Analysis of gene regulatory sequencing data: ChIP-seq, ATAC-seq and Hi-C

PrerequisitesNew

This advanced course will cover high-throughput sequencing data processing, ChIP-seq data analysis (including alignment, peak calling), differences in analyses methods for transcription factors (TF) binding and epigenomic datasets, a range of downstream analysis methods for extracting meaningful biology from ChIP-seq data and will provide an introduction to the analysis of open chromatin with ATAC-seq and long-distance interactions with chromosomal conformation capture based Hi-C datasets.

Materials for this course can be found here.

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.

• Graduate students, Postdocs and Staff members from the University of Cambridge, Affiliated Institutions and other external Institutions or individuals
• Further details regarding eligibility criteria are available here

• This is an advanced course with a focus on the most current methods, tools and workflows for analysis of gene regulation related sequencing data. A good understanding of the experimental techniques generating regulatory genomic data-types (ChIP-seq, ATAC-seq, Hi-C) is assumed.
• Participants should have completed a Unix course and an intermediate R programming course such as Statistical Analysis using R or Data Analysis and Visualisation in R.
• Prior experience with R/Bioconductor packages such as tidyr, dplyr, ggplot2, biomaRt and GenomicRanges is recommended.

Number of sessions: 2

Bioinformatics, ChIP-seq, Data visualisation, Data handing, Epigenomics

After this course you should be able to:

• Process and quality control short read sequencing data
• Align short reads to a reference genome and identify TF binding or epigenomic histone modifications using ChIP-seq peak calling
• Annotate peaks, detect functional enrichment, identify motifs, motif enrichment and perform other downstream analyses of ChIP-seq data
• Identifying TF direct targets and differential binding analysis
• Understand ATAC-seq and Hi-C data processing workflows

During this course you will learn about:

• Analysis of transcription factor (TF) and epigenomic (histone mark) ChIP-seq data
• Identifying open chromatin regions using ATAC-seq
• Analysis of long distance chromatin interactions using Hi-C

Presentations, demonstrations and practicals

• Free for University of Cambridge students
• £ 50/day for all University of Cambridge staff, including postdocs, and participants from Affiliated Institutions. Please note that these charges are recovered by us at the Institutional level
• £ 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

2 days

A number of times per year

• Statistical Analysis using R
• Data Manipulation and Visualisation in R