#!/bin/bash
#SBATCH -t 6:00:00
#SBATCH --nodes=1 --ntasks-per-node=1
#SBATCH --export=NONE
#SBATCH --mail-user=jamie_wandzilak@uri.edu
#SBATCH --mail-type=BEGIN,END,FAIL

module load bowtie2/2.2.4

cd /data/kramseylab/compressed_fastq/2001_RNA-Seq/

for f in *_R1.fastq;
do
        PREFIX1="${f%_R1.fastq}"
        bowtie2 -N 1 -L 20 -i S,1,0.50 -D 20 --non-deterministic -x /data/kramseylab/genomefiles/LVSReference -1 $PREFIX1\_R1.fastq -2 $PREFIX1\_R2.fastq -S /data/kramseylab/sam/rnaseq_LVS_sam/$PREFIX1.sam

done