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.

Cufflinks is a part of the Tuxedo suite. Template:App Location

Available Versions

• 1.0.3 - Legacy version.
• 1.1.0 - This is the version used by Galaxy. Beware the file format change from 1.0.3.
• 1.3.0 - Default.

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