This is a 4½ hour workshop. The morning session (10 am - 12 pm) starts with a presentation from the Genomics Research Core on best practices in sample handling, followed by a brief introduction to techniques, platforms, and methods used in bulk RNA-Seq experiments. The afternoon session (1 pm - 3:30 pm) focuses on software demonstration using the HSLS-licensed CLC Genomics Workbench.
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
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.