Mercurial > repos > bgruening > deeptools_bam_compare

annotate bamCompare.xml @ 3:2f27bfe8b570 draft

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planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2e8510e4f4015f51f7726de5697ba2de9b4e2f4c
author bgruening
date Wed, 09 Mar 2016 18:30:04 -0500
parents e237a134059a
children 8e41fe2f3661
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1 <tool id="deeptools_bam_compare" name="bamCompare" version="@WRAPPER_VERSION@.0">
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2 <description>normalizes and compares two BAM files to obtain the ratio, log2ratio or difference between them</description>
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3 <macros>
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4 <token name="@BINARY@">bamCompare</token>
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5 <import>deepTools_macros.xml</import>
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6 </macros>
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7 <expand macro="requirements" />
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8 <command>
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9 <![CDATA[
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10 ln -s '$bamFile1' one.bam &&
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11 ln -s '${bamFile1.metadata.bam_index}' one.bam.bai &&
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12 ln -s '$bamFile2' two.bam &&
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13 ln -s '${bamFile2.metadata.bam_index}' two.bam.bai &&
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15 @BINARY@
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16 @THREADS@
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17 --bamfile1 one.bam
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18 --bamfile2 two.bam
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19
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20 --outFileName '$outFileName'
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21 --outFileFormat '$outFileFormat'
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23 --binSize $binSize
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24
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25 #if $scaling.method == 'SES':
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26 --scaleFactorsMethod SES
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27 --sampleLength $scaling.sampleLength
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28 --numberOfSamples $scaling.numberOfSamples
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29 #elif $scaling.method == 'readCount':
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30 --scaleFactorsMethod readCount
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31 #elif $scaling.method == 'own':
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32 --scaleFactors '$scaling.scaleFactor1:$scaling.scaleFactor2'
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33 #end if
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34
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35 --ratio $comparison.type
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36
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37 #if $comparison.type == 'subtract':
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38 #if $comparison.normalization.type == 'rpkm':
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39 --normalizeUsingRPKM
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40 #elif $comparison.normalization.type == '1x':
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41
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42 #if $comparison.normalization.effectiveGenomeSize.effectiveGenomeSize_opt == "specific":
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43 --normalizeTo1x $comparison.normalization.effectiveGenomeSize.effectiveGenomeSize
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44 #else:
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45 --normalizeTo1x $comparison.normalization.effectiveGenomeSize.effectiveGenomeSize_opt
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46 #end if
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47
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48 #end if
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49 #elif $comparison.type in ['ratio','log2']:
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50 --pseudocount $comparison.pseudocount
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51 #end if
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52
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53 #if str($region).strip() != '':
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54 --region '$region'
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55 #end if
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56
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57 #if $advancedOpt.showAdvancedOpt == "yes":
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58 #if $advancedOpt.smoothLength:
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59 --smoothLength '$advancedOpt.smoothLength'
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60 #end if
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61
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62 @ADVANCED_OPTS_READ_PROCESSING@
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63 $advancedOpt.skipNAs
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64
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65 #if str($advancedOpt.ignoreForNormalization).strip() != '':
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66 --ignoreForNormalization '$advancedOpt.ignoreForNormalization'
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67 #end if
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68 #end if
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69 ]]>
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70 </command>
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71 <inputs>
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72 <param argument="--bamFile1" format="bam" type="data" label="First BAM file (e.g. treated sample)"
3
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73 help=""/>
0
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74 <param argument="--bamFile2" format="bam" type="data" label="Second BAM file (e.g. control sample)"
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75 help=""/>
0
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76
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77 <param argument="--binSize" type="integer" value="50" min="1"
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78 label="Bin size in bases"
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79 help="The genome will be divided into bins of the specified size. For each bin, the overlaping number of fragments (or reads) will be reported.
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80 If only half a fragment overlaps then this fraction will be reported."/>
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81
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82 <conditional name="scaling">
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83 <param name="method" type="select"
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84 label="Method to use for scaling the largest sample to the smallest">
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85 <option value="readCount" selected="true">read count</option>
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86 <option value="SES">signal extraction scaling (SES), check with plotFingerprint before using it!</option>
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87 <option value="own">enter own scaling factors</option>
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88 </param>
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89 <when value="SES">
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90 <param argument="--sampleLength" type="integer" value="1000" min="10"
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91 label="Length in bases used to sample the genome and compute the size or scaling factors."
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92 help="The default is fine. Only change it if you know what you are doing." />
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93 <param argument="--numberOfSamples" type="integer" value="100000" min="0"
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94 label="Number of samplings taken from the genome to compute the scaling factors"
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95 help="" />
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96 </when>
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97 <when value="readCount" />
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98 <when value="own">
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99 <expand macro="scaleFactors" />
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100 </when>
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101 </conditional>
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102
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103 <conditional name="comparison">
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104 <param name="type" type="select"
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105 label="How to compare the two files"
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106 help="The default is to output the log2ratio between the two samples.
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107 The reciprocal ratio returns the negative of the inverse of the ratio if
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108 the ratio is less than 0. The resulting values are interpreted as negative fold changes.">
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109 <option value="log2" selected="true">Compute log2 of the number of reads ratio</option>
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110 <option value="ratio">Compute the ratio of the number of reads</option>
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111 <option value="subtract">Compute difference (subtract input from treatment) of the number of reads</option>
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112 <option value="add">Compute the sum of number of reads</option>
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113 <option value="reciprocal_ratio">Computes the fold change. If the fold change is less than 1, the negative of the inverse is reported. E.g. A fold change of 10 to 5 would be reported not as 0.5 but as -2</option>
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114 </param>
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115 <when value="log2">
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116 <expand macro="pseudocount" />
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117 </when>
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118 <when value="ratio">
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119 <expand macro="pseudocount" />
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120 </when>
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121 <when value="add" />
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122 <when value="reciprocal_ratio">
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123 <expand macro="pseudocount" />
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124 </when>
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125 <when value="subtract">
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126 <conditional name="normalization">
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127 <param name="type" type="select" label="Normalization method" >
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128 <option value="1x">Normalize coverage to 1x</option>
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129 <option value="rpkm">Normalize to fragments (reads) per kilobase per million (RPKM)</option>
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130 <option value="no">Do not normalize or scale</option>
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131 </param>
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132 <when value="rpkm" />
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133 <when value="no" />
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134 <when value="1x">
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135 <expand macro="effectiveGenomeSize" />
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136 </when>
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137 </conditional>
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138 </when>
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139 </conditional>
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140
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141 <param name="outFileFormat" type="select" label="Coverage file format">
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142 <option value="bigwig" selected="true">bigwig</option>
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143 <option value="bedgraph">bedgraph</option>
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144 </param>
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145 <expand macro="region_limit_operation" />
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146 <conditional name="advancedOpt">
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147 <param name="showAdvancedOpt" type="select" label="Show advanced options" >
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148 <option value="no" selected="true">no</option>
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149 <option value="yes">yes</option>
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150 </param>
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151 <when value="no" />
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152 <when value="yes">
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153 <expand macro="smoothLength" />
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154 <expand macro="read_processing_options" />
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155
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156 <expand macro="skipNAs" />
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157 <param argument="--ignoreForNormalization" type="text" value="" size="50"
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158 label="regions that should be excluded for calculating the scaling factor"
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159 help="Sometimes it makes sense to exclude certain regions when calculating the scaling factor.
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160 For example, if you know of copy number variations between samples then you may want to exclude these.
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161 Another typical example is the difference in chromosome X copies between males and females in many species.
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162 Example inputs are chrX,chrY,chr3 or chr10:12220-128932" />
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163 </when>
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164 </conditional>
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165 </inputs>
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166 <outputs>
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167 <data format="bigwig" name="outFileName">
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168 <change_format>
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169 <when input="outFileFormat" value="bigwig" format="bigwig" />
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170 <when input="outFileFormat" value="bedgraph" format="bedgraph" />
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171 </change_format>
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172 </data>
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173 </outputs>
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174 <tests>
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175 <test>
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176 <param name="bamFile1" value="bowtie2-test1.bam" ftype="bam" />
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177 <param name="bamFile2" value="bowtie2-test1.bam" ftype="bam" />
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178 <param name="showAdvancedOpt" value="no" />
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179 <param name="outFileFormat" value="bigwig" />
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180 <param name="outFileFormat" value="bedgraph" />
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181 <param name="binSize" value="5" />
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182 <param name="type" value="ratio" />
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183 <output name="outFileName" file="bamCompare_result1.bg" ftype="bedgraph" />
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184 </test>
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185 <test>
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186 <param name="bamFile1" value="bowtie2-test1.bam" ftype="bam" />
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187 <param name="bamFile2" value="bowtie2-test1.bam" ftype="bam" />
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188 <param name="showAdvancedOpt" value="yes" />
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189 <param name="outFileFormat" value="bigwig" />
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190 <param name="outFileFormat" value="bigwig" />
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191 <param name="binSize" value="10" />
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192 <param name="type" value="ratio" />
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193 <output name="outFileName" file="bamCompare_result2.bw" ftype="bigwig" />
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194 </test>
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195 </tests>
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196 <help>
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197 <![CDATA[
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198
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199 What it does
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200 -------------
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201
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202 This tool can be used to generate a bigWig or bedGraph file based on **two BAM** files that are compared to each other while being simultaneously normalized for sequencing depth.
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203
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204 To compare the BAM files to each other, the genome is partitioned into bins of equal size, then the number of reads found in each BAM file is counted per bin, and finally a summary value reported.
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205 This value can be the ratio of the number of reads per bin, the log2 of the ratio, or the difference.
0
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206
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207 This tool can normalize the number of reads in each BAM file using the SES method proposed in Diaz et al. (2012). "Normalization, bias correction, and peak
0
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208 calling for ChIP-seq". Statistical applications in genetics and molecular
1
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209 biology, 11(3).
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210
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211 Normalization based on read counts is also available.
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212
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213 By default, if reads are from a paired-end sequencing run and reads are properly paired, the fragment length reported in the BAM file is used.
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214
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215 **Note:** *For paired-end sequencing samples, each read mate is treated independently to avoid a bias when a mixture of concordant and discordant pairs are present. This means that _each end_ will be extended to match the fragment length.*
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216
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217 .. image:: $PATH_TO_IMAGES/norm_IGVsnapshot_indFiles.png
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218 :width: 600
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219 :height: 336
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220
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221 Output files
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222 --------------
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223
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224 ``bamCompare`` produces the same kind of output as ``bamCoverage``.
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225 The difference is that you now obtain 1 coverage file that is based on 2 BAM files: a bedGraph or a bigwig file containing the bin location and the resulting comparison values.
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226
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227 Like BAM files, bigWig files are compressed, binary files. If you would like to see the coverage values, choose the bedGraph output. For more information on typical NGS file formats, see our `Glossary <http://deeptools.readthedocs.org/en/latest/content/help_glossary.html#file-formats>`_
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228
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229 .. image:: $PATH_TO_IMAGES/bamCompare_output.png
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230 :width: 600
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231 :height: 436
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232
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233 -----
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234
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235 @REFERENCES@
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236 ]]>
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237 </help>
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238 <expand macro="citations" />
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239 </tool>