Note: This page relates to the 2013 single-cell Hi-C paper. For the recent 2017 paper, see single-cel Hi-C: pipeline and analysis

Scell_hicpipe is a set of scripts the process single cell Hi-C libraries, as was done in the paper "Single-cell Hi-C reveals cell-to-cell variability in chromosome structure" by Takashi Nagano, Yaniv Lubling, Tim J. Stevens, Stefan Schoenfelder, Eitan Yaffe, Wendy Dean, Ernest D. Laue, Amos Tanay & Peter Fraser (Nature, 2013). The input for the pipeline is a list of mapped read pairs and a list of restriction enzyme sites in the genome, and the output is a list of interacting fragment end pairs. The pipeline itself is scell_hicpipe_core_1_2.tar.gz, and an example input dataset (for cell-5 in the above Nagano et al. paper) can be found in scell_hicpipe_test_project_1_0.tar.gz. The list of domains inferred from the ensemble Hi-C map and used in the above paper is available here: Nagano2013_SuppTable1.xlsx For questions and more information please email Yaniv Lubling