HiC数据处理之juicer

1. Try

安装juicer和3ddna。

建立fastq文件夹，cat分别合并 R1和R2测序文件。

建立reference文件夹，放入.fa文件，用以下命令进行预处理

mamba activate juicer
mamba install -y bwa
bwa index genome.fa
bwa index genome.fa

python ~/software/juicer-1.6/misc/generate_site_positions.py MboI genome genome.fa
awk 'BEGIN{OFS="\t"}{print $1, $NF}' genome_MboI.txt  > skgenome.chrom.size

mkdir fastq
ln -s /mnt/caigui/41_sk_genome_129M/37_hicpro/fastq/sample1/reads_R1.fastq.gz fastq
ln -s /mnt/caigui/41_sk_genome_129M/37_hicpro/fastq/sample1/reads_R2.fastq.gz fastq

# 整理目录如下

运行

nohup ~/software/juicer-1.6/CPU/juicer.sh \
    -g genome \
    -s MboI \
    -z /mnt/caigui/41_sk_genome_129M/39_juicer/genome.fa \
    -y /mnt/caigui/41_sk_genome_129M/39_juicer/genome_MboI.txt \
    -p /mnt/caigui/41_sk_genome_129M/39_juicer/skgenome.chrom.size \
    -D /home/caigui/software/juicer-1.6/ \
    -t 40 &> juicer.log &

juicer处理结果中的align文件夹中的inter_30.hic可以进行可视化

2. 使用juicer_tools进行下游分析

https://github.com/aidenlab/Juicebox/releases/download/v2.20.00/juicer_tools.2.20.00.jar

cd ~/software/juicer_tools
wget https://github.com/aidenlab/Juicebox/releases/download/v2.20.00/juicer_tools.2.20.00.jar

cd /mnt/caigui/41_sk_genome_129M/39_juicer/aligned
java -jar ~/software/juicer_tools/juicer_tools.2.20.00.jar arrowhead inter_30.hic inter_30.hic.arrowhead