Reading interactions¶

hictk supports reading interactions from .hic and .cool files using 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 1kbp

7   7   1745
7   12  1766
7   17  1078
...

Use the option --join to instead dump interactions in bedgraph2 format:

user@dev:/tmp$ hictk dump data/4DNFIZ1ZVXC8.mcool --resolution 1kbp --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 1kbp | head -n 3

 7   1745
 12  1766
 17  1078

user@dev:/tmp$ hictk dump data/4DNFIZ1ZVXC8.mcool::/resolutions/1000 | head -n 3

 7   1745
 12  1766
 17  1078

Dump balanced or expected interactions:

user@dev:/tmp$ hictk dump data/4DNFIZ1ZVXC8.hic9 --resolution 1kbp --join --balance SCALE | head -n 3

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 1kbp --join --matrix-type expected | head -n 3

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 1kbp --join --range chr3L:20,000,000-25,000,000 | head -n 3

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 1kbp --join --range chr3L:20,000,000-25,000,000 --range2 chrX | head -n 3

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 | head -n 3

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 | head -n 3

1000
5000
10000

See hictk dump help message for the complete list of supported tables.

Dump cis or trans interactions only:

user@dev:/tmp$ hictk dump data/4DNFIZ1ZVXC8.hic9 --resolution 1kbp --cis-only --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

user@dev:/tmp$ hictk dump data/4DNFIZ1ZVXC8.hic9 --resolution 1kbp --trans-only --join | head -n 3

chr2L 7000    8000    chr2R   27000   28000   1
chr2L 7000    8000    chr2R   322000  323000  1
chr2L 7000    8000    chr2R   397000  398000  1