Introduction: The Hi­C tool is a graphical user interface(GUI) implementation and compilation of the Bayesian 3D constructor for Hi­C data (BACH) and BACH­MIX, an extended BACH algorithm to characterize structural variations of chromatin folding. The tool’s purpose is to allow a more user friendly way of data input. This manual will explain how to use the software and the various functionalities. Setup: For the program to work, R is required. Please install R and add it to the environment path. 1. From the desktop, right­click My Computer and click Properties. 2. Go to Advanced System Setting. 3. In the Advance tab, click on environment variables. 4. Under the System variables section, find Path, highlight it and click Edit. 5. Add the path to R into the line, separated by a semi­colon. ( ; ) Example: if R is installed under C:\Program Files\R\R­3.0.1 then add “;C:\Program Files\R\R­3.0.1\bin" into the path. Some users have problem with D3DCOMPILER_43.dll error. This problem can be solved by downloading the latest DirectX from microsoft. To start the program, simply double click HiC.exe The Program Files: There are hidden folders, executables and .dll files within the folder. They are crucial to the execution of the program and should not be tampered with. 1. HiC.exe: This is the main executable, double click to execute the program. 2. BACH_result: The default folder for storing results of BACH algorithm. 3. BACH_MIX_result: The default folder for storing results of BACH­MIX algorithm. 4. Saves: The default folder where user’s settings will be saved. 5. BACH_input.txt: Text file which stores the parameters of the last BACH algorithm execution. 6. BACH_MIX_input.txt: Text file which stores the parameters of the last BACH­MIX algorithm execution. The Main functionalities: Main Menu: The main menu displays the option of running either BACH or BACH­MIX algorithm. BACH: The BACH algorithm is as following. Heatmap File/Covariate File/Output Directory: The files can be chosen by clicking the button on the right. A file dialog will appear. Simply choose the file desired. Output directory is by default in the same folder as HiC.exe, under folder BACH_result Other parameters: The program will display the default values. Simply specify the desired values by typing in the numbers in appropriate boxes. BACH­MIX algorithm: File for genomic region A, B/ Heatmap file/ Covariate file/ Nuisance parameters file, Output file path: The files can be chosen by clicking the button on the right. A file dialog will appear. Simply choose the file desired. Output directory is by default in the same folder as HiC.exe, under folder BACH_MIX_result. Other parameters: The program will display the default values. Simply specify the desired values by typing in the numbers in appropriate boxes. Additional Features: The tool features additional features for both algorithms on the toolbars. 1. Files: a. Quick Load Last Run:This function will allow the users fast access to the parameters entered in the last execution of the respective algorithm. b. Save Setup: This function will allow the users to save current parameters into a file (.bsave for BACH, .bmsave for BACH­MIX). This allows the user to easily access frequently used parameters. c. Load Setup: This function will allow the users to load previously saved setup. 2. Help: a. Help: A help menu for general usage of the program. By selecting from the combo box on the top left hand corner, the user can easily get information on a particular aspect of the program. b. About: Displays the tool’s information. The tool is designed and developed by Yikai Lee, using Qt 5.0.2 under the LGPL license. The Qt libraries used have not been modified. The software as well as both algorithms are open source. Comments, suggestions, questions are welcomed, and should be directed to Ming Hu. If you are interested, a copy of source code will be provided upon request. Email: [email protected]..