Previous Workshops
RNA-seq
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
- Library design
- 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
TBD
