Quickstart (CLI)

First, install hictk with one of the methods listed in the Installation section.

Next, verify that hictk was installed correctly with:

user@dev:/tmp$ hictk --version
hictk-v2.2.0

Command line interface

hictk CLI supports performing common operations on .hic and .cool files directly from the shell.

Verifying file integrity

hictk validate interactions.cool --validate-index

hictk validate interactions.hic

For more detailed examples refer to File validation

Reading interactions

hictk supports reading interactions from .hic and .cool files through the hictk dump command:

user@dev:/tmp$ hictk dump interactions.cool
0     0       1745
0     1       2844
0     2       409
...

user@dev:/tmp$ hictk dump interactions.cool --join
chr2L 0       10000   chr2L   0       10000   1745
chr2L 0       10000   chr2L   10000   20000   2844
chr2L 0       10000   chr2L   20000   30000   409
...

For more detailed examples refer to Reading interactions

Other operations

• Balancing Hi-C matrices

• Converting single-resolution files to multi-resolution

• Creating .cool and .hic files

• Dumping tabular information to stdout

• File validation

• Format conversion

• Reading file metadata

API

Refer to Quickstart (API).