RNASeq Data preprocessing using Shell commands in linux

Next-Generation Sequencing (NGS) opens a window to a deeper understanding of biological processes by offering a comprehensive view of genomes and gene expression. In NGS experiments, the raw data is captured in a file format known as FASTq, and mastering the handling of these files is crucial for bioinformaticians. This involves using shell commands in a Linux environment.

In this module, you'll become acquainted with the Linux system and shell commands, learn about various data file formats, and discover how to select and retrieve raw files from the Gene Expression Omnibus (GEO). Additionally, you'll gain hands-on experience in preprocessing FASTq files, including quality control, aligning them to a reference genome, and generating gene expression matrices

Learning objectives:

• Linux for NGS data analysis
• Data Retrieval (NCBI SRA)
• Understanding Fastq files and other data types
• Quality control check
• Retrieval of proper reference genome (Human, Mouse)
• Alignment of reads using reference Genome.
• Generation of gene expression matrices.