RNA-Seq workshop

This course covers differential transcriptomics as applied to modern short-read datasets where a suitable reference genome is available.
The course assumes you have attended the Unix and Perl and/or short-read genomics workshops and/or have previous experience with the Linux command line.

The target audience is anyone wanting further training in bioinformatics: PhD, post-docs, technicians, and faculty staff.
Biologists and other researchers are more and more likely to encounter short-read datasets in their everyday research. Participants will be able to take the techniques and skills they learn back to their groups to continue making their own research easier and more effective.

Course content

  • Theory behind transcriptome analysis using high throughput sequencing.
  • Setting up and accessing your own Linux virtual machine in the Amazon cloud computing environment.
  • Introduction to RNA-Seq
  • Setting up and accessing your own Linux virtual machine in the Amazon cloud computing environment
  • Accessing the virtual machine using the NX client
  • Quality control of raw RNA-Seq data
  • Mapping reads to a reference genome
  • Assigning reads to known genomic features
  • An introduction to R
  • Identifying differentially expressed genes with DESeq2
  • GO term enrichment analysis using topGO

Course details

Attendance: Registration not yet available

Dates: TBA   (half a day per week plus homework).

Prerequisites: Participants must be comfortable with the Linux command line and have attended the Introduction to R course.

Location: (TBC) Hatherley B12, Streatham Campus, University of Exeter

Please ensure you can attend the entire series of workshops. Places will be allocated on a first-come first-served basis up to a maximum of 50 places.

Instructors:


Dr Ryan Ames - R.Ames@exeter.ac.uk
Paul O'Neill - P.A.O'Neill@exeter.ac.uk