3D 基因组分析
1. 构建接触矩阵
1.1 将HI-C数据比对到参考基因组
# 构建bwa索引
bwa index -p ref/genome ref/genome.fa
# 比对（注意，双端的测序数据要分开比对）
bwa mem -A1 -B4 -E50 -L0 t 1 genome.fasta leaf_Rep1_R1.fastq.gz | samtools view -hb –threads 1 -o leaf_Rep1_R1.bam –
bwa mem -A1 -B4 -E50 -L0 t 1 genome.fasta leaf_Rep1_R2.fastq.gz | samtools view -hb –threads 1 -o leaf_Rep1_R2.bam –
1.2 生成酶切片段
hicFindRestSite –fasta genome.fa –searchPattern GATC -o rest_site.bed
1.3 构建接触矩阵
hicBuildMatrix –samFiles leaf_Rep1_R1.bam leaf_Rep1_R2.bam –genomeAssembly genome.fa –outBam leaf_Rep1.bam –outFileName leaf_Rep1.cool –QCfolder leaf_Rep1 –restrictionCutFile rest_site.bed –binSize 1000 –threads 1 –minDistance 500 –maxLibraryInsertSize 1500 –inputBufferSize 400000 –restrictionSequence GATC –danglingSequence GATC