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1 <tool id="defuse" name="DeFuse" version="1.5">
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2 <description>identify fusion transcripts</description>
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3 <requirements>
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4 <requirement type="package" version="0.5.0">defuse</requirement>
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5 <requirement type="package">bowtie</requirement>
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6 <requirement type="package">blat</requirement>
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7 <requirement type="package">fatotwobit</requirement>
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8 </requirements>
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9 <command interpreter="command"> /bin/bash $shscript </command>
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10 <inputs>
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11 <param name="left_pairendreads" type="data" format="fastq" label="left part of read pairs" help="The left and right reads pairs must be in the same order, and not have any unpaired reads. (FASTQ interlacer will pair reads and remove the unpaired. FASTQ de-interlacer will separate the result into left and right reads.)"/>
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12 <param name="right_pairendreads" type="data" format="fastq" label="right part of read pairs" help="In the same order as the left reads"/>
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13 <conditional name="refGenomeSource">
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14 <param name="genomeSource" type="select" label="Will you select a built-in DeFuse Reference Dataset, or supply a configuration from your history" help="">
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15 <option value="indexed">Use a built-in DeFuse Reference Dataset</option>
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16 <option value="history">Use a configuration from your history that specifies the DeFuse Reference Dataset</option>
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17 </param>
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18 <when value="indexed">
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19 <param name="index" type="select" label="Select a Reference Dataset" help="if your genome of interest is not listed - contact Galaxy team">
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20 <options from_file="defuse.loc">
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21 <column name="name" index="1"/>
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22 <column name="value" index="2"/>
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23 <filter type="sort_by" column="0" />
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24 <validator type="no_options" message="No indexes are available" />
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25 </options>
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26 </param>
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27 <conditional name="defuse_param">
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28 <param name="settings" type="select" label="Defuse parameter settings" help="">
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29 <option value="preSet">Default settings</option>
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30 <option value="full">Full parameter list</option>
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31 </param>
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32 <when value="preSet" />
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33 <when value="full">
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34 <param name="max_insert_size" type="integer" value="500" optional="true" label="Bowtie max_insert_size" />
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35 <param name="dna_concordant_length" type="integer" value="2000" optional="true" label="Minimum gene fusion range dna_concordant_length" />
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36 <param name="discord_read_trim" type="integer" value="50" optional="true" label="Trim length for discordant reads discord_read_trim" help="(split reads are not trimmed)" />
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37 <param name="clustering_precision" type="float" value=".95" optional="true" label="Filter clustering_precision">
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38 <validator type="in_range" message="Choose a value between .1 and 1.0" min=".1" max="1"/>
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39 </param>
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40 <param name="span_count_threshold" type="integer" value="5" optional="true" label="Filter span_count_threshold" />
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41 <param name="split_count_threshold" type="integer" value="3" optional="true" label="Filter split_count_threshold" />
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42 <param name="percent_identity_threshold" type="float" value=".90" optional="true" label="Filter percent_identity_threshold">
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43 <validator type="in_range" message="Choose a value between .1 and 1.0" min=".1" max="1"/>
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44 </param>
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45 <param name="max_dist_pos" type="integer" value="600" optional="true" label="Filter max_dist_pos" />
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46 <param name="num_dist_genes" type="integer" value="500" optional="true" label="Filter num_dist_genes" />
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47 <param name="split_min_anchor" type="integer" value="4" optional="true" label="Filter split_min_anchor" />
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48 <param name="max_concordant_ratio" type="float" value="0.1" optional="true" label="Filter max_concordant_ratio">
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49 <validator type="in_range" message="Choose a value between 0.0 and 1.0" min="0" max="1"/>
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50 </param>
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51 <param name="splice_bias" type="integer" value="10" optional="true" label="Filter splice_bias" />
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52 <param name="probability_threshold" type="float" value="0.50" optional="true" label="Filter probability_threshold">
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53 <validator type="in_range" message="Choose a value between 0.0 and 1.0" min="0" max="1"/>
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54 </param>
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55 <param name="covariance_sampling_density" type="float" value="0.01" optional="true" label="covariance_sampling_density">
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56 <help>Position density when calculating covariance</help>
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57 <validator type="in_range" message="Choose a value between 0.0 and 1.0" min="0" max="1"/>
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58 </param>
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59 <param name="denovo_assembly" type="select" label="denovo_assembly" help="">
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60 <option value="">Use Default</option>
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61 <option value="no">no</option>
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62 <option value="yes">yes</option>
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63 </param>
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64 <!--
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65 <param name="positive_controls" type="data" format="txt" optional=true label="Defuse positive_controls" help=""/>
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66 -->
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67 </when> <!-- full -->
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68 </conditional> <!-- defuse_param -->
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69 </when>
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70 <when value="history">
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71 <param name="config" type="data" format="txt" label="Defuse Config file" help=""/>
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72 </when> <!-- history -->
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73 </conditional> <!-- refGenomeSource -->
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74 <param name="keep_output" type="boolean" checked="true" truevalue="yes" falsevalue="no" label="Save DeFuse working directory files"/>
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75 <param name="do_get_reads" type="boolean" checked="false" truevalue="yes" falsevalue="no" label="Run get_reads on each cluster"/>
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76 </inputs>
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77 <configfiles>
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78 <configfile name="defuse_config">
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79 #import ast
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80 #if $refGenomeSource.genomeSource == "history":
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81 #include raw $refGenomeSource.config.__str__
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82 #else
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83 #set $ref_dict = dict($ast.literal_eval($refGenomeSource.index.value))
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84 #
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85 # Configuration file for defuse
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86 #
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87 # At a minimum, change all values enclused by []
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88 #
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89
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90 # Directory where the defuse code was unpacked
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91 ## Default location in the tool/defuse directory
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92 # source_directory = ${__root_dir__}/tools/defuse
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93 source_directory = #slurp
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94 #try
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95 $ref_dict['source_directory']
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96 #except
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97 __DEFUSE_PATH__
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98 #end try
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99
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100 # Directory where you want your dataset
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101 dataset_directory = #slurp
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102 #try
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103 $ref_dict['dataset_directory']
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104 #except
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105 /project/db/genomes/Hsapiens/hg19/defuse
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106 #end try
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107
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108 # Input genome and gene models
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109 gene_models = #slurp
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110 #try
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111 $ref_dict['gene_models']
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112 #except
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113 \$(dataset_directory)/Homo_sapiens.GRCh37.62.gtf
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114 #end try
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115 genome_fasta = #slurp
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116 #try
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117 $ref_dict['genome_fasta']
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118 #except
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119 \$(dataset_directory)/Homo_sapiens.GRCh37.62.dna.chromosome.fa
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120 #end try
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121
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122 # Repeat table from ucsc genome browser
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123 repeats_filename = #slurp
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124 #try
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125 $ref_dict['repeats_filename']
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126 #except
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127 \$(dataset_directory)/rmsk.txt
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128 #end try
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129
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130 # EST info downloaded from ucsc genome browser
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131 est_fasta = #slurp
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132 #try
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133 $ref_dict['est_fasta']
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134 #except
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135 \$(dataset_directory)/est.fa
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136 #end try
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137 est_alignments = #slurp
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138 #try
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139 $ref_dict['est_alignments']
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140 #except
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141 \$(dataset_directory)/intronEst.txt
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142 #end try
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143
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144 # Unigene clusters downloaded from ncbi
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145 unigene_fasta = #slurp
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146 #try
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147 $ref_dict['unigene_fasta']
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148 #except
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149 \$(dataset_directory)/Hs.seq.uniq
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150 #end try
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151
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152 # Paths to external tools
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153 bowtie_bin = #slurp
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154 #try
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155 $ref_dict['bowtie_bin']
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156 #except
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157 __BOWTIE_BIN__
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158 #end try
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159 bowtie_build_bin = #slurp
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160 #try
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161 $ref_dict['bowtie_build_bin']
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162 #except
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163 __BOWTIE_BUILD_BIN__
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164 #end try
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165 blat_bin = #slurp
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166 #try
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167 $ref_dict['blat_bin']
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168 #except
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169 __BLAT_BIN__
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170 #end try
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171 fatotwobit_bin = #slurp
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172 #try
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173 $ref_dict['fatotwobit_bin']
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174 #except
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175 __FATOTWOBIT_BIN__
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176 #end try
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177 r_bin = #slurp
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178 #try
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179 $ref_dict['r_bin']
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180 #except
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181 __R_BIN__
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182 #end try
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183 rscript_bin = #slurp
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184 #try
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185 $ref_dict['rscript_bin']
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186 #except
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187 __RSCRIPT_BIN__
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188 #end try
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189
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190 #raw
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191 # Dataset files
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192 dataset_prefix = $(dataset_directory)/defuse
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193 chromosome_prefix = $(dataset_prefix).dna.chromosomes
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194 exons_fasta = $(dataset_prefix).exons.fa
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195 cds_fasta = $(dataset_prefix).cds.fa
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196 cdna_regions = $(dataset_prefix).cdna.regions
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197 cdna_fasta = $(dataset_prefix).cdna.fa
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198 reference_fasta = $(dataset_prefix).reference.fa
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199 rrna_fasta = $(dataset_prefix).rrna.fa
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200 ig_gene_list = $(dataset_prefix).ig.gene.list
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201 repeats_regions = $(dataset_directory)/repeats.regions
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202 est_split_fasta1 = $(dataset_directory)/est.1.fa
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203 est_split_fasta2 = $(dataset_directory)/est.2.fa
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204 est_split_fasta3 = $(dataset_directory)/est.3.fa
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205 est_split_fasta4 = $(dataset_directory)/est.4.fa
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206 est_split_fasta5 = $(dataset_directory)/est.5.fa
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207 est_split_fasta6 = $(dataset_directory)/est.6.fa
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208 est_split_fasta7 = $(dataset_directory)/est.7.fa
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209 est_split_fasta8 = $(dataset_directory)/est.8.fa
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210 est_split_fasta9 = $(dataset_directory)/est.9.fa
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211
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212 # Fasta files with bowtie indices for prefiltering reads for concordantly mapping pairs
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213 prefilter1 = $(unigene_fasta)
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214
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215 # deFuse scripts and tools
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216 scripts_directory = $(source_directory)/scripts
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217 tools_directory = $(source_directory)/tools
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218 data_directory = $(source_directory)/data
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219 #end raw
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220
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221 # Path to samtools, 0.1.8 is compiled for you, use other versions at your own risk
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222 samtools_bin = #slurp
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223 #try
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224 $ref_dict['samtools_bin']
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225 #except
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226 \$(source_directory)/external/samtools-0.1.8/samtools
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227 #end try
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228
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229 # Bowtie parameters
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230 bowtie_threads = #slurp
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231 #try
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232 $ref_dict['bowtie_threads']
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233 #except
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234 4
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235 #end try
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236 bowtie_quals = #slurp
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237 #try
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238 $ref_dict['bowtie_quals']
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239 #except
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240 --phred33-quals
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241 #end try
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242 max_insert_size = #slurp
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243 #if $refGenomeSource.defuse_param.settings == "full" and $refGenomeSource.defuse_param.max_insert_size.__str__ != "":
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244 $refGenomeSource.defuse_param.max_insert_size
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245 #else
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246 #try
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247 $ref_dict['max_insert_size']
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248 #except
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249 500
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250 #end try
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251 #end if
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252
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253 # Parameters for building the dataset
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254 chromosomes = #slurp
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255 #try
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256 $ref_dict.chromosomes
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257 #except
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258 1,2,3,4,5,6,7,8,9,10,11,12,13,14,15,16,17,18,19,20,21,22,X,Y,MT
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259 #end try
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260 mt_chromosome = #slurp
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261 #try
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262 $ref_dict['mt_chromosome']
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263 #except
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264 MT
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265 #end try
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266 gene_sources = #slurp
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267 #try
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268 $ref_dict['gene_sources']
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269 #except
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270 IG_C_gene,IG_D_gene,IG_J_gene,IG_V_gene,processed_transcript,protein_coding
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271 #end try
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272 ig_gene_sources = #slurp
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273 #try
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274 $ref_dict['ig_gene_sources']
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275 #except
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276 IG_C_gene,IG_D_gene,IG_J_gene,IG_V_gene,IG_pseudogene
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277 #end try
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278 rrna_gene_sources = #slurp
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279 #try
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280 $ref_dict['rrna_gene_sources']
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281 #except
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282 Mt_rRNA,rRNA,rRNA_pseudogene
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283 #end try
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284
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285 # Blat sequences per job
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286 num_blat_sequences = #slurp
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287 #try
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288 $ref_dict['num_blat_sequences']
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289 #except
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290 10000
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291 #end try
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292
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293 # Minimum gene fusion range
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294 dna_concordant_length = #slurp
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295 #if $refGenomeSource.defuse_param.settings == "full" and $refGenomeSource.defuse_param.dna_concordant_length.__str__ != "":
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296 $refGenomeSource.defuse_param.dna_concordant_length
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297 #else
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298 #try
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299 $ref_dict['dna_concordant_length']
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300 #except
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301 2000
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302 #end try
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303 #end if
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304
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305 # Trim length for discordant reads (split reads are not trimmed)
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306 discord_read_trim = #slurp
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307 #if $refGenomeSource.defuse_param.settings == "full" and $refGenomeSource.defuse_param.discord_read_trim.__str__ != "":
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308 $refGenomeSource.defuse_param.discord_read_trim
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309 #else
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310 #try
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311 $ref_dict['discord_read_trim']
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312 #except
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313 50
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314 #end try
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315 #end if
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316
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317 # Filtering parameters
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318 clustering_precision = #slurp
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319 #if $refGenomeSource.defuse_param.settings == "full" and $refGenomeSource.defuse_param.clustering_precision.__str__ != ""
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320 $refGenomeSource.defuse_param.clustering_precision
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321 #else
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322 #try
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323 $ref_dict['clustering_precision']
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324 #except
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325 0.95
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326 #end try
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327 #end if
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328 span_count_threshold = #slurp
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329 #if $refGenomeSource.defuse_param.settings == "full" and $refGenomeSource.defuse_param.span_count_threshold.__str__ != ""
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330 $refGenomeSource.defuse_param.span_count_threshold
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331 #else
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332 #try
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333 $ref_dict['span_count_threshold']
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334 #except
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335 5
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336 #end try
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337 #end if
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338 split_count_threshold = #slurp
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339 #if $refGenomeSource.defuse_param.settings == "full" and $refGenomeSource.defuse_param.split_count_threshold.__str__ != ""
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340 $refGenomeSource.defuse_param.split_count_threshold
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341 #else
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342 #try
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343 $ref_dict['split_count_threshold']
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344 #except
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345 3
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346 #end try
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347 #end if
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348 percent_identity_threshold = #slurp
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349 #if $refGenomeSource.defuse_param.settings == "full" and $refGenomeSource.defuse_param.percent_identity_threshold.__str__ != ""
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350 $refGenomeSource.defuse_param.percent_identity_threshold
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351 #else
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352 #try
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353 $ref_dict['percent_identity_threshold']
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354 #except
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355 0.90
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356 #end try
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357 #end if
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358 max_dist_pos = #slurp
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359 #if $refGenomeSource.defuse_param.settings == "full" and $refGenomeSource.defuse_param.max_dist_pos.__str__ != ""
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360 $refGenomeSource.defuse_param.max_dist_pos
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361 #else
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362 #try
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363 $ref_dict['max_dist_pos']
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364 #except
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365 600
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366 #end try
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367 #end if
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368 num_dist_genes = #slurp
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369 #if $refGenomeSource.defuse_param.settings == "full" and $refGenomeSource.defuse_param.num_dist_genes.__str__ != ""
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370 $refGenomeSource.defuse_param.num_dist_genes
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371 #else
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372 #try
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373 $ref_dict['num_dist_genes']
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|
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374 #except
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|
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375 500
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|
|
376 #end try
|
|
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377 #end if
|
|
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378 split_min_anchor = #slurp
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|
|
379 #if $refGenomeSource.defuse_param.settings == "full" and $refGenomeSource.defuse_param.split_min_anchor.__str__ != ""
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|
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380 $refGenomeSource.defuse_param.split_min_anchor
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|
|
381 #else
|
|
|
382 #try
|
|
|
383 $ref_dict['split_min_anchor']
|
|
|
384 #except
|
|
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385 4
|
|
|
386 #end try
|
|
|
387 #end if
|
|
|
388 max_concordant_ratio = #slurp
|
|
|
389 #if $refGenomeSource.defuse_param.settings == "full" and $refGenomeSource.defuse_param.max_concordant_ratio.__str__ != ""
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|
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390 $refGenomeSource.defuse_param.max_concordant_ratio
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|
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391 #else
|
|
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392 #try
|
|
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393 $ref_dict['max_concordant_ratio']
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|
|
394 #except
|
|
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395 0.1
|
|
|
396 #end try
|
|
|
397 #end if
|
|
|
398 splice_bias = #slurp
|
|
|
399 #if $refGenomeSource.defuse_param.settings == "full" and $refGenomeSource.defuse_param.splice_bias.__str__ != ""
|
|
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400 $refGenomeSource.defuse_param.splice_bias
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|
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401 #else
|
|
|
402 #try
|
|
|
403 $ref_dict['splice_bias']
|
|
|
404 #except
|
|
|
405 10
|
|
|
406 #end try
|
|
|
407 #end if
|
|
|
408 denovo_assembly = #slurp
|
|
|
409 #if $refGenomeSource.defuse_param.settings == "full" and $refGenomeSource.defuse_param.denovo_assembly.__str__ != ""
|
|
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410 $refGenomeSource.defuse_param.denovo_assembly
|
|
|
411 #else
|
|
|
412 #try
|
|
|
413 $ref_dict['denovo_assembly']
|
|
|
414 #except
|
|
|
415 no
|
|
|
416 #end try
|
|
|
417 #end if
|
|
|
418 probability_threshold = #slurp
|
|
|
419 #if $refGenomeSource.defuse_param.settings == "full" and $refGenomeSource.defuse_param.probability_threshold.__str__ != ""
|
|
|
420 $refGenomeSource.defuse_param.probability_threshold
|
|
|
421 #else
|
|
|
422 #try
|
|
|
423 $ref_dict['probability_threshold']
|
|
|
424 #except
|
|
|
425 0.50
|
|
|
426 #end try
|
|
|
427 #end if
|
|
|
428 positive_controls = \$(data_directory)/controls.txt
|
|
|
429
|
|
|
430 # Position density when calculating covariance
|
|
|
431 covariance_sampling_density = #slurp
|
|
|
432 #if $refGenomeSource.defuse_param.settings == "full" and $refGenomeSource.defuse_param.covariance_sampling_density.__str__ != ""
|
|
|
433 $refGenomeSource.defuse_param.covariance_sampling_density
|
|
|
434 #else
|
|
|
435 #try
|
|
|
436 $ref_dict['covariance_sampling_density']
|
|
|
437 #except
|
|
|
438 0.01
|
|
|
439 #end try
|
|
|
440 #end if
|
|
|
441
|
|
|
442
|
|
|
443 # Number of reads for each job in split
|
|
|
444 reads_per_job = 1000000
|
|
|
445
|
|
|
446 # Number of regions for each breakpoint sequence job in split
|
|
|
447 regions_per_job = 20
|
|
|
448
|
|
|
449 #raw
|
|
|
450 # If you have command line 'mail' and wish to be notified
|
|
|
451 # mailto = andrew.mcpherson@gmail.com
|
|
|
452
|
|
|
453 # Remove temp files
|
|
|
454 remove_job_files = yes
|
|
|
455 remove_job_temp_files = yes
|
|
|
456
|
|
|
457 # Converting to fastq
|
|
|
458 # Fastq converter config format 1 for reads stored in separate files for each end
|
|
|
459 # data_lane_rexex_N is a perl regex which stores the lane id in $1
|
|
|
460 # data_end_regex_N is a perl regex which stores the end, 1 or 2, in $1
|
|
|
461 # data_compress_regex_N is a perl regex which stores the compression extension in $1
|
|
|
462 # data_convert_N is the associated conversion utility that takes data at stdin and outputs fastq at stdout
|
|
|
463 # Fastq converter config format 2 for reads stored in separate files for each end
|
|
|
464 # data_lane_regex_N is a perl regex which stores the lane id in $1
|
|
|
465 # data_compress_regex_N is a perl regex which stores the compression extension in $1
|
|
|
466 # data_end1_converter_N is the associated conversion utility that takes data at stdin and outputs fastq for end 1 at stdout
|
|
|
467 # data_end2_converter_N is the associated conversion utility that takes data at stdin and outputs fastq for end 2 at stdout
|
|
|
468
|
|
|
469 data_lane_regex_1 = ^(.+)_[12]_export\.txt.*$
|
|
|
470 data_end_regex_1 = ^.+_([12])_export\.txt.*$
|
|
|
471 data_compress_regex_1 = ^.+_[12]_export\.txt(.*)$
|
|
|
472 data_converter_1 = $(scripts_directory)/fq_all2std.pl export2std
|
|
|
473
|
|
|
474 data_lane_regex_2 = ^(.+)_[12]_concat_qseq\.txt.*$
|
|
|
475 data_end_regex_2 = ^.+_([12])_concat_qseq\.txt.*$
|
|
|
476 data_compress_regex_2 = ^.+_[12]_concat_qseq\.txt(.*)$
|
|
|
477 data_converter_2 = $(scripts_directory)/qseq2fastq.pl
|
|
|
478
|
|
|
479 data_lane_regex_3 = ^(.+)\.bam.*$
|
|
|
480 data_compress_regex_3 = ^.+\.bam(.*)$
|
|
|
481 data_end1_converter_3 = samtools view - | filter_sam_mate.pl 1 | sam_to_fastq.pl
|
|
|
482 data_end2_converter_3 = samtools view - | filter_sam_mate.pl 2 | sam_to_fastq.pl
|
|
|
483
|
|
|
484 data_lane_regex_4 = ^(.+).[12].fastq.*$
|
|
|
485 data_end_regex_4 = ^.+.([12]).fastq.*$
|
|
|
486 data_compress_regex_4 = ^.+.[12].fastq(.*)$
|
|
|
487 data_converter_4 = cat
|
|
|
488 #end raw
|
|
|
489
|
|
|
490 #end if
|
|
|
491
|
|
|
492 </configfile>
|
|
|
493 <configfile name="shscript">
|
|
|
494 #!/bin/bash
|
|
|
495 ## define some things for cheetah proccessing
|
|
|
496 #set $ds = chr(36)
|
|
|
497 #set $amp = chr(38)
|
|
|
498 #set $gt = chr(62)
|
|
|
499 #set $lt = chr(60)
|
|
|
500 #set $echo_cmd = 'echo'
|
|
|
501 ## Find the defuse.pl in the galaxy tool path
|
|
|
502 #import Cheetah.FileUtils
|
|
|
503 ## declare a bash function for converting a results tsv into html with links to the get_reads output files
|
|
|
504 results2html() {
|
|
|
505 rlts=${ds}1
|
|
|
506 rslt_name=`basename ${ds}rlts`
|
|
|
507 html=${ds}2
|
|
|
508 echo '${lt}html${gt}${lt}head${gt}${lt}title${gt}Defuse '${ds}rslt_name'${lt}/title${gt}${lt}/head${gt}${lt}body${gt}' ${gt} ${ds}html
|
|
|
509 echo '${lt}h2${gt}Defuse '${ds}rslt_name'${lt}/h2${gt}${lt}table${gt}' ${gt}${gt} ${ds}html
|
|
|
510 if [ -z "${ds}3" ]
|
|
|
511 then
|
|
|
512 awk '${ds}1 ~ /cluster_id/{printf("${lt}tr${gt}");for (i = 1; i ${lt}= NF; i++) {printf("${lt}th${gt}%s${lt}/th${gt}", ${ds}i);}; printf("${lt}/tr${gt}\n");}\
|
|
|
513 ${ds}1 ~ /[1-9][0-9]*/{printf("${lt}tr${gt}");for (i = 1; i ${lt}= NF; i++) {printf("${lt}td${gt}%s${lt}/td${gt}", ${ds}i);}; printf("${lt}/tr${gt}\n");}' ${ds}rlts ${gt}${gt} ${ds}html
|
|
|
514 echo '${lt}/table${gt}' ${gt}${gt} ${ds}html
|
|
|
515 echo '${lt}/body${gt}${lt}/html${gt}' ${gt}${gt} ${ds}html
|
|
|
516 else
|
|
|
517 export _EFP=${ds}3
|
|
|
518 mkdir -p ${ds}_EFP
|
|
|
519 awk '${ds}1 ~ /cluster_id/{printf("${lt}tr${gt}");for (i = 1; i ${lt}= NF; i++) {printf("${lt}th${gt}%s${lt}/th${gt}", ${ds}i);}; printf("${lt}/tr${gt}\n");}\
|
|
|
520 ${ds}1 ~ /[1-9][0-9]*/{fn="cluster_"${ds}1"_reads.txt"; \
|
|
|
521 printf("${lt}tr${gt}${lt}td${gt}${lt}a href=\"%s\"${gt}%s${lt}/a${gt}${lt}/td${gt}",fn, ${ds}1);for (i = 2; i ${lt}= NF; i++) {printf("${lt}td${gt}%s${lt}/td${gt}", ${ds}i);}; printf("${lt}/tr${gt}\n");}' ${ds}rlts ${gt}${gt} ${ds}html
|
|
|
522 echo '${lt}/table${gt}' ${gt}${gt} ${ds}html
|
|
|
523 echo '${lt}/body${gt}${lt}/html${gt}' ${gt}${gt} ${ds}html
|
|
|
524 for i in `awk '${ds}1 ~ /[1-9][0-9]*/{print ${ds}1}' ${ds}rlts`;
|
|
|
525 do fn=cluster_${ds}{i}_reads.txt;
|
|
|
526 pn=${ds}_EFP/${ds}fn;
|
|
|
527 perl \${DEFUSE_PATH}/scripts/get_reads.pl -c $defuse_config -o output_dir -i ${ds}i ${gt} ${ds}pn;
|
|
|
528 done
|
|
|
529 fi
|
|
|
530 }
|
|
|
531 ## substitute pathnames into config file
|
|
1
|
532 if `grep __DEFUSE_PATH__ $defuse_config ${gt} /dev/null`;then sed -i'.tmp' "s#__DEFUSE_PATH__#\${DEFUSE_PATH}#" $defuse_config; fi
|
|
|
533 if `grep __SAMTOOLS_BIN__ $defuse_config ${gt} /dev/null` ${amp}${amp} SAMTOOLS_BIN=`which samtools`;then sed -i'.tmp' "s#__SAMTOOLS_BIN__#\${SAMTOOLS_BIN}#" $defuse_config; fi
|
|
|
534 if `grep __BOWTIE_BIN__ $defuse_config ${gt} /dev/null` ${amp}${amp} BOWTIE_BIN=`which bowtie`;then sed -i'.tmp' "s#__BOWTIE_BIN__#\${BOWTIE_BIN}#" $defuse_config; fi
|
|
|
535 if `grep __BOWTIE_BUILD_BIN__ $defuse_config ${gt} /dev/null` ${amp}${amp} BOWTIE_BUILD_BIN=`which bowtie-build`;then sed -i'.tmp' "s#__BOWTIE_BUILD_BIN__#\${BOWTIE_BUILD_BIN}#" $defuse_config; fi
|
|
|
536 if `grep __BLAT_BIN__ $defuse_config ${gt} /dev/null` ${amp}${amp} BLAT_BIN=`which blat`;then sed -i'.tmp' "s#__BLAT_BIN__#\${BLAT_BIN}#" $defuse_config; fi
|
|
|
537 if `grep __FATOTWOBIT_BIN__ $defuse_config ${gt} /dev/null` ${amp}${amp} FATOTWOBIT_BIN=`which fatotwobit`;then sed -i'.tmp' "s#__FATOTWOBIT_BIN__#\${FATOTWOBIT_BIN}#" $defuse_config; fi
|
|
|
538 if `grep __R_BIN__ $defuse_config ${gt} /dev/null` ${amp}${amp} R_BIN=`which R`;then sed -i'.tmp' "s#__R_BIN__#\${R_BIN}#" $defuse_config; fi
|
|
|
539 if `grep __RSCRIPT_BIN__ $defuse_config ${gt} /dev/null` ${amp}${amp} RSCRIPT_BIN=`which Rscript`;then sed -i'.tmp' "s#__RSCRIPT_BIN__#\${RSCRIPT_BIN}#" $defuse_config; fi
|
|
0
|
540
|
|
|
541
|
|
|
542 ## copy config to output
|
|
|
543 cp $defuse_config $config_txt
|
|
|
544 ## make a data_dir and ln -s the input fastq
|
|
|
545 mkdir -p data_dir
|
|
|
546 ln -s $left_pairendreads data_dir/reads_1.fastq
|
|
|
547 ln -s $right_pairendreads data_dir/reads_2.fastq
|
|
|
548 ## ln to output_dir in from_work_dir
|
|
|
549 #if $defuse_out.__str__ != 'None':
|
|
|
550 mkdir -p $defuse_out.extra_files_path
|
|
|
551 ln -s $defuse_out.extra_files_path output_dir
|
|
|
552 #else
|
|
|
553 mkdir -p output_dir
|
|
|
554 #end if
|
|
|
555 ## run defuse.pl
|
|
|
556 perl \${DEFUSE_PATH}/scripts/defuse.pl -c $defuse_config -d data_dir -o output_dir -p 8
|
|
|
557 ## copy primary results to output datasets
|
|
|
558 if [ -e output_dir/log/defuse.log ]; then cp output_dir/log/defuse.log $defuse_log; fi
|
|
|
559 if [ -e output_dir/results.tsv ]; then cp output_dir/results.tsv $results_tsv; fi
|
|
|
560 if [ -e output_dir/results.filtered.tsv ]; then cp output_dir/results.filtered.tsv $results_filtered_tsv; fi
|
|
|
561 if [ -e output_dir/results.classify.tsv ]; then cp output_dir/results.classify.tsv $results_classify_tsv; fi
|
|
|
562 ## create html with links for output_dir
|
|
|
563 #if $defuse_out.__str__ != 'None':
|
|
|
564 if [ -e $defuse_out ]
|
|
|
565 then
|
|
|
566 echo '${lt}html${gt}${lt}head${gt}${lt}title${gt}Defuse Output${lt}/title${gt}${lt}/head${gt}${lt}body${gt}' ${gt} $defuse_out
|
|
|
567 echo '${lt}h2${gt}Defuse Output Files${lt}/h2${gt}${lt}ul${gt}' ${gt}${gt} $defuse_out
|
|
|
568 pushd $defuse_out.extra_files_path
|
|
|
569 for f in `find -L . -maxdepth 1 -type f`;
|
|
|
570 do fn=`basename ${ds}f`; echo '${lt}li${gt}${lt}a href="'${ds}fn'"${gt}'${ds}fn'${lt}/a${gt}${lt}/li${gt}' ${gt}${gt} $defuse_out;
|
|
|
571 done
|
|
|
572 popd
|
|
|
573 echo '${lt}/ul${gt}' ${gt}${gt} $defuse_out
|
|
|
574 echo '${lt}/body${gt}${lt}/html${gt}' ${gt}${gt} $defuse_out
|
|
|
575 fi
|
|
|
576 #end if
|
|
|
577 ## run get_reads.pl on each cluster
|
|
|
578 #if $fusion_reads.__str__ != 'None':
|
|
|
579 if [ -e output_dir/results.filtered.tsv -a -e $fusion_reads ]
|
|
|
580 then
|
|
|
581 mkdir -p $fusion_reads.extra_files_path
|
|
|
582 results2html output_dir/results.filtered.tsv $fusion_reads $fusion_reads.extra_files_path
|
|
|
583 fi
|
|
|
584 #end if
|
|
|
585 </configfile>
|
|
|
586 </configfiles>
|
|
|
587 <outputs>
|
|
|
588 <data format="txt" name="config_txt" label="${tool.name} on ${on_string}: config.txt"/>
|
|
|
589 <data format="txt" name="defuse_log" label="${tool.name} on ${on_string}: defuse.log" />
|
|
|
590 <data format="html" name="defuse_out" label="${tool.name} on ${on_string}: defuse_output">
|
|
|
591 <filter>keep_output == True</filter>
|
|
|
592 </data>
|
|
|
593 <data format="html" name="fusion_reads" label="${tool.name} on ${on_string}: fusion_reads">
|
|
|
594 <filter>do_get_reads == True</filter>
|
|
|
595 </data>
|
|
|
596 <data format="tabular" name="results_tsv" label="${tool.name} on ${on_string}: results.tsv" />
|
|
|
597 <data format="tabular" name="results_filtered_tsv" label="${tool.name} on ${on_string}: results.filtered.tsv" />
|
|
|
598 <data format="tabular" name="results_classify_tsv" label="${tool.name} on ${on_string}: results.classify.tsv" />
|
|
|
599 </outputs>
|
|
|
600 <tests>
|
|
|
601 </tests>
|
|
|
602 <help>
|
|
|
603 **DeFuse**
|
|
|
604
|
|
|
605 DeFuse_ is a software package for gene fusion discovery using RNA-Seq data. The software uses clusters of discordant paired end alignments to inform a split read alignment analysis for finding fusion boundaries. The software also employs a number of heuristic filters in an attempt to reduce the number of false positives and produces a fully annotated output for each predicted fusion.
|
|
|
606
|
|
|
607 Journal reference: http://www.ploscompbiol.org/article/info%3Adoi%2F10.1371%2Fjournal.pcbi.1001138
|
|
|
608
|
|
|
609 .. _DeFuse: http://sourceforge.net/apps/mediawiki/defuse/index.php?title=Main_Page
|
|
|
610
|
|
|
611 ------
|
|
|
612
|
|
|
613 **Inputs**
|
|
|
614
|
|
|
615 DeFuse requires 2 fastq files for paried reads, one with the left mate of the paired reads, and a second fastq with the the right mate of the paired reads (**with reads in the same order as in the first fastq dataset**).
|
|
|
616
|
|
|
617 If your fastq files have reads in different orders or include unpaired reads, you can preprocess them with **FASTQ interlacer** to create a single interlaced fastq dataset with only the paired reads and input that to **FASTQ de-interlacer** to separate the reads into a left fastq and right fastq.
|
|
|
618
|
|
|
619 DeFuse uses a Reference Dataset to search for gene fusions. The Reference Dataset is generated from the following sources in DeFuse_Version_0.4_:
|
|
|
620 - genome_fasta from Ensembl
|
|
|
621 - gene_models from Ensembl
|
|
|
622 - repeats_filename from UCSC RepeatMasker rmsk.txt
|
|
|
623 - est_fasta from UCSC
|
|
|
624 - est_alignments from UCSC intronEst.txt
|
|
|
625 - unigene_fasta from NCBI
|
|
|
626
|
|
|
627 .. _DeFuse_Version_0.4: http://sourceforge.net/apps/mediawiki/defuse/index.php?title=DeFuse_Version_0.4.2
|
|
|
628
|
|
|
629 ------
|
|
|
630
|
|
|
631 **Outputs**
|
|
|
632
|
|
|
633 The galaxy history will contain 5 outputs: the config.txt file that provides DeFuse with its parameters, the defuse.log which details what DeFuse has done and can be useful in determining any errors, and the 3 results files that defuse generates.
|
|
|
634
|
|
|
635 DeFuse generates 3 results files: results.txt, results.filtered.txt, and results.classify.txt. All three files have the same format, though results.classify.txt has a probability column from the application of the classifier to results.txt, and results.filtered.txt has been filtered according to the threshold probability as set in config.txt.
|
|
|
636
|
|
|
637 The file format is tab delimited with one prediction per line, and the following fields per prediction (not necessarily in this order):
|
|
|
638
|
|
|
639 - **Identification**
|
|
|
640 - cluster_id : random identifier assigned to each prediction
|
|
|
641 - library_name : library name given on the command line of defuse
|
|
|
642 - gene1 : ensembl id of gene 1
|
|
|
643 - gene2 : ensembl id of gene 2
|
|
|
644 - gene_name1 : name of gene 1
|
|
|
645 - gene_name2 : name of gene 2
|
|
|
646 - **Evidence**
|
|
|
647 - break_predict : breakpoint prediction method, denovo or splitr, that is considered most reliable
|
|
|
648 - concordant_ratio : proportion of spanning reads considered concordant by blat
|
|
|
649 - denovo_min_count : minimum kmer count across denovo assembled sequence
|
|
|
650 - denovo_sequence : fusion sequence predicted by debruijn based denovo sequence assembly
|
|
|
651 - denovo_span_pvalue : p-value, lower values are evidence the prediction is a false positive
|
|
|
652 - gene_align_strand1 : alignment strand for spanning read alignments to gene 1
|
|
|
653 - gene_align_strand2 : alignment strand for spanning read alignments to gene 2
|
|
|
654 - min_map_count : minimum of the number of genomic mappings for each spanning read
|
|
|
655 - max_map_count : maximum of the number of genomic mappings for each spanning read
|
|
|
656 - mean_map_count : average of the number of genomic mappings for each spanning read
|
|
|
657 - num_multi_map : number of spanning reads that map to more than one genomic location
|
|
|
658 - span_count : number of spanning reads supporting the fusion
|
|
|
659 - span_coverage1 : coverage of spanning reads aligned to gene 1 as a proportion of expected coverage
|
|
|
660 - span_coverage2 : coverage of spanning reads aligned to gene 2 as a proportion of expected coverage
|
|
|
661 - span_coverage_min : minimum of span_coverage1 and span_coverage2
|
|
|
662 - span_coverage_max : maximum of span_coverage1 and span_coverage2
|
|
|
663 - splitr_count : number of split reads supporting the prediction
|
|
|
664 - splitr_min_pvalue : p-value, lower values are evidence the prediction is a false positive
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665 - splitr_pos_pvalue : p-value, lower values are evidence the prediction is a false positive
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666 - splitr_sequence : fusion sequence predicted by split reads
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667 - splitr_span_pvalue : p-value, lower values are evidence the prediction is a false positive
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668 - **Annotation**
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669 - adjacent : fusion between adjacent genes
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670 - altsplice : fusion likely the product of alternative splicing between adjacent genes
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671 - break_adj_entropy1 : di-nucleotide entropy of the 40 nucleotides adjacent to the fusion splice in gene 1
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672 - break_adj_entropy2 : di-nucleotide entropy of the 40 nucleotides adjacent to the fusion splice in gene 2
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673 - break_adj_entropy_min : minimum of break_adj_entropy1 and break_adj_entropy2
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674 - breakpoint_homology : number of nucleotides at the fusion splice that align equally well to gene 1 or gene 2
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675 - breakseqs_estislands_percident : maximum percent identity of fusion sequence alignments to est islands
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676 - cdna_breakseqs_percident : maximum percent identity of fusion sequence alignments to cdna
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677 - deletion : fusion produced by a genomic deletion
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678 - est_breakseqs_percident : maximum percent identity of fusion sequence alignments to est
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679 - eversion : fusion produced by a genomic eversion
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680 - exonboundaries : fusion splice at exon boundaries
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681 - expression1 : expression of gene 1 as number of concordant pairs aligned to exons
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682 - expression2 : expression of gene 2 as number of concordant pairs aligned to exons
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683 - gene_chromosome1 : chromosome of gene 1
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684 - gene_chromosome2 : chromosome of gene 2
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685 - gene_end1 : end position for gene 1
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686 - gene_end2 : end position for gene 2
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687 - gene_location1 : location of breakpoint in gene 1
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688 - gene_location2 : location of breakpoint in gene 2
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689 - gene_start1 : start of gene 1
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690 - gene_start2 : start of gene 2
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691 - gene_strand1 : strand of gene 1
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692 - gene_strand2 : strand of gene 2
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693 - genome_breakseqs_percident : maximum percent identity of fusion sequence alignments to genome
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694 - genomic_break_pos1 : genomic position in gene 1 of fusion splice / breakpoint
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695 - genomic_break_pos2 : genomic position in gene 2 of fusion splice / breakpoint
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696 - genomic_strand1 : genomic strand in gene 1 of fusion splice / breakpoint, retained sequence upstream on this strand, breakpoint is downstream
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697 - genomic_strand2 : genomic strand in gene 2 of fusion splice / breakpoint, retained sequence upstream on this strand, breakpoint is downstream
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698 - interchromosomal : fusion produced by an interchromosomal translocation
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699 - interrupted_index1 : ratio of coverage before and after the fusion splice / breakpoint in gene 1
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700 - interrupted_index2 : ratio of coverage before and after the fusion splice / breakpoint in gene 2
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701 - inversion : fusion produced by genomic inversion
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702 - orf : fusion combines genes in a way that preserves a reading frame
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703 - probability : probability produced by classification using adaboost and example positives/negatives (only given in results.classified.txt)
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704 - read_through : fusion involving adjacent potentially resulting from co-transcription rather than genome rearrangement
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705 - repeat_proportion1 : proportion of the spanning reads in gene 1 that span a repeat region
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706 - repeat_proportion2 : proportion of the spanning reads in gene 2 that span a repeat region
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707 - max_repeat_proportion : max of repeat_proportion1 and repeat_proportion2
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708 - splice_score : number of nucleotides similar to GTAG at fusion splice
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709 - num_splice_variants : number of potential splice variants for this gene pair
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710 - splicing_index1 : number of concordant pairs in gene 1 spanning the fusion splice / breakpoint, divided by number of spanning reads supporting the fusion with gene 2
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711 - splicing_index2 : number of concordant pairs in gene 2 spanning the fusion splice / breakpoint, divided by number of spanning reads supporting the fusion with gene 1
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712
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713
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714 **Example**
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715
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716 results.tsv::
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717
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718 cluster_id splitr_sequence splitr_count splitr_span_pvalue splitr_pos_pvalue splitr_min_pvalue adjacent altsplice break_adj_entropy1 break_adj_entropy2 break_adj_entropy_min break_predict breakpoint_homology breakseqs_estislands_percident cdna_breakseqs_percident concordant_ratio deletion est_breakseqs_percident eversion exonboundaries expression1 expression2 gene1 gene2 gene_align_strand1 gene_align_strand2 gene_chromosome1 gene_chromosome2 gene_end1 gene_end2 gene_location1 gene_location2 gene_name1 gene_name2 gene_start1 gene_start2 gene_strand1 gene_strand2 genome_breakseqs_percident genomic_break_pos1 genomic_break_pos2 genomic_strand1 genomic_strand2 interchromosomal interrupted_index1 interrupted_index2 inversion library_name max_map_count max_repeat_proportion mean_map_count min_map_count num_multi_map num_splice_variants orf read_through repeat_proportion1 repeat_proportion2 span_count span_coverage1 span_coverage2 span_coverage_max span_coverage_min splice_score splicing_index1 splicing_index2
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719 1169 GCTTACTGTATGCCAGGCCCCAGAGGGGCAACCACCCTCTAAAGAGAGCGGCTCCTGCCTCCCAGAAAGCTCACAGACTGTGGGAGGGAAACAGGCAGCAGGTGAAGATGCCAAATGCCAGGATATCTGCCCTGTCCTTGCTTGATGCAGCTGCTGGCTCCCACGTTCTCCCCAGAATCCCCTCACACTCCTGCTGTTTTCTCTGCAGGTTGGCAGAGCCCCATGAGGGCAGGGCAGCCACTTTGTTCTTGGGCGGCAAACCTCCCTGGGCGGCACGGAAACCACGGTGAGAAGGGGGCAGGTCGGGCACGTGCAGGGACCACGCTGCAGG|TGTACCCAACAGCTCCGAAGAGACAGCGACCATCGAGAACGGGCCATGATGACGATGGCGGTTTTGTCGAAAAGAAAAGGGGGAAATGTGGGGAAAAGCAAGAGAGATCAGATTGTTACTGTGTCTGTGTAGAAAGAAGTAGACATGGGAGACTCCATTTTGTTCTGTACTAAGAAAAATTCTTCTGCCTTGAGATTCGGTGACCCCACCCCCAACCCCGTGCTCTCTGAAACATGTGCTGTGTCCACTCAGGGTTGAATGGATTAAGGGCGGTGCGAGACGTGCTTT 2 0.000436307890680442 0.110748295953850 0.0880671602973091 N Y 3.19872427442695 3.48337348351473 3.19872427442695 splitr 0 0 0 0 Y 0 N N 0 0 ENSG00000105549 ENSG00000213753 + - 19 19 376013 59111168 intron upstream THEG AC016629.2 361750 59084870 - + 0 375099 386594 + - N 8.34107429512245 - N output_dir 82 0.677852348993289 40.6666666666667 1 11 1 N N 0.361271676300578 0.677852348993289 12 0.758602776578432 0.569678713445872 0.758602776578432 0.569678713445872 2 0.416666666666667 -
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720 3596 TGGGGGTTGAGGCTTCTGTTCCCAGGTTCCATGACCTCAGAGGTGGCTGGTGAGGTTATGACCTTTGCCCTCCAGCCCTGGCTTAAAACCTCAGCCCTAGGACCTGGTTAAAGGAAGGGGAGATGGAGCTTTGCCCCGACCCCCCCCCGTTCCCCTCACCTGTCAGCCCGAGCTGGGCCAGGGCCCCTAGGTGGGGAACTGGGCCGGGGGGCGGGCACAAGCGGAGGTGGTGCCCCCAAAAGGGCTCCCGGTGGGGTCTTGCTGAGAAGGTGAGGGGTTCCCGGGGCCGCAGCAGGTGGTGGTGGAGGAGCCAAGCGGCTGTAGAGCAAGGGGTGAGCAGGTTCCAGACCGTAGAGGCGGGCAGCGGCCACGGCCCCGGGTCCAGTTAGCTCCTCACCCGCCTCATAGAAGCGGGGTGGCCTTGCCAGGCGTGGGGGTGCTGCC|TTCCTTGGATGTGGTAGCCGTTTCTCAGGCTCCCTCTCCGGAATCGAACCCTGATTCCCCGTCACCCGTGGTCACCATGGTAGGCACGGCGACTACCATCGAAAGTTGATAGGGCAGACGTTCGAATGGGTCGTCGCCGCCACGGGGGGCGTGCGATCAGCCCGAGGTTATCTAGAGTCACCAAAGCCGCCGGCGCCCGCCCCCCGGCCGGGGCCGGAGAGGGGCTGACCGGGTTGGTTTTGATCTGATAAATGCACGCATCCCCCCCGCGAAGGGGGTCAGCGCCCGTCGGCATGTATTAGCTCTAGAATTACCACAGTTATCCAAGTAGGAGAGGAGCGAGCGACCAAAGGAACCATAACTGATTTAATGAGCCATTCGCAGTTTCACTGTACCGGCCGTGCGTACTTAGACATGCATGGCTTAATCTTTGAGACAAGCATATGCTACTGGCAGG 250 7.00711162298275e-72 0.00912124762512338 0.00684237452309549 N N 3.31745197152461 3.47233119514066 3.31745197152461 splitr 7 0.0157657657657656 0 0 N 0.0135135135135136 N N 0 0 ENSG00000156860 ENSG00000212932 - + 16 21 30682131 48111157 coding upstream FBRS RPL23AP4 30670289 48110676 + + 0.0157657657657656 30680678 9827473 - + Y - - N output_dir 2 1 1.11111111111111 1 1 1 N N 0 1 9 0.325530693397641 0.296465452915709 0.325530693397641 0.296465452915709 2 - -
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721
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722 </help>
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723 </tool>
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