RNA-Seq and ChiP-Seq Data Analysis Course - Campinas, Brazil - 07-10 April 2014

Date:

 Monday 7 Thursday 10 April 2014

Venue: 

Faculdade de Ciencias Medicas, Campinas - R. Tessália Vieira de Camargo, Campinas,  - SP,  13083-887, Brazil

Application opens: 

Tuesday 11 March 2014

Application deadline: 

Friday 28 March 2014

Participation: 

Open application with selection

Contact: 

Johanna Langrish

Registration closed

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Course Overview

This course will 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 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.

Audience

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.

Learning outcomes

After this course you will be able to:

  • Use bioinformatics tools to analyses RNA-Seq and ChIP-Seq data
  • Discuss methods for processing NGS data
  • Evaluate a range of different analytical approaches

Programme

Time Topic Trainer
Day 1 - Monday 07 April 2014
08:30 - 09:15 Overview of the course G. Rustici
09:15 - 10:15 Lecture: Introduction to the high-throughput sequencing data analysis workflows, with examples from R B. Carvalho
10:15 - 10:30 Tea/Coffee Break  
10:30 - 11:00 Practical: Introduction to R/Bioconductor B. Carvalho
11:00 - 11:45 Lecture: Short read representation, manipulation and quality assessment N. Delhomme
11:45 - 12:30 Practical: Short read representation, manipulation and quality assessment N. Delhomme
12:30 - 14:30 Lunch
14:30 - 15:00 Lecture: Mapping strategies for sequence reads B. Carvalho
15:00 - 17:30 Practical: Mapping B. Carvalho
17:30 - 18:00 Q&A Session
Day 2 - Tuesday 08 April 2014
09:00 - 10:00 Lecture: Estimating expression over genes and exons N. Delhomme
10:00 - 10:15 Tea/coffee break  
10:15 - 11:15 Practical: Estimating expression over genes and exons N. Delhomme 
11:15 - 12:30 Practical: Discovering novel transcribed regions N. Delhomme
12:30 - 14:30 Lunch  
14:30 - 16:00 Lecture: Statistical concepts and methodologies for data analysis B. Carvalho
16:00 - 16:15 Tea/Coffee Break  
16:15 - 17:30 Practical: Statistical concepts and methodologies for data analysis B. Carvalho
17:30 - 18:00 Q&A Session
Day 3 - Wednesday 09 April 2014
09:00 - 10:00 Lecture: RNA-seq analysis R. Loos/M. Kostadima
10:00 - 11:00 Practical: Transcriptome assembly R. Loos/M. Kostadima
11:00 - 11:15 Tea/Coffee Break
11:15 - 12:30 Practical: Differential gene expression R. Loos/M. Kostadima
12:30 - 13:30 Lunch  
13:30 - 14:30 Practical: Differential gene expression R. Loos/M. Kostadima
14:30 - 16:00 Lecture & Practical: Differential exon usage R. Loos/M. Kostadima
16:00 - 16:15 Tea/Coffee Break  
16:15 - 17:30 Lecture: Downstream functional analysis G. Rustici
17:30 - 18:00 Q&A Session  
Day 4 - Thursday 10 April 2014
09:00 - 10:00 Lecture: Introduction to ChIP-Seq data and analysis R. Loos/M. Kostadima
10:00 - 10:30 Practical: Peak Calling R. Loos/M. Kostadima
10:30 - 10:45 Tea/Coffee Break
10:45 - 12:30 Practical: Peak annotation R. Loos/M. Kostadima
12:30 - 13:30 Lunch
13:30 - 14:30 Practical: Motif analysis R. Loos/M. Kostadima
14:30 - 14:45 Tea/Coffee Break  
14:45 - 16:30 Lecture & Practical: Integrative analysis R. Loos/M. Kostadima
16:30 - 17:00 Q&A Session  

Additional information:

Please note: The official language for this course is English.  To benefit from this course, it is essential that participants are able to communication in English.