Bioinformatics Methods for Transcriptomics

This course will cover bioinformatics methods for analyzing transcriptomic RNA sequencing data generated with the short read (RNA-seq) and long read (PacBio, ONT) sequencing. In its four modules, the course addresses the core transcriptomics questions: What are the genes and transcripts expressed in a given sample or condition of an experiment?, What are their expression levels?, and What are the differences in gene expression and splicing patterns between conditions? It provides hands-on instruction on how to use popular and/or emerging tools such as STAR, PsiCLASS, DESeq2, rMATS, MntJULiP, Minimap2 and IsoQuant. This is an intermediate level course, and assumes basic knowledge on using command line bioinformatics tools in a Unix-type environment

• Analyze RNA sequencing data using advanced tools like STAR and DESeq2
• Identify expressed genes and transcripts in samples
• Compare expression and splicing patterns between conditions
• Use bioinformatics software in Linux environments for analysis
• Interpret transcriptomic and splicing results accurately

• Basic familiarity with bioinformatics concepts and terminology
• Willingness to engage in applied exercises or case-based work