Cufflinks

Description

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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. Template:App Location

Available Versions

• 1.0.3
• 1.1.0 - Default - (Beware the file format change)

Running the application using modules

To use cufflinks with the environment modules system at HPC the following commands are available:

Get module information for cufflinks:

$module spider cufflinks

Load the default application module:

$module load cufflinks

The modulefile for this software adds the directory with executable files to the shell execution PATH and sets the following environment variables:

• HPC_CUFFLINKS_DIR - directory where cufflinks is located.
• HPC_CUFFLINKS_BIN - executable directory
• HPC_CUFFLINKS_DOC - readme directory