Advanced sequence analysis - Illumina Sequencing

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People landing here might also be interested in my October 2014 course in Bioinformatics for transcriptomics. This course will include RNA-seq data analysis in R.

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Course provider:
University of Manchester
Contact:
Heather Vincent (heather.vincent@manchester.ac.uk)
Summary:
This advanced bioinformatics course is suitable for those with a first degree in either a biological science or in computer science. It covers the most recent methods for biological sequence analysis. It could be taken as an individual short course, for professional development, and could be combined with one of more units from our theme in Computational Systems Biology :-

Bioinformatics for Systems Biology
Mathematics for metabolic modelling
Computational Systems Biology
Bioinformatics for transcriptomics.

A student successfully completing four units could graduate with a Postgraduate Certificate. Those people who wish to complete the Masters degree will be required to successfully complete six modules and a research project.
Syllabus:
This course provides an introduction to the data and methods for projects requiring Next Generation Sequence data analysis. The examples are from Illumina sequencing. It will cover :
  • genes, genomes and genome sequencing;
  • technologies for high throughput sequencing;
  • understanding the data;
  • mapping to a genome;
  • RNA-seq : quantification and differential expression;
  • ChIP-seq.

For practical work students will have accounts on our Galaxy server.
Assessment:

The assessment methods:

  1. There will be a tutorial exercise for each of the above topics.  These exercises will be brief: they are included as one means of maintaining a dialogue between all of our bioinformatics students. This exchange is particularly important for bioinformatics, which spans traditional academic disciplines.
  2. The main assessment will be a data analysis project and report.  At the discretion of the examiners, you may also be required to attend a viva voce examination.
Further details:
If you do not have much previous experience with the main bioinformatics services, databases and software, you might find it useful to prepare yourself by working through 'A practical guide to Bioinformatics' in EMBER. This is a very useful self-study introduction to bioinformatics. Please let me know if you have any problems in accessing EMBER.

All the learning materials that you need will be provided within the Moodle Virtual Learning Environment (VLE). The tools provided will allow you to navigate and search through the specially written textbook, practical exercises in bioinformatics and references to other useful texts and URLs. The textbook is provided as a set of web pages. It will be used to provide the necessary background to the focus of the course, which is problem-based learning.
You will interact with your tutor, and with other learners, through bulletin boards. Our students and graduates can continue to use the programme bulletin boards after a course has ended, so we now have a large and supportive online community.
Technical requirements:
This module is entirely web-based, so a reliable internet connection is essential.
References:
Veeramah, K. (2009), "Next generation sequencing technologies", in Veeramah, K. (ed.), Introduction to Human Genetics: Fundamentals and latest advances, The Biomedical & Life Sciences Collection, Henry Stewart Talks Ltd, London
(Full access is available to registered students.)

Lawrence E. Hunter
The Processes of Life: An Introduction to Molecular Biology
MIT Press
ISBN-13: 978-0262013055

The above book, written for computer scientists, will be a useful reference text for many of our bioinformatics courses. An online textbook, and recommendations for additional reading, are provided within the Virtual Learning Environment.

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Updated 27 March 2014 by Heather Vincent