CRUK: Using Genome Browsers to visualise high-throughput data

Modern genomics technologies are able to produce large volumes of data that often leave researchers feeling overwhelmed and unsure of how to begin the process of biological interpretation.

In this course, we explain the common file formats generated by sequencing technologies and how they can be manipulated and explored by non bioinformaticians. The main tools that we will use are the Integrative Genomics Viewer (IGV) and University of Santa Cruz (UCSC) genome browser.

This event is part of a series of training courses organized in collaboration with Dr. Mark Dunning at CRUK Cambridge Institute. The materials for the course were developed in collaboration with Dr. Thomas Carroll from the MRC CSC.

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

• 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

Number of sessions: 1

After this course you should be able to:

• Use IGV to explore your own sequencing data
• Navigate to, and explore, regions of interest in a reference genome
• Retrieve annotation for a genomic region

During this course you will learn about:

• How to run IGV
• Navigating the IGV interface and moving around genomes
• Loading and visualising data in IGV
• Exploring RNA-seq data in IGV
• Understanding the UCSC interface
• Basic searches in USCC
• Viewing tracks in UCSC
• Retrieving DNA sequences and annotation

Presentation and demonstrations

• This course requires you to bring a laptop that can access wireless internet. Users with a Raven password will be able to access the Eduroam network. Otherwise users will be given access to the Cancer Research Uk wireless network for the duration of the course.
• You may need to install specific software on our laptop prior to the course. Further announcements will follow with details of the software requirements for this course. If you need advice on software installation, please contact the course organiser, Mark Dunning at Mark.Dunning@cruk.cam.ac.uk
• Refreshments and lunches are not provided. Participants will be able to purchase refreshments and lunches from the building vending machines and canteen by charging money on their security/visitor card. Please note that additional options are also available from the main Addenbrookes food court.

• Please arrive 20 minutes prior to the advertised start time. The Cancer Research Uk Cambridge Institute is not open to the public and the training room is located beyond security barriers. Therefore you should allow time to sign-in at Reception.
• Upon arrival at Reception, you will be issued with a pink security/visitor card and lanyard, which you will need to pass the security barriers and access the training room. You should wear this card around your neck at all times.
• The security/visitor card is also used to purchase refreshments and food from the canteen or vending machines. You will need to 'charge' the card with money before you can use it. Any unused money left on the card will be refunded at the end of the course.

One full day session

Once a year

• CRUK: Introduction to Statistical Analysis using R Commander
• Introduction to Unix shell