<p>Turns out HiC file does store such metadata.</p>

<p><code>straw</code> tool from Aiden Lab contains a script (<a href="https://github.com/aidenlab/straw/blob/master/python/read_hic_header.py" rel="nofollow noreferrer">read_hic_header.py</a>) that prints out the metadata from a given HiC file. Usage: <code>read_hic_header.py &lt;hic file or URL&gt; [verbose]</code></p>

<p>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 <a href="https://github.com/rraadd88/straw.git" rel="nofollow noreferrer">fork</a>.</p>

<pre><code>from straw import straw_module
straw_module.read_metadata(infile,verbose=False)

Args
    infile: str, path to the HiC file 
    verbose: bool, print the metadata if True else return the metadata
Returns
    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). 
</code></pre>

CC BY-SA 4.0
2020-04-06T14:54:06.203Z
2020-04-06T14:54:06.203Z
user345394
<p>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.</p>

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

<p>(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.).</p>

<reference-genome><chromosome-capture><hi-c>
How to identify the reference genome assembly used to create a .hic file?
# How to identify the reference genome assembly used to create a .hic file?

(Asked by: username_0 on 2020-04-05)

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.).

**Tags:** reference-genome, chromosome-capture, hi-c

---

## 1 answers

### Answer by username_0 on 2020-04-06. Score: 1 | Accepted answer

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  [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
straw_module.read_metadata(infile,verbose=False)

Args
    infile: str, path to the HiC file 
    verbose: bool, print the metadata if True else return the metadata
Returns
    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).


---

