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Johns Hopkins University

Bioinformatics Methods for Transcriptomics

Johns Hopkins University via Coursera

Overview

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.

Syllabus

  • 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

Taught by

Liliana Florea, PhD

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