This class will consist of a flipped classroom – a pre-recorded video and a hands-on session – covering bulk RNA-seq data analysis using CLC Genomics workbench software. Upon registration, you will receive links to workshop materials, including PowerPoint slides, lecture videos, and practice exercises, that you can view on your schedule. During the class, we will learn how to solve the exercise problems.
Participants will learn how to
- access the CLCbio Genomics Server hosted on the HTC Cluster by Pitt CRC
- import RNA-Seq FASTQ reads from a GEO dataset
- assess the quality of RNA-Seq data
- align reads to a reference genome
- estimate known gene and transcript expression
- perform differential expression analysis
- visualize data by generating PCA and heatmaps
Target Audience
Experimental biologists seeking to analyze bulk RNA-Seq data generated through experiments or retrieved from a repository such as GEO. The software covered in the workshop operates through a user-friendly, point-and-click graphical user interface, so neither programming experience nor familiarity with the command-line interface is required.