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Thu 24 Nov - Fri 25 Nov 2016
09:30 - 17:30

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

Provided by: Bioinformatics


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

Thu 24 Nov - Fri 25 Nov 2016

Description

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.

Target audience
  • 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
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.
Sessions

Number of sessions: 2

# Date Time Venue Trainers
1 Thu 24 Nov 2016   09:30 - 17:30 09:30 - 17:30 Bioinformatics Training Room, Craik-Marshall Building, Downing Site map Dr Shamith Samarajiwa,  Dr Dora Bihary
2 Fri 25 Nov 2016   09:30 - 17:30 09:30 - 17:30 Bioinformatics Training Room, Craik-Marshall Building, Downing Site map Dr Shamith Samarajiwa,  Dr Dora Bihary
Topics covered

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

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
Aims

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
Format

Presentations, demonstrations and practicals

Timetable

Day 1 Topics Speaker(s)
9:30 – 17:30 Data processing for Next Generation Sequencing Shamith Samarajiwa, Dora Bihary
Alignment to reference genomes and QC
Introduction to ChIP-seq
Quality control methods for ChIP-seq
Introduction to BedTools, Genomic Ranges, ChIPseeker, Rtracklayer
Downloading public ChIP-seq datasets
Day 2
9:30 – 17:30 Downstream analysis of ChIP-seq data Shamith Samarajiwa, Dora Bihary
Differential binding analysis
Identifying direct targets of Transcription Factors
Introduction to the analysis of long distance interactions (Hi-C)
Introduction to the analysis of specialised interaction data
Charging
  • 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
Duration

2 days

Frequency

A number of times per year

Related courses
Theme
Specialized Training

Booking / availability