├── .gitignore ├── Dockerfile ├── LICENSE ├── README.md ├── Ref-Ready └── Dockerfile ├── controls ├── docker.sysctrl ├── docker_test.ctrl ├── glitch.sysctrl ├── inactive │ ├── amlAzt.ctrl │ ├── amlAzt.list │ ├── bcell.ctrl │ ├── bcell.list │ ├── dlbcl.ctrl │ ├── dlbcl.list │ ├── dlbcl2.ctrl │ ├── dlbcl2.list │ ├── gm12878.ctrl │ ├── gsc.ctrl │ ├── gsc.list │ ├── hl.ctrl │ ├── hl.list │ ├── hl_old.list │ ├── hodgkin.ctrl │ ├── hs2253.ctrl │ ├── hs2253a.list │ ├── hs2254.ctrl │ ├── hs2254.list │ ├── parameter_old.ctrl │ └── xhost.ctrl ├── input.list ├── old │ ├── colon.ctrl │ ├── colon.list │ ├── genesis.sysctrl │ ├── glitch.sysctrl │ ├── gm12878.list │ ├── gm12878_2.ctrl │ ├── gm12878_2.list │ ├── simH1.ctrl │ ├── simH1.list │ └── xhost.sysctrl ├── parameter.ctrl ├── sandbox.ctrl ├── synTALL_test.ctrl ├── synTALL_test.list ├── system.sysctrl └── template │ ├── input.list │ ├── parameter.ctrl │ └── system.sysctrl ├── docs ├── DIR_MAP.md ├── ERRORS_CODES.md ├── INSTALL.README └── OUTPUT.md ├── lions.sh ├── lions_opt.sh ├── manuscript ├── Figures │ ├── ANN │ │ ├── Up_ANN.svg │ │ ├── Up_ANN_.svg │ │ ├── Up_Classification.svg │ │ ├── Up_FDR.svg │ │ └── Up_ROC.svg │ ├── F1_LIONS_pipeline.pdf │ ├── F1_LIONS_pipeline.svg │ ├── F2_Chimeric_Fragments.pdf │ ├── F2_Chimeric_Fragments.svg │ ├── F3_ROC.pdf │ ├── F3_ROC.svg │ ├── SF1_CAGE.pdf │ ├── SF1_CAGE.svg │ ├── SF2_HL_RTPCR.pdf │ ├── SF2_HL_RTPCR.svg │ ├── SF3_TE_Exon_Intersection.pdf │ ├── SF3_TE_Exon_Intersection.svg │ ├── SF4_Flowchart.pdf │ ├── SF4_Flowchart.svg │ ├── SF5_K562_FHAD1.pdf │ ├── SF5_K562_FHAD1.svg │ ├── V1 │ │ ├── F1_LIONS_pipeline.pdf │ │ ├── F2_Chimeric_Fragments.pdf │ │ ├── F3_CAGE.pdf │ │ ├── SF1_TE_Exon_Intersection.pdf │ │ └── SF2_Flowchart.pdf │ ├── v2 │ │ ├── F1_LIONS_pipeline.pdf │ │ ├── F2_Chimeric_Fragments.pdf │ │ ├── F3_Alt_Graph_typegm12878_cage_fpkm_CDF.eps │ │ ├── F3_CAGE_old.pdf │ │ ├── SF1_TE_Exon_Intersection.pdf │ │ └── SF2_Flowchart.pdf │ ├── v3 │ │ ├── Alt_Graph_typegm12878_cage_fpkm_CDF.eps │ │ ├── CAGE_hmm.pzf │ │ ├── Contribution.svg │ │ ├── F1_LIONS_pipeline.svg │ │ ├── F2_Chimeric_Fragments.svg │ │ ├── F3_CAGE.svg │ │ ├── F3_CAGE_working.svg │ │ ├── SF1_TE_Exon_Intersection.svg │ │ ├── SF2_Flowchart.svg │ │ ├── SF2_Flowchart_noRI.pdf │ │ ├── SF4_LIONS_workflow.svg │ │ ├── SF5_Brunswick_workflow.svg │ │ ├── TE_Exon_Intersection.svg │ │ └── TE_Exon_Intersection.svg.2015_07_01_16_34_15.0.svg │ └── v4_bx │ │ ├── F1_LIONS_pipeline.pdf │ │ ├── F2_Chimeric_Fragments.pdf │ │ ├── F3_ROC.pdf │ │ ├── SF1_CAGE.pdf │ │ ├── SF2_HL_RTPCR.pdf │ │ ├── SF3_TE_Exon_Intersection.pdf │ │ ├── SF4_Flowchart.pdf │ │ └── SF5_K562_FHAD1.pdf ├── LIONS_Manuscript_V1.doc ├── LIONS_Manuscript_v2.doc ├── Manuscript.odt ├── Paper_Outline.pdf ├── Sept30-2014-version.docx ├── Tables │ ├── S1_RNA_Seq_Libraries.xlsx │ └── Table S1.xlsx ├── biorxiv │ ├── BIORXIV-2017-149864v1-Mager.pdf │ ├── F1_LIONS_pipeline.pdf │ ├── F2_Chimeric_Fragments.pdf │ ├── F3_ROC.pdf │ ├── LIONS_Figures.pdf │ ├── LIONS_Supplementary_Figures.pdf │ ├── LIONS_manuscript.odt │ ├── LIONS_manuscript.pdf │ ├── LIONS_manuscript_text.pdf │ ├── LIONS_manuscript_v4.doc │ ├── S1_Data_Sets.xls │ ├── S2_primer_sequences.xls │ ├── SF1_CAGE.pdf │ ├── SF2_HL_RTPCR.pdf │ ├── SF3_TE_Exon_Intersection.pdf │ ├── SF4_Flowchart.pdf │ ├── SF5_K562_FHAD1.pdf │ ├── V3 │ │ ├── LIONS_manuscript_v3.doc │ │ ├── S1_Data_Sets.xlsx │ │ └── S2_primer_sequences.xlsx │ ├── V4_submission │ │ ├── F1_LIONS_pipeline.pdf │ │ ├── F2_Chimeric_Fragments.pdf │ │ ├── F3_ROC.pdf │ │ ├── LIONS_Figures.pdf │ │ ├── LIONS_Supplementary_Figures.pdf │ │ ├── LIONS_manuscript.odt │ │ ├── LIONS_manuscript_text.pdf │ │ ├── LIONS_manuscript_v4.doc │ │ ├── S1_Data_Sets.xlsx │ │ ├── S2_primer_sequences.xlsx │ │ ├── SF1_CAGE.pdf │ │ ├── SF2_HL_RTPCR.pdf │ │ ├── SF3_TE_Exon_Intersection.pdf │ │ ├── SF4_Flowchart.pdf │ │ └── SF5_K562_FHAD1.pdf │ ├── drafts │ │ ├── LIONS_manuscript.odt │ │ ├── LIONS_manuscript_0602-DMcomments.doc │ │ ├── LIONS_manuscript_170612-DMcomments_wchanges.doc │ │ └── LIONS_manuscript_170612.doc │ └── drafts2 │ │ ├── F1_LIONS_pipeline.pdf │ │ ├── F2_Chimeric_Fragments.pdf │ │ ├── F3_ROC.pdf │ │ ├── F3_ROC.svg │ │ ├── LIONS_figures_170607.pdf │ │ ├── LIONS_manuscript_170612-DMcomments.doc │ │ ├── LIONS_manuscript_changes.odt │ │ ├── S1_Data_Accessions.xlsx │ │ ├── S2_primer_sequences.xlsx │ │ ├── SF1_CAGE.pdf │ │ ├── SF2_HL_RTPCR.pdf │ │ ├── SF3_TE_Exon_Intersection.pdf │ │ ├── SF4_Flowchart.pdf │ │ └── SF5_K562_FHAD1.pdf ├── compiled_data │ ├── CAGE_hmm.pzf │ ├── Figure2 │ │ ├── Figure2B_data.pzf │ │ └── LIONS_Figure2.xlsx │ ├── Figure3 │ │ ├── LCSV.eps │ │ ├── LCSV_posneg.svg │ │ ├── LCSV_t.test.txt │ │ ├── Layout 1.pdf │ │ ├── Layout 2.pdf │ │ ├── Layout_wInput.pdf │ │ ├── ROC_LIONS.pzf │ │ └── Stats_Analysis.xlsx │ └── col_figures │ │ ├── ColvCtrl_data.png │ │ ├── ColvCtrl_sim.png │ │ └── colon_Clustering_OLD.png ├── faseb │ ├── abstract-FASEB_v2.docx │ └── faseb15.pdf └── oldManuscript ├── scripts ├── Brunswick │ ├── 1_simulateData │ │ ├── 0_README │ │ ├── 1_initTranscriptome.sh │ │ ├── 2_runFlux │ │ │ ├── h1_100m.par │ │ │ ├── hg19 │ │ │ │ ├── 1_linkFaGenomeHere │ │ │ │ └── 2_FastaSplit.sh │ │ │ ├── runFlux.sh │ │ │ └── template │ │ │ │ ├── h1_100m.par │ │ │ │ └── runFlux.sh │ │ ├── 3_fluxSimExpToGTF.r │ │ ├── 4_ANN_training.r │ │ ├── 5_ANN_dataMerge.r │ │ └── etc │ │ │ ├── ANN.list │ │ │ ├── ANN_graph.R │ │ │ ├── ANN_merge_old.r │ │ │ ├── ANN_training_manual.r │ │ │ ├── annLoop.sh │ │ │ ├── fluxSimExpToGTF.r │ │ │ ├── fqPairSplit.sh │ │ │ ├── input.list │ │ │ ├── proLoop.sh │ │ │ ├── rmUgtf_assembly.r │ │ │ └── rmUgtf_chromHMM.R │ ├── 2_trainModel │ │ ├── 1_FireItUp.sh │ │ ├── _0_README │ │ ├── chimNeuro.R │ │ └── matches.sh │ └── 3_refineModel │ │ ├── 1_annROC.R │ │ ├── 2_annParse.R │ │ └── 3_chimNSort.R ├── ChimericAnalysis │ ├── .Rhistory │ ├── chimGroup.R │ ├── chimGroup_old.R │ ├── ucscPaint.sh │ └── wigChr.sh ├── ChimericReadTool │ ├── .Rhistory │ ├── ChimericReadTool.sh │ ├── RNAgetrRes.sh │ ├── __pycache__ │ │ ├── intervalTree.cpython-32.pyc │ │ ├── intervalTree.cpython-33.pyc │ │ ├── intervalTree.cpython-34.pyc │ │ └── intervalTree.cpython-35.pyc │ ├── chimAnnSort.R │ ├── chimIntLookup.R │ ├── chimIntersect.sh │ ├── chimSort.R │ ├── chimericReadSearch.py │ ├── crt_source.zip │ ├── debugScripts.tar.gz │ ├── exon_scan.sh │ ├── intervalTree.py │ └── sandbox.py ├── Initialize │ ├── .Rhistory │ ├── initializeBin.sh │ ├── initializeLIONS.sh │ ├── initializeRes.sh │ ├── initializeScripts.sh │ ├── input.list.awk │ └── rmResource.R ├── RNAseqPipeline │ ├── RNAgetRes.sh │ ├── RNAseqCoverageCalculator.sh │ ├── RNAseqMaster.sh │ ├── RNAseqPipeline.sh │ ├── RPKM.sh │ ├── TE_stats.sh │ ├── WIG_RPKM.sh │ ├── bin │ │ ├── BAM2WIG.jar │ │ ├── RegionsCoverageFromWigCalculator.jar │ │ └── RegionsCoverageFromWigCalculator_May6_2011.jar │ ├── resourceGeneration │ │ ├── EnsemblResourceGenerator.sh │ │ ├── GencodeGenerate.sh │ │ ├── RefSeqGenerate.sh │ │ ├── RepeatMaskerGenerate.sh │ │ ├── buildResourceGTF.sh │ │ └── buildResources.sh │ └── source │ │ ├── RNAgetRes.oct2013.sh │ │ ├── RNAgetRes.sh │ │ ├── RNAgetRes_0905.sh │ │ ├── RNAseqCoverageCalculator.sh │ │ ├── RNAseqMaster.sh │ │ ├── RNAseqPipeline.sh │ │ ├── RPKM.sh │ │ ├── TE_stats.sh │ │ ├── WIG_RPKM.sh │ │ ├── pipe.tar.gz │ │ └── resourceGeneration │ │ ├── EnsemblResourceGenerator.sh │ │ ├── GencodeGenerate.sh │ │ ├── RefSeqGenerate.sh │ │ ├── RepeatMaskerGenerate.sh │ │ └── buildResources.sh ├── eastLion.sh ├── lion2bed.sh ├── preflight_check.sh └── westLion.sh ├── software ├── Cython-0.22.zip ├── pysam-master.zip ├── python-pip_1.5.6.orig.tar.gz ├── samtools_0.1.19 ├── setuptools-14.3.zip ├── software.README └── wigToBigWig ├── source_refs.sh ├── todo └── user_guide ├── LIONS_UG.pdf └── LIONS_UG.tex /.gitignore: -------------------------------------------------------------------------------- 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