== ====== ===========================================
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459 chr18 394599 396513 DiffBind 0 \. 1914|7.15|5.55|7.89|-2.35|7.06e-24|9.84e-21
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460 chr18 111566 112005 DiffBind 0 \. 439|5.71|6.53|3.63|2.89|1.27e-08|8.88e-06
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461 chr18 346463 347342 DiffBind 0 \. 879|5|5.77|3.24|2.52|6.51e-06|0.00303
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462 chr18 399013 400382 DiffBind 0 \. 1369|7.62|7|8.05|-1.04|1.04e-05|0.00364
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463 chr18 371109 372102 DiffBind 0 \. 993|4.63|3.07|5.36|-2.3|8.1e-05|0.0226
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464 ====== ====== ====== ======== ===== ====== ===========================================
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465
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466 Columns contain the following data:
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467
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468 * **Chrom**: Chromosome name
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469 * **Start**: Start position of site
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470 * **End**: End position of site
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471 * **Score**: 0
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472 * **Name**: DiffBind
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473 * **Strand**: Strand
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474 * **Comment**: The pipe ("|") separated values in this column correspond to:
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475
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476 * *width*: Length of site
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477 * *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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478 * *Conc_Group1*: Mean concentration over the first group (e.g. Responsive)
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479 * *Conc_Group2*: Mean concentration over second group (e.g. Resistant)
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480 * *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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481 * *p.value*: P-value confidence measure for identifying these sites as differentially bound
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482 * *FDR*: a multiple testing corrected FDR p-value
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483
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484 Example - **BED format**:
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485
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486 ===== ====== ====== ======== ===== ======
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487 Chrom Start End Name Score Strand
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488 ===== ====== ====== ======== ===== ======
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489 chr18 394599 396513 DiffBind 0 \.
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490 chr18 111566 112005 DiffBind 0 \.
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491 chr18 346463 347342 DiffBind 0 \.
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492 chr18 399013 400382 DiffBind 0 \.
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493 chr18 371109 372102 DiffBind 0 \.
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494 ===== ====== ====== ======== ===== ======
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495
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496 Example - **Tabular format**:
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497
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498 ===== ====== ====== ======== ===== ====== ==== =============== ============== ===== ======== ========
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499 Chrom Start End Name Score Strand Conc Conc_Responsive Conc_Resistant Fold p.value FDR
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500 ===== ====== ====== ======== ===== ====== ==== =============== ============== ===== ======== ========
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501 chr18 394599 396513 DiffBind 0 \. 7.15 5.55 7.89 -2.35 7.06E-24 9.84E-21
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502 chr18 111566 112005 DiffBind 0 \. 5.71 6.53 3.63 2.89 1.27E-08 8.88E-06
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503 chr18 346463 347342 DiffBind 0 \. 5 5.77 3.24 2.52 6.51E-06 0.00303
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504 chr18 399013 400382 DiffBind 0 \. 7.62 7 8.05 -1.04 1.04E-05 0.00364
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505 chr18 371109 372102 DiffBind 0 \. 4.63 3.07 5.36 -2.3 8.10E-05 0.0226
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506 ===== ====== ====== ======== ===== ====== ==== =============== ============== ===== ======== ========
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507
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508
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509 **Binding Affinity Matrix**
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510
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511 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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512 differential analysis. Note that this output is a tabular 0-based format.
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513
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514 Example:
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515
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516 ===== ====== ====== ========= ========= ========== ==========
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517 Chrom Start End MCF7_ER_1 MCF7_ER_2 BT474_ER_1 BT474_ER_2
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518 ===== ====== ====== ========= ========= ========== ==========
fa56d93f7980 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diffbind commit 11f68fe2b872f5abc5b660adb10336b0955fa0ee
iuc
parents: 11
diff changeset
519 chr18 111567 112005 137.6152 59.87837 29.41393 19.95945
fa56d93f7980 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diffbind commit 11f68fe2b872f5abc5b660adb10336b0955fa0ee
iuc
parents: 11
diff changeset
520 chr18 189223 189652 19.95945 12.60597 11.55547 23.11095
fa56d93f7980 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diffbind commit 11f68fe2b872f5abc5b660adb10336b0955fa0ee
iuc
parents: 11
diff changeset
521 chr18 215232 216063 11.55547 15.75746 31.51493 72.48434
fa56d93f7980 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diffbind commit 11f68fe2b872f5abc5b660adb10336b0955fa0ee
iuc
parents: 11
diff changeset
522 chr18 311530 312172 17.85846 11.55547 54.62588 43.07040
fa56d93f7980 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diffbind commit 11f68fe2b872f5abc5b660adb10336b0955fa0ee
iuc
parents: 11
diff changeset
523 chr18 346464 347342 75.63583 40.96941 21.00995 16.80796
fa56d93f7980 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diffbind commit 11f68fe2b872f5abc5b660adb10336b0955fa0ee
iuc
parents: 11
diff changeset
524 chr18 356560 357362 11.55547 14.70696 57.77737 53.57538
fa56d93f7980 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diffbind commit 11f68fe2b872f5abc5b660adb10336b0955fa0ee
iuc
parents: 11
diff changeset
525 chr18 371110 372102 8.403982 9.454479 81.93882 82.98932
fa56d93f7980 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diffbind commit 11f68fe2b872f5abc5b660adb10336b0955fa0ee
iuc
parents: 11
diff changeset
526 chr18 394600 396513 56.72687 43.07040 510.5419 438.0575
fa56d93f7980 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diffbind commit 11f68fe2b872f5abc5b660adb10336b0955fa0ee
iuc
parents: 11
diff changeset
527 chr18 399014 400382 156.5241 117.6557 558.8648 496.8854
fa56d93f7980 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diffbind commit 11f68fe2b872f5abc5b660adb10336b0955fa0ee
iuc
parents: 11
diff changeset
528 chr18 498906 500200 767.9138 278.3819 196.4430 181.7361
fa56d93f7980 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diffbind commit 11f68fe2b872f5abc5b660adb10336b0955fa0ee
iuc
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diff changeset
529 ===== ====== ====== ========= ========= ========== ==========
9
6171163112de planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diffbind commit 9de99de5fb4c62f889814ea43b8800ce8d28eb83
iuc
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diff changeset
530
10
d7725c5596ab planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diffbind commit f970dcbe9d0e4c3714b1db74c404ea34223cf8ed
iuc
parents: 9
diff changeset
531 -----
9
6171163112de planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diffbind commit 9de99de5fb4c62f889814ea43b8800ce8d28eb83
iuc
parents:
diff changeset
532
6171163112de planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diffbind commit 9de99de5fb4c62f889814ea43b8800ce8d28eb83
iuc
parents:
diff changeset
533 **More Information**
6171163112de planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diffbind commit 9de99de5fb4c62f889814ea43b8800ce8d28eb83
iuc
parents:
diff changeset
534
6171163112de planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diffbind commit 9de99de5fb4c62f889814ea43b8800ce8d28eb83
iuc
parents:
diff changeset
535 Generally, processing data with DiffBind involves five phases:
6171163112de planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diffbind commit 9de99de5fb4c62f889814ea43b8800ce8d28eb83
iuc
parents:
diff changeset
536
6171163112de planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diffbind commit 9de99de5fb4c62f889814ea43b8800ce8d28eb83
iuc
parents:
diff changeset
537 #. Reading in peaksets
6171163112de planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diffbind commit 9de99de5fb4c62f889814ea43b8800ce8d28eb83
iuc
parents:
diff changeset
538 #. Occupancy analysis
6171163112de planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diffbind commit 9de99de5fb4c62f889814ea43b8800ce8d28eb83
iuc
parents:
diff changeset
539 #. Counting reads
6171163112de planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diffbind commit 9de99de5fb4c62f889814ea43b8800ce8d28eb83
iuc
parents:
diff changeset
540 #. Differential binding affinity analysis
6171163112de planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diffbind commit 9de99de5fb4c62f889814ea43b8800ce8d28eb83
iuc
parents:
diff changeset
541 #. Plotting and reporting
6171163112de planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diffbind commit 9de99de5fb4c62f889814ea43b8800ce8d28eb83
iuc
parents:
diff changeset
542
6171163112de planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diffbind commit 9de99de5fb4c62f889814ea43b8800ce8d28eb83
iuc
parents:
diff changeset
543
10
d7725c5596ab planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diffbind commit f970dcbe9d0e4c3714b1db74c404ea34223cf8ed
iuc
parents: 9
diff changeset
544 **Reading in peaksets**:
9
6171163112de planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diffbind commit 9de99de5fb4c62f889814ea43b8800ce8d28eb83
iuc
parents:
diff changeset
545
6171163112de planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diffbind commit 9de99de5fb4c62f889814ea43b8800ce8d28eb83
iuc
parents:
diff changeset
546 The first step is to read in a set of peaksets and associated
10
d7725c5596ab planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diffbind commit f970dcbe9d0e4c3714b1db74c404ea34223cf8ed
iuc
parents: 9
diff changeset
547 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
d7725c5596ab planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diffbind commit f970dcbe9d0e4c3714b1db74c404ea34223cf8ed
iuc
parents: 9
diff changeset
548 in a genome). A single experiment can have more than
9
6171163112de planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diffbind commit 9de99de5fb4c62f889814ea43b8800ce8d28eb83
iuc
parents:
diff changeset
549 one associated peakset; e.g. if multiple peak callers are used for comparison purposes
6171163112de planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diffbind commit 9de99de5fb4c62f889814ea43b8800ce8d28eb83
iuc
parents:
diff changeset
550 each sample would have more than one line in the sample sheet. Once the peaksets
6171163112de planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diffbind commit 9de99de5fb4c62f889814ea43b8800ce8d28eb83
iuc
parents:
diff changeset
551 are read in, a merging function finds all overlapping peaks and derives a single set of
6171163112de planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diffbind commit 9de99de5fb4c62f889814ea43b8800ce8d28eb83
iuc
parents:
diff changeset
552 unique genomic intervals covering all the supplied peaks (a consensus peakset for the
6171163112de planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diffbind commit 9de99de5fb4c62f889814ea43b8800ce8d28eb83
iuc
parents:
diff changeset
553 experiment).
6171163112de planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diffbind commit 9de99de5fb4c62f889814ea43b8800ce8d28eb83
iuc
parents:
diff changeset
554
10
d7725c5596ab planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diffbind commit f970dcbe9d0e4c3714b1db74c404ea34223cf8ed
iuc
parents: 9
diff changeset
555 **Occupancy analysis**:
9
6171163112de planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diffbind commit 9de99de5fb4c62f889814ea43b8800ce8d28eb83
iuc
parents:
diff changeset
556
6171163112de planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diffbind commit 9de99de5fb4c62f889814ea43b8800ce8d28eb83
iuc
parents:
diff changeset
557 Peaksets, especially those generated by peak callers, provide
6171163112de planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diffbind commit 9de99de5fb4c62f889814ea43b8800ce8d28eb83
iuc
parents:
diff changeset
558 an insight into the potential occupancy of the protein being ChIPed for at specific
6171163112de planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diffbind commit 9de99de5fb4c62f889814ea43b8800ce8d28eb83
iuc
parents:
diff changeset
559 genomic loci. After the peaksets have been loaded, it can be useful to perform some
6171163112de planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diffbind commit 9de99de5fb4c62f889814ea43b8800ce8d28eb83
iuc
parents:
diff changeset
560 exploratory plotting to determine how these occupancy maps agree with each other,
6171163112de planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diffbind commit 9de99de5fb4c62f889814ea43b8800ce8d28eb83
iuc
parents:
diff changeset
561 e.g. between experimental replicates (re-doing the ChIP under the same conditions),
6171163112de planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diffbind commit 9de99de5fb4c62f889814ea43b8800ce8d28eb83
iuc
parents:
diff changeset
562 between different peak callers on the same experiment, and within groups of samples
6171163112de planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diffbind commit 9de99de5fb4c62f889814ea43b8800ce8d28eb83
iuc
parents:
diff changeset
563 representing a common experimental condition. DiffBind provides functions to enable
6171163112de planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diffbind commit 9de99de5fb4c62f889814ea43b8800ce8d28eb83
iuc
parents:
diff changeset
564 overlaps to be examined, as well as functions to determine how well similar samples
6171163112de planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diffbind commit 9de99de5fb4c62f889814ea43b8800ce8d28eb83
iuc
parents:
diff changeset
565 cluster together. Beyond quality control, the product of an occupancy analysis may be
6171163112de planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diffbind commit 9de99de5fb4c62f889814ea43b8800ce8d28eb83
iuc
parents:
diff changeset
566 a consensus peakset, representing an overall set of candidate binding sites to be used
6171163112de planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diffbind commit 9de99de5fb4c62f889814ea43b8800ce8d28eb83
iuc
parents:
diff changeset
567 in further analysis.
6171163112de planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diffbind commit 9de99de5fb4c62f889814ea43b8800ce8d28eb83
iuc
parents:
diff changeset
568
10
d7725c5596ab planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diffbind commit f970dcbe9d0e4c3714b1db74c404ea34223cf8ed
iuc
parents: 9
diff changeset
569 **Counting reads**:
9
6171163112de planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diffbind commit 9de99de5fb4c62f889814ea43b8800ce8d28eb83
iuc
parents:
diff changeset
570
6171163112de planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diffbind commit 9de99de5fb4c62f889814ea43b8800ce8d28eb83
iuc
parents:
diff changeset
571 Once a consensus peakset has been derived, DiffBind can use the
6171163112de planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diffbind commit 9de99de5fb4c62f889814ea43b8800ce8d28eb83
iuc
parents:
diff changeset
572 supplied sequence read files to count how many reads overlap each interval for each
6171163112de planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diffbind commit 9de99de5fb4c62f889814ea43b8800ce8d28eb83
iuc
parents:
diff changeset
573 unique sample. The peaks in the consensus peakset may be re-centered and trimmed
6171163112de planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diffbind commit 9de99de5fb4c62f889814ea43b8800ce8d28eb83
iuc
parents:
diff changeset
574 based on calculating their summits (point of greatest read overlap) in order to provide
6171163112de planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diffbind commit 9de99de5fb4c62f889814ea43b8800ce8d28eb83
iuc
parents:
diff changeset
575 more standardized peak intervals. The final result of counting is a binding affinity matrix
6171163112de planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diffbind commit 9de99de5fb4c62f889814ea43b8800ce8d28eb83
iuc
parents:
diff changeset
576 containing a (normalized) read count for each sample at every potential binding site.
6171163112de planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diffbind commit 9de99de5fb4c62f889814ea43b8800ce8d28eb83
iuc
parents:
diff changeset
577 With this matrix, the samples can be re-clustered using affinity, rather than occupancy,
6171163112de planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diffbind commit 9de99de5fb4c62f889814ea43b8800ce8d28eb83
iuc
parents:
diff changeset
578 data. The binding affinity matrix is used for QC plotting as well as for subsequent
6171163112de planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diffbind commit 9de99de5fb4c62f889814ea43b8800ce8d28eb83
iuc
parents:
diff changeset
579 differential analysis.
6171163112de planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diffbind commit 9de99de5fb4c62f889814ea43b8800ce8d28eb83
iuc
parents:
diff changeset
580
10
d7725c5596ab planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diffbind commit f970dcbe9d0e4c3714b1db74c404ea34223cf8ed
iuc
parents: 9
diff changeset
581 **Differential binding affinity analysis**:
9
6171163112de planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diffbind commit 9de99de5fb4c62f889814ea43b8800ce8d28eb83
iuc
parents:
diff changeset
582
6171163112de planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diffbind commit 9de99de5fb4c62f889814ea43b8800ce8d28eb83
iuc
parents:
diff changeset
583 The core functionality of DiffBind is the
6171163112de planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diffbind commit 9de99de5fb4c62f889814ea43b8800ce8d28eb83
iuc
parents:
diff changeset
584 differential binding affinity analysis, which enables binding sites to be identified that
6171163112de planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diffbind commit 9de99de5fb4c62f889814ea43b8800ce8d28eb83
iuc
parents:
diff changeset
585 are statistically significantly differentially bound between sample groups. To accomplish
6171163112de planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diffbind commit 9de99de5fb4c62f889814ea43b8800ce8d28eb83
iuc
parents:
diff changeset
586 this, first a contrast (or contrasts) is established, dividing the samples into groups to
12
fa56d93f7980 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diffbind commit 11f68fe2b872f5abc5b660adb10336b0955fa0ee
iuc
parents: 11
diff changeset
587 be compared. Next the core analysis routines are executed, by default using DESeq2.
9
6171163112de planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diffbind commit 9de99de5fb4c62f889814ea43b8800ce8d28eb83
iuc
parents:
diff changeset
588 This will assign a p-value and FDR to each candidate binding site indicating confidence
6171163112de planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diffbind commit 9de99de5fb4c62f889814ea43b8800ce8d28eb83
iuc
parents:
diff changeset
589 that they are differentially bound.
6171163112de planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diffbind commit 9de99de5fb4c62f889814ea43b8800ce8d28eb83
iuc
parents:
diff changeset
590
10
d7725c5596ab planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diffbind commit f970dcbe9d0e4c3714b1db74c404ea34223cf8ed
iuc
parents: 9
diff changeset
591 **Plotting and reporting**:
9
6171163112de planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diffbind commit 9de99de5fb4c62f889814ea43b8800ce8d28eb83
iuc
parents:
diff changeset
592
6171163112de planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diffbind commit 9de99de5fb4c62f889814ea43b8800ce8d28eb83
iuc
parents:
diff changeset
593 Once one or more contrasts have been run, DiffBind provides
6171163112de planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diffbind commit 9de99de5fb4c62f889814ea43b8800ce8d28eb83
iuc
parents:
diff changeset
594 a number of functions for reporting and plotting the results. MA plots give an
6171163112de planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diffbind commit 9de99de5fb4c62f889814ea43b8800ce8d28eb83
iuc
parents:
diff changeset
595 overview of the results of the analysis, while correlation heatmaps and PCA plots show
6171163112de planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diffbind commit 9de99de5fb4c62f889814ea43b8800ce8d28eb83
iuc
parents:
diff changeset
596 how the groups cluster based on differentially bound sites. Boxplots show the distribution
6171163112de planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diffbind commit 9de99de5fb4c62f889814ea43b8800ce8d28eb83
iuc
parents:
diff changeset
597 of reads within differentially bound sites corresponding to whether they gain or
6171163112de planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diffbind commit 9de99de5fb4c62f889814ea43b8800ce8d28eb83
iuc
parents:
diff changeset
598 lose affinity between the two sample groups. A reporting mechanism enables differentially
6171163112de planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diffbind commit 9de99de5fb4c62f889814ea43b8800ce8d28eb83
iuc
parents:
diff changeset
599 bound sites to be extracted for further processing, such as annotation, motif, and
11
4c7ab9995f9e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diffbind commit cc4c1c4131518b9cbf986a1f252767ff73ca938e
iuc
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diff changeset
600 pathway analyses.
10
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parents: 9
diff changeset
601
d7725c5596ab planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diffbind commit f970dcbe9d0e4c3714b1db74c404ea34223cf8ed
iuc
parents: 9
diff changeset
602 -----
9
6171163112de planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diffbind commit 9de99de5fb4c62f889814ea43b8800ce8d28eb83
iuc
parents:
diff changeset
603
6171163112de planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diffbind commit 9de99de5fb4c62f889814ea43b8800ce8d28eb83
iuc
parents:
diff changeset
604 **References**
6171163112de planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diffbind commit 9de99de5fb4c62f889814ea43b8800ce8d28eb83
iuc
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diff changeset
605
6171163112de planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diffbind commit 9de99de5fb4c62f889814ea43b8800ce8d28eb83
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606 DiffBind Authors: Rory Stark, Gordon Brown (2011)
6171163112de planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diffbind commit 9de99de5fb4c62f889814ea43b8800ce8d28eb83
iuc
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diff changeset
607 Wrapper authors: Bjoern Gruening, Pavankumar Videm
6171163112de planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diffbind commit 9de99de5fb4c62f889814ea43b8800ce8d28eb83
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608
11
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diff changeset
609 .. _DiffBind: https://bioconductor.org/packages/release/bioc/html/DiffBind.html
4c7ab9995f9e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diffbind commit cc4c1c4131518b9cbf986a1f252767ff73ca938e
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610 .. _`Bioconductor package`: https://bioconductor.org/packages/release/bioc/html/DiffBind.html
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611 .. _`DiffBind User Guide`: https://bioconductor.org/packages/release/bioc/vignettes/DiffBind/inst/doc/DiffBind.pdf
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612 .. _`Bioconductor post`: https://support.bioconductor.org/p/69924/
13
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613 .. _here: https://galaxyproject.org/learn/datatypes/#interval
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614 .. _`Biostars post`: https://www.biostars.org/p/84686/
11
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615
9
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616 ]]>
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617 </help>
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618 <citations>
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619 <citation type="doi">doi:10.1038/nature10730</citation>
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620 </citations>
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621 </tool>