Mercurial > repos > iuc > macs2

annotate macs2_callpeak.xml @ 12:38769345062e draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit 09ef7ee96fadeef22273029ea23d1e140ce96737
author iuc
date Thu, 22 Mar 2018 09:43:37 -0400
parents cb785e26207c
children 01cded2297b7
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38769345062e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit 09ef7ee96fadeef22273029ea23d1e140ce96737
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1 <tool id="macs2_callpeak" name="MACS2 callpeak" version="@VERSION_STRING@.3" 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 @home_dir@
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12
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13 #set $temp_stderr = 'macs2_stderr'
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14 (macs2 callpeak
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16 --name 'MACS2'
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18 ## Treatment File(s)
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20 #if str($treatment.t_multi_select) == "Yes":
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21 -t ${ ' '.join( [ "'%s'" % $x for $x in $treatment.input_treatment_file] ) }
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22 #else
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23 -t '$treatment.input_treatment_file'
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24 #end if
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25
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26 ## Control File(s)
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28 #if str($control.c_select) == "Yes":
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29 #if str($control.c_multiple.c_multi_select) == "Yes":
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30 -c ${ ' '.join( [ "'%s'" % $x for $x in $control.c_multiple.input_control_file] ) }
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31 #else
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32 -c '$control.c_multiple.input_control_file'
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33 #end if
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34 #end if
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35
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36 --format $format
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37
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38 @effective_genome_size@
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39
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40 ## advanced options
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42 $advanced_options.nolambda
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43 $advanced_options.to_large
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45 #if $advanced_options.ratio:
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46 --ratio $advanced_options.ratio
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47 #end if
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49 #if $advanced_options.slocal:
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50 --slocal $advanced_options.slocal
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51 #end if
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53 #if $advanced_options.llocal:
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54 --llocal $advanced_options.llocal
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55 #end if
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56
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57 #if $advanced_options.broad_options.broad_options_selector == "broad":
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58 --broad
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59 --broad-cutoff='${ advanced_options.broad_options.broad_cutoff }'
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60 #else
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61 $advanced_options.broad_options.call_summits
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62 #end if
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63
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64 #if str( $advanced_options.keep_dup_options.keep_dup_options_selector ) == "user":
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65 --keep-dup '${ advanced_options.keep_dup_options.user_keepdup }'
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66 #else
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67 --keep-dup '${ advanced_options.keep_dup_options.keep_dup_options_selector }'
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68 #end if
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69
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70
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71 ## With --bdg two additional output files will be generated.
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72 #if "bdg" in str($outputs).split(','):
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73 --bdg
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74 #end if
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75
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76 ## cutoff selection
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77 #if str( $cutoff_options.cutoff_options_selector ) == "qvalue":
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78 --qvalue '${ cutoff_options.qvalue }'
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79 #elif str( $cutoff_options.cutoff_options_selector ) == "pvalue":
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80 #if str($cutoff_options.pvalue).strip() != "":
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81 --pvalue '${ cutoff_options.pvalue }'
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82 #end if
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83 #end if
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84
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85 ## model options
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86 #if $nomodel_type.nomodel_type_selector == "nomodel":
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87 --nomodel
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88 --extsize '${ nomodel_type.extsize }'
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89 --shift '${ nomodel_type.shift}'
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90 #else
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91 --mfold '${nomodel_type.mfold_lower}' '${nomodel_type.mfold_upper}'
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93 #if $nomodel_type.band_width:
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94 --bw '${nomodel_type.band_width}'
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95 #end if
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96 #end if
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97
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98 2>&1 > $temp_stderr)
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99 #if "peaks_tabular" in str($outputs).split(','):
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100 &&
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101 cp MACS2_peaks.xls '${ output_tabular }'
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102 #end if
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103
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104 ## run R to create pdf from model script
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105 #if $nomodel_type.nomodel_type_selector == "create_model" and "pdf" in str($outputs).split(',') and $format != "BAMPE":
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106 &&
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107 Rscript MACS2_model.r > MACS2_model.r.log
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108 #end if
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109
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110 #if 'html' in str($outputs).split(','):
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111 ## if output files exists, move them to the files_path and create a html result page linking to them
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112 &&
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113 (
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114 count=`ls -1 MACS2* 2>/dev/null | wc -l`;
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115 if [ \$count != 0 ];
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116 then
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117 mkdir '${ output_extra_files.files_path }' &&
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118 cp -r MACS2* '${ output_extra_files.files_path }' &&
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119 python '$__tool_directory__/dir2html.py'
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120 '${ output_extra_files.files_path }' $temp_stderr > '${ output_extra_files }';
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121 fi;
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122 )
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123 #end if
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124 &&
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125 exit_code_for_galaxy=\$? &&
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126 cat $temp_stderr 2>&1 &&
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127 (exit \$exit_code_for_galaxy)
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128 ]]></command>
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129 <inputs>
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130 <conditional name="treatment">
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131 <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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132 <option value="No" selected="True">No</option>
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133 <option value="Yes">Yes</option>
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134 </param>
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135 <when value="No" >
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136 <param name="input_treatment_file" argument="-t" type="data" format="bam,sam,bed" label="ChIP-Seq Treatment File" />
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137 </when>
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138 <when value="Yes">
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139 <param name="input_treatment_file" argument="-t" type="data" format="bam,sam,bed" multiple="true" label="ChIP-Seq Treatment File" />
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140 </when>
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141 </conditional>
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142
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143 <conditional name="control">
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144 <param name="c_select" type="select" label="Do you have a Control File?" >
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145 <option value="Yes">Yes</option>
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146 <option value="No" selected="True">No</option>
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147 </param>
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148 <when value="Yes">
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149 <conditional name="c_multiple">
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150 <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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151 <option value="No" selected="True">No</option>
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152 <option value="Yes">Yes</option>
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153 </param>
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154 <when value="No" >
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155 <param name="input_control_file" argument="-c" type="data" format="bam,sam,bed" label="ChIP-Seq Control File" />
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156 </when>
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157 <when value="Yes">
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158 <param name="input_control_file" argument="-c" type="data" format="bam,sam,bed" multiple="true" label="ChIP-Seq Control File" />
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159 </when>
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160 </conditional>
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161 </when>
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162 <when value="No" />
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163 </conditional>
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164
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165 <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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166 <option value="BAM" selected="True">Single-end BAM</option>
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167 <option value="BAMPE">Paired-end BAM</option>
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168 <option value="BED">Single-end BED</option>
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169 </param>
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170
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171 <expand macro="conditional_effective_genome_size" />
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172
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173 <conditional name="nomodel_type">
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174 <param name="nomodel_type_selector" type="select" label="Build Model">
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175 <option value="nomodel">Do not build the shifting model (--nomodel)</option>
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176 <option value="create_model" selected="true">Build the shifting model</option>
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177 </param>
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178 <when value="create_model">
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179 <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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180 <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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181 <param name="band_width" type="integer" value="300"
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182 label="Band width for picking regions to compute fragment size"
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183 help=" You can set this parameter as the medium fragment size expected from sonication or size selection (--bw). Default: 300" />
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184 </when>
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185 <when value="nomodel">
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186 <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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187 <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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188 </when>
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189 </conditional>
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190
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191 <conditional name="cutoff_options">
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192 <param name="cutoff_options_selector" type="select" label="Peak detection based on" help="default uses q-value">
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193 <option value="qvalue" selected="true">q-value</option>
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194 <option value="pvalue">p-value</option>
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195 </param>
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196 <when value="pvalue">
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197 <param name="pvalue" type="float" value="" label="p-value cutoff for peak detection" help="default: not set (--pvalue)"/>
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198 </when>
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199 <when value="qvalue">
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200 <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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201 </when>
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202 </conditional>
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203
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204 <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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205 <option value="peaks_tabular">Peaks as tabular file</option>
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206 <option value="summits">Peak summits</option>
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207 <option value="bdg" >Scores in bedGraph files (--bdg)</option>
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208 <option value="html">Summary page (html)</option>
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209 <option value="pdf">Plot in PDF (only available if a model is created and if BAMPE is not used)</option>
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210 </param>
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211
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212 <section name="advanced_options" title="Advanced Options">
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213 <param name="to_large" type="boolean" truevalue="--to-large" falsevalue="" checked="False" optional="True"
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214 label="When set, scale the small sample up to the bigger sample"
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215 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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216 <param name="nolambda" type="boolean" truevalue="--nolambda" falsevalue="" checked="False" optional="True"
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217 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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218 <param name="ratio" type="float" optional="True"
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219 label="When set, use a custom scaling ratio of ChIP/control (e.g. calculated using NCIS) for linear scaling"
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220 help="(--ratio) Default: ignore"/>
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221 <param name="slocal" type="integer" optional="True" label="The small nearby region in basepairs to calculate dynamic lambda"
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222 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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223 <param name="llocal" type="integer" optional="True" label="The large nearby region in basepairs to calculate dynamic lambda"
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224 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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225 <conditional name="broad_options">
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226 <param name="broad_options_selector" type="select"
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227 label="Composite broad regions" help="by putting nearby highly enriched regions into a broad region with loose cutoff (--broad)">
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228 <option value="nobroad" selected="true">No broad regions</option>
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229 <option value="broad">broad regions</option>
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230 </param>
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231 <when value="broad">
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232 <param name="broad_cutoff" type="float" label="Cutoff for broad region" value="0.1"
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233 help="value is either p-value or q-value as specified above (--broad-cutoff)"/>
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234 </when>
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235 <when value="nobroad">
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236 <param name="call_summits" type="boolean" truevalue="--call-summits" falsevalue="" checked="False"
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237 label="Use a more sophisticated signal processing approach to find subpeak summits in each enriched peak region"
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238 help="(--call-summits)"/>
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239 </when>
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240 </conditional>
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241 <expand macro="keep_duplicates" />
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242 </section>
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243 </inputs>
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244 <outputs>
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245 <!--callpeaks output-->
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246 <data name="output_tabular" format="tabular" default_identifier_source="input_treatment_file" label="${tool.name} on ${on_string} (Peaks in tabular format)">
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247 <filter> outputs and 'peaks_tabular' in outputs</filter>
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248 </data>
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249 <data name="output_broadpeaks" format="bed" from_work_dir="MACS2_peaks.broadPeak" default_identifier_source="input_treatment_file" label="${tool.name} on ${on_string} (broad Peaks)">
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250 <filter>
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251 ((
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252 advanced_options['broad_options']['broad_options_selector'] == "broad"
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253 ))
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254 </filter>
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255 </data>
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256 <data name="output_gappedpeaks" format="bed" from_work_dir="MACS2_peaks.gappedPeak" default_identifier_source="input_treatment_file" label="${tool.name} on ${on_string} (gapped Peaks)">
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257 <filter>
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258 ((
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259 advanced_options['broad_options']['broad_options_selector'] == "broad"
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260 ))
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261 </filter>
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262 </data>
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263 <data name="output_narrowpeaks" format="bed" from_work_dir="MACS2_peaks.narrowPeak" default_identifier_source="input_treatment_file" label="${tool.name} on ${on_string} (narrow Peaks)">
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264 <filter>
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265 ((
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266 advanced_options['broad_options']['broad_options_selector'] == "nobroad"
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267 ))
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268 </filter>
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269 </data>
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270 <data name="output_summits" format="bed" from_work_dir="MACS2_summits.bed" default_identifier_source="input_treatment_file" label="${tool.name} on ${on_string} (summits in BED)">
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271 <filter>outputs and 'summits' in outputs</filter>
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272 </data>
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273 <data name="output_plot" format="pdf" from_work_dir="MACS2_model.pdf" default_identifier_source="input_treatment_file" label="${tool.name} on ${on_string} (plot)">
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274 <filter>
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275 ((
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276 outputs and 'pdf' in outputs and
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277 nomodel_type['nomodel_type_selector'] == "create_model" and
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278 format != "BAMPE"
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279 ))
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280 </filter>
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281 </data>
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282 <data name="output_treat_pileup" format="bedgraph" from_work_dir="MACS2_treat_pileup.bdg" default_identifier_source="input_treatment_file" label="${tool.name} on ${on_string} (Bedgraph Treatment)">
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283 <filter>outputs and 'bdg' in outputs</filter>
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284 </data>
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285 <data name="output_control_lambda" format="bedgraph" from_work_dir="MACS2_control_lambda.bdg" default_identifier_source="input_treatment_file" label="${tool.name} on ${on_string} (Bedgraph Control)">
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286 <filter>outputs and 'bdg' in outputs</filter>
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287 </data>
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288 <data name="output_extra_files" format="html" default_identifier_source="input_treatment_file" label="${tool.name} on ${on_string} (html report)">
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289 <filter>outputs and 'html' in outputs</filter>
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290 </data>
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291 </outputs>
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292 <tests>
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293 <test expect_num_outputs="5">
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294 <param name="input_treatment_file" value="ChIP_200K.bed" ftype="bed"/>
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295 <param name="c_select" value="Yes"/>
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296 <param name="input_control_file" value="Control_200K.bed" ftype="bed"/>
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297 <param name="format" value="BED" />
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298 <param name="cutoff_options_selector" value="qvalue"/>
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299 <param name="qvalue" value="0.05"/>
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300 <param name="band_width" value="300"/>
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301 <param name="outputs" value="peaks_tabular,bdg,html"/>
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302 <param name="effective_genome_size_options_selector" value="user_defined" />
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303 <param name="gsize" value="3300000000" />
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304 <param name="lower" value="5" />
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305 <param name="upper" value="50" />
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306 <output name="output_control_lambda" compare="contains" file="callpeak_control_part.bdg" lines_diff="1"/>
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307 <output name="output_treat_pileup" compare="contains" file="callpeak_treatment_part.bdg" lines_diff="1"/>
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308 <output name="output_tabular" compare="contains" file="callpeak_part.tabular" lines_diff="1"/>
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309 <output name="output_extra_files">
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310 <assert_contents>
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311 <has_text text="Additional output created by MACS2" />
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312 </assert_contents>
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313 </output>
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314 </test>
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315 <!-- Ensure pdf can be output -->
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316 <test expect_num_outputs="2">
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317 <param name="input_treatment_file" value="ChIP_200K.bed" ftype="bed"/>
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318 <param name="c_select" value="Yes"/>
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319 <param name="input_control_file" value="Control_200K.bed" ftype="bed"/>
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320 <param name="format" value="BED" />
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321 <param name="cutoff_options_selector" value="qvalue"/>
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322 <param name="qvalue" value="0.05"/>
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323 <param name="band_width" value="300"/>
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324 <param name="outputs" value="pdf"/>
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325 <param name="effective_genome_size_options_selector" value="user_defined" />
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326 <param name="gsize" value="3300000000" />
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327 <param name="lower" value="5" />
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328 <param name="upper" value="50" />
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329 <output name="output_plot" file="magic.pdf" ftype="pdf" compare="contains" />
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330 </test>
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331 <!-- Ensure BAMPE works -->
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332 <test expect_num_outputs="1">
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333 <param name="input_treatment_file" ftype="bam" value="bwa-mem-test1.bam"/>
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334 <param name="format" value="BAMPE" />
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335 <param name="effective_genome_size_options_selector" value="user_defined"/>
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336 <param name="gsize" value="3300000000"/>
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337 <param name="nomodel_type_selector" value="nomodel"/>
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338 <param name="nolambda" value="True"/>
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339 <!-- 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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340 <param name="outputs" value="pdf"/>
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341 <output name="output_narrowpeaks" file="callpeak_bampe_narrow.bed"/>
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342 </test>
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343 </tests>
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344 <help><![CDATA[
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345
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346 .. class:: infomark
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347
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348 **What it does**
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349
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350 **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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351
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352 -----
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353
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354 **Inputs**
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355
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356 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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357
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358 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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359
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360 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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361
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362 *Effective Genome Size*
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363
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364 PLEASE assign this parameter to fit your needs!
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365
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366 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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367
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368 hs: 2.7e9
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369 mm: 1.87e9
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370 ce: 9e7
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371 dm: 1.2e8
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372
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373 Or see the **deepTools** website for updated information on calculating `Effective Genome Size`_.
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374
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375 -----
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376
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377 **Outputs**
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378
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379 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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380
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381 * **a BED file of peaks** (default)
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382 * a tabular file of peaks
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383 * a BED file of peak summits
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384 * two bedGraph files of scores, for treatment pileup and control lambda
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385 * a HTML summary page
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386 * a PDF plot (if model is built)
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387 * a BED file of broad peaks (if **Composite broad regions** is selected under Advanced Options)
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388 * a BED file of gapped peaks (if **Composite broad regions** is selected under Advanced Options)
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389
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390 **Peaks BED File**
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391
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392 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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393
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394 Example:
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395
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396 ======= ========= ======= ============ ==== === ======= ======== ======= =======
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397 1 2 3 4 5 6 7 8 9 **10**
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398 ======= ========= ======= ============ ==== === ======= ======== ======= =======
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399 chr1 840081 840400 MACS2_peak_1 69 . 4.89872 10.50944 6.91052 158
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400 chr1 919419 919785 MACS2_peak_2 87 . 5.85158 12.44148 8.70936 130
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401 chr1 937220 937483 MACS2_peak_3 66 . 4.87632 10.06728 6.61759 154
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402 ======= ========= ======= ============ ==== === ======= ======== ======= =======
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403
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404 Columns contain the following data:
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405
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406 * **1st**: chromosome name
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407 * **2nd**: start position of peak
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408 * **3rd**: end position of peak
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409 * **4th**: name of peak
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410 * **5th**: integer score for display in genome browser (e.g. UCSC)
e8a060164e11 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit 4e2bb09986aebf442f2981e8d77aa512d4c86b90
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411 * **6th**: strand, either "." (=no strand) or "+" or "-"
e8a060164e11 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit 4e2bb09986aebf442f2981e8d77aa512d4c86b90
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412 * **7th**: fold-change
e8a060164e11 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit 4e2bb09986aebf442f2981e8d77aa512d4c86b90
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413 * **8th**: -log10pvalue
e8a060164e11 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit 4e2bb09986aebf442f2981e8d77aa512d4c86b90
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414 * **9th**: -log10qvalue
e8a060164e11 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit 4e2bb09986aebf442f2981e8d77aa512d4c86b90
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415 * **10th**: relative summit position to peak start
e8a060164e11 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit 4e2bb09986aebf442f2981e8d77aa512d4c86b90
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416
e8a060164e11 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit 4e2bb09986aebf442f2981e8d77aa512d4c86b90
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417
e8a060164e11 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit 4e2bb09986aebf442f2981e8d77aa512d4c86b90
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418 **Peaks tabular File**
e8a060164e11 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit 4e2bb09986aebf442f2981e8d77aa512d4c86b90
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419
9
acbd3fb47f90 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit 586ecaebf9e6020fac2674fbda368e293d1c9bc2
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420 A tabular file which contains information about called peaks. You can open it in Excel and sort/filter using Excel functions.
8
e8a060164e11 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit 4e2bb09986aebf442f2981e8d77aa512d4c86b90
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421
e8a060164e11 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit 4e2bb09986aebf442f2981e8d77aa512d4c86b90
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422 Example:
e8a060164e11 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit 4e2bb09986aebf442f2981e8d77aa512d4c86b90
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423
e8a060164e11 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit 4e2bb09986aebf442f2981e8d77aa512d4c86b90
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424 ======= ========= ======= ========== ============== ========== ================== =================== ================== =============
e8a060164e11 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit 4e2bb09986aebf442f2981e8d77aa512d4c86b90
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425 **chr** **start** **end** **length** **abs_summit** **pileup** **-log10(pvalue)** **fold_enrichment** **-log10(qvalue)** **name**
e8a060164e11 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit 4e2bb09986aebf442f2981e8d77aa512d4c86b90
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426 ======= ========= ======= ========== ============== ========== ================== =================== ================== =============
e8a060164e11 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit 4e2bb09986aebf442f2981e8d77aa512d4c86b90
iuc
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427 chr1 840082 840400 319 840240 4.00 10.50944 4.89872 6.91052 MACS2_peak_1
e8a060164e11 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit 4e2bb09986aebf442f2981e8d77aa512d4c86b90
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428 chr1 919420 919785 366 919550 5.00 12.44148 5.85158 8.70936 MACS2_peak_2
e8a060164e11 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit 4e2bb09986aebf442f2981e8d77aa512d4c86b90
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429 chr1 937221 937483 263 937375 4.00 10.06728 4.87632 6.61759 MACS2_peak_3
e8a060164e11 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit 4e2bb09986aebf442f2981e8d77aa512d4c86b90
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430 ======= ========= ======= ========== ============== ========== ================== =================== ================== =============
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431
e8a060164e11 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit 4e2bb09986aebf442f2981e8d77aa512d4c86b90
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432 Columns contain the following data:
e8a060164e11 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit 4e2bb09986aebf442f2981e8d77aa512d4c86b90
iuc
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433
e8a060164e11 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit 4e2bb09986aebf442f2981e8d77aa512d4c86b90
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434 * **chr**: chromosome name
e8a060164e11 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit 4e2bb09986aebf442f2981e8d77aa512d4c86b90
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435 * **start**: start position of peak
e8a060164e11 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit 4e2bb09986aebf442f2981e8d77aa512d4c86b90
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436 * **end**: end position of peak
e8a060164e11 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit 4e2bb09986aebf442f2981e8d77aa512d4c86b90
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437 * **length**: length of peak region
e8a060164e11 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit 4e2bb09986aebf442f2981e8d77aa512d4c86b90
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438 * **abs_summit**: absolute peak summit position
e8a060164e11 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit 4e2bb09986aebf442f2981e8d77aa512d4c86b90
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439 * **pileup**: pileup height at peak summit
e8a060164e11 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit 4e2bb09986aebf442f2981e8d77aa512d4c86b90
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440 * **-log10(pvalue)**: -log10(pvalue) for the peak summit (e.g. pvalue =1e-10, then this value should be 10)
e8a060164e11 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit 4e2bb09986aebf442f2981e8d77aa512d4c86b90
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441 * **fold_enrichment**: fold enrichment for this peak summit against random Poisson distribution with local lambda
e8a060164e11 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit 4e2bb09986aebf442f2981e8d77aa512d4c86b90
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442 * **-log10(qvalue)**: -log10(qvalue) at peak summit
e8a060164e11 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit 4e2bb09986aebf442f2981e8d77aa512d4c86b90
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443 * **name**: name of peak
e8a060164e11 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit 4e2bb09986aebf442f2981e8d77aa512d4c86b90
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444
e8a060164e11 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit 4e2bb09986aebf442f2981e8d77aa512d4c86b90
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445 *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)*
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446
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447
e8a060164e11 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit 4e2bb09986aebf442f2981e8d77aa512d4c86b90
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448 **Summits BED File**
e8a060164e11 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit 4e2bb09986aebf442f2981e8d77aa512d4c86b90
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449
e8a060164e11 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit 4e2bb09986aebf442f2981e8d77aa512d4c86b90
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450 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.
e8a060164e11 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit 4e2bb09986aebf442f2981e8d77aa512d4c86b90
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451
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452 Example:
e8a060164e11 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit 4e2bb09986aebf442f2981e8d77aa512d4c86b90
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453
9
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454 ======= ========= ======= ============ =======
8
e8a060164e11 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit 4e2bb09986aebf442f2981e8d77aa512d4c86b90
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455 1 2 3 4 **5**
e8a060164e11 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit 4e2bb09986aebf442f2981e8d77aa512d4c86b90
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456 ======= ========= ======= ============ =======
e8a060164e11 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit 4e2bb09986aebf442f2981e8d77aa512d4c86b90
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457 chr1 840239 840240 MACS2_peak_1 6.91052
e8a060164e11 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit 4e2bb09986aebf442f2981e8d77aa512d4c86b90
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458 chr1 919549 919550 MACS2_peak_2 8.70936
e8a060164e11 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit 4e2bb09986aebf442f2981e8d77aa512d4c86b90
iuc
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459 chr1 937374 937375 MACS2_peak_3 6.61759
e8a060164e11 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit 4e2bb09986aebf442f2981e8d77aa512d4c86b90
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460 ======= ========= ======= ============ =======
e8a060164e11 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit 4e2bb09986aebf442f2981e8d77aa512d4c86b90
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461
e8a060164e11 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit 4e2bb09986aebf442f2981e8d77aa512d4c86b90
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462 Columns contain the following data:
e8a060164e11 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit 4e2bb09986aebf442f2981e8d77aa512d4c86b90
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463
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464 * **1st**: chromosome name
e8a060164e11 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit 4e2bb09986aebf442f2981e8d77aa512d4c86b90
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465 * **2nd**: start position of peak
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466 * **3rd**: end position of peak
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467 * **4th**: name of peak
e8a060164e11 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit 4e2bb09986aebf442f2981e8d77aa512d4c86b90
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468 * **5th**: -log10qvalue
e8a060164e11 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit 4e2bb09986aebf442f2981e8d77aa512d4c86b90
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469
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470
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471 **BedGraph Files**
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472
e8a060164e11 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit 4e2bb09986aebf442f2981e8d77aa512d4c86b90
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473 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`_.
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474
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475
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476 Example:
e8a060164e11 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit 4e2bb09986aebf442f2981e8d77aa512d4c86b90
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477
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478 **Treatment pileup file**
e8a060164e11 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit 4e2bb09986aebf442f2981e8d77aa512d4c86b90
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479
e8a060164e11 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit 4e2bb09986aebf442f2981e8d77aa512d4c86b90
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480 ======= ========= ======= =======
e8a060164e11 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit 4e2bb09986aebf442f2981e8d77aa512d4c86b90
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481 1 2 3 **4**
e8a060164e11 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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iuc
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483 chr1 840146 840147 3.00000
e8a060164e11 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit 4e2bb09986aebf442f2981e8d77aa512d4c86b90
iuc
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484 chr1 840147 840332 4.00000
e8a060164e11 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit 4e2bb09986aebf442f2981e8d77aa512d4c86b90
iuc
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485 chr1 840332 840335 3.00000
e8a060164e11 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit 4e2bb09986aebf442f2981e8d77aa512d4c86b90
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486 ======= ========= ======= =======
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487
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488
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489 **Control lambda file**
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490
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491 ======= ========= ======= =======
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492 1 2 3 **4**
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493 ======= ========= ======= =======
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494 chr1 800953 801258 0.02536
e8a060164e11 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit 4e2bb09986aebf442f2981e8d77aa512d4c86b90
iuc
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495 chr1 801258 801631 0.25364
e8a060164e11 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit 4e2bb09986aebf442f2981e8d77aa512d4c86b90
iuc
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496 chr1 801631 801885 0.99858
e8a060164e11 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit 4e2bb09986aebf442f2981e8d77aa512d4c86b90
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497 ======= ========= ======= =======
e8a060164e11 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit 4e2bb09986aebf442f2981e8d77aa512d4c86b90
iuc
parents: 7
diff changeset
498
e8a060164e11 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit 4e2bb09986aebf442f2981e8d77aa512d4c86b90
iuc
parents: 7
diff changeset
499 Columns contain the following data:
e8a060164e11 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit 4e2bb09986aebf442f2981e8d77aa512d4c86b90
iuc
parents: 7
diff changeset
500
e8a060164e11 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit 4e2bb09986aebf442f2981e8d77aa512d4c86b90
iuc
parents: 7
diff changeset
501 * **1st**: chromosome name
e8a060164e11 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit 4e2bb09986aebf442f2981e8d77aa512d4c86b90
iuc
parents: 7
diff changeset
502 * **2nd**: start position of peak
e8a060164e11 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit 4e2bb09986aebf442f2981e8d77aa512d4c86b90
iuc
parents: 7
diff changeset
503 * **3rd**: end position of peak
e8a060164e11 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit 4e2bb09986aebf442f2981e8d77aa512d4c86b90
iuc
parents: 7
diff changeset
504 * **4th**: treatment pileup score or control local lambda score
e8a060164e11 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit 4e2bb09986aebf442f2981e8d77aa512d4c86b90
iuc
parents: 7
diff changeset
505
e8a060164e11 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit 4e2bb09986aebf442f2981e8d77aa512d4c86b90
iuc
parents: 7
diff changeset
506
e8a060164e11 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit 4e2bb09986aebf442f2981e8d77aa512d4c86b90
iuc
parents: 7
diff changeset
507 **Broad peaks File**
e8a060164e11 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit 4e2bb09986aebf442f2981e8d77aa512d4c86b90
iuc
parents: 7
diff changeset
508
e8a060164e11 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit 4e2bb09986aebf442f2981e8d77aa512d4c86b90
iuc
parents: 7
diff changeset
509 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.
e8a060164e11 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit 4e2bb09986aebf442f2981e8d77aa512d4c86b90
iuc
parents: 7
diff changeset
510
e8a060164e11 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit 4e2bb09986aebf442f2981e8d77aa512d4c86b90
iuc
parents: 7
diff changeset
511 Example:
e8a060164e11 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit 4e2bb09986aebf442f2981e8d77aa512d4c86b90
iuc
parents: 7
diff changeset
512
9
acbd3fb47f90 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit 586ecaebf9e6020fac2674fbda368e293d1c9bc2
iuc
parents: 8
diff changeset
513 ======= ========= ======= ============ ==== === ======= ======= =======
8
e8a060164e11 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit 4e2bb09986aebf442f2981e8d77aa512d4c86b90
iuc
parents: 7
diff changeset
514 1 2 3 4 5 6 7 8 9
9
acbd3fb47f90 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit 586ecaebf9e6020fac2674fbda368e293d1c9bc2
iuc
parents: 8
diff changeset
515 ======= ========= ======= ============ ==== === ======= ======= =======
8
e8a060164e11 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit 4e2bb09986aebf442f2981e8d77aa512d4c86b90
iuc
parents: 7
diff changeset
516 chr1 840081 840400 MACS2_peak_1 52 . 4.08790 8.57605 5.21506
e8a060164e11 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit 4e2bb09986aebf442f2981e8d77aa512d4c86b90
iuc
parents: 7
diff changeset
517 chr1 919419 919785 MACS2_peak_2 56 . 4.37270 8.90436 5.60462
e8a060164e11 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit 4e2bb09986aebf442f2981e8d77aa512d4c86b90
iuc
parents: 7
diff changeset
518 chr1 937220 937483 MACS2_peak_3 48 . 4.02343 8.06676 4.86861
9
acbd3fb47f90 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit 586ecaebf9e6020fac2674fbda368e293d1c9bc2
iuc
parents: 8
diff changeset
519 ======= ========= ======= ============ ==== === ======= ======= =======
8
e8a060164e11 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit 4e2bb09986aebf442f2981e8d77aa512d4c86b90
iuc
parents: 7
diff changeset
520
e8a060164e11 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit 4e2bb09986aebf442f2981e8d77aa512d4c86b90
iuc
parents: 7
diff changeset
521
e8a060164e11 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit 4e2bb09986aebf442f2981e8d77aa512d4c86b90
iuc
parents: 7
diff changeset
522 Columns contain the following data:
e8a060164e11 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit 4e2bb09986aebf442f2981e8d77aa512d4c86b90
iuc
parents: 7
diff changeset
523
e8a060164e11 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit 4e2bb09986aebf442f2981e8d77aa512d4c86b90
iuc
parents: 7
diff changeset
524 * **1st**: chromosome name
e8a060164e11 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit 4e2bb09986aebf442f2981e8d77aa512d4c86b90
iuc
parents: 7
diff changeset
525 * **2nd**: start position of peak
e8a060164e11 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit 4e2bb09986aebf442f2981e8d77aa512d4c86b90
iuc
parents: 7
diff changeset
526 * **3rd**: end position of peak
e8a060164e11 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit 4e2bb09986aebf442f2981e8d77aa512d4c86b90
iuc
parents: 7
diff changeset
527 * **4th**: name of peak
e8a060164e11 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit 4e2bb09986aebf442f2981e8d77aa512d4c86b90
iuc
parents: 7
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528 * **5th**: integer score for display in genome browser (e.g. UCSC)
e8a060164e11 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit 4e2bb09986aebf442f2981e8d77aa512d4c86b90
iuc
parents: 7
diff changeset
529 * **6th**: strand, either "." (=no strand) or "+" or "-"
e8a060164e11 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit 4e2bb09986aebf442f2981e8d77aa512d4c86b90
iuc
parents: 7
diff changeset
530 * **7th**: fold-change
e8a060164e11 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit 4e2bb09986aebf442f2981e8d77aa512d4c86b90
iuc
parents: 7
diff changeset
531 * **8th**: -log10pvalue
e8a060164e11 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit 4e2bb09986aebf442f2981e8d77aa512d4c86b90
iuc
parents: 7
diff changeset
532 * **9th**: -log10qvalue
e8a060164e11 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit 4e2bb09986aebf442f2981e8d77aa512d4c86b90
iuc
parents: 7
diff changeset
533
e8a060164e11 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit 4e2bb09986aebf442f2981e8d77aa512d4c86b90
iuc
parents: 7
diff changeset
534
e8a060164e11 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit 4e2bb09986aebf442f2981e8d77aa512d4c86b90
iuc
parents: 7
diff changeset
535 **Gapped peaks File**
e8a060164e11 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit 4e2bb09986aebf442f2981e8d77aa512d4c86b90
iuc
parents: 7
diff changeset
536
e8a060164e11 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit 4e2bb09986aebf442f2981e8d77aa512d4c86b90
iuc
parents: 7
diff changeset
537 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.
e8a060164e11 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit 4e2bb09986aebf442f2981e8d77aa512d4c86b90
iuc
parents: 7
diff changeset
538
e8a060164e11 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit 4e2bb09986aebf442f2981e8d77aa512d4c86b90
iuc
parents: 7
diff changeset
539 Example:
e8a060164e11 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit 4e2bb09986aebf442f2981e8d77aa512d4c86b90
iuc
parents: 7
diff changeset
540
e8a060164e11 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit 4e2bb09986aebf442f2981e8d77aa512d4c86b90
iuc
parents: 7
diff changeset
541 ======= ========= ======= ============ ==== === ======= ======= === === === === ======= ======= =======
e8a060164e11 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit 4e2bb09986aebf442f2981e8d77aa512d4c86b90
iuc
parents: 7
diff changeset
542 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15
e8a060164e11 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit 4e2bb09986aebf442f2981e8d77aa512d4c86b90
iuc
parents: 7
diff changeset
543 ======= ========= ======= ============ ==== === ======= ======= === === === === ======= ======= =======
e8a060164e11 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit 4e2bb09986aebf442f2981e8d77aa512d4c86b90
iuc
parents: 7
diff changeset
544 chr1 840081 840400 MACS2_peak_1 52 . 840081 840400 0 1 319 0 4.08790 8.57605 5.21506
e8a060164e11 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit 4e2bb09986aebf442f2981e8d77aa512d4c86b90
iuc
parents: 7
diff changeset
545 chr1 919419 919785 MACS2_peak_2 56 . 919419 919785 0 1 366 0 4.37270 8.90436 5.60462
e8a060164e11 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit 4e2bb09986aebf442f2981e8d77aa512d4c86b90
iuc
parents: 7
diff changeset
546 chr1 937220 937483 MACS2_peak_3 48 . 937220 937483 0 1 263 0 4.02343 8.06676 4.86861
e8a060164e11 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit 4e2bb09986aebf442f2981e8d77aa512d4c86b90
iuc
parents: 7
diff changeset
547 ======= ========= ======= ============ ==== === ======= ======= === === === === ======= ======= =======
e8a060164e11 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit 4e2bb09986aebf442f2981e8d77aa512d4c86b90
iuc
parents: 7
diff changeset
548
e8a060164e11 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit 4e2bb09986aebf442f2981e8d77aa512d4c86b90
iuc
parents: 7
diff changeset
549 Columns contain the following data:
e8a060164e11 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit 4e2bb09986aebf442f2981e8d77aa512d4c86b90
iuc
parents: 7
diff changeset
550
e8a060164e11 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit 4e2bb09986aebf442f2981e8d77aa512d4c86b90
iuc
parents: 7
diff changeset
551 * **1st**: chromosome name
e8a060164e11 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit 4e2bb09986aebf442f2981e8d77aa512d4c86b90
iuc
parents: 7
diff changeset
552 * **2nd**: start position of peak
e8a060164e11 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit 4e2bb09986aebf442f2981e8d77aa512d4c86b90
iuc
parents: 7
diff changeset
553 * **3rd**: end position of peak
e8a060164e11 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit 4e2bb09986aebf442f2981e8d77aa512d4c86b90
iuc
parents: 7
diff changeset
554 * **4th**: name of peak
e8a060164e11 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit 4e2bb09986aebf442f2981e8d77aa512d4c86b90
iuc
parents: 7
diff changeset
555 * **5th**: 10*-log10qvalue, to be more compatible to show grey levels on UCSC browser
e8a060164e11 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit 4e2bb09986aebf442f2981e8d77aa512d4c86b90
iuc
parents: 7
diff changeset
556 * **6th**: strand, either "." (=no strand) or "+" or "-"
9
acbd3fb47f90 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit 586ecaebf9e6020fac2674fbda368e293d1c9bc2
iuc
parents: 8
diff changeset
557 * **7th**: start of the first narrow peak in the region
8
e8a060164e11 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit 4e2bb09986aebf442f2981e8d77aa512d4c86b90
iuc
parents: 7
diff changeset
558 * **8th**: end of the peak
9
acbd3fb47f90 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit 586ecaebf9e6020fac2674fbda368e293d1c9bc2
iuc
parents: 8
diff changeset
559 * **9th**: RGB color key, default colour is 0
8
e8a060164e11 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit 4e2bb09986aebf442f2981e8d77aa512d4c86b90
iuc
parents: 7
diff changeset
560 * **10th**: number of blocks, including the starting 1bp and ending 1bp of broad regions
e8a060164e11 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit 4e2bb09986aebf442f2981e8d77aa512d4c86b90
iuc
parents: 7
diff changeset
561 * **11th**: length of each block, comma-separated values if multiple
e8a060164e11 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit 4e2bb09986aebf442f2981e8d77aa512d4c86b90
iuc
parents: 7
diff changeset
562 * **12th**: start of each block, comma-separated values if multiple
9
acbd3fb47f90 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit 586ecaebf9e6020fac2674fbda368e293d1c9bc2
iuc
parents: 8
diff changeset
563 * **13th**: fold-change
acbd3fb47f90 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit 586ecaebf9e6020fac2674fbda368e293d1c9bc2
iuc
parents: 8
diff changeset
564 * **14th**: -log10pvalue
8
e8a060164e11 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit 4e2bb09986aebf442f2981e8d77aa512d4c86b90
iuc
parents: 7
diff changeset
565 * **15th**: -log10qvalue
e8a060164e11 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit 4e2bb09986aebf442f2981e8d77aa512d4c86b90
iuc
parents: 7
diff changeset
566
e8a060164e11 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit 4e2bb09986aebf442f2981e8d77aa512d4c86b90
iuc
parents: 7
diff changeset
567 -----
e8a060164e11 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit 4e2bb09986aebf442f2981e8d77aa512d4c86b90
iuc
parents: 7
diff changeset
568
e8a060164e11 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit 4e2bb09986aebf442f2981e8d77aa512d4c86b90
iuc
parents: 7
diff changeset
569 **More Information**
e8a060164e11 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit 4e2bb09986aebf442f2981e8d77aa512d4c86b90
iuc
parents: 7
diff changeset
570
5
beb902da6e5f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit e10f301c7f8c54a7d12df4e631527197baccf70b
iuc
parents: 4
diff changeset
571 MACS2 performs the following analysis steps:
0
fe62ba547975 Uploaded
iuc
parents:
diff changeset
572
8
e8a060164e11 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit 4e2bb09986aebf442f2981e8d77aa512d4c86b90
iuc
parents: 7
diff changeset
573 * Artificially extends reads to expected fragment length, and generates coverage map along genome.
e8a060164e11 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit 4e2bb09986aebf442f2981e8d77aa512d4c86b90
iuc
parents: 7
diff changeset
574 * 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.
e8a060164e11 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit 4e2bb09986aebf442f2981e8d77aa512d4c86b90
iuc
parents: 7
diff changeset
575 * 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.
e8a060164e11 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit 4e2bb09986aebf442f2981e8d77aa512d4c86b90
iuc
parents: 7
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576
0
fe62ba547975 Uploaded
iuc
parents:
diff changeset
577
8
e8a060164e11 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit 4e2bb09986aebf442f2981e8d77aa512d4c86b90
iuc
parents: 7
diff changeset
578 **Tips of fine-tuning peak calling**
e8a060164e11 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit 4e2bb09986aebf442f2981e8d77aa512d4c86b90
iuc
parents: 7
diff changeset
579
e8a060164e11 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit 4e2bb09986aebf442f2981e8d77aa512d4c86b90
iuc
parents: 7
diff changeset
580 Check out these other MACS2 tools:
e8a060164e11 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit 4e2bb09986aebf442f2981e8d77aa512d4c86b90
iuc
parents: 7
diff changeset
581
e8a060164e11 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit 4e2bb09986aebf442f2981e8d77aa512d4c86b90
iuc
parents: 7
diff changeset
582 * **MACS2 bdgcmp** can be used on the callpeak bedGraph files or bedGraph files from other resources to calculate score track.
e8a060164e11 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit 4e2bb09986aebf442f2981e8d77aa512d4c86b90
iuc
parents: 7
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583 * **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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584 * 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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586 .. class:: warningmark
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587
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588 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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589
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590 .. _MACS2: https://github.com/taoliu/MACS
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591 .. _`Effective Genome Size`: http://deeptools.readthedocs.io/en/latest/content/feature/effectiveGenomeSize.html
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592 .. _`UCSC website here`: https://genome.ucsc.edu/goldenPath/help/bedgraph.html
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594 @citation@
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595 ]]></help>
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596 <expand macro="citations" />
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597 </tool>