New Correlation Plot Tool and Link to GeneCards Now Available in GDC Data Portal
The GDC Uhlenbeck Release includes a new Correlation Plot Tool, link to GeneCards, and other enhancements in the GDC 2.0 Data Portal. Primary features include:
Analyze Data
Why do CNVs of different genes in the GDC Data Portal differ from other genomic portals?
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This discrepancy is due to differences in the data processing pipelines used by the GDC and other genomic portals. At the GDC, gene-level CNVs are derived from a mix of standardized pipelines. For TCGA projects, the CNV values are prioritized in the following order: SNP6 ABSOLUTE (LiftOver) > SNP6 ASCAT3 > WGS AscatNGS > SNP6 ASCAT2. All of these workflows produce absolute integer copy number values.
How are the five categories of copy number changes determined?
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The GDC begins with integer-level estimates of absolute copy number generated by either the ASCAT or ABSOLUTE pipeline. To establish a baseline, an integer-valued sample ploidy is computed as follows:
How does the GDC choose the default transcript for each variant?
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When a mutation overlaps multiple transcripts or genes, the GDC annotates all consequences in the all_effects column of the MAF file and in the CONSEQUENCE table on the Mutation Summary Page. One transcript is then selected as the default for detailed annotation and visualization where a single consequence is shown.
New Single Cell RNA-Seq Tool and CNV Categories Available in the GDC Data Portal
The GDC 2.4 Röntgen Release brings a range of new features aimed at enhancing data analysis and user experience.
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?
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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.
8000+ New WGS Variant Calls Now Available in the GDC!
The GDC is excited to announce the release of 8000+ new whole genome sequencing (WGS) variant calls as part of Data Release 42. Highlights of this release include:
New GDC Data Portal Features in the Pauling Release (GDC 2.3)
The latest GDC 2.3 Pauling Release introduces several new features designed to enhance user experience and improve data analysis.
Join the GDC Analysis Tool Challenge!
The NCI GDC Analysis Tool Challenge is a collaborative competition aimed at enhancing cancer research by integrating innovative analysis tools with the GDC.
In the GDC Data Portal, where is the histogram of top frequently mutated genes for a cohort?
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To view the top frequently mutated genes for a cohort, first build a cohort using the Cohort Builder and then select the Mutation Frequency tool in the Analysis Center