Learn how to set up and execute a comprehensive RNA-Seq pipeline from scratch in this 32-minute tutorial video. Walk through the entire process of processing bulk RNA-Seq reads, from quality control to generating a counts matrix for downstream analysis. Explore essential steps including FastQC for quality control, Trimmomatic for read trimming, HISAT2 for alignment, and featureCounts for quantification. Gain insights into run times, memory requirements, and aligner accuracies for various tools. Follow along with provided code and data links to build your own pipeline using bash in a Linux environment. Discover best practices, learn about splice-aware aligners, and understand when to trim reads. Perfect for bioinformatics beginners and researchers looking to enhance their RNA-Seq analysis skills.