Extract text from genomic contact matrices (HIC)
To convert HIC contact matrices to another format, you need Juicebox or other Data software.
To convert other file formats to the "Genomic Contact Matrix" file type, you need software like Juicebox or a similar tool.
The .HIC file is a highly compressed biological data format used to store chromosome contact maps generated by Hi-C sequencing. These files serve as the primary storage mechanism for visualizing 3D genome architecture. The main software used to open and interact with these files is Juicebox and its associated command-line utility, Juicer Tools, both developed by Aiden Lab.
Users often face massive challenges when handling .HIC files. Because they store millions of pairwise genomic interactions across multiple resolutions, these files routinely exceed several gigabytes in size. It is a proprietary, closed binary format that is completely unreadable by standard software. Attempting to open a .HIC file in standard text editors or spreadsheet applications will instantly crash your system. Furthermore, you cannot natively view these files in web browsers or generic data visualization tools.
To perform custom bioinformatics analysis in Python or R, users usually need to convert or extract the embedded data into flat formats like TXT, CSV, or .BEDPE. Be warned: extracting a highly compressed .HIC file into a raw text matrix will result in massive file sizes and the complete loss of the format's fast-zooming indexing structure.
Because of its extreme specialization, standard online file converters will fail to process a .HIC file. Often, only the original bioinformatics software can properly read or export the multi-resolution 2D genomic data. However, convert.guru can still identify the file format, inspect the file, and show text or internal content. Because our analysis detects the underlying ZIP-based compression structure embedded within many .HIC files, viewing raw metadata or partial extraction may still be possible. Just drag and drop your file to see what it is and convert it if supported.
Convert.Guru analyzes your HIC file, detects the exact format, and lets you read the text inside.
Users also converted HEIC, GPX, PHO and QZTP files.
If you want to convert HIC file to , you can use Juicebox or similar software from the "Genomic Contact Data Storage" category. In the File menu, look for Save As… or Export….
To convert files to HIC, try Juicebox or another comparable tool in the "Genomic Contact Data Storage" category.
The history of Convert.Guru began over 25 years ago in California with Tom Simondi’s file-format database. A former contributor to Space Shuttle development and a software pioneer of the 1980s, Simondi established a trusted resource for file type analysis that was even referenced by Microsoft Windows XP. Today, we use modern technology to process and convert thousands of file formats while continually improving our HIC converter.