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How to download GDC gene-expression quantification files: repository filters and manifests
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Summary
Bill demonstrated how to find gene expression quantification files in the GDC repository, filter to RNA‑Seq gene expression quantification, add selected files to the cart (54 files, 228 MB) or export a manifest for the GDC Data Transfer Tool; he noted most gene-expression data shown are open access while some STAR-derived files may be controlled access.
Bill walked attendees through downloading gene expression quantification files from the GDC repository and described two common workflows: browser cart download for modest-sized sets or using a manifest with the GDC Data Transfer Tool for larger transfers.
To find files Bill applied facet filters in the repository view: experimental strategy = RNA-Seq and data type = gene expression quantification. For the demo cohort this produced 54 quantification files totaling 228 MB; Bill added them to the cart and noted an in-browser download is feasible for that size. He cautioned that STAR counts or splice-junction quantification files can include controlled-access content, which requires appropriate authorization, whereas the files used in the demo were open access.
For automated or repeatable workflows Bill showed how to export a manifest from the cart and pass it to the GDC Data Transfer Tool. He also outlined associated downloads available from the repository page: clinical/sample sheets and metadata tables that many researchers request alongside expression files.
Bill reiterated that the visualization and most gene-expression data demonstrated are available without logging in: “This can be done by anyone with access to the Internet.” He closed the download demo by pointing attendees to documentation pages and the support email (support@nci-gdc.datacommons.io) for help with manifests, controlled-access queries or data-transfer troubleshooting.
Practical details extracted from the demo: the repository hit count (example shown as 2,900 harmonized files before filtering), the filtered selection (54 gene expression quantification files), and the total download size for the selected files (228 MB). For reproducibility use manifests with the Data Transfer Tool and consult GDC documentation for controlled-access procedures.
