RNA-Seq exercise


This exercise was set by Remco Loos and Myrto Kostadima from the EMBL-EBI. The exercise involves using a sample RNA-Seq dataset from zebrafish to perform a number of basic tasks:

  • Aligning RNA-Seq data to the genome.
  • Transcriptome reconstruction.
  • Comparison of gene expression between two different conditions.

The exercise materials are available for your to work through at your leisure.



Click here to download the worksheet and files.

Before you download this folder, be aware that it is more than 650MB.


You will need to install the following programmes and commands on your computer in order to carry out this practical:



In the NGS workshop, the files were pre-installed on the course computers in specific file locations. The commands in the worksheet direct to those file locations: you will need to alter the commands to go to the locations where you have saved your files.