EMBO Practical Course on Analysis of High-Throughput Sequencing Data
supported by AWS in Education Grant award
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.
|Sunday 20 October 2013 - delegates arrive and check in to accommodation|
|Day 1 - Monday 21 October 2013|
|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|
|15:00||Practical: Mapping||Ernest Turro|
|Day 2 - Tuesday 22 October 2013|
|09:00||Lecture: Representing and manipulating alignments||Nicolas Delhomme|
|09:45||Practical: 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||Working without a reference genome||Nicolas Delhomme|
|Day 3 - Wednesday 23 October 2013|
|09:00||Lecture: Differential expression||Simon Anders|
|10:00||Lecture: Alternative exon usage||Simon Anders|
|11:15||Lecture: Multiple testing||John Marioni|
|13:30||Practical: Differential expression with RNA seq||Simon Anders|
|15:45||Practical: Differential expression with RNA seq||Simon Anders|
|Day 4 - Thursday 24 October 2013|
|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||Leonor Quintais|
|13:30||Practical: Small non-coding RNA Analysis||Leonor Quintais|
|15:00||Poster session I|
|17:00||Coach departs WTCC to Cambridge|
|19:30||Dinner at Jesus College, Cambridge|
|Day 5 - Friday 25 October 2013|
|09:00||Introduction to Galaxy and the Galaxy Ecosystem||Francis Ouellette|
|10:00||RNA-Seq Analysis with Galaxy||Francis Ouellette|
|13:00||RNA-Seq Analysis with Galaxy||Francis Ouellette|
|15:15||RNA-Seq Analysis with Galaxy||Francis Ouellette|
|16:30||Poster session II|
|Day 6 - Saturday 26 October 2013|
|09:00||Lecture: Introduction to ChIP-Seq data and analysis||Bori Gerle & Kathi Zarnack|
|10:00||Lecture: Peak-callers||Bori Gerle & Kathi Zarnack|
|10:45||Practical: Peak-callers||Bori Gerle & Kathi Zarnack|
|13:30||Lecture: ChIP-Seq data analysis with Bioconductor||Bori Gerle & Kathi Zarnack|
|14:45||Practical: ChIP-Seq data analysis with Bioconductor||Bori Gerle & Kathi Zarnack|
|16:00||Course feedback and wrap up and delegates to depart|
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 23 August 2013 (12:00 midday GMT). There will be a maximum of 40 participants on this course. Successful applicants will be notified by 6 September 2013 and will then be asked to confirm their place on the course by re-registering and paying the course fee.
Academic Registration fee £365
Industry Registration fee £850 (€1000)
Registration includes the following:
* Use of EBI I.T. Training Room during the 6 day course.
To apply for this event please use the following link. Items marked * are mandatory. Incomplete applications will not be processed.
Application is now closed