Cufflinks

Software Summary

Mesabi

Default Module:

2.2.1

Other Modules Available:

2.2.1-haswell, 2.0.0, 2.1.1, 2.2.0, 2.2.1

Last Updated On:

Tuesday, August 29, 2023

Mesabi K40

Default Module:

Other Modules Available:

Last Updated On:

Mangi

Default Module:

2.2.1

Other Modules Available:

2.2.1-haswell, 2.0.0, 2.1.1, 2.2.0, 2.2.1

Last Updated On:

Tuesday, August 29, 2023

Mangi v100

Default Module:

Other Modules Available:

Last Updated On:

NICE

Default Module:

Other Versions Available:

Last Updated On:

Tuesday, August 29, 2023

Support Level:

Secondary Support

Software Access Level:

Open Access

Home Page:

Link

Software Categories:

Genetics

Software Description

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.

Software Documentation

Software Documentation Tabs

General Linux

To run this software interactively in a Linux environment run the commands:

module load cufflinks
cufflinks [options] <aligned_reads.(sam/bam)> ...

Cufflinks programs may also be submitted to a queue using PBS script such as the one below:

#PBS -l nodes=3:ppn=8,pmem=1000mb,walltime=8:00:00
#PBS -m abe
#PBS -M sample_email@umn.edu

module load cufflinks

cufflinks -p $PBS_NP <aligned_reads.sam/bam>

Note the use of -p $PBS_NP; this option is used to specify the number of threads used by Cufflinks.

To see a list of options, type the command

cufflinks -h

Significant changes (improvements) have been made to Cufflinks command-line options, and to how Cufflinks calculates differential expression. Output file formats have also been changed.

Additional Information

Cufflinks Manual