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.
Note
Please follow the recommended citation guidelines from the developers when you use the tool in research.
Versions
Cluster |
Version(s) |
|---|---|
ANVIL |
2.2.1 |
BELL |
2.2.1 |
GAUTSCHI |
2.2.1 |
NEGISHI |
2.2.1 |
SCHOLAR |
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 -p wholenode # Partition name
#SBATCH -t 1:00:00
#SBATCH -N 1
#SBATCH -n 1
#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
module biocontainers cufflinks
# Your cufflinks workflow...
#!/bin/bash
#SBATCH -A mygroup # Group name
#SBATCH -p cpu # Partition name
#SBATCH -q normal # QOS name (optional)
#SBATCH -t 1:00:00
#SBATCH -N 1
#SBATCH -n 1
#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
module biocontainers cufflinks
# Your cufflinks workflow...
#!/bin/bash
#SBATCH -A mygroup # Group name
#SBATCH -p ai # Partition name
#SBATCH --gres=gpu:1 # Number of GPUs
#SBATCH -q normal # QOS name (optional)
#SBATCH -t 1:00:00
#SBATCH -N 1
#SBATCH -n 1
#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
module biocontainers cufflinks
# Your cufflinks workflow...
#!/bin/bash
#SBATCH -A mygroup # Group name
#SBATCH -p a100 # Partition name
#SBATCH --gres=gpu:1 # Number of GPUs
#SBATCH --mem=2G # Memory
#SBATCH -q normal # QOS name (optional)
#SBATCH -t 1:00:00
#SBATCH -N 1
#SBATCH -n 1
#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
module biocontainers cufflinks
# Your cufflinks workflow...
#!/bin/bash
#SBATCH -A queue # Queue name
#SBATCH -t 1:00:00
#SBATCH -N 1
#SBATCH -n 1
#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
module biocontainers cufflinks
# Your cufflinks workflow...