RNA-Seq and ChiP-Seq Data Analysis

Date: Wednesday, July 9, 2014 to Thursday, July 10, 2014
Venue: European Bioinformatics Institute, CB10 1SD, United Kingdom
Registration Opens Date: Wednesday, May 7, 2014
Participation: First come, first served

*Registration for this course has now closed, the maximum number of participants has been reached*

If you want to be placed on the waiting list in case of a cancellation please email training@dixa-fp7.eu

Is it right for me?

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. 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.

What will I learn?

Lectures will give insight into how biological knowledge can be generated from RNA-seq and ChIP-seq 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 RNA-seq and ChIP-seq data under the guidance of the lecturers and teaching assistants. Familiarity with the technology and biological use cases of high throughput sequencing is required, as is some experience with R/Bioconductor.

What will it cover?

The course covers data analysis of RNA-Seq and ChIP-Seq experiments.

Topics will include: alignment, data handling and visualisation, region identification, differential expression, data quality assessment and statistical analysis, using R/Bioconductor.

Course material

The course material is available through the link below:


Course participants have been sent the login details by email.

If you did not participate in the course but would like access to the material please email training@dixa-fp7.eu to request access.


Day 1 - Wednesday 9 July - Introduction to sequencing and ChIP-seq analysis

09:00 - 09:10   Welcome and introduction                                                                       

09:10 - 10:00   Lecture: Next generation sequencing overview (+exercise)                

10:00 - 10:15   Tea/coffee break        

10:15 - 10:45   Lecture & Practical: NGS quality control      

10:45 - 12:00   Lecture & Practical: Sequence alignment       

12:00 - 13:00   Lunch 

13:00 - 13:30   Lecture: Introduction to ChIP-seq     

13:30 - 15:00   Practical: ChIP-seq - peak calling and annotation      

15:00 - 15:15   Tea/coffee break        

15:15 - 17:00   Practical: ChIP-seq - motif analysis    

17:00 - 17:30   DiXa project overview            

18:45 - 19:30   Pre-dinner drinks, Hinxton Hall        

19:30   Workshop dinner Hinxton Hall

Day 2 - Thursday 10 July- RNA-seq data analysis

09:00 - 10:00   Lecture: Benchmarking of aligners for sequencing data       

10:00 - 10:15   Tea/coffee break        

10:15 - 11:30   Lecture: Introduction to RNA-seq     

11:30 - 12:30   Practical: RNA-seq - Alignment and splice junction identification   

12:30 - 13:30   Lunch 

13:30 - 14:15   Practical: RNA-seq - Transcriptome assembly            

14:15 - 15:15   Practical: RNA-seq analysis - Differential expression analysis          

15:15 - 15:30   Tea/coffee break        

15:30 - 16:00   Practical: RNA-seq analysis - Differential expression analysis          

16:00 - 17:00   Lecture: On the empirical evaluation of RNA-seq gene profiling pipelines   

17:00   Close


*Registration for this course has now closed, the maximum number of participants has been reached*

If you want to be placed on the waiting listin case of a cancellation please email training@dixa-fp7.eu

The registration fee for this course is £100 and includes:

  • Lunch, and refreshment breaks
  • Course drinks & dinner on the 9th July 2014
  • Course materials
  • Use of a computer in the IT Training Room throughout the course

Event Speakers

Nuno Fonseca, EMBL-EBI
Remco Loos, EMBL-EBI
Nils Koelling , EMBL-EBI
Myrto Kostadima, Cambridge University
Botond Sipos, EMBL-EBI, United Kingdom
Maria Xenophontos, EMBL-EBI