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Tue 15 Mar - Fri 18 Mar 2016
09:30 - 17:30

Venue: Bioinformatics Training Room, Craik-Marshall Building, Downing Site

Provided by: Bioinformatics


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Introduction to high-throughput sequencing data analysis

Tue 15 Mar - Fri 18 Mar 2016

Description

This course provides an introduction to high-throughput sequencing (HTS) data analysis methodologies. Lectures will give insight into how biological knowledge can be generated from RNA-seq, ChIP-seq and DNA-seq experiments and illustrate different ways of analyzing such data. Practicals will consist of computer exercises that will enable the participants to apply statistical methods to the analysis of RNA-seq, ChIP-seq and DNA-seq data under the guidance of the lecturers and teaching assistants. It is aimed at researchers who are applying or planning to apply HTS technologies and bioinformatics methods in their research.

The timetable can be found here.

Please note that if you are not eligible for a University of Cambridge Raven account you will need to Book or register Interest 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

The course will include an introduction to Unix and R but to get the most out of the course we suggest acquiring:

  • Basic experience of command line UNIX
  • Sufficient UNIX experience might be obtained from one of the many UNIX tutorials available online.
  • Basic knowledge of the R syntax
  • For a real beginner's introduction into R see here. More advanced R instructions can be found at Quick-R or An Introduction to R
Sessions

Number of sessions: 4

# Date Time Venue Trainers
1 Tue 15 Mar 2016   09:30 - 17:30 09:30 - 17:30 Bioinformatics Training Room, Craik-Marshall Building, Downing Site map M.A. Kostadima,  Roman Kreuzhuber,  Frederik Otzen Bagger
2 Wed 16 Mar 2016   09:30 - 17:30 09:30 - 17:30 Bioinformatics Training Room, Craik-Marshall Building, Downing Site map M.A. Kostadima,  Romina Petersen,  M. Xenophontos
3 Thu 17 Mar 2016   09:30 - 17:30 09:30 - 17:30 Bioinformatics Training Room, Craik-Marshall Building, Downing Site map M.A. Kostadima,  Nils Koelling
4 Fri 18 Mar 2016   09:30 - 17:30 09:30 - 17:30 Bioinformatics Training Room, Craik-Marshall Building, Downing Site map Dr Stefan Gräf
Aims

During this course you will learn about:

  • HTS technology
  • Quality control of raw reads: FASTQC and fastx toolkit
  • Considerations on experiment design for ChIP-seq and RNA-seq
  • Read alignment to a reference genome: Bowtie and Tophat
  • File format conversion and processing: UCSC tools and samtools
  • Peak calling: MACS
  • Motif analysis: MEME
  • Quantification of expression and guided transcriptome assembly: Cufflinks
  • Analysis of variants
Format

Presentations, demonstrations and practicals

Duration

4

Frequency

A number of times per year

Theme
Specialized Training

Booking / availability