Learn the essential steps of RNA sequencing data analysis in this 30-minute tutorial. Explore the process of downloading sequencing data using SRA Toolkit on both Windows and Ubuntu/Linux systems. Master the conversion of SRA files to FASTQ format, perform quality checks with FastQC, and trim FASTQ files using Trimmomatic. Discover how to align reads to a reference genome using STAR, create and index BAM files with samtools, and calculate gene expression using FeatureCounts. Gain practical skills in handling and processing sequencing data for your research or bioinformatics projects.
Overview
Syllabus
Downloading sequencing data on windows - SRA Tool kit - Step 1.
Converting SRA into FASTQ file - SRA Tool kit - Step 2.
FASTQ quality check (FastQC) - Step 3.
Trimming of FastQ file (Trimmomatic) - Step 4.
FastQ to BAM - Align reads to the reference genome with STAR - Step 5.
Indexing BAM file using samtools - Step 6.
Caculate gene expression with FeatureCounts - Step 7.
Downloading sequencing data on ubuntu/linux - SRA toolkit.
Taught by
Farhan Haq
