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


module load bowtie2/2.2.4

cd data/kramseylab/compressed_fastq/WGRS_Fno
bowtie2 -N 1 -L 20 -i S,1,0.50 -D 20 --non-deterministic -x /data/kramseylab/genomefiles/FnotReference -1 /data/kramseylab/compressed_fastq/WGRS_Fno/LADL--07-285A_R1.fastq -2	/data/kramseylab/compressed_fastq/WGRS_Fno/LADL--07-285A_R2.fastq -S /data/kramseylab/sam/FnotAlignments.sam 




#module load bowtie2/2.2.4

#cd data/kramseylab/compressed_fastq/WGRS_Fno
#bowtie2 -N 1 -L 20 -i S,1,0.50 -D 20 --non-deterministic -x 
#/data/kramseylab/genomefiles/FnotReference -1 
#/data/kramseylab/compressed_fastq/WGRS_Fno/LADL--07-285A_R1.fastq -2	
#/data/kramseylab/compressed_fastq/WGRS_Fno/LADL--07-285A_R2.fastq -S	
#/data/kramseylab/sam/FnotAlignments.sam