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annotate diffbind.xml @ 20:11cd8b1ae397 draft

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planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diffbind commit affbc59222cde9be21e91fa1f9194930a070b830
author iuc
date Sun, 28 Jan 2018 04:25:49 -0500
parents ab544462062a
children
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1 <tool id="diffbind" name="DiffBind" version="2.6.5.0">
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2 <description> differential binding analysis of ChIP-Seq peak data</description>
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3 <requirements>
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4 <requirement type="package" version="2.6.5">bioconductor-diffbind</requirement>
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5 <requirement type="package" version="1.20.0">r-getopt</requirement>
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6 <!--added rmysql requirement to remove: "Warning: namespace ‘RMySQL’ is not available"-->
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7 <requirement type="package" version="0.10.11">r-rmysql</requirement>
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8 </requirements>
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9 <stdio>
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10 <regex match="Execution halted"
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11 source="both"
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12 level="fatal"
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13 description="Execution halted." />
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14 <regex match="Input-Error 01"
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15 source="both"
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16 level="fatal"
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17 description="Error in your input parameters: Make sure you only apply factors to selected samples." />
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18 <regex match="Error in"
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19 source="both"
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20 level="fatal"
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21 description="An undefined error occured, please check your intput carefully and contact your administrator." />
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22 </stdio>
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23 <version_command><![CDATA[
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24 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: ")," getopt version" $(R --vanilla --slave -e "library(getopt); cat(sessionInfo()\$otherPkgs\$getopt\$Version)" 2> /dev/null | grep -v -i "WARNING: ")", rmysql version" $(R --vanilla --slave -e "library(rmysql); cat(sessionInfo()\$otherPkgs\$rmysql\$Version)" 2> /dev/null | grep -v -i "WARNING: ")
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25 ]]></version_command>
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26 <command><![CDATA[
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27 ## seems that diffbind also needs file extensions to work properly
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28 #set $counter = 1
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29 #for $sample in $samples:
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30 ln -s $sample.bamreads #echo str($counter) + "_bamreads.bam"# &&
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31 ln -s ${sample.bamreads.metadata.bam_index} #echo str($counter) + "_bamreads.bai"# &&
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32 #if str( $sample.bamcontrol ) != 'None':
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33 ln -s $sample.bamcontrol #echo str($counter) + "_bamcontrol.bam"# &&
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34 ln -s ${sample.bamcontrol.metadata.bam_index} #echo str($counter) + "_bamcontrol.bai"# &&
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35 #end if
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36 #set $counter = $counter + 1
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37 #end for
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38
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39 Rscript '$__tool_directory__/diffbind.R'
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40 -i $infile
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41 -o '$outfile'
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42 -p '$plots'
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43 -f $format
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44 -t $th
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45
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46 #if $binding_affinity_matrix:
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47 -b
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48 #end if
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49 ]]>
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50 </command>
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51 <configfiles>
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52 <configfile name="infile"><![CDATA[
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53 #set $counter = 1
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54 #for $sample in $samples:
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55 #if str( $sample.bamcontrol ) != 'None' and $counter == 1:
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56 SampleID,Tissue,Factor,Condition,Replicate,bamReads,bamControl,Peaks
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57 #elif $counter == 1:
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58 SampleID,Tissue,Factor,Condition,Replicate,bamReads,Peaks
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59 #end if
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60 #if str( $sample.bamcontrol ) != 'None':
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61 $sample.sample_id,$sample.tissue,$sample.factor,$sample.condition,$sample.replicate,#echo str($counter) + '_bamreads.bam'#,#echo str($counter) + '_bamcontrol.bam'#,$sample.peaks
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62 #else:
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63 $sample.sample_id,$sample.tissue,$sample.factor,$sample.condition,$sample.replicate,#echo str($counter) + '_bamreads.bam'#,$sample.peaks
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64 #end if
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65 #set $counter = $counter + 1
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66 #end for]]></configfile>
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67 </configfiles>
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68 <inputs>
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69 <repeat name="samples" title="Samples" min="2">
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70 <param name="sample_id" type="text" value="Sample ID" label="Specify a sample id" help="e.g. BT474.1-" />
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71 <param name="tissue" type="text" value="Tissue" label="Specify the tissue" help="e.g. BT474" />
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72 <param name="factor" type="text" value="Factor Name" label="Specify a factor name" help="e.g. ER" />
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73 <param name="condition" type="text" value="Condition" label="Specify the condition" help="e.g. Resistent" />
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74 <param name="replicate" type="integer" value="1" label="Specify the replicate number" help="e.g. 1" />
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75 <param name="bamreads" type="data" format="bam" label="Read BAM file" help="Specify the Read BAM file, used for Peak calling."/>
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76 <param name="bamcontrol" type="data" format="bam" optional="True" label="Control BAM file" help="If specifying a control BAM file for this sample, then all samples are required to specify one."/>
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77 <param name="peaks" type="data" format="bed" label="Peak file" help="Result of your Peak calling experiment."/>
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78 </repeat>
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79 <param name="th" type="float" value="1" min="0" max="1"
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80 label="FDR Threshold"
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81 help="Significance threshold; all sites with FDR less than or equal to this value will be included in the report. A value of 1 will include all binding sites in the report. Default: 1"/>
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82 <param name="pdf" type="boolean" truevalue="" falsevalue="" checked="true"
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83 label="Visualising the analysis results"
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84 help="output an additional PDF file" />
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85 <param name="format" type="select" label="Output Format">
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86 <option value="bed">BED</option>
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87 <option value="gff">GFF</option>
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88 <option value="wig">WIG</option>
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89 </param>
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90 <param name="binding_affinity_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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91 </inputs>
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92 <outputs>
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93 <data name="outfile" format="bed" label="Differential binding sites on ${on_string}">
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94 <change_format>
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95 <when input="format" value="wig" format="wig" />
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96 <when input="format" value="gff" format="gff" />
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97 </change_format>
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98 </data>
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99 <data name="plots" format="pdf" label="Differential binding sites on ${on_string}">
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100 <filter>pdf == True</filter>
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101 </data>
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102 <data name="binding_matrix" format="tabular" from_work_dir="bmatrix.tab" label="Differential binding sites on ${on_string}">
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103 <filter>binding_affinity_matrix == True</filter>
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104 </data>
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105 </outputs>
20
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106 <tests>
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107 <test>
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108 <repeat name="samples">
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109 <param name="sample_id" value="BT4741" />
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110 <param name="tissue" value="BT474" />
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111 <param name="factor" value="ER" />
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112 <param name="condition" value="Resistant" />
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113 <param name="replicate" value="1" />
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114 <param name="bamreads" ftype="bam" value="BT474_ER_1.bam" />
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115 <param name="peaks" ftype="bed" value="BT474_ER_1.bed.gz" />
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116 </repeat>
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117 <repeat name="samples">
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118 <param name="sample_id" value="BT4742" />
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119 <param name="tissue" value="BT474" />
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120 <param name="factor" value="ER" />
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121 <param name="condition" value="Resistant" />
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122 <param name="replicate" value="2" />
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123 <param name="bamreads" ftype="bam" value="BT474_ER_2.bam" />
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124 <param name="peaks" ftype="bed" value="BT474_ER_2.bed.gz" />
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125 </repeat>
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126 <repeat name="samples">
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127 <param name="sample_id" value="MCF71" />
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128 <param name="tissue" value="MCF7" />
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129 <param name="factor" value="ER" />
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130 <param name="condition" value="Responsive" />
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131 <param name="replicate" value="1" />
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132 <param name="bamreads" ftype="bam" value="MCF7_ER_1.bam" />
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133 <param name="peaks" ftype="bed" value="MCF7_ER_1.bed.gz" />
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134 </repeat>
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135 <repeat name="samples">
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136 <param name="sample_id" value="MCF72" />
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137 <param name="tissue" value="MCF7" />
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138 <param name="factor" value="ER" />
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139 <param name="condition" value="Responsive" />
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140 <param name="replicate" value="2" />
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141 <param name="bamreads" ftype="bam" value="MCF7_ER_2.bam" />
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142 <param name="peaks" ftype="bed" value="MCF7_ER_2.bed.gz" />
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143 </repeat>
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144 <param name="pdf" value="True" />
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145 <param name="binding_affinity_matrix" value="True" />
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146 <output name="outfile" value="out_diffbind.bed" />
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147 <output name="binding_matrix" value="out_binding.matrix" />
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148 </test>
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149 </tests>
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150 <help><![CDATA[
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151
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152 .. class:: infomark
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153
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154 **What it does**
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155
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156 DiffBind_ is a `Bioconductor package`_ that provides functions for processing ChIP-Seq data enriched for genomic loci where specific
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157 protein/DNA binding occurs, including peak sets identified by ChIP-Seq peak callers and
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158 aligned sequence read datasets. It is designed to work with multiple peak sets simultaneously,
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159 representing different ChIP experiments (antibodies, transcription factor and/or histone
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160 marks, experimental conditions, replicates) as well as managing the results of multiple peak
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161 callers.
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162
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163 The primary emphasis of DiffBind is on identifying sites that are differentially bound
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164 between two sample groups. It includes functions to support the processing of peak sets,
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165 including overlapping and merging peak sets, counting sequencing reads overlapping intervals
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166 in peak sets, and identifying statistically significantly differentially bound sites based on
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167 evidence of binding affinity (measured by differences in read densities). To this end it uses
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168 statistical routines developed in an RNA-Seq context (primarily the Bioconductor packages
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169 edgeR and DESeq2 ). Additionally, the package builds on Rgraphics routines to provide a
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170 set of standardized plots to aid in binding analysis.
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171
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172 The `DiffBind User Guide`_ includes a brief overview of the processing flow, followed by four sections of
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173 examples: the first focusing on the core task of obtaining differentially bound sites based on
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174 affinity data, the second working through the main plotting routines, the third discussing the
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175 use of a blocking factor, and the fourth revisiting occupancy data (peak calls) in more detail,
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176 as well as comparing the results of an occupancy-based analysis with an affinity-based one.
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177 Finally, certain technical aspects of the how these analyses are accomplished are detailed.
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178
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179 Note DiffBind requires a minimum of four samples (two groups with two replicates each).
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180
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181 .. _DiffBind: https://bioconductor.org/packages/release/bioc/html/DiffBind.html
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182 .. _`Bioconductor package`: https://bioconductor.org/packages/release/bioc/html/DiffBind.html
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183 .. _`DiffBind User Guide`: https://bioconductor.org/packages/release/bioc/vignettes/DiffBind/inst/doc/DiffBind.pdf
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184
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185 **Inputs**
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186
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187 DiffBind works primarily with peaksets, which are sets of genomic intervals representing
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188 candidate protein binding sites. Each interval consists of a chromosome, a start and end
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189 position, and usually a score of some type indicating confidence in, or strength of, the peak.
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190 Associated with each peakset are metadata relating to the experiment from which the peakset
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191 was derived. Additionally, files containing mapped sequencing reads (generally .bam files) can
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192 be associated with each peakset (one for the ChIP data, and optionally another representing
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193 a control sample)
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194
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195 **Sample Information**
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196
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197 You have to specify your sample information in the tool form above.
11cd8b1ae397 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diffbind commit affbc59222cde9be21e91fa1f9194930a070b830
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198
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199 Example:
11cd8b1ae397 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diffbind commit affbc59222cde9be21e91fa1f9194930a070b830
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200
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201 ============= ========== ========== ============= =============
11cd8b1ae397 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diffbind commit affbc59222cde9be21e91fa1f9194930a070b830
iuc
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202 **SampleID** **Tissue** **Factor** **Condition** **Replicate**
11cd8b1ae397 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diffbind commit affbc59222cde9be21e91fa1f9194930a070b830
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203 ------------- ---------- ---------- ------------- -------------
11cd8b1ae397 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diffbind commit affbc59222cde9be21e91fa1f9194930a070b830
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204 BT4741 BT474 ER Resistant 1
11cd8b1ae397 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diffbind commit affbc59222cde9be21e91fa1f9194930a070b830
iuc
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205 BT4742 BT474 ER Resistant 2
11cd8b1ae397 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diffbind commit affbc59222cde9be21e91fa1f9194930a070b830
iuc
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206 MCF71 MCF7 ER Responsive 1
11cd8b1ae397 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diffbind commit affbc59222cde9be21e91fa1f9194930a070b830
iuc
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207 MCF72 MCF7 ER Responsive 2
11cd8b1ae397 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diffbind commit affbc59222cde9be21e91fa1f9194930a070b830
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208 MCF73 MCF7 ER Responsive 3
11cd8b1ae397 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diffbind commit affbc59222cde9be21e91fa1f9194930a070b830
iuc
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209 T47D1 T47D ER Responsive 1
11cd8b1ae397 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diffbind commit affbc59222cde9be21e91fa1f9194930a070b830
iuc
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210 T47D2 T47D ER Responsive 2
11cd8b1ae397 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diffbind commit affbc59222cde9be21e91fa1f9194930a070b830
iuc
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211 MCF7r1 MCF7 ER Resistant 1
11cd8b1ae397 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diffbind commit affbc59222cde9be21e91fa1f9194930a070b830
iuc
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212 MCF7r2 MCF7 ER Resistant 2
11cd8b1ae397 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diffbind commit affbc59222cde9be21e91fa1f9194930a070b830
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213 ZR751 ZR75 ER Responsive 1
11cd8b1ae397 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diffbind commit affbc59222cde9be21e91fa1f9194930a070b830
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214 ZR752 ZR75 ER Responsive 2
11cd8b1ae397 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diffbind commit affbc59222cde9be21e91fa1f9194930a070b830
iuc
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215 ============= ========== ========== ============= =============
11cd8b1ae397 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diffbind commit affbc59222cde9be21e91fa1f9194930a070b830
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216
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217 Or provide a sample sheet tabular file such as below.
15
aefe2a771a95 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diffbind commit 10052765d6b712cf7d38356af4251fcc38a339b6-dirty
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218
20
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219 Example:
11cd8b1ae397 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diffbind commit affbc59222cde9be21e91fa1f9194930a070b830
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220
11cd8b1ae397 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diffbind commit affbc59222cde9be21e91fa1f9194930a070b830
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221 ======== ====== ====== ========== ========== ========= ==================== ========= ===================== ================= ==========
11cd8b1ae397 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diffbind commit affbc59222cde9be21e91fa1f9194930a070b830
iuc
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222 SampleID Tissue Factor Condition Treatment Replicate bamReads ControlID bamControl Peaks PeakCaller
11cd8b1ae397 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diffbind commit affbc59222cde9be21e91fa1f9194930a070b830
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223 ======== ====== ====== ========== ========== ========= ==================== ========= ===================== ================= ==========
11cd8b1ae397 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diffbind commit affbc59222cde9be21e91fa1f9194930a070b830
iuc
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224 BT4741 BT474 ER Resistant Full-Media 1 Chr18_BT474_ER_1.bam BT474c Chr18_BT474_input.bam BT474_ER_1.bed.gz bed
11cd8b1ae397 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diffbind commit affbc59222cde9be21e91fa1f9194930a070b830
iuc
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225 BT4742 BT474 ER Resistant Full-Media 2 Chr18_BT474_ER_2.bam BT474c Chr18_BT474_input.bam BT474_ER_2.bed.gz bed
11cd8b1ae397 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diffbind commit affbc59222cde9be21e91fa1f9194930a070b830
iuc
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226 MCF71 MCF7 ER Responsive Full-Media 1 Chr18_MCF7_ER_1.bam MCF7c Chr18_MCF7_input.bam MCF7_ER_1.bed.gz bed
11cd8b1ae397 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diffbind commit affbc59222cde9be21e91fa1f9194930a070b830
iuc
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227 MCF72 MCF7 ER Responsive Full-Media 2 Chr18_MCF7_ER_2.bam MCF7c Chr18_MCF7_input.bam MCF7_ER_2.bed.gz bed
11cd8b1ae397 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diffbind commit affbc59222cde9be21e91fa1f9194930a070b830
iuc
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228 MCF73 MCF7 ER Responsive Full-Media 3 Chr18_MCF7_ER_3.bam MCF7c Chr18_MCF7_input.bam MCF7_ER_3.bed.gz bed
11cd8b1ae397 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diffbind commit affbc59222cde9be21e91fa1f9194930a070b830
iuc
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229 T47D1 T47D ER Responsive Full-Media 1 Chr18_T47D_ER_1.bam T47Dc Chr18_T47D_input.bam T47D_ER_1.bed.gz bed
11cd8b1ae397 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diffbind commit affbc59222cde9be21e91fa1f9194930a070b830
iuc
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230 T47D2 T47D ER Responsive Full-Media 2 Chr18_T47D_ER_2.bam T47Dc Chr18_T47D_input.bam T47D_ER_2.bed.gz bed
11cd8b1ae397 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diffbind commit affbc59222cde9be21e91fa1f9194930a070b830
iuc
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231 MCF7r1 MCF7 ER Resistant Full-Media 1 Chr18_TAMR_ER_1.bam TAMRc Chr18_TAMR_input.bam TAMR_ER_1.bed.gz bed
11cd8b1ae397 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diffbind commit affbc59222cde9be21e91fa1f9194930a070b830
iuc
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232 MCF7r2 MCF7 ER Resistant Full-Media 2 Chr18_TAMR_ER_2.bam TAMRc Chr18_TAMR_input.bam TAMR_ER_2.bed.gz bed
11cd8b1ae397 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diffbind commit affbc59222cde9be21e91fa1f9194930a070b830
iuc
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233 ZR751 ZR75 ER Responsive Full-Media 1 Chr18_ZR75_ER_1.bam ZR75c Chr18_ZR75_input.bam ZR75_ER_1.bed.gz bed
11cd8b1ae397 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diffbind commit affbc59222cde9be21e91fa1f9194930a070b830
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234 ZR752 ZR75 ER Responsive Full-Media 2 Chr18_ZR75_ER_2.bam ZR75c Chr18_ZR75_input.bam ZR75_ER_2.bed.gz bed
11cd8b1ae397 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diffbind commit affbc59222cde9be21e91fa1f9194930a070b830
iuc
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235 ======== ====== ====== ========== ========== ========= ==================== ========= ===================== ================= ==========
11cd8b1ae397 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diffbind commit affbc59222cde9be21e91fa1f9194930a070b830
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236
15
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237
20
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238 **Peak files**
11cd8b1ae397 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diffbind commit affbc59222cde9be21e91fa1f9194930a070b830
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239
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240 Result of your Peak calling experiment in bed format, one file for each sample is required.
11cd8b1ae397 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diffbind commit affbc59222cde9be21e91fa1f9194930a070b830
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241
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242 Example:
11cd8b1ae397 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diffbind commit affbc59222cde9be21e91fa1f9194930a070b830
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243
11cd8b1ae397 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diffbind commit affbc59222cde9be21e91fa1f9194930a070b830
iuc
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244 ======= ======= ======= =============== =======
11cd8b1ae397 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diffbind commit affbc59222cde9be21e91fa1f9194930a070b830
iuc
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245 1 2 3 4 **5**
11cd8b1ae397 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diffbind commit affbc59222cde9be21e91fa1f9194930a070b830
iuc
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246 ======= ======= ======= =============== =======
11cd8b1ae397 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diffbind commit affbc59222cde9be21e91fa1f9194930a070b830
iuc
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247 chr18 215562 216063 MACS_peak_16037 56.11
11cd8b1ae397 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diffbind commit affbc59222cde9be21e91fa1f9194930a070b830
iuc
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248 chr18 311530 312105 MACS_peak_16038 222.49
11cd8b1ae397 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diffbind commit affbc59222cde9be21e91fa1f9194930a070b830
iuc
parents: 19
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249 chr18 356656 357315 MACS_peak_16039 92.06
11cd8b1ae397 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diffbind commit affbc59222cde9be21e91fa1f9194930a070b830
iuc
parents: 19
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250 chr18 371110 372092 MACS_peak_16040 123.86
11cd8b1ae397 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diffbind commit affbc59222cde9be21e91fa1f9194930a070b830
iuc
parents: 19
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251 chr18 395116 396464 MACS_peak_16041 1545.39
11cd8b1ae397 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diffbind commit affbc59222cde9be21e91fa1f9194930a070b830
iuc
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252 chr18 399014 400382 MACS_peak_16042 1835.19
11cd8b1ae397 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diffbind commit affbc59222cde9be21e91fa1f9194930a070b830
iuc
parents: 19
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253 chr18 499134 500200 MACS_peak_16043 748.32
11cd8b1ae397 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diffbind commit affbc59222cde9be21e91fa1f9194930a070b830
iuc
parents: 19
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254 chr18 503518 504552 MACS_peak_16044 818.30
11cd8b1ae397 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diffbind commit affbc59222cde9be21e91fa1f9194930a070b830
iuc
parents: 19
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255 chr18 531672 532274 MACS_peak_16045 159.30
11cd8b1ae397 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diffbind commit affbc59222cde9be21e91fa1f9194930a070b830
iuc
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256 chr18 568326 569282 MACS_peak_16046 601.11
11cd8b1ae397 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diffbind commit affbc59222cde9be21e91fa1f9194930a070b830
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257 ======= ======= ======= =============== =======
0
8d48d5591389 Uploaded
bgruening
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258
16
128584543be7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diffbind commit 78d26b3a3bbaf30d4d1367a0361618876fe69ae7
bgruening
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259 * BAM file which contains the mapped sequencing reads can be associated with each peakset
128584543be7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diffbind commit 78d26b3a3bbaf30d4d1367a0361618876fe69ae7
bgruening
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260 * Control BAM file represents a control dataset and are optional, but have to specified for all when used.
20
11cd8b1ae397 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diffbind commit affbc59222cde9be21e91fa1f9194930a070b830
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261
15
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262
20
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263 **Outputs**
0
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264
15
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bgruening
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265 As output format you can choose BED, GFF, WIG.
aefe2a771a95 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diffbind commit 10052765d6b712cf7d38356af4251fcc38a339b6-dirty
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266
20
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267 Example:
11cd8b1ae397 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diffbind commit affbc59222cde9be21e91fa1f9194930a070b830
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268
11cd8b1ae397 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diffbind commit affbc59222cde9be21e91fa1f9194930a070b830
iuc
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269 ======== ====== =======+
11cd8b1ae397 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diffbind commit affbc59222cde9be21e91fa1f9194930a070b830
iuc
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270 seqnames ranges strand Conc Conc_Resistant
11cd8b1ae397 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diffbind commit affbc59222cde9be21e91fa1f9194930a070b830
iuc
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271
11cd8b1ae397 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diffbind commit affbc59222cde9be21e91fa1f9194930a070b830
iuc
parents: 19
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272 2452 chr18 [64490686, 64491186] * | 6.36 1.39
11cd8b1ae397 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diffbind commit affbc59222cde9be21e91fa1f9194930a070b830
iuc
parents: 19
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273 1291 chr18 [34597713, 34598213] * | 5.33 0.22
11cd8b1ae397 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diffbind commit affbc59222cde9be21e91fa1f9194930a070b830
iuc
parents: 19
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274 976 chr18 [26860997, 26861497] * | 7.3 3.13
11cd8b1ae397 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diffbind commit affbc59222cde9be21e91fa1f9194930a070b830
iuc
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275 2338 chr18 [60892900, 60893400] * | 7.13 1.84
11cd8b1ae397 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diffbind commit affbc59222cde9be21e91fa1f9194930a070b830
iuc
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276 2077 chr18 [55569087, 55569587] * | 5.52 1.89
11cd8b1ae397 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diffbind commit affbc59222cde9be21e91fa1f9194930a070b830
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277
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iuc
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278 Conc_Responsive Fold p-value FDR
11cd8b1ae397 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diffbind commit affbc59222cde9be21e91fa1f9194930a070b830
iuc
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279 <numeric> <numeric> <numeric> <numeric>
11cd8b1ae397 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diffbind commit affbc59222cde9be21e91fa1f9194930a070b830
iuc
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280 2452 7 -5.61 3.57e-10 1.02e-06
11cd8b1ae397 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diffbind commit affbc59222cde9be21e91fa1f9194930a070b830
iuc
parents: 19
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281 1291 5.97 -5.75 1.1e-09 1.57e-06
11cd8b1ae397 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diffbind commit affbc59222cde9be21e91fa1f9194930a070b830
iuc
parents: 19
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282 976 7.92 -4.79 1.1e-08 1.05e-05
11cd8b1ae397 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diffbind commit affbc59222cde9be21e91fa1f9194930a070b830
iuc
parents: 19
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283 2338 7.77 -5.93 1.68e-08 1.17e-05
11cd8b1ae397 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diffbind commit affbc59222cde9be21e91fa1f9194930a070b830
iuc
parents: 19
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284 2077 6.13 -4.23 2.36e-08 1.17e-05
11cd8b1ae397 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diffbind commit affbc59222cde9be21e91fa1f9194930a070b830
iuc
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285
11cd8b1ae397 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diffbind commit affbc59222cde9be21e91fa1f9194930a070b830
iuc
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286 The value columns show the
11cd8b1ae397 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diffbind commit affbc59222cde9be21e91fa1f9194930a070b830
iuc
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287 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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288 Conc_Resistant mean concentration over the first (Resistant) group
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289 Conc_Responsive mean concentration over second (Responsive) group
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290 Fold column shows the difference in mean concentrations between the two groups (Conc_Resistant - Conc_Responsive), with a positive value indicating increased binding affinity in the Resistant group and a negative value indicating increased binding affinity in the Responsive group.
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291 p-value confidence measure for identifying these sites as differentially bound
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292 FDR a multiple testing corrected FDR p-value
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293
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294
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295 **Binding Affinity Matrix**
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296
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297 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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298 differential analysis.
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299
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300 Example:
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301
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302 ====== ====== ====== ========== ========== ========= ====== ========= ====
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303 ID Tissue Factor Condition Treatment Replicate Caller Intervals FRiP
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304 ====== ====== ====== ========== ========== ========= ====== ========= ====
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305 BT4741 BT474 ER Resistant Full-Media 1 counts 2845 0.16
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306 BT4742 BT474 ER Resistant Full-Media 2 counts 2845 0.15
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307 MCF71 MCF7 ER Responsive Full-Media 1 counts 2845 0.27
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308 MCF72 MCF7 ER Responsive Full-Media 2 counts 2845 0.17
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309 MCF73 MCF7 ER Responsive Full-Media 3 counts 2845 0.23
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310 T47D1 T47D ER Responsive Full-Media 1 counts 2845 0.10
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311 T47D2 T47D ER Responsive Full-Media 2 counts 2845 0.06
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312 MCF7r1 MCF7 ER Resistant Full-Media 1 counts 2845 0.20
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313 MCF7r2 MCF7 ER Resistant Full-Media 2 counts 2845 0.13
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314 ZR751 ZR75 ER Responsive Full-Media 1 counts 2845 0.32
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315 ZR752 ZR75 ER Responsive Full-Media 2 counts 2845 0.22
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316 ====== ====== ====== ========== ========== ========= ====== ========= ====
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317
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318
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319
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320 **More Information**
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321
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322 Generally, processing data with DiffBind involves five phases:
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323
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324 #. Reading in peaksets
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325 #. Occupancy analysis
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326 #. Counting reads
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327 #. Differential binding affinity analysis
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328 #. Plotting and reporting
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329
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330
20
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331 * **Reading in peaksets**:
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332
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333 The first step is to read in a set of peaksets and associated
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334 metadata. Peaksets are derived either from ChIP-Seq peak callers, such as MACS
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335 ([1]), or using some other criterion (e.g. genomic windows, or all the promoter regions
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336 in a genome). The easiest way to read in peaksets is using a comma-separated value
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337 (csv) sample sheet with one line for each peakset. (Spreadsheets in Excel® format, with
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338 a .xls or .xlsx suffix, are also accepted.) A single experiment can have more than
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339 one associated peakset; e.g. if multiple peak callers are used for comparison purposes
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340 each sample would have more than one line in the sample sheet. Once the peaksets
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341 are read in, a merging function finds all overlapping peaks and derives a single set of
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342 unique genomic intervals covering all the supplied peaks (a consensus peakset for the
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343 experiment).
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344
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345 * **Occupancy analysis**:
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346
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347 Peaksets, especially those generated by peak callers, provide
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348 an insight into the potential occupancy of the protein being ChIPed for at specific
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349 genomic loci. After the peaksets have been loaded, it can be useful to perform some
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350 exploratory plotting to determine how these occupancy maps agree with each other,
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351 e.g. between experimental replicates (re-doing the ChIP under the same conditions),
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352 between different peak callers on the same experiment, and within groups of samples
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353 representing a common experimental condition. DiffBind provides functions to enable
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354 overlaps to be examined, as well as functions to determine how well similar samples
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355 cluster together. Beyond quality control, the product of an occupancy analysis may be
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356 a consensus peakset, representing an overall set of candidate binding sites to be used
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357 in further analysis.
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358
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359 * **Counting reads**:
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360
20
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361 Once a consensus peakset has been derived, DiffBind can use the
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362 supplied sequence read files to count how many reads overlap each interval for each
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363 unique sample. The peaks in the consensus peakset may be re-centered and trimmed
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364 based on calculating their summits (point of greatest read overlap) in order to provide
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365 more standardized peak intervals. The final result of counting is a binding affinity matrix
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366 containing a (normalized) read count for each sample at every potential binding site.
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367 With this matrix, the samples can be re-clustered using affinity, rather than occupancy,
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368 data. The binding affinity matrix is used for QC plotting as well as for subsequent
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369 differential analysis.
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370
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371 * **Differential binding affinity analysis**:
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372
20
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373 The core functionality of DiffBind is the
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374 differential binding affinity analysis, which enables binding sites to be identified that
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375 are statistically significantly differentially bound between sample groups. To accomplish
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376 this, first a contrast (or contrasts) is established, dividing the samples into groups to
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377 be compared. Next the core analysis routines are executed, by default using DESeq2 .
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378 This will assign a p-value and FDR to each candidate binding site indicating confidence
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379 that they are differentially bound.
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380
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381 * **Plotting and reporting**:
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382
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383 Once one or more contrasts have been run, DiffBind provides
11cd8b1ae397 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diffbind commit affbc59222cde9be21e91fa1f9194930a070b830
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384 a number of functions for reporting and plotting the results. MA plots give an
11cd8b1ae397 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diffbind commit affbc59222cde9be21e91fa1f9194930a070b830
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385 overview of the results of the analysis, while correlation heatmaps and PCA plots show
11cd8b1ae397 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diffbind commit affbc59222cde9be21e91fa1f9194930a070b830
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386 how the groups cluster based on differentially bound sites. Boxplots show the distribution
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387 of reads within differentially bound sites corresponding to whether they gain or
11cd8b1ae397 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diffbind commit affbc59222cde9be21e91fa1f9194930a070b830
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388 lose affinity between the two sample groups. A reporting mechanism enables differentially
11cd8b1ae397 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diffbind commit affbc59222cde9be21e91fa1f9194930a070b830
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389 bound sites to be extracted for further processing, such as annotation, motif, and
11cd8b1ae397 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diffbind commit affbc59222cde9be21e91fa1f9194930a070b830
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390 pathway analyses.
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391
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392 **References**
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393
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394 DiffBind Authors: Rory Stark, Gordon Brown (2011)
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395 Wrapper authors: Bjoern Gruening, Pavankumar Videm
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396
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397 ]]>
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398 </help>
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399 <citations>
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400 <citation type="doi">doi:10.1038/nature10730</citation>
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401 </citations>
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402 </tool>