Mercurial > repos > jjohnson > defuse
annotate defuse.xml @ 14:038a5210392a draft
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| author | jjohnson |
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| date | Tue, 12 Dec 2017 10:02:00 -0500 |
| parents | 3a4876d01c7e |
| children | bdd93719cede |
| rev | line source |
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1 <tool id="defuse" name="DeFuse" version="@DEFUSE_VERSION@.1"> |
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2 <description>identify fusion transcripts</description> |
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3 <macros> |
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4 <import>macros.xml</import> |
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5 </macros> |
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6 <requirements> |
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7 <expand macro="defuse_requirement" /> |
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8 <expand macro="mapping_requirements" /> |
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9 <expand macro="r_requirements" /> |
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10 </requirements> |
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3
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DeFuse - Allow user to save the workspace, create an html file with links to the files in the workspace.
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11 <command interpreter="command"> /bin/bash $shscript </command> |
| 1 | 12 <inputs> |
| 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.)"/> | |
| 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 <param name="library_name" type="text" value="unknown" label="library name" help="Value to put in the results library_name column"> |
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16 <validator type="length" min="1"/> |
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17 </param> |
| 1 | 18 <conditional name="refGenomeSource"> |
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19 <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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20 <option value="indexed">Use a built-in DeFuse Reference Dataset</option> |
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21 <option value="history">Use a configuration from your history that specifies the DeFuse Reference Dataset</option> |
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22 </param> |
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23 <when value="indexed"> |
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24 <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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25 <options from_file="defuse_reference.loc"> |
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26 <column name="name" index="1"/> |
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27 <column name="value" index="3"/> |
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28 <filter type="sort_by" column="0" /> |
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29 <validator type="no_options" message="No indexes are available" /> |
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30 </options> |
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31 </param> |
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32 </when> |
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33 <when value="history"> |
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34 <param name="config" type="data" format="defuse.conf" label="Defuse Config file" help=""/> |
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35 </when> <!-- history --> |
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36 </conditional> <!-- refGenomeSource --> |
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37 <conditional name="defuse_param"> |
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38 <param name="settings" type="select" label="Defuse parameter settings" help=""> |
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39 <option value="preSet">Default settings</option> |
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40 <option value="full">Full parameter list</option> |
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41 </param> |
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42 <when value="preSet" /> |
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43 <when value="full"> |
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44 <param name="max_insert_size" type="integer" value="500" optional="true" label="Bowtie max_insert_size" /> |
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45 <param name="dna_concordant_length" type="integer" value="2000" optional="true" label="Minimum gene fusion range dna_concordant_length" /> |
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46 <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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47 <param name="calculate_extra_annotations" type="select" label="Calculate extra annotations, fusion splice index and interrupted index" help=""> |
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48 <option value="">Use Default</option> |
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49 <option value="no">no</option> |
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50 <option value="yes">yes</option> |
| 1 | 51 </param> |
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52 <param name="clustering_precision" type="float" value=".95" optional="true" label="Filter clustering_precision"> |
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53 <validator type="in_range" message="Choose a value between .1 and 1.0" min=".1" max="1"/> |
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54 </param> |
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55 <param name="span_count_threshold" type="integer" value="5" optional="true" label="Filter span_count_threshold" /> |
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56 <param name="percent_identity_threshold" type="float" value=".90" optional="true" label="Filter percent_identity_threshold"> |
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57 <validator type="in_range" message="Choose a value between .1 and 1.0" min=".1" max="1"/> |
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58 </param> |
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59 <param name="split_min_anchor" type="integer" value="4" optional="true" label="Filter split_min_anchor" /> |
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60 <param name="splice_bias" type="integer" value="10" optional="true" label="Filter splice_bias" /> |
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61 <param name="probability_threshold" type="float" value="0.50" optional="true" label="Filter probability_threshold"> |
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62 <validator type="in_range" message="Choose a value between 0.0 and 1.0" min="0" max="1"/> |
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63 </param> |
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64 <param name="multi_exon_transcripts_stats" type="select" label="Use multiple exon transcripts for stats calculations" help="should be enabled for very small libraries"> |
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65 <option value="no" select="true">no</option> |
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66 <option value="yes">yes</option> |
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67 </param> |
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68 <param name="covariance_sampling_density" type="float" value="0.01" optional="true" label="covariance_sampling_density"> |
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69 <help>Position density when calculating covariance</help> |
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70 <validator type="in_range" message="Choose a value between 0.0 and 1.0" min="0" max="1"/> |
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71 </param> |
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72 <param name="max_paired_alignments" type="integer" value="10" optional="true" label="max_paired_alignments"> |
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73 <help>Maximum number of alignments for a read pair, Pairs with more alignments are filtered, default is 10</help> |
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74 <validator type="in_range" message="Choose a value between 0.0 and 1.0" min="1" max="100"/> |
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75 </param> |
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76 <param name="denovo_assembly" type="select" label="denovo_assembly" help=""> |
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77 <option value="">Use Default</option> |
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78 <option value="no">no</option> |
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79 <option value="yes">yes</option> |
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80 </param> |
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81 <!-- |
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82 <param name="positive_controls" type="data" format="txt" optional=true label="Defuse positive_controls" help=""/> |
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83 --> |
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84 <param name="reads_per_job" type="integer" value="1000000" optional="true" label="Number of reads for each job in split" /> |
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85 </when> <!-- full --> |
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86 </conditional> <!-- defuse_param --> |
| 6 | 87 <param name="keep_output" type="boolean" checked="true" truevalue="yes" falsevalue="no" label="Save DeFuse working directory files" |
| 88 help="The defuse output working directory can be helpful for determining errors that may have occurred during the run, | |
| 89 but they require considerable diskspace, and should be deleted and purged when no longer needed."/> | |
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90 <param name="breakpoints_bam" type="boolean" checked="false" truevalue="yes" falsevalue="no" label="Generate a Bam file for the fusions"/> |
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91 <param name="do_get_reads" type="boolean" checked="false" truevalue="yes" falsevalue="no" label="Run get_reads on each cluster"/> |
| 1 | 92 </inputs> |
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93 <stdio> |
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94 <exit_code range="1:" level="fatal" description="Error Running Defuse" /> |
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95 </stdio> |
| 6 | 96 <outputs> |
| 97 <data format="txt" name="config_txt" label="${tool.name} on ${on_string}: config.txt"/> | |
| 98 <data format="txt" name="defuse_log" label="${tool.name} on ${on_string}: defuse.log" /> | |
| 99 <data format="html" name="defuse_out" label="${tool.name} on ${on_string}: defuse_output (purge when no longer needed)"> | |
| 100 <filter>keep_output == True</filter> | |
| 101 </data> | |
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102 <data format="defuse.results.tsv" name="results_classify_tsv" label="${tool.name} on ${on_string}: results.classify.tsv" /> |
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103 <data format="defuse.results.tsv" name="results_filtered_tsv" label="${tool.name} on ${on_string}: results.filtered.tsv" /> |
| 6 | 104 <data format="html" name="fusion_reads" label="${tool.name} on ${on_string}: fusion_reads"> |
| 105 <filter>do_get_reads == True</filter> | |
| 106 </data> | |
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107 <data format="bam" name="fusions_bam" label="${tool.name} on ${on_string}: fusions.bam"> |
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108 <filter>breakpoints_bam == True</filter> |
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109 </data> |
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110 <!-- |
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111 expression_plot |
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112 circos plot |
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113 --> |
| 6 | 114 </outputs> |
| 1 | 115 <configfiles> |
| 116 <configfile name="defuse_config"> | |
|
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117 #import re |
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118 #set $ds = chr(36) |
| 1 | 119 #if $refGenomeSource.genomeSource == "history": |
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120 #set config_file = $refGenomeSource.config.__str__ |
| 1 | 121 #else |
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122 #set config_file = $refGenomeSource.index.value |
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123 #end if |
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124 #set pat = '^\s*([^#=][^=]*?)\s*=\s*(.*?)\s*$' |
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125 #set fh = open($config_file) |
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126 #set keys = ['dataset_directory','ensembl_organism','ensembl_prefix','ensembl_version','ensembl_genome_version','ucsc_genome_version','ncbi_organism','ncbi_prefix','chromosomes','mt_chromosome','gene_sources','ig_gene_sources','rrna_gene_sources'] |
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127 #set kv = [] |
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128 #for $line in $fh: |
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129 #set m = $re.match($pat,$line) |
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130 #if $m and len($m.groups()) == 2: |
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131 ## #echo $line |
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132 #if $m.groups()[0] in keys: |
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133 #set k = $m.groups()[0] |
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134 #if k == 'dataset_directory' and $refGenomeSource.genomeSource == "indexed": |
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135 ## The DataManager is conifgured to place the config file in the same directory as the defuse_data: dataset_directory |
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136 #set v = $os.path.dirname($config_file) |
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137 #else: |
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138 #set v = $m.groups()[1] |
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139 #end if |
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140 #set kv = $kv + [[$k, $v]] |
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141 #end if |
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142 #end if |
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143 #end for |
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144 ## #echo $kv |
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145 #set ref_dict = dict($kv) |
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146 ## #echo $ref_dict |
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147 ## include raw $refGenomeSource.config.__str__ |
| 1 | 148 # |
| 149 # Configuration file for defuse | |
| 150 # | |
| 151 # At a minimum, change all values enclused by [] | |
| 152 # | |
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153 |
| 1 | 154 # Directory where the defuse code was unpacked |
| 155 ## Default location in the tool/defuse directory | |
| 156 # source_directory = ${__root_dir__}/tools/defuse | |
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157 source_directory = __DEFUSE_PATH__ |
| 1 | 158 |
| 159 # Directory where you want your dataset | |
| 160 dataset_directory = #slurp | |
| 161 #try | |
| 162 $ref_dict['dataset_directory'] | |
| 163 #except | |
| 164 /project/db/genomes/Hsapiens/hg19/defuse | |
| 165 #end try | |
| 166 | |
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167 # Organism IDs |
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168 ensembl_organism = #slurp |
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169 #try |
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170 $ref_dict['ensembl_organism'] |
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171 #except |
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172 homo_sapiens |
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173 #end try |
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174 |
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175 ensembl_prefix = #slurp |
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176 #try |
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177 $ref_dict['ensembl_prefix'] |
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178 #except |
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179 Homo_sapiens |
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180 #end try |
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181 |
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182 ensembl_version = #slurp |
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183 #try |
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184 $ref_dict['ensembl_version'] |
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185 #except |
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186 71 |
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187 #end try |
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188 |
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189 ensembl_genome_version = #slurp |
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190 #try |
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191 $ref_dict['ensembl_genome_version'] |
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192 #except |
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193 GRCh37 |
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194 #end try |
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195 |
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196 ucsc_genome_version = #slurp |
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197 #try |
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198 $ref_dict['ucsc_genome_version'] |
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199 #except |
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200 hg19 |
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201 #end try |
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202 |
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203 ncbi_organism = #slurp |
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204 #try |
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205 $ref_dict['ncbi_organism'] |
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206 #except |
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207 Homo_sapiens |
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208 #end try |
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209 |
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210 ncbi_prefix = #slurp |
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211 #try |
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212 $ref_dict['ncbi_prefix'] |
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213 #except |
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214 Hs |
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215 #end try |
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216 |
| 1 | 217 # Input genome and gene models |
| 218 gene_models = #slurp | |
| 219 #try | |
| 220 $ref_dict['gene_models'] | |
| 221 #except | |
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222 \$(dataset_directory)/\$(ensembl_prefix).\$(ensembl_genome_version).\$(ensembl_version).gtf |
| 1 | 223 #end try |
| 224 genome_fasta = #slurp | |
| 225 #try | |
| 226 $ref_dict['genome_fasta'] | |
| 227 #except | |
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228 \$(dataset_directory)/\$(ensembl_prefix).\$(ensembl_genome_version).\$(ensembl_version).dna.chromosomes.fa |
| 1 | 229 #end try |
| 230 | |
| 231 # Repeat table from ucsc genome browser | |
| 232 repeats_filename = #slurp | |
| 233 #try | |
| 234 $ref_dict['repeats_filename'] | |
| 235 #except | |
| 236 \$(dataset_directory)/rmsk.txt | |
| 237 #end try | |
| 238 | |
| 239 # EST info downloaded from ucsc genome browser | |
| 240 est_fasta = #slurp | |
| 241 #try | |
| 242 $ref_dict['est_fasta'] | |
| 243 #except | |
| 244 \$(dataset_directory)/est.fa | |
| 245 #end try | |
| 246 est_alignments = #slurp | |
| 247 #try | |
| 248 $ref_dict['est_alignments'] | |
| 249 #except | |
| 250 \$(dataset_directory)/intronEst.txt | |
| 251 #end try | |
| 252 | |
| 253 # Unigene clusters downloaded from ncbi | |
| 254 unigene_fasta = #slurp | |
| 255 #try | |
| 256 $ref_dict['unigene_fasta'] | |
| 257 #except | |
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258 \$(dataset_directory)/\$(ncbi_prefix).seq.uniq |
| 1 | 259 #end try |
| 260 | |
| 261 # Paths to external tools | |
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262 bowtie_bin = __BOWTIE_BIN__ |
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263 bowtie_build_bin = __BOWTIE_BUILD_BIN__ |
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264 blat_bin = __BLAT_BIN__ |
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265 fatotwobit_bin = __FATOTWOBIT_BIN__ |
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266 gmap_bin = __GMAP_BIN__ |
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267 gmap_bin = __GMAP_BIN__ |
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268 gmap_setup_bin = __GMAP_SETUP_BIN__ |
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269 r_bin = __R_BIN__ |
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270 rscript_bin = __RSCRIPT_BIN__ |
| 1 | 271 |
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272 # Directory where you want your dataset |
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273 gmap_index_directory = #slurp |
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274 #try |
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275 $ref_dict['gmap_index_directory'] |
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276 #except |
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277 #raw |
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278 $(dataset_directory)/gmap |
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279 #end raw |
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280 #end try |
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281 |
| 1 | 282 #raw |
| 283 # Dataset files | |
| 284 dataset_prefix = $(dataset_directory)/defuse | |
| 285 chromosome_prefix = $(dataset_prefix).dna.chromosomes | |
| 286 exons_fasta = $(dataset_prefix).exons.fa | |
| 287 cds_fasta = $(dataset_prefix).cds.fa | |
| 288 cdna_regions = $(dataset_prefix).cdna.regions | |
| 289 cdna_fasta = $(dataset_prefix).cdna.fa | |
| 290 reference_fasta = $(dataset_prefix).reference.fa | |
| 291 rrna_fasta = $(dataset_prefix).rrna.fa | |
| 292 ig_gene_list = $(dataset_prefix).ig.gene.list | |
| 293 repeats_regions = $(dataset_directory)/repeats.regions | |
| 294 est_split_fasta1 = $(dataset_directory)/est.1.fa | |
| 295 est_split_fasta2 = $(dataset_directory)/est.2.fa | |
| 296 est_split_fasta3 = $(dataset_directory)/est.3.fa | |
| 297 est_split_fasta4 = $(dataset_directory)/est.4.fa | |
| 298 est_split_fasta5 = $(dataset_directory)/est.5.fa | |
| 299 est_split_fasta6 = $(dataset_directory)/est.6.fa | |
| 300 est_split_fasta7 = $(dataset_directory)/est.7.fa | |
| 301 est_split_fasta8 = $(dataset_directory)/est.8.fa | |
| 302 est_split_fasta9 = $(dataset_directory)/est.9.fa | |
| 303 | |
| 304 # Fasta files with bowtie indices for prefiltering reads for concordantly mapping pairs | |
| 305 prefilter1 = $(unigene_fasta) | |
| 306 | |
| 307 # deFuse scripts and tools | |
| 308 scripts_directory = $(source_directory)/scripts | |
| 309 tools_directory = $(source_directory)/tools | |
| 310 data_directory = $(source_directory)/data | |
| 311 #end raw | |
| 312 | |
| 313 # Path to samtools, 0.1.8 is compiled for you, use other versions at your own risk | |
| 314 samtools_bin = #slurp | |
| 315 #try | |
| 316 $ref_dict['samtools_bin'] | |
| 317 #except | |
| 318 \$(source_directory)/external/samtools-0.1.8/samtools | |
| 319 #end try | |
| 320 | |
| 321 # Bowtie parameters | |
| 322 bowtie_threads = #slurp | |
| 323 #try | |
| 324 $ref_dict['bowtie_threads'] | |
| 325 #except | |
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326 4 |
| 1 | 327 #end try |
| 328 bowtie_quals = #slurp | |
| 329 #try | |
| 330 $ref_dict['bowtie_quals'] | |
| 331 #except | |
| 332 --phred33-quals | |
| 333 #end try | |
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334 bowtie_params = #slurp |
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335 #try |
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336 $ref_dict['bowtie_params'] |
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337 #except |
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338 --chunkmbs 200 |
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339 #end try |
| 1 | 340 max_insert_size = #slurp |
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341 #if $defuse_param.settings == "full" and $defuse_param.max_insert_size.__str__ != "": |
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342 $defuse_param.max_insert_size |
| 1 | 343 #else |
| 344 #try | |
| 345 $ref_dict['max_insert_size'] | |
| 346 #except | |
| 347 500 | |
| 348 #end try | |
| 349 #end if | |
| 350 | |
| 351 # Parameters for building the dataset | |
| 352 chromosomes = #slurp | |
| 353 #try | |
| 354 $ref_dict.chromosomes | |
| 355 #except | |
| 356 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 | |
| 357 #end try | |
| 358 mt_chromosome = #slurp | |
| 359 #try | |
| 360 $ref_dict['mt_chromosome'] | |
| 361 #except | |
| 362 MT | |
| 363 #end try | |
| 364 gene_sources = #slurp | |
| 365 #try | |
| 366 $ref_dict['gene_sources'] | |
| 367 #except | |
| 368 IG_C_gene,IG_D_gene,IG_J_gene,IG_V_gene,processed_transcript,protein_coding | |
| 369 #end try | |
| 370 ig_gene_sources = #slurp | |
| 371 #try | |
| 372 $ref_dict['ig_gene_sources'] | |
| 373 #except | |
| 374 IG_C_gene,IG_D_gene,IG_J_gene,IG_V_gene,IG_pseudogene | |
| 375 #end try | |
| 376 rrna_gene_sources = #slurp | |
| 377 #try | |
| 378 $ref_dict['rrna_gene_sources'] | |
| 379 #except | |
| 380 Mt_rRNA,rRNA,rRNA_pseudogene | |
| 381 #end try | |
| 382 | |
| 383 # Blat sequences per job | |
| 384 num_blat_sequences = #slurp | |
| 385 #try | |
| 386 $ref_dict['num_blat_sequences'] | |
| 387 #except | |
| 388 10000 | |
| 389 #end try | |
| 390 | |
| 391 # Minimum gene fusion range | |
| 392 dna_concordant_length = #slurp | |
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393 #if $defuse_param.settings == "full" and $defuse_param.dna_concordant_length.__str__ != "": |
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394 $defuse_param.dna_concordant_length |
| 1 | 395 #else |
| 396 #try | |
| 397 $ref_dict['dna_concordant_length'] | |
| 398 #except | |
| 399 2000 | |
| 400 #end try | |
| 401 #end if | |
| 402 | |
| 403 # Trim length for discordant reads (split reads are not trimmed) | |
| 404 discord_read_trim = #slurp | |
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405 #if $defuse_param.settings == "full" and $defuse_param.discord_read_trim.__str__ != "": |
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406 $defuse_param.discord_read_trim |
| 1 | 407 #else |
| 408 #try | |
| 409 $ref_dict['discord_read_trim'] | |
| 410 #except | |
| 411 50 | |
| 412 #end try | |
| 413 #end if | |
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414 # Calculate extra annotations, fusion splice index and interrupted index |
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415 calculate_extra_annotations = #slurp |
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416 #if $defuse_param.settings == "full" and $defuse_param.calculate_extra_annotations.__str__ != "": |
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417 $defuse_param.calculate_extra_annotations |
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418 #else |
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419 #try |
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420 $ref_dict['calculate_extra_annotations'] |
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421 #except |
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422 no |
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423 #end try |
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424 #end if |
| 1 | 425 # Filtering parameters |
| 426 clustering_precision = #slurp | |
|
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427 #if $defuse_param.settings == "full" and $defuse_param.clustering_precision.__str__ != "" |
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428 $defuse_param.clustering_precision |
| 1 | 429 #else |
| 430 #try | |
| 431 $ref_dict['clustering_precision'] | |
| 432 #except | |
| 433 0.95 | |
| 434 #end try | |
| 435 #end if | |
| 436 span_count_threshold = #slurp | |
|
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437 #if $defuse_param.settings == "full" and $defuse_param.span_count_threshold.__str__ != "" |
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438 $defuse_param.span_count_threshold |
| 1 | 439 #else |
| 440 #try | |
| 441 $ref_dict['span_count_threshold'] | |
| 442 #except | |
| 443 5 | |
| 444 #end try | |
| 445 #end if | |
| 446 percent_identity_threshold = #slurp | |
|
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447 #if $defuse_param.settings == "full" and $defuse_param.percent_identity_threshold.__str__ != "" |
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448 $defuse_param.percent_identity_threshold |
| 1 | 449 #else |
| 450 #try | |
| 451 $ref_dict['percent_identity_threshold'] | |
| 452 #except | |
| 453 0.90 | |
| 454 #end try | |
| 455 #end if | |
| 456 split_min_anchor = #slurp | |
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457 #if $defuse_param.settings == "full" and $defuse_param.split_min_anchor.__str__ != "" |
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458 $defuse_param.split_min_anchor |
| 1 | 459 #else |
| 460 #try | |
| 461 $ref_dict['split_min_anchor'] | |
| 462 #except | |
| 463 4 | |
| 464 #end try | |
| 465 #end if | |
| 466 splice_bias = #slurp | |
|
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467 #if $defuse_param.settings == "full" and $defuse_param.splice_bias.__str__ != "" |
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468 $defuse_param.splice_bias |
| 1 | 469 #else |
| 470 #try | |
| 471 $ref_dict['splice_bias'] | |
| 472 #except | |
| 473 10 | |
| 474 #end try | |
| 475 #end if | |
| 476 denovo_assembly = #slurp | |
|
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477 #if $defuse_param.settings == "full" and $defuse_param.denovo_assembly.__str__ != "" |
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478 $defuse_param.denovo_assembly |
| 1 | 479 #else |
| 480 #try | |
| 481 $ref_dict['denovo_assembly'] | |
| 482 #except | |
| 483 no | |
| 484 #end try | |
| 485 #end if | |
| 486 probability_threshold = #slurp | |
|
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487 #if $defuse_param.settings == "full" and $defuse_param.probability_threshold.__str__ != "" |
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488 $defuse_param.probability_threshold |
| 1 | 489 #else |
| 490 #try | |
| 491 $ref_dict['probability_threshold'] | |
| 492 #except | |
| 493 0.50 | |
| 494 #end try | |
| 495 #end if | |
| 496 positive_controls = \$(data_directory)/controls.txt | |
| 497 | |
|
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498 # Use multiple exon transcripts for stats calculations (yes/no) |
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499 # should be enabled for very small libraries |
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500 multi_exon_transcripts_stats = #slurp |
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501 #if $defuse_param.settings == "full" and $defuse_param.multi_exon_transcripts_stats.__str__ != "" |
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502 $defuse_param.multi_exon_transcripts_stats |
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503 #else |
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504 #try |
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505 $ref_dict['multi_exon_transcripts_stats'] |
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506 #except |
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507 no |
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508 #end try |
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509 #end if |
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510 |
| 1 | 511 # Position density when calculating covariance |
| 512 covariance_sampling_density = #slurp | |
|
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513 #if $defuse_param.settings == "full" and $defuse_param.covariance_sampling_density.__str__ != "" |
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514 $defuse_param.covariance_sampling_density |
| 1 | 515 #else |
| 516 #try | |
| 517 $ref_dict['covariance_sampling_density'] | |
| 518 #except | |
| 519 0.01 | |
| 520 #end try | |
| 521 #end if | |
| 522 | |
|
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523 # Maximum number of alignments for a read pair |
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524 # Pairs with more alignments are filtered |
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525 max_paired_alignments = #slurp |
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526 #if $defuse_param.settings == "full" and $defuse_param.max_paired_alignments.__str__ != "" |
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527 $defuse_param.max_paired_alignments |
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528 #else |
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529 #try |
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530 $ref_dict['max_paired_alignments'] |
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531 #except |
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532 10 |
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533 #end try |
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534 #end if |
| 1 | 535 |
| 536 # Number of reads for each job in split | |
|
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537 reads_per_job = #slurp |
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538 #if $defuse_param.settings == "full" and $defuse_param.reads_per_job.__str__ != "" |
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539 $defuse_param.reads_per_job |
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540 #else |
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541 #try |
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542 $ref_dict['reads_per_job'] |
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543 #except |
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544 1000000 |
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545 #end try |
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546 #end if |
| 1 | 547 |
| 548 #raw | |
| 549 # If you have command line 'mail' and wish to be notified | |
| 550 # mailto = andrew.mcpherson@gmail.com | |
| 551 | |
| 552 # Remove temp files | |
| 553 remove_job_files = yes | |
| 554 remove_job_temp_files = yes | |
| 555 | |
|
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556 qsub_params = "" |
| 1 | 557 |
| 558 #end raw | |
| 559 | |
| 560 | |
| 561 </configfile> | |
|
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562 <configfile name="shscript"> |
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563 #!/bin/bash |
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564 ## define some things for cheetah proccessing |
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565 #set $ds = chr(36) |
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566 #set $amp = chr(38) |
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567 #set $gt = chr(62) |
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568 #set $lt = chr(60) |
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569 #set $echo_cmd = 'echo' |
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570 ## Find the defuse.pl in the galaxy tool path |
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571 #import Cheetah.FileUtils |
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572 ## declare a bash function for converting a results tsv into html with links to the get_reads output files |
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573 results2html() { |
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574 rlts=${ds}1 |
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575 rslt_name=`basename ${ds}rlts` |
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576 html=${ds}2 |
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577 echo '${lt}html${gt}${lt}head${gt}${lt}title${gt}Defuse '${ds}rslt_name'${lt}/title${gt}${lt}/head${gt}${lt}body${gt}' ${gt} ${ds}html |
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578 echo '${lt}h2${gt}Defuse '${ds}rslt_name'${lt}/h2${gt}${lt}table${gt}' ${gt}${gt} ${ds}html |
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579 if [ -z "${ds}3" ] |
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580 then |
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581 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");}\ |
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582 ${ds}1 ~ /[1-9][0-9]*/{printf("${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} ${ds}html |
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583 echo '${lt}/table${gt}' ${gt}${gt} ${ds}html |
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584 echo '${lt}/body${gt}${lt}/html${gt}' ${gt}${gt} ${ds}html |
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585 else |
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586 export _EFP=${ds}3 |
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587 mkdir -p ${ds}_EFP |
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588 awk '${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");}\ |
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589 ${ds}1 ~ /[1-9][0-9]*/{fn="cluster_"${ds}1"_reads.txt"; \ |
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590 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} ${ds}html |
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591 echo '${lt}/table${gt}' ${gt}${gt} ${ds}html |
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592 echo '${lt}/body${gt}${lt}/html${gt}' ${gt}${gt} ${ds}html |
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593 for i in `awk '${ds}1 ~ /[1-9][0-9]*/{print ${ds}1}' ${ds}rlts`; |
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594 do fn=cluster_${ds}{i}_reads.txt; |
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595 pn=${ds}_EFP/${ds}fn; |
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596 perl \${DEFUSE_PATH}/scripts/get_reads.pl -c $defuse_config -o output_dir -i ${ds}i ${gt} ${ds}pn; |
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597 done |
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598 fi |
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599 } |
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600 ## substitute pathnames into config file |
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601 if `grep __DEFUSE_PATH__ $defuse_config ${gt} /dev/null`;then sed -i'.tmp' "s#__DEFUSE_PATH__#\${DEFUSE_PATH}#" $defuse_config; fi |
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602 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 |
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603 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 |
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604 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 |
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605 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 |
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606 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 |
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607 if `grep __GMAP_BIN__ $defuse_config ${gt} /dev/null` ${amp}${amp} GMAP_BIN=`which gmap`;then sed -i'.tmp' "s#__GMAP_BIN__#\${GMAP_BIN}#" $defuse_config; fi |
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608 if `grep __GMAP_SETUP_BIN__ $defuse_config ${gt} /dev/null` ${amp}${amp} GMAP_SETUP_BIN=`which gmap_setup`;then sed -i'.tmp' "s#__GMAP_SETUP_BIN__#\${GMAP_SETUP_BIN}#" $defuse_config; fi |
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609 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 |
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610 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 |
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611 |
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612 |
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613 ## copy config to output |
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614 cp $defuse_config $config_txt |
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615 ## make a data_dir and ln -s the input fastq |
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616 mkdir -p data_dir |
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617 ## ln -s "$left_pairendreads" data_dir/reads_1.fastq |
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618 ## ln -s "$right_pairendreads" data_dir/reads_2.fastq |
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619 cp "$left_pairendreads" data_dir/reads_1.fastq |
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620 cp "$right_pairendreads" data_dir/reads_2.fastq |
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621 ## ln to output_dir in from_work_dir |
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622 #if $defuse_out.__str__ != 'None': |
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623 mkdir -p $defuse_out.dataset.extra_files_path |
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624 ln -s $defuse_out.dataset.extra_files_path output_dir |
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625 #else |
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626 mkdir -p output_dir |
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627 #end if |
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628 ## run defuse.pl |
| 13 | 629 perl \${DEFUSE_PATH}/scripts/defuse.pl -name "$library_name" -c $defuse_config -1 data_dir/reads_1.fastq -2 data_dir/reads_2.fastq -o output_dir -p \$GALAXY_SLOTS; |
| 630 exit_code_for_galaxy=\$?; | |
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631 ## copy primary results to output datasets |
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632 if [ -e output_dir/log/defuse.log ]; then cp output_dir/log/defuse.log $defuse_log; fi |
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633 ## if [ -e output_dir/results.tsv ]; then cp output_dir/results.tsv $results_tsv; fi |
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634 if [ -e output_dir/results.filtered.tsv ]; then cp output_dir/results.filtered.tsv $results_filtered_tsv; fi |
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635 if [ -e output_dir/results.classify.tsv ]; then cp output_dir/results.classify.tsv $results_classify_tsv; fi |
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636 #if $breakpoints_bam: |
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637 if [ -e output_dir/results.filtered.tsv ] ${amp}${amp} [ -e output_dir/breakpoints.genome.psl ] |
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638 then |
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639 awk "\\$10 ~ /^(`awk '\\$1 ~ /[0-9]+/{print \\$1}' output_dir/results.filtered.tsv | tr '\n' '|'`)\\$/{print \\$0}" output_dir/breakpoints.genome.psl > breakpoints.genome.filtered.psl ${amp}${amp} |
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640 psl2sam.pl breakpoints.genome.filtered.psl > breakpoints.genome.filtered.sam ${amp}${amp} |
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641 samtools view -b -T /panfs/roc/rissdb/galaxy/genomes/NCBIM37/defuse/defuse.reference.fa -o breakpoints.genome.filtered.bam breakpoints.genome.filtered.sam ${amp}${amp} |
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642 samtools sort breakpoints.genome.filtered.bam breakpoints ${amp}${amp} |
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643 ## samtools index breakpoints.bam |
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644 cp breakpoints.bam $fusions_bam |
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645 fi |
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646 #end if |
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647 ## create html with links for output_dir |
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648 #if $defuse_out.__str__ != 'None': |
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649 if [ -e $defuse_out ] |
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650 then |
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651 echo '${lt}html${gt}${lt}head${gt}${lt}title${gt}Defuse Output${lt}/title${gt}${lt}/head${gt}${lt}body${gt}' ${gt} $defuse_out |
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652 echo '${lt}h2${gt}Defuse Output Files${lt}/h2${gt}${lt}ul${gt}' ${gt}${gt} $defuse_out |
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653 pushd $defuse_out.dataset.extra_files_path |
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654 for f in `find -L . -maxdepth 1 -type f`; |
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655 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} $defuse_out; |
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656 done |
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657 popd |
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658 echo '${lt}/ul${gt}' ${gt}${gt} $defuse_out |
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659 echo '${lt}/body${gt}${lt}/html${gt}' ${gt}${gt} $defuse_out |
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660 fi |
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661 #end if |
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662 ## run get_reads.pl on each cluster |
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663 #if $fusion_reads.__str__ != 'None': |
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664 if [ -e output_dir/results.filtered.tsv -a -e $fusion_reads ] |
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665 then |
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666 mkdir -p $fusion_reads.dataset.extra_files_path |
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667 results2html output_dir/results.filtered.tsv $fusion_reads $fusion_reads.dataset.extra_files_path |
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668 fi |
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669 #end if |
| 13 | 670 (exit \$exit_code_for_galaxy) |
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671 </configfile> |
| 1 | 672 </configfiles> |
| 6 | 673 |
| 1 | 674 <tests> |
| 675 </tests> | |
| 676 <help> | |
| 677 **DeFuse** | |
| 678 | |
| 679 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. | |
| 680 | |
| 681 Journal reference: http://www.ploscompbiol.org/article/info%3Adoi%2F10.1371%2Fjournal.pcbi.1001138 | |
| 682 | |
| 683 .. _DeFuse: http://sourceforge.net/apps/mediawiki/defuse/index.php?title=Main_Page | |
| 684 | |
| 685 ------ | |
| 686 | |
| 687 **Inputs** | |
| 688 | |
| 689 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**). | |
| 690 | |
| 691 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. | |
| 692 | |
| 693 DeFuse uses a Reference Dataset to search for gene fusions. The Reference Dataset is generated from the following sources in DeFuse_Version_0.4_: | |
| 694 - genome_fasta from Ensembl | |
| 695 - gene_models from Ensembl | |
| 696 - repeats_filename from UCSC RepeatMasker rmsk.txt | |
| 697 - est_fasta from UCSC | |
| 698 - est_alignments from UCSC intronEst.txt | |
| 699 - unigene_fasta from NCBI | |
| 700 | |
| 701 .. _DeFuse_Version_0.4: http://sourceforge.net/apps/mediawiki/defuse/index.php?title=DeFuse_Version_0.4.2 | |
| 702 | |
| 703 ------ | |
| 704 | |
| 705 **Outputs** | |
| 706 | |
| 707 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. | |
| 708 | |
| 709 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. | |
| 710 | |
| 711 The file format is tab delimited with one prediction per line, and the following fields per prediction (not necessarily in this order): | |
| 712 | |
| 713 - **Identification** | |
| 714 - cluster_id : random identifier assigned to each prediction | |
| 715 - library_name : library name given on the command line of defuse | |
| 716 - gene1 : ensembl id of gene 1 | |
| 717 - gene2 : ensembl id of gene 2 | |
| 718 - gene_name1 : name of gene 1 | |
| 719 - gene_name2 : name of gene 2 | |
| 720 - **Evidence** | |
| 721 - break_predict : breakpoint prediction method, denovo or splitr, that is considered most reliable | |
| 722 - concordant_ratio : proportion of spanning reads considered concordant by blat | |
| 723 - denovo_min_count : minimum kmer count across denovo assembled sequence | |
| 724 - denovo_sequence : fusion sequence predicted by debruijn based denovo sequence assembly | |
| 725 - denovo_span_pvalue : p-value, lower values are evidence the prediction is a false positive | |
| 726 - gene_align_strand1 : alignment strand for spanning read alignments to gene 1 | |
| 727 - gene_align_strand2 : alignment strand for spanning read alignments to gene 2 | |
| 728 - min_map_count : minimum of the number of genomic mappings for each spanning read | |
| 729 - max_map_count : maximum of the number of genomic mappings for each spanning read | |
| 730 - mean_map_count : average of the number of genomic mappings for each spanning read | |
| 731 - num_multi_map : number of spanning reads that map to more than one genomic location | |
| 732 - span_count : number of spanning reads supporting the fusion | |
| 733 - span_coverage1 : coverage of spanning reads aligned to gene 1 as a proportion of expected coverage | |
| 734 - span_coverage2 : coverage of spanning reads aligned to gene 2 as a proportion of expected coverage | |
| 735 - span_coverage_min : minimum of span_coverage1 and span_coverage2 | |
| 736 - span_coverage_max : maximum of span_coverage1 and span_coverage2 | |
| 737 - splitr_count : number of split reads supporting the prediction | |
| 738 - splitr_min_pvalue : p-value, lower values are evidence the prediction is a false positive | |
| 739 - splitr_pos_pvalue : p-value, lower values are evidence the prediction is a false positive | |
| 740 - splitr_sequence : fusion sequence predicted by split reads | |
| 741 - splitr_span_pvalue : p-value, lower values are evidence the prediction is a false positive | |
| 742 - **Annotation** | |
| 743 - adjacent : fusion between adjacent genes | |
| 744 - altsplice : fusion likely the product of alternative splicing between adjacent genes | |
| 745 - break_adj_entropy1 : di-nucleotide entropy of the 40 nucleotides adjacent to the fusion splice in gene 1 | |
| 746 - break_adj_entropy2 : di-nucleotide entropy of the 40 nucleotides adjacent to the fusion splice in gene 2 | |
| 747 - break_adj_entropy_min : minimum of break_adj_entropy1 and break_adj_entropy2 | |
| 748 - breakpoint_homology : number of nucleotides at the fusion splice that align equally well to gene 1 or gene 2 | |
| 749 - breakseqs_estislands_percident : maximum percent identity of fusion sequence alignments to est islands | |
| 750 - cdna_breakseqs_percident : maximum percent identity of fusion sequence alignments to cdna | |
| 751 - deletion : fusion produced by a genomic deletion | |
| 752 - est_breakseqs_percident : maximum percent identity of fusion sequence alignments to est | |
| 753 - eversion : fusion produced by a genomic eversion | |
| 754 - exonboundaries : fusion splice at exon boundaries | |
| 755 - expression1 : expression of gene 1 as number of concordant pairs aligned to exons | |
| 756 - expression2 : expression of gene 2 as number of concordant pairs aligned to exons | |
| 757 - gene_chromosome1 : chromosome of gene 1 | |
| 758 - gene_chromosome2 : chromosome of gene 2 | |
| 759 - gene_end1 : end position for gene 1 | |
| 760 - gene_end2 : end position for gene 2 | |
| 761 - gene_location1 : location of breakpoint in gene 1 | |
| 762 - gene_location2 : location of breakpoint in gene 2 | |
| 763 - gene_start1 : start of gene 1 | |
| 764 - gene_start2 : start of gene 2 | |
| 765 - gene_strand1 : strand of gene 1 | |
| 766 - gene_strand2 : strand of gene 2 | |
| 767 - genome_breakseqs_percident : maximum percent identity of fusion sequence alignments to genome | |
| 768 - genomic_break_pos1 : genomic position in gene 1 of fusion splice / breakpoint | |
| 769 - genomic_break_pos2 : genomic position in gene 2 of fusion splice / breakpoint | |
| 770 - genomic_strand1 : genomic strand in gene 1 of fusion splice / breakpoint, retained sequence upstream on this strand, breakpoint is downstream | |
| 771 - genomic_strand2 : genomic strand in gene 2 of fusion splice / breakpoint, retained sequence upstream on this strand, breakpoint is downstream | |
| 772 - interchromosomal : fusion produced by an interchromosomal translocation | |
| 773 - interrupted_index1 : ratio of coverage before and after the fusion splice / breakpoint in gene 1 | |
| 774 - interrupted_index2 : ratio of coverage before and after the fusion splice / breakpoint in gene 2 | |
| 775 - inversion : fusion produced by genomic inversion | |
| 776 - orf : fusion combines genes in a way that preserves a reading frame | |
| 777 - probability : probability produced by classification using adaboost and example positives/negatives (only given in results.classified.txt) | |
| 778 - read_through : fusion involving adjacent potentially resulting from co-transcription rather than genome rearrangement | |
| 779 - repeat_proportion1 : proportion of the spanning reads in gene 1 that span a repeat region | |
| 780 - repeat_proportion2 : proportion of the spanning reads in gene 2 that span a repeat region | |
| 781 - max_repeat_proportion : max of repeat_proportion1 and repeat_proportion2 | |
| 782 - splice_score : number of nucleotides similar to GTAG at fusion splice | |
| 783 - num_splice_variants : number of potential splice variants for this gene pair | |
| 784 - 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 | |
| 785 - 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 | |
| 786 | |
| 787 | |
| 788 **Example** | |
| 789 | |
| 790 results.tsv:: | |
| 791 | |
| 792 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 | |
| 793 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 - | |
| 794 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 - - | |
| 795 | |
| 796 </help> | |
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797 <expand macro="citations"/> |
| 1 | 798 </tool> |