hicSumMatrix is combining two (or more) contact matrices of the same size to one. This is useful if replicates of an Hi-C experiment should be merged into one contact matrix to increase the coverage of the data. With Hi-C, real contacts are sometimes difficult to be distinguished from noise, especially with a low contact count. The more contacts are given, the more likely it is that a high number of contacts are biologically releveant. It is therefore common to merge biological and technical replicates of Hi-C experiments and hicSumMatrix address this concern.
This tool takes two or more Hi-C contact matrices and sum the contacts into one matrix. It is recommended to use uncorrected and unmerged matrices as input (use the direct output from hicBuildMatrix). Bin merging (hicMergeMatrixBins) and Hi-C contact matrix correction (hicCorrectMatrix) must be performed afterwards.
hicSumMatrix outputs a Hi-C contact matrix comprising the sum of all the contacts of the Hi-C matrices used as input.