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


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.



Dr Shamith Samarajiwa, MRC Cancer Unit

Dr Dora Bihary, MRC Cancer Unit


Audience and Prerequisites

  • 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.
  • Graduate students, Postdocs and Staff members from the University of Cambridge, Affiliated Institutions and other external Institutions or individuals


Syllabus, Tools and Resources

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


Learning Objectives

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



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