Mercurial > repos > jjohnson > defuse
annotate defuse.xml @ 9:d9017e11cde5
Fix toolshed location in tool_dependencies.xml
| author | Jim Johnson <jj@umn.edu> |
|---|---|
| date | Wed, 05 Jun 2013 15:52:32 -0500 |
| parents | 06675bd664ee |
| children | 08e9244aeab8 |
| rev | line source |
|---|---|
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06675bd664ee
Update to DeFuse verion 0.6.1 and change tool dependencies for autoinstall
Jim Johnson <jj@umn.edu>
parents:
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1 <tool id="defuse" name="DeFuse" version="1.6.1"> |
| 0 | 2 <description>identify fusion transcripts</description> |
| 3 <requirements> | |
|
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06675bd664ee
Update to DeFuse verion 0.6.1 and change tool dependencies for autoinstall
Jim Johnson <jj@umn.edu>
parents:
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changeset
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4 <requirement type="package" version="0.6.1">defuse</requirement> |
| 6 | 5 <requirement type="package" version="0.1.18">samtools</requirement> |
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06675bd664ee
Update to DeFuse verion 0.6.1 and change tool dependencies for autoinstall
Jim Johnson <jj@umn.edu>
parents:
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changeset
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6 <requirement type="package" version="1.0.0">bowtie</requirement> |
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06675bd664ee
Update to DeFuse verion 0.6.1 and change tool dependencies for autoinstall
Jim Johnson <jj@umn.edu>
parents:
7
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changeset
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7 <requirement type="package" version="2013-05-09">gmap</requirement> |
|
06675bd664ee
Update to DeFuse verion 0.6.1 and change tool dependencies for autoinstall
Jim Johnson <jj@umn.edu>
parents:
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changeset
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8 <requirement type="package" version="283">kent</requirement> |
| 0 | 9 </requirements> |
| 10 <command interpreter="command"> /bin/bash $shscript </command> | |
| 11 <inputs> | |
| 12 <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.)"/> | |
| 13 <param name="right_pairendreads" type="data" format="fastq" label="right part of read pairs" help="In the same order as the left reads"/> | |
| 14 <conditional name="refGenomeSource"> | |
| 15 <param name="genomeSource" type="select" label="Will you select a built-in DeFuse Reference Dataset, or supply a configuration from your history" help=""> | |
| 16 <option value="indexed">Use a built-in DeFuse Reference Dataset</option> | |
| 17 <option value="history">Use a configuration from your history that specifies the DeFuse Reference Dataset</option> | |
| 18 </param> | |
| 19 <when value="indexed"> | |
| 20 <param name="index" type="select" label="Select a Reference Dataset" help="if your genome of interest is not listed - contact Galaxy team"> | |
| 21 <options from_file="defuse.loc"> | |
| 22 <column name="name" index="1"/> | |
| 23 <column name="value" index="2"/> | |
| 24 <filter type="sort_by" column="0" /> | |
| 25 <validator type="no_options" message="No indexes are available" /> | |
| 26 </options> | |
| 27 </param> | |
| 28 <conditional name="defuse_param"> | |
| 29 <param name="settings" type="select" label="Defuse parameter settings" help=""> | |
| 30 <option value="preSet">Default settings</option> | |
| 31 <option value="full">Full parameter list</option> | |
| 32 </param> | |
| 33 <when value="preSet" /> | |
| 34 <when value="full"> | |
| 35 <param name="max_insert_size" type="integer" value="500" optional="true" label="Bowtie max_insert_size" /> | |
| 36 <param name="dna_concordant_length" type="integer" value="2000" optional="true" label="Minimum gene fusion range dna_concordant_length" /> | |
| 37 <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)" /> | |
| 38 <param name="clustering_precision" type="float" value=".95" optional="true" label="Filter clustering_precision"> | |
| 39 <validator type="in_range" message="Choose a value between .1 and 1.0" min=".1" max="1"/> | |
| 40 </param> | |
| 41 <param name="span_count_threshold" type="integer" value="5" optional="true" label="Filter span_count_threshold" /> | |
| 42 <param name="split_count_threshold" type="integer" value="3" optional="true" label="Filter split_count_threshold" /> | |
| 43 <param name="percent_identity_threshold" type="float" value=".90" optional="true" label="Filter percent_identity_threshold"> | |
| 44 <validator type="in_range" message="Choose a value between .1 and 1.0" min=".1" max="1"/> | |
| 45 </param> | |
| 46 <param name="max_dist_pos" type="integer" value="600" optional="true" label="Filter max_dist_pos" /> | |
| 47 <param name="num_dist_genes" type="integer" value="500" optional="true" label="Filter num_dist_genes" /> | |
| 48 <param name="split_min_anchor" type="integer" value="4" optional="true" label="Filter split_min_anchor" /> | |
| 49 <param name="max_concordant_ratio" type="float" value="0.1" optional="true" label="Filter max_concordant_ratio"> | |
| 50 <validator type="in_range" message="Choose a value between 0.0 and 1.0" min="0" max="1"/> | |
| 51 </param> | |
| 52 <param name="splice_bias" type="integer" value="10" optional="true" label="Filter splice_bias" /> | |
| 53 <param name="probability_threshold" type="float" value="0.50" optional="true" label="Filter probability_threshold"> | |
| 54 <validator type="in_range" message="Choose a value between 0.0 and 1.0" min="0" max="1"/> | |
| 55 </param> | |
| 56 <param name="covariance_sampling_density" type="float" value="0.01" optional="true" label="covariance_sampling_density"> | |
| 57 <help>Position density when calculating covariance</help> | |
| 58 <validator type="in_range" message="Choose a value between 0.0 and 1.0" min="0" max="1"/> | |
| 59 </param> | |
| 60 <param name="denovo_assembly" type="select" label="denovo_assembly" help=""> | |
| 61 <option value="">Use Default</option> | |
| 62 <option value="no">no</option> | |
| 63 <option value="yes">yes</option> | |
| 64 </param> | |
| 65 <!-- | |
| 66 <param name="positive_controls" type="data" format="txt" optional=true label="Defuse positive_controls" help=""/> | |
| 67 --> | |
| 68 </when> <!-- full --> | |
| 69 </conditional> <!-- defuse_param --> | |
| 70 </when> | |
| 71 <when value="history"> | |
| 72 <param name="config" type="data" format="txt" label="Defuse Config file" help=""/> | |
| 73 </when> <!-- history --> | |
| 74 </conditional> <!-- refGenomeSource --> | |
| 5 | 75 <param name="keep_output" type="boolean" checked="true" truevalue="yes" falsevalue="no" label="Save DeFuse working directory files" |
| 76 help="The defuse output working directory can be helpful for determining errors that may have occurred during the run, | |
| 77 but they require considerable diskspace, and should be deleted and purged when no longer needed."/> | |
| 3 | 78 <param name="do_get_reads" type="boolean" checked="true" truevalue="yes" falsevalue="no" label="Run get_reads on each cluster"/> |
| 0 | 79 </inputs> |
| 5 | 80 <outputs> |
| 81 <data format="txt" name="config_txt" label="${tool.name} on ${on_string}: config.txt"/> | |
| 82 <data format="txt" name="defuse_log" label="${tool.name} on ${on_string}: defuse.log" /> | |
| 83 <data format="html" name="defuse_out" label="${tool.name} on ${on_string}: defuse_output (purge when no longer needed)"> | |
| 84 <filter>keep_output == True</filter> | |
| 85 </data> | |
| 86 <data format="tabular" name="results_tsv" label="${tool.name} on ${on_string}: results.tsv" /> | |
| 87 <data format="tabular" name="results_classify_tsv" label="${tool.name} on ${on_string}: results.classify.tsv" /> | |
| 88 <data format="tabular" name="results_filtered_tsv" label="${tool.name} on ${on_string}: results.filtered.tsv" /> | |
| 89 <data format="html" name="fusion_reads" label="${tool.name} on ${on_string}: fusion_reads"> | |
| 90 <filter>do_get_reads == True</filter> | |
| 91 </data> | |
| 92 </outputs> | |
| 0 | 93 <configfiles> |
| 94 <configfile name="defuse_config"> | |
| 95 #import ast | |
| 96 #if $refGenomeSource.genomeSource == "history": | |
| 97 #include raw $refGenomeSource.config.__str__ | |
| 98 #else | |
| 99 #set $ref_dict = dict($ast.literal_eval($refGenomeSource.index.value)) | |
| 100 # | |
| 101 # Configuration file for defuse | |
| 102 # | |
| 103 # At a minimum, change all values enclused by [] | |
| 104 # | |
| 105 | |
| 106 # Directory where the defuse code was unpacked | |
| 107 ## Default location in the tool/defuse directory | |
| 108 # source_directory = ${__root_dir__}/tools/defuse | |
| 109 source_directory = #slurp | |
| 110 #try | |
| 111 $ref_dict['source_directory'] | |
| 112 #except | |
| 113 __DEFUSE_PATH__ | |
| 114 #end try | |
| 115 | |
| 116 # Directory where you want your dataset | |
| 117 dataset_directory = #slurp | |
| 118 #try | |
| 119 $ref_dict['dataset_directory'] | |
| 120 #except | |
| 121 /project/db/genomes/Hsapiens/hg19/defuse | |
| 122 #end try | |
| 123 | |
| 124 # Input genome and gene models | |
| 125 gene_models = #slurp | |
| 126 #try | |
| 127 $ref_dict['gene_models'] | |
| 128 #except | |
| 129 \$(dataset_directory)/Homo_sapiens.GRCh37.62.gtf | |
| 130 #end try | |
| 131 genome_fasta = #slurp | |
| 132 #try | |
| 133 $ref_dict['genome_fasta'] | |
| 134 #except | |
| 135 \$(dataset_directory)/Homo_sapiens.GRCh37.62.dna.chromosome.fa | |
| 136 #end try | |
| 137 | |
| 138 # Repeat table from ucsc genome browser | |
| 139 repeats_filename = #slurp | |
| 140 #try | |
| 141 $ref_dict['repeats_filename'] | |
| 142 #except | |
| 143 \$(dataset_directory)/rmsk.txt | |
| 144 #end try | |
| 145 | |
| 146 # EST info downloaded from ucsc genome browser | |
| 147 est_fasta = #slurp | |
| 148 #try | |
| 149 $ref_dict['est_fasta'] | |
| 150 #except | |
| 151 \$(dataset_directory)/est.fa | |
| 152 #end try | |
| 153 est_alignments = #slurp | |
| 154 #try | |
| 155 $ref_dict['est_alignments'] | |
| 156 #except | |
| 157 \$(dataset_directory)/intronEst.txt | |
| 158 #end try | |
| 159 | |
| 160 # Unigene clusters downloaded from ncbi | |
| 161 unigene_fasta = #slurp | |
| 162 #try | |
| 163 $ref_dict['unigene_fasta'] | |
| 164 #except | |
| 165 \$(dataset_directory)/Hs.seq.uniq | |
| 166 #end try | |
| 167 | |
| 168 # Paths to external tools | |
| 169 bowtie_bin = #slurp | |
| 170 #try | |
| 171 $ref_dict['bowtie_bin'] | |
| 172 #except | |
| 173 __BOWTIE_BIN__ | |
| 174 #end try | |
| 175 bowtie_build_bin = #slurp | |
| 176 #try | |
| 177 $ref_dict['bowtie_build_bin'] | |
| 178 #except | |
| 179 __BOWTIE_BUILD_BIN__ | |
| 180 #end try | |
| 181 blat_bin = #slurp | |
| 182 #try | |
| 183 $ref_dict['blat_bin'] | |
| 184 #except | |
| 185 __BLAT_BIN__ | |
| 186 #end try | |
| 187 fatotwobit_bin = #slurp | |
| 188 #try | |
| 189 $ref_dict['fatotwobit_bin'] | |
| 190 #except | |
| 191 __FATOTWOBIT_BIN__ | |
| 192 #end try | |
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193 gmap_bin = #slurp |
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194 #try |
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195 $ref_dict['gmap_bin'] |
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196 #except |
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197 __GMAP_BIN__ |
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198 #end try |
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199 gmap_bin = #slurp |
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200 #try |
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201 $ref_dict['gmap_bin'] |
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202 #except |
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203 __GMAP_BIN__ |
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204 #end try |
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205 gmap_setup_bin = #slurp |
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206 #try |
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207 $ref_dict['gmap_setup_bin'] |
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208 #except |
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209 __GMAP_SETUP_BIN__ |
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210 #end try |
| 0 | 211 r_bin = #slurp |
| 212 #try | |
| 213 $ref_dict['r_bin'] | |
| 214 #except | |
| 215 __R_BIN__ | |
| 216 #end try | |
| 217 rscript_bin = #slurp | |
| 218 #try | |
| 219 $ref_dict['rscript_bin'] | |
| 220 #except | |
| 221 __RSCRIPT_BIN__ | |
| 222 #end try | |
| 223 | |
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224 # Directory where you want your dataset |
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225 gmap_index_directory = #slurp |
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226 #try |
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227 $ref_dict['gmap_index_directory'] |
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228 #except |
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229 \$(dataset_directory)/gmap |
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230 #end try |
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231 |
| 0 | 232 #raw |
| 233 # Dataset files | |
| 234 dataset_prefix = $(dataset_directory)/defuse | |
| 235 chromosome_prefix = $(dataset_prefix).dna.chromosomes | |
| 236 exons_fasta = $(dataset_prefix).exons.fa | |
| 237 cds_fasta = $(dataset_prefix).cds.fa | |
| 238 cdna_regions = $(dataset_prefix).cdna.regions | |
| 239 cdna_fasta = $(dataset_prefix).cdna.fa | |
| 240 reference_fasta = $(dataset_prefix).reference.fa | |
| 241 rrna_fasta = $(dataset_prefix).rrna.fa | |
| 242 ig_gene_list = $(dataset_prefix).ig.gene.list | |
| 243 repeats_regions = $(dataset_directory)/repeats.regions | |
| 244 est_split_fasta1 = $(dataset_directory)/est.1.fa | |
| 245 est_split_fasta2 = $(dataset_directory)/est.2.fa | |
| 246 est_split_fasta3 = $(dataset_directory)/est.3.fa | |
| 247 est_split_fasta4 = $(dataset_directory)/est.4.fa | |
| 248 est_split_fasta5 = $(dataset_directory)/est.5.fa | |
| 249 est_split_fasta6 = $(dataset_directory)/est.6.fa | |
| 250 est_split_fasta7 = $(dataset_directory)/est.7.fa | |
| 251 est_split_fasta8 = $(dataset_directory)/est.8.fa | |
| 252 est_split_fasta9 = $(dataset_directory)/est.9.fa | |
| 253 | |
| 254 # Fasta files with bowtie indices for prefiltering reads for concordantly mapping pairs | |
| 255 prefilter1 = $(unigene_fasta) | |
| 256 | |
| 257 # deFuse scripts and tools | |
| 258 scripts_directory = $(source_directory)/scripts | |
| 259 tools_directory = $(source_directory)/tools | |
| 260 data_directory = $(source_directory)/data | |
| 261 #end raw | |
| 262 | |
| 263 # Path to samtools, 0.1.8 is compiled for you, use other versions at your own risk | |
| 264 samtools_bin = #slurp | |
| 265 #try | |
| 266 $ref_dict['samtools_bin'] | |
| 267 #except | |
| 268 \$(source_directory)/external/samtools-0.1.8/samtools | |
| 269 #end try | |
| 270 | |
| 271 # Bowtie parameters | |
| 272 bowtie_threads = #slurp | |
| 273 #try | |
| 274 $ref_dict['bowtie_threads'] | |
| 275 #except | |
| 276 4 | |
| 277 #end try | |
| 278 bowtie_quals = #slurp | |
| 279 #try | |
| 280 $ref_dict['bowtie_quals'] | |
| 281 #except | |
| 282 --phred33-quals | |
| 283 #end try | |
| 284 max_insert_size = #slurp | |
| 285 #if $refGenomeSource.defuse_param.settings == "full" and $refGenomeSource.defuse_param.max_insert_size.__str__ != "": | |
| 286 $refGenomeSource.defuse_param.max_insert_size | |
| 287 #else | |
| 288 #try | |
| 289 $ref_dict['max_insert_size'] | |
| 290 #except | |
| 291 500 | |
| 292 #end try | |
| 293 #end if | |
| 294 | |
| 295 # Parameters for building the dataset | |
| 296 chromosomes = #slurp | |
| 297 #try | |
| 298 $ref_dict.chromosomes | |
| 299 #except | |
| 300 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 | |
| 301 #end try | |
| 302 mt_chromosome = #slurp | |
| 303 #try | |
| 304 $ref_dict['mt_chromosome'] | |
| 305 #except | |
| 306 MT | |
| 307 #end try | |
| 308 gene_sources = #slurp | |
| 309 #try | |
| 310 $ref_dict['gene_sources'] | |
| 311 #except | |
| 312 IG_C_gene,IG_D_gene,IG_J_gene,IG_V_gene,processed_transcript,protein_coding | |
| 313 #end try | |
| 314 ig_gene_sources = #slurp | |
| 315 #try | |
| 316 $ref_dict['ig_gene_sources'] | |
| 317 #except | |
| 318 IG_C_gene,IG_D_gene,IG_J_gene,IG_V_gene,IG_pseudogene | |
| 319 #end try | |
| 320 rrna_gene_sources = #slurp | |
| 321 #try | |
| 322 $ref_dict['rrna_gene_sources'] | |
| 323 #except | |
| 324 Mt_rRNA,rRNA,rRNA_pseudogene | |
| 325 #end try | |
| 326 | |
| 327 # Blat sequences per job | |
| 328 num_blat_sequences = #slurp | |
| 329 #try | |
| 330 $ref_dict['num_blat_sequences'] | |
| 331 #except | |
| 332 10000 | |
| 333 #end try | |
| 334 | |
| 335 # Minimum gene fusion range | |
| 336 dna_concordant_length = #slurp | |
| 337 #if $refGenomeSource.defuse_param.settings == "full" and $refGenomeSource.defuse_param.dna_concordant_length.__str__ != "": | |
| 338 $refGenomeSource.defuse_param.dna_concordant_length | |
| 339 #else | |
| 340 #try | |
| 341 $ref_dict['dna_concordant_length'] | |
| 342 #except | |
| 343 2000 | |
| 344 #end try | |
| 345 #end if | |
| 346 | |
| 347 # Trim length for discordant reads (split reads are not trimmed) | |
| 348 discord_read_trim = #slurp | |
| 349 #if $refGenomeSource.defuse_param.settings == "full" and $refGenomeSource.defuse_param.discord_read_trim.__str__ != "": | |
| 350 $refGenomeSource.defuse_param.discord_read_trim | |
| 351 #else | |
| 352 #try | |
| 353 $ref_dict['discord_read_trim'] | |
| 354 #except | |
| 355 50 | |
| 356 #end try | |
| 357 #end if | |
| 358 | |
| 359 # Filtering parameters | |
| 360 clustering_precision = #slurp | |
| 361 #if $refGenomeSource.defuse_param.settings == "full" and $refGenomeSource.defuse_param.clustering_precision.__str__ != "" | |
| 362 $refGenomeSource.defuse_param.clustering_precision | |
| 363 #else | |
| 364 #try | |
| 365 $ref_dict['clustering_precision'] | |
| 366 #except | |
| 367 0.95 | |
| 368 #end try | |
| 369 #end if | |
| 370 span_count_threshold = #slurp | |
| 371 #if $refGenomeSource.defuse_param.settings == "full" and $refGenomeSource.defuse_param.span_count_threshold.__str__ != "" | |
| 372 $refGenomeSource.defuse_param.span_count_threshold | |
| 373 #else | |
| 374 #try | |
| 375 $ref_dict['span_count_threshold'] | |
| 376 #except | |
| 377 5 | |
| 378 #end try | |
| 379 #end if | |
| 380 split_count_threshold = #slurp | |
| 381 #if $refGenomeSource.defuse_param.settings == "full" and $refGenomeSource.defuse_param.split_count_threshold.__str__ != "" | |
| 382 $refGenomeSource.defuse_param.split_count_threshold | |
| 383 #else | |
| 384 #try | |
| 385 $ref_dict['split_count_threshold'] | |
| 386 #except | |
| 387 3 | |
| 388 #end try | |
| 389 #end if | |
| 390 percent_identity_threshold = #slurp | |
| 391 #if $refGenomeSource.defuse_param.settings == "full" and $refGenomeSource.defuse_param.percent_identity_threshold.__str__ != "" | |
| 392 $refGenomeSource.defuse_param.percent_identity_threshold | |
| 393 #else | |
| 394 #try | |
| 395 $ref_dict['percent_identity_threshold'] | |
| 396 #except | |
| 397 0.90 | |
| 398 #end try | |
| 399 #end if | |
| 400 max_dist_pos = #slurp | |
| 401 #if $refGenomeSource.defuse_param.settings == "full" and $refGenomeSource.defuse_param.max_dist_pos.__str__ != "" | |
| 402 $refGenomeSource.defuse_param.max_dist_pos | |
| 403 #else | |
| 404 #try | |
| 405 $ref_dict['max_dist_pos'] | |
| 406 #except | |
| 407 600 | |
| 408 #end try | |
| 409 #end if | |
| 410 num_dist_genes = #slurp | |
| 411 #if $refGenomeSource.defuse_param.settings == "full" and $refGenomeSource.defuse_param.num_dist_genes.__str__ != "" | |
| 412 $refGenomeSource.defuse_param.num_dist_genes | |
| 413 #else | |
| 414 #try | |
| 415 $ref_dict['num_dist_genes'] | |
| 416 #except | |
| 417 500 | |
| 418 #end try | |
| 419 #end if | |
| 420 split_min_anchor = #slurp | |
| 421 #if $refGenomeSource.defuse_param.settings == "full" and $refGenomeSource.defuse_param.split_min_anchor.__str__ != "" | |
| 422 $refGenomeSource.defuse_param.split_min_anchor | |
| 423 #else | |
| 424 #try | |
| 425 $ref_dict['split_min_anchor'] | |
| 426 #except | |
| 427 4 | |
| 428 #end try | |
| 429 #end if | |
| 430 max_concordant_ratio = #slurp | |
| 431 #if $refGenomeSource.defuse_param.settings == "full" and $refGenomeSource.defuse_param.max_concordant_ratio.__str__ != "" | |
| 432 $refGenomeSource.defuse_param.max_concordant_ratio | |
| 433 #else | |
| 434 #try | |
| 435 $ref_dict['max_concordant_ratio'] | |
| 436 #except | |
| 437 0.1 | |
| 438 #end try | |
| 439 #end if | |
| 440 splice_bias = #slurp | |
| 441 #if $refGenomeSource.defuse_param.settings == "full" and $refGenomeSource.defuse_param.splice_bias.__str__ != "" | |
| 442 $refGenomeSource.defuse_param.splice_bias | |
| 443 #else | |
| 444 #try | |
| 445 $ref_dict['splice_bias'] | |
| 446 #except | |
| 447 10 | |
| 448 #end try | |
| 449 #end if | |
| 450 denovo_assembly = #slurp | |
| 451 #if $refGenomeSource.defuse_param.settings == "full" and $refGenomeSource.defuse_param.denovo_assembly.__str__ != "" | |
| 452 $refGenomeSource.defuse_param.denovo_assembly | |
| 453 #else | |
| 454 #try | |
| 455 $ref_dict['denovo_assembly'] | |
| 456 #except | |
| 457 no | |
| 458 #end try | |
| 459 #end if | |
| 460 probability_threshold = #slurp | |
| 461 #if $refGenomeSource.defuse_param.settings == "full" and $refGenomeSource.defuse_param.probability_threshold.__str__ != "" | |
| 462 $refGenomeSource.defuse_param.probability_threshold | |
| 463 #else | |
| 464 #try | |
| 465 $ref_dict['probability_threshold'] | |
| 466 #except | |
| 467 0.50 | |
| 468 #end try | |
| 469 #end if | |
| 470 positive_controls = \$(data_directory)/controls.txt | |
| 471 | |
| 472 # Position density when calculating covariance | |
| 473 covariance_sampling_density = #slurp | |
| 474 #if $refGenomeSource.defuse_param.settings == "full" and $refGenomeSource.defuse_param.covariance_sampling_density.__str__ != "" | |
| 475 $refGenomeSource.defuse_param.covariance_sampling_density | |
| 476 #else | |
| 477 #try | |
| 478 $ref_dict['covariance_sampling_density'] | |
| 479 #except | |
| 480 0.01 | |
| 481 #end try | |
| 482 #end if | |
| 483 | |
| 484 | |
| 485 # Number of reads for each job in split | |
| 486 reads_per_job = 1000000 | |
| 487 | |
| 488 # Number of regions for each breakpoint sequence job in split | |
| 489 regions_per_job = 20 | |
| 490 | |
| 491 #raw | |
| 492 # If you have command line 'mail' and wish to be notified | |
| 493 # mailto = andrew.mcpherson@gmail.com | |
| 494 | |
| 495 # Remove temp files | |
| 496 remove_job_files = yes | |
| 497 remove_job_temp_files = yes | |
| 498 | |
| 499 # Converting to fastq | |
| 500 # Fastq converter config format 1 for reads stored in separate files for each end | |
| 501 # data_lane_rexex_N is a perl regex which stores the lane id in $1 | |
| 502 # data_end_regex_N is a perl regex which stores the end, 1 or 2, in $1 | |
| 503 # data_compress_regex_N is a perl regex which stores the compression extension in $1 | |
| 504 # data_convert_N is the associated conversion utility that takes data at stdin and outputs fastq at stdout | |
| 505 # Fastq converter config format 2 for reads stored in separate files for each end | |
| 506 # data_lane_regex_N is a perl regex which stores the lane id in $1 | |
| 507 # data_compress_regex_N is a perl regex which stores the compression extension in $1 | |
| 508 # data_end1_converter_N is the associated conversion utility that takes data at stdin and outputs fastq for end 1 at stdout | |
| 509 # data_end2_converter_N is the associated conversion utility that takes data at stdin and outputs fastq for end 2 at stdout | |
| 510 | |
| 511 data_lane_regex_1 = ^(.+)_[12]_export\.txt.*$ | |
| 512 data_end_regex_1 = ^.+_([12])_export\.txt.*$ | |
| 513 data_compress_regex_1 = ^.+_[12]_export\.txt(.*)$ | |
| 514 data_converter_1 = $(scripts_directory)/fq_all2std.pl export2std | |
| 515 | |
| 516 data_lane_regex_2 = ^(.+)_[12]_concat_qseq\.txt.*$ | |
| 517 data_end_regex_2 = ^.+_([12])_concat_qseq\.txt.*$ | |
| 518 data_compress_regex_2 = ^.+_[12]_concat_qseq\.txt(.*)$ | |
| 519 data_converter_2 = $(scripts_directory)/qseq2fastq.pl | |
| 520 | |
| 521 data_lane_regex_3 = ^(.+)\.bam.*$ | |
| 522 data_compress_regex_3 = ^.+\.bam(.*)$ | |
| 523 data_end1_converter_3 = samtools view - | filter_sam_mate.pl 1 | sam_to_fastq.pl | |
| 524 data_end2_converter_3 = samtools view - | filter_sam_mate.pl 2 | sam_to_fastq.pl | |
| 525 | |
| 526 data_lane_regex_4 = ^(.+).[12].fastq.*$ | |
| 527 data_end_regex_4 = ^.+.([12]).fastq.*$ | |
| 528 data_compress_regex_4 = ^.+.[12].fastq(.*)$ | |
| 529 data_converter_4 = cat | |
| 530 #end raw | |
| 531 | |
| 532 #end if | |
| 533 | |
| 534 </configfile> | |
| 535 <configfile name="shscript"> | |
| 536 #!/bin/bash | |
| 537 ## define some things for cheetah proccessing | |
| 538 #set $ds = chr(36) | |
| 539 #set $amp = chr(38) | |
| 540 #set $gt = chr(62) | |
| 541 #set $lt = chr(60) | |
| 542 #set $echo_cmd = 'echo' | |
| 543 ## Find the defuse.pl in the galaxy tool path | |
| 544 #import Cheetah.FileUtils | |
| 545 ## declare a bash function for converting a results tsv into html with links to the get_reads output files | |
| 546 results2html() { | |
| 547 rlts=${ds}1 | |
| 548 rslt_name=`basename ${ds}rlts` | |
| 549 html=${ds}2 | |
| 550 echo '${lt}html${gt}${lt}head${gt}${lt}title${gt}Defuse '${ds}rslt_name'${lt}/title${gt}${lt}/head${gt}${lt}body${gt}' ${gt} ${ds}html | |
| 551 echo '${lt}h2${gt}Defuse '${ds}rslt_name'${lt}/h2${gt}${lt}table${gt}' ${gt}${gt} ${ds}html | |
| 552 if [ -z "${ds}3" ] | |
| 553 then | |
| 554 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");}\ | |
| 555 ${ds}1 ~ /[1-9][0-9]*/{printf("${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} ${ds}html | |
| 556 echo '${lt}/table${gt}' ${gt}${gt} ${ds}html | |
| 557 echo '${lt}/body${gt}${lt}/html${gt}' ${gt}${gt} ${ds}html | |
| 558 else | |
| 559 export _EFP=${ds}3 | |
| 560 mkdir -p ${ds}_EFP | |
| 561 awk '${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");}\ | |
| 562 ${ds}1 ~ /[1-9][0-9]*/{fn="cluster_"${ds}1"_reads.txt"; \ | |
| 563 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} ${ds}html | |
| 564 echo '${lt}/table${gt}' ${gt}${gt} ${ds}html | |
| 565 echo '${lt}/body${gt}${lt}/html${gt}' ${gt}${gt} ${ds}html | |
| 566 for i in `awk '${ds}1 ~ /[1-9][0-9]*/{print ${ds}1}' ${ds}rlts`; | |
| 567 do fn=cluster_${ds}{i}_reads.txt; | |
| 568 pn=${ds}_EFP/${ds}fn; | |
| 569 perl \${DEFUSE_PATH}/scripts/get_reads.pl -c $defuse_config -o output_dir -i ${ds}i ${gt} ${ds}pn; | |
| 570 done | |
| 571 fi | |
| 572 } | |
| 573 ## substitute pathnames into config file | |
| 1 | 574 if `grep __DEFUSE_PATH__ $defuse_config ${gt} /dev/null`;then sed -i'.tmp' "s#__DEFUSE_PATH__#\${DEFUSE_PATH}#" $defuse_config; fi |
| 575 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 | |
| 576 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 | |
| 577 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 | |
| 578 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 | |
| 2 | 579 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 |
|
7
f4eadbd2e7c1
Add gmap_setup_bin and gmap_index_directory to defuse.xml config file generation
Jim Johnson <jj@umn.edu>
parents:
6
diff
changeset
|
580 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 |
|
f4eadbd2e7c1
Add gmap_setup_bin and gmap_index_directory to defuse.xml config file generation
Jim Johnson <jj@umn.edu>
parents:
6
diff
changeset
|
581 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 |
| 1 | 582 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 |
| 583 if `grep __RSCRIPT_BIN__ $defuse_config ${gt} /dev/null` ${amp}${amp} RSCRIPT_BIN=`which Rscript`;then sed -i'.tmp' "s#__RSCRIPT_BIN__#\${RSCRIPT_BIN}#" $defuse_config; fi | |
| 0 | 584 |
| 585 | |
| 586 ## copy config to output | |
| 587 cp $defuse_config $config_txt | |
| 588 ## make a data_dir and ln -s the input fastq | |
| 589 mkdir -p data_dir | |
| 590 ln -s $left_pairendreads data_dir/reads_1.fastq | |
| 591 ln -s $right_pairendreads data_dir/reads_2.fastq | |
| 592 ## ln to output_dir in from_work_dir | |
| 593 #if $defuse_out.__str__ != 'None': | |
| 594 mkdir -p $defuse_out.extra_files_path | |
| 595 ln -s $defuse_out.extra_files_path output_dir | |
| 596 #else | |
| 597 mkdir -p output_dir | |
| 598 #end if | |
| 599 ## run defuse.pl | |
| 600 perl \${DEFUSE_PATH}/scripts/defuse.pl -c $defuse_config -d data_dir -o output_dir -p 8 | |
| 601 ## copy primary results to output datasets | |
| 602 if [ -e output_dir/log/defuse.log ]; then cp output_dir/log/defuse.log $defuse_log; fi | |
| 603 if [ -e output_dir/results.tsv ]; then cp output_dir/results.tsv $results_tsv; fi | |
| 604 if [ -e output_dir/results.filtered.tsv ]; then cp output_dir/results.filtered.tsv $results_filtered_tsv; fi | |
| 605 if [ -e output_dir/results.classify.tsv ]; then cp output_dir/results.classify.tsv $results_classify_tsv; fi | |
| 606 ## create html with links for output_dir | |
| 607 #if $defuse_out.__str__ != 'None': | |
| 608 if [ -e $defuse_out ] | |
| 609 then | |
| 610 echo '${lt}html${gt}${lt}head${gt}${lt}title${gt}Defuse Output${lt}/title${gt}${lt}/head${gt}${lt}body${gt}' ${gt} $defuse_out | |
| 611 echo '${lt}h2${gt}Defuse Output Files${lt}/h2${gt}${lt}ul${gt}' ${gt}${gt} $defuse_out | |
| 612 pushd $defuse_out.extra_files_path | |
| 613 for f in `find -L . -maxdepth 1 -type f`; | |
| 614 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} $defuse_out; | |
| 615 done | |
| 616 popd | |
| 617 echo '${lt}/ul${gt}' ${gt}${gt} $defuse_out | |
| 618 echo '${lt}/body${gt}${lt}/html${gt}' ${gt}${gt} $defuse_out | |
| 619 fi | |
| 620 #end if | |
| 621 ## run get_reads.pl on each cluster | |
| 622 #if $fusion_reads.__str__ != 'None': | |
| 623 if [ -e output_dir/results.filtered.tsv -a -e $fusion_reads ] | |
| 624 then | |
| 625 mkdir -p $fusion_reads.extra_files_path | |
| 626 results2html output_dir/results.filtered.tsv $fusion_reads $fusion_reads.extra_files_path | |
| 627 fi | |
| 628 #end if | |
| 629 </configfile> | |
| 630 </configfiles> | |
| 5 | 631 |
| 0 | 632 <tests> |
| 633 </tests> | |
| 634 <help> | |
| 635 **DeFuse** | |
| 636 | |
| 637 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. | |
| 638 | |
| 639 Journal reference: http://www.ploscompbiol.org/article/info%3Adoi%2F10.1371%2Fjournal.pcbi.1001138 | |
| 640 | |
| 641 .. _DeFuse: http://sourceforge.net/apps/mediawiki/defuse/index.php?title=Main_Page | |
| 642 | |
| 643 ------ | |
| 644 | |
| 645 **Inputs** | |
| 646 | |
| 647 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**). | |
| 648 | |
| 649 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. | |
| 650 | |
| 651 DeFuse uses a Reference Dataset to search for gene fusions. The Reference Dataset is generated from the following sources in DeFuse_Version_0.4_: | |
| 652 - genome_fasta from Ensembl | |
| 653 - gene_models from Ensembl | |
| 654 - repeats_filename from UCSC RepeatMasker rmsk.txt | |
| 655 - est_fasta from UCSC | |
| 656 - est_alignments from UCSC intronEst.txt | |
| 657 - unigene_fasta from NCBI | |
| 658 | |
| 659 .. _DeFuse_Version_0.4: http://sourceforge.net/apps/mediawiki/defuse/index.php?title=DeFuse_Version_0.4.2 | |
| 660 | |
| 661 ------ | |
| 662 | |
| 663 **Outputs** | |
| 664 | |
| 665 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. | |
| 666 | |
| 667 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. | |
| 668 | |
| 669 The file format is tab delimited with one prediction per line, and the following fields per prediction (not necessarily in this order): | |
| 670 | |
| 671 - **Identification** | |
| 672 - cluster_id : random identifier assigned to each prediction | |
| 673 - library_name : library name given on the command line of defuse | |
| 674 - gene1 : ensembl id of gene 1 | |
| 675 - gene2 : ensembl id of gene 2 | |
| 676 - gene_name1 : name of gene 1 | |
| 677 - gene_name2 : name of gene 2 | |
| 678 - **Evidence** | |
| 679 - break_predict : breakpoint prediction method, denovo or splitr, that is considered most reliable | |
| 680 - concordant_ratio : proportion of spanning reads considered concordant by blat | |
| 681 - denovo_min_count : minimum kmer count across denovo assembled sequence | |
| 682 - denovo_sequence : fusion sequence predicted by debruijn based denovo sequence assembly | |
| 683 - denovo_span_pvalue : p-value, lower values are evidence the prediction is a false positive | |
| 684 - gene_align_strand1 : alignment strand for spanning read alignments to gene 1 | |
| 685 - gene_align_strand2 : alignment strand for spanning read alignments to gene 2 | |
| 686 - min_map_count : minimum of the number of genomic mappings for each spanning read | |
| 687 - max_map_count : maximum of the number of genomic mappings for each spanning read | |
| 688 - mean_map_count : average of the number of genomic mappings for each spanning read | |
| 689 - num_multi_map : number of spanning reads that map to more than one genomic location | |
| 690 - span_count : number of spanning reads supporting the fusion | |
| 691 - span_coverage1 : coverage of spanning reads aligned to gene 1 as a proportion of expected coverage | |
| 692 - span_coverage2 : coverage of spanning reads aligned to gene 2 as a proportion of expected coverage | |
| 693 - span_coverage_min : minimum of span_coverage1 and span_coverage2 | |
| 694 - span_coverage_max : maximum of span_coverage1 and span_coverage2 | |
| 695 - splitr_count : number of split reads supporting the prediction | |
| 696 - splitr_min_pvalue : p-value, lower values are evidence the prediction is a false positive | |
| 697 - splitr_pos_pvalue : p-value, lower values are evidence the prediction is a false positive | |
| 698 - splitr_sequence : fusion sequence predicted by split reads | |
| 699 - splitr_span_pvalue : p-value, lower values are evidence the prediction is a false positive | |
| 700 - **Annotation** | |
| 701 - adjacent : fusion between adjacent genes | |
| 702 - altsplice : fusion likely the product of alternative splicing between adjacent genes | |
| 703 - break_adj_entropy1 : di-nucleotide entropy of the 40 nucleotides adjacent to the fusion splice in gene 1 | |
| 704 - break_adj_entropy2 : di-nucleotide entropy of the 40 nucleotides adjacent to the fusion splice in gene 2 | |
| 705 - break_adj_entropy_min : minimum of break_adj_entropy1 and break_adj_entropy2 | |
| 706 - breakpoint_homology : number of nucleotides at the fusion splice that align equally well to gene 1 or gene 2 | |
| 707 - breakseqs_estislands_percident : maximum percent identity of fusion sequence alignments to est islands | |
| 708 - cdna_breakseqs_percident : maximum percent identity of fusion sequence alignments to cdna | |
| 709 - deletion : fusion produced by a genomic deletion | |
| 710 - est_breakseqs_percident : maximum percent identity of fusion sequence alignments to est | |
| 711 - eversion : fusion produced by a genomic eversion | |
| 712 - exonboundaries : fusion splice at exon boundaries | |
| 713 - expression1 : expression of gene 1 as number of concordant pairs aligned to exons | |
| 714 - expression2 : expression of gene 2 as number of concordant pairs aligned to exons | |
| 715 - gene_chromosome1 : chromosome of gene 1 | |
| 716 - gene_chromosome2 : chromosome of gene 2 | |
| 717 - gene_end1 : end position for gene 1 | |
| 718 - gene_end2 : end position for gene 2 | |
| 719 - gene_location1 : location of breakpoint in gene 1 | |
| 720 - gene_location2 : location of breakpoint in gene 2 | |
| 721 - gene_start1 : start of gene 1 | |
| 722 - gene_start2 : start of gene 2 | |
| 723 - gene_strand1 : strand of gene 1 | |
| 724 - gene_strand2 : strand of gene 2 | |
| 725 - genome_breakseqs_percident : maximum percent identity of fusion sequence alignments to genome | |
| 726 - genomic_break_pos1 : genomic position in gene 1 of fusion splice / breakpoint | |
| 727 - genomic_break_pos2 : genomic position in gene 2 of fusion splice / breakpoint | |
| 728 - genomic_strand1 : genomic strand in gene 1 of fusion splice / breakpoint, retained sequence upstream on this strand, breakpoint is downstream | |
| 729 - genomic_strand2 : genomic strand in gene 2 of fusion splice / breakpoint, retained sequence upstream on this strand, breakpoint is downstream | |
| 730 - interchromosomal : fusion produced by an interchromosomal translocation | |
| 731 - interrupted_index1 : ratio of coverage before and after the fusion splice / breakpoint in gene 1 | |
| 732 - interrupted_index2 : ratio of coverage before and after the fusion splice / breakpoint in gene 2 | |
| 733 - inversion : fusion produced by genomic inversion | |
| 734 - orf : fusion combines genes in a way that preserves a reading frame | |
| 735 - probability : probability produced by classification using adaboost and example positives/negatives (only given in results.classified.txt) | |
| 736 - read_through : fusion involving adjacent potentially resulting from co-transcription rather than genome rearrangement | |
| 737 - repeat_proportion1 : proportion of the spanning reads in gene 1 that span a repeat region | |
| 738 - repeat_proportion2 : proportion of the spanning reads in gene 2 that span a repeat region | |
| 739 - max_repeat_proportion : max of repeat_proportion1 and repeat_proportion2 | |
| 740 - splice_score : number of nucleotides similar to GTAG at fusion splice | |
| 741 - num_splice_variants : number of potential splice variants for this gene pair | |
| 742 - 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 | |
| 743 - 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 | |
| 744 | |
| 745 | |
| 746 **Example** | |
| 747 | |
| 748 results.tsv:: | |
| 749 | |
| 750 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 | |
| 751 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 - | |
| 752 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 - - | |
| 753 | |
| 754 </help> | |
| 755 </tool> |