[{"data":1,"prerenderedAt":891},["ShallowReactive",2],{"navigation":3,"/genomics-platform/managing-data/overview":421,"/genomics-platform/managing-data/overview-surround":887},[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":67,"_dir":422,"_draft":423,"_partial":423,"_locale":424,"title":425,"description":426,"navigation":427,"body":428,"_type":881,"_id":882,"_source":883,"_file":884,"_stem":885,"_extension":886},"managing-data",false,"","Working With Our Data","In this overview, we will explain how to manage your data request(s) from St. Jude Cloud's genomics platform My Dashboard page and how to access and manage your data (once it has been vended to you) from within a DNAnexus project.\nThe DNAnexus genomic ecosystem is the backbone for the computation and storage in St. Jude Cloud.\nThis means that each data request in St. Jude Cloud corresponds to a project in DNAnexus.\nIf you'd like, you can read an introduction to the DNAnexus ecosystem here.\nIf you haven't already, follow this guide to request access to St. Jude data in this secure cloud ecosystem.",{"title":5},{"type":429,"children":430,"toc":875},"root",[431,475,482,517,526,569,575,580,585,605,613,618,741,762,768,773,839,845,869],{"type":432,"tag":433,"props":434,"children":435},"element","p",{},[436,439,448,450,457,459,466,468,473],{"type":437,"value":438},"text","In this overview, we will explain how to manage your data request(s) from St. Jude Cloud's genomics platform ",{"type":432,"tag":440,"props":441,"children":445},"a",{"href":442,"rel":443},"https://platform.stjude.cloud/dashboard",[444],"nofollow",[446],{"type":437,"value":447},"My Dashboard page",{"type":437,"value":449}," and how to access and manage your data (once it has been vended to you) from within a DNAnexus project.\nThe ",{"type":432,"tag":440,"props":451,"children":454},{"href":452,"rel":453},"https://www.dnanexus.com/",[444],[455],{"type":437,"value":456},"DNAnexus",{"type":437,"value":458}," genomic ecosystem is the backbone for the computation and storage in St. Jude Cloud.\nThis means that each data request in St. Jude Cloud corresponds to a project in DNAnexus.\nIf you'd like, you can read an introduction to the DNAnexus ecosystem ",{"type":432,"tag":440,"props":460,"children":463},{"href":461,"rel":462},"https://documentation.dnanexus.com/",[444],[464],{"type":437,"value":465},"here",{"type":437,"value":467},".\nIf you haven't already, follow ",{"type":432,"tag":440,"props":469,"children":470},{"href":40},[471],{"type":437,"value":472},"this guide",{"type":437,"value":474}," to request access to St. Jude data in this secure cloud ecosystem.",{"type":432,"tag":476,"props":477,"children":479},"h2",{"id":478},"managing-your-data-requests",[480],{"type":437,"value":481},"Managing Your Data Requests",{"type":432,"tag":433,"props":483,"children":484},{},[485,487,493,495,501,503,508,510,515],{"type":437,"value":486},"Below is a snapshot of the ",{"type":432,"tag":440,"props":488,"children":490},{"href":442,"rel":489},[444],[491],{"type":437,"value":492},"My Dashboard",{"type":437,"value":494}," on our Genomics Platform.\nFrom this page you can check the status of your data request, complete an ",{"type":432,"tag":440,"props":496,"children":498},{"href":497},"/genomics-platform/getting-started/filling-out-the-daa#the-electronic-data-access-agreement-process",[499],{"type":437,"value":500},"EDAA",{"type":437,"value":502}," draft, upload a revised ",{"type":432,"tag":440,"props":504,"children":505},{"href":43},[506],{"type":437,"value":507},"DAA",{"type":437,"value":509}," or an ",{"type":432,"tag":440,"props":511,"children":512},{"href":79},[513],{"type":437,"value":514},"Extension Addendum",{"type":437,"value":516},", or link to your DNAnexus project folder for a specific data request.",{"type":432,"tag":433,"props":518,"children":519},{},[520],{"type":432,"tag":521,"props":522,"children":525},"img",{"alt":523,"src":524},"manage-data-page","/img/genomics-platform/managing-data/overview/docs-manage-data-page-labelled-tagged.png",[],{"type":432,"tag":527,"props":528,"children":531},"callout",{"color":529,"icon":530},"blue","i-heroicons-arrows-right-left",[532,541],{"type":432,"tag":433,"props":533,"children":534},{},[535],{"type":432,"tag":536,"props":537,"children":538},"strong",{},[539],{"type":437,"value":540},"Pending Request Types",{"type":432,"tag":542,"props":543,"children":544},"ol",{},[545,551,556],{"type":432,"tag":546,"props":547,"children":548},"li",{},[549],{"type":437,"value":550},"Request 1 is an Open Draft, meaning the requester has not yet finished the setup wizard and the DocuSign envelope has not yet been sent to any of the signatories.",{"type":432,"tag":546,"props":552,"children":553},{},[554],{"type":437,"value":555},"Request 2, listed in the Projects section, has been sent to the signatories, but has not been completed by all of them.\nThis status will look like the Request 3 when all of the signatories sign the document and it is ready to be sent to the Data Access Committee(s).",{"type":432,"tag":546,"props":557,"children":558},{},[559,561,567],{"type":437,"value":560},"Request 3 is pending approval from the Data Access Committee(s), and the status will change from Pending to either Approved or Rejected, based on their decision.\nAll submitted manual-process Data Access Agreements will show up on your My Dashboard page like Request 3.\nIf you have a question about the status of your data request which is not answered on the \"My Dashboard\" page, you can email us at ",{"type":432,"tag":440,"props":562,"children":564},{"href":563},"mailto:support@stjude.cloud",[565],{"type":437,"value":566},"support@stjude.cloud",{"type":437,"value":568},".",{"type":432,"tag":476,"props":570,"children":572},{"id":571},"accessing-your-data",[573],{"type":437,"value":574},"Accessing Your Data",{"type":432,"tag":433,"props":576,"children":577},{},[578],{"type":437,"value":579},"Once your data access request is approved, the data you requested from St. Jude Cloud will automatically be distributed to a DNAnexus project with the same name that you entered through the data request setup wizard.",{"type":432,"tag":433,"props":581,"children":582},{},[583],{"type":437,"value":584},"To ensure that your data is properly vended, it is important for you to sign in to your St. Jude Cloud account following your approval.",{"type":432,"tag":433,"props":586,"children":587},{},[588,590,595,597,603],{"type":437,"value":589},"From your ",{"type":432,"tag":440,"props":591,"children":593},{"href":442,"rel":592},[444],[594],{"type":437,"value":492},{"type":437,"value":596}," page, click on a specific data request name to navigate directly to your corresponding project in DNAnexus.\n(You can also follow the link in the approval email from ",{"type":432,"tag":440,"props":598,"children":600},{"href":599},"mailto:notifications@stjude.cloud",[601],{"type":437,"value":602},"notifications@stjude.cloud",{"type":437,"value":604},".)",{"type":432,"tag":433,"props":606,"children":607},{},[608],{"type":432,"tag":521,"props":609,"children":612},{"alt":610,"src":611},"dx project page","/img/genomics-platform/managing-data/overview/DX-project-page.png",[],{"type":432,"tag":433,"props":614,"children":615},{},[616],{"type":437,"value":617},"When the data is vended, the directory structure of your DNAnexus project will look something like this:",{"type":432,"tag":619,"props":620,"children":624},"pre",{"className":621,"code":622,"language":623,"meta":424,"style":424},"language-bash shiki shiki-themes material-theme-lighter material-theme material-theme-palenight","project_space/\n├── restricted/\n│   ├── bam/\n│   ├── gVCF/\n│   ├── Somatic_VCF/\n│   └── CNV/\n└── SAMPLE_INFO.txt\n","bash",[625],{"type":432,"tag":626,"props":627,"children":628},"code",{"__ignoreMap":424},[629,641,656,675,692,709,727],{"type":432,"tag":630,"props":631,"children":634},"span",{"class":632,"line":633},"line",1,[635],{"type":432,"tag":630,"props":636,"children":638},{"style":637},"--shiki-light:#E2931D;--shiki-default:#FFCB6B;--shiki-dark:#FFCB6B",[639],{"type":437,"value":640},"project_space/\n",{"type":432,"tag":630,"props":642,"children":644},{"class":632,"line":643},2,[645,650],{"type":432,"tag":630,"props":646,"children":647},{"style":637},[648],{"type":437,"value":649},"├──",{"type":432,"tag":630,"props":651,"children":653},{"style":652},"--shiki-light:#91B859;--shiki-default:#C3E88D;--shiki-dark:#C3E88D",[654],{"type":437,"value":655}," restricted/\n",{"type":432,"tag":630,"props":657,"children":659},{"class":632,"line":658},3,[660,665,670],{"type":432,"tag":630,"props":661,"children":662},{"style":637},[663],{"type":437,"value":664},"│",{"type":432,"tag":630,"props":666,"children":667},{"style":652},[668],{"type":437,"value":669},"   ├──",{"type":432,"tag":630,"props":671,"children":672},{"style":652},[673],{"type":437,"value":674}," bam/\n",{"type":432,"tag":630,"props":676,"children":678},{"class":632,"line":677},4,[679,683,687],{"type":432,"tag":630,"props":680,"children":681},{"style":637},[682],{"type":437,"value":664},{"type":432,"tag":630,"props":684,"children":685},{"style":652},[686],{"type":437,"value":669},{"type":432,"tag":630,"props":688,"children":689},{"style":652},[690],{"type":437,"value":691}," gVCF/\n",{"type":432,"tag":630,"props":693,"children":695},{"class":632,"line":694},5,[696,700,704],{"type":432,"tag":630,"props":697,"children":698},{"style":637},[699],{"type":437,"value":664},{"type":432,"tag":630,"props":701,"children":702},{"style":652},[703],{"type":437,"value":669},{"type":432,"tag":630,"props":705,"children":706},{"style":652},[707],{"type":437,"value":708}," Somatic_VCF/\n",{"type":432,"tag":630,"props":710,"children":712},{"class":632,"line":711},6,[713,717,722],{"type":432,"tag":630,"props":714,"children":715},{"style":637},[716],{"type":437,"value":664},{"type":432,"tag":630,"props":718,"children":719},{"style":652},[720],{"type":437,"value":721},"   └──",{"type":432,"tag":630,"props":723,"children":724},{"style":652},[725],{"type":437,"value":726}," CNV/\n",{"type":432,"tag":630,"props":728,"children":730},{"class":632,"line":729},7,[731,736],{"type":432,"tag":630,"props":732,"children":733},{"style":637},[734],{"type":437,"value":735},"└──",{"type":432,"tag":630,"props":737,"children":738},{"style":652},[739],{"type":437,"value":740}," SAMPLE_INFO.txt\n",{"type":432,"tag":433,"props":742,"children":743},{},[744,746,752,754,760],{"type":437,"value":745},"The ",{"type":432,"tag":626,"props":747,"children":749},{"className":748},[],[750],{"type":437,"value":751},"SAMPLE_INFO.txt",{"type":437,"value":753}," file provides all the ",{"type":432,"tag":440,"props":755,"children":757},{"href":756},"/genomics-platform/about-our-data/metadata-and-clinical-information#metadata",[758],{"type":437,"value":759},"metadata",{"type":437,"value":761}," associated with the request, and the restricted folder contains all the data for which you were approved separated by file type.",{"type":432,"tag":476,"props":763,"children":765},{"id":764},"using-your-data",[766],{"type":437,"value":767},"Using Your Data",{"type":432,"tag":433,"props":769,"children":770},{},[771],{"type":437,"value":772},"There are two primary ways you can interact with data vended to you in St. Jude Cloud:",{"type":432,"tag":774,"props":775,"children":776},"ul",{},[777,803],{"type":432,"tag":546,"props":778,"children":779},{},[780,785,787,792,794,801],{"type":432,"tag":536,"props":781,"children":782},{},[783],{"type":437,"value":784},"Cloud access",{"type":437,"value":786},".\nYou can choose to work with the data in DNAnexus' genomics cloud ecosystem.\nThis is our suggested method of interaction, as you can avoid downloading the data to your local servers (which both takes time and is error prone).\nIf you choose to leverage this approach, you can either wrap your own analysis pipeline as a cloud app (see ",{"type":432,"tag":440,"props":788,"children":789},{"href":92},[790],{"type":437,"value":791},"our guide",{"type":437,"value":793},") or leverage any of DNAnexus' publicly available apps (see ",{"type":432,"tag":440,"props":795,"children":798},{"href":796,"rel":797},"https://documentation.dnanexus.com/user/running-apps-and-workflows",[444],[799],{"type":437,"value":800},"DNAnexus' guide",{"type":437,"value":802},").",{"type":432,"tag":546,"props":804,"children":805},{},[806,811,813,819,821,825,827],{"type":432,"tag":536,"props":807,"children":808},{},[809],{"type":437,"value":810},"Download the data",{"type":437,"value":812}," (",{"type":432,"tag":814,"props":815,"children":816},"em",{},[817],{"type":437,"value":818},"not suggested",{"type":437,"value":820},").\nThe second way to interact with data vended to you in St. Jude Cloud is by downloading the data to your local servers.\nIf you wish to do this, you can download the data on the command line (see ",{"type":432,"tag":440,"props":822,"children":823},{"href":86},[824],{"type":437,"value":791},{"type":437,"value":826},").\n",{"type":432,"tag":536,"props":828,"children":829},{},[830,832,838],{"type":437,"value":831},"Note that you must have indicated you wish to download the data in your ",{"type":432,"tag":440,"props":833,"children":835},{"href":834},"/genomics-platform/getting-started/filling-out-the-daa#the-data-access-agreement",[836],{"type":437,"value":837},"data access agreement",{"type":437,"value":568},{"type":432,"tag":476,"props":840,"children":842},{"id":841},"similar-topics",[843],{"type":437,"value":844},"Similar Topics",{"type":432,"tag":433,"props":846,"children":847},{},[848,853,857,861,864],{"type":432,"tag":440,"props":849,"children":850},{"href":55},[851],{"type":437,"value":852},"About our Data",{"type":432,"tag":854,"props":855,"children":856},"br",{},[],{"type":432,"tag":440,"props":858,"children":859},{"href":40},[860],{"type":437,"value":39},{"type":432,"tag":854,"props":862,"children":863},{},[],{"type":432,"tag":440,"props":865,"children":866},{"href":70},[867],{"type":437,"value":868},"Upload/Download Data (local)",{"type":432,"tag":870,"props":871,"children":872},"style",{},[873],{"type":437,"value":874},"html .light .shiki span {color: var(--shiki-light);background: var(--shiki-light-bg);font-style: var(--shiki-light-font-style);font-weight: var(--shiki-light-font-weight);text-decoration: var(--shiki-light-text-decoration);}html.light .shiki span {color: var(--shiki-light);background: var(--shiki-light-bg);font-style: var(--shiki-light-font-style);font-weight: var(--shiki-light-font-weight);text-decoration: var(--shiki-light-text-decoration);}html .default .shiki span {color: var(--shiki-default);background: var(--shiki-default-bg);font-style: var(--shiki-default-font-style);font-weight: var(--shiki-default-font-weight);text-decoration: var(--shiki-default-text-decoration);}html .shiki span {color: var(--shiki-default);background: var(--shiki-default-bg);font-style: var(--shiki-default-font-style);font-weight: var(--shiki-default-font-weight);text-decoration: var(--shiki-default-text-decoration);}html .dark .shiki span {color: var(--shiki-dark);background: var(--shiki-dark-bg);font-style: var(--shiki-dark-font-style);font-weight: var(--shiki-dark-font-weight);text-decoration: var(--shiki-dark-text-decoration);}html.dark .shiki span {color: var(--shiki-dark);background: var(--shiki-dark-bg);font-style: var(--shiki-dark-font-style);font-weight: var(--shiki-dark-font-weight);text-decoration: var(--shiki-dark-text-decoration);}",{"title":424,"searchDepth":643,"depth":643,"links":876},[877,878,879,880],{"id":478,"depth":643,"text":481},{"id":571,"depth":643,"text":574},{"id":764,"depth":643,"text":767},{"id":841,"depth":643,"text":844},"markdown","content:3.genomics-platform:3.managing-data:1.overview.md","content","3.genomics-platform/3.managing-data/1.overview.md","3.genomics-platform/3.managing-data/1.overview","md",[888,889],{"_path":61,"title":60,"description":424},{"_path":70,"title":890,"description":424},"Uploading Data from your Local Computer",1791243637610]