Hands-On RNA-Seq Analysis Crash Course: From FASTQ to Differential Expression

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Hands-On RNA-Seq Analysis Crash Course: From FASTQ to Differential Expression

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About Course

This RNA-Seq Data Analysis course is going to be a game changer for you. In the modern era of genomics and transcriptomics, we are witnessing an explosion of RNA sequencing data. If you want to survive and grow in research, academia, or the bioinformatics industry, learning RNA-Seq is no longer optional it’s essential. Traditional biology is no longer sufficient to handle this scale of data. This is where computational biology and bioinformatics come into play, helping researchers make sense of massive datasets through efficient pipelines and analysis tools.

RNA-Seq (RNA sequencing) is one of the most powerful technologies used to study gene expression and discover differentially expressed genes (DEGs). It helps uncover the molecular mechanisms behind diseases, responses to treatments, and regulatory pathways in all living organisms.

Keeping this demand in view, we have brought you a complete hands-on crash course on RNA-Seq analysis that takes you from raw FASTQ files all the way to DEGs and gene enrichment results. This course will help you master the complete pipeline of RNA-Seq analysis using a blend of command-line tools and R programming.

This course is divided into 9 comprehensive sections:

(1) Course & Linux Introduction
(2) Basic Linux for Bioinformatics
(3) Foundations of RNA-Seq
(4) Data Acquisition & Preprocessing
(5) Mapping to the Reference Genome
(6) Quantification & Normalization
(7) R and RStudio Setup
(8) Downstream Analysis: DEGs & GSEA
(9) Final Quiz & Capstone Project

This course is a unique blend of theory and hands-on practice. First, you will learn the basics of RNA-Seq and Linux. Then, you will perform real-time preprocessing, alignment, quantification, and downstream analysis using publicly available RNA-Seq data. You’ll also be completing assignments and a capstone project, giving you the practical experience needed to confidently handle real-world datasets.

You’ll work with some of the most widely used bioinformatics tools such as:

  • FastQC for quality check

  • BWA for alignment

  • Samtools and FeatureCounts for BAM file handling and quantification

  • R and DESeq2 for DEG analysis

  • clusterProfiler for enrichment and pathway analysis

We assure you that by the end of this course, you will be able to build your own RNA-Seq analysis pipeline from scratch using command-line tools and R. This will not only add a valuable skill to your CV but also transform the way you look at transcriptomics and biological data analysis.

We hope this course will be worth your time and investment and it will open up new opportunities for you in the ever-evolving field of bioinformatics.

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What Will You Learn?

  • Understand the basics of Linux and command-line operations essential for bioinformatics.
  • Set up your bioinformatics environment on Windows using Linux (WSL) or VirtualBox.
  • Retrieve RNA-Seq datasets from public databases like NCBI SRA or ENA.
  • Perform quality control and preprocessing on FASTQ files.
  • Learn how to align RNA-Seq reads to a reference genome using tools like HISAT2, STAR, or BWA.
  • Quantify gene expression levels from alignment files (BAM).
  • Use R and RStudio to perform downstream analyses including: Differential gene expression analysis (DGEA) and Gene set enrichment analysis (GSEA) Analysis.
  • Work on real-life assignments and a capstone project that solidify your skills and build your portfolio.
  • Hands-on approach: Real datasets, practical workflows, and terminal-based commands.
  • No prior experience required: Beginner-friendly and fully guided.
  • Portfolio-ready assignments and a capstone project for showcasing your skills.

Course Content

Course Introduction

  • Introduction of the Course
    04:59

Basic Linux For Bioinformatics

Foundations of RNA-Seq

Data Acquisition & Preprocessing

Mapping to the Reference Genome

Quantification & Normalization

R and R Studio

Downstream Analyses

Final Project & Quiz

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Your Instructor

Abdul Rehman Ikram

Bioinformatician | Data Analyst | Computational Biologist

Abdul is a distinguished bioinformatician, data analyst, and computational biologist known for his exceptional contributions to the field of biomedical research. With a passion for integrating technology and biology, Abdul has carved a niche for himself, leveraging cutting-edge computational techniques to unravel complex biological data.

Driven by a curiosity to decode the complexities of life, Abdul believes in the power of interdisciplinary approaches. He is committed to mentoring the next generation of scientists, fostering a culture of innovation and continuous learning.

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