External Data

Download Data Files

Download Short-Read Archive, Gene Expression Omnibus, or Recount3 data from their respective databases, files from URL, or gene sequences

Workflow Walkthrough

  1. Navigate to the Download Data Files workflow. You can use the search bar at the top-right corner to find the workflow, or use the External Data filter on the left-hand side.
  2. Select version 1.1.2 from the dropdown menu in the top right corner. When ready to begin analysis, click the “Run Workflow” button.
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  4. To start, select the type of data you wish to retrieve - either Short Read Archive (SRA) data, Gene Omnibus Expression (GEO) data, Recount3 data, a URL, or gene sequences from a platform-supported genome. Depending on the resource you wish to access, you will be asked to provide a file containing the IDs of the data to retrieve - SRA IDs, GEO IDs, or the Recount3 project ID respectively. URL access will require additional information.
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  6. Give the workflow a unique name, and review the workflow inputs and parameters. When ready to submit, click “Run Workflow”.
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  8. N.B. - be sure to double check the design files when using retrieved files in a later workflow run. Some workflows, such as RNASeq, may require some rearranging of the automatically retrieved design files, which can be performed when selecting the design file.

Results Walkthrough

  1. To begin, find the workflow run in the Activity tab. Select your workflow.
  2. On this page, you can view an array of information about your workflow run. To find your downloaded files, select the Files tab.
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  4. In the Files tab, select the Output folder to view all output files.
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  6. Alternately, you can find retrieved files in the pipeline-outputs folder.
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  8. Once in the folder, select getncbi.
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  10. Find the folder corresponding to your workflow run, then select output to view files.