- 09:30 - 10:30; Introduction to Functional Genomics (AM)
- 10:30 - 12:30; Introduction (Recap) of R (AM)
- 12:30 - 13:30; LUNCH
- 13:30 - 14:30 Principles of Experimental Design (MF)
- 14:30 - 17:00; Data Processing for Next Generation Sequencing (JK / DB)
- Introduction to next generation sequencing (JK)
- A brief Introduction to genomic file formats (DB)
- Quality control and artefact removal (DB)
- Practical - Learn to use FastQC and Cutadapt on a sample dataset
- Short Read alignment and quality control (JK)
- Practical - Alignment to reference genomes using BWA and STAR
- 09:30 - 10:30; Introduction to RNA-seq (AS)
- 10:30 - 12:30; Importing and QC of RNA-seq data (AS)
- 12:30 - 13:30; LUNCH
- 13:30 - 17:00; Differential Expression (DM)
- 09:30 - 11:00; Annotation and Visualisation of Differential Expression (SB)
- 11:00 - 12:30; Gene set analysis and Gene Ontology testing (AM)
- 12:30 - 13:30; LUNCH
- 13:30 - 17:00; (SS / DB)
- Introduction to ChIP-seq
- Quality control methods for ChIP-seq
- Introduction to BedTools, GenomicRanges et al
- 09:30 - 17:00; (SS / DB)
- Downloading public ChIP-seq data
- Downstream analysis of public ChIP-seq datasets
- 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
- 09:30 - 12:30; Introduction to single-cell sequencing (DM)