# 5.2. Hi-C dataset format¶

An Hi-C dataset is a folder containing the heatmaps and a metadata.json file.

As its name suggests, the JSON file holds basic metadata about the dataset. Its format is the following:

{
"Binsize": 5000,
"Assembly": "droYak2",
"Species": "Drosophila yakuba",
"Comment": "nm_none - No NaN",
"Date": "",
"Dataset": "Dyak_c",
"Dims": {
"2R|2R": [1234, 1234],
"4|X": [345, 2345],
...
}
"MapFiles": {
"2R|2R": "2R_2R.tsv.gz",
"4|X": "4_X.tsv.gz",
...
}
}


Note

The MapFiles maps to the key-value store of the heatmaps files. The files can be named in any way, but not the key. They must be of the form X|Y.

## 5.2.2. Heatmap files¶

There are one file per matrix. The matrices are written as tabulated-separated files, optionally gzipped. There is no header row, and 3 columns:

• row position (an integer),
• column position (an integer),
• value (a floating-point number).

In order to save space, only the non-empty boxes from the matrices are written (the matrices are sparse).