Analysis of High-Throughput Sequencing Data

Date:

 Tuesday 7 Friday 10 November 2017

Venue: 

European Bioinformatics Institute (EMBL-EBI) - Training Room 1 - Wellcome Genome Campus, Hinxton, Cambridge,  CB10 1SD, United Kingdom

Application opens: 

Thursday July 13 2017

Application deadline: 

Friday September 08 2017

Participation: 

Open application with selection

Contact: 

Johanna Langrish

Registration fee: 

£520 - (Including Accommodation)

Registration closed

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Overview

The aim of this course is to familiarise participants with 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 high-throughput sequencing 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 sequencing data under the guidance of the lecturers and teaching assistants.

Audience

This course is aimed at 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 Unix and R/Bioconductor.

Outcomes

During this course you will learn about:

  • High-throughput sequencing technology
  • Quality control of raw reads
  • Considerations on experiment design for variant calling and RNA-seq
  • Read alignment to a reference genome
  • File format conversion and processing
  • Methodologies for variant calling
  • Quantification of expression and differential expression analysis and differential exon usage: R, DESeq, DEXSeq
  • Single cell RNA-seq analysis

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
  • Compare and apply appropriate short read aligners
  • Perform variant calling analysis
  • Perform alignment and quantification of expression for RNA-seq datasets
  • Understand the challenges of single cell sequencing analysis

Programme

 

Time Topic Trainer
Day 1 - Tuesday 07 November 2017
09:00 - 09:30 Registration  
09:30 - 10:00 Welcome and introduction Chiara Batini
10:00 - 10:30 Lecture: Introduction to NGS technologies and library preparation  Chiara Batini
10:30 - 10:45 Tea/coffee break  
10:45 - 12:30 Lecture and practicals: Introduction to data types and data QC Matthew Blades
12:30 - 13:30 Lunch  
13:30 - 15:00 Lecture and practicals: Mapping; SAM/BAM format Chiara Batini
15:00 - 15:15 Tea/coffee break   
15:15 - 17:00 Lecture and practicals: BAM refinement [Local Realignment, Base quality recalibration] Chiara Batini 
17:00 - 18:30 Recap and group activity  
19:00 Dinner at the Wellcome Trust Conference Centre, Hinxton  
Day 2 - Wednesday 08 November 2017
09:00 - 11:00 Lecture and practicals: BAM refinement [Duplicate removal, BAM handling, BAM visualization] Chiara Batini
11:00 - 11:15 Tea/coffee break  
11:15 - 12:30 Lecture and practicals: BAM refinement [Duplicate removal, BAM handling, BAM visualization] Chiara Batini
12:30 - 13:30 Lunch  
13:30 - 15:15 Lecture and practicals: Variant calling - SNPs Chiara Batini
15:15 - 15:30 Tea/coffee break  
15:30 - 17:00 Lecture and practicals: Filtering variants Chiara Batini
17:00 - 18:30 Recap and group activity  
19:00 - 19:30 EBI/Campus Fireworks Display  
19:30 Dinner at the Wellcome Trust Conference Centre, Hinxton  
Day 3 - Thursday 09 November 2017
09:30 - 10:00  Lecture: Introduction to RNA-seq Nils Koelling, Konrad Rudolph
10:00 - 10:15  Tea/coffee break  
10:15 - 12:00  Practical: RNA-seq analysis - alignment Nils Koelling, Konrad Rudolph
12:00 - 13:00  Lunch  
13:00 - 15:00  Practical: RNA-seq - Transcriptome assembly Nils Koelling, Konrad Rudolph
15:00 - 15:15  Tea/coffee break  
15:15 - 17:30  Practical: RNA-seq analysis - Differential expression analysis Nils Koelling, Konrad Rudolph
19:00  Dinner at the Red Lion Pub, Hinxton  
Day 4 - Friday 10 November 2017
09:30 - 10:30 Lecture: Downstream analysis Nils Koelling, Konrad Rudolph
10:30 - 10:45 Tea/coffee break  
10:45 - 12:00 Practical: Downstream analysis Nils Koelling, Konrad Rudolph
12:00 - 13:00 Lunch  
13:00 - 14:00 Lecture: Single cell sequencing Aaron Lun
14:00 - 15:00 Practical: Single cell sequencing Aaron Lun 
15:00 - 15:15 Tea/coffee break  
15:15 - 16:30  Practical: Single cell sequencing Aaron Lun
16:30 Coach to Cambridge Train station