Accessing Genomic Data
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The GDC Data Portal is a groundbreaking tool that enables a better understanding of cancer biology by allowing researchers to:
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Documentation
Data Access Tools
The GDC provides web-based tools and API endpoints for searching, viewing and downloading data as well as client tools for downloading large volumes of data.
Controlled Data Access Policy
Any user requesting access to GDC controlled data must apply for access to the data through the database of Genotypes and Phenotypes (dbGaP):
High Quality Datasets
The GDC obtains datasets from NCI programs which maintain tissue collection strategies that couple quantity with quality. Data validation is performed on all data submitted to the GDC.
What’s New with the GDC and Cancer Research
Cancer Research Highlights and Publications:
Why do some genes show no expression in STAR results across all samples, even though I can see mapped reads in the raw RNA-Seq data?
STAR gene expression quantification excludes reads that are mapped to multiple different genes. This can cause some genes to appear with zero expression in the final counts, even if mapped reads are present in the raw data.
One common reason for this is gene overlap. These genes often have their exons entirely encompassed within other genes, and in such cases, STAR cannot assign reads to them because they are ambiguous. To check if a gene falls into this category, you can refer to the following lists: Stranded Counting Overlap Gene List: overlap.gene.stranded.tsv, and Strandless Counting Overlap Gene List: overlap.gene.strandless.tsv.
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