Cufflinks

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Transcript assembly, differential expression, and differential regulation for RNA Sequencing

Introduction

Cufflinks is a bioinformatics program designed to assemble genetic transcripts and analyze these RNA sequences for differential expression and differential regulation.

Cufflinks is readily available upon login for the HPC and Spear systems and does not require the use of a module. To run Cufflinks, log in to either an HPC or Spear node and enter cufflinks. This will show all of the available options for the program. The manual contains further details regarding these options as well as instructions on how to run the program.