Archivo por meses: mayo 2015

Cufflinks

Genética, Software de Cálculo

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/

 

TopHat

Genética, Software, Software de Cálculo

Información general

TopHat is a fast splice junction mapper for RNA-Seq reads. It aligns RNA-Seq reads to mammalian-sized genomes using the ultra high-throughput short read aligner Bowtie, and then analyzes the mapping results to identify splice junctions between exons.

Versión instalada

2.1.1

Cómo usar

Un ejemplo sería para el script de torque sería:

#!/bin/bash
#PBS -l nodes=1:ppn=8: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=$(wc -l $PBS_NODEFILE)

tophat --bowtie1 -p $NPROCS -G genes.gtf -o C1_R1_thout genome GSM794483_C1_R1_1.fq.gz GSM794483_C1_R1_2.fq.gz

Más información

Página web de TopHat.