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Johns Hopkins University

Bioinformatics Methods for Transcriptomics

Johns Hopkins University via Coursera

Overview

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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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