Cufflinks

Software Description:

Transcriptome assembly and differential expression analysis for RNA-Seq.

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.

Software Home Page: Cufflinks

Software Documentation:

To run this software in a Linux environment on LCC,
run the command(s):

#To load module
module load ccs/conda/cufflinks-2.2.1

#To unload module
conda deactivate

#To load module version 2.1.1 
module load ccs/cufflinks/2.1.1

#To load module version 2.0.0
module load ccs/cufflinks/2.0.0

#To unload module per version
module unload ccs/cufflinks/2.1.1
OR
module unload ccs/cufflinks/2.0.0