#!/bin/sh

wget -O GRCm39.fasta.gz https://ftp.ncbi.nlm.nih.gov/genomes/all/GCA/000/001/635/GCA_000001635.9_GRCm39/GCA_000001635.9_GRCm39_genomic.fna.gz
gunzip GRCm39.fasta.gz
bwa index GRCm39.fasta
samtools faidx GRCm39.fasta
cut -f1,2 GRCm39.fasta.fai > GRCm39.fasta.chrom.sizes
python /home/aapopov/tool/juicer1.6_compact-main/misc/generate_site_positions.py DpnII GRCm39 /data/aapopov/Projects/ChickenOocyt/Mouse_genome/GRCm39.fasta
/data/aapopov/Projects/ChickenOocyt/NSN_mouse_oocytes/juicer_start.sh