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Analysis of high-throughput sequencing data

5 – 10 September 2016 | Cambridge, United Kingdom

Registration deadline

5 June 2016

Abstract submission deadline

5 June 2016

Selected participants will be notified by

20 June 2016

Payment deadline

20 July 2016

Apply now!

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About the practical course

Course overview

The aim of this course is to familiarise the participants with advanced data analysis methodologies and provide hands-on training on the latest analytical approaches. Lectures will give insight into how biological knowledge can be generated from High-throughput sequencing 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 sequencing data under the guidance of the lecturers and teaching assistants.


This course is aimed at advanced PhD students and post-doctoral researchers who are applying or planning to apply high throughput sequencing technologies and bioinformatics methods in their research. Familiarity with the technology and biological use cases of high throughput sequencing is required, as is some experience with R/Bioconductor. Syllabus, tools and resources During this course you will learn about:
  • High-throughput sequencing 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: STAR and BWA
  • File format conversion and processing
  • Peak calling: MACS, USeq and SISSR
  • Motif analysis: MEME
  • Quantification of expression and differential expression analysis and differential exon usage: R, edgeR, DESeq2, DEXSeq

Learning outcomes

After this course you should be able to:
  • Understand the advantages and limitations of the high-throughput assays presented
  • Assess the quality of your datasets
  • Compare and apply appropriate short read aligners
  • Perform alignment and peak calling of ChIP-seq datasets
  • Perform alignment and quantification of expression for RNA-seq datasets
  • Understand the challenges of single cell sequencing analysis






Registration deadline

5 June 2016

Abstract submission deadline

5 June 2016

Selected participants will be notified by

20 June 2016

Payment deadline

20 July 2016



£340 (GBP)


£340 (GBP)


£760 (GBP)





Registration includes:

  • 6 nights of accommodation from Sunday 4th of September to Friday 9th of September included
  • All meals
  • Course materials

The registration fee does not include travel to and from the venue or any extra nights of accommodation after the course.  

Selection Criteria

  • Applicants will be selected based on:
  • Relevance of their current research/work to the objectives of the course

  • Knowledge of the programming language/system (R and Unix) used in the practical sessions
  • Quality of their application
  • Scientific excellence of the previous research
  • Priority will be given to applicants with HTS data ready to be analyzed

Application Guidelines

Please provide a brief description of your research, focusing on how you are using, or planning to use, HTS applications in your work. Abstracts should be no longer than 100 words.


There will be no poster sessions but participants will be given 5 minutes each to give a brief presentation about their work. Further instructions will be provided to selected participants.


Successful applicants will be emailed payment details for the online credit card system.




Cathy Hemmings

Phone: +44 (0)1223 333614




venue map


University of Cambridge

Bioinformatics Training Facility

Craik-Marshall Building

Downing Site

University of Cambridge



United Kingdom


Accommodation Details

  • Participants will be accommodated at the University of Cambridge’s Gonville & Cauis College, in the Harvey Court Building on the West Road site, in single occupancy en-suite rooms.
  • On arrival at the College, they should report to the Porters’ Lodge. The Porters' Lodge is manned 24 hours a day.
  • Check in will be from 2.30pm on Sunday 4th September 2016 and check out by 10.00am on Saturday 10th September 2016.
  • Breakfast will be served in the Harvey Court Dining Room between 8.15 am - 9.15 am
  • Evening meals will be served in the Harvey Court Dining Room
  • All accommodation is based on standard single occupancy en-suite rooms.
  • Refundable deposits may be required for keys or swipe cards. Please have the necessary £5/£10 ready on arrival.
  • A formal dinner will be held on one of the evenings.

Travel Information

Directions to Cambridge

By Air

Cambridge is within easy reach of several London’s airports.  London Stansted is located just 30 miles to the South of the city, with easy access by train and coach.  Cambridge is also within easy reach of London Heathrow and London Gatwick.

By Train

There are services to Cambridge from both King's Cross and Liverpool Street in London. Non-stop trains from King's Cross take about 45 minutes. On trains from the North towards London, change at Peterborough for connections to Cambridge. For more detailed train information from your nearest station use the rail planner here.

By Coach

There are hourly coach services from London Victoria, and less frequent coaches from some airports and from other major cities. These stop at Drummer Street Bus Station, or on Parkside; both these termini are very close to the course venue. Check the National Express website for bus details.

By Car

This is not recommended, because of severe traffic problems, and expensive parking charges. Unfortunately, there is no on-site parking available for visitors to the University. Park and ride services operate from some peripheral sites. For details see the Cambridge City Council Park & Ride website.