Cufflinks

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Achtung.png 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