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.
• Accessing the virtual machine using the NX client.
• Introduction to R.
• Introduction to SQL databases.
• Illumina RNAseq quality control.
• Mapping reads to a reference genome sequence.
• Differential expression analysis.
• Visualisation, clustering and plotting results.
• RNASeq statistics.
• Identifying and visualising introns and splice variants.

Course details