skip to navigation skip to content
- Select training provider - (Bioinformatics)
Mon 30 Nov - Wed 2 Dec 2015
09:30 - 17:30

Venue: Bioinformatics Training Room, Craik-Marshall Building

Provided by: Bioinformatics


Booking

Bookings cannot be made on this event (Event is completed).


Other dates:

No more events

[ Show past events ]



Register interest
Register your interest - if you would be interested in additional dates being scheduled.


Booking / availability

Analysis of high-throughput sequencing data with Bioconductor
Prerequisites

Mon 30 Nov - Wed 2 Dec 2015

Description

This course provides an introduction to the tools available through the Bioconductor project for manipulating and analysing high-throughput sequencing (HTS) 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 visualize HTS data, which can be applied to any type of sequencing experiment.

The course timetable is available here.

Please note that if you are not eligible for a University of Cambridge Raven account you will need to book by linking here.

Target audience
  • Graduate students, Postdocs and Staff members from the University of Cambridge, Affiliated Institutions and other external Institutions or individuals
  • Further details regarding eligibility criteria are available here
  • Further details regarding the charging policy are available here
Prerequisites
  • A knowledge of current sequencing technologies, data formats (e.g. fastq and bam) and alignment
  • A 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
Sessions

Number of sessions: 3

# Date Time Venue Trainers
1 Mon 30 Nov 2015   09:30 - 17:30 09:30 - 17:30 Bioinformatics Training Room, Craik-Marshall Building map Mark Dunning,  Oscar Rueda,  Bernard Pereira,  Ines de Santiago
2 Tue 1 Dec 2015   09:30 - 17:30 09:30 - 17:30 Bioinformatics Training Room, Craik-Marshall Building map Mark Dunning,  Oscar Rueda,  Bernard Pereira,  Ines de Santiago
3 Wed 2 Dec 2015   09:30 - 17:30 09:30 - 17:30 Bioinformatics Training Room, Craik-Marshall Building map Mark Dunning,  Oscar Rueda,  Bernard Pereira,  Ines de Santiago
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
Aims

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 HTS results with Bioconductor.
  • Importing ChIP-Seq peaks and performing downstream analysis.
  • Integrating ChIP-Seq and RNA-Seq data.
Format

Presentations and practicals

Duration

3

Frequency

A number of times per year

Related courses
Theme
Bioinformatics

Booking / availability