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Analysis workflow for Hi-C (A), cHi-C (B) and scHi-C (C). All the workflows use the hicBuildMatrix to create the individual contact matrices. Hi-C and cHi-C supports HiCExplorer’s h5 and cool interaction matrix file format; however, scHi-C pipeline creates one cool file per cell. These files can then be merged into a single multi-cool (scool) matrix with scHicMergeToSCool.
