The challenge is to analyze RNA-seq data from this paper https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6257967/.
The goal is to conduct an independent analysis on your own and compare the results with those provided by the authors.
You can use any tools of your choice. You can work individually or in groups.
In the end, you need to prepare a written report and a brief 10-minute power-point presentation highlighting the steps of the analysis, major discoveries, the questions and problems you encountered during the analysis.
On May 27th, we will discuss the results and questions.
IMPORTANT (if you use the CRG cluster)
Since many steps of the RNA-seq analysis are computationally extensive, you have to run them on the CRG cluster either interactively (via qlogin) or as a batch job (using qsub); for detail, refer to http://www.linux.crg.es/index.php/Cluster_summary_help.
Also, make sure to check the parameters of programms you will be using, as some of them allow multi-threading.