juicer 学习

首先下载juicer后，另建一个juicer-work的文件夹，juicer-work里面各个文件夹的位置要放对，reference, fastq等，注意script里放上CPU或其他集群里的common文件夹。

1. bwa index mygenome.fasta

2. python generate_site_positions.py HindIII Aox-genome ../reference/Aox-genome.fasta

确保选择了正确的酶，在generate_site_positions.py里可以看到各个酶的名字及序列

3.awk 'BEGIN{OFS="\t"}{print $1, $NF}' Aox-genome_HindIII.txt > Aox-genome.chrom.sizes

4. nohup ./scripts/juicer.sh -d /sas/supercloud-kong/zhaocaiyao/software/juicer-work/ -p restriction_sites/Aox-genome.chrom.sizes -y restriction_sites/Aox-genome_HindIII.txt -z reference/Aox-genome-V0.FINAL.fasta -D ./ -t 10 &