[{"data":1,"prerenderedAt":545},["ShallowReactive",2],{"navigation":3,"/genomics-platform/analyzing-data/visualizing-ngs-data":421,"/genomics-platform/analyzing-data/visualizing-ngs-data-surround":539},[4,19,25,131,197],{"title":5,"_path":6,"children":7,"icon":18},"Overview","/overview",[8,9,12,15],{"title":5,"_path":6},{"title":10,"_path":11},"About our Ecosystem","/overview/ecosystem",{"title":13,"_path":14},"Citing St. Jude Cloud","/overview/citing-stjude-cloud",{"title":16,"_path":17},"Frequently Asked Questions","/overview/faq","sjc-icon:child-logo",{"title":20,"_path":21,"children":22,"icon":24},"CC4K","/cc4k",[23],{"title":5,"_path":21},"sjc-icon:ontology-tree",{"title":26,"_path":27,"children":28,"icon":130},"Genomics Platform","/genomics-platform",[29,49,62,80,99],{"title":30,"_path":31,"children":32},"Getting Started","/genomics-platform/getting-started",[33,35,38,41,44,46],{"title":5,"_path":34},"/genomics-platform/getting-started/overview",{"title":36,"_path":37},"Accounts and Billing","/genomics-platform/getting-started/accounts-and-billing",{"title":39,"_path":40},"Making a Data Request","/genomics-platform/getting-started/making-a-data-request",{"title":42,"_path":43},"Filling Out the DAA","/genomics-platform/getting-started/filling-out-the-daa",{"title":16,"_path":45},"/genomics-platform/getting-started/faq",{"title":47,"_path":48},"Glossary","/genomics-platform/getting-started/glossary",{"title":50,"_path":51,"children":52},"About Our Data","/genomics-platform/about-our-data",[53,56,59],{"title":54,"_path":55},"Data Sets and Data Access Units","/genomics-platform/about-our-data/data-sets-and-data-access-units",{"title":57,"_path":58},"File Formats and Sequencing Information","/genomics-platform/about-our-data/file-formats-and-sequencing-information",{"title":60,"_path":61},"Metadata and Clinical Information","/genomics-platform/about-our-data/metadata-and-clinical-information",{"title":63,"_path":64,"children":65},"Managing Data","/genomics-platform/managing-data",[66,68,71,74,77],{"title":5,"_path":67},"/genomics-platform/managing-data/overview",{"title":69,"_path":70},"Upload/Download Data (Local)","/genomics-platform/managing-data/upload-download-data-local",{"title":72,"_path":73},"Upload/Download Data (Cluster)","/genomics-platform/managing-data/upload-download-data-cluster",{"title":75,"_path":76},"Upload/Download Data (DNAnexus)","/genomics-platform/managing-data/upload-download-data-dnanexus",{"title":78,"_path":79},"Renewing Your DAA","/genomics-platform/managing-data/renewing-your-daa",{"title":81,"_path":82,"children":83},"Analyzing Data","/genomics-platform/analyzing-data",[84,87,90,93,96],{"title":85,"_path":86},"Command Line Interaction","/genomics-platform/analyzing-data/command-line-interaction",{"title":88,"_path":89},"Running Our Workflows","/genomics-platform/analyzing-data/running-our-workflows",{"title":91,"_path":92},"Creating a Cloud Application","/genomics-platform/analyzing-data/creating-a-cloud-app",{"title":94,"_path":95},"Interactive Nodes","/genomics-platform/analyzing-data/interactive-nodes",{"title":97,"_path":98},"Visualizing NGS Data","/genomics-platform/analyzing-data/visualizing-ngs-data",{"title":100,"_path":101,"children":102},"Workflow Guides","/genomics-platform/workflow-guides",[103,106,109,112,115,118,121,124,127],{"title":104,"_path":105},"ChIP-Seq Peak Calling","/genomics-platform/workflow-guides/chipseq",{"title":107,"_path":108},"cis-X","/genomics-platform/workflow-guides/cisx",{"title":110,"_path":111},"MethylationToActivity","/genomics-platform/workflow-guides/methylation-to-activity",{"title":113,"_path":114},"Mutational Signatures","/genomics-platform/workflow-guides/mutational-signatures",{"title":116,"_path":117},"Rapid RNA-Seq","/genomics-platform/workflow-guides/rapid-rnaseq",{"title":119,"_path":120},"RNA-Seq Expression Classification","/genomics-platform/workflow-guides/rnaseq-expression-classification",{"title":122,"_path":123},"SEAseq","/genomics-platform/workflow-guides/seaseq",{"title":125,"_path":126},"SequencErr","/genomics-platform/workflow-guides/sequencerr",{"title":128,"_path":129},"WARDEN Differential Gene Expression","/genomics-platform/workflow-guides/warden","sjc-icon:genomics-platform",{"title":132,"_path":133,"children":134,"icon":196},"PeCan","/pecan",[135,149,156,174,181,190],{"title":5,"_path":136,"children":137},"/pecan/overview",[138,140,143,146],{"title":30,"_path":139},"/pecan/overview/getting-started",{"title":141,"_path":142},"Methods and Data","/pecan/overview/methods-and-data",{"title":144,"_path":145},"Videos","/pecan/overview/videos",{"title":147,"_path":148},"FAQ","/pecan/overview/faq",{"title":150,"_path":151,"children":152},"Cohort Building","/pecan/cohort-building",[153],{"title":154,"_path":155},"Create Custom Cohorts","/pecan/cohort-building/cohort-building",{"title":157,"_path":158,"children":159},"Data Facets","/pecan/data-facets",[160,163,165,168,171],{"title":161,"_path":162},"Variants","/pecan/data-facets/variants",{"title":113,"_path":164},"/pecan/data-facets/mutational-signatures",{"title":166,"_path":167},"Expression","/pecan/data-facets/expression",{"title":169,"_path":170},"Histology","/pecan/data-facets/histology",{"title":172,"_path":173},"Use Cases","/pecan/data-facets/use-cases",{"title":175,"_path":176,"children":177},"Accessibility","/pecan/accessibility",[178],{"title":179,"_path":180},"Keyboard Shortcuts","/pecan/accessibility/keyboard-shortcuts",{"title":182,"_path":183,"children":184},"PeCan PIE","/pecan/pecan-pie",[185,188],{"title":186,"_path":187},"What is PIE","/pecan/pecan-pie/what-is-pie",{"title":147,"_path":189},"/pecan/pecan-pie/faq",{"title":191,"_path":192,"children":193},"Release Notes","/pecan/release-notes",[194],{"title":195,"_path":192},"PeCan Release Notes","sjc-icon:pecan",{"title":198,"_path":199,"children":200,"icon":420},"Visualization Community","/visualization-community",[201,215,246,307,411],{"title":5,"_path":202,"children":203},"/visualization-community/overview",[204,207,210,213],{"title":205,"_path":206},"What is Visualization Community","/visualization-community/overview/what-is-visualization-community",{"title":208,"_path":209},"What are ProteinPaint and GenomePaint","/visualization-community/overview/what-are-proteinpaint-and-genome-paint",{"title":211,"_path":212},"Data Types","/visualization-community/overview/data-types-and-graphs",{"title":147,"_path":214},"/visualization-community/overview/faq",{"title":30,"_path":216,"children":217},"/visualization-community/getting-started",[218,220,223,226,229,232,235,238,241,243],{"title":5,"_path":219},"/visualization-community/getting-started/overview",{"title":221,"_path":222},"How to Sign-in","/visualization-community/getting-started/how-to-sign-in",{"title":224,"_path":225},"How to Use the VisEditor","/visualization-community/getting-started/how-to-use-the-viseditor",{"title":227,"_path":228},"Tracks and Apps","/visualization-community/getting-started/tracks-and-apps",{"title":230,"_path":231},"Manage Your Data","/visualization-community/getting-started/manage-your-data",{"title":233,"_path":234},"Collections & Communities","/visualization-community/getting-started/collections-and-communities",{"title":236,"_path":237},"Public vs. Private Visualizations","/visualization-community/getting-started/public-vs-private-visualizations",{"title":239,"_path":240},"Embedding","/visualization-community/getting-started/embedding",{"title":144,"_path":242},"/visualization-community/getting-started/videos",{"title":244,"_path":245},"NEW Data Download","/visualization-community/getting-started/new-data-download",{"title":247,"_path":248,"children":249},"Code Block Library","/visualization-community/code-block-library",[250,253,256,259,262,265,268,271,274,277,280,283,286,289,292,295,298,301,304],{"title":251,"_path":252},"Code Block Basics","/visualization-community/code-block-library/code-block-basics",{"title":254,"_path":255},"Allelic Imbalance","/visualization-community/code-block-library/allelic-imbalance",{"title":257,"_path":258},"Arc","/visualization-community/code-block-library/arc",{"title":260,"_path":261},"BAM","/visualization-community/code-block-library/bam",{"title":263,"_path":264},"BigWig","/visualization-community/code-block-library/bigwig",{"title":266,"_path":267},"BigWig Stranded","/visualization-community/code-block-library/bigwig-stranded",{"title":269,"_path":270},"Expression Rank","/visualization-community/code-block-library/expression-rank",{"title":272,"_path":273},"Hi-C","/visualization-community/code-block-library/hi-c",{"title":275,"_path":276},"Heatmap","/visualization-community/code-block-library/heatmap",{"title":278,"_path":279},"JSON BED","/visualization-community/code-block-library/json-bed",{"title":281,"_path":282},"Lollipop","/visualization-community/code-block-library/lollipop",{"title":284,"_path":285},"MA Volcano","/visualization-community/code-block-library/ma-volcano",{"title":287,"_path":288},"Profile Gene Value","/visualization-community/code-block-library/profile-gene-value",{"title":290,"_path":291},"RNA Splice Junction","/visualization-community/code-block-library/rna-splice-junction",{"title":293,"_path":294},"Single Cell","/visualization-community/code-block-library/single-cell",{"title":296,"_path":297},"Splice Junctions Cohort","/visualization-community/code-block-library/splice-junctions-cohort",{"title":299,"_path":300},"Track List and Facet Table","/visualization-community/code-block-library/track-list-and-facet-table",{"title":302,"_path":303},"t-SNE","/visualization-community/code-block-library/t-sne",{"title":305,"_path":306},"VCF","/visualization-community/code-block-library/vcf",{"title":308,"_path":309,"children":310},"ProteinPaint","/visualization-community/proteinpaint",[311,313,316,318,321,324,327,330,333,336,339,342,345,348,351,354,357,360,363,366,369,372,375,378,381,384,387,390,393,396,399,402,405,408],{"title":308,"_path":312},"/visualization-community/proteinpaint/proteinpaint",{"title":314,"_path":315},"Introduction","/visualization-community/proteinpaint/introduction",{"title":30,"_path":317},"/visualization-community/proteinpaint/getting-started",{"title":319,"_path":320},"Loading Datasets","/visualization-community/proteinpaint/loading-datasets",{"title":322,"_path":323},"Viewing SNV/Indel Mutations","/visualization-community/proteinpaint/viewing-snv-indel-mutations",{"title":325,"_path":326},"Viewing Gene Fusions","/visualization-community/proteinpaint/viewing-gene-fusions",{"title":328,"_path":329},"Viewing Expression Data","/visualization-community/proteinpaint/viewing-expression-data",{"title":331,"_path":332},"Filtering Mutations","/visualization-community/proteinpaint/filtering-mutations",{"title":334,"_path":335},"Exporting Figures and Data","/visualization-community/proteinpaint/exporting-figures-and-data",{"title":337,"_path":338},"Using the Gene Table","/visualization-community/proteinpaint/using-the-gene-table",{"title":340,"_path":341},"Using the Sample Table","/visualization-community/proteinpaint/using-the-sample-table",{"title":343,"_path":344},"Using the Heatmap","/visualization-community/proteinpaint/using-the-heatmap",{"title":346,"_path":347},"Using Disease Pie Charts","/visualization-community/proteinpaint/using-disease-pie-charts",{"title":349,"_path":350},"Stratifying Mutations by Cancer Subtype","/visualization-community/proteinpaint/stratifying-mutations-by-cancer-subtype",{"title":352,"_path":353},"SNV and Indel","/visualization-community/proteinpaint/snv-and-indel",{"title":355,"_path":356},"SV and fusion transcript","/visualization-community/proteinpaint/sv-and-fusion-transcript",{"title":358,"_path":359},"Copy Number Variants","/visualization-community/proteinpaint/copy-number-variants",{"title":361,"_path":362},"Internal tandem duplications","/visualization-community/proteinpaint/internal-tandem-duplications",{"title":364,"_path":365},"Intragenic deletion","/visualization-community/proteinpaint/intragenic-deletion",{"title":367,"_path":368},"Truncation, N-loss, or C-loss","/visualization-community/proteinpaint/truncation",{"title":370,"_path":371},"JSON-BED","/visualization-community/proteinpaint/json-bed",{"title":373,"_path":374},"Splice Junction","/visualization-community/proteinpaint/splice-junction",{"title":376,"_path":377},"Profile-Gene-Value","/visualization-community/proteinpaint/profile-gene-value",{"title":379,"_path":380},"Bampile","/visualization-community/proteinpaint/bampile",{"title":382,"_path":383},"Add Custom Protein Domains","/visualization-community/proteinpaint/add-custom-protein-domains",{"title":385,"_path":386},"Using Custom Tracks","/visualization-community/proteinpaint/using-custom-tracks",{"title":388,"_path":389},"Visualize Your Mutation Data","/visualization-community/proteinpaint/visualize-your-mutation-data",{"title":391,"_path":392},"Loading SNV/Indel Mutations from a File","/visualization-community/proteinpaint/loading-mutations-from-file",{"title":394,"_path":395},"Uploaded Mutation Data User Interface","/visualization-community/proteinpaint/uploaded-mutation-data",{"title":397,"_path":398},"Loading a TCGA MAF File","/visualization-community/proteinpaint/loading-tcga-maf-file",{"title":400,"_path":401},"Using a VCF File","/visualization-community/proteinpaint/using-vcf-file",{"title":403,"_path":404},"Embedding ProteinPaint","/visualization-community/proteinpaint/embedding-proteinpaint",{"title":406,"_path":407},"URL Parameters","/visualization-community/proteinpaint/url-parameters",{"title":409,"_path":410},"Organizing Data into a Study View","/visualization-community/proteinpaint/study-view",{"title":412,"_path":413,"children":414},"GenomePaint","/visualization-community/genomepaint",[415,417],{"title":412,"_path":416},"/visualization-community/genomepaint/genomepaint",{"title":418,"_path":419},"GenomePaint User Guide","/visualization-community/genomepaint/genomepaint-user-guide","sjc-icon:viz",{"_path":98,"_dir":422,"_draft":423,"_partial":423,"_locale":424,"title":97,"description":425,"body":426,"_type":533,"_id":534,"_source":535,"_file":536,"_stem":537,"_extension":538},"analyzing-data",false,"","In the future, we will release an alpha version of the GenomePaint visualization tool on St. Jude Cloud.\nIn the meantime, the best way to visualize NGS data on St. Jude Cloud is using IGV.\nYou can use the desktop or web browser versions of IGV.",{"type":427,"children":428,"toc":523},"root",[429,445,452,468,474,479,486,495,501,509,515],{"type":430,"tag":431,"props":432,"children":433},"element","p",{},[434,437,443],{"type":435,"value":436},"text","In the future, we will release an ",{"type":430,"tag":438,"props":439,"children":440},"strong",{},[441],{"type":435,"value":442},"alpha version",{"type":435,"value":444}," of the GenomePaint visualization tool on St. Jude Cloud.\nIn the meantime, the best way to visualize NGS data on St. Jude Cloud is using IGV.\nYou can use the desktop or web browser versions of IGV.",{"type":430,"tag":446,"props":447,"children":449},"h2",{"id":448},"desktop-igv",[450],{"type":435,"value":451},"Desktop IGV",{"type":430,"tag":431,"props":453,"children":454},{},[455,457,466],{"type":435,"value":456},"DNAnexus has an existing guide on viewing files in DNAnexus using the desktop version of IGV.\nYou can view the guide ",{"type":430,"tag":458,"props":459,"children":463},"a",{"href":460,"rel":461},"https://documentation.dnanexus.com/science/using-igv-with-dnanexus",[462],"nofollow",[464],{"type":435,"value":465},"here",{"type":435,"value":467},".",{"type":430,"tag":446,"props":469,"children":471},{"id":470},"web-browser-igv",[472],{"type":435,"value":473},"Web Browser IGV",{"type":430,"tag":431,"props":475,"children":476},{},[477],{"type":435,"value":478},"Within any DNAnexus project, you can view the data in the IGV web browser by doing the following steps.",{"type":430,"tag":480,"props":481,"children":483},"h3",{"id":482},"select-visualize",[484],{"type":435,"value":485},"Select \"Visualize\"",{"type":430,"tag":431,"props":487,"children":488},{},[489],{"type":430,"tag":490,"props":491,"children":494},"img",{"alt":492,"src":493},"igv visualizer","/img/genomics-platform/analyzing-data/visualizing-ngs-data/visualizer-igv-1.png",[],{"type":430,"tag":480,"props":496,"children":498},{"id":497},"select-igv-v200",[499],{"type":435,"value":500},"Select IGV v2.0.0",{"type":430,"tag":431,"props":502,"children":503},{},[504],{"type":430,"tag":490,"props":505,"children":508},{"alt":506,"src":507},"igv visualizer 2.0","/img/genomics-platform/analyzing-data/visualizing-ngs-data/visualizer-igv-2.png",[],{"type":430,"tag":480,"props":510,"children":512},{"id":511},"select-the-files-you-want-to-view",[513],{"type":435,"value":514},"Select the files you want to view",{"type":430,"tag":431,"props":516,"children":517},{},[518],{"type":430,"tag":490,"props":519,"children":522},{"alt":520,"src":521},"igv visualizer file selection","/img/genomics-platform/analyzing-data/visualizing-ngs-data/visualizer-igv-3.png",[],{"title":424,"searchDepth":524,"depth":524,"links":525},2,[526,527],{"id":448,"depth":524,"text":451},{"id":470,"depth":524,"text":473,"children":528},[529,531,532],{"id":482,"depth":530,"text":485},3,{"id":497,"depth":530,"text":500},{"id":511,"depth":530,"text":514},"markdown","content:3.genomics-platform:4.analyzing-data:5.visualizing-ngs-data.md","content","3.genomics-platform/4.analyzing-data/5.visualizing-ngs-data.md","3.genomics-platform/4.analyzing-data/5.visualizing-ngs-data","md",[540,543],{"_path":95,"title":541,"description":542},"Interactive Nodes in the Cloud","Apart from creating and running cloud apps, you can request an interactive node in the cloud to use for iterative development.\nThis can be particularly useful if you want to run some quick analyses on the cloud, want to run tools without creating an app, or want to submit jobs similar to bsub on the local St. Jude HPC.",{"_path":105,"title":544,"description":424},"ChIP-Seq",1791243637906]