Setup RNA-Seq Pipeline From Scratch - Fastq to Counts - Step-by-Step Tutorial

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.

Intro
- Applications of RNA-Seq data
Schematic detailed workflow
What are splice-aware aligners?
Workflow for this tutorial
Comparison of run times, memory usage and aligner accuracies for various aligners
Which aligner should I choose?
Pre-requistes to build this pipeline things that will not be covered in this video
Set-up before building the pipeline
Some good practices while building a pipeline
Quality control: FastQC
To trim or to not trim?
Trimming reads: Trimmomatic
Align reads: HISAT2
Read quantification: featureCounts