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Cufflinks

Cufflinks

Description

Cufflinks assembles transcripts, estimates their abundances, and tests for differential expression and regulation in RNA-Seq samples. It accepts aligned RNA-Seq reads and assembles the alignments into a parsimonious set of transcripts. Cufflinks then estimates the relative abundances of these transcripts based on how many reads support each one, taking into account biases in library preparation protocols.


Available

Version on CSC's Servers

Taito: 2.1.1, 2.2.1
FGI grid: 2.1.1
Chipster graphical user interface


Usage

To set up Cufflinks environment in Taito, give command

module load biokit 

After that you can start cufflinks by giving command:

cufflinks 


Discipline

Biosciences

References


Support

servicedesk@csc.fi


Manual

More information about Cufflinks can be found from the Cufflinks home page