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#!/bin/bash
#$ -V
#$ -cwd
#$ -pe 12way 12
#$ -q normal
#$ -l h_rt=00:30:00
#$ -A BME_2012
#$ -o output.$JOB_ID
#$ -e error.$JOB_ID
##$ -m be
##$ -M <your email would go here>
#$ -N align_bwa_01
module load bwa/0.6.2
bwa aln -t 12 -f SRR030257_1.sai NC_012967.1.fasta SRR030257_1.fastq
bwa aln -t 12 -f SRR030257_2.sai NC_012967.1.fasta SRR030257_2.fastq
bwa sampe -f SRR030257.sam NC_012967.1.fasta SRR030257_1.sai SRR030257_2.sai SRR030257_1.fastq SRR030257_2.fastq
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