Additional file 3: Table S2. of HiC-bench: comprehensive and reproducible Hi-C data analysis designed for parameter exploration and benchmarking

HiC-bench input-output objects. The table summarizes the inputs and outputs of the TAD-calling task using three different methods with parameter values stored in the params files (column 2). The first column describes the tree structure of the input directories that are essentially the different Hi-C matrices for each sample, before (filtered) and after matrix correction using different methods (e.g., IC). The second column lists all the different parameter scripts and the third column corresponds to the tree structure of the generated output objects. (XLSX 10 kb)