In this repository I am storing the data and the code used to produce the RNA-seq analysis I did to fulfill the requirements of the "Advanced Technology Report in Bioscience".
This advanced technology report describes a limma-based approach to analyze RNA sequencing data and extract gene-level statistics to perform gene set analysis using the package PIANO (Platform for integrative analysis of omics data). The report is mainly focused on the analysis performed after generating a gene-count file with the nf-core RNA-seq pipeline. How to map the reads to a reference genome will be briefly discussed from a theoretical point of view, but no code will be shown or discussed. After a brief introduction on RNA-sequencing principles, the code used to perform the analysis will be described and explained step by step. The procedure and results are based on Y. lipolitica but can be easily adjusted to different organisms as well. All the code is available in this GitHub directory.