#190927_align.sh
#Alignment of WGRS data

for f in *_R1_001.fastq.gz;

do
  PREFIX="${f%_R1_001.fastq.gz}"

  bowtie2 -N 1 -D 20 -R 3 -L 20 -i S,1,0.50 --non-deterministic --no-mixed -p 6 -x ~/Google\ Drive\ File\ Stream/Shared\ drives/KRamsey\ Lab/GenomeInfo/LVS_genome_info/LVSgenome -1 $PREFIX\_R1_001.fastq.gz -2 $PREFIX\_R2_001.fastq.gz -S $PREFIX.sam

shift
done