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Analysis of high-throughput sequencing data with Bioconductor


This course provides an introduction to the tools available through the Bioconductor project for manipulating and analysing high-throughput sequencing data. We will present workflows for the analysis of ChIP-Seq and RNA-seq data starting from aligned reads in 'bam' format. We will also describe the various resources available through Bioconductor to annotate and visualise NGS data, which can be applied to any type of sequencing experiment.



Mark Dunning, CRUK

Oscar Rueda, CRUK

Bernard Pereira, CRUK

Ines de Santiago, CRUK


Audience and Prerequisites

  • very basic knowledge of UNIX would be an advantage, but nothing will be assumed and extremely little will be required. Attendees should be comfortable with using the R statistical language to read and manipulate data, and produce simple graphs.
  • Graduate students, Postdocs and Staff members from the University of Cambridge, Affiliated Institutions and other external Institutions or individuals


Syllabus, Tools and Resources

During this course you will learn about:

  • Quality assessment of raw sequencing reads and aligned reads using R.
  • Differential expression analysis using edgeR and Deseq.
  • Annotating NGS results with Bioconductor.
  • Importing ChIP-Seq peaks and performing downstream analysis.
  • Integrating ChIP- and RNA-seq data.


Learning Objectives

After this course you should be able to:

  • Know what tools are available in Bioconductor for NGS analysis and understand the basic object-types that are utilised
  • Given a set of gene identifiers, find out whereabouts in the genome they are located, and vice-versa (i.e. go from genomic coordinates to genes)
  • Produce a list of differentially-expressed genes from an RNA-seq experiment
  • Import a set of ChIP-seq peaks and investigate their Biological context



Book Here



Day 1

Introduction to NGS sequencing Mark Dunning
Strings and Ranges Mark Dunning

Copy-Number Analysis Oscar Rueda
Linear Models and Experimental Design Oscar Rueda
Day 2

Introduction to RNA-seq Mark Dunning
RNA-seq Analysis Mark Dunning, Oscar Rueda
Afternoon Genomic Annotation and Visualisation Mark Dunning, Shamith Samarajiwa
Day 3
Morning Introduction to ChIP-seq Suraj Menon, Shamith Samarajiwa
ChIP-Seq Analysis Suraj Menon, Shamith Samarajiwa
Afternoon Downstream analysis of ChIP data Suraj Menon, Shamith Samarajiwa