FastqToBam

Build hg38 index

• bowtie2-build Homo_sapiens_assembly38.fasta hg38

Transfer fastq to sam file

• bowtie2 -x hg38 -1 111_R1.fq.gz -2 111_R2.fq.gz -S 111.sam --thread 20

Transfer sam to bam file

• samtools view -bS 111.sam -o 111.bam

Sort bam

• samtools sort 111.bam -o 111.sorted.bam --threads 20

Index bam

• samtools index 111.sorted.bam