Advanced RNA-Seq and ChiP-Seq Data Analysis
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Date:
Monday 11 - Thursday 14 May 2015Venue:
European Bioinformatics Institute (EMBL-EBI) - Wellcome Genome Campus, Hinxton, Cambridge, CB10 1SD, United KingdomParticipation:
Open application with selectionContact:
Frank O’DonnellRegistration fee:
£525Registration closed
Overview
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. 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.
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. Familiarity with the technology and biological use cases of high throughput sequencing is required, as is some experience with R/Bioconductor.
Syllabus, tools and resources
During this course you will learn about:
- High-throughput sequencing technology
- Quality control of raw reads: FASTQC and fastx toolkit
- Considerations on experiment design for ChIP-seq and RNA-seq
- Read alignment to a reference genome: Bowtie and Tophat
- File format conversion and processing
- Peak calling: MACS, USeq and SISSR
- Motif analysis: MEME
- Quantification of expression and differential expression analysis and differential exon usage: R, DeSeq, DEXSeq
Outcomes
After this course you should be able to:
- Understand the advantages and limitations of the high-throughput assays presented
- Assess the quality of your datasets
- Understand the difference between short read aligners
- Perform alignment and peak calling of ChIP-seq datasets
- Perform alignment and quantification of expression of RNA-seq datasets
Programme
| Time | Topic | Trainer |
|---|---|---|
| Day 1 - Monday 11 May 2015 | ||
| 08:15 | Registration | |
| 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 |
| 10:15 | Tea/coffee break | |
| 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 |
| 12:30 | Lunch | |
| 13:30 | Lecture/Practical: Genes and Genomes (continued) | Nicolas Delhomme & Bastian Schiffthaler |
| 14:00 | Lecture: Mapping strategies for sequence reads | Ernest Turro |
| 15:00 | Tea/coffee break | |
| 15:15 | Practical: Mapping | Ernest Turro |
| 17:30 | Q&A session | |
| 19:30 | Evening meal | |
| 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 |
| 10:30 | Tea/coffee break | |
| 10:45 | Practical: Representing and manipulating alignments | Nicolas Delhomme & Bastian Schiffthaler |
| 12:30 | Lunch | |
| 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 |
| 15:30 | Tea/coffee break | |
| 15:45 | Practical: Discovering novel transcribed regions | Nicolas Delhomme & Bastian Schiffthaler |
| 16:30 | Working without a reference genome | Nicolas Delhomme & Bastian Schiffthaler |
| 17:30 | Q&A session | |
| 19:30 | Dinner | |
| 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 |
| 11:00 | Tea/coffee break | |
| 11:15 | Lecture: Multiple testing | TBC |
| 12:30 | Lunch | |
| 13:30 | Practical: Differential expression with RNA seq | Alessandra Vigilante & Bori Gerle |
| 15:30 | Tea/coffee break | |
| 15:45 | Practical: Differential expression with RNA seq (cont.) | Alessandra Vigilante & Bori Gerle |
| 17:30 | Q&A session | |
| 17:45 | Lecture: Single Cell sequencing | Sarah Teichmann |
| 19:30 | Dinner | |
| 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 |
| 10:30 | Tea/coffee break | |
| 10:45 | Practical: Peak-callers | Bori Gerle & Alessandra Vigilante |
| 12:30 | Lunch | |
| 13:30 | Practical: ChIP-Seq data analysis with Bioconductor | Bori Gerle & Alessandra Vigilante |
| 14:30 | Tea/coffee break | |
| 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 | |
In association with
How to apply
This event has now closed.
Number of places
30 places
Organisers
Gabriella Rustici - School of Biological Sciences of the University of Cambridge
Trainers
Gabriella Rustici - EMBL-EBI, UK
Nicolas Delhomme - UPSC, Umeå, Sweden
Bastian Schiffthaler - Umeå University, Sweden
Sarah Teichmann - EMBL-EBI, UK
Ernest Turro - University of Cambridge
Alessandra Vigilante - EMBL-EBI, UK
Bori Mifsud - Queen Mary University, London