Differential Gene Expression Analysis on the Cancer Genomics Cloud (CGC)
RNA sequencing (RNA-Seq) is a high throughput technique that provides qualitative and quantitative information about RNA biology including transcriptome-wide expression quantification, discovery of novel genes and gene isoforms, and differential expression.
Tutorial Goal
- Create virtual cancer cohorts using the Integrated Canine Data Commons (ICDC).
- Conduct differential gene expression (DGE) within the Cancer Genomics Cloud (CGC), the cloud analysis platform that interoperates with the ICDC.
Note
This example RNA-Seq analysis uses 6 Binary Alignment Mapping (BAM) files derived from 6 canine individuals enrolled in the UBC02 study. 3 files are from tumor tissues sequenced from diseased individuals and 3 files are from normal tissues sequenced from healthy individuals.
Table of Contents
| Lesson Name | Description |
|---|---|
| Overview of RNA-Seq | History of RNA-Seq |
| Building a Cohort on the ICDC | Build cohort on the ICDC and export files to the CGC |
| Navigating the CGC | Set up project, inspect files, and copy tools into project |
| Analyzing sample files | Run samtools, htseq-count, and DESeq2 |