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.

• Module 1: Course Introduction and Gene expression analysis of RNA-seq data
• Module 2: Alternative splicing analysis of RNA-seq data
• Module 3: Transcriptome reconstruction with long RNA sequencing reads
• Module 4: Differential expression and differential splicing analysis with long RNA sequencing reads