Mercurial > repos > bgruening > hicexplorer_hicbuildmatrix

annotate hicBuildMatrix.xml @ 8:707f691c974c draft

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planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457
author bgruening
date Wed, 07 Mar 2018 03:42:32 -0500
parents be42758f532e
children 495ae38f6e0d
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707f691c974c planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457
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1 <tool id="hicexplorer_hicbuildmatrix" name="@BINARY@" version="@WRAPPER_VERSION@.0">
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2 <description>creates a contact matrix</description>
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3 <macros>
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4 <token name="@BINARY@">hicBuildMatrix</token>
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5 <import>macros.xml</import>
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6 </macros>
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7 <expand macro="requirements" >
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8 <requirement type="package" version="1.6">samtools</requirement>
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9 </expand>
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10 <command detect_errors="exit_code"><![CDATA[
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9767c021cd58 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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12 mkdir ./QCfolder &&
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13 mkdir $qc.files_path &&
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14 hicBuildMatrix
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9767c021cd58 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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16 --samFiles
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17 #for $repeat in $samFiles:
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18 '${repeat.samFile}'
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19 #end for
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20
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21 #if $restrictionCutFileBinSize_conditional.restrictionCutFileBinSize_selector == "optionRestrictionCutFile":
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22 --restrictionCutFile '$restrictionCutFileBinSize_conditional.restrictionCutFile'
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23 --minDistance $restrictionCutFileBinSize_conditional.minDistance
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24 --maxLibraryInsertSize $restrictionCutFileBinSize_conditional.maxLibraryInsertSize
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25 #end if
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2
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27 #if $restrictionCutFileBinSize_conditional.restrictionCutFileBinSize_selector == "optionBinSize":
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28 --binSize $restrictionCutFileBinSize_conditional.binSize
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29 #end if
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9767c021cd58 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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9767c021cd58 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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32 #if $restrictionSequence:
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33 --restrictionSequence '$restrictionSequence'
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34 #end if
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35
9767c021cd58 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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36 #if $region:
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37 --region '$region'
9767c021cd58 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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38 #end if
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39
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be42758f532e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit d76f2040a05a5f8752cbfe9a8bc1ef9efae45c01
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40 --outFileName matrix.$outputFormat
be42758f532e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit d76f2040a05a5f8752cbfe9a8bc1ef9efae45c01
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41
0
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42 --outBam ./unsorted.bam
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43
2
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44 $keepSelfCircles
0
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9767c021cd58 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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46 #if $minMappingQuality and $minMappingQuality is not None:
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47 --minMappingQuality $minMappingQuality
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48 #end if
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49
2
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50 #if $danglingSequence:
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51 --danglingSequence '$danglingSequence'
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52 #end if
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53
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54 --threads @THREADS@
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55
0
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56 --QCfolder ./QCfolder
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57 &&
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58 mv ./QCfolder/* $qc.files_path/
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59 &&
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60 mv $qc.files_path/hicQC.html $qc
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61 && mv $qc.files_path/*.log raw_qc
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62 && mv matrix.$outputFormat matrix
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63 && samtools sort ./unsorted.bam -o sorted.bam
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64
0
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65 ]]>
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66 </command>
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67 <inputs>
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68 <repeat max="2" min="2" name="samFiles" title="Sam/Bam files to process">
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69 <param name="samFile" type="data" format="sam,bam"/>
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70 </repeat>
2
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71 <conditional name="restrictionCutFileBinSize_conditional">
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72 <param name="restrictionCutFileBinSize_selector" type="select" label="Choose to use a restriction cut file or a bin size">
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73 <option value="optionRestrictionCutFile">Restriction cut file</option>
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74 <option value="optionBinSize" selected="True">Bin size</option>
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75 </param>
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76 <when value="optionRestrictionCutFile">
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77 <param argument="--restrictionCutFile" type="data" format="bed" optional="true" label="BED file with all restriction cut places"
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78 help="Should contaion only mappable restriction sites. If given, the bins are set to match the restriction fragments
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79 (i.e. the region between one restriction site and the next)." />
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80 <param argument="--minDistance" type="integer" value="" optional="true" label="Minimum distance between restriction sites"
2
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81 help="Restriction sites that are closer that this distance are merged into one.
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82 This option only applies if --restrictionCutFile is given."/>
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83 <param argument="--maxLibraryInsertSize" type="integer" value="" optional="true"
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84 label="Maximum library insert size defines different cut offs based on the maximum expected library size"
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85 help="*This is not the average fragment size* but the higher end of the fragment size distribution (obtained using for example Fragment Analyzer)
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86 which usually is between 800 to 1500 bp. If this value if not known use the default of 1000. The insert value is used to decide if two mates
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87 belong to the same fragment (by checking if they are within this max insert size) and to decide if a mate
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88 is too far away from the nearest restriction site." />
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89 </when>
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90 <when value="optionBinSize">
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91 <param argument="--binSize" type="integer" value="" optional="true" label="Bin size in bp"
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92 help="If used, the restriction cut places (if given) are used to only consider reads that are in the vicinity of the resctriction sites.
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93 Otherwise all reads in the interval are considered. "/>
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94 </when>
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95 </conditional>
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96
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97 <param argument="--restrictionSequence" type="text" optional="true" label="Sequence of the restriction site"
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98 help="This is used to discard reads that end/start with such sequence and that are considered un-ligated fragments or
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99 &quot;dangling-ends&quot;. If not given, such statistics will not be available." />
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100
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101 <expand macro="region" />
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102
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103 <param argument="--keepSelfCircles" type="boolean" truevalue="--keepSelfCircles" falsevalue=""
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104 label="Keep self circles"
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105 help="If set, outward facing reads without any restriction fragment (self circles) are kept. They will be counted and shown in the QC plots." />
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106
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107 <expand macro="minMappingQuality" />
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108
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109 <param argument="--danglingSequence" type="text" optional="true" label="The dangling sequence"
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110 help="Dangling end sequence left by the restriction enzyme. For DpnII for example,
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111 the dangling end is the same restriction sequence. This is used
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112 to discard reads that end/start with such sequence
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113 and that are considered un-ligated fragments or
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114 'dangling-ends'. If not given, such statistics will
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115 not be available."/>
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116 <param name='outputFormat' type='select' label="Output file format">
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117 <option value='h5'>HiCExplorer format</option>
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118 <option value="cool">cool</option>
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119 </param>
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120 </inputs>
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121 <outputs>
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122 <data name="outBam" from_work_dir="sorted.bam" format="bam" label="${tool.name} BAM file on ${on_string}"/>
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123 <data name="outFileName" from_work_dir="matrix" format="h5" label="${tool.name} MATRIX on ${on_string}">
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124 <change_format>
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125 <when input="outputFormat" value="cool" format="cool" />
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126 </change_format>
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127 </data>
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128 <data name="qc" format="html" label="${tool.name} QC"/>
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129
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130 <data name="raw_qc" from_work_dir='raw_qc' format='txt' label="${tool.name} raw QC" />
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131 </outputs>
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132 <tests>
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133 <test>
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134 <repeat name="samFiles">
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135 <param name="samFile" value="small_test_R1_unsorted.sam"/>
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136 </repeat>
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137 <repeat name="samFiles">
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138 <param name="samFile" value="small_test_R2_unsorted.sam"/>
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139 </repeat>
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140 <conditional name="restrictionCutFileBinSize_conditional">
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141 <param name="restrictionCutFileBinSize_selector" value="optionBinSize"/>
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142 <param name="binSize" value="5000"/>
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143 </conditional>
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144 <param name='outputFormat' value='h5'/>
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145
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146 <output name="outBam" file="small_test_matrix_result_sorted.bam" ftype="bam"/>
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147 <output name="outFileName" file="small_test_matrix_2.h5" ftype="h5" compare="sim_size"/>
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148 <output name="raw_qc" file='raw_qc_report' compare='diff' lines_diff='2'/>
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149 </test>
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150 </tests>
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151 <help><![CDATA[
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152
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153 Creation of the contact matrix
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154 ===============================
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155
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156 ``hicBuildMatrix`` creates a contact matrix based on Hi-C read pairs. It requires two sam or bam files
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157 corresponding to the first and second mates of the paired-end H-C reads. The sam and bam files should
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158 not be sorted by position. There are two main options to create the Hi-C contact matrix, either by
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159 fixed bin size (eg. 10.000 bp) or by bins of variable restriction fragment size length.
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160 ``hicBuildMatrix`` generates a quality control output that can be used to analyze the quality of the Hi-C reads.
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161
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162 Input
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163 -----
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164
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165 `hicBuildMatrix` is having the following parameters:
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166
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167 Parameters
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168 __________
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169
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170
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171 - two input BAM/SAM files
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172 - a bin size
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173 - a restriction cut file as an alternative to the bin size
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174 - restriction sequence: e.g. HindIII: GATC
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175
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176
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177
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178 Output
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179 ------
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180
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181 `hicBuildMatrix` creates as an output:
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182 - the contact matrix
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183 - a bam file with the accepted alignments
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184 - a quality report.
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185
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186 Example plot
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187 -----------------------------------------------------------------
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188 .. image:: $PATH_TO_IMAGES/SRR027956.svg
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189 :width: 70%
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190
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191 Contact matrix created with `hicPlotMatrix`.
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192
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193 Quality report
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194 --------------
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195
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196 The quality report gives you information about:
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197
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198 - how many pairs were used to build the contact matrix
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199 - dangling end pairs: These are reads that start with the restriction site and constitute reads that were digested but no ligated.
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200 - same fragment pairs: These are read mates, facing inward, separated by up to 800 bp that do not have a restriction enzyme in between. These read pairs are not valid Hi-C pairs.
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201 - self circles: Self circles are defined as pairs within 25kb with 'outward' read orientation
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202 - self ligations: These are read pairs with a restriction site in between that are within 800 bp.
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203
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204 Contact distance:
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205 _________________
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206 - inter chromosomal
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207 - short range < 20 kb
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208 - long range
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209
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210 Read orientation:
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211 _________________
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212 - inward pairs
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213 - outward pairs
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214 - left pairs
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215 - right pairs
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216
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217 .. image:: $PATH_TO_IMAGES/hicQC.png
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218 :width: 70 %
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219
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220
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221 | For more information about HiCExplorer please consider our documentation on readthedocs.io_.
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222
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223 .. _readthedocs.io: http://hicexplorer.readthedocs.io/en/latest/index.html
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224
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225
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226 ]]></help>
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227 <expand macro="citations" />
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228 </tool>