High-throughput sequencing of RNA libraries (RNA-seq) has become increasingly common and largely supplanted gene microarrays for transcriptome profiling. When processed appropriately, RNA-seq data has the potential to provide a considerably more detailed view of the transcriptome. The CBW has developed a 3-day course providing an introduction to RNA-seq data analysis followed by integrated tutorials demonstrating the use of popular RNA-seq analysis packages. The tutorials are designed as self-contained units that include example data (Illumina paired-end RNA-seq data) and detailed instructions for installation of all required bioinformatics tools (HISAT, StringTie, etc.). De novo assembly of transcripts will be covered.

Participants will gain practical experience and skills to be able to:

Perform command-line Linux based analysis on the cloud
Assess quality of RNA-seq data
Align RNA-seq data to a reference genome
Estimate known gene and transcript expression
Perform differential expression analysis
Discover novel isoforms
Assemble RNA-seq data into transcripts
Visualize and summarize the output of RNA-seq analyses in R