Raw FASTQ Files to Gene Count Matrix using Linux & Bioinformatics Tools

Basic Course Information

• Course Title: Raw FASTQ Files to Gene Count Matrix Using Linux & Bioinformatics Tools

• Duration: 5 Days

• Course Level: Beginner

• Category: Bioinformatics / RNA-Seq / NGS Data Analysis

• Course Format: Online Practical Training

• Language: English

• Prerequisites: No prior knowledge of Linux or bioinformatics required

• Operating System: Windows 10/11 (using WSL2 or Ubuntu Linux)

• Required Equipment: Laptop or desktop computer with a stable internet connection

• Software & Tools: Ubuntu Linux, Conda, SRA Toolkit, FastQC, fastp, HISAT2, SAMtools, and featureCounts

• Practical Training: Real RNA-Seq datasets from NCBI SRA

• Final Output: Quality-controlled sequencing reads, aligned BAM files, and an analysis-ready gene count matrix

• Target Audience: BS, MSc, MPhil, PhD students, postdoctoral researchers, biologists, geneticists, and bioinformatics enthusiasts

Course Requirements

• Laptop or Computer: Windows 10/11 with at least 8 GB RAM (16 GB recommended).

• Internet Connection: Stable internet access for downloading software, tools, and RNA-Seq datasets.

• Operating System: Windows with WSL2 (Ubuntu Linux) or a computer running Ubuntu Linux.

• Software Installation: All required bioinformatics tools will be installed during the course with step-by-step guidance.

• Prior Knowledge: No previous experience in Linux, programming, RNA-Seq, or bioinformatics is required.

• Educational Background: Basic understanding of biology or genetics is helpful but not mandatory.

• Learning Commitment: Willingness to participate in practical exercises and work with real sequencing datasets.

• Storage Space: At least 30–50 GB of free disk space recommended for software installation and practice datasets.

Intended Audience

This course is designed for students, researchers, and professionals who want to develop practical skills in RNA-Seq data processing using Linux and bioinformatics tools.

• Undergraduate Students: BS/BSc students in biology, biotechnology, genetics, and related disciplines.

• Postgraduate Students: MSc, MPhil, and PhD scholars working with molecular biology, genomics, and transcriptomics.

• Postdoctoral Researchers: Researchers interested in applying RNA-Seq data processing techniques to their scientific projects.

• Biologists and Geneticists: Professionals seeking practical experience in next-generation sequencing (NGS) data analysis.

• Bioinformatics Beginners: Individuals with no prior experience in Linux or RNA-Seq analysis.

• Research Scientists: Professionals working in plant sciences, agriculture, microbiology, biomedical sciences, and molecular genetics.

• Data Analysts: Individuals interested in expanding their skills into genomics and computational biology.

No prior programming or Linux experience is required. The course starts with fundamental concepts and progresses to a complete practical RNA-Seq preprocessing workflow.