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1 <tool id="ncPRO-ANNOTATION" name="Annotation">
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2 <description>of mapped reads</description>
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3 <requirements>
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4 <container type="docker">institutcuriengsintegration/ncproseqgalaxy:1.6.5</container>
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5 </requirements>
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6 <command interpreter="bash">
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7
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8 ncPRO-ANNOTATION.sh
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9 -i $input
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10 -g $genome
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11 -t $cond.datatype
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12 -e $cond['database']$cond['borne']$cond['N1']"_"$cond['N2']
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13 -u $ucsc_track
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14 -n $rpm
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15 -l $outlog
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16 #if str($cond.datatype) == "matmir":
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17 #if str($cond['allmiRNA']) == "True":
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18 -o $out_mirna
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19 -a $out_all_mirna
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20 #else
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21 -o $out_mirna
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22 #end if
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23 #elif str($cond.datatype) == 'trna':
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24 -o $out_trna
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25 #elif str($cond.datatype) == 'premir':
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26 #if str($cond['allmiRNA']) == "True":
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27 -o $out_premirna
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28 -a $out_all_premirna
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29 #else
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30 -o $out_premirna
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31 #end if
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32 #elif str($cond.datatype) == 'rfam':
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33 -o $out_rfam
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34 #elif str($cond.datatype) == 'rmsk':
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35 -o $out_rmsk
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36 #end if
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37
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38 #if str($ucsc_track) == 'True':
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39 -v $out_ucsc
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40 #end if
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41 -r ${__root_dir__}
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42 -p $projectName
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43 </command>
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44
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45 <inputs>
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46 <param name="projectName" type="text" value="Project_1" size="20" label="Give a project name" >
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47 <sanitizer invalid_char="">
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48 <valid initial="string.letters,string.digits"><add value="_"/></valid>
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49 </sanitizer>
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50 </param>
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51 <param name="input" type="data" format="bam" label="Select your input file format" help="Aligned file (BAM) is required."/>
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52 <param name="genome" type="select" label="Select a reference genome" help="All the samples have to belong to the same species."> <!-- values should be the same as annotation files names, this value goes to ORGANISM in config file-->
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53 <option value="human_hg19">hg19</option>
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54 <option value="mouse_mm10">mm10</option>
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55 <option value="mouse_mm9">mm9</option>
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56 <option value="zebrafish_Zv9">Zv9</option>
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57 <option value="athaliana_TAIR9">TAIR9</option>
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58 <option value="zebrafinch_taeGut1">taeGut1</option>
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59 <option value="chicken_galGal3">galGal3</option>
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60 <option value="rat_rn4">rn4</option>
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61 <option value="rat_rn5">rn5</option>
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62 <option value="platypus_ornAna1">ornAna1</option>
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63 <option value="opossum_monDom5">monDom5</option>
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64 <option value="macaca_rheMac2">rheMac2</option>
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65 <option value="horse_equCab2">equCab2</option>
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66 <option value="dog_canFam2">canFam2</option>
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67 <option value="dmelanogaster_dm3">dm3</option>
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68 <option value="cow_bosTau4">bosTau4</option>
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69 <option value="celegans_ce6">ce6</option>
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70 </param>
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71
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72 <conditional name="cond">
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73 <param name="datatype" type="select" label="Annotate mapped reads against the following database" help="ncPRO-seq allows to calculate the reads coverage for each feature of an annotation database.">
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74 <option value="matmir">mature miRNAs from miRBase</option>
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75 <option value="premir">precursor miRNAs from miRBase</option>
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76 <option value="trna">tRNA from UCSC</option>
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77 <option value="rfam">Other ncRNAs from RFAM</option>
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78 <option value="rmsk">Repeats from RepeatMasker</option>
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79 <option value="other">Other custom annotation file</option>
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80 </param>
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81
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82
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83 <!--OTHER annotation files -->
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84
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85 <when value="other">
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86 <param name="database" type="data" format="gff3" label="Select a file for reads annotation" help="standard gff3 format is required."/>
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87 <!-- this is only to make my life easier .. None of this will be used !!-->
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88 <param name="borne" type="hidden" value="," />
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89 <param name="N1" type="hidden" value="0"/>
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90 <param name="N2" type="hidden" value="0"/>
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91
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92
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93 <!-- None of this will be used !!-->
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94 </when>
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95 <!--END OTHER annotation files -->
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96
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97 <when value="matmir">
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98
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99 <!-- mature mi RNA : NO repeats in annotation !-->
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100
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101 <param name="borne" type="select" label="Method" help="Only read alignments which have 100% overlap with annotations will be counted. Thus, it can be interesing to modified the coordinates of genomic annotation according to your biological question.">
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102 <option value="_e_">Extend the annotation</option>
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103 <option value="_i_">Shorten the annotation</option>
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104 <option value="_s_">Focus on the 5' end</option>
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105 <option value="_t_">Focus on the 3' end</option>
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106
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107
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108 </param>
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109 <param name="database" type="hidden" value="miRNA" />
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110 <param name="N1" type="text" size="4" value="+0" label="From">
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111 <help>Fill this field with +/- value</help>
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112 </param>
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113 <param name="N2" type="text" size="4" value="+0" label="To">
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114 <help>Fill this field with +/- value</help>
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115 </param>
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116 <param name="allmiRNA" type="boolean" value="False" truevalue="True" falsevalue="False" label="All miRBase miRNA" help="Create a result file with all miRBase RNA (even if the miRNA mappes with 0 sequence)"/>
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117 </when>
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118
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119
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120 <!-- PRE miRNA : NO repeats in annotation -->
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121 <when value="premir">
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122
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123 <param name="borne" type="select" label="Method" help="Only read alignments which have 100% overlap with annotations will be counted. Thus, it can be interesing to modified the coordinates of genomic annotation according to your biological question.">
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124 <option value="_e_">Extend the annotation</option>
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125 <option value="_i_">Shorten the annotation</option>
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126 <option value="_s_">Focus on the 5' end</option>
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127 <option value="_t_">Focus on the 3' end</option>
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128
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129 </param>
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130 <param name="database" type="hidden" value="miRNA" />
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131 <param name="N1" type="text" size="4" value="+0" label="From">
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132 <help>Fill this field with +/- value</help>
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133 </param>
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134 <param name="N2" type="text" size="4" value="+0" label="To">
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135 <help>Fill this field with +/- value</help>
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136 </param>
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137 <param name="allmiRNA" type="boolean" value="False" truevalue="True" falsevalue="False" label="All miRBase miRNA" help="Create a result file with all miRBase RNA (even if the miRNA mappes with 0 sequence)"/>
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138 </when>
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139
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140
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141 <!-- TRNA : NO repeats in annotation -->
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142 <when value="trna">
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143 <param name="borne" type="select" label="Method" help="Only read alignments which have 100% overlap with annotations will be counted. Thus, it can be interesing to modified the coordinates of genomic annotation according to your biological question.">
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144 <option value="_e_">Extend the annotation</option>
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145 <option value="_i_">Shorten the annotation</option>
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146 <option value="_s_">Focus on the 5' end</option>
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147 <option value="_t_">Focus on the 3' end</option>
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148 </param>
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149 <param name="database" type="hidden" value="tRNA" />
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150 <param name="N1" type="text" size="4" value="+0" label="From">
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151 <help>Fill this field with +/- value</help>
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152 </param>
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153 <param name="N2" type="text" size="4" value="+0" label="To">
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154 <help>Fill this field with +/- value</help>
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155 </param>
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156 </when>
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157
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158
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159
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160 <!-- RFAM -->
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161 <when value="rfam">
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162 <param name="database" type="select" label="Select a sub-family to focus on"> <!-- sub-families are listed in annotation/rfam_items.txt-->
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163 <option value="5_8S_rRNA">5_8S_rRNA</option>
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164 <option value="5S_rRNA">5S_rRNA</option>
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165 <option value="7SK">7SK</option>
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166 <option value="ACA64">ACA64</option>
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167 <option value="Antizyme_FSE">Antizyme_FSE</option>
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168 <option value="CAESAR">CAESAR</option>
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169 <option value="CPEB3_ribozyme">CPEB3_ribozyme</option>
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170 <option value="Gammaretro_CES">Gammaretro_CES</option>
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171 <option value="G-CSF_SLDE">G-CSF_SLDE</option>
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172 <option value="GP_knot1">GP_knot1</option>
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173 <option value="GRIK4_3p_UTR">GRIK4_3p_UTR</option>
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174 <option value="Histone3">Histone3</option>
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175 <option value="IRE">IRE</option>
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176 <option value="IRES_Bag1">IRES_Bag1</option>
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177 <option value="IRES_Bip">IRES_Bip</option>
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178 <option value="IRES_c-myc">IRES_c-myc</option>
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179 <option value="IRES_c-sis">IRES_c-sis</option>
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180 <option value="IRES_Cx32">IRES_Cx32</option>
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181 <option value="IRES_Cx43">IRES_Cx43</option>
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182 <option value="IRES_FGF1">IRES_FGF1</option>
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183 <option value="IRES_HIF1">IRES_HIF1</option>
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184 <option value="IRES_IGF2">IRES_IGF2</option>
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185 <option value="IRES_Kv1_4">IRES_Kv1_4</option>
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186 <option value="IRES_L-myc">IRES_L-myc</option>
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187 <option value="IRES_mnt">IRES_mnt</option>
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188 <option value="IRES_n-myc">IRES_n-myc</option>
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189 <option value="IRES_TrkB">IRES_TrkB</option>
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190 <option value="IRES_VEGF_A">IRES_VEGF_A</option>
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191 <option value="K_chan_RES">K_chan_RES</option>
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192 <option value="let-7">let-7</option>
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193 <option value="lin-4">lin-4</option>
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194 <option value="NRON">NRON</option>
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195 <option value="p27_CRE">p27_CRE</option>
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196 <option value="Prion_pknot">Prion_pknot</option>
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197 <option value="REN-SRE">REN-SRE</option>
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198 <option value="RF_site4">RF_site4</option>
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199 <option value="RF_site5">RF_site5</option>
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200 <option value="RF_site9">RF_site9</option>
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201 <option value="RNase_MRP">RNase_MRP</option>
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202 <option value="RNaseP_nuc">RNaseP_nuc</option>
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203 <option value="SCARNA1">SCARNA1</option>
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204 <option value="SCARNA11">SCARNA11</option>
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205 <option value="SCARNA13">SCARNA13</option>
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206 <option value="SCARNA14">SCARNA14</option>
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207 <option value="SCARNA15">SCARNA15</option>
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208 <option value="SCARNA16">SCARNA16</option>
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209 <option value="SCARNA17">SCARNA17</option>
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210 <option value="SCARNA18">SCARNA18</option>
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211 <option value="SCARNA20">SCARNA20</option>
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212 <option value="SCARNA21">SCARNA21</option>
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213 <option value="SCARNA23">SCARNA23</option>
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214 <option value="SCARNA24">SCARNA24</option>
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215 <option value="SCARNA3">SCARNA3</option>
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216 <option value="SCARNA4">SCARNA4</option>
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217 <option value="SCARNA6">SCARNA6</option>
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218 <option value="SCARNA8">SCARNA8</option>
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219 <option value="SECIS">SECIS</option>
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220 <option value="snoMBII-202">snoMBII-202</option>
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221 <option value="snoR38">snoR38</option>
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222 <option value="SNORA1">SNORA1</option>
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223 <option value="SNORA11">SNORA11</option>
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224 <option value="SNORA12">SNORA12</option>
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225 <option value="SNORA13">SNORA13</option>
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226 <option value="SNORA14">SNORA14</option>
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227 <option value="SNORA15">SNORA15</option>
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228 <option value="SNORA16">SNORA16</option>
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229 <option value="SNORA17">SNORA17</option>
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230 <option value="SNORA18">SNORA18</option>
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231 <option value="SNORA19">SNORA19</option>
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232 <option value="SNORA2">SNORA2</option>
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233 <option value="SNORA20">SNORA20</option>
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234 <option value="SNORA21">SNORA21</option>
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235 <option value="SNORA22">SNORA22</option>
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236 <option value="SNORA23">SNORA23</option>
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237 <option value="SNORA24">SNORA24</option>
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238 <option value="SNORA25">SNORA25</option>
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239 <option value="SNORA26">SNORA26</option>
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240 <option value="SNORA27">SNORA27</option>
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241 <option value="SNORA28">SNORA28</option>
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242 <option value="SNORA29">SNORA29</option>
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243 <option value="SNORA3">SNORA3</option>
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244 <option value="SNORA30">SNORA30</option>
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245 <option value="SNORA31">SNORA31</option>
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246 <option value="SNORA32">SNORA32</option>
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247 <option value="SNORA33">SNORA33</option>
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248 <option value="SNORA35">SNORA35</option>
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249 <option value="SNORA36">SNORA36</option>
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250 <option value="SNORA38">SNORA38</option>
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251 <option value="SNORA4">SNORA4</option>
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252 <option value="SNORA40">SNORA40</option>
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253 <option value="SNORA41">SNORA41</option>
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254 <option value="SNORA42">SNORA42</option>
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255 <option value="SNORA43">SNORA43</option>
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256 <option value="SNORA44">SNORA44</option>
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257 <option value="SNORA46">SNORA46</option>
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258 <option value="SNORA47">SNORA47</option>
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259 <option value="SNORA48">SNORA48</option>
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260 <option value="SNORA49">SNORA49</option>
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261 <option value="SNORA5">SNORA5</option>
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262 <option value="SNORA50">SNORA50</option>
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263 <option value="SNORA51">SNORA51</option>
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264 <option value="SNORA52">SNORA52</option>
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265 <option value="SNORA53">SNORA53</option>
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266 <option value="SNORA54">SNORA54</option>
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267 <option value="SNORA55">SNORA55</option>
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268 <option value="SNORA57">SNORA57</option>
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269 <option value="SNORA58">SNORA58</option>
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270 <option value="SNORA61">SNORA61</option>
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271 <option value="SNORA62">SNORA62</option>
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272 <option value="SNORA63">SNORA63</option>
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273 <option value="SNORA64">SNORA64</option>
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274 <option value="SNORA65">SNORA65</option>
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275 <option value="SNORA66">SNORA66</option>
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276 <option value="SNORA67">SNORA67</option>
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277 <option value="SNORA68">SNORA68</option>
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278 <option value="SNORA69">SNORA69</option>
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279 <option value="SNORA7">SNORA7</option>
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280 <option value="SNORA70">SNORA70</option>
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281 <option value="SNORA71">SNORA71</option>
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282 <option value="SNORA72">SNORA72</option>
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283 <option value="SNORA73">SNORA73</option>
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284 <option value="SNORA74">SNORA74</option>
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285 <option value="SNORA75">SNORA75</option>
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286 <option value="SNORA76">SNORA76</option>
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287 <option value="SNORA77">SNORA77</option>
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288 <option value="SNORA79">SNORA79</option>
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289 <option value="SNORA8">SNORA8</option>
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290 <option value="SNORA81">SNORA81</option>
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291 <option value="SNORA84">SNORA84</option>
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292 <option value="SNORA9">SNORA9</option>
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293 <option value="SNORD100">SNORD100</option>
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294 <option value="SNORD101">SNORD101</option>
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295 <option value="SNORD102">SNORD102</option>
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296 <option value="SNORD103">SNORD103</option>
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297 <option value="SNORD105">SNORD105</option>
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298 <option value="SNORD107">SNORD107</option>
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299 <option value="SNORD11">SNORD11</option>
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300 <option value="SNORD110">SNORD110</option>
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301 <option value="SNORD111">SNORD111</option>
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302 <option value="SNORD113">SNORD113</option>
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303 <option value="SNORD115">SNORD115</option>
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304 <option value="SNORD116">SNORD116</option>
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305 <option value="SNORD11B">SNORD11B</option>
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306 <option value="SNORD12">SNORD12</option>
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307 <option value="SNORD121A">SNORD121A</option>
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308 <option value="SNORD123">SNORD123</option>
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309 <option value="SNORD124">SNORD124</option>
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310 <option value="SNORD125">SNORD125</option>
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311 <option value="SNORD127">SNORD127</option>
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312 <option value="SNORD14">SNORD14</option>
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313 <option value="SNORD15">SNORD15</option>
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314 <option value="SNORD16">SNORD16</option>
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315 <option value="SNORD17">SNORD17</option>
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316 <option value="SNORD18">SNORD18</option>
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317 <option value="SNORD19">SNORD19</option>
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318 <option value="SNORD19B">SNORD19B</option>
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319 <option value="SNORD20">SNORD20</option>
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320 <option value="SNORD21">SNORD21</option>
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321 <option value="SNORD22">SNORD22</option>
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322 <option value="SNORD23">SNORD23</option>
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323 <option value="SNORD24">SNORD24</option>
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324 <option value="SNORD25">SNORD25</option>
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325 <option value="SNORD26">SNORD26</option>
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326 <option value="SNORD27">SNORD27</option>
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327 <option value="SNORD28">SNORD28</option>
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328 <option value="SNORD29">SNORD29</option>
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329 <option value="SNORD30">SNORD30</option>
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330 <option value="SNORD31">SNORD31</option>
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331 <option value="SNORD33">SNORD33</option>
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332 <option value="SNORD34">SNORD34</option>
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333 <option value="SNORD35">SNORD35</option>
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334 <option value="SNORD36">SNORD36</option>
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335 <option value="SNORD37">SNORD37</option>
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336 <option value="SNORD38">SNORD38</option>
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337 <option value="SNORD41">SNORD41</option>
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338 <option value="SNORD42">SNORD42</option>
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339 <option value="SNORD43">SNORD43</option>
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340 <option value="SNORD45">SNORD45</option>
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341 <option value="SNORD46">SNORD46</option>
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342 <option value="SNORD47">SNORD47</option>
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343 <option value="SNORD48">SNORD48</option>
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344 <option value="SNORD49">SNORD49</option>
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345 <option value="SNORD5">SNORD5</option>
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346 <option value="SNORD50">SNORD50</option>
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347 <option value="SNORD51">SNORD51</option>
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348 <option value="SNORD52">SNORD52</option>
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349 <option value="SNORD53">SNORD53</option>
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350 <option value="SNORD55">SNORD55</option>
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351 <option value="SNORD56">SNORD56</option>
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352 <option value="SNORD57">SNORD57</option>
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353 <option value="SNORD58">SNORD58</option>
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354 <option value="SNORD59">SNORD59</option>
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355 <option value="SNORD60">SNORD60</option>
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356 <option value="SNORD61">SNORD61</option>
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357 <option value="SNORD62">SNORD62</option>
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358 <option value="SNORD63">SNORD63</option>
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359 <option value="SNORD64">SNORD64</option>
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360 <option value="SNORD65">SNORD65</option>
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361 <option value="SNORD66">SNORD66</option>
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362 <option value="SNORD67">SNORD67</option>
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363 <option value="SNORD69">SNORD69</option>
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364 <option value="SNORD70">SNORD70</option>
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365 <option value="SNORD71">SNORD71</option>
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366 <option value="SNORD72">SNORD72</option>
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367 <option value="SNORD73">SNORD73</option>
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368 <option value="SNORD74">SNORD74</option>
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369 <option value="SNORD75">SNORD75</option>
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370 <option value="SNORD78">SNORD78</option>
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371 <option value="SNORD79">SNORD79</option>
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372 <option value="SNORD81">SNORD81</option>
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373 <option value="SNORD82">SNORD82</option>
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374 <option value="SNORD83">SNORD83</option>
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375 <option value="SNORD86">SNORD86</option>
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|
376 <option value="SNORD87">SNORD87</option>
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|
377 <option value="SNORD88">SNORD88</option>
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|
|
378 <option value="SNORD89">SNORD89</option>
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379 <option value="SNORD90">SNORD90</option>
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380 <option value="SNORD91">SNORD91</option>
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381 <option value="SNORD92">SNORD92</option>
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382 <option value="SNORD93">SNORD93</option>
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383 <option value="SNORD94">SNORD94</option>
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384 <option value="SNORD95">SNORD95</option>
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385 <option value="SNORD96">SNORD96</option>
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386 <option value="SNORD98">SNORD98</option>
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|
387 <option value="SNORD99">SNORD99</option>
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388 <option value="SNORND104">SNORND104</option>
|
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|
389 <option value="snosnR60_Z15">snosnR60_Z15</option>
|
|
|
390 <option value="snoU105B">snoU105B</option>
|
|
|
391 <option value="snoU109">snoU109</option>
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|
392 <option value="snoU13">snoU13</option>
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|
393 <option value="snoU2_19">snoU2_19</option>
|
|
|
394 <option value="snoU2-25">snoU2-25</option>
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|
395 <option value="snoU2-30">snoU2-30</option>
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|
|
396 <option value="snoU54">snoU54</option>
|
|
|
397 <option value="snoU6-53">snoU6-53</option>
|
|
|
398 <option value="snoU6-77">snoU6-77</option>
|
|
|
399 <option value="snoU82P">snoU82P</option>
|
|
|
400 <option value="snoU83B">snoU83B</option>
|
|
|
401 <option value="snoU85">snoU85</option>
|
|
|
402 <option value="snoU89">snoU89</option>
|
|
|
403 <option value="snoU90">snoU90</option>
|
|
|
404 <option value="snoU97">snoU97</option>
|
|
|
405 <option value="snoZ17">snoZ17</option>
|
|
|
406 <option value="snoZ30">snoZ30</option>
|
|
|
407 <option value="snoZ39">snoZ39</option>
|
|
|
408 <option value="snoZ40">snoZ40</option>
|
|
|
409 <option value="snR39B">snR39B</option>
|
|
|
410 <option value="Spi-1">Spi-1</option>
|
|
|
411 <option value="SSU_rRNA_5">SSU_rRNA_5</option>
|
|
|
412 <option value="Telomerase-vert">Telomerase-vert</option>
|
|
|
413 <option value="tRNA">tRNA</option>
|
|
|
414 <option value="U1">U1</option>
|
|
|
415 <option value="U11">U11</option>
|
|
|
416 <option value="U12">U12</option>
|
|
|
417 <option value="U1A_PIE">U1A_PIE</option>
|
|
|
418 <option value="U2">U2</option>
|
|
|
419 <option value="U3">U3</option>
|
|
|
420 <option value="U4">U4</option>
|
|
|
421 <option value="U4atac">U4atac</option>
|
|
|
422 <option value="U5">U5</option>
|
|
|
423 <option value="U6">U6</option>
|
|
|
424 <option value="U6atac">U6atac</option>
|
|
|
425 <option value="U7">U7</option>
|
|
|
426 <option value="U8">U8</option>
|
|
|
427 <option value="Vault">Vault</option>
|
|
|
428 <option value="Vimentin3">Vimentin3</option>
|
|
|
429 <option value="Y_RNA">Y_RNA</option>
|
|
|
430 </param>
|
|
|
431
|
|
|
432
|
|
|
433 <param name="borne" type="select" label="Method" help="Only read alignments which have 100% overlap with annotations will be counted. Thus, it can be interesing to modified the coordinates of genomic annotation according to your biological question.">
|
|
|
434 <option value="_e_">Extend the annotation</option>
|
|
|
435 <option value="_i_">Shorten the annotation</option>
|
|
|
436 <option value="_s_">Focus on the 5' end</option>
|
|
|
437 <option value="_t_">Focus on the 3' end</option>
|
|
|
438 </param>
|
|
|
439 <param name="N1" type="text" size="4" value="+0" label="From">
|
|
|
440 <help>Fill this field with +/- value</help>
|
|
|
441 </param>
|
|
|
442 <param name="N2" type="text" size="4" value="+0" label="To">
|
|
|
443 <help>Fill this field with +/- value</help>
|
|
|
444 </param>
|
|
|
445
|
|
|
446 </when>
|
|
|
447
|
|
|
448 <!-- sub-families are listed in annotation/rmsk_items.txt -->
|
|
|
449 <when value="rmsk">
|
|
|
450 <param name="database" type="select" label="Select a sub-family to focus on:">
|
|
|
451 <option value="AcHobo">AcHobo</option>
|
|
|
452 <option value="Alu">Alu</option>
|
|
|
453 <option value="B2">B2</option>
|
|
|
454 <option value="B4">B4</option>
|
|
|
455 <option value="centr">centr</option>
|
|
|
456 <option value="Charlie">Charlie</option>
|
|
|
457 <option value="CR1">CR1</option>
|
|
|
458 <option value="DNA">DNA</option>
|
|
|
459 <option value="ERV">ERV</option>
|
|
|
460 <option value="ERV1">ERV1</option>
|
|
|
461 <option value="ERVK">ERVK</option>
|
|
|
462 <option value="ERVL">ERVL</option>
|
|
|
463 <option value="Gypsy">Gypsy</option>
|
|
|
464 <option value="hAT">hAT</option>
|
|
|
465 <option value="Helitron">Helitron</option>
|
|
|
466 <option value="ID">ID</option>
|
|
|
467 <option value="IAP">IAP</option>
|
|
|
468 <option value="L1">L1</option>
|
|
|
469 <option value="L1Md_T">L1Md_T</option>
|
|
|
470 <option value="L1Md_Gf">L1Md_Gf</option>
|
|
|
471 <option value="L1Md_A">L1Md_A</option>
|
|
|
472 <option value="L2">L2</option>
|
|
|
473 <option value="Low_complexity">Low_complexity</option>
|
|
|
474 <option value="LTR">LTR</option>
|
|
|
475 <option value="MaLR">MaLR</option>
|
|
|
476 <option value="Mariner">Mariner</option>
|
|
|
477 <option value="MER1_type">MER1_type</option>
|
|
|
478 <option value="MER2_type">MER2_type</option>
|
|
|
479 <option value="MIR">MIR</option>
|
|
|
480 <option value="MuDR">MuDR</option>
|
|
|
481 <option value="PiggyBac">PiggyBac</option>
|
|
|
482 <option value="rRNA">rRNA</option>
|
|
|
483 <option value="RTE">RTE</option>
|
|
|
484 <option value="Satellite">Satellite</option>
|
|
|
485 <option value="scRNA">scRNA</option>
|
|
|
486 <option value="Simple_repeat">Simple_repeat</option>
|
|
|
487 <option value="SINE">SINE</option>
|
|
|
488 <option value="snRNA">snRNA</option>
|
|
|
489 <option value="srpRNA">srpRNA</option>
|
|
|
490 <option value="Tc2">Tc2</option>
|
|
|
491 <option value="TcMar">TcMar</option>
|
|
|
492 <option value="Tigger">Tigger</option>
|
|
|
493 <option value="Tip100">Tip100</option>
|
|
|
494 <option value="tRNA">tRNA</option>
|
|
|
495 </param>
|
|
|
496
|
|
|
497
|
|
|
498 <param name="borne" type="select" label="Method" help="Only read alignments which have 100% overlap with annotations will be counted. Thus, it can be interesing to modified the coordinates of genomic annotation according to your biological question.">
|
|
|
499 <option value="_e_">Extend the annotation</option>
|
|
|
500 <option value="_i_">Shorten the annotation</option>
|
|
|
501 <option value="_s_">Focus on the 5' end</option>
|
|
|
502 <option value="_t_">Focus on the 3' end</option>
|
|
|
503 </param>
|
|
|
504 <param name="N1" type="text" size="4" value="+0" label="From">
|
|
|
505 <help>Fill this field with +/- value</help>
|
|
|
506 </param>
|
|
|
507 <param name="N2" type="text" size="4" value="+0" label="To">
|
|
|
508 <help>Fill this field with +/- value</help>
|
|
|
509 </param>
|
|
|
510
|
|
|
511
|
|
|
512 </when>
|
|
|
513 </conditional>
|
|
|
514
|
|
|
515
|
|
|
516 <param name="rpm" type="boolean" value="False" truevalue="True" falsevalue="False" label="Reads Per Million (RPM) normalization of reads counts" />
|
|
|
517 <param name="ucsc_track" type="boolean" value="False" truevalue="True" falsevalue="False" label="Create IGV tracks for ncRNA visualization" />
|
|
|
518
|
|
|
519
|
|
|
520 </inputs>
|
|
|
521
|
|
|
522 <outputs>
|
|
|
523 <data format="tabular" name="out_mirna" label="miRNA annotation table">
|
|
|
524 <filter>(str(cond['datatype']) == "matmir")</filter>
|
|
|
525 </data>
|
|
|
526 <data format="tabular" name="out_all_mirna" label="miRNA annotation table with all miRBase RNA">
|
|
|
527 <filter>((str(cond['datatype']) == "matmir") and (cond['allmiRNA'] == True))</filter>
|
|
|
528 </data>
|
|
|
529 <data format="tabular" name="out_premirna" label="premiRNA annotation table">
|
|
|
530 <filter>(str(cond['datatype']) == "premir")</filter>
|
|
|
531 </data>
|
|
|
532 <data format="tabular" name="out_all_premirna" label="premiRNA annotation table with all miRBase RNA">
|
|
|
533 <filter>((str(cond['datatype']) == "premir") and (cond['allmiRNA'] == True))</filter>
|
|
|
534 </data>
|
|
|
535 <data format="tabular" name="out_trna" label="tRNA annotation table">
|
|
|
536 <filter>(str(cond['datatype']) == "trna")</filter>
|
|
|
537 </data>
|
|
|
538 <data format="tabular" name="out_rfam" label="ncRNA annotation table">
|
|
|
539 <filter>(str(cond['datatype']) == "rfam")</filter>
|
|
|
540 </data>
|
|
|
541 <data format="tabular" name="out_rmsk" label="repeats annotation table">
|
|
|
542 <filter>(str(cond['datatype']) == "rmsk")</filter>
|
|
|
543 </data>
|
|
|
544
|
|
|
545 <data format="bed" name="out_ucsc" label="annotation tracks (testing sens track)">
|
|
|
546 <filter>(str(ucsc_track) == 'True')</filter>
|
|
|
547 </data>
|
|
|
548
|
|
|
549 <data format="txt" name="outlog" label="ncPRO log">
|
|
|
550 </data>
|
|
|
551 </outputs>
|
|
|
552 <help>
|
|
|
553
|
|
|
554 **What ncPRO-seq does ?**
|
|
|
555
|
|
|
556 ------
|
|
|
557
|
|
|
558 ncPRO-seq is a tool for annotation and profiling of ncRNAs from smallRNA sequencing data. It aims to interrogate and perform detailed analysis on small RNAs derived from annotated non-coding regions in miRBase, Rfam and repeatMasker, and regions defined by users. A command line version and an online version are available at http://ncpro.curie.fr.
|
|
|
559 If you use the ncPRO-seq tool for your analysis, please cite the following paper :
|
|
|
560 Chen C., Servant N., Toedling J., Sarazin A., Marchais A., Duvernois-Berthet E., Cognat V., Colot V., Voinnet O., Heard E., Ciaudo C. and Barillot E. (2012) ncPRO-seq: a tool for annotation and profiling analysis of ncRNAs from small RNA-seq.Bioinformatics.28(23):3147-9.
|
|
|
561
|
|
|
562 # Copyleft ↄ⃝ 2012 Institut Curie
|
|
|
563 # Author(s): Jocelyn Brayet, Laurene Syx, Chongjian Chen, Nicolas Servant(Institut Curie) 2012 - 2015
|
|
|
564 # Contact: bioinfo.ncproseq@curie.fr
|
|
|
565 # This software is distributed without any guarantee under the terms of the GNU General
|
|
|
566 # Public License, either Version 2, June 1991 or Version 3, June 2007.
|
|
|
567
|
|
|
568 ------
|
|
|
569
|
|
|
570 **Input Formats**
|
|
|
571
|
|
|
572 Aligned file (BAM) is allowed. See ncPRO-seq Alignment and quality control for more details.
|
|
|
573
|
|
|
574 ------
|
|
|
575
|
|
|
576 **Annotation**
|
|
|
577
|
|
|
578 To find overlaps between read alignments and genomic annotations, intersectBed tool in
|
|
|
579 BEDTools is implemented. Only read alignments which have 100% overlap with annotations are reported
|
|
|
580 by setting -f option in intersectBed to 1.
|
|
|
581
|
|
|
582 -Reads with multiple mapping sites
|
|
|
583 A major challenging problem using NGS sequencing data is the annotation of reads aligned at multiple
|
|
|
584 locations. Most of the available frameworks resolve this situation by discarding these reads or by
|
|
|
585 providing random annotations. Here, we propose to keep all the reads aligned to the genome, and to
|
|
|
586 weight them by the number of mapping sites. Suppose a read can be aligned 5 times to the genome,
|
|
|
587 for each mapping site, the read would be counted as 0.2, i.e. 1/5.
|
|
|
588
|
|
|
589 -Annotation
|
|
|
590 There are four types of extended items which can be used to modify coordinates.
|
|
|
591 1- shorten [+-]N1 bp at 5' end, [+-]N2 bp at 3' end
|
|
|
592 2- extend [+-]N1 bp at 5' end, [+-]N2 bp at 3' end
|
|
|
593 3- get coordinates for sub-region from position N1 to N2 indexed from 5' end
|
|
|
594 4- get coordinates for sub-region from position N1 to N2 indexed from 3' end
|
|
|
595
|
|
|
596 For instance, due to the inaccurate processing of precursor miRNAs by Dicer or downstream miRNA remodelling, mature miRNAs often have end heterogeneities comparing to their annotations in miRBase. Thus, when analyzing mature miRNAs, it is necessary to extend miRNA annotation several bases (e.g. 2 bases) in both upstream and downstream region.
|
|
|
597
|
|
|
598 </help>
|
|
|
599 </tool>
|
