I have a bunch of .hic files of different species. But, I don't know which reference genome assembly (e.g. GRCh37 or GRCh38 in the case of human genome) the genomic co-ordinates of the .hic file correspond to. So I wonder if there is any way to figure out the version of the reference genome assembly from a .hic file.

Therefore, my question is: Does .hic file contain metadata such as the version of reference genome assembly? If yes, then how could I access it?

(I could obtain the information I need by digging into the methods sections of each paper corresponding to each .hic file. But it would be much better if I could get that right-away from the .hic file.).


1 Answer 1


Turns out HiC file does store such metadata.

straw tool from Aiden Lab contains a script (read_hic_header.py) that prints out the metadata from a given HiC file. Usage: read_hic_header.py <hic file or URL> [verbose]

In order to obtain the metadata in the form of a dictionary, one may consider using a function of the same tool that is currently available in my fork.

from straw import straw_module

    infile: str, path to the HiC file 
    verbose: bool, print the metadata if True else return the metadata
    metadata: dict, the metadata is returned if verbose is False. 
                Keys of the metadata: 
                HiC version, 
                Master index, 
                Genome ID (str), 
                Attribute dictionary (dict), 
                Chromosomes (dict), 
                chromosomes2length (dict), 
                Base pair-delimited resolutions (list), 
                Fragment-delimited resolutions (list). 

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