| Autor: |
Kyukwang Kim, Inkyung Jung |
| Jazyk: |
angličtina |
| Rok vydání: |
2021 |
| Předmět: |
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| Zdroj: |
Computational and Structural Biotechnology Journal, Vol 19, Iss , Pp 3149-3159 (2021) |
| Druh dokumentu: |
article |
| ISSN: |
2001-0370 |
| DOI: |
10.1016/j.csbj.2021.05.041 |
| Popis: |
Hi-C and capture Hi-C have greatly advanced our understanding of the principles of higher-order chromatin structure. In line with the evolution of the Hi-C protocols, there is a demand for an advanced computational method that can be applied to the various forms of Hi-C protocols and effectively remove innate biases. To resolve this issue, we developed an implicit normalization method named “covNorm” and implemented it as an R package. The proposed method can perform a complete procedure of data processing for Hi-C and its variants. Starting from the negative binomial model-based normalization for DNA fragment coverages, removal of genomic distance-dependent background and calling of the significant interactions can be applied sequentially. The performance evaluation of covNorm showed enhanced or similar reproducibility in terms of HiC-spector score, correlation of compartment A/B profiles, and detection of reproducible significant long-range chromatin contacts compared to baseline methods in the benchmark datasets. The developed method is powerful in terms of effective normalization of Hi-C and capture Hi-C data, detection of long-range chromatin contacts, and readily extendibility to the other derivative Hi-C protocols. The covNorm R package is freely available at GitHub: https://github.com/kaistcbfg/covNormRpkg. |
| Databáze: |
Directory of Open Access Journals |
| Externí odkaz: |
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