Course Objectives & pre-requisites

NB – The listing below is a draft. It should be broadly correct but may change before the Summer School is run.
It is advisable to have basic familiarity with R and the command line.
An R Crash course is available here and a good introduction to the Linux command line is here

Experimental design

  • Key aspects of experimental design
    – Experimental variables
    – Power: variance and replicates
    – Bias: confounding factors, randomisation, and controls
  • Design parameters for Functional sequencing experiments
  • Experimental design process at CRUK-CI

Data processing for Next Generation Sequencing

  • A brief introduction to file formats
  • Quality control and artefact removal
  • Short read alignment to a reference genome

RNAseq using R

  • Learn how to analyse RNA-seq count data, using R.
  • Reading data into R, quality control and performing differential expression analysis and gene set testing, with a focus on the edgeR analysis workflow.
  • You will learn how to generate common plots for analysis and visualisation of gene expression data, such as boxplots and heatmaps.
  • You will also be learning how alignment and counting of raw RNA-seq data can be performed in R.
  • This workshop is aimed at biologists interested in learning how to perform differential expression analysis of RNA-seq data when reference genomes are available

Single Cell RNAseq

  • Normalise scRNA-seq data using the scater package
  • Visualise the data and apply dimensionality reduction
  • Use available tools for analysing differential expression
  • Use available methods for clustering
  • Use available methods for pseudo-time alignment

ChIP-seq and ATAC-seq Analysis

  • Introduction to ChIP-seq
  • Peak Calling
  • Quality control methods for ChIP-seq
  • Useful software fora nalysis of genomic data
  • Downstream analysis of ChIP-seq and ATAC-seq data
  • Identifying direct targets of Transcription Factors
  • Differential binding analysis
  • Introduction to Epigenomics and Chromatin Interactions