RNA-Seq refers to high throughput sequencing methods that probes the entire transcriptomic landscape of a given tissue or sample of interest. The data acquired from such experiments can be used to explore the overall RNA profile of a sample as well as comparing samples under various conditions. While extremely powerful, RNA-Seq is susceptible to numerous experimental pitfalls and requires intimate knowledge of the experimental procedures and data analysis methods. When conducted properly RNA-Seq can reveal information about gene/transcript expression, splicing and the effects of mutations. In this session we will take a thorough look at a comprehensive RNA-Seq pipeline, from sample processing methods to final differential expression analysis. Relevant R / BioConductor packages will be introduced. We will have the opportunity to investigate numerous quality control metrics, perform genomic alignment, differential expression and pathway enrichment analysis. We will cover several “gotcha”s and common mistakes in experimental design and data analysis. Basic familiarity with R and Linux command line will be beneficial but not required. All necessary commands and parameters will be explained during the class. Participants will be offered hands-on practice in which they will use RStudio to run R/BioConductor scripts for data analysis as well as the Integrative Genomic Viewer (IGV) software to visualize genomic data on their laptopsLevel: IntermediateLength: 3 HoursFormat: Lecture + Hands-onPrerequisites: Basic R and Linux beneficial but not required :: Tues. June 4 ::09:00 to 12:00---------------------------------------------------------------------Registration linkCompute Ontario Summer School is a series of online courses on Advanced Research Computing, High Performance Computing, Research Data Management, and Research Software. It runs from June 3 to June 21, 2024. The courses are delivered each workday from 9:00am to 4:30pm (EDT) with a lunch break,  in two parallel streams. Pick-and-choose the course(s) you want to attend. Registration is free. Please register early as  courses have a limited capacity. The Summer School is jointly delivered by SHARCNET, SciNet, Centre for Advanced Computing, in collaboration with the Alliance and RDM experts from across Ontario and Canada.