Mercurial > repos > iuc > macs2

annotate macs2_callpeak.xml @ 59:ea526bc73f8a draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit 30858afbdbe0223d07d2936a8469295bcbeda786
author iuc
date Mon, 15 Oct 2018 06:48:49 -0400
parents 567665ed8cdb
children 75bd115a2085
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
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1 <tool id="macs2_callpeak" name="MACS2 callpeak" version="@VERSION_STRING@.5" profile="17.09">
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2 <description>Call peaks from alignment results</description>
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3 <macros>
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4 <import>macs2_macros.xml</import>
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5 </macros>
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6 <expand macro="requirements">
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7 </expand>
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8 <expand macro="stdio" />
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9 <expand macro="version_command" />
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10 <command><![CDATA[
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11 #import re
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12
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13 @home_dir@
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14 #set $temp_stderr = 'macs2_stderr'
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15
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16 (macs2 callpeak
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17
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18 ## Treatment File(s)
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20 #if str($treatment.t_multi_select) == "Yes":
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21 -t ${ ' '.join( [ "'%s'" % $x for $x in $treatment.input_treatment_file] ) }
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22 #set identifier = re.sub('[^\w\-]', '_', str($treatment.input_treatment_file[0].element_identifier))
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23 #else
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24 -t '$treatment.input_treatment_file'
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25 #set identifier = re.sub('[^\w\-]', '_', str($treatment.input_treatment_file.element_identifier))
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26 #end if
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28 --name $identifier
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29
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30 ## Control File(s)
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32 #if str($control.c_select) == "Yes":
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33 #if str($control.c_multiple.c_multi_select) == "Yes":
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34 -c ${ ' '.join( [ "'%s'" % $x for $x in $control.c_multiple.input_control_file] ) }
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35 #else
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36 -c '$control.c_multiple.input_control_file'
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37 #end if
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38 #end if
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39
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40 --format $format
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41
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42 @effective_genome_size@
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44 ## advanced options
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46 $advanced_options.nolambda
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47 $advanced_options.to_large
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48 $advanced_options.spmr
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50 #if $advanced_options.ratio:
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51 --ratio $advanced_options.ratio
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52 #end if
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54 #if $advanced_options.slocal:
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55 --slocal $advanced_options.slocal
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56 #end if
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58 #if $advanced_options.llocal:
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59 --llocal $advanced_options.llocal
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60 #end if
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61
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62 #if $advanced_options.broad_options.broad_options_selector == "broad":
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63 --broad
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64 --broad-cutoff='${ advanced_options.broad_options.broad_cutoff }'
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65 #else
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66 $advanced_options.broad_options.call_summits
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67 #end if
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68
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69 #if str( $advanced_options.keep_dup_options.keep_dup_options_selector ) == "user":
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70 --keep-dup '${ advanced_options.keep_dup_options.user_keepdup }'
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71 #else
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72 --keep-dup '${ advanced_options.keep_dup_options.keep_dup_options_selector }'
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73 #end if
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74
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75
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76 ## With --bdg two additional output files will be generated.
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77 #if "bdg" in str($outputs).split(','):
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78 --bdg
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79 #end if
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80
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81 ## cutoff selection
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82 #if str( $cutoff_options.cutoff_options_selector ) == "qvalue":
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83 --qvalue '${ cutoff_options.qvalue }'
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84 #elif str( $cutoff_options.cutoff_options_selector ) == "pvalue":
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85 #if str($cutoff_options.pvalue).strip() != "":
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86 --pvalue '${ cutoff_options.pvalue }'
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87 #end if
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88 #end if
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90 ## model options
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91 #if $nomodel_type.nomodel_type_selector == "nomodel":
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92 --nomodel
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93 --extsize '${ nomodel_type.extsize }'
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94 --shift '${ nomodel_type.shift}'
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95 #else
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96 --mfold '${nomodel_type.mfold_lower}' '${nomodel_type.mfold_upper}'
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98 #if $nomodel_type.band_width:
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99 --bw '${nomodel_type.band_width}'
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100 #end if
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101 #end if
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102
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103 2>&1 > $temp_stderr)
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104 #if "peaks_tabular" in str($outputs).split(','):
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105 &&
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106 cp ${identifier}_peaks.xls '${ output_tabular }'
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107 #end if
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108
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109 ## run R to create pdf from model script
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110 #if $nomodel_type.nomodel_type_selector == "create_model" and "pdf" in str($outputs).split(',') and $format != "BAMPE":
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111 &&
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112 Rscript ${identifier}_model.r > ${identifier}_model.r.log
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113 #end if
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114
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115 #if 'html' in str($outputs).split(','):
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116 ## if output files exists, move them to the files_path and create a html result page linking to them
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117 &&
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118 (
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119 count=`ls -1 ${identifier}* 2>/dev/null | wc -l`;
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120 if [ \$count != 0 ];
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121 then
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122 mkdir '${ output_extra_files.files_path }' &&
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123 cp -r ${identifier}* '${ output_extra_files.files_path }' &&
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124 python '$__tool_directory__/dir2html.py'
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125 '${ output_extra_files.files_path }' $temp_stderr > '${ output_extra_files }';
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126 fi;
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127 )
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128 #end if
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129 &&
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130 exit_code_for_galaxy=\$? &&
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131 cat $temp_stderr 2>&1 &&
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132 (exit \$exit_code_for_galaxy)
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133 ]]></command>
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134 <inputs>
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135 <conditional name="treatment">
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136 <param name="t_multi_select" type="select" label="Are you pooling Treatment Files?" help="For more information, see Help section below" >
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137 <option value="No" selected="True">No</option>
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138 <option value="Yes">Yes</option>
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139 </param>
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140 <when value="No" >
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141 <param name="input_treatment_file" argument="-t" type="data" format="bam,sam,bed" label="ChIP-Seq Treatment File" />
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142 </when>
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143 <when value="Yes">
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144 <param name="input_treatment_file" argument="-t" type="data" format="bam,sam,bed" multiple="true" label="ChIP-Seq Treatment File" />
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145 </when>
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146 </conditional>
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147
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148 <conditional name="control">
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149 <param name="c_select" type="select" label="Do you have a Control File?" >
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150 <option value="Yes">Yes</option>
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151 <option value="No" selected="True">No</option>
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152 </param>
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153 <when value="Yes">
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154 <conditional name="c_multiple">
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155 <param name="c_multi_select" type="select" label="Are you pooling Control Files?" help="For more information, see Help section below" >
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156 <option value="No" selected="True">No</option>
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157 <option value="Yes">Yes</option>
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158 </param>
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159 <when value="No" >
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160 <param name="input_control_file" argument="-c" type="data" format="bam,sam,bed" label="ChIP-Seq Control File" />
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161 </when>
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162 <when value="Yes">
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163 <param name="input_control_file" argument="-c" type="data" format="bam,sam,bed" multiple="true" label="ChIP-Seq Control File" />
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164 </when>
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165 </conditional>
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166 </when>
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167 <when value="No" />
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168 </conditional>
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169
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170 <param name="format" type="select" label="Format of Input Files" help="For Paired-end BAM (BAMPE) the 'Build model step' will be ignored and the real fragments will be used for each template defined by leftmost and rightmost mapping positions (--format). Default: Single-end BAM">
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171 <option value="BAM" selected="True">Single-end BAM</option>
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172 <option value="BAMPE">Paired-end BAM</option>
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173 <option value="BED">Single-end BED</option>
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174 </param>
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175
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176 <expand macro="conditional_effective_genome_size" />
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177
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178 <conditional name="nomodel_type">
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179 <param name="nomodel_type_selector" type="select" label="Build Model">
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180 <option value="nomodel">Do not build the shifting model (--nomodel)</option>
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181 <option value="create_model" selected="true">Build the shifting model</option>
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182 </param>
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183 <when value="create_model">
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184 <param name="mfold_lower" type="integer" value="5" label="Set lower mfold bound" help="Select the lower region within MFOLD range of high confidence enrichment ratio against background to build model. Fold-enrichment in regions must be higher than lower limit (--mfold). Default: 5" />
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185 <param name="mfold_upper" type="integer" value="50" label="Set upper mfold bound" help="Select the upper region within MFOLD range of high confidence enrichment ratio against background to build model. Fold-enrichment in regions must be lower than the upper limit (--mfold). Default: 50"/>
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186 <param name="band_width" type="integer" value="300"
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187 label="Band width for picking regions to compute fragment size"
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188 help=" You can set this parameter as the medium fragment size expected from sonication or size selection (--bw). Default: 300" />
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189 </when>
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190 <when value="nomodel">
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191 <param name="extsize" type="integer" value="200" label="Set extension size" help="The arbitrary extension size in bp. When nomodel is true, MACS will use this value as fragment size to extend each read towards 3-prime; end, then pile them up. It is exactly twice the number of obsolete SHIFTSIZE. In previous language, each read is moved 5-prime-to-3-prime direction to middle of fragment by 0.5 d, then extended to both direction with 0.5 d. This is equivalent to say each read is extended towards 5-prime-to-3-prime into a d size fragment. --extsize (this option) and --shift (the option below) can be combined when necessary. See --shift option below. Default: 200 (--extsize)."/>
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192 <param name="shift" type="integer" value="0" label="Set shift size" help="(NOT the legacy --shiftsize option!) The arbitrary shift in bp. Use discretion while setting it other than default value. When NOMODEL is set, MACS will use this value to move cutting ends (5-prime) towards 5-prime-to-3-prime direction then apply EXTSIZE to extend them to fragments. When this value is negative, ends will be moved toward 3-prime-to-5-prime direction. Recommended to keep it as default 0 for ChIP-Seq datasets, or -1 * 0.5 of --extsize (option above) together with --extsize option for detecting enriched cutting loci such as certain DNAseI-Seq datasets. Note, you can't set values other than 0 if format is paired-end data (BAMPE). Default: 0 (--shift)."/>
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193 </when>
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194 </conditional>
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195
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196 <conditional name="cutoff_options">
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197 <param name="cutoff_options_selector" type="select" label="Peak detection based on" help="default uses q-value">
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198 <option value="qvalue" selected="true">q-value</option>
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199 <option value="pvalue">p-value</option>
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200 </param>
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201 <when value="pvalue">
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202 <param name="pvalue" type="float" value="" label="p-value cutoff for peak detection" help="default: not set (--pvalue)"/>
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203 </when>
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204 <when value="qvalue">
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205 <param name="qvalue" type="float" value="0.05" label="Minimum FDR (q-value) cutoff for peak detection" help="The q-value (minimum FDR) cutoff to call significant regions. Default is 0.05. For broad marks, you can try 0.05 as cutoff. Q-values are calculated from p-values using Benjamini-Hochberg procedure. (--qvalue)"/>
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206 </when>
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207 </conditional>
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208
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209 <param name="outputs" type="select" display="checkboxes" multiple="True" optional="True" label="Additional Outputs" help="PDF is only created when the model is built">
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210 <option value="peaks_tabular">Peaks as tabular file (compatible wih MultiQC)</option>
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211 <option value="summits">Peak summits</option>
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212 <option value="bdg" >Scores in bedGraph files (--bdg)</option>
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213 <option value="html">Summary page (html)</option>
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214 <option value="pdf">Plot in PDF (only available if a model is created and if BAMPE is not used)</option>
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215 </param>
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216
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217 <section name="advanced_options" title="Advanced Options">
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218 <param name="to_large" type="boolean" truevalue="--to-large" falsevalue="" checked="False" optional="True"
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219 label="When set, scale the small sample up to the bigger sample"
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220 help="By default, the bigger dataset will be scaled down towards the smaller dataset, which will lead to smaller p/qvalues and more specific results. Keep in mind that scaling down will bring down background noise more. (--to-large). Default: No"/>
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221 <param name="nolambda" type="boolean" truevalue="--nolambda" falsevalue="" checked="False" optional="True"
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222 label="Use fixed background lambda as local lambda for every peak region" help="up to 9X more time consuming (--nolambda). Default: No"/>
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223 <param name="spmr" type="boolean" truevalue="--SPMR" falsevalue="" checked="False" optional="True"
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224 label="Save signal per million reads for fragment pileup profiles"
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225 help="Requires 'Scores in bedGraph files (--bdg)' output to be selected. (--SPMR). Default: No"/>
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226 <param name="ratio" type="float" optional="True"
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227 label="When set, use a custom scaling ratio of ChIP/control (e.g. calculated using NCIS) for linear scaling"
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228 help="(--ratio) Default: ignore"/>
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229 <param name="slocal" type="integer" optional="True" label="The small nearby region in basepairs to calculate dynamic lambda"
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230 help="This is used to capture the bias near the peak summit region. Invalid if there is no control data. If you set this to 0, MACS will skip slocal lambda calculation. *Note* that MACS will always perform a d-size local lambda calculation. The final local bias should be the maximum of the lambda value from d, slocal, and llocal size windows. (--slocal). Default: 1000"/>
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231 <param name="llocal" type="integer" optional="True" label="The large nearby region in basepairs to calculate dynamic lambda"
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232 help="This is used to capture the surround bias. If you set this to 0, MACS will skip llocal lambda calculation. *Note* that MACS will always perform a d-size local lambda calculation. The final local bias should be the maximum of the lambda value from d, slocal, and llocal size windows. (--llocal) Default: 10000"/>
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233 <conditional name="broad_options">
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234 <param name="broad_options_selector" type="select"
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235 label="Composite broad regions" help="by putting nearby highly enriched regions into a broad region with loose cutoff (--broad)">
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236 <option value="nobroad" selected="true">No broad regions</option>
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237 <option value="broad">broad regions</option>
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238 </param>
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239 <when value="broad">
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240 <param name="broad_cutoff" type="float" label="Cutoff for broad region" value="0.1"
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241 help="value is either p-value or q-value as specified above (--broad-cutoff)"/>
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242 </when>
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243 <when value="nobroad">
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244 <param name="call_summits" type="boolean" truevalue="--call-summits" falsevalue="" checked="False"
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245 label="Use a more sophisticated signal processing approach to find subpeak summits in each enriched peak region"
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246 help="(--call-summits)"/>
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247 </when>
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248 </conditional>
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249 <expand macro="keep_duplicates" />
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250 </section>
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251 </inputs>
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252 <outputs>
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253 <!--callpeaks output-->
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254 <data name="output_tabular" format="tabular" default_identifier_source="treatment|input_treatment_file" label="${tool.name} on ${on_string} (Peaks in tabular format)">
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255 <filter> outputs and 'peaks_tabular' in outputs</filter>
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256 </data>
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257 <data name="output_broadpeaks" format="bed" from_work_dir="*_peaks.broadPeak" default_identifier_source="treatment|input_treatment_file" label="${tool.name} on ${on_string} (broad Peaks)">
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258 <filter>
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259 ((
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260 advanced_options['broad_options']['broad_options_selector'] == "broad"
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261 ))
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262 </filter>
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263 </data>
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264 <data name="output_gappedpeaks" format="bed" from_work_dir="*_peaks.gappedPeak" default_identifier_source="treatment|input_treatment_file" label="${tool.name} on ${on_string} (gapped Peaks)">
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265 <filter>
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266 ((
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267 advanced_options['broad_options']['broad_options_selector'] == "broad"
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268 ))
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269 </filter>
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270 </data>
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271 <data name="output_narrowpeaks" format="bed" from_work_dir="*_peaks.narrowPeak" default_identifier_source="treatment|input_treatment_file" label="${tool.name} on ${on_string} (narrow Peaks)">
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272 <filter>
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273 ((
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274 advanced_options['broad_options']['broad_options_selector'] == "nobroad"
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275 ))
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276 </filter>
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277 </data>
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278 <data name="output_summits" format="bed" from_work_dir="*_summits.bed" default_identifier_source="treatment|input_treatment_file" label="${tool.name} on ${on_string} (summits in BED)">
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279 <filter>outputs and 'summits' in outputs</filter>
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280 </data>
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281 <data name="output_plot" format="pdf" from_work_dir="*_model.pdf" default_identifier_source="treatment|input_treatment_file" label="${tool.name} on ${on_string} (plot)">
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282 <filter>
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283 ((
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284 outputs and 'pdf' in outputs and
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285 nomodel_type['nomodel_type_selector'] == "create_model" and
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286 format != "BAMPE"
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287 ))
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288 </filter>
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289 </data>
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290 <data name="output_treat_pileup" format="bedgraph" from_work_dir="*_treat_pileup.bdg" default_identifier_source="treatment|input_treatment_file" label="${tool.name} on ${on_string} (Bedgraph Treatment)">
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291 <filter>outputs and 'bdg' in outputs</filter>
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292 </data>
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293 <data name="output_control_lambda" format="bedgraph" from_work_dir="*_control_lambda.bdg" default_identifier_source="treatment|input_treatment_file" label="${tool.name} on ${on_string} (Bedgraph Control)">
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294 <filter>outputs and 'bdg' in outputs</filter>
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295 </data>
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296 <data name="output_extra_files" format="html" default_identifier_source="treatment|input_treatment_file" label="${tool.name} on ${on_string} (html report)">
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297 <filter>outputs and 'html' in outputs</filter>
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298 </data>
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299 </outputs>
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300 <tests>
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301 <test expect_num_outputs="5">
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302 <param name="input_treatment_file" value="ChIP_200K.bed" ftype="bed"/>
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303 <param name="c_select" value="Yes"/>
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304 <param name="input_control_file" value="Control_200K.bed" ftype="bed"/>
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305 <param name="format" value="BED" />
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306 <param name="cutoff_options_selector" value="qvalue"/>
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307 <param name="qvalue" value="0.05"/>
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308 <param name="band_width" value="300"/>
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309 <param name="outputs" value="peaks_tabular,bdg,html"/>
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310 <param name="effective_genome_size_options_selector" value="user_defined" />
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311 <param name="gsize" value="3300000000" />
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312 <param name="lower" value="5" />
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313 <param name="upper" value="50" />
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314 <output name="output_control_lambda" compare="contains" file="callpeak_control_part.bdg" lines_diff="1"/>
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315 <output name="output_treat_pileup" compare="contains" file="callpeak_treatment_part.bdg" lines_diff="1"/>
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316 <output name="output_tabular" compare="contains" file="callpeak_part.tabular" lines_diff="3"/>
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317 <output name="output_extra_files">
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318 <assert_contents>
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319 <has_text text="Additional output created by MACS2" />
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320 </assert_contents>
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321 </output>
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322 </test>
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323 <!-- Ensure pdf can be output -->
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324 <test expect_num_outputs="2">
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325 <param name="input_treatment_file" value="ChIP_200K.bed" ftype="bed"/>
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326 <param name="c_select" value="Yes"/>
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327 <param name="input_control_file" value="Control_200K.bed" ftype="bed"/>
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328 <param name="format" value="BED" />
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329 <param name="cutoff_options_selector" value="qvalue"/>
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330 <param name="qvalue" value="0.05"/>
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331 <param name="band_width" value="300"/>
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332 <param name="outputs" value="pdf"/>
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333 <param name="effective_genome_size_options_selector" value="user_defined" />
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334 <param name="gsize" value="3300000000" />
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335 <param name="lower" value="5" />
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336 <param name="upper" value="50" />
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337 <output name="output_plot" file="magic.pdf" ftype="pdf" compare="contains" />
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338 </test>
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339 <!-- Ensure BAMPE works -->
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340 <test expect_num_outputs="1">
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341 <param name="input_treatment_file" ftype="bam" value="bwa-mem-test1.bam"/>
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342 <param name="format" value="BAMPE" />
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343 <param name="effective_genome_size_options_selector" value="user_defined"/>
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344 <param name="gsize" value="3300000000"/>
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345 <param name="nomodel_type_selector" value="nomodel"/>
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346 <param name="nolambda" value="True"/>
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347 <!-- we select PDF as output, but since we are in BAMPE mode, this will not ignored and the expect_num_outputs stays one. -->
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348 <param name="outputs" value="pdf"/>
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349 <output name="output_narrowpeaks" file="callpeak_bampe_narrow.bed"/>
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350 </test>
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351 </tests>
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352 <help><![CDATA[
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353
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354 .. class:: infomark
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355
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356 **What it does**
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357
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358 **callpeak** is the main function of the MACS2_ package. MACS identifies enriched binding sites in ChIP-seq experiments. It captures the influence of genome complexity to evaluate the significance of enriched ChIP regions, and improves the spatial resolution of binding sites through combining the information of both sequencing tag position and orientation.
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359
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360 -----
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361
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362 **Inputs**
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363
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364 MACS can be used for ChIP-Seq data (Treatment) alone, or with a Control sample with the increase of specificity (recommended).
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365
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366 A Treatment File is the only REQUIRED parameter for MACS. The file can be in BAM or BED format and this tool will autodetect the format using the first treatment file provided as input. If you have more than one alignment file per sample, you can select to pool them above. MACS can pool files together e.g. as `-t A B C` for treatment or `-c A B C` for control.
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367
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368 Both single-end and paired-end mapping results can be input and you can specify if the data is from paired-end reads above. Paired-end mapping results can be input to MACS as a single BAM file, and just the left mate (5' end) tag will be automatically kept. However, when paired-end format (BAMPE) is specified, MACS will use the real fragments inferred from alignment results for reads pileup.
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369
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370 *Effective Genome Size*
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371
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372 PLEASE assign this parameter to fit your needs!
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373
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374 It's the mappable genome size or effective genome size which is defined as the genome size which can be sequenced. Because of the repetitive features on the chromsomes, the actual mappable genome size will be smaller than the original size, about 90% or 70% of the genome size. The default hs -- 2.7e9 is recommended for UCSC human hg18 assembly. Here are all precompiled parameters for effective genome size from the MACS2_ website:
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375
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376 hs: 2.7e9
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377 mm: 1.87e9
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378 ce: 9e7
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379 dm: 1.2e8
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380
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381 Or see the **deepTools** website for updated information on calculating `Effective Genome Size`_.
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382
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383 -----
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384
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385 **Outputs**
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386
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387 This tool produces a BED file of narrowPeaks as default output. It can also produce additional outputs, which can be selected under the **Additional Outputs** option above.
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388
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389 * **a BED file of peaks** (default)
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390 * a tabular file of peaks (compatible wih MultiQC)
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391 * a BED file of peak summits
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392 * two bedGraph files of scores, for treatment pileup and control lambda
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393 * a HTML summary page
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394 * a PDF plot (if model is built)
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395 * a BED file of broad peaks (if **Composite broad regions** is selected under Advanced Options)
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396 * a BED file of gapped peaks (if **Composite broad regions** is selected under Advanced Options)
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397
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398 **Peaks BED File**
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399
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400 The default output is the narrowPeak BED file (BED6+4 format). This contains the peak locations, together with peak summit, pvalue and qvalue. You can load it to UCSC genome browser.
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401
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402 Example:
6c9ea5f92ddb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit 4e2bb09986aebf442f2981e8d77aa512d4c86b90
iuc
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403
6c9ea5f92ddb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit 4e2bb09986aebf442f2981e8d77aa512d4c86b90
iuc
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404 ======= ========= ======= ============ ==== === ======= ======== ======= =======
6c9ea5f92ddb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit 4e2bb09986aebf442f2981e8d77aa512d4c86b90
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405 1 2 3 4 5 6 7 8 9 **10**
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8f6b37d29df5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit 586ecaebf9e6020fac2674fbda368e293d1c9bc2
iuc
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406 ======= ========= ======= ============ ==== === ======= ======== ======= =======
58
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iuc
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407 chr1 840081 840400 treat1_peak_1 69 . 4.89872 10.50944 6.91052 158
567665ed8cdb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit c9c5c4dd15aed950ed9b43a294ce6c41f5732a23
iuc
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408 chr1 919419 919785 treat1_peak_2 87 . 5.85158 12.44148 8.70936 130
567665ed8cdb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit c9c5c4dd15aed950ed9b43a294ce6c41f5732a23
iuc
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409 chr1 937220 937483 treat1_peak_3 66 . 4.87632 10.06728 6.61759 154
52
6c9ea5f92ddb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit 4e2bb09986aebf442f2981e8d77aa512d4c86b90
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410 ======= ========= ======= ============ ==== === ======= ======== ======= =======
6c9ea5f92ddb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit 4e2bb09986aebf442f2981e8d77aa512d4c86b90
iuc
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411
6c9ea5f92ddb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit 4e2bb09986aebf442f2981e8d77aa512d4c86b90
iuc
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412 Columns contain the following data:
6c9ea5f92ddb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit 4e2bb09986aebf442f2981e8d77aa512d4c86b90
iuc
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413
6c9ea5f92ddb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit 4e2bb09986aebf442f2981e8d77aa512d4c86b90
iuc
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414 * **1st**: chromosome name
6c9ea5f92ddb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit 4e2bb09986aebf442f2981e8d77aa512d4c86b90
iuc
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415 * **2nd**: start position of peak
6c9ea5f92ddb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit 4e2bb09986aebf442f2981e8d77aa512d4c86b90
iuc
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416 * **3rd**: end position of peak
6c9ea5f92ddb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit 4e2bb09986aebf442f2981e8d77aa512d4c86b90
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417 * **4th**: name of peak
6c9ea5f92ddb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit 4e2bb09986aebf442f2981e8d77aa512d4c86b90
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418 * **5th**: integer score for display in genome browser (e.g. UCSC)
6c9ea5f92ddb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit 4e2bb09986aebf442f2981e8d77aa512d4c86b90
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419 * **6th**: strand, either "." (=no strand) or "+" or "-"
6c9ea5f92ddb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit 4e2bb09986aebf442f2981e8d77aa512d4c86b90
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420 * **7th**: fold-change
6c9ea5f92ddb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit 4e2bb09986aebf442f2981e8d77aa512d4c86b90
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421 * **8th**: -log10pvalue
6c9ea5f92ddb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit 4e2bb09986aebf442f2981e8d77aa512d4c86b90
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422 * **9th**: -log10qvalue
6c9ea5f92ddb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit 4e2bb09986aebf442f2981e8d77aa512d4c86b90
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423 * **10th**: relative summit position to peak start
6c9ea5f92ddb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit 4e2bb09986aebf442f2981e8d77aa512d4c86b90
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424
6c9ea5f92ddb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit 4e2bb09986aebf442f2981e8d77aa512d4c86b90
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425
6c9ea5f92ddb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit 4e2bb09986aebf442f2981e8d77aa512d4c86b90
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426 **Peaks tabular File**
6c9ea5f92ddb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit 4e2bb09986aebf442f2981e8d77aa512d4c86b90
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427
58
567665ed8cdb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit c9c5c4dd15aed950ed9b43a294ce6c41f5732a23
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428 A tabular file which contains information about called peaks. You can open it in Excel and sort/filter using Excel functions. This file is compatible with **MultiQC**.
52
6c9ea5f92ddb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit 4e2bb09986aebf442f2981e8d77aa512d4c86b90
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429
6c9ea5f92ddb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit 4e2bb09986aebf442f2981e8d77aa512d4c86b90
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430 Example:
6c9ea5f92ddb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit 4e2bb09986aebf442f2981e8d77aa512d4c86b90
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431
6c9ea5f92ddb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit 4e2bb09986aebf442f2981e8d77aa512d4c86b90
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432 ======= ========= ======= ========== ============== ========== ================== =================== ================== =============
6c9ea5f92ddb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit 4e2bb09986aebf442f2981e8d77aa512d4c86b90
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433 **chr** **start** **end** **length** **abs_summit** **pileup** **-log10(pvalue)** **fold_enrichment** **-log10(qvalue)** **name**
6c9ea5f92ddb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit 4e2bb09986aebf442f2981e8d77aa512d4c86b90
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434 ======= ========= ======= ========== ============== ========== ================== =================== ================== =============
58
567665ed8cdb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit c9c5c4dd15aed950ed9b43a294ce6c41f5732a23
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435 chr1 840082 840400 319 840240 4.00 10.50944 4.89872 6.91052 treat1_peak_1
567665ed8cdb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit c9c5c4dd15aed950ed9b43a294ce6c41f5732a23
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436 chr1 919420 919785 366 919550 5.00 12.44148 5.85158 8.70936 treat1_peak_2
567665ed8cdb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit c9c5c4dd15aed950ed9b43a294ce6c41f5732a23
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437 chr1 937221 937483 263 937375 4.00 10.06728 4.87632 6.61759 treat1_peak_3
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6c9ea5f92ddb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit 4e2bb09986aebf442f2981e8d77aa512d4c86b90
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438 ======= ========= ======= ========== ============== ========== ================== =================== ================== =============
6c9ea5f92ddb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit 4e2bb09986aebf442f2981e8d77aa512d4c86b90
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439
6c9ea5f92ddb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit 4e2bb09986aebf442f2981e8d77aa512d4c86b90
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440 Columns contain the following data:
6c9ea5f92ddb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit 4e2bb09986aebf442f2981e8d77aa512d4c86b90
iuc
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441
6c9ea5f92ddb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit 4e2bb09986aebf442f2981e8d77aa512d4c86b90
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442 * **chr**: chromosome name
6c9ea5f92ddb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit 4e2bb09986aebf442f2981e8d77aa512d4c86b90
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443 * **start**: start position of peak
6c9ea5f92ddb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit 4e2bb09986aebf442f2981e8d77aa512d4c86b90
iuc
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444 * **end**: end position of peak
6c9ea5f92ddb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit 4e2bb09986aebf442f2981e8d77aa512d4c86b90
iuc
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445 * **length**: length of peak region
6c9ea5f92ddb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit 4e2bb09986aebf442f2981e8d77aa512d4c86b90
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446 * **abs_summit**: absolute peak summit position
6c9ea5f92ddb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit 4e2bb09986aebf442f2981e8d77aa512d4c86b90
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447 * **pileup**: pileup height at peak summit
6c9ea5f92ddb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit 4e2bb09986aebf442f2981e8d77aa512d4c86b90
iuc
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448 * **-log10(pvalue)**: -log10(pvalue) for the peak summit (e.g. pvalue =1e-10, then this value should be 10)
6c9ea5f92ddb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit 4e2bb09986aebf442f2981e8d77aa512d4c86b90
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449 * **fold_enrichment**: fold enrichment for this peak summit against random Poisson distribution with local lambda
6c9ea5f92ddb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit 4e2bb09986aebf442f2981e8d77aa512d4c86b90
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450 * **-log10(qvalue)**: -log10(qvalue) at peak summit
6c9ea5f92ddb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit 4e2bb09986aebf442f2981e8d77aa512d4c86b90
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451 * **name**: name of peak
6c9ea5f92ddb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit 4e2bb09986aebf442f2981e8d77aa512d4c86b90
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452
6c9ea5f92ddb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit 4e2bb09986aebf442f2981e8d77aa512d4c86b90
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453 *Note that these tabular file coordinates are 1-based which is different than the 0-based BED format (compare the start values in the BED and tabular Example above)*
6c9ea5f92ddb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit 4e2bb09986aebf442f2981e8d77aa512d4c86b90
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454
6c9ea5f92ddb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit 4e2bb09986aebf442f2981e8d77aa512d4c86b90
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455
6c9ea5f92ddb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit 4e2bb09986aebf442f2981e8d77aa512d4c86b90
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456 **Summits BED File**
6c9ea5f92ddb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit 4e2bb09986aebf442f2981e8d77aa512d4c86b90
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457
6c9ea5f92ddb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit 4e2bb09986aebf442f2981e8d77aa512d4c86b90
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458 A BED file which contains the peak summits locations for every peaks. The 5th column in this file is -log10qvalue, the same as in the Peaks BED file. If you want to find the motifs at the binding sites, this file is recommended. The file can be loaded directly to UCSC genome browser. Remove the beginning track line if you want to analyze it by other tools.
6c9ea5f92ddb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit 4e2bb09986aebf442f2981e8d77aa512d4c86b90
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459
6c9ea5f92ddb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit 4e2bb09986aebf442f2981e8d77aa512d4c86b90
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diff changeset
460 Example:
6c9ea5f92ddb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit 4e2bb09986aebf442f2981e8d77aa512d4c86b90
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461
53
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462 ======= ========= ======= ============ =======
52
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463 1 2 3 4 **5**
6c9ea5f92ddb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit 4e2bb09986aebf442f2981e8d77aa512d4c86b90
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464 ======= ========= ======= ============ =======
58
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465 chr1 840239 840240 treat1_peak_1 6.91052
567665ed8cdb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit c9c5c4dd15aed950ed9b43a294ce6c41f5732a23
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466 chr1 919549 919550 treat1_peak_2 8.70936
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467 chr1 937374 937375 treat1_peak_3 6.61759
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468 ======= ========= ======= ============ =======
6c9ea5f92ddb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit 4e2bb09986aebf442f2981e8d77aa512d4c86b90
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469
6c9ea5f92ddb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit 4e2bb09986aebf442f2981e8d77aa512d4c86b90
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470 Columns contain the following data:
6c9ea5f92ddb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit 4e2bb09986aebf442f2981e8d77aa512d4c86b90
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471
6c9ea5f92ddb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit 4e2bb09986aebf442f2981e8d77aa512d4c86b90
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472 * **1st**: chromosome name
6c9ea5f92ddb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit 4e2bb09986aebf442f2981e8d77aa512d4c86b90
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473 * **2nd**: start position of peak
6c9ea5f92ddb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit 4e2bb09986aebf442f2981e8d77aa512d4c86b90
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474 * **3rd**: end position of peak
6c9ea5f92ddb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit 4e2bb09986aebf442f2981e8d77aa512d4c86b90
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475 * **4th**: name of peak
6c9ea5f92ddb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit 4e2bb09986aebf442f2981e8d77aa512d4c86b90
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476 * **5th**: -log10qvalue
6c9ea5f92ddb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit 4e2bb09986aebf442f2981e8d77aa512d4c86b90
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477
6c9ea5f92ddb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit 4e2bb09986aebf442f2981e8d77aa512d4c86b90
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478
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479 **BedGraph Files**
6c9ea5f92ddb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit 4e2bb09986aebf442f2981e8d77aa512d4c86b90
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480
6c9ea5f92ddb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit 4e2bb09986aebf442f2981e8d77aa512d4c86b90
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481 MACS2 will output two kinds of bedGraph files if the --bdg option is selected under the Additional Outputs option above, which contain the scores for the treatment fragment pileup and control local lambda, respectively. BedGraph files can be imported into genome browsers, such as UCSC genome browser, or be converted into even smaller bigWig files. For more information on bedGraphs, see the `UCSC website here`_.
6c9ea5f92ddb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit 4e2bb09986aebf442f2981e8d77aa512d4c86b90
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482
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483
6c9ea5f92ddb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit 4e2bb09986aebf442f2981e8d77aa512d4c86b90
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484 Example:
6c9ea5f92ddb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit 4e2bb09986aebf442f2981e8d77aa512d4c86b90
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485
6c9ea5f92ddb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit 4e2bb09986aebf442f2981e8d77aa512d4c86b90
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486 **Treatment pileup file**
6c9ea5f92ddb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit 4e2bb09986aebf442f2981e8d77aa512d4c86b90
iuc
parents: 51
diff changeset
487
6c9ea5f92ddb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit 4e2bb09986aebf442f2981e8d77aa512d4c86b90
iuc
parents: 51
diff changeset
488 ======= ========= ======= =======
6c9ea5f92ddb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit 4e2bb09986aebf442f2981e8d77aa512d4c86b90
iuc
parents: 51
diff changeset
489 1 2 3 **4**
6c9ea5f92ddb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit 4e2bb09986aebf442f2981e8d77aa512d4c86b90
iuc
parents: 51
diff changeset
490 ======= ========= ======= =======
6c9ea5f92ddb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit 4e2bb09986aebf442f2981e8d77aa512d4c86b90
iuc
parents: 51
diff changeset
491 chr1 840146 840147 3.00000
6c9ea5f92ddb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit 4e2bb09986aebf442f2981e8d77aa512d4c86b90
iuc
parents: 51
diff changeset
492 chr1 840147 840332 4.00000
6c9ea5f92ddb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit 4e2bb09986aebf442f2981e8d77aa512d4c86b90
iuc
parents: 51
diff changeset
493 chr1 840332 840335 3.00000
6c9ea5f92ddb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit 4e2bb09986aebf442f2981e8d77aa512d4c86b90
iuc
parents: 51
diff changeset
494 ======= ========= ======= =======
6c9ea5f92ddb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit 4e2bb09986aebf442f2981e8d77aa512d4c86b90
iuc
parents: 51
diff changeset
495
6c9ea5f92ddb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit 4e2bb09986aebf442f2981e8d77aa512d4c86b90
iuc
parents: 51
diff changeset
496
6c9ea5f92ddb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit 4e2bb09986aebf442f2981e8d77aa512d4c86b90
iuc
parents: 51
diff changeset
497 **Control lambda file**
6c9ea5f92ddb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit 4e2bb09986aebf442f2981e8d77aa512d4c86b90
iuc
parents: 51
diff changeset
498
6c9ea5f92ddb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit 4e2bb09986aebf442f2981e8d77aa512d4c86b90
iuc
parents: 51
diff changeset
499 ======= ========= ======= =======
6c9ea5f92ddb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit 4e2bb09986aebf442f2981e8d77aa512d4c86b90
iuc
parents: 51
diff changeset
500 1 2 3 **4**
6c9ea5f92ddb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit 4e2bb09986aebf442f2981e8d77aa512d4c86b90
iuc
parents: 51
diff changeset
501 ======= ========= ======= =======
6c9ea5f92ddb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit 4e2bb09986aebf442f2981e8d77aa512d4c86b90
iuc
parents: 51
diff changeset
502 chr1 800953 801258 0.02536
6c9ea5f92ddb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit 4e2bb09986aebf442f2981e8d77aa512d4c86b90
iuc
parents: 51
diff changeset
503 chr1 801258 801631 0.25364
6c9ea5f92ddb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit 4e2bb09986aebf442f2981e8d77aa512d4c86b90
iuc
parents: 51
diff changeset
504 chr1 801631 801885 0.99858
6c9ea5f92ddb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit 4e2bb09986aebf442f2981e8d77aa512d4c86b90
iuc
parents: 51
diff changeset
505 ======= ========= ======= =======
6c9ea5f92ddb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit 4e2bb09986aebf442f2981e8d77aa512d4c86b90
iuc
parents: 51
diff changeset
506
6c9ea5f92ddb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit 4e2bb09986aebf442f2981e8d77aa512d4c86b90
iuc
parents: 51
diff changeset
507 Columns contain the following data:
6c9ea5f92ddb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit 4e2bb09986aebf442f2981e8d77aa512d4c86b90
iuc
parents: 51
diff changeset
508
6c9ea5f92ddb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit 4e2bb09986aebf442f2981e8d77aa512d4c86b90
iuc
parents: 51
diff changeset
509 * **1st**: chromosome name
6c9ea5f92ddb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit 4e2bb09986aebf442f2981e8d77aa512d4c86b90
iuc
parents: 51
diff changeset
510 * **2nd**: start position of peak
6c9ea5f92ddb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit 4e2bb09986aebf442f2981e8d77aa512d4c86b90
iuc
parents: 51
diff changeset
511 * **3rd**: end position of peak
6c9ea5f92ddb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit 4e2bb09986aebf442f2981e8d77aa512d4c86b90
iuc
parents: 51
diff changeset
512 * **4th**: treatment pileup score or control local lambda score
6c9ea5f92ddb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit 4e2bb09986aebf442f2981e8d77aa512d4c86b90
iuc
parents: 51
diff changeset
513
6c9ea5f92ddb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit 4e2bb09986aebf442f2981e8d77aa512d4c86b90
iuc
parents: 51
diff changeset
514
6c9ea5f92ddb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit 4e2bb09986aebf442f2981e8d77aa512d4c86b90
iuc
parents: 51
diff changeset
515 **Broad peaks File**
6c9ea5f92ddb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit 4e2bb09986aebf442f2981e8d77aa512d4c86b90
iuc
parents: 51
diff changeset
516
6c9ea5f92ddb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit 4e2bb09986aebf442f2981e8d77aa512d4c86b90
iuc
parents: 51
diff changeset
517 If the broad option (--broad) is selected unded Advanced Options above, MACS2 will output a broadPeaks file. When this flag is on, MACS will try to composite broad regions in BED12 ( a gene-model-like format ) by putting nearby highly enriched regions into a broad region with loose cutoff. The broad region is controlled by another cutoff through --broad-cutoff. The maximum length of broad region length is 4 times of d from MACS. The broad peaks file is in BED6+3 format which is similar to the narrowPeak file, except for missing the 10th column for annotating peak summits.
6c9ea5f92ddb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit 4e2bb09986aebf442f2981e8d77aa512d4c86b90
iuc
parents: 51
diff changeset
518
6c9ea5f92ddb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit 4e2bb09986aebf442f2981e8d77aa512d4c86b90
iuc
parents: 51
diff changeset
519 Example:
6c9ea5f92ddb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit 4e2bb09986aebf442f2981e8d77aa512d4c86b90
iuc
parents: 51
diff changeset
520
53
8f6b37d29df5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit 586ecaebf9e6020fac2674fbda368e293d1c9bc2
iuc
parents: 52
diff changeset
521 ======= ========= ======= ============ ==== === ======= ======= =======
52
6c9ea5f92ddb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit 4e2bb09986aebf442f2981e8d77aa512d4c86b90
iuc
parents: 51
diff changeset
522 1 2 3 4 5 6 7 8 9
53
8f6b37d29df5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit 586ecaebf9e6020fac2674fbda368e293d1c9bc2
iuc
parents: 52
diff changeset
523 ======= ========= ======= ============ ==== === ======= ======= =======
58
567665ed8cdb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit c9c5c4dd15aed950ed9b43a294ce6c41f5732a23
iuc
parents: 57
diff changeset
524 chr1 840081 840400 treat1_peak_1 52 . 4.08790 8.57605 5.21506
567665ed8cdb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit c9c5c4dd15aed950ed9b43a294ce6c41f5732a23
iuc
parents: 57
diff changeset
525 chr1 919419 919785 treat1_peak_2 56 . 4.37270 8.90436 5.60462
567665ed8cdb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit c9c5c4dd15aed950ed9b43a294ce6c41f5732a23
iuc
parents: 57
diff changeset
526 chr1 937220 937483 treat1_peak_3 48 . 4.02343 8.06676 4.86861
53
8f6b37d29df5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit 586ecaebf9e6020fac2674fbda368e293d1c9bc2
iuc
parents: 52
diff changeset
527 ======= ========= ======= ============ ==== === ======= ======= =======
52
6c9ea5f92ddb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit 4e2bb09986aebf442f2981e8d77aa512d4c86b90
iuc
parents: 51
diff changeset
528
6c9ea5f92ddb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit 4e2bb09986aebf442f2981e8d77aa512d4c86b90
iuc
parents: 51
diff changeset
529
6c9ea5f92ddb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit 4e2bb09986aebf442f2981e8d77aa512d4c86b90
iuc
parents: 51
diff changeset
530 Columns contain the following data:
6c9ea5f92ddb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit 4e2bb09986aebf442f2981e8d77aa512d4c86b90
iuc
parents: 51
diff changeset
531
6c9ea5f92ddb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit 4e2bb09986aebf442f2981e8d77aa512d4c86b90
iuc
parents: 51
diff changeset
532 * **1st**: chromosome name
6c9ea5f92ddb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit 4e2bb09986aebf442f2981e8d77aa512d4c86b90
iuc
parents: 51
diff changeset
533 * **2nd**: start position of peak
6c9ea5f92ddb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit 4e2bb09986aebf442f2981e8d77aa512d4c86b90
iuc
parents: 51
diff changeset
534 * **3rd**: end position of peak
6c9ea5f92ddb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit 4e2bb09986aebf442f2981e8d77aa512d4c86b90
iuc
parents: 51
diff changeset
535 * **4th**: name of peak
6c9ea5f92ddb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit 4e2bb09986aebf442f2981e8d77aa512d4c86b90
iuc
parents: 51
diff changeset
536 * **5th**: integer score for display in genome browser (e.g. UCSC)
6c9ea5f92ddb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit 4e2bb09986aebf442f2981e8d77aa512d4c86b90
iuc
parents: 51
diff changeset
537 * **6th**: strand, either "." (=no strand) or "+" or "-"
6c9ea5f92ddb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit 4e2bb09986aebf442f2981e8d77aa512d4c86b90
iuc
parents: 51
diff changeset
538 * **7th**: fold-change
6c9ea5f92ddb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit 4e2bb09986aebf442f2981e8d77aa512d4c86b90
iuc
parents: 51
diff changeset
539 * **8th**: -log10pvalue
6c9ea5f92ddb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit 4e2bb09986aebf442f2981e8d77aa512d4c86b90
iuc
parents: 51
diff changeset
540 * **9th**: -log10qvalue
6c9ea5f92ddb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit 4e2bb09986aebf442f2981e8d77aa512d4c86b90
iuc
parents: 51
diff changeset
541
6c9ea5f92ddb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit 4e2bb09986aebf442f2981e8d77aa512d4c86b90
iuc
parents: 51
diff changeset
542
6c9ea5f92ddb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit 4e2bb09986aebf442f2981e8d77aa512d4c86b90
iuc
parents: 51
diff changeset
543 **Gapped peaks File**
6c9ea5f92ddb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit 4e2bb09986aebf442f2981e8d77aa512d4c86b90
iuc
parents: 51
diff changeset
544
6c9ea5f92ddb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit 4e2bb09986aebf442f2981e8d77aa512d4c86b90
iuc
parents: 51
diff changeset
545 If the broad option (--broad) is selected unded Advanced Options above, MACS2 will also output a gappedPeaks file. The gappedPeak file is in BED12+3 format and contains both the broad region and narrow peaks. The file can be loaded directly to UCSC genome browser.
6c9ea5f92ddb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit 4e2bb09986aebf442f2981e8d77aa512d4c86b90
iuc
parents: 51
diff changeset
546
6c9ea5f92ddb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit 4e2bb09986aebf442f2981e8d77aa512d4c86b90
iuc
parents: 51
diff changeset
547 Example:
6c9ea5f92ddb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit 4e2bb09986aebf442f2981e8d77aa512d4c86b90
iuc
parents: 51
diff changeset
548
6c9ea5f92ddb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit 4e2bb09986aebf442f2981e8d77aa512d4c86b90
iuc
parents: 51
diff changeset
549 ======= ========= ======= ============ ==== === ======= ======= === === === === ======= ======= =======
6c9ea5f92ddb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit 4e2bb09986aebf442f2981e8d77aa512d4c86b90
iuc
parents: 51
diff changeset
550 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15
6c9ea5f92ddb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit 4e2bb09986aebf442f2981e8d77aa512d4c86b90
iuc
parents: 51
diff changeset
551 ======= ========= ======= ============ ==== === ======= ======= === === === === ======= ======= =======
58
567665ed8cdb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit c9c5c4dd15aed950ed9b43a294ce6c41f5732a23
iuc
parents: 57
diff changeset
552 chr1 840081 840400 treat1_peak_1 52 . 840081 840400 0 1 319 0 4.08790 8.57605 5.21506
567665ed8cdb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit c9c5c4dd15aed950ed9b43a294ce6c41f5732a23
iuc
parents: 57
diff changeset
553 chr1 919419 919785 treat1_peak_2 56 . 919419 919785 0 1 366 0 4.37270 8.90436 5.60462
567665ed8cdb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit c9c5c4dd15aed950ed9b43a294ce6c41f5732a23
iuc
parents: 57
diff changeset
554 chr1 937220 937483 treat1_peak_3 48 . 937220 937483 0 1 263 0 4.02343 8.06676 4.86861
52
6c9ea5f92ddb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit 4e2bb09986aebf442f2981e8d77aa512d4c86b90
iuc
parents: 51
diff changeset
555 ======= ========= ======= ============ ==== === ======= ======= === === === === ======= ======= =======
6c9ea5f92ddb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit 4e2bb09986aebf442f2981e8d77aa512d4c86b90
iuc
parents: 51
diff changeset
556
6c9ea5f92ddb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit 4e2bb09986aebf442f2981e8d77aa512d4c86b90
iuc
parents: 51
diff changeset
557 Columns contain the following data:
6c9ea5f92ddb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit 4e2bb09986aebf442f2981e8d77aa512d4c86b90
iuc
parents: 51
diff changeset
558
6c9ea5f92ddb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit 4e2bb09986aebf442f2981e8d77aa512d4c86b90
iuc
parents: 51
diff changeset
559 * **1st**: chromosome name
6c9ea5f92ddb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit 4e2bb09986aebf442f2981e8d77aa512d4c86b90
iuc
parents: 51
diff changeset
560 * **2nd**: start position of peak
6c9ea5f92ddb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit 4e2bb09986aebf442f2981e8d77aa512d4c86b90
iuc
parents: 51
diff changeset
561 * **3rd**: end position of peak
6c9ea5f92ddb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit 4e2bb09986aebf442f2981e8d77aa512d4c86b90
iuc
parents: 51
diff changeset
562 * **4th**: name of peak
6c9ea5f92ddb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit 4e2bb09986aebf442f2981e8d77aa512d4c86b90
iuc
parents: 51
diff changeset
563 * **5th**: 10*-log10qvalue, to be more compatible to show grey levels on UCSC browser
6c9ea5f92ddb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit 4e2bb09986aebf442f2981e8d77aa512d4c86b90
iuc
parents: 51
diff changeset
564 * **6th**: strand, either "." (=no strand) or "+" or "-"
53
8f6b37d29df5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit 586ecaebf9e6020fac2674fbda368e293d1c9bc2
iuc
parents: 52
diff changeset
565 * **7th**: start of the first narrow peak in the region
52
6c9ea5f92ddb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit 4e2bb09986aebf442f2981e8d77aa512d4c86b90
iuc
parents: 51
diff changeset
566 * **8th**: end of the peak
53
8f6b37d29df5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit 586ecaebf9e6020fac2674fbda368e293d1c9bc2
iuc
parents: 52
diff changeset
567 * **9th**: RGB color key, default colour is 0
52
6c9ea5f92ddb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit 4e2bb09986aebf442f2981e8d77aa512d4c86b90
iuc
parents: 51
diff changeset
568 * **10th**: number of blocks, including the starting 1bp and ending 1bp of broad regions
6c9ea5f92ddb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit 4e2bb09986aebf442f2981e8d77aa512d4c86b90
iuc
parents: 51
diff changeset
569 * **11th**: length of each block, comma-separated values if multiple
6c9ea5f92ddb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit 4e2bb09986aebf442f2981e8d77aa512d4c86b90
iuc
parents: 51
diff changeset
570 * **12th**: start of each block, comma-separated values if multiple
53
8f6b37d29df5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit 586ecaebf9e6020fac2674fbda368e293d1c9bc2
iuc
parents: 52
diff changeset
571 * **13th**: fold-change
8f6b37d29df5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit 586ecaebf9e6020fac2674fbda368e293d1c9bc2
iuc
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572 * **14th**: -log10pvalue
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573 * **15th**: -log10qvalue
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575 -----
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576
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577 **More Information**
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578
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579 MACS2 performs the following analysis steps:
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580
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581 * Artificially extends reads to expected fragment length, and generates coverage map along genome.
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582 * Assumes background reads are Poisson distributed. Mean of the Poisson is locally variable and is estimated from control experiment (if available) in 5Kbp or 10Kbp around examined location.
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583 * For a given location, asks do we see more reads than we would have expected from the Poisson (p < 0.00005)? If Yes, MACS2 calls a peak.
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584
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585
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586 **Tips of fine-tuning peak calling**
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587
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588 Check out these other MACS2 tools:
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589
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590 * **MACS2 bdgcmp** can be used on the callpeak bedGraph files or bedGraph files from other resources to calculate score track.
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591 * **MACS2 bdgpeakcall** can be used on the file generated from bdgcmp or bedGraph file from other resources to call peaks with given cutoff, maximum-gap between nearby mergable peaks and minimum length of peak. bdgbroadcall works similarly to bdgpeakcall, however it will output a broad peaks file in BED12 format.
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592 * Differential calling tool **MACS2 bdgdiff**, can be used on 4 bedGraph files which are scores between treatment 1 and control 1, treatment 2 and control 2, treatment 1 and treatment 2, treatment 2 and treatment 1. It will output the consistent and unique sites according to parameter settings for minimum length, maximum gap and cutoff.
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593
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594 .. class:: warningmark
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595
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596 If MACS2 fails, it is usually because it cannot build the model for peaks. You may want to extend **mfold** range by increasing the upper bound or play with **Build model** options. For more information, see the MACS2_ website.
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597
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598 .. _MACS2: https://github.com/taoliu/MACS
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599 .. _`Effective Genome Size`: http://deeptools.readthedocs.io/en/latest/content/feature/effectiveGenomeSize.html
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600 .. _`UCSC website here`: https://genome.ucsc.edu/goldenPath/help/bedgraph.html
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601
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602 @citation@
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603 ]]></help>
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604 <expand macro="citations" />
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605 </tool>