Advanced RNA-Seq and ChiP-Seq Data Analysis
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.
|Day 1 - Monday 11 May 2015|
|08:30||Overview of the course||Gabriella Rustici|
|09:15||Lecture: Introduction to the high-throughput sequencing data analysis workflows, with examples from R||Nicolas Delhomme & Bastian Schiffthaler|
|10:30||Lecture/Practical: Short read representation, manipulation and quality assessment||Nicolas Delhomme & Bastian Schiffthaler|
|11:30||Lecture/Practical: Genes and Genomes||Nicolas Delhomme & Bastian Schiffthaler|
|13:30||Lecture/Practical: Genes and Genomes (continued)||Nicolas Delhomme & Bastian Schiffthaler|
|14:00||Lecture: Mapping strategies for sequence reads||Ernest Turro|
|15:15||Practical: Mapping||Ernest Turro|
|Day 2 - Tuesday 12 May 2015|
|09:00||Lecture: Representing and manipulating alignments||Nicolas Delhomme & Bastian Schiffthaler|
|09:45||Practical: Representing and manipulating alignments||Nicolas Delhomme & Bastian Schiffthaler|
|10:45||Practical: Representing and manipulating alignments||Nicolas Delhomme & Bastian Schiffthaler|
|13:30||Lecture: Estimating expression over genes and exons||Nicolas Delhomme & Bastian Schiffthaler|
|14:30||Practical: Estimating expression over genes and exons||Nicolas Delhomme & Bastian Schiffthaler|
|15:45||Practical: Discovering novel transcribed regions||Nicolas Delhomme & Bastian Schiffthaler|
|16:30||Working without a reference genome||Nicolas Delhomme & Bastian Schiffthaler|
|Day 3 - Wednesday 13 May 2015|
|09:00||Lecture: Normalizing RNA-seq data||Alessandra Vigilante & Bori Gerle|
|10:00||Lecture: Differential expression||Alessandra Vigilante & Bori Gerle|
|11:15||Lecture: Multiple testing||TBC|
|13:30||Practical: Differential expression with RNA seq||Alessandra Vigilante & Bori Gerle|
|15:45||Practical: Differential expression with RNA seq (cont.)||Alessandra Vigilante & Bori Gerle|
|17:45||Lecture: Single Cell sequencing||Sarah Teichmann|
|Day 4 - Thursday 14 May 2015|
|09:00||Lecture: Introduction to ChIP-Seq data and analysis||Bori Gerle & Alessandra Vigilante|
|10:00||Lecture: Peak-callers||Bori Gerle & Alessandra Vigilante|
|10:45||Practical: Peak-callers||Bori Gerle & Alessandra Vigilante|
|13:30||Practical: ChIP-Seq data analysis with Bioconductor||Bori Gerle & Alessandra Vigilante|
|14:45||Practical: ChIP-Seq data analysis with Bioconductor||Bori Gerle & Alessandra Vigilante|
|16:00||Course closing comments and feedback session||All|
|16:20||Coach to Cambridge train station|
Application will be via a selection process therefore applicants should be aware that, in order to be considered for place on this course, they MUST complete:
A 300 word PDF document containing 3 sections:
- 100 word paragraph on your work history
- 100 word description of your current research interests
- 100 word biography
Incomplete applications will NOT be considered. Details of how to submit these extra documents will be provided on your application confirmation email.
Application registration closes 27 March 2015 (12:00 midday GMT). There will be a maximum of 30 participants on this course. Successful applicants will be notified by 10 April 2015 and will then be asked to confirm their place on the course by re-registering and paying the course fee.
Some of our courses are eligible for a discount for members of the Industry programme. For more information see: http://www.ebi.ac.uk/training/industry-programme-partners-discounted-rates
Please note that the registration fee includes:
- All meals listed in the agenda (breakfast, lunch, dinner and refreshment breaks)
- The evening meals will be at the Wellcome Trust Conference Centre
- A USB stick and access to course materials
- Use of a computer in the EMBL-EBI IT Training Room throughout the course
- Accommodation at the Wellcome Trust Conference Centre for 3 nights (11-14 May 2015)
To apply for this event please use the following link. Items marked * are mandatory. Incomplete applications will not be processed.