STAR.pbs

#!/bin/bash

## Introductory Example for running STAR
## Copyright (c) 2013 The Center for Advanced Research Computing
##                            at The University of New Mexico

#PBS -lnodes=1:ppn=8
#PBS -lwalltime=24:00:00
#PBS -S /bin/bash

# Load the environment modules system
# source /etc/profile.d/modules.sh

# Load the environment module for STAR version 2.4.2a
module load star/2.4.2a/gcc/4.8.4

# Change to the directory that this job was submitted from
cd $PBS_O_WORKDIR

# Call the executable to run on your input file. 
# !!!!  You must replace <parameters> to match your calculation !!!!
STAR --runThreadN 8 --runMode alignReads --genomeDir ./genomeDir/Smansoni --readFilesIn BpMollR1_1_paired.fq BpMollR1_2_paired.fq --outFileNamePrefix BpMollR1 --outReadsUnmapped Fastx --outSAMtype BAM SortedByCoordinate