SAM Format

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Mapped within the insert size and in correct orientation:

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Tag

• NM:i:0: number of reads
• MD:Z:60A: 60 match, A mutation

随机读取基因组的任意位置

samtools index -@ 2 input.bam
samtools view -h input.bam char:5000-5500

deuplication

DNA remove duplications by Picard
RNA remove duplications by UMI

去重的经验

• 比较好的解决方案是文库构建时加入UMI或barcode
• RNA表达量分析，一般不去重
• DNA数据分析一般去重
  • Chip-seq
  • m6A-seq
  • ATAC-seq, DNase-seq, MNase-seq
  • Hi-C
  • BS-seq

reference

https://samformat.info/sam-format-flag