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.
module load cufflinks cufflinks [options] <aligned_reads.(sam/bam)> ...
#PBS -l nodes=3:ppn=8,pmem=1000mb,walltime=8:00:00 #PBS -m abe #PBS -M email@example.com module load cufflinks cufflinks -p $PBS_NP <aligned_reads.sam/bam>