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1 <tool id="defuse" name="DeFuse" version="1.0">
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2 <description>identify fusion transcripts</description>
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3 <requirements>
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4 <requirement type="binary"></requirement>
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5 </requirements>
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6 <command interpreter="perl">
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7 scripts/defuse.pl
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8 -c `cp $defuse_config $config_txt; echo $defuse_config`
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9 -d `mkdir -p data_dir; ln -s $left_pairendreads data_dir/reads_1.fastq; ln -s $right_pairendreads data_dir/reads_2.fastq; echo data_dir`
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10 -o output_dir -p 8
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11 </command>
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12 <inputs>
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13 <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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14 <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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15 <conditional name="refGenomeSource">
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16 <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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17 <option value="indexed">Use a built-in DeFuse Reference Dataset</option>
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18 <option value="history">Use a configuration from your history that specifies the DeFuse Reference Dataset</option>
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19 </param>
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20 <when value="indexed">
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21 <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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22 <options from_file="defuse.loc">
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23 <column name="name" index="1"/>
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24 <column name="value" index="2"/>
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25 <filter type="sort_by" column="0" />
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26 <validator type="no_options" message="No indexes are available" />
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27 </options>
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28 </param>
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29 <conditional name="defuse_param">
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30 <param name="settings" type="select" label="Defuse parameter settings" help="">
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31 <option value="preSet">Default settings</option>
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32 <option value="full">Full parameter list</option>
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33 </param>
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34 <when value="preSet" />
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35 <when value="full">
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36 <param name="max_insert_size" type="integer" value="500" optional="true" label="Bowtie max_insert_size" />
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37 <param name="dna_concordant_length" type="integer" value="2000" optional="true" label="Minimum gene fusion range dna_concordant_length" />
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38 <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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39 <param name="clustering_precision" type="float" value=".95" optional="true" label="Filter clustering_precision">
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40 <validator type="in_range" message="Choose a value between .1 and 1.0" min=".1" max="1"/>
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41 </param>
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42 <param name="span_count_threshold" type="integer" value="5" optional="true" label="Filter span_count_threshold" />
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43 <param name="split_count_threshold" type="integer" value="3" optional="true" label="Filter split_count_threshold" />
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44 <param name="percent_identity_threshold" type="float" value=".90" optional="true" label="Filter percent_identity_threshold">
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45 <validator type="in_range" message="Choose a value between .1 and 1.0" min=".1" max="1"/>
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46 </param>
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47 <param name="max_dist_pos" type="integer" value="600" optional="true" label="Filter max_dist_pos" />
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48 <param name="num_dist_genes" type="integer" value="500" optional="true" label="Filter num_dist_genes" />
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49 <param name="split_min_anchor" type="integer" value="4" optional="true" label="Filter split_min_anchor" />
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50 <param name="max_concordant_ratio" type="float" value="0.1" optional="true" label="Filter max_concordant_ratio">
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51 <validator type="in_range" message="Choose a value between 0.0 and 1.0" min="0" max="1"/>
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52 </param>
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53 <param name="splice_bias" type="integer" value="10" optional="true" label="Filter splice_bias" />
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54 <param name="probability_threshold" type="float" value="0.50" optional="true" label="Filter probability_threshold">
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55 <validator type="in_range" message="Choose a value between 0.0 and 1.0" min="0" max="1"/>
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56 </param>
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57 <param name="covariance_sampling_density" type="float" value="0.01" optional="true" label="covariance_sampling_density">
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58 <help>Position density when calculating covariance</help>
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59 <validator type="in_range" message="Choose a value between 0.0 and 1.0" min="0" max="1"/>
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60 </param>
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61 <param name="denovo_assembly" type="select" label="denovo_assembly" help="">
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62 <option value="">Use Default</option>
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63 <option value="no">no</option>
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64 <option value="yes">yes</option>
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65 </param>
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66 <!--
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67 <param name="positive_controls" type="data" format="txt" optional=true label="Defuse positive_controls" help=""/>
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68 -->
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69 </when> <!-- full -->
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70 </conditional> <!-- defuse_param -->
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71 </when>
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72 <when value="history">
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73 <param name="config" type="data" format="txt" label="Defuse Config file" help=""/>
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74 </when> <!-- history -->
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75 </conditional> <!-- refGenomeSource -->
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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 # Gene/Transcript id pattern
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90 gene_id_pattern = #slurp
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91 #try
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92 $ref_dict['gene_id_pattern']
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93 transcript_id_pattern = #slurp
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94 #except
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95 ENSG\d+
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96 #end try
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97 #try
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98 $ref_dict['transcript_id_pattern']
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99 #except
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100 ENST\d+
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101 #end try
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102
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103 # Directory where the defuse code was unpacked
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104 ## Default location in the tool/defuse directory
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105 # source_directory = ${__root_dir__}/tools/defuse
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106 source_directory = #slurp
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107 #try
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108 $ref_dict['source_directory']
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109 #except
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110 ${__root_dir__}/tools/defuse
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111 #end try
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112
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113 # Directory where you want your dataset
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114 dataset_directory = #slurp
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115 #try
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116 $ref_dict['dataset_directory']
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117 #except
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118 /project/db/genomes/Hsapiens/hg19/defuse
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119 #end try
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120
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121 # Input genome and gene models
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122 gene_models = #slurp
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123 #try
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124 $ref_dict['gene_models']
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125 #except
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126 \$(dataset_directory)/Homo_sapiens.GRCh37.62.gtf
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127 #end try
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128 genome_fasta = #slurp
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129 #try
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130 $ref_dict['genome_fasta']
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131 #except
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132 \$(dataset_directory)/Homo_sapiens.GRCh37.62.dna.chromosome.fa
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133 #end try
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134
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135 # Repeat table from ucsc genome browser
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136 repeats_filename = #slurp
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137 #try
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138 $ref_dict['repeats_filename']
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139 #except
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140 \$(dataset_directory)/rmsk.txt
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141 #end try
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142
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143 # EST info downloaded from ucsc genome browser
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144 est_fasta = #slurp
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145 #try
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146 $ref_dict['est_fasta']
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147 #except
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148 \$(dataset_directory)/est.fa
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149 #end try
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150 est_alignments = #slurp
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151 #try
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152 $ref_dict['est_alignments']
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153 #except
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154 \$(dataset_directory)/intronEst.txt
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155 #end try
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156
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157 # Unigene clusters downloaded from ncbi
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158 unigene_fasta = #slurp
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159 #try
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160 $ref_dict['unigene_fasta']
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161 #except
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162 \$(dataset_directory)/Hs.seq.uniq
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163 #end try
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164
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165 # Paths to external tools
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166 bowtie_bin = #slurp
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167 #try
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168 $ref_dict['bowtie_bin']
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169 #except
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170 /soft/bowtie/0.12.7/bowtie
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171 #end try
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172 bowtie_build_bin = #slurp
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173 #try
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174 $ref_dict['bowtie_build_bin']
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175 #except
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176 /soft/bowtie/0.12.7/bowtie-build
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177 #end try
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178 blat_bin = #slurp
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179 #try
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180 $ref_dict['blat_bin']
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181 #except
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182 /soft/blat/34/bin/blat
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183 #end try
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184 fatotwobit_bin = #slurp
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185 #try
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186 $ref_dict['fatotwobit_bin']
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187 #except
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188 /soft/blat/34/bin/faToTwoBit
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189 #end try
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190 r_bin = #slurp
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191 #try
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192 $ref_dict['r_bin']
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193 #except
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194 /project/sdml-sles11-weblocal/R-2.12.1/bin/R
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195 #end try
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196 rscript_bin = #slurp
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197 #try
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198 $ref_dict['rscript_bin']
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199 #except
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200 /project/sdml-sles11-weblocal/R-2.12.1/bin/Rscript
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201 #end try
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202
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203 #raw
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204 # Dataset files
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205 dataset_prefix = $(dataset_directory)/defuse
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206 chromosome_prefix = $(dataset_prefix).dna.chromosomes
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207 exons_fasta = $(dataset_prefix).exons.fa
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208 cds_fasta = $(dataset_prefix).cds.fa
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209 cdna_regions = $(dataset_prefix).cdna.regions
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210 cdna_fasta = $(dataset_prefix).cdna.fa
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211 reference_fasta = $(dataset_prefix).reference.fa
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212 rrna_fasta = $(dataset_prefix).rrna.fa
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213 ig_gene_list = $(dataset_prefix).ig.gene.list
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214 repeats_regions = $(dataset_directory)/repeats.regions
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215 est_split_fasta1 = $(dataset_directory)/est.1.fa
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216 est_split_fasta2 = $(dataset_directory)/est.2.fa
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217 est_split_fasta3 = $(dataset_directory)/est.3.fa
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218 est_split_fasta4 = $(dataset_directory)/est.4.fa
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219 est_split_fasta5 = $(dataset_directory)/est.5.fa
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220 est_split_fasta6 = $(dataset_directory)/est.6.fa
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221 est_split_fasta7 = $(dataset_directory)/est.7.fa
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222 est_split_fasta8 = $(dataset_directory)/est.8.fa
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223 est_split_fasta9 = $(dataset_directory)/est.9.fa
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224
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225 # Fasta files with bowtie indices for prefiltering reads for concordantly mapping pairs
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226 prefilter1 = $(unigene_fasta)
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227
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228 # deFuse scripts and tools
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229 scripts_directory = $(source_directory)/scripts
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230 tools_directory = $(source_directory)/tools
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231 data_directory = $(source_directory)/data
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232 #end raw
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233
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234 # Path to samtools, 0.1.8 is compiled for you, use other versions at your own risk
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235 samtools_bin = #slurp
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236 #try
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237 $ref_dict['samtools_bin']
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238 #except
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239 \$(source_directory)/external/samtools-0.1.8/samtools
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240 #end try
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241
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242 # Bowtie parameters
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243 bowtie_threads = #slurp
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244 #try
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245 $ref_dict['bowtie_threads']
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246 #except
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247 1
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248 #end try
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249 bowtie_quals = #slurp
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250 #try
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251 $ref_dict['bowtie_quals']
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252 #except
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253 --phred33-quals
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254 #end try
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255 max_insert_size = #slurp
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256 #if $refGenomeSource.defuse_param.settings == "full" and $refGenomeSource.defuse_param.max_insert_size.__str__ != "":
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257 $refGenomeSource.defuse_param.max_insert_size
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258 #else
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259 #try
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260 $ref_dict['max_insert_size']
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261 #except
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262 500
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263 #end try
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264 #end if
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265
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266 # Parameters for building the dataset
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267 chromosomes = #slurp
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268 #try
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269 $ref_dict.chromosomes
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270 #except
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271 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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272 #end try
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273 mt_chromosome = #slurp
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274 #try
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275 $ref_dict['mt_chromosome']
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276 #except
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277 MT
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278 #end try
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279 gene_sources = #slurp
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280 #try
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281 $ref_dict['gene_sources']
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282 #except
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283 IG_C_gene,IG_D_gene,IG_J_gene,IG_V_gene,processed_transcript,protein_coding
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284 #end try
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285 ig_gene_sources = #slurp
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286 #try
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287 $ref_dict['ig_gene_sources']
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288 #except
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289 IG_C_gene,IG_D_gene,IG_J_gene,IG_V_gene,IG_pseudogene
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290 #end try
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291 rrna_gene_sources = #slurp
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292 #try
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293 $ref_dict['rrna_gene_sources']
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294 #except
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295 Mt_rRNA,rRNA,rRNA_pseudogene
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296 #end try
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297
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298 # Blat sequences per job
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299 num_blat_sequences = #slurp
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300 #try
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301 $ref_dict['num_blat_sequences']
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302 #except
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303 10000
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304 #end try
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305
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306 # Minimum gene fusion range
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307 dna_concordant_length = #slurp
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308 #if $refGenomeSource.defuse_param.settings == "full" and $refGenomeSource.defuse_param.dna_concordant_length.__str__ != "":
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309 $refGenomeSource.defuse_param.dna_concordant_length
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310 #else
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311 #try
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312 $ref_dict['dna_concordant_length']
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313 #except
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314 2000
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315 #end try
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316 #end if
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317
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318 # Trim length for discordant reads (split reads are not trimmed)
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319 discord_read_trim = #slurp
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320 #if $refGenomeSource.defuse_param.settings == "full" and $refGenomeSource.defuse_param.discord_read_trim.__str__ != "":
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321 $refGenomeSource.defuse_param.discord_read_trim
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322 #else
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323 #try
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324 $ref_dict['discord_read_trim']
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325 #except
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326 50
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327 #end try
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328 #end if
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329
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330 # Filtering parameters
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331 clustering_precision = #slurp
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332 #if $refGenomeSource.defuse_param.settings == "full" and $refGenomeSource.defuse_param.clustering_precision.__str__ != ""
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333 $refGenomeSource.defuse_param.clustering_precision
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334 #else
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335 #try
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336 $ref_dict['clustering_precision']
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337 #except
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338 0.95
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339 #end try
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340 #end if
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341 span_count_threshold = #slurp
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342 #if $refGenomeSource.defuse_param.settings == "full" and $refGenomeSource.defuse_param.span_count_threshold.__str__ != ""
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343 $refGenomeSource.defuse_param.span_count_threshold
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344 #else
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345 #try
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346 $ref_dict['span_count_threshold']
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347 #except
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348 5
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349 #end try
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350 #end if
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351 split_count_threshold = #slurp
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352 #if $refGenomeSource.defuse_param.settings == "full" and $refGenomeSource.defuse_param.split_count_threshold.__str__ != ""
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353 $refGenomeSource.defuse_param.split_count_threshold
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354 #else
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355 #try
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356 $ref_dict['split_count_threshold']
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357 #except
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358 3
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359 #end try
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360 #end if
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361 percent_identity_threshold = #slurp
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362 #if $refGenomeSource.defuse_param.settings == "full" and $refGenomeSource.defuse_param.percent_identity_threshold.__str__ != ""
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363 $refGenomeSource.defuse_param.percent_identity_threshold
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364 #else
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365 #try
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366 $ref_dict['percent_identity_threshold']
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367 #except
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368 0.90
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369 #end try
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370 #end if
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371 max_dist_pos = #slurp
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372 #if $refGenomeSource.defuse_param.settings == "full" and $refGenomeSource.defuse_param.max_dist_pos.__str__ != ""
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373 $refGenomeSource.defuse_param.max_dist_pos
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374 #else
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375 #try
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376 $ref_dict['max_dist_pos']
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377 #except
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378 600
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379 #end try
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380 #end if
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381 num_dist_genes = #slurp
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382 #if $refGenomeSource.defuse_param.settings == "full" and $refGenomeSource.defuse_param.num_dist_genes.__str__ != ""
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383 $refGenomeSource.defuse_param.num_dist_genes
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384 #else
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385 #try
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386 $ref_dict['num_dist_genes']
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387 #except
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388 500
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389 #end try
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390 #end if
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391 split_min_anchor = #slurp
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392 #if $refGenomeSource.defuse_param.settings == "full" and $refGenomeSource.defuse_param.split_min_anchor.__str__ != ""
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393 $refGenomeSource.defuse_param.split_min_anchor
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394 #else
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395 #try
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396 $ref_dict['split_min_anchor']
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397 #except
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398 4
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399 #end try
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400 #end if
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401 max_concordant_ratio = #slurp
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402 #if $refGenomeSource.defuse_param.settings == "full" and $refGenomeSource.defuse_param.max_concordant_ratio.__str__ != ""
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403 $refGenomeSource.defuse_param.max_concordant_ratio
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404 #else
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405 #try
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406 $ref_dict['max_concordant_ratio']
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407 #except
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408 0.1
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409 #end try
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410 #end if
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411 splice_bias = #slurp
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412 #if $refGenomeSource.defuse_param.settings == "full" and $refGenomeSource.defuse_param.splice_bias.__str__ != ""
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413 $refGenomeSource.defuse_param.splice_bias
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414 #else
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415 #try
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416 $ref_dict['splice_bias']
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417 #except
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418 10
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419 #end try
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420 #end if
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421 denovo_assembly = #slurp
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422 #if $refGenomeSource.defuse_param.settings == "full" and $refGenomeSource.defuse_param.denovo_assembly.__str__ != ""
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423 $refGenomeSource.defuse_param.denovo_assembly
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424 #else
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425 #try
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426 $ref_dict['denovo_assembly']
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427 #except
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428 no
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429 #end try
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430 #end if
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431 probability_threshold = #slurp
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432 #if $refGenomeSource.defuse_param.settings == "full" and $refGenomeSource.defuse_param.probability_threshold.__str__ != ""
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433 $refGenomeSource.defuse_param.probability_threshold
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434 #else
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|
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435 #try
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|
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436 $ref_dict['probability_threshold']
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|
437 #except
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|
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438 0.50
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|
|
439 #end try
|
|
|
440 #end if
|
|
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441 positive_controls = \$(data_directory)/controls.txt
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442
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443 # Position density when calculating covariance
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444 covariance_sampling_density = #slurp
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|
|
445 #if $refGenomeSource.defuse_param.settings == "full" and $refGenomeSource.defuse_param.covariance_sampling_density.__str__ != ""
|
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446 $refGenomeSource.defuse_param.covariance_sampling_density
|
|
|
447 #else
|
|
|
448 #try
|
|
|
449 $ref_dict['covariance_sampling_density']
|
|
|
450 #except
|
|
|
451 0.01
|
|
|
452 #end try
|
|
|
453 #end if
|
|
|
454
|
|
|
455
|
|
|
456 # Number of reads for each job in split
|
|
|
457 reads_per_job = 1000000
|
|
|
458
|
|
|
459 # Number of regions for each breakpoint sequence job in split
|
|
|
460 regions_per_job = 20
|
|
|
461
|
|
|
462 #raw
|
|
|
463 # If you have command line 'mail' and wish to be notified
|
|
|
464 # mailto = andrew.mcpherson@gmail.com
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|
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465
|
|
|
466 # Remove temp files
|
|
|
467 remove_job_files = yes
|
|
|
468 remove_job_temp_files = yes
|
|
|
469
|
|
|
470 # Converting to fastq
|
|
|
471 # Fastq converter config format 1 for reads stored in separate files for each end
|
|
|
472 # data_lane_rexex_N is a perl regex which stores the lane id in $1
|
|
|
473 # data_end_regex_N is a perl regex which stores the end, 1 or 2, in $1
|
|
|
474 # data_compress_regex_N is a perl regex which stores the compression extension in $1
|
|
|
475 # data_convert_N is the associated conversion utility that takes data at stdin and outputs fastq at stdout
|
|
|
476 # Fastq converter config format 2 for reads stored in separate files for each end
|
|
|
477 # data_lane_regex_N is a perl regex which stores the lane id in $1
|
|
|
478 # data_compress_regex_N is a perl regex which stores the compression extension in $1
|
|
|
479 # data_end1_converter_N is the associated conversion utility that takes data at stdin and outputs fastq for end 1 at stdout
|
|
|
480 # data_end2_converter_N is the associated conversion utility that takes data at stdin and outputs fastq for end 2 at stdout
|
|
|
481
|
|
|
482 data_lane_regex_1 = ^(.+)_[12]_export\.txt.*$
|
|
|
483 data_end_regex_1 = ^.+_([12])_export\.txt.*$
|
|
|
484 data_compress_regex_1 = ^.+_[12]_export\.txt(.*)$
|
|
|
485 data_converter_1 = $(scripts_directory)/fq_all2std.pl export2std
|
|
|
486
|
|
|
487 data_lane_regex_2 = ^(.+)_[12]_concat_qseq\.txt.*$
|
|
|
488 data_end_regex_2 = ^.+_([12])_concat_qseq\.txt.*$
|
|
|
489 data_compress_regex_2 = ^.+_[12]_concat_qseq\.txt(.*)$
|
|
|
490 data_converter_2 = $(scripts_directory)/qseq2fastq.pl
|
|
|
491
|
|
|
492 data_lane_regex_3 = ^(.+)\.bam.*$
|
|
|
493 data_compress_regex_3 = ^.+\.bam(.*)$
|
|
|
494 data_end1_converter_3 = samtools view - | filter_sam_mate.pl 1 | sam_to_fastq.pl
|
|
|
495 data_end2_converter_3 = samtools view - | filter_sam_mate.pl 2 | sam_to_fastq.pl
|
|
|
496
|
|
|
497 data_lane_regex_4 = ^(.+).[12].fastq.*$
|
|
|
498 data_end_regex_4 = ^.+.([12]).fastq.*$
|
|
|
499 data_compress_regex_4 = ^.+.[12].fastq(.*)$
|
|
|
500 data_converter_4 = cat
|
|
|
501 #end raw
|
|
|
502
|
|
|
503 #end if
|
|
|
504
|
|
|
505 </configfile>
|
|
|
506 </configfiles>
|
|
|
507 <outputs>
|
|
|
508 <data format="txt" name="config_txt" label="${tool.name} on ${on_string}: config.txt"/>
|
|
|
509 <data format="txt" name="defuse_log" label="${tool.name} on ${on_string}: defuse.log" from_work_dir="output_dir/log/defuse.log"/>
|
|
|
510 <data format="tabular" name="results_tsv" label="${tool.name} on ${on_string}: results.tsv" from_work_dir="output_dir/results.tsv"/>
|
|
|
511 <data format="tabular" name="results_filtered_tsv" label="${tool.name} on ${on_string}: results.filtered.tsv" from_work_dir="output_dir/results.filtered.tsv"/>
|
|
|
512 <data format="tabular" name="results_classify_tsv" label="${tool.name} on ${on_string}: results.classify.tsv" from_work_dir="output_dir/results.classify.tsv"/>
|
|
|
513 </outputs>
|
|
|
514 <tests>
|
|
|
515 </tests>
|
|
|
516 <help>
|
|
|
517 **DeFuse**
|
|
|
518
|
|
|
519 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.
|
|
|
520
|
|
|
521 Journal reference: http://www.ploscompbiol.org/article/info%3Adoi%2F10.1371%2Fjournal.pcbi.1001138
|
|
|
522
|
|
|
523 .. _DeFuse: http://sourceforge.net/apps/mediawiki/defuse/index.php?title=Main_Page
|
|
|
524
|
|
|
525 ------
|
|
|
526
|
|
|
527 **Inputs**
|
|
|
528
|
|
|
529 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**).
|
|
|
530
|
|
|
531 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.
|
|
|
532
|
|
|
533 DeFuse uses a Reference Dataset to search for gene fusions. The Reference Dataset is generated from the following sources in DeFuse_Version_0.4_:
|
|
|
534 - genome_fasta from Ensembl
|
|
|
535 - gene_models from Ensembl
|
|
|
536 - repeats_filename from UCSC RepeatMasker rmsk.txt
|
|
|
537 - est_fasta from UCSC
|
|
|
538 - est_alignments from UCSC intronEst.txt
|
|
|
539 - unigene_fasta from NCBI
|
|
|
540
|
|
|
541 .. _DeFuse_Version_0.4: http://sourceforge.net/apps/mediawiki/defuse/index.php?title=DeFuse_Version_0.4.2
|
|
|
542
|
|
|
543 ------
|
|
|
544
|
|
|
545 **Outputs**
|
|
|
546
|
|
|
547 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.
|
|
|
548
|
|
|
549 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.
|
|
|
550
|
|
|
551 The file format is tab delimited with one prediction per line, and the following fields per prediction (not necessarily in this order):
|
|
|
552
|
|
|
553 - **Identification**
|
|
|
554 - cluster_id : random identifier assigned to each prediction
|
|
|
555 - library_name : library name given on the command line of defuse
|
|
|
556 - gene1 : ensembl id of gene 1
|
|
|
557 - gene2 : ensembl id of gene 2
|
|
|
558 - gene_name1 : name of gene 1
|
|
|
559 - gene_name2 : name of gene 2
|
|
|
560 - **Evidence**
|
|
|
561 - break_predict : breakpoint prediction method, denovo or splitr, that is considered most reliable
|
|
|
562 - concordant_ratio : proportion of spanning reads considered concordant by blat
|
|
|
563 - denovo_min_count : minimum kmer count across denovo assembled sequence
|
|
|
564 - denovo_sequence : fusion sequence predicted by debruijn based denovo sequence assembly
|
|
|
565 - denovo_span_pvalue : p-value, lower values are evidence the prediction is a false positive
|
|
|
566 - gene_align_strand1 : alignment strand for spanning read alignments to gene 1
|
|
|
567 - gene_align_strand2 : alignment strand for spanning read alignments to gene 2
|
|
|
568 - min_map_count : minimum of the number of genomic mappings for each spanning read
|
|
|
569 - max_map_count : maximum of the number of genomic mappings for each spanning read
|
|
|
570 - mean_map_count : average of the number of genomic mappings for each spanning read
|
|
|
571 - num_multi_map : number of spanning reads that map to more than one genomic location
|
|
|
572 - span_count : number of spanning reads supporting the fusion
|
|
|
573 - span_coverage1 : coverage of spanning reads aligned to gene 1 as a proportion of expected coverage
|
|
|
574 - span_coverage2 : coverage of spanning reads aligned to gene 2 as a proportion of expected coverage
|
|
|
575 - span_coverage_min : minimum of span_coverage1 and span_coverage2
|
|
|
576 - span_coverage_max : maximum of span_coverage1 and span_coverage2
|
|
|
577 - splitr_count : number of split reads supporting the prediction
|
|
|
578 - splitr_min_pvalue : p-value, lower values are evidence the prediction is a false positive
|
|
|
579 - splitr_pos_pvalue : p-value, lower values are evidence the prediction is a false positive
|
|
|
580 - splitr_sequence : fusion sequence predicted by split reads
|
|
|
581 - splitr_span_pvalue : p-value, lower values are evidence the prediction is a false positive
|
|
|
582 - **Annotation**
|
|
|
583 - adjacent : fusion between adjacent genes
|
|
|
584 - altsplice : fusion likely the product of alternative splicing between adjacent genes
|
|
|
585 - break_adj_entropy1 : di-nucleotide entropy of the 40 nucleotides adjacent to the fusion splice in gene 1
|
|
|
586 - break_adj_entropy2 : di-nucleotide entropy of the 40 nucleotides adjacent to the fusion splice in gene 2
|
|
|
587 - break_adj_entropy_min : minimum of break_adj_entropy1 and break_adj_entropy2
|
|
|
588 - breakpoint_homology : number of nucleotides at the fusion splice that align equally well to gene 1 or gene 2
|
|
|
589 - breakseqs_estislands_percident : maximum percent identity of fusion sequence alignments to est islands
|
|
|
590 - cdna_breakseqs_percident : maximum percent identity of fusion sequence alignments to cdna
|
|
|
591 - deletion : fusion produced by a genomic deletion
|
|
|
592 - est_breakseqs_percident : maximum percent identity of fusion sequence alignments to est
|
|
|
593 - eversion : fusion produced by a genomic eversion
|
|
|
594 - exonboundaries : fusion splice at exon boundaries
|
|
|
595 - expression1 : expression of gene 1 as number of concordant pairs aligned to exons
|
|
|
596 - expression2 : expression of gene 2 as number of concordant pairs aligned to exons
|
|
|
597 - gene_chromosome1 : chromosome of gene 1
|
|
|
598 - gene_chromosome2 : chromosome of gene 2
|
|
|
599 - gene_end1 : end position for gene 1
|
|
|
600 - gene_end2 : end position for gene 2
|
|
|
601 - gene_location1 : location of breakpoint in gene 1
|
|
|
602 - gene_location2 : location of breakpoint in gene 2
|
|
|
603 - gene_start1 : start of gene 1
|
|
|
604 - gene_start2 : start of gene 2
|
|
|
605 - gene_strand1 : strand of gene 1
|
|
|
606 - gene_strand2 : strand of gene 2
|
|
|
607 - genome_breakseqs_percident : maximum percent identity of fusion sequence alignments to genome
|
|
|
608 - genomic_break_pos1 : genomic position in gene 1 of fusion splice / breakpoint
|
|
|
609 - genomic_break_pos2 : genomic position in gene 2 of fusion splice / breakpoint
|
|
|
610 - genomic_strand1 : genomic strand in gene 1 of fusion splice / breakpoint, retained sequence upstream on this strand, breakpoint is downstream
|
|
|
611 - genomic_strand2 : genomic strand in gene 2 of fusion splice / breakpoint, retained sequence upstream on this strand, breakpoint is downstream
|
|
|
612 - interchromosomal : fusion produced by an interchromosomal translocation
|
|
|
613 - interrupted_index1 : ratio of coverage before and after the fusion splice / breakpoint in gene 1
|
|
|
614 - interrupted_index2 : ratio of coverage before and after the fusion splice / breakpoint in gene 2
|
|
|
615 - inversion : fusion produced by genomic inversion
|
|
|
616 - orf : fusion combines genes in a way that preserves a reading frame
|
|
|
617 - probability : probability produced by classification using adaboost and example positives/negatives (only given in results.classified.txt)
|
|
|
618 - read_through : fusion involving adjacent potentially resulting from co-transcription rather than genome rearrangement
|
|
|
619 - repeat_proportion1 : proportion of the spanning reads in gene 1 that span a repeat region
|
|
|
620 - repeat_proportion2 : proportion of the spanning reads in gene 2 that span a repeat region
|
|
|
621 - max_repeat_proportion : max of repeat_proportion1 and repeat_proportion2
|
|
|
622 - splice_score : number of nucleotides similar to GTAG at fusion splice
|
|
|
623 - num_splice_variants : number of potential splice variants for this gene pair
|
|
|
624 - 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
|
|
|
625 - 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
|
|
|
626
|
|
|
627
|
|
|
628 **Example**
|
|
|
629
|
|
|
630 results.tsv::
|
|
|
631
|
|
|
632 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
|
|
|
633 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 -
|
|
|
634 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 - -
|
|
|
635
|
|
|
636 </help>
|
|
|
637 </tool>
|
