Analysis of ChIP-seq data (ONLINE LIVE TRAINING)

Updated

Chromatin immunoprecipitation followed by sequencing (ChIP-seq) is a method used to identify binding sites for transcription factors, histone modifications and other DNA-binding proteins across the genome. In this course, we will cover the fundamentals of ChIP-seq data analysis, from raw data to downstream applications.

We will start with an introduction to ChIP-seq methods, including important considerations when designing your experiments. We will cover the bioinformatic steps in a standard ChIP-seq analysis workflow, covering raw data quality control, trimming/filtering, mapping, duplicate removal, post-mapping quality control, peak calling and peak annotation. We will discuss metrics used for quality assessment of the called peaks when multiple replicates are available, as well as the analysis of differential binding across sample groups. Throughout the course we will also cover tools and packages that can be used for visualising and exploring your results.

If you do not have a University of Cambridge Raven account please book or register your interest here.

• Our courses are only free for registered University of Cambridge students. All other participants will be charged according to our charging policy.
• Attendance will be taken on all courses and a charge is applied for non-attendance, including for University of Cambridge students. After you have booked a place, if you are unable to attend any of the live sessions, please email the Bioinfo Team.
• Further details regarding eligibility criteria are available here.

• This course is aimed at researchers with no prior experience in the analysis of ChIP-seq data, who would like to get started in processing their data using a standardised pipeline and perform downstream analysis and visualisation of their results.

• Basic understanding of high-throughput sequencing technologies.
  • Watch this iBiology video for an excellent overview.
• A working knowledge of the UNIX command line (course registration page).
  • If you are not able to attend this prerequisite course, please work through our Unix command line materials ahead of the course (up to section 7).
• A working knowledge of R (course registration page).
  • If you are not able to attend this prerequisite course, please work through our R materials ahead of the course.

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

During this course you will learn about:

• How ChIP-seq data is generated and what information it provides about the (epi)genome
• Experimental design considerations needed when performing ChIP-seq experiments
• The bioinformatic steps involved in processing ChIP-seq data
• How to interpret and assess the quality of your data and results
• How to perform differential binding analysis to compare different groups of samples

After this course you should be able to:

• Apply the nf-core/chipseq pipeline to perform peak calling and annotation from raw sequencing data
• Perform differential binding analysis to compare different groups of samples
• Analyse, explore and visualise your results using both standard and dedicated R/Bioconductor packages.

Presentations, demonstrations and practicals

Under revision

• Free for registered 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

1

A couple of times a year

• Introduction to R for Biologists (IN-PERSON)
• Analysis of bulk RNA-seq data (IN-PERSON)
• Analysis of DNA Methylation using Sequencing (IN-PERSON)
• Analysis of single cell RNA-seq data (IN-PERSON)