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annotate edger-repenrich.xml @ 9:db32bb7bda01 draft

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planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/repenrich commit ccf4b178d13aeedf7214f2400e7411bcfa3e73b4-dirty
author artbio
date Tue, 11 Dec 2018 12:50:46 -0500
parents 5dd4791c7b70
children 6f4143893463
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9
db32bb7bda01 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/repenrich commit ccf4b178d13aeedf7214f2400e7411bcfa3e73b4-dirty
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1 <tool id="edger-repenrich" name="edgeR-repenrich" version="1.5.3">
0
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2 <description>Determines differentially expressed features from RepEnrich counts</description>
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3 <requirements>
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4 <requirement type="package" version="3.16.5">bioconductor-edger</requirement>
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5 <requirement type="package" version="3.30.13">bioconductor-limma</requirement>
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6 <requirement type="package" version="1.20.0">r-getopt</requirement>
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7 <requirement type="package" version="0.2.15">r-rjson</requirement>
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8 </requirements>
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9 <stdio>
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10 <regex match="Execution halted"
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11 source="both"
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12 level="fatal"
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13 description="Execution halted." />
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14 <regex match="Error in"
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15 source="both"
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16 level="fatal"
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17 description="An undefined error occurred, please check your input carefully and contact your administrator." />
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18 <regex match="Fatal error"
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19 source="both"
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20 level="fatal"
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21 description="An undefined error occurred, please check your input carefully and contact your administrator." />
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22 </stdio>
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23 <version_command>
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24 <![CDATA[
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25 echo $(R --version | grep version | grep -v GNU)", edgeR version" $(R --vanilla --slave -e "library(edgeR) &&
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26 cat(sessionInfo()\$otherPkgs\$edgeR\$Version)" 2> /dev/null | grep -v -i "WARNING: ")
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27 ]]>
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28 </version_command>
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29 <command>
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30 <![CDATA[
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31 #import json
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32 Rscript '${__tool_directory__}/edgeR_repenrich.R'
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33 --factorName '$factorName'
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34
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35 --levelNameA '$factorLevel_A'
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36 #set $factorlevelsA = list()
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37 #for $file in $countsFiles_A:
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38 $factorlevelsA.append(str($file))
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39 #end for
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40 $factorlevelsA.reverse()
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41 --levelAfiles '#echo json.dumps(factorlevelsA)#'
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42
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43 --levelNameB '$factorLevel_B'
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44 #set $factorlevelsB = list()
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45 #for $file in $countsFiles_B:
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46 $factorlevelsB.append(str($file))
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47 #end for
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48 $factorlevelsB.reverse()
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49 --levelBfiles '#echo json.dumps(factorlevelsB)#'
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50
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51 #set $alignedA = list()
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52 #for file in $alignmentFiles_A:
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53 $alignedA.append(str($file))
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54 #end for
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55 $alignedA.reverse()
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56 --alignmentA '#echo json.dumps(alignedA)#'
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57
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58 #set $alignedB = list()
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59 #for file in $alignmentFiles_B:
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60 $alignedB.append(str($file))
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61 #end for
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62 $alignedB.reverse()
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63 --alignmentB '#echo json.dumps(alignedB)#'
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64
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65 -o 'edger_out'
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66
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67 -p '$plots'
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68 #if $normCounts:
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69 -n '$counts_out'
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70 #end if
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71 -o '$edger_out'
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72 ]]>
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73 </command>
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74 <inputs>
3
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75 <param name="factorName" type="text" value="FactorName" label="Specify a factor name, e.g. genotype or age or drug_x"
0
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76 help="Only letters, numbers and underscores will be retained in this field">
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77 <sanitizer>
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78 <valid initial="string.letters,string.digits"><add value="_" /></valid>
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79 </sanitizer>
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80 </param>
3
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81 <param name="factorLevel_A" type="text" value="FactorLevel1" label="Specify a factor level, typical values could be 'mutant' or 'Drug_X'"
0
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82 help="Only letters, numbers and underscores will be retained in this field">
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83 <sanitizer>
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84 <valid initial="string.letters,string.digits"><add value="_" /></valid>
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85 </sanitizer>
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86 </param>
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87 <param name="countsFiles_A" type="data" format="tabular" multiple="true" label="Counts file(s)" help="Count files must have been generated by repenrich" />
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88 <param name="alignmentFiles_A" type="data" format="tabular" multiple="true" label="Number of aligned reads file(s)" help="files of total aligned reads generated by repenrich"/>
3
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89 <param name="factorLevel_B" type="text" value="FactorLevel2" label="Specify a factor level, typical values could be 'wildtype' or 'control'"
0
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90 help="Only letters, numbers and underscores will be retained in this field">
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91 <sanitizer>
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92 <valid initial="string.letters,string.digits"><add value="_" /></valid>
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93 </sanitizer>
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94 </param>
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95 <param name="countsFiles_B" type="data" format="tabular" multiple="true" label="Counts file(s)" help="Count files must have been generated by repenrich tool" />
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96 <param name="alignmentFiles_B" type="data" format="tabular" multiple="true" label="Number of aligned reads file(s)" help="files of total aligned reads generated by repenrich"/>
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97 <param name="normCounts" type="boolean" truevalue="1" falsevalue="0" checked="false"
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98 label="Output normalized counts table" />
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99 </inputs>
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100 <outputs>
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101 <data format="tabular" name="edger_out" label="edgeR: ${factorLevel_A} compared to ${factorLevel_B}">
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102 <actions>
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103 <action name="column_names" type="metadata" default="Tag,log2(FC),FDR,Class,Type" />
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104 </actions>
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105 </data>
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106 <data format="pdf" name="plots" label="edgeR plots" />
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107 <data format="tabular" name="counts_out" label="Normalized counts file">
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108 <filter>normCounts == True</filter>
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109 </data>
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110 </outputs>
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111 <tests>
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112 <test>
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113 <param name="factorName" value="Genotype"/>
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114 <param name="factorLevel_A" value="Mutant"/>
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115 <param name="countsFiles_A" value="355_fraction_counts.tab,356_fraction_counts.tab"/>
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116 <param name="alignmentFiles_A" value="aligned_355.tab,aligned_356.tab"/>
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117 <param name="factorLevel_B" value="Wildtype"/>
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118 <param name="countsFiles_B" value="353_fraction_counts.tab,354_fraction_counts.tab"/>
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119 <param name="alignmentFiles_B" value="aligned_353.tab,aligned_354.tab"/>
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120 <param name="normCounts" value="True"/>
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121 <output name="counts_out" file="Normalized_counts_file.tab"/>
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122 <output name="plots" file="edgeR_plots.pdf"/>
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123 <output name="edger_out" file="edgeR_result_file.tab"/>
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124
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125 </test>
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126 </tests>
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127 <help>
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128 <![CDATA[
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129 .. class:: infomark
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130
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131 **What it does**
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132
1
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133 Estimate Distance between samples (MDS) and Biological Coefficient Variation (BCV) in count
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134 data from high-throughput sequencing assays and test for differential expression using edgeR_.
0
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135
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136 **Inputs**
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137
1
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138 edger-repenrich takes count tables generated by repenrich as inputs. A repenrich count table looks
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139 like:
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140
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141 ============== ========== ========== ==========
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142 LSU-rRNA_Dme rRNA rRNA 3659329
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143 -------------- ---------- ---------- ----------
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144 FW3_DM LINE Jockey 831
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145 -------------- ---------- ---------- ----------
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146 DMTOM1_LTR LTR Gypsy 1004
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147 -------------- ---------- ---------- ----------
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148 R1_DM LINE R1 7343
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149 -------------- ---------- ---------- ----------
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150 TAHRE LINE Jockey 4560
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151 -------------- ---------- ---------- ----------
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152 G4_DM LINE Jockey 3668
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153 -------------- ---------- ---------- ----------
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154 BS LINE Jockey 7296
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155 -------------- ---------- ---------- ----------
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156 Stalker2_I-int LTR Gypsy 12252
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157 -------------- ---------- ---------- ----------
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158 Stalker3_LTR LTR Gypsy 593
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159 -------------- ---------- ---------- ----------
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160 TABOR_I-int LTR Gypsy 3947
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161 -------------- ---------- ---------- ----------
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162 G7_DM LINE Jockey 162
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163 -------------- ---------- ---------- ----------
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164 BEL_I-int LTR Pao 23757
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165 -------------- ---------- ---------- ----------
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166 Gypsy6_I-int LTR Gypsy 7489
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167 ============== ========== ========== ==========
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168
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169 Count tables must be
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170 generated for each sample individually. Here, edgeR_ is handling a single factor
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171 (genotype, age, treatment, etc) that effect your experiment. This factor has two
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172 levels/states (for instance, "wild-type" and "mutant".
0
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173 You need to select appropriate count table from your history for each factor level.
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174
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175 The following table gives some examples of factors and their levels:
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176
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177 ========= ============== ===============
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178 Factor Factorlevel1 Factorlevel2
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179 --------- -------------- ---------------
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180 Treatment Treated Untreated
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181 --------- -------------- ---------------
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182 Genotype Knockdown Wildtype
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183 --------- -------------- ---------------
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184 TimePoint Day4 Day1
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185 --------- -------------- ---------------
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186 Gender Female Male
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187 ========= ============== ===============
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188
1
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189 *Note*: Output log2 fold changes are based on primary factor level 1 vs. factor level2.
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190 Here the order of factor levels is important. For example, for the factor 'Treatment' given
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191 in above table, edgeR computes fold changes of 'Treated' samples against 'Untreated',
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192 i.e. the values correspond to up or down regulations of genes in Treated samples.
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193
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194 *Number of aligned reads*:
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195
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196 A file containing the number of reads aligned to transposons by repenrich must me provided
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197 to edger-repenrich. This file is a single-column tabular file containing a single value.
0
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198
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199 **Output**
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200
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201 edgeR_ generates a tabular file containing the different columns and results visualized in a PDF:
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202
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203 ====== =============================================================================
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204 Column Description
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205 ------ -----------------------------------------------------------------------------
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206 1 Tag (transposon element ID)
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207 2 the logarithm (to basis 2) of the fold change (See the note in inputs section)
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208 3 p value adjusted for multiple testing with the Benjamini-Hochberg procedure
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209 which controls false discovery rate (FDR)
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210 4 Class the transposon belongs to
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211 5 Type the transposon belongs to
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212 ====== =============================================================================
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213
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214 .. _edgeR: http://www.bioconductor.org/packages/release/bioc/html/edgeR.html
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215 ]]>
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216
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217 **Note**: This edgeR_ wrapper was adapted from code available at https://github.com/nskvir/RepEnrich
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218
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219 </help>
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220 <citations>
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221 <citation type="doi">10.1093/bioinformatics/btp616</citation>
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222 </citations>
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223 </tool>