.. Copyright (C) 2023 Roberto Rossini SPDX-License-Identifier: MIT Quickstart (CLI) ################ First, install hictk with one of the methods listed in the :doc:`Installation <./installation>` section. Next, verify that hictk was installed correctly with: .. code-block:: console 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 ------------------------ .. code-block:: sh hictk validate interactions.cool --validate-index hictk validate interactions.hic For more detailed examples refer to :doc:`File validation <./file_validation>` Reading interactions -------------------- hictk supports reading interactions from .hic and .cool files through the ``hictk dump`` command: .. code-block:: console 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 :doc:`Reading interactions <./reading_interactions>` Other operations ---------------- * :doc:`Balancing Hi-C matrices <./balancing_matrices>` * :doc:`Converting single-resolution files to multi-resolution <./creating_multires_files>` * :doc:`Creating .cool and .hic files <./creating_cool_and_hic_files>` * :doc:`Dumping tabular information to stdout <./reading_interactions>` * :doc:`File validation <./file_validation>` * :doc:`Format conversion <./format_conversion>` * :doc:`Reading file metadata <./file_metadata>` API === Refer to :doc:`Quickstart (API) <./quickstart_api>`.