annotate bamCoverage.xml @ 20:827fe3df85c3 draft

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date Mon, 09 Jul 2018 19:06:38 -0400
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1 <tool id="deeptools_bam_coverage" name="bamCoverage" version="@WRAPPER_VERSION@.0">
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2 <description>generates a coverage bigWig file from a given BAM or CRAM file</description>
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3 <macros>
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4 <token name="@BINARY@">bamCoverage</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 '$bamInput' one.bam &&
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11 #if $bamInput.ext == 'bam':
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12 ln -s '${bamInput.metadata.bam_index}' one.bam.bai &&
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13 #else:
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14 ln -s '${bamInput.metadata.cram_index}' one.bam.crai &&
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15 #end if
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17 @BINARY@
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18 @THREADS@
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19
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20 --bam one.bam
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21 --outFileName '$outFileName'
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22 --outFileFormat '$outFileFormat'
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24 --binSize $binSize
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26 #if $scaling.type=='rpkm':
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27 --normalizeUsing RPKM
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28 #elif $scaling.type=='cpm':
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29 --normalizeUsing CPM
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30 #elif $scaling.type=='bpm':
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31 --normalizeUsing BPM
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32 #elif $scaling.type=='1x':
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33 --normalizeUsing RPGC
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34 #if $scaling.effectiveGenomeSize.effectiveGenomeSize_opt == "specific":
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35 --effectiveGenomeSize $scaling.effectiveGenomeSize.effectiveGenomeSize
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36 #else:
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37 --effectiveGenomeSize $scaling.effectiveGenomeSize.effectiveGenomeSize_opt
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38 #end if
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39 #end if
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41 #if str($region).strip() != '':
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42 --region '$region'
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43 #end if
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44 $exactScaling
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46 #if $advancedOpt.showAdvancedOpt == "yes":
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47 #if str($advancedOpt.scaleFactor).strip() != '':
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48 --scaleFactor $advancedOpt.scaleFactor
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49 #end if
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50
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51 #if $advancedOpt.smoothLength:
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52 --smoothLength '$advancedOpt.smoothLength'
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53 #end if
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55 @ADVANCED_OPTS_READ_PROCESSING@
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56 $advancedOpt.skipNAs
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58 #if str($advancedOpt.ignoreForNormalization).strip() != '':
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59 --ignoreForNormalization $advancedOpt.ignoreForNormalization
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60 #end if
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62 #if str($advancedOpt.filterRNAstrand) != 'no':
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63 --filterRNAstrand '$advancedOpt.filterRNAstrand'
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64 #end if
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65
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66 #if $advancedOpt.Offset:
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67 --Offset $advancedOpt.Offset
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68 #end if
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69
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70 @blacklist@
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71 #end if
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72 ]]>
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73 </command>
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74
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75 <inputs>
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76 <param name="bamInput" format="bam,cram" type="data" label="BAM/CRAM file"
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77 help=""/>
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78
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79 <param name="binSize" type="integer" value="50" min="1"
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80 label="Bin size in bases"
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81 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. If only half a fragment overlaps, this fraction will be reported. "/>
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82
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83 <conditional name="scaling">
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84 <param name="type" type="select" label="Scaling/Normalization method" >
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85 <option value="1x">Normalize coverage to 1x</option>
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86 <option value="rpkm">Normalize to reads per kilobase per million (RPKM)</option>
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87 <option value="cpm">Normalize to counts per million (CPM), same as CPM in RNA-seq</option>
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88 <option value="bpm">Normalize to bins per million (BPM), same as TPM in RNA-seq</option>
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89 <option value="no">Do not normalize or scale</option>
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90 </param>
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91 <when value="rpkm"/>
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92 <when value="cpm"/>
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93 <when value="bpm"/>
0
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94 <when value="no"/>
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95 <when value="1x">
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96 <expand macro="effectiveGenomeSize" />
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97 </when>
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98 </conditional>
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99
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100 <param name="outFileFormat" type="select" label="Coverage file format">
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101 <option value="bigwig" selected="true">bigwig</option>
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102 <option value="bedgraph">bedgraph</option>
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103 </param>
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104
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105 <expand macro="exactScaling" />
0
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106 <expand macro="region_limit_operation" />
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107
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108 <conditional name="advancedOpt">
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109 <param name="showAdvancedOpt" type="select" label="Show advanced options" >
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110 <option value="no" selected="true">no</option>
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111 <option value="yes">yes</option>
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112 </param>
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113 <when value="no" />
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114 <when value="yes">
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115 <expand macro="scaleFactor" />
0
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116 <expand macro="smoothLength" />
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117
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118 <param argument="ignoreForNormalization" type="text" value=""
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119 label="Regions that should be excluded for normalization"
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120 help="A list of chromosome names separated by spaces
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121 containing those chromosomes that should be excluded
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122 during normalization. This is useful when
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123 considering samples with unequal coverage across
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124 chromosomes, like male and female samples. Example: chrX chrM" />
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125
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126 <expand macro="skipNAs" />
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127 <expand macro="read_processing_options" />
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128
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129 <param argument="--MNase" type="boolean" truevalue="--MNase" falsevalue=""
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130 label="Determine nucleosome positions from MNase-seq data"
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131 help="Only the 3 nucleotides at the center of each fragment are counted. The fragment ends are defined by the two mate reads. *NOTE*: Requires paired-end data. By default, only fragments between 130 and 200 bases will be used, though this can be changed with the --minFragmentLength and --maxFragmentLength options." />
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132
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133 <param argument="--Offset" type="text" value="" optional="True"
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134 label="Offset inside each alignment to use for the signal location."
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135 help="Uses this offset inside of each read as the signal. This is useful in
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136 cases like RiboSeq or GROseq, where only the 12th, 15th or 1st base aligned
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137 should be used to denote where the signal is (rather than the span of the
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138 whole alignment). This can be paired with the --filterRNAstrand option. Note
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139 that negative values indicate offsets from the end of each read. A value of
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140 1 indicates the first base of the alignment (taking alignment orientation
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141 into account). Likewise, a value of -1 is the last base of the alignment. An
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142 offset of 0 is not permitted. If two values (separated by spaces) are specified, then they will be
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143 used to specify a range of positions. Note that specifying something like
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144 --Offset 5 -1 will result in the 5th through last position being used, which
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145 is equivalent to trimming 4 bases from the 5-prime end of alignments." />
0
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146
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147 <param argument="filterRNAstrand" type="select" label="Only include reads originating from fragments from the forward or reverse strand."
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148 help="By default (the no option), all reads are processed, regardless of the strand they originated from. For RNAseq, it can be useful to separately create bigWig files for the forward or reverse strands.
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149 Note that this tools assumes that a dUTP-based method was used, so fragments will be assigned to the reverse strand if the second read in a pair is reverse complemented.">
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150 <option value="no" selected="true">no</option>
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151 <option value="forward">forward</option>
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152 <option value="reverse">reverse</option>
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153 </param>
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154 <expand macro="blacklist" />
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155
0
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156 </when>
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157 </conditional>
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158 </inputs>
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159 <outputs>
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160 <data format="bigwig" name="outFileName">
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161 <change_format>
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162 <when input="outFileFormat" value="bigwig" format="bigwig" />
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163 <when input="outFileFormat" value="bedgraph" format="bedgraph" />
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164 </change_format>
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165 </data>
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166 </outputs>
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167 <tests>
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168 <test>
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169 <param name="bamInput" value="bowtie2 test1.bam" ftype="bam" />
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170 <param name="outFileFormat" value="bigwig" />
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171 <param name="showAdvancedOpt" value="no" />
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172 <param name="binSize" value="10" />
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173 <param name="type" value="no" />
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174 <output name="outFileName" file="bamCoverage_result1.bw" ftype="bigwig" />
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175 </test>
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176 <test>
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177 <param name="bamInput" value="bowtie2 test1.bam" ftype="bam" />
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178 <param name="outFileFormat" value="bigwig" />
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179 <param name="showAdvancedOpt" value="no" />
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180 <param name="effectiveGenomeSize_opt" value="specific" />
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181 <param name="effectiveGenomeSize" value="2451960000" />
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182 <param name="binSize" value="10" />
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183 <output name="outFileName" file="bamCoverage_result2.bw" ftype="bigwig" />
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184 </test>
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185 <test>
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186 <param name="bamInput" value="bowtie2 test1.bam" ftype="bam" />
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187 <param name="outFileFormat" value="bedgraph" />
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188 <param name="showAdvancedOpt" value="no" />
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189 <param name="effectiveGenomeSize_opt" value="specific" />
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190 <param name="effectiveGenomeSize" value="2451960000" />
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191 <param name="binSize" value="10" />
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192 <output name="outFileName" file="bamCoverage_result3.bg" ftype="bedgraph" />
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193 </test>
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194 <test>
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195 <param name="bamInput" value="phiX.bam" ftype="bam" />
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196 <param name="outFileFormat" value="bigwig" />
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197 <param name="showAdvancedOpt" value="no" />
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198 <param name="effectiveGenomeSize_opt" value="specific" />
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199 <param name="effectiveGenomeSize" value="2451960000" />
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200 <param name="binSize" value="10" />
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201 <output name="outFileName" file="bamCoverage_result4.bw" ftype="bigwig" />
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202 </test>
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203 <test>
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204 <param name="bamInput" value="phiX.bam" ftype="bam" />
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205 <param name="outFileFormat" value="bedgraph" />
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206 <param name="showAdvancedOpt" value="yes" />
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207 <param name="effectiveGenomeSize_opt" value="specific" />
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208 <param name="effectiveGenomeSize" value="2451960000" />
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209 <param name="binSize" value="10" />
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210 <output name="outFileName" file="bamCoverage_result4.bg" ftype="bedgraph" />
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211 </test>
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212 <test>
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213 <param name="bamInput" value="phiX.bam" ftype="bam" />
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214 <param name="outFileFormat" value="bigwig" />
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215 <param name="showAdvancedOpt" value="yes" />
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216 <param name="filterRNAstrand" value="reverse" />
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217 <param name="effectiveGenomeSize_opt" value="specific" />
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218 <param name="effectiveGenomeSize" value="2451960000" />
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219 <param name="binSize" value="10" />
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220 <output name="outFileName" file="bamCoverage_result5.bw" ftype="bigwig" />
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221 </test>
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222 <test>
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223 <param name="bamInput" value="bowtie2 test1.bam" ftype="bam" />
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224 <param name="outFileFormat" value="bigwig" />
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225 <param name="showAdvancedOpt" value="yes" />
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226 <param name="binSize" value="10" />
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227 <param name="Offset" value="-4 -1" />
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228 <param name="doExtend" value="yes" />
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229 <param name="minMappingQuality" value="0" />
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230 <param name="type" value="no" />
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231 <output name="outFileName" file="bamCoverage_result6.bw" ftype="bigwig" />
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232 </test>
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233 </tests>
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234 <help>
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235 <![CDATA[
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236
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237 What it does
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238 --------------
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239
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240 Given a BAM file, this tool generates a bigWig or bedGraph file of fragment or
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241 read coverages. The way the method works is by first calculating all the
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242 number of reads (either extended to match the fragment length or not) that
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243 overlap each bin in the genome. Various options are available to normalize the reads:
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244 1) using a given scaling factor
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245 2) RPKM (reads per kilobase per million) : RPKM (per bin) = number of reads per bin / ( number of mapped reads (in millions) * bin length (kb) ).
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246 3) CPM (counts per million) : CPM (per bin) = number of reads per bin / number of mapped reads (in millions).
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247 4) BPM (bins per million) : BPM (per bin) = number of reads per bin / sum of all reads per bin (in millions).
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248 5) RPGC (1x sequencing depth ) : number of reads per bin /(total number of mapped reads * fragment length / effective genome size)
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249
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250 In the case of paired-end mapping, each read mate is treated
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251 independently to avoid a bias when a mixture of concordant and discordant
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252 pairs is present. This means that *each end* will be extended to match the
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253 fragment length.
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254
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255 See the usage hints below.
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256
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257 .. image:: $PATH_TO_IMAGES/norm_IGVsnapshot_indFiles.png
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258 :width: 600
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259 :height: 336
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260
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261 Output
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262 -------------
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263
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264 ``bamCoverage`` produces a coverage file, either in bigWig or bedGraph format, where for each bin the number of overlapping reads (possibly normalized) is noted.
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265
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266 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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267
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268 .. image:: $PATH_TO_IMAGES/bamCoverage_output.png
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269 :width: 600
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270 :height: 450
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271
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272 Usage hints
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273 ------------
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275 * A smaller ``bin size`` value will result in a higher resolution of the coverage track but also in a larger file size.
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276 * The ``1x normalization`` (RPGC) requires the input of a value for the **effective genome size**, which is the mappable part of the reference genome. Of course, this value is species-specific.
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277 * It might be useful for some studies to exclude certain chromosomes in order to avoid biases, e.g. chromosome X for many mammals where the males contain a pair of each autosome, but often only a single X chromosome.
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278 * By default, the read length is **NOT** extended! This is the preferred setting for **spliced-read** data like RNA-seq, where one usually wants to rely on the detected read locations only. A read extension would neglect potential splice sites in the unmapped part of the fragment.
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279 Other data, e.g. ChIP-seq, where fragments are known to map contiuously, should be processed with read extension (``--extendReads [INT]``).
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280 * For paired-end data, the fragment length is generally defined by the two read mates. The user-provided fragment length is only used as a fallback for singletons or mate reads that map too far apart (with a distance greater than four times the fragment length or if the mates are located on different chromosomes).
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282 WARNING: If you already normalized for GC bias using ``correctGCbias``, you should absolutely **NOT** set the parameter ``--ignoreDuplicates``!
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283
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285 -----
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287 @REFERENCES@
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288 ]]>
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289 </help>
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290 <expand macro="citations" />
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291 </tool>