This tutorial teaches learners how to download sequencing data on Windows and Ubuntu/Linux, convert SRA files into FASTQ format, perform quality checks, trim files, align reads to a reference genome, index BAM files, and calculate gene expression using various tools like FastQC, Trimmomatic, STAR, samtools, and FeatureCounts. The course aims to equip participants with the skills needed to handle sequencing data effectively. The teaching method involves a step-by-step approach to guide learners through the process. This course is intended for individuals interested in bioinformatics, genomics, or molecular biology who want to learn how to work with sequencing data.
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
