ScHi-CSim: a flexible simulator that generates high-fidelity single-cell Hi-C data for benchmarking.

ABSTRACT: Single-cell Hi-C technology provides an unprecedented opportunity to reveal chromatin structure in individual cells. However, high sequencing cost impedes the generation of biological Hi-C data with high sequencing depths and multiple replicates for downstream analysis. Here, we developed a single-cell Hi-C simulator (scHi-CSim) that generates high-fidelity data for benchmarking. scHi-CSim merges neighboring cells to overcome the sparseness of data, samples interactions in distance-stratified chromosomes to maintain the heterogeneity of single cells, and estimates the empirical distribution of restriction fragments to generate simulated data. We demonstrated that scHi-CSim can generate high-fidelity data by comparing the performance of single-cell clustering and detection of chromosomal hi

SUBMITTER: Fan S 

PROVIDER: S-EPMC10308180 | biostudies-literature | 2023 Jun

REPOSITORIES: biostudies-literature