Mercurial > repos > jjohnson > defuse
annotate create_reference_dataset.xml @ 14:d975e466d443
Add stdio tag to create_reference_dataset.xml
| author | Jim Johnson <jj@umn.edu> |
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| date | Mon, 10 Jun 2013 05:43:53 -0500 |
| parents | 85693cb5339f |
| children | 547d8db4673e |
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85693cb5339f
Correct tool_id create_reference_dataset.xml
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1 <tool id="create_defuse_reference" name="Create DeFuse Reference" version="1.6.1"> |
| 12 | 2 <description>create a defuse reference from Ensembl and UCSC sources</description> |
| 3 <requirements> | |
| 4 <requirement type="package" version="0.6.1">defuse</requirement> | |
| 5 <requirement type="package" version="0.1.18">samtools</requirement> | |
| 6 <requirement type="package" version="1.0.0">bowtie</requirement> | |
| 7 <requirement type="package" version="2013-05-09">gmap</requirement> | |
| 8 <requirement type="package" version="latest">kent</requirement> | |
| 9 </requirements> | |
| 10 <command interpreter="command"> /bin/bash $shscript </command> | |
| 11 <inputs> | |
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12 <param name="ensembl_genome_version" type="text" value="" label="Ensembl Genome Version" help="Example: GRCh37"/> |
| 12 | 13 <param name="ensembl_version" type="integer" value="" label="Esembl Release Version" help="Example: 71"/> |
| 14 <param name="ucsc_genome_version" type="text" value="" label="UCSC Genome Version" help="Example: hg19"/> | |
| 15 <param name="chromosomes" type="text" value="" label="Chromosomes" help="Example: 1,2,3,4,5,6,7,8,9,10,11,12,13,14,15,16,17,18,19,20,21,22,X,Y,MT"/> | |
| 16 <param name="mt_chromosome" type="text" value="MT" label="Mitochonrial Chromosome" /> | |
| 17 <param name="gene_sources" type="text" value="IG_C_gene,IG_D_gene,IG_J_gene,IG_V_gene,processed_transcript,protein_coding" label="Gene sources" /> | |
| 18 <param name="ig_gene_sources" type="text" value="IG_C_gene,IG_D_gene,IG_J_gene,IG_V_gene,IG_pseudogene" label="IG Gene sources" /> | |
| 19 <param name="rrna_gene_sources" type="text" value="Mt_rRNA,rRNA,rRNA_pseudogene" label="Ribosomal Gene sources" /> | |
| 20 </inputs> | |
| 21 <outputs> | |
| 22 <data format="txt" name="config_txt" label="${tool.name} on ${on_string}: config.txt"/> | |
| 23 </outputs> | |
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24 <stdio> |
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25 <exit_code range="1:" level="fatal" description="Error running Create DeFuse Reference" /> |
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26 <regex match="Error:" |
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27 source="both" |
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28 level="fatal" |
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29 description="Error running Create DeFuse Reference" /> |
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parents:
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30 |
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31 </stdio> |
| 12 | 32 <configfiles> |
| 33 <configfile name="defuse_config"> | |
| 34 #import ast | |
| 35 # | |
| 36 # Configuration file for defuse | |
| 37 # | |
| 38 # At a minimum, change all values enclused by [] | |
| 39 # | |
| 40 | |
| 41 # Directory where the defuse code was unpacked | |
| 42 ## Default location in the tool/defuse directory | |
| 43 # source_directory = ${__root_dir__}/tools/defuse | |
| 44 source_directory = __DEFUSE_PATH__ | |
| 45 | |
| 46 ensembl_version = $ensembl_version | |
| 47 ensembl_genome_version = $ensembl_genome_version | |
| 48 ucsc_genome_version = $ucsc_genome_version | |
| 49 | |
| 50 # Directory where you want your dataset | |
| 51 dataset_directory = $config_txt.extra_files_path | |
| 52 | |
| 53 #raw | |
| 54 # Input genome and gene models | |
| 55 gene_models = $(dataset_directory)/Homo_sapiens.$(ensembl_genome_version).$(ensembl_version).gtf | |
| 56 genome_fasta = $(dataset_directory)/Homo_sapiens.$(ensembl_genome_version).$(ensembl_version).dna.chromosomes.fa | |
| 57 | |
| 58 # Repeat table from ucsc genome browser | |
| 59 repeats_filename = $(dataset_directory)/repeats.txt | |
| 60 | |
| 61 # EST info downloaded from ucsc genome browser | |
| 62 est_fasta = $(dataset_directory)/est.fa | |
| 63 est_alignments = $(dataset_directory)/intronEst.txt | |
| 64 | |
| 65 # Unigene clusters downloaded from ncbi | |
| 66 unigene_fasta = $(dataset_directory)/Hs.seq.uniq | |
| 67 #end raw | |
| 68 | |
| 69 # Paths to external tools | |
| 70 samtools_bin = __SAMTOOLS_BIN__ | |
| 71 bowtie_bin = __BOWTIE_BIN__ | |
| 72 bowtie_build_bin = __BOWTIE_BUILD_BIN__ | |
| 73 blat_bin = __BLAT_BIN__ | |
| 74 fatotwobit_bin = __FATOTWOBIT_BIN__ | |
| 75 gmap_bin = __GMAP_BIN__ | |
| 76 gmap_setup_bin = __GMAP_SETUP_BIN__ | |
| 77 r_bin = __R_BIN__ | |
| 78 rscript_bin = __RSCRIPT_BIN__ | |
| 79 | |
| 80 #raw | |
| 81 # Directory where you want your dataset | |
| 82 gmap_index_directory = $(dataset_directory)/gmap | |
| 83 #end raw | |
| 84 | |
| 85 #raw | |
| 86 # Dataset files | |
| 87 dataset_prefix = $(dataset_directory)/defuse | |
| 88 chromosome_prefix = $(dataset_prefix).dna.chromosomes | |
| 89 exons_fasta = $(dataset_prefix).exons.fa | |
| 90 cds_fasta = $(dataset_prefix).cds.fa | |
| 91 cdna_regions = $(dataset_prefix).cdna.regions | |
| 92 cdna_fasta = $(dataset_prefix).cdna.fa | |
| 93 reference_fasta = $(dataset_prefix).reference.fa | |
| 94 rrna_fasta = $(dataset_prefix).rrna.fa | |
| 95 ig_gene_list = $(dataset_prefix).ig.gene.list | |
| 96 repeats_regions = $(dataset_directory)/repeats.regions | |
| 97 est_split_fasta1 = $(dataset_directory)/est.1.fa | |
| 98 est_split_fasta2 = $(dataset_directory)/est.2.fa | |
| 99 est_split_fasta3 = $(dataset_directory)/est.3.fa | |
| 100 est_split_fasta4 = $(dataset_directory)/est.4.fa | |
| 101 est_split_fasta5 = $(dataset_directory)/est.5.fa | |
| 102 est_split_fasta6 = $(dataset_directory)/est.6.fa | |
| 103 est_split_fasta7 = $(dataset_directory)/est.7.fa | |
| 104 est_split_fasta8 = $(dataset_directory)/est.8.fa | |
| 105 est_split_fasta9 = $(dataset_directory)/est.9.fa | |
| 106 | |
| 107 # Fasta files with bowtie indices for prefiltering reads for concordantly mapping pairs | |
| 108 prefilter1 = $(unigene_fasta) | |
| 109 | |
| 110 # deFuse scripts and tools | |
| 111 scripts_directory = $(source_directory)/scripts | |
| 112 tools_directory = $(source_directory)/tools | |
| 113 data_directory = $(source_directory)/data | |
| 114 #end raw | |
| 115 | |
| 116 #raw | |
| 117 # Bowtie parameters | |
| 118 bowtie_threads = 1 | |
| 119 bowtie_quals = --phred33-quals | |
| 120 max_insert_size = 500 | |
| 121 #end raw | |
| 122 | |
| 123 # Parameters for building the dataset | |
| 124 chromosomes = $chromosomes | |
| 125 mt_chromosome = $mt_chromosome | |
| 126 gene_sources = $gene_sources | |
| 127 ig_gene_sources = $ig_gene_sources | |
| 128 rrna_gene_sources = $rrna_gene_sources | |
| 129 | |
| 130 #raw | |
| 131 # Blat sequences per job | |
| 132 num_blat_sequences = 10000 | |
| 133 | |
| 134 # Minimum gene fusion range | |
| 135 dna_concordant_length = 2000 | |
| 136 | |
| 137 # Trim length for discordant reads (split reads are not trimmed) | |
| 138 discord_read_trim = 50 | |
| 139 | |
| 140 # Calculate extra annotations, fusion splice index and interrupted index | |
| 141 calculate_extra_annotations = no | |
| 142 | |
| 143 # Filtering parameters | |
| 144 clustering_precision = 0.95 | |
| 145 span_count_threshold = 5 | |
| 146 percent_identity_threshold = 0.90 | |
| 147 split_min_anchor = 4 | |
| 148 splice_bias = 10 | |
| 149 positive_controls = $(data_directory)/controls.txt | |
| 150 probability_threshold = 0.50 | |
| 151 | |
| 152 # Position density when calculating covariance | |
| 153 covariance_sampling_density = 0.01 | |
| 154 | |
| 155 # Number of reads for each job in split | |
| 156 reads_per_job = 1000000 | |
| 157 | |
| 158 # If you have command line 'mail' and wish to be notified | |
| 159 mailto = andrew.mcpherson@gmail.com | |
| 160 | |
| 161 # Remove temp files | |
| 162 remove_job_files = yes | |
| 163 remove_job_temp_files = yes | |
| 164 #end raw | |
| 165 </configfile> | |
| 166 <configfile name="shscript"> | |
| 167 #!/bin/bash | |
| 168 ## define some things for cheetah proccessing | |
| 169 #set $ds = chr(36) | |
| 170 #set $amp = chr(38) | |
| 171 #set $gt = chr(62) | |
| 172 #set $lt = chr(60) | |
| 173 #set $echo_cmd = 'echo' | |
| 174 ## Find the defuse.pl in the galaxy tool path | |
| 175 #import Cheetah.FileUtils | |
| 176 ## substitute pathnames into config file | |
| 177 if `grep __DEFUSE_PATH__ $defuse_config ${gt} /dev/null`;then sed -i'.tmp' "s#__DEFUSE_PATH__#\${DEFUSE_PATH}#" $defuse_config; fi | |
| 178 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 | |
| 179 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 | |
| 180 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 | |
| 181 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 | |
| 182 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 | |
| 183 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 | |
| 184 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 | |
| 185 if `grep __GMAP_INDEX_DIR__ $defuse_config ${gt} /dev/null` ${amp}${amp} GMAP_INDEX_DIR=`pwd`/gmap;then sed -i'.tmp' "s#__GMAP_INDEX_DIR__#\${GMAP_INDEX_DIR}#" $defuse_config; fi | |
| 186 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 | |
| 187 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 | |
| 188 | |
| 189 ## copy config to output | |
| 190 cp $defuse_config $config_txt | |
| 191 ## make a data_dir and ln -s the input fastq | |
| 192 mkdir -p $config_txt.extra_files_path | |
| 193 ## run defuse.pl | |
| 194 perl \${DEFUSE_PATH}/scripts/create_reference_dataset.pl -c $defuse_config | |
| 195 </configfile> | |
| 196 </configfiles> | |
| 197 | |
| 198 <tests> | |
| 199 </tests> | |
| 200 <help> | |
| 201 **DeFuse** | |
| 202 | |
| 203 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. | |
| 204 | |
| 205 Journal reference: http://www.ploscompbiol.org/article/info%3Adoi%2F10.1371%2Fjournal.pcbi.1001138 | |
| 206 | |
| 207 .. _DeFuse: http://sourceforge.net/apps/mediawiki/defuse/index.php?title=Main_Page | |
| 208 | |
| 209 ------ | |
| 210 | |
| 211 **Inputs** | |
| 212 | |
| 213 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**). | |
| 214 | |
| 215 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. | |
| 216 | |
| 217 DeFuse uses a Reference Dataset to search for gene fusions. The Reference Dataset is generated from the following sources in DeFuse_Version_0.4_: | |
| 218 - genome_fasta from Ensembl | |
| 219 - gene_models from Ensembl | |
| 220 - repeats_filename from UCSC RepeatMasker rmsk.txt | |
| 221 - est_fasta from UCSC | |
| 222 - est_alignments from UCSC intronEst.txt | |
| 223 - unigene_fasta from NCBI | |
| 224 | |
| 225 .. _DeFuse_Version_0.4: http://sourceforge.net/apps/mediawiki/defuse/index.php?title=DeFuse_Version_0.4.2 | |
| 226 | |
| 227 ------ | |
| 228 | |
| 229 **Outputs** | |
| 230 | |
| 231 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. | |
| 232 | |
| 233 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. | |
| 234 | |
| 235 The file format is tab delimited with one prediction per line, and the following fields per prediction (not necessarily in this order): | |
| 236 | |
| 237 - **Identification** | |
| 238 - cluster_id : random identifier assigned to each prediction | |
| 239 - library_name : library name given on the command line of defuse | |
| 240 - gene1 : ensembl id of gene 1 | |
| 241 - gene2 : ensembl id of gene 2 | |
| 242 - gene_name1 : name of gene 1 | |
| 243 - gene_name2 : name of gene 2 | |
| 244 - **Evidence** | |
| 245 - break_predict : breakpoint prediction method, denovo or splitr, that is considered most reliable | |
| 246 - concordant_ratio : proportion of spanning reads considered concordant by blat | |
| 247 - denovo_min_count : minimum kmer count across denovo assembled sequence | |
| 248 - denovo_sequence : fusion sequence predicted by debruijn based denovo sequence assembly | |
| 249 - denovo_span_pvalue : p-value, lower values are evidence the prediction is a false positive | |
| 250 - gene_align_strand1 : alignment strand for spanning read alignments to gene 1 | |
| 251 - gene_align_strand2 : alignment strand for spanning read alignments to gene 2 | |
| 252 - min_map_count : minimum of the number of genomic mappings for each spanning read | |
| 253 - max_map_count : maximum of the number of genomic mappings for each spanning read | |
| 254 - mean_map_count : average of the number of genomic mappings for each spanning read | |
| 255 - num_multi_map : number of spanning reads that map to more than one genomic location | |
| 256 - span_count : number of spanning reads supporting the fusion | |
| 257 - span_coverage1 : coverage of spanning reads aligned to gene 1 as a proportion of expected coverage | |
| 258 - span_coverage2 : coverage of spanning reads aligned to gene 2 as a proportion of expected coverage | |
| 259 - span_coverage_min : minimum of span_coverage1 and span_coverage2 | |
| 260 - span_coverage_max : maximum of span_coverage1 and span_coverage2 | |
| 261 - splitr_count : number of split reads supporting the prediction | |
| 262 - splitr_min_pvalue : p-value, lower values are evidence the prediction is a false positive | |
| 263 - splitr_pos_pvalue : p-value, lower values are evidence the prediction is a false positive | |
| 264 - splitr_sequence : fusion sequence predicted by split reads | |
| 265 - splitr_span_pvalue : p-value, lower values are evidence the prediction is a false positive | |
| 266 - **Annotation** | |
| 267 - adjacent : fusion between adjacent genes | |
| 268 - altsplice : fusion likely the product of alternative splicing between adjacent genes | |
| 269 - break_adj_entropy1 : di-nucleotide entropy of the 40 nucleotides adjacent to the fusion splice in gene 1 | |
| 270 - break_adj_entropy2 : di-nucleotide entropy of the 40 nucleotides adjacent to the fusion splice in gene 2 | |
| 271 - break_adj_entropy_min : minimum of break_adj_entropy1 and break_adj_entropy2 | |
| 272 - breakpoint_homology : number of nucleotides at the fusion splice that align equally well to gene 1 or gene 2 | |
| 273 - breakseqs_estislands_percident : maximum percent identity of fusion sequence alignments to est islands | |
| 274 - cdna_breakseqs_percident : maximum percent identity of fusion sequence alignments to cdna | |
| 275 - deletion : fusion produced by a genomic deletion | |
| 276 - est_breakseqs_percident : maximum percent identity of fusion sequence alignments to est | |
| 277 - eversion : fusion produced by a genomic eversion | |
| 278 - exonboundaries : fusion splice at exon boundaries | |
| 279 - expression1 : expression of gene 1 as number of concordant pairs aligned to exons | |
| 280 - expression2 : expression of gene 2 as number of concordant pairs aligned to exons | |
| 281 - gene_chromosome1 : chromosome of gene 1 | |
| 282 - gene_chromosome2 : chromosome of gene 2 | |
| 283 - gene_end1 : end position for gene 1 | |
| 284 - gene_end2 : end position for gene 2 | |
| 285 - gene_location1 : location of breakpoint in gene 1 | |
| 286 - gene_location2 : location of breakpoint in gene 2 | |
| 287 - gene_start1 : start of gene 1 | |
| 288 - gene_start2 : start of gene 2 | |
| 289 - gene_strand1 : strand of gene 1 | |
| 290 - gene_strand2 : strand of gene 2 | |
| 291 - genome_breakseqs_percident : maximum percent identity of fusion sequence alignments to genome | |
| 292 - genomic_break_pos1 : genomic position in gene 1 of fusion splice / breakpoint | |
| 293 - genomic_break_pos2 : genomic position in gene 2 of fusion splice / breakpoint | |
| 294 - genomic_strand1 : genomic strand in gene 1 of fusion splice / breakpoint, retained sequence upstream on this strand, breakpoint is downstream | |
| 295 - genomic_strand2 : genomic strand in gene 2 of fusion splice / breakpoint, retained sequence upstream on this strand, breakpoint is downstream | |
| 296 - interchromosomal : fusion produced by an interchromosomal translocation | |
| 297 - interrupted_index1 : ratio of coverage before and after the fusion splice / breakpoint in gene 1 | |
| 298 - interrupted_index2 : ratio of coverage before and after the fusion splice / breakpoint in gene 2 | |
| 299 - inversion : fusion produced by genomic inversion | |
| 300 - orf : fusion combines genes in a way that preserves a reading frame | |
| 301 - probability : probability produced by classification using adaboost and example positives/negatives (only given in results.classified.txt) | |
| 302 - read_through : fusion involving adjacent potentially resulting from co-transcription rather than genome rearrangement | |
| 303 - repeat_proportion1 : proportion of the spanning reads in gene 1 that span a repeat region | |
| 304 - repeat_proportion2 : proportion of the spanning reads in gene 2 that span a repeat region | |
| 305 - max_repeat_proportion : max of repeat_proportion1 and repeat_proportion2 | |
| 306 - splice_score : number of nucleotides similar to GTAG at fusion splice | |
| 307 - num_splice_variants : number of potential splice variants for this gene pair | |
| 308 - 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 | |
| 309 - 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 | |
| 310 | |
| 311 | |
| 312 **Example** | |
| 313 | |
| 314 results.tsv:: | |
| 315 | |
| 316 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 | |
| 317 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 - | |
| 318 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 - - | |
| 319 | |
| 320 </help> | |
| 321 </tool> |