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, 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
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