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Cuffmerge2 merges together several Cufflinks assemblies. It also handles running Cuffcompare. The main purpose of this script is to make it easier to make an assembly GTF file suitable for use with Cuffdiff.

Cuffmerge2 provides an interface to Cuffmerge 2+ to merge reference GTF files for multple Cufflinks outputs. This step is recommended by the authors of the Cufflinks package.

App Creator

Sheldon Mckay

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 -> cuffmerge

Input File(s)




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, no further configuration needed.


Output File(s)


merged.gtf and


 as output.

Related Tutuorials

RNA-Seq Tutorial (DE 1.8)

Tool Source for App