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Differential Gene Expression Analysis on Cavatica Cloud Platform

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.

The goal of this tutorial is to enable you to:

  1. create virtual cancer cohorts using the NIH Common Fund-supported Gabriella Miller Kids First Data Portal (KF Portal).
  2. analyze differential gene expression (DGE) on Cavatica, an integrated cloud based platform.

You will learn two different approaches for DGE analysis using open access human cancer data on Cavatica: (a) using a public workflow app and (b) running code from an analysis script on an instance with RStudio computational environment.

Table of contents

Est. Time Lesson Name Description
10 mins An Introduction to RNA-Seq Background about RNA-Seq
20 mins Selecting Kids First Cancer Cohort Select Kids First open access cancer RNA-Seq files and push to Cavatica
20 mins Cavatica - View, Filter, Tag and Download Filter imported data, tag and download relevant metadata from Cavatica
20 mins Setup DESeq2 Public App Setting up the workflow app based on DESeq2 on Cavatica
15 mins Phenotype File and Upload to Cavatica Reformat metadata file and upload it to Cavatica
50 mins Analysis with DESeq2 Public App Run the DESeq2 app with appropriate inputs and computational settings
60 mins Analysis using Data Cruncher Analysis on an instance in the RStudio environment

Learning Objectives

  • learn to build virtual cohorts on KF portal
  • learn to navigate project folder and perform file operations on Cavatica
  • learn to upload and download data from Cavatica
  • learn to search, copy, and edit public workflow apps on Cavatica
  • learn to perform differential gene expression (DGE) analysis using DESeq2 app
  • learn to setup analysis environment and execute code for DGE analysis

Login Credentials

You do not need eRA Commons ID to do the lesson!

  • Background: Knowledge of biology and rudimentary genetics.
  • Technology: Basic knowledge of R and command line. Familiarity with RStudio is useful.
  • Financial: Pilot funds ($100) are provided to every user on Cavatica with linked KF accounts.
  • Time: Initial account setup may take hours to a day for verification. Setup of eRA Commons ID may take days and is institute dependent.
  • DESeq2 app < $1.00
  • Analysis with R < $1.00

Last update: December 10, 2021