EMBO Practical Course on Analysis of High-Throughput Sequencing Data
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 (basic understanding of the R syntax and ability to manipulate R objects) and the Unix/Linux operating system.
What will it cover?
The course covers data analysis of RNA-Seq and ChIP-Seq experiments.
Topics will include: short read alignment using Bowtie/BWA; data handling and visualisation, region identification, differential expression, data quality assessment and statistical analysis, using R/Bioconductor.
|Day 1 - Monday 20 October 2014|
|08:30||Overview of the course||Gabriella Rustici|
|09:15||Lecture: Introduction to the high-throughput sequencing data analysis workflows, with examples from R||Martin Morgan|
|10:30||Lecture/Practical: Short read representation, manipulation and quality assessment||Martin Morgan|
|11:30||Lecture/Practical: Genes and Genomes||Martin Morgan|
|13:30||Lecture/Practical: Genes and Genomes (continued)||Martin Morgan|
|14:00||Lecture: Mapping strategies for sequence reads||Ernest Turro|
|15:15||Practical: Mapping||Ernest Turro|
|Day 2 - Tuesday 21 October 2014|
|09:00||Lecture: Representing and manipulating alignments||Nicolas Delhomme|
|09:45||Pratical: Representing and manipulating alignments||Nicolas Delhomme|
|10:45||Practical: Representing and manipulating alignments||Nicolas Delhomme|
|13:30||Lecture: Estimating expression over genes and exons||Nicolas Delhomme|
|14:30||Practical: Estimating expression over genes and exons||Nicolas Delhomme|
|15:45||Practical: Discovering novel transcribed regions||Nicolas Delhomme|
|16:30||Challenges and solutions working with new plant genomes||Nathaniel Street|
|Day 3 - Wednesday 22 October 2014|
|09:00||Lecture: Differential expression||Wolfgang Huber|
|10:00||Lecture: Alternative exon usage||Wolfgang Huber|
|11:15||Lecture: Multiple testing||John Marioni|
|13:30||Practical: Differential expression with RNA seq||Wolfgang Huber|
|15:45||Practical: Differential expression with RNA seq||Wolfgang Huber|
|Day 4 - Thursday 23 October 2014|
|09:00||Lecture: Single cell sequencing||John Marioni|
|10:15||Lecture: Small non-coding RNA Analysis||Anton Enright|
|11:30||Practical: Small non-coding RNA Analysis||Enright's Lab|
|13:30||Practical: Small non-coding RNA Analysis||Enright's Lab|
|15:00||Poster session 1|
|17:00||Coach departs WTCC to Cambridge|
|19:30||College dinner, Cambridge|
|Day 5 - Friday 24 October 2014|
|09:00||Leture: Introduction to ChIP-Seq data and analysis||Alessandra Vigilante & Bori Gerle|
|10:00||Lecture: Peak-callers||Alessandra Vigilante & Bori Gerle|
|10:45||Practical: Peak-callers||Alessandra Vigilante & Bori Gerle|
|13:30||Lecture: ChIP-Seq data analysis with Bioconductor||Alessandra Vigilante & Bori Gerle|
|14:45||Practical: ChIP-Seq data analysis with Bioconductor||Alessandra Vigilante & Bori Gerle|
|17:00||Poster session II|
|Day 6 - Saturday 25 October 2014|
|09:00||Lecture: Chromosome conformation in gene expression||Bori Gerle & Elodie Darbo|
|09:30||Lecture: Introduction to HiC data analysis||Bori Gerle & Elodie Darbo|
|10:15||Practical: HiC data analysis in R||Bori Gerle & Elodie Darbo|
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 the application page as well as submit a short CV, research interests and a letter of support from their supervisor or another senior co-worker. Incomplete applications will NOT be considered. Details of how to submit these extra documents will be provided on your application confirmation email.
Application closes on 15 August 2014 (12:00 midday GMT). Successful applicants will be notified by 29 August 2014, and will then be asked to confirm their place on the course by re-registering and paying the course fee.
Academic Registration: £270.00
Industry Registration: £1,000.00
Registration includes the following:
* Use of EBI Training Room during the 6 day course