All raw and processed files placed:
	Server aquarium - /data/aapopov/Projects/ChickenOocyt/NSN_mouse_oocytes/
Data SRAs: 
	described in the names of directories
Genome: 
	GenCode GCA_000001635.9 - GRCm39
Juicer:
	Experiment description: Juicer version 1.6; BWA 0.7.17-r1188; 20 threads; openjdk version "1.8.0_152-release"; /home/aapopov/tool/juicer1.6_compact-main/scripts/juicer.sh -g GRCm39 -d /data/aapopov/Projects/ChickenOocyt/NSN_mouse_oocytes/SRR3343947_pass -s DpnII -y /data/aapopov/Projects/ChickenOocyt/Mouse_genome/GRCm39_DpnII.txt -p /data/aapopov/Projects/ChickenOocyt/Mouse_genome/GRCm39.fasta.chrom.sizes -D /home/aapopov/tool/juicer1.6_compact-main -z /data/aapopov/Projects/ChickenOocyt/Mouse_genome/GRCm39.fasta -t 20


Cooler:
	cooler cload pairs -c1 2 -p1 3 -c2 6 -p2 7 /data/aapopov/Projects/ChickenOocyt/Mouse_genome/GRCm39_for_cooler.fasta.chrom.sizes:1000 ...

hicConvertFormat:
	hicConvertFormat --matrices ${DIR}_1000.cool --outFileName ${DIR}.mcool --inputFormat cool --resolutions 1000 5000 10000 20000 50000 100000 300000 500000 1000000 --outputFormat mcool