1. 构建基因组index

  1. hisat2-build \
  2.   -p 20\
  3.   ./genome.fa \
  4.   ./reference \
  5.   &> hisat2-build.log

2. 比对

  1. hisat2 \
  2.   --new-summary \
  3.   -p 20 \
  4.   -x ./reference \
  5.   -1 ${sample}_1.fastp.fq.gz \
  6.   -2 ${sample}_2.fastp.fq.gz \
  7.   -S ${sample}.sam  \
  8.   &> ${sample}.log

3. sam2bam并sort

  1. samtools sort \
  2.   ../tpm/${sample}.sam \
  3.   -o ${sample}.sort.bam \
  4.   -@ 20
  • samtools sort
  • samtools view

参考

HISAT2 github 地址：http://daehwankimlab.github.io/hisat2/

samtools：http://samtools.sourceforge.net/