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Thu 2 May - Fri 3 May 2019
09:30, ...

Venue: Bioinformatics Training Room, Craik-Marshall Building, Downing Site

Provided by: Bioinformatics


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ChIP-seq and ATAC-seq analysis
PrerequisitesUpdated

Thu 2 May - Fri 3 May 2019

Description

The primary aim of this course is to familiarise participants with the analysis of ChIP-seq and ATAC-seq data and provide hands-on training on the latest analytical approaches.

The course starts with an introduction to ChIP-seq experiments for the detection of genome-wide DNA binding sites of transcription factors and other proteins. We first show data quality control and basic analytical steps such as alignment, peak calling and motif analysis, followed by practical examples on how to work with biological replicates and fundamental quality metrics for ChIP-seq datasets. On the second day, we then focus on the analysis of differential binding, comparing between different samples. We will also give an introduction to ATAC-seq data analysis for the detection of regions of open chromatin.

The training room is located on the first floor and there is currently no wheelchair or level access available to this level.

Please note that if you are not eligible for a University of Cambridge Raven account you will need to book or register your interest by linking here.

Target audience
  • Graduate students, Postdocs and Staff members from the University of Cambridge, Affiliated Institutions and other external Institutions or individuals
  • Please be aware that these courses are only free for University of Cambridge students. All other participants will be charged a registration fee in some form. Registration fees and further details regarding the charging policy are available here.
  • Further details regarding eligibility criteria are available here
Prerequisites
Sessions

Number of sessions: 2

# Date Time Venue Trainers
1 Thu 2 May   09:30 - 17:30 09:30 - 17:30 Bioinformatics Training Room, Craik-Marshall Building, Downing Site map Dr Sandra Cortijo,  Denis Seyres,  Sergio Martinez Cuesta,  Ashley Sawle
2 Fri 3 May   09:30 - 17:00 09:30 - 17:00 Bioinformatics Training Room, Craik-Marshall Building, Downing Site map Dr Sandra Cortijo,  Denis Seyres,  Sergio Martinez Cuesta,  Ashley Sawle
Topics covered

Bioinformatics, Epigenomics, Functional genomics, Data visualisation, Data handing, Data mining, ChIP-seq

Objectives

After this course you should be able to:

  • Understand quality of high-throughput sequencing data
  • Assess the quality of your ChIP-seq datasets and reproducibility of replicates
  • Perform alignment and peak calling of ChIP-seq datasets
  • Compare samples by performing differential binding analysis
  • Detect regions of open chromatin by analysing ATAC-seq datasets
  • Visualize multiple layers of epigenomic data
Aims

During this course you will learn about:

  • Considerations on experimental design for ChIP-seq
  • Quality control of raw reads
  • Read alignment to a reference genome
  • Peak calling and motif analysis
  • Differential binding analysis
  • Quality control, processing and analysis of ATAC-seq data
Format

Presentations, demonstrations and practicals

Timetable

Day 1 Topics
09:30 - 10:30 Lecture: Introduction to ChIP-seq, data analysis and QC metrics
10:30 - 11:00 Practical: Introduction to ChIP-seq, data analysis and QC metrics
11:00 - 11:15 Tea/coffee break
11:15 - 12:30 Practical: Introduction to ChIP-seq, data analysis and QC metrics (continued)
12:30 - 13:30 Lunch (not provided)
13:30 - 15:15 Lecture/practical: ChIP-seq data analysis part 1
15:15 - 15:30 Tea/coffee break
15:30 - 17:30 Lecture/practical: ChIP-seq data analysis part 2
Day 2
09:30 - 10:15 Practicals: ChIP-seq part 3 (cont.) & working with biological replicates
10:15 - 10:30 Tea/coffee break
10:30 - 11:15 Lecture: Differential binding analysis
11:15 - 13:00 Practical: Differential binding analysis
13:00 - 14:00 Lunch (not provided)
14:00 - 14:45 Lecture: Introduction to ATAC-seq data analysis
14:45 - 15:00 Tea/coffee break
14:00 - 17:00 Practical: ATAC-seq data analysis
Registration fees
  • Free for University of Cambridge students
  • £ 50/day for all University of Cambridge staff, including postdocs, temporary visitors (students and researchers) and participants from Affiliated Institutions. Please note that these charges are recovered by us at the Institutional level
  • It remains the participant's responsibility to acquire prior approval from the relevant group leader, line manager or budget holder to attend the course. It is requested that people booking only do so with the agreement of the relevant party as costs will be charged back to your Lab Head or Group Supervisor.
  • £ 50/day for all other academic participants from external Institutions and charitable organizations. These charges must be paid at registration
  • £ 100/day for all Industry participants. These charges must be paid at registration
  • Further details regarding the charging policy are available here
Duration

2

Frequency

2 times a year

Related courses
Theme
Specialized Training

Booking / availability