Introduction to RNA Seq Analysis
Gene expression is central to cell biology. Disease pathways often involve changes in the expression levels of at least some genes. RNA-seq has become one of the most popular experimental methods to quantify gene expression levels. This 2-day hands-on workshop will provide an introduction to a typical bulk RNA-seq protocol and focus on the data analysis steps for recovering actionable insights.
You’ll learn how to perform quality check of the raw data in the typical format provided by sequencing centers, process it by trimming adapters, map trimmed reads to a reference genome, and tally gene-wise counts. You’ll learn to analyze high-throughput data using docker, learn about various methods of quality control at each step, and interpret data formats such as FASTQ, BAM, and GFF. No prior RNA-seq experience is required.
This is an introductory workshop in the RNA-Seq Analysis series. No prior experience required. No prerequisites.
Click here to download the materials.
RNA-seq data can be analyzed using online tool like the Galaxy platform, or on other systems like a high-performance compute (HPC) cluster, as well as locally on your own computer using containerization software such as docker. Before the workshop, download and install Docker Desktop by clicking here.
You can access these materials remotely at any time and go through them at your own pace. Here's how:
-
Download the materials here and unzip the contents.
-
Inside the downloaded folder is a slide deck that contains notes below each slide where you can find links to recommended reading material.
-
Each section contains relevant background on the tools/tech and describes files that should be used as input to the tools. Please go through these step-by-step and read the suggested reading material.
Refer to our workshop materials for pathway analysis and materials from the UCSF library for bulk RNA-seq analysis, which focuses on differential gene expression analysis. The library hosts its materials on the UCSF Collaborative Learning Environment, which you can visit by following a link in the description of their materials.