Reading interactions#
hictk supports reading interactions from .hic and .cool files through the hictk dump command.
By default, interactions are dumped to stdout in COO format (row, column, count):
user@dev:/tmp$ hictk dump data/4DNFIZ1ZVXC8.hic9 --resolution 1000
7 7 1745
7 12 1766
7 17 1078
...
Use option --join to instead dump interactions in bedgraph2 format:
user@dev:/tmp$ hictk dump data/4DNFIZ1ZVXC8.mcool --resolution 1000 --join | head -n 3
chr2L 7000 8000 chr2L 7000 8000 1745
chr2L 7000 8000 chr2L 12000 13000 1766
chr2L 7000 8000 chr2L 17000 18000 1078
...
All operations work on .hic as well as .[m]cool files:
user@dev:/tmp$ hictk dump data/4DNFIZ1ZVXC8.mcool --resolution 1000
7 7 1745
7 12 1766
7 17 1078
...
user@dev:/tmp$ hictk dump data/4DNFIZ1ZVXC8.mcool::/resolutions/1000
7 7 1745
7 12 1766
7 17 1078
...
Dump balanced or expected interactions:
user@dev:/tmp$ hictk dump data/4DNFIZ1ZVXC8.hic9 --resolution 1000 --join --balance SCALE
chr2L 7000 8000 chr2L 7000 8000 1681.679565429688
chr2L 7000 8000 chr2L 12000 13000 1386.554565429688
chr2L 7000 8000 chr2L 17000 18000 878.9703979492188
...
user@dev:/tmp$ hictk dump data/4DNFIZ1ZVXC8.hic9 --resolution 1000 --join --matrix-type expected
chr2L 7000 8000 chr2L 7000 8000 88.33206176757812
chr2L 7000 8000 chr2L 12000 13000 63.43805313110352
chr2L 7000 8000 chr2L 17000 18000 31.78345680236816
...
Dump interactions overlapping a region of interest:
user@dev:/tmp$ hictk dump data/4DNFIZ1ZVXC8.hic9 --resolution 1000 --join --range chr3L:20,000,000-25,000,000
chr3L 20002000 20003000 chr3L 20002000 20003000 2390
chr3L 20002000 20003000 chr3L 20007000 20008000 1285
chr3L 20002000 20003000 chr3L 20012000 20013000 490
...
user@dev:/tmp$ hictk dump data/4DNFIZ1ZVXC8.hic9 --resolution 1000 --join --range chr3L:20,000,000-25,000,000 --range2 chrX
chr3L 20002000 20003000 chrX 52000 53000 1
chr3L 20002000 20003000 chrX 157000 158000 1
chr3L 20002000 20003000 chrX 352000 353000 1
...
Dump tables other than pixels:
user@dev:/tmp$ hictk dump data/4DNFIZ1ZVXC8.hic9 --table chroms
chr2L 23513712
chr2R 25286936
chr3L 28110227
...
user@dev:/tmp$ hictk dump data/4DNFIZ1ZVXC8.hic9 --table normalizations
SCALE
VC
VC_SQRT
user@dev:/tmp$ hictk dump data/4DNFIZ1ZVXC8.hic9 --table resolutions
1000
5000
10000
...
Dump cis or trans interactions only:
user@dev:/tmp$ hictk dump data/4DNFIZ1ZVXC8.hic9 --resolution 1000 --cis-only --join
chr2L 7000 8000 chr2L 7000 8000 1745
chr2L 7000 8000 chr2L 12000 13000 1766
chr2L 7000 8000 chr2L 17000 18000 1078
...
user@dev:/tmp$ hictk dump data/4DNFIZ1ZVXC8.hic9 --resolution 1000 --trans-only --join
chr2L 7000 8000 chr2R 27000 28000 1
chr2L 7000 8000 chr2R 322000 323000 1
chr2L 7000 8000 chr2R 397000 398000 1
...