[{"data":1,"prerenderedAt":920},["ShallowReactive",2],{"navigation":3,"/visualization-community/getting-started/manage-your-data":421,"/visualization-community/getting-started/manage-your-data-surround":913},[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":231,"_dir":422,"_draft":423,"_partial":423,"_locale":424,"title":230,"description":425,"body":426,"_type":907,"_id":908,"_source":909,"_file":910,"_stem":911,"_extension":912},"getting-started",false,"","In this section, you will learn how and where to find your data so that you can use our visualization editors.",{"type":427,"children":428,"toc":902},"root",[429,436,508,513,539,558,565,570,598,603,622,627,652,657,671,676,706,711,730,735,764,769,801,806,812,866,871,896],{"type":430,"tag":431,"props":432,"children":433},"element","p",{},[434],{"type":435,"value":425},"text",{"type":430,"tag":437,"props":438,"children":441},"callout",{"color":439,"icon":440},"blue","i-heroicons-light-bulb",[442,451],{"type":430,"tag":431,"props":443,"children":444},{},[445],{"type":430,"tag":446,"props":447,"children":448},"strong",{},[449],{"type":435,"value":450},"Tip",{"type":430,"tag":452,"props":453,"children":454},"ul",{},[455,470,475,488],{"type":430,"tag":456,"props":457,"children":458},"li",{},[459,461,468],{"type":435,"value":460},"The ",{"type":430,"tag":462,"props":463,"children":465},"code",{"className":464},[],[466],{"type":435,"value":467},"\u003Curl>",{"type":435,"value":469}," key is case in-sensitive.",{"type":430,"tag":456,"props":471,"children":472},{},[473],{"type":435,"value":474},"Dropbox storage url keys will not work since these are binary files.",{"type":430,"tag":456,"props":476,"children":477},{},[478,480,486],{"type":435,"value":479},"Amazon (AWS) and DNAnexus are two examples that ",{"type":430,"tag":462,"props":481,"children":483},{"className":482},[],[484],{"type":435,"value":485},"runproteinpaint()",{"type":435,"value":487}," can access.",{"type":430,"tag":456,"props":489,"children":490},{},[491,492,498,500,506],{"type":435,"value":460},{"type":430,"tag":462,"props":493,"children":495},{"className":494},[],[496],{"type":435,"value":497},"\u003Cfile>",{"type":435,"value":499}," key is only for internal St. Jude users to access the HPC within the ",{"type":430,"tag":462,"props":501,"children":503},{"className":502},[],[504],{"type":435,"value":505},"\u003Ctp>",{"type":435,"value":507}," directory.",{"type":430,"tag":431,"props":509,"children":510},{},[511],{"type":435,"value":512},"Follow the below tutorials if you want to upload data to DNAnexus:",{"type":430,"tag":452,"props":514,"children":515},{},[516,529],{"type":430,"tag":456,"props":517,"children":518},{},[519,521,527],{"type":435,"value":520},"if you have your data stored in DNAnexus, go ",{"type":430,"tag":522,"props":523,"children":524},"a",{"href":76},[525],{"type":435,"value":526},"here",{"type":435,"value":528},".",{"type":430,"tag":456,"props":530,"children":531},{},[532,534,538],{"type":435,"value":533},"if you have your data stored on your local and want to upload to DNAnexus, go ",{"type":430,"tag":522,"props":535,"children":536},{"href":70},[537],{"type":435,"value":526},{"type":435,"value":528},{"type":430,"tag":437,"props":540,"children":543},{"color":541,"icon":542},"orange","i-heroicons-exclamation-circle",[544],{"type":430,"tag":431,"props":545,"children":546},{},[547,552,556],{"type":430,"tag":446,"props":548,"children":549},{},[550],{"type":435,"value":551},"Warning",{"type":430,"tag":553,"props":554,"children":555},"br",{},[],{"type":435,"value":557},"\nYou must follow the below tutorial to extend your links after you upload your data.\nOtherwise, the links in DNAnexus are available for 24h only and therefore your visualization will not render after that allotted time.",{"type":430,"tag":559,"props":560,"children":562},"h2",{"id":561},"accessing-dnanexus-from-the-command-line-to-extend-your-file-duration",[563],{"type":435,"value":564},"Accessing DNAnexus from the command line (to extend your file duration)",{"type":430,"tag":431,"props":566,"children":567},{},[568],{"type":435,"value":569},"First, you will want to check if you have python installed.",{"type":430,"tag":571,"props":572,"children":576},"pre",{"className":573,"code":574,"language":575,"meta":424,"style":424},"language-bash shiki shiki-themes material-theme-lighter material-theme material-theme-palenight","python --version\n","bash",[577],{"type":430,"tag":462,"props":578,"children":579},{"__ignoreMap":424},[580],{"type":430,"tag":581,"props":582,"children":585},"span",{"class":583,"line":584},"line",1,[586,592],{"type":430,"tag":581,"props":587,"children":589},{"style":588},"--shiki-light:#E2931D;--shiki-default:#FFCB6B;--shiki-dark:#FFCB6B",[590],{"type":435,"value":591},"python",{"type":430,"tag":581,"props":593,"children":595},{"style":594},"--shiki-light:#91B859;--shiki-default:#C3E88D;--shiki-dark:#C3E88D",[596],{"type":435,"value":597}," --version\n",{"type":430,"tag":431,"props":599,"children":600},{},[601],{"type":435,"value":602},"Then, check if you have python3 installed",{"type":430,"tag":571,"props":604,"children":606},{"className":573,"code":605,"language":575,"meta":424,"style":424},"python3 --version\n",[607],{"type":430,"tag":462,"props":608,"children":609},{"__ignoreMap":424},[610],{"type":430,"tag":581,"props":611,"children":612},{"class":583,"line":584},[613,618],{"type":430,"tag":581,"props":614,"children":615},{"style":588},[616],{"type":435,"value":617},"python3",{"type":430,"tag":581,"props":619,"children":620},{"style":594},[621],{"type":435,"value":597},{"type":430,"tag":431,"props":623,"children":624},{},[625],{"type":435,"value":626},"now install DNAnexus.",{"type":430,"tag":571,"props":628,"children":630},{"className":573,"code":629,"language":575,"meta":424,"style":424},"pip3 install dxpy\n",[631],{"type":430,"tag":462,"props":632,"children":633},{"__ignoreMap":424},[634],{"type":430,"tag":581,"props":635,"children":636},{"class":583,"line":584},[637,642,647],{"type":430,"tag":581,"props":638,"children":639},{"style":588},[640],{"type":435,"value":641},"pip3",{"type":430,"tag":581,"props":643,"children":644},{"style":594},[645],{"type":435,"value":646}," install",{"type":430,"tag":581,"props":648,"children":649},{"style":594},[650],{"type":435,"value":651}," dxpy\n",{"type":430,"tag":431,"props":653,"children":654},{},[655],{"type":435,"value":656},"Open DNAnexus to ensure you can access it from the command line.",{"type":430,"tag":571,"props":658,"children":660},{"className":573,"code":659,"language":575,"meta":424,"style":424},"dx\n",[661],{"type":430,"tag":462,"props":662,"children":663},{"__ignoreMap":424},[664],{"type":430,"tag":581,"props":665,"children":666},{"class":583,"line":584},[667],{"type":430,"tag":581,"props":668,"children":669},{"style":588},[670],{"type":435,"value":659},{"type":430,"tag":431,"props":672,"children":673},{},[674],{"type":435,"value":675},"Get your token by logging into DNAnexus.\nNavigate to your profile icon.\nSelect the API token in the top navbar.\nSelect to generate the token.\nThen go to your terminal and enter:",{"type":430,"tag":571,"props":677,"children":679},{"className":573,"code":678,"language":575,"meta":424,"style":424},"dx login --token add_token_here\n",[680],{"type":430,"tag":462,"props":681,"children":682},{"__ignoreMap":424},[683],{"type":430,"tag":581,"props":684,"children":685},{"class":583,"line":584},[686,691,696,701],{"type":430,"tag":581,"props":687,"children":688},{"style":588},[689],{"type":435,"value":690},"dx",{"type":430,"tag":581,"props":692,"children":693},{"style":594},[694],{"type":435,"value":695}," login",{"type":430,"tag":581,"props":697,"children":698},{"style":594},[699],{"type":435,"value":700}," --token",{"type":430,"tag":581,"props":702,"children":703},{"style":594},[704],{"type":435,"value":705}," add_token_here\n",{"type":430,"tag":431,"props":707,"children":708},{},[709],{"type":435,"value":710},"Pick a project to enter and then type the below to see all files in that project.",{"type":430,"tag":571,"props":712,"children":714},{"className":573,"code":713,"language":575,"meta":424,"style":424},"dx ls\n",[715],{"type":430,"tag":462,"props":716,"children":717},{"__ignoreMap":424},[718],{"type":430,"tag":581,"props":719,"children":720},{"class":583,"line":584},[721,725],{"type":430,"tag":581,"props":722,"children":723},{"style":588},[724],{"type":435,"value":690},{"type":430,"tag":581,"props":726,"children":727},{"style":594},[728],{"type":435,"value":729}," ls\n",{"type":430,"tag":431,"props":731,"children":732},{},[733],{"type":435,"value":734},"You can type the below to see the durations.",{"type":430,"tag":571,"props":736,"children":738},{"className":573,"code":737,"language":575,"meta":424,"style":424},"dx make_download_url file_name.txt --help\n",[739],{"type":430,"tag":462,"props":740,"children":741},{"__ignoreMap":424},[742],{"type":430,"tag":581,"props":743,"children":744},{"class":583,"line":584},[745,749,754,759],{"type":430,"tag":581,"props":746,"children":747},{"style":588},[748],{"type":435,"value":690},{"type":430,"tag":581,"props":750,"children":751},{"style":594},[752],{"type":435,"value":753}," make_download_url",{"type":430,"tag":581,"props":755,"children":756},{"style":594},[757],{"type":435,"value":758}," file_name.txt",{"type":430,"tag":581,"props":760,"children":761},{"style":594},[762],{"type":435,"value":763}," --help\n",{"type":430,"tag":431,"props":765,"children":766},{},[767],{"type":435,"value":768},"Now, set your duration.",{"type":430,"tag":571,"props":770,"children":772},{"className":573,"code":771,"language":575,"meta":424,"style":424},"dx make_download_url file_name.txt --duration 100y\n",[773],{"type":430,"tag":462,"props":774,"children":775},{"__ignoreMap":424},[776],{"type":430,"tag":581,"props":777,"children":778},{"class":583,"line":584},[779,783,787,791,796],{"type":430,"tag":581,"props":780,"children":781},{"style":588},[782],{"type":435,"value":690},{"type":430,"tag":581,"props":784,"children":785},{"style":594},[786],{"type":435,"value":753},{"type":430,"tag":581,"props":788,"children":789},{"style":594},[790],{"type":435,"value":758},{"type":430,"tag":581,"props":792,"children":793},{"style":594},[794],{"type":435,"value":795}," --duration",{"type":430,"tag":581,"props":797,"children":798},{"style":594},[799],{"type":435,"value":800}," 100y\n",{"type":430,"tag":431,"props":802,"children":803},{},[804],{"type":435,"value":805},"Use the new URL as VisCom's url key, be sure to save this to reference later.",{"type":430,"tag":559,"props":807,"children":809},{"id":808},"accessing-the-hpc",[810],{"type":435,"value":811},"Accessing the HPC",{"type":430,"tag":452,"props":813,"children":814},{},[815,826],{"type":430,"tag":456,"props":816,"children":817},{},[818,820,825],{"type":435,"value":819},"If you have your data stored on the HPC and want to move it to DNAnexus, follow these ",{"type":430,"tag":522,"props":821,"children":822},{"href":73},[823],{"type":435,"value":824},"instructions",{"type":435,"value":528},{"type":430,"tag":456,"props":827,"children":828},{},[829,831,836,838,843,845],{"type":435,"value":830},"In order to allow ProteinPaint's server to access your data on the HPC, you must move it to to the ",{"type":430,"tag":462,"props":832,"children":834},{"className":833},[],[835],{"type":435,"value":505},{"type":435,"value":837}," directory.\nTo access this, sign in (see ",{"type":430,"tag":522,"props":839,"children":840},{"href":222},[841],{"type":435,"value":842},"this",{"type":435,"value":844}," tutorial) and type",{"type":430,"tag":571,"props":846,"children":848},{"className":573,"code":847,"language":575,"meta":424,"style":424},"cd /research/rgs01/resgen/legacy/gb_customTracks/tp\n",[849],{"type":430,"tag":462,"props":850,"children":851},{"__ignoreMap":424},[852],{"type":430,"tag":581,"props":853,"children":854},{"class":583,"line":584},[855,861],{"type":430,"tag":581,"props":856,"children":858},{"style":857},"--shiki-light:#6182B8;--shiki-default:#82AAFF;--shiki-dark:#82AAFF",[859],{"type":435,"value":860},"cd",{"type":430,"tag":581,"props":862,"children":863},{"style":594},[864],{"type":435,"value":865}," /research/rgs01/resgen/legacy/gb_customTracks/tp\n",{"type":430,"tag":431,"props":867,"children":868},{},[869],{"type":435,"value":870},"Here, you can make a new directory to store your data.",{"type":430,"tag":437,"props":872,"children":873},{"color":439,"icon":440},[874],{"type":430,"tag":431,"props":875,"children":876},{},[877,881,884,886,894],{"type":430,"tag":446,"props":878,"children":879},{},[880],{"type":435,"value":450},{"type":430,"tag":553,"props":882,"children":883},{},[],{"type":435,"value":885},"\nThe data must be on the ",{"type":430,"tag":522,"props":887,"children":891},{"href":888,"rel":889},"https://proteinpaint.stjude.org",[890],"nofollow",[892],{"type":435,"value":893},"proteinpaint.stjude.org",{"type":435,"value":895}," server and not ppr1, otherwise your visualizations have to be viewed by VPN.",{"type":430,"tag":897,"props":898,"children":899},"style",{},[900],{"type":435,"value":901},"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":903,"depth":903,"links":904},2,[905,906],{"id":561,"depth":903,"text":564},{"id":808,"depth":903,"text":811},"markdown","content:5.visualization-community:2.getting-started:5.manage-your-data.md","content","5.visualization-community/2.getting-started/5.manage-your-data.md","5.visualization-community/2.getting-started/5.manage-your-data","md",[914,917],{"_path":228,"title":915,"description":916},"Tracks versus Apps","Visualization Community supports GenomePaint and ProteinPaint tracks and apps.\nAll data types supported can be found here.",{"_path":234,"title":918,"description":919},"Collections and Communities","In this section, you will learn how to create a collection and/or community within VisCom.",1791243634660]