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. To quantify the expression levels, RNA-seq has become one of the most popular experimental methods. This 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.
We will start with raw data in the typical format that is provided by sequencing centers. We will process it by trimming adapters, mapping trimmed reads to a reference genome, tallying gene-wise counts, and end with differential gene expression analysis. We will also look at various methods of quality control at each step, learn to interpret data formats such as FASTQ, BAM, and GFF, and discuss the relevant tools and technology. No prior RNA-seq experience is required. Bring your laptop and power adapter!
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 on the Galaxy platform, or on other systems as well as locally on your own computer. More details about other systems to be added soon.
You can access these materials remotely at any time and go through them at your own pace. Here's how:
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Download the materials here and unzip the contents.
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Inside the downloaded folder is a slide deck that contains notes below each slide where you can find links to recommended reading material, including a link to get started with Galaxy.
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Each section contains relevant background on the tools/tech and describes files that should be used as input to tools on Galaxy. 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.