#!/bin/bash
#SBATCH -t 2:00:00
#SBATCH --nodes=1 --ntasks-per-node=1
#SBATCH --export=NONE

#module load Bowtie2/2.3.5.1-GCC-8.3.0

#bowtie2 -x /data/mramseylab/genomes/hpara/hpara -q -k 1 -U /data/mramseylab/raw_reads/2014_whiteley/SRR1045151.fastq -S SRR1045151.sam
#bowtie2 -x /data/mramseylab/genomes/hpara/hpara -q -k 1 -U /data/mramseylab/raw_reads/2014_whiteley/SRR1045152.fastq -S SRR1045152.sam
#bowtie2 -x /data/mramseylab/genomes/hpara/hpara -q -k 1 -U /data/mramseylab/raw_reads/2014_whiteley/SRR1045153.fastq -S SRR1045153.sam
#bowtie2 -x /data/mramseylab/genomes/hpara/hpara -q -k 1 -U /data/mramseylab/raw_reads/2014_whiteley/SRR1045154.fastq -S SRR1045154.sam
#bowtie2 -x /data/mramseylab/genomes/hpara/hpara -q -k 1 -U /data/mramseylab/raw_reads/2014_whiteley/SRR1045155.fastq -S SRR1045155.sam
#bowtie2 -x /data/mramseylab/genomes/hpara/hpara -q -k 1 -U /data/mramseylab/raw_reads/2014_whiteley/SRR1045157.fastq -S SRR1045157.sam
#bowtie2 -x /data/mramseylab/genomes/hpara/hpara -q -k 1 -U /data/mramseylab/raw_reads/2014_whiteley/SRR1534916.fastq -S SRR1534916.sam
#bowtie2 -x /data/mramseylab/genomes/hpara/hpara -q -k 1 -U /data/mramseylab/raw_reads/2014_whiteley/SRR1534917.fastq -S SRR1534917.sam

module load SAMtools/1.9-foss-2018b

samtools view -S -b SRR1045151.sam > SRR1045151.bam