Previous Workshops


RNA-seq workshop 25-26 September 2019

With this workshop we aim to illustrate some of the methodologies applied to Next-Generation Sequencing technologies with a focus on RNA-seq in particular. The course will cover the bioinformatics aspects of RNA-seq data analysis. 

This workshop is organised by Imperial BRC Genomics and is intended for people at Imperial.  Please register here

Tentative schedule:

Wednesday 25 SEP

Introduction (3h30m) 13.00-16.30

  • Introduction to the course
    • Course overview
    • Why have a general understanding
    • RNA-seq vs microarrays
  • Intro to RNA-seq, history, process overview, main concepts and sequencers 
    • History, starting with Sanger sequencing
    • Sequencing technologies
    • Process overview, from library prep to raw digital data (Illumina, other technologies)
    • Main concepts (coverage, paired- vs single-end, read length, strandedness)
    • Comparison of sequencers, Illumina devices
  • 15m break / questions
  • Applications 
    • Gene expression profiling, DE 
    • Splicing events, isoform usage 
    • Expressed variants, allele-specific expression 
    • New transcript(ome)s, fusion genes 
  • Experimental design 
    • Library design 
      • Type of library (directionality, polyA vs total vs rRNA dep)
      • Type of sequencing (length, paired)
      • How many reads per sample
    • Sample design 
      • Power analysis 
      • Replicates (technical vs biological, number, batches)
      • Paired samples
      • Pooling
      • Reference samples
  • 30m questions

Thursday 26 SEP

Bioinformatics (2h30m) 09.30-12.00

  • Recap of process overview and main concepts (15m)
  • QC to DE 
    • FASTQ and annotation formats
    • Pre-alignment quality control
    • Alignment
    • SAM/BAM format
    • Post-alignment quality control
    • Quantification and normalization
    • Differential expression
    • Filtering
  • 15m break / questions
  • Methods for downstream analyses 
  • Computational resources to store data and run the analyses
    • CX1 and AX4, and the Research Data Storage (RDS)

Bioinformatics practical (3h30m) 13.00-16.30

Introduction to UNIX