Practical Workshop on High-Throughput Sequencing Data Analysis

Announced on October 9,2014

Due to the typhoon #19 the HTSA2014 original program has been changed

There may be some change to the speakers.

           We've compiled all the course material in a zip file and sent to participants via email shortly.

Important dates:

  • Workshop dates: 6 Oct - 10 Oct 2014
  • Application deadline: 15 July 2014
  • Notification of participation: 31 July 2014 (planned)

Workshop description:

This workshop aims to familiarize participants with the analysis of high-throughput sequencing (HTS) data and provide hands-on training on the latest analytical approaches. The course consists of a well balanced mixture of lectures, giving insight into how to analyze HTS data, and practicals, consisting of computational exercises that will enable participants to apply statistical methods to the analysis of RNA-seq and ChIP-seq data, under the guidance of the lecturers and teaching assistants.
Topics will include:
  • Quality control of sequencing reads
  • Data handling and visualization
  • Genomic mapping
  • Statistical concepts for data analysis
  • RNA-seq data analysis
  • ChIP-seq data analysis
  • Functional analyses
Lectures on analysis methodologies will be complemented by presentations from leading scientists, who will give first-hand examples of how biological knowledge can be gained from RNA-seq and ChIP-seq experiments.


  • Nicholas Luscombe, OIST, Japan
  • Jonathan Miller, OIST, Japan
  • Gabriella Rustici, University of Cambridge
  • Hidetoshi Saze, OIST, Japan


The 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 (basic understanding of the R syntax and ability to manipulate R objects) and the Unix/Linux operating system.

Invited Speakers/Instructors:

  • Benilton Carvalho, State University of Campinas (UNICAMP), Brazil
  • Nicolas Delhomme, Umeå University, Sweden
  • Alistair Forrest, RIKEN Center for Life Sciences Technologies, Japan
  • Hiroko Ohmiya, RIKEN Advanced Center for Computing and Communication, Japan
  • Anna Poetsch, Cancer Research UK, UK
  • Bastian Schiffthaler, Umeå University, Sweden
  • Alessandra Vigilante, University College London, UK 


Applicants are asked to provide a short description of their research project and their motivation to participate in this course. The full application form can be found here. As part of the application, you will need to provide contact details for a referee. A request for a letter of support will be automatically sent to the referee once you submit your application.

Application deadline is 15 July 2014.

Participants will be selected based on their applications. In order to be considered for a place on this workshop, applicants MUST complete the application form fully. Incomplete applications will NOT be considered.

OIST is deeply committed to the advancement of women in science, in Japan and worldwide. Women are strongly encouraged to apply.


How much does it cost?

It is free! OIST will cover all course and accommodation costs for accepted participants. In addition, we have a small number of travel scholarships to subsidise the cost of transport to Okinawa. Please see Application Form for more details. 

Do I need a visa?

OIST will help arrange a visa if needed.

Can I bring my own computer to the course?

Computers with the required software programmes will be provided to all participants during the time of the course. We strongly encourage participants to use these computers! If you prefer to bring your own laptop, please contact us at least 2 weeks prior to the course about required system specifications and installed software.

I need more information.

Please address inquiries and questions to the High-Throughput Sequence Analysis Workshop Team (



Day 1 - Mon 6 October   
9:00 - 9:30 Registration and welcoming  
9:30 - 10:00 Set-up time (if people bring their own computers)  
10:00 - 10:45 Lecture: Introduction to HTS technologies and their biological applications Nick Luscombe 
10:45 -11:00 Coffee break  
11:00 - 11:30 Lecture/practical: Introduction to Unix Hiroko Ohmiya/Alessandra Vigilante 
11:30 - 12:00 Lecture: Understanding the high-throughput sequencing data analysis workflow Nicolas Delhomme 
12:00 - 12:30 Lecture: Introduction to R/Bioconductor Hiroko Ohmiya/Nicolas Delhomme 
12:30 - 13:30  Lunch  
13:30 - 14:00 Lecture: Introduction to R/Bioconductor (continued) Hiroko Ohmiya/Nicolas Delhomme 
14:00 - 15:00 Lecture: File formats and QC Anna Poetsch 
15:00- 16:00 Practical: QC with fastQC and R/Bioconductor Anna Poetsch/Alessandra Vigilante 
16:00 - 16:15 Coffee break  
16:15 - 17:30 Lecture: Mapping strategies, tools and file formats Anna Poetsch 
17:30 - 18:00 Recap on the HTS workflows + Q&A session  
18:00 - 18:40 Talk: Decoding the genome of a non-model organism Chuya Shinzato 
20:00-22:00 Dinner, followed by Q&A session about evening's presentation  
Day 2 - Tue 7 October   
09:00 - 09:45 Lecture: Representing and manipulating alignments   Nicolas Delhomme / Bastian Schiffthaler 
09:45 - 10:30 Practical: Representing and manipulating alignments   
10:30 - 10:45 Tea/coffee break  
10:45 - 12:30 Practical: Representing and manipulating alignments (continued) Nicolas Delhomme / Bastian Schiffthaler 
12:30 - 13:30 Lunch  
13:30 - 14:30 Lecture: Estimating expression over genes and exons Nicolas Delhomme / Bastian Schiffthaler 
14:30 - 15:30 Practical:  Estimating expression over genes and exons Nicolas Delhomme / Bastian Schiffthaler 
15:30 - 15:45 Tea/coffee break  
15:45 - 16:30 Practical: Discovering novel transcribed regions Nicolas Delhomme / Bastian Schiffthaler 
16:30 - 17:00 Q&A session   
19:00 - 21:00 Poster session I (with dinner)  
Day 3 - Wed 8 October   
9:00 - 10:30 Lecture: Statistical concepts and methodologies for data analysis Benilton Carvalho 
10:30 - 10:45 Tea/coffee break  
10:45 - 12:30 Practical: Statistical concepts and methodologies for data analysis Benilton Carvalho 
12:30 - 13:30 Lunch  
13:30 - 19:00 Excursion  
20:00 - 22:00 Poster session II (with dinner)  
Day 4 - Thu 9 October   
09:00 - 09:45 Lecture: Normalizing RNA-seq data Alessandra Vigilante 
09:45 - 10:30 Lecture: Differential expression Alessandra Vigilante 
10:30 - 10:45 Tea/coffee break  
10:45 - 12:30 Practical: Differential expression with RNA seq Anna Poetsch/Alessandra Vigilante 
12:30 - 13:30 Lunch  
13:30 - 15:30 Practical: Differential expression with RNA seq (continued) Anna Poetsch/Alessandra Vigilante 
15:30 - 15:45 Tea/coffee break  
15:45 - 17:00 Lecture: Downstream functional analysis Gabriella Rustici 
17:00 - 18:00 Talk: The FANTOM5 project  - genome wide atlases of promoters and enhancers Alistair Forrest 
18:00 - 19:00 Practical: Interactive visualization and analysis of large-scale sequencing datasets using ZENBU Jessica Severin 
20:00 - 22:00 Dinner  
Day 5 - Fri 10 October   
09:00 - 10:00 Lecture: Introduction to ChIP-Seq data and analysis Anna Poetsch 
10:00 - 10:30 Lecture: Peak-callers Anna Poetsch 
10:30 - 10:45 Tea/coffee break  
10:45 - 12:30 Practical: Peak-callers Anna Poetsch/Alessandra Vigilante 
12:30 - 13:30 Lunch  
13:30 - 14:00 Talk:  OIST - history, mission and recent developments George Iwama 
14:00 - 14:30 Practical: ChIP-Seq data analysis with Bioconductor Anna Poetsch/Alessandra Vigilante 
14:30 - 14:45 Tea/coffee break  
14:45 - 16:30 Practical: ChIP-Seq data analysis with Bioconductor Anna Poetsch/Alessandra Vigilante 
16:30 - 17:30 Talk: HTS - What's next? Nick Luscombe 
17:30 Course feedback and wrap up All 
from 19:30 Conference dinner