Cufflinks

Description

From the Cufflinks home page: 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.

Version

2.2.1

Authorized Users

CIRCE account holders
RRA account holders
SC account holders

Platforms

CIRCE cluster
RRA cluster
SC cluster

Modules

Cufflinks requires the following module file to run:

apps/cufflinks/2.2.1

See Modules for more information.

Running Cufflinks on CIRCE

The Cufflinks user guide is essential to understanding the application and making the most of it. The guide and this page should help you to get started with your simulations. Please refer to the Documentation section for a link to the guide.

Note on CIRCE: Make sure to run your jobs from your $WORK directory!
Note: Scripts are provided as examples only. Your SLURM executables, tools, and options may vary from the example below. For help on submitting jobs to the queue, see our SLURM User’s Guide.

Submitting a Job

The Cufflinks user guide is essential to understanding the application and making the most of it. The guide and this page should help you to get started with your simulations. Please refer to the Documentation section for a link to the guide.

Note on CIRCE: Make sure to run your jobs from your $WORK directory!
Note: Scripts are provided as examples only. Your SLURM executables, tools, and options may vary from the example below. For help on submitting jobs to the queue, see our SLURM User’s Guide.

You must create a submit script (for testing, call it “cufflinks-test.sh”) like the following to run Cufflinks:

#!/bin/bash
#
#SBATCH --comment=cufflinks-test
#SBATCH --nodes=1
#SBATCH --ntasks-per-node=2 
#SBATCH --job-name=cufflinks-test
#SBATCH --output=output.%j.cufflinks-test
#SBATCH --time=00:10:00

#### SLURM task using 1 Node with 2 Processors per Node cufflinks test to run for 10 minutes.

module purge
module load apps/cufflinks/2.2.1

CUFFLINKS_OUTPUT="${PWD}"

cufflinks --quiet --num-threads $SLURM_NTASKS --output-dir $CUFFLINKS_OUTPUT input.bam

Next, you can change to your job’s directory, and run the sbatch command to submit the job:

[user@login0 ~]$ cd my/jobdir
[user@login0 jobdir]$ sbatch ./cufflinks-test.sh

You can view the status of your job with the “squeue -u <username>” command

Documentation

Home Page, User Guides, and Manuals

Cufflinks Home Page
- http://cole-trapnell-lab.github.io/cufflinks/
Cufflinks User Manual:
- http://cole-trapnell-lab.github.io/cufflinks/manual/

More Job Information

See the following for more detailed job submission information:

Reporting Bugs

Report bugs with Cufflinks to the IT Help Desk: rc-help@usf.edu