Hi-C Processing

Hi-C files are fun and very variable in their format. Here is wrapper that uses hicstraw to bring a .hic-file into coordinate format, with one file per chromosome and each file with bin | bin | contact. Due to the size of Hi-C files, no example is provided here. There is an alternative bash wrapper in the STARE repository that uses juicer’s dump.

HiCStraw

With hicstraw to write the coo-format from a .hic-file with one file per chromosome. Works with a local hic-file or remote URL.

usage: HiCStraw.py [-h] --hic HIC --normalization NORMALIZATION
                   [--resolution RESOLUTION] --out_folder OUT_FOLDER

Named Arguments

--hic

Path to .hic file or an URL.

--normalization

Which normalization to apply, has to be present in the hic file, will otherwise fail.

--resolution

Resolution with which to write the output.

Default: 5000

--out_folder

Folder where the files (one per chr) will be written to.