Download Data Files
Download Short-Read Archive, Gene Expression Omnibus, or Recount3 data from their respective databases, files from URL, or gene sequences
- 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.
- Select version 1.1.2 from the dropdown menu in the top right corner. When ready to begin analysis, click the “Run Workflow” button.
- 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.
- Give the workflow a unique name, and review the workflow inputs and parameters. When ready to submit, click “Run Workflow”.
- 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.
- To begin, find the workflow run in the Activity tab. Select your workflow.
- On this page, you can view an array of information about your workflow run. To find your downloaded files, select the Files tab.
- In the Files tab, select the Output folder to view all output files.
- Alternately, you can find retrieved files in the pipeline-outputs folder.
- Once in the folder, select getncbi.
- Find the folder corresponding to your workflow run, then select output to view files.