cufflinks
Link to section 'Description' of 'cufflinks' Description
Cufflinks assembles transcripts, estimates their abundances, and tests for differential expression and regulation in RNA-Seq samples.
Link to section 'Versions' of 'cufflinks' Versions
- Anvil: 2.2.1
Link to section 'Module' of 'cufflinks' Module
You can load the modules by:
module load cufflinks
Link to section 'Example job' of 'cufflinks' Example job
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 load cufflinks
cufflinks -p 8 -G transcript.gtf --library-type fr-unstranded -o cufflinks_output tophat_out/accepted_hits.bam