Important dates:

  • Workshop dates: 30 Sep - 4 Oct 2013
  • Application deadline: 31 May 2013
  • Notification of participation: 30 June 2013
  • Deadline for your photograph and short biography for our website: end of July 2013

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.
 

Organizers:

  • Nicholas Luscombe, OIST, Japan
  • Jonathan Miller, OIST, Japan
  • John Marioni, EMBL European Bioinformatics Institute, UK
  • Mikita Suyama, Kyushu University, Japan
  • Kathi Zarnack, CRUK London Research Institute, UK 

Prerequisites:

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:

  • Piero Carninci, Riken Center for Life Sciences Technologies, Japan
  • Byung-Kwan Cho, Korean Advanced Institute of Science & Technology, Korea
  • Jing-Dong Jackie Han, CAS-MPG Institute for Computational Biology, Shanghai, China
  • Nicolas Delhomme, Umeå University, Sweden
  • Benilton Carvalho, State University of Campinas (UNICAMP), Brazil
  • Gabriella Rustici, EMBL European Bioinformatics Institute, UK 
  • Bori Gerle, University College London, UK 

Application:

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 31st May 2013.

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.

Room and board will be covered for all workshop participants. Cost of transportation to Okinawa will be subsidised up to 100%. OIST will help with arranging visas, if necessary. OIST is deeply committed to the advancement of women in science, in Japan and worldwide. Women are strongly encouraged to apply.

Please address inquiries and questions to the High-Throughput Sequence Analysis Workshop Team (htsa2013@oist.jp).

FAQ:

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.

 

Program:

Day 1 - Introduction and Quality Control
Primary instructors: Nicolas Delhomme, Benilton Carvalho
 
Lectures and practicals: 
  • Introduction to NGS technologies and applications
  • Introduction to Linux, R and Bioconductor
  • File formats 
  • QC with fastQC and R/Bioconductor 
 
Day 2 - Mapping and data processing
Primary instructors: Kathi Zarnack, Nicolas Delhomme
 
Lectures and practicals: 
  • Mapping strategies, tools and output formats
  • Tour through the Bioconductor packages
 
Day 3 - Statistics and Normalisation
Primary instructors: Benilton Carvalho, John Marioni
 
Lectures and practicals: 
  • Statistical concepts and methodologies for data analyses
  • Normalisation of RNA-seq data

 

Day 4 - Differential expression and exon usage
Primary instructors: John Marioni, Kathi Zarnack, Nicolas Delhomme
 
Lectures and practicals: 
  • Differential expression 
  • Multiple testing
  • Differential expression with RNA-seq data 
  • RNA-seq analyses using easyRNAseq
  • Downstream functional analyses (including GO, etc)
 
Day 5 - ChIP-seq analyses
Primary instructors: Bori Gerle, Kathi Zarnack
 
Lectures and practicals: 
  • Introduction to ChIP-seq
  • ChIP-seq analysis
  • Differential analysis of ChIP-seq data

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