Share a PBS script for STAR (version 2.7.3a) alignment for RNA-seq dataset (pair-end) running in MCRI PBS system. STAR manual can be downloaded here.

#!/bin/sh
set -eu
cd ~/hpc/project/RnaseqBacterial/extdata/rnaseq
mkdir temp
mkdir bam
for i in $(ls *.fastq | rev | cut -c 14- | rev | uniq)
do
echo \#PBS -N $i  > $i.job
echo \#PBS -l nodes=1:ppn=6 >> $i.job
echo \#PBS -M Guo.shicheng\@marshfieldresearch.org >> $i.job
echo \#PBS -m abe  >> $i.job
echo \#PBS -o $(pwd)/temp/ >>$i.job
echo \#PBS -e $(pwd)/temp/ >>$i.job
echo cd $(pwd) >> $i.job
OPTS_P1="--outReadsUnmapped Fastx --outSAMtype BAM SortedByCoordinate --limitBAMsortRAM 100000000000 --genomeLoad LoadAndKeep --seedSearchStartLmax 8 --outFilterMultimapNmax 100 --outFilterMismatchNoverLmax 0.5"
genomeDir="/gpfs/home/guosa/hpc/db/hg19/STAR"
echo STAR --runThreadN 6 --outBAMsortingThreadN 6 --genomeDir $genomeDir --outFileNamePrefix ~/hpc/project/RnaseqBacterial/extdata/rnaseq/bam/$i --readFilesIn $i\_R1_001.fastq $i\_R2_001.fastq >> $i.job
qsub $i.job
done