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.

To run this software interactively in a Linux environment run the commands:
module load cufflinks
cufflinks [options] <aligned_reads.(sam/bam)> ...
Cufflinks programs may also be submitted to a queue using PBS script such as the one below:
#PBS -l nodes=3:ppn=8,pmem=1000mb,walltime=8:00:00
#PBS -m abe

module load cufflinks

cufflinks -p $PBS_NP <aligned_reads.sam/bam>
Note the use of -p $PBS_NP; this option is used to specify the number of threads used by Cufflinks.
To see a list of options, type the command
cufflinks -h
Significant changes (improvements) have been made to Cufflinks command-line options, and to how Cufflinks calculates differential expression. Output file formats have also been changed.
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