_R1.fastq.gz

Index the reference sequence for bwa

bwa index -p Cash9_R1_ref Cash9_R1_ref.fa

Align the reads to the reference sequence using bwa mem and output as a SAM file

bwa mem -t 8 Cash9_R1_ref Cash9/Crispr/Cash9_R1.fastq.gz > Cash9/Crispr/Cash9-AlignedReads-BWA-MEM.sam