Información general

Cufflinks is a reference-guided assembler for RNA-Seq experiments. It
simultaneously assembles transcripts from reads and estimates their relative
abundances, without using a reference annotation. The software expects as
input RNA-Seq read alignments in SAM format (http://samtools.sourceforge.net).

Versión instalada

2.2.0

Cómo usar

#!/bin/bash
#PBS -l nodes=1:ppn=4:rh7
#PBS -l mem=8gb
#PBS -l walltime=24:00:00

cd $PBS_O_WORKDIR

export PATH=/software/anaconda2/bin:$PATH
export LD_LIBRARY_PATH=/software/anaconda2/lib:$LD_LIBRARY_PATH

NPROCS=$( cat $PBS_NODEFILE | wc -l )

cufflinks -p $NPROCS -o C1_R2_clout C1_R2_thout/accepted_hits.bam

Más información

http://cole-trapnell-lab.github.io/cufflinks/