Difference between revisions of "Applications/Cufflinks"
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With linkages to the following modules too: | With linkages to the following modules too: | ||
| − | * | + | * [[applications/Bowtie1|Bowtie1]] |
| + | * [[applications/Bowtie2|Bowtie2]] | ||
* [[applications/Samtools|Samtools]] | * [[applications/Samtools|Samtools]] | ||
| + | * [[applications/Tophat|Tophat]] | ||
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<pre style="background-color: black; color: white; border: 2px solid black; font-family: monospace, sans-serif;"> | <pre style="background-color: black; color: white; border: 2px solid black; font-family: monospace, sans-serif;"> | ||
| − | [username@login01 ~]$ module load cufflinks/2.2.1 | + | [username@login01 ~]$ module add cufflinks/2.2.1 |
| + | |||
| + | </pre> | ||
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| + | ===Batch Job=== | ||
| + | <!-- Edited from: https://wiki.rc.usf.edu/index.php/Cufflinks#Submitting_a_Job --> | ||
| + | <pre> | ||
| + | #!/bin/bash | ||
| + | #SBATCH -J cufflinks-test | ||
| + | #SBATCH -n 1 | ||
| + | #SBATCH --ntasks-per-node=2 | ||
| + | #SBATCH --output=output.%j.out | ||
| + | #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 cufflinks/2.2.1 | ||
| + | |||
| + | CUFFLINKS_OUTPUT="${PWD}" | ||
| + | cufflinks --quiet --num-threads $SLURM_NTASKS --output-dir $CUFFLINKS_OUTPUT input.bam | ||
</pre> | </pre> | ||
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* [http://cole-trapnell-lab.github.io/cufflinks/ http://cole-trapnell-lab.github.io/cufflinks/] | * [http://cole-trapnell-lab.github.io/cufflinks/ http://cole-trapnell-lab.github.io/cufflinks/] | ||
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Latest revision as of 16:55, 16 November 2022
Application Details
- Description: The Cufflinks suite of tools can be used to perform a number of different types of analyses for RNA-Seq experiments. The Cufflinks suite includes a number of different programs that work together to perform these analyses.
- Version: 2.2.1
- Modules: cufflinks/2.2.1
- Licence: Open source (Github)
Usage Examples
Cufflinks assembles transcripts, estimates their abundances, and tests for differential expression and regulation in RNA-Seq samples. It accepts aligned RNA-Seq reads and assembles the alignments into a parsimonious set of transcripts. Cufflinks then estimates the relative abundances of these transcripts based on how many reads support each one, taking into account biases in library preparation protocols.
It provides the following tools:
- cuffcompare
- cuffdiff
- cufflinks
- cuffmerge
- cuffnorm
- cuffquant
- gffread
- gtf_to_sam
With linkages to the following modules too:
[username@login01 ~]$ module add cufflinks/2.2.1
Batch Job
#!/bin/bash
#SBATCH -J cufflinks-test
#SBATCH -n 1
#SBATCH --ntasks-per-node=2
#SBATCH --output=output.%j.out
#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 cufflinks/2.2.1
CUFFLINKS_OUTPUT="${PWD}"
cufflinks --quiet --num-threads $SLURM_NTASKS --output-dir $CUFFLINKS_OUTPUT input.bam