StaticSection

Matrix Aggregation and Normalization

For Capture Hi-C, the Hi-C pipeline is run with the default restriction enzyme-based intra-fragment contact filtering, but matrix balancing is not performed.

4DN DCIC provides a Hi-C matrix in two different formats: .mcool format and .hic format. The two files are generated from the same pairs file as input filtered contact list. Both files contain multiple resolutions.

** .hic format**

• A .hic file is produced by Juicertools (version 1.8.9-cuda8) and can be visualized using Juicebox
• The matrix is normalized using the VC, VC_SQRT, KR methods.

** .mcool format**

• An .mcool file is produced by Cooler (version 0.7.6) and can be visualized using HiGlass.
• The diagonal and the rows/columns with a low value are removed from the matrix.
• The .mcool file also contains the normalization vectors generated by Juicertools (same as in a .hic file generated from the same pairs file)

Resolutions: Both mcool and hic files contain the following resolutions.

• 1kb, 2kb, 5kb, 10kb, 25kb, 50kb, 100kb, 250kb, 500kb, 1Mb, 2.5Mb, 5Mb, 10Mb