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How does the GDC choose the default transcript for each variant?

Submitted by gaheens on

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. 

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?

Submitted by gaheens on

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. 

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