Protocol for identifying differentially expressed genes using the RumBall RNA-seq analysis platform

Abstract

Summary: Here, we present a protocol for the identification of differentially expressed genes through RNA sequencing analysis. Starting with FASTQ files from public datasets, this protocol leverages RumBall within a self-contained Docker system. We describe the steps for software setup, obtaining data, read mapping, sample normalization, statistical modeling, and gene ontology enrichment. We then detail procedures for interpreting results with plots and tables. RumBall internally utilizes popular tools, ensuring a comprehensive understanding of the analysis process. : Publisher’s note: Undertaking any experimental protocol requires adherence to local institutional guidelines for laboratory safety and ethics.

Keywords

• Bioinformatics
• Sequence analysis
• RNA-seq