RNA-Seq Differential Expression Analysis

For initial inspection of RNA-Seq experiments, the CCCB offers a suite of standard offerings based around differential analysis of transcript expression, including:

  • Quality report produced by the Broad Institute's RNA-SeQC tool
  • Differential expression analysis performed by DESeq
  • Integer read counts (determined via subRead's featureCounts tool) for reads mapped to the reference genome.  Includes normalization (performed by DESeq) to account for library size.
  • A heatmap of the most highly expressed genes, including basic hierarchical clustering
  • Gene-set enrichment analysis for gene sets in the canonical pathways (GSEA, Broad Institute)

In addition to these basic offerings, the CCCB can consult on more detailed and specific analyses tailored to the needs of your RNA-Seq study.  Common additions include differential isoform expression and splice variant detection and quantification.


Basic mRNASeq Workflow