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Use the BaseSpace Downloader to download run-related data, either FASTQ files (if applicable) or SAV files.
Select the run in the run list, or navigate to the run details page.
Select File, point to Download, and then select Run.
Select the file type you want to download:
FASTQ — FASTQ files.
Sequencing Analysis Viewer (SAV) — InterOp and other files required to run SAV.
Select Download.
The BaseSpace Downloader guides you through the download process, and starts the download of the files to the desired location.
When viewing lists of files (e.g., run files, analysis files, or files in a search result), you can preview and download them individually.
Click on the name of the file you want to download.
A preview of the file will appear, for supported file formats.
Select Download.
The file will download automatically. This method does not use the BaseSpace Downloader.
Use the BaseSpace Downloader to download a package of all files in a project.
Select a project in the project list, or navigate to a project details page.
Select the File icon, point to Download, then select Project.
Select Download.
The BaseSpace Downloader guides you through the download process, and starts the download of the files to the desired location.
Use the BaseSpace Downloader to download a package of analysis files.
Select one or more analyses from the analysis list, or navigate to an analysis details page.
Select the File icon, point to Download, then select Analysis.
Select the file type you want to download:
All files including VCF, BAM, & FASTQ
VCF files only
BAM files only
Select Download.
The BaseSpace Downloader guides you through the download process, and starts the download of the files to the desired location.
Use the BaseSpace Downloader to download FASTQ or general datasets. Datasets are linked to biosamples and are listed on the Datasets tab of the biosample details page. To download a files from a run, see Download Run Data Files.
From the Biosamples or Projects list, click on the desired biosample or project.
Select the FASTQs or Other Datasets tab.
[Optional] Select a dataset name to view a list of file details.
Select the checkboxes for the desired datasets.
Select the File icon, point to Download, then select Dataset.
Select Download.
The BaseSpace Downloader guides you through the download process, and starts the download of the files to the desired location.
Use the BaseSpace Sequence Hub Downloader to download whole samples or individual files from a specific sample.
From a Run or Project, select the Samples tab.
Select the checkboxes for the desired sample or samples.
Select File, Download, then select Sample.
Select Download. The BaseSpace Sequence Hub Downloader guides you through the download process, and starts the download of the files to the desired location.
From a Run or Project, select the Samples tab.
Click the name of the desired sample to access the sample details page.
In the Sample Files section, select the checkboxes of the file or files to download.
The BaseSpace Sequence Hub Downloader guides you through the download process, and starts the download of the files to the desired location.
BaseSpace Sequence Hub allows you to download data as a package, individually, or as a group of FASTQ files.
When installing the Windows version of the BaseSpace Downloader on a restricted environment, it is important to allow digicert Extended Validation (EV) code signing certificates.
See the following pages for more details on downloading specific types of data: