Cufflinks

Introduction

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.

For more information, please check its website: https://biocontainers.pro/tools/cufflinks and its home page on Github.

Versions

• 2.2.1

Commands

• cuffcompare

• cuffdiff

• cufflinks

• cuffmerge

• cuffnorm

• cuffquant

• gffread

• gtf_to_sam

Module

You can load the modules by:

module load biocontainers
module load cufflinks

Example job

Warning

Using #!/bin/sh -l as shebang in the slurm job script will cause the failure of some biocontainer modules. Please use #!/bin/bash instead.

To run Cufflinks on our clusters:

#!/bin/bash
#SBATCH -A myallocation     # Allocation name
#SBATCH -t 1:00:00
#SBATCH -N 1
#SBATCH -n 8
#SBATCH --job-name=cufflinks
#SBATCH --mail-type=FAIL,BEGIN,END
#SBATCH --error=%x-%J-%u.err
#SBATCH --output=%x-%J-%u.out

module --force purge
ml biocontainers cufflinks

cufflinks -p 8 -G transcript.gtf --library-type fr-unstranded -o cufflinks_output tophat_out/accepted_hits.bam