Cufflinks

Legacy documentation This page describes a service provided by a retired ACENET system. Most ACENET services are currently provided by national systems, for which please visit https://docs.computecanada.ca.

Description

Cufflinks assembles transcripts, estimates their abundances, and tests for differential expression and regulation in RNA-Seq samples.

Modulefile

cufflinks

Documentation

Cufflinks homepage

Usage

Here is an example of a submission script processing the test data from the Cufflinks website:

#$ -cwd
#$ -l h_rt=01:00:00
#$ -pe openmp 2
module load python cufflinks
cufflinks --num-threads $NSLOTS  test_data.sam