Crispr/Cash9
_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
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