Cuffdiff performs differential transcript abundance analysis for two or more RNA-Seq samples.

App Creator

Roger Barthelson

Quick Start

Test Data

Test data for this app appears directly in the Discovery Environment in the Data window under Community Data -> iplantcollaborative -> example_data -> cuffdiff

Input File(s)

Use the following files from the directory above as test input:






Parameters Used in App

When the app is run in the Discovery Environment, use the following parameters with the above input file(s) to get the output provided in the next section below.

  • Default parameters only, and WT vs hy5 sample names


Output File(s)

Expect a series of files describing the expression for genes and transcripts as output in a cuffdiff_out directory and a series of sorted files of significantly features that have significantly different expression in the sorted_data directory. 

Related Tutorials

RNA-Seq Tutorial (DE 1.8)

Tool Source for App