Recipe: Identify and visualize expressed transcripts in RNA-Seq data
4 videos • 1,027 views • by GenomeSpace This recipe provides an outline of one method to identify and visualize genes and isoforms that are highly expressed in RNA-Seq data. Given a set of raw RNA-Seq reads, the goal is to align the reads to a reference genome, estimate expression abundance levels for reference genes and isoforms, filter out low-expressed genes and isoforms, and visualize the read alignments and their expression levels. In particular, this Recipe uses the UCSC Table Browser to retrieve a reference genome to align RNA-Seq reads against. We also uses several modules in GenePattern to align the reads against the reference genome, and to identify differentially expressed genes when comparing two conditions. Finally, we use IGV to visualize the differentially expressed genes.