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Measuring the reproducibility and quality of Hi-C data
- Source :
- Genome Biology, Vol 20, Iss 1, Pp 1-19 (2019)
- Publication Year :
- 2019
- Publisher :
- BMC, 2019.
-
Abstract
- Abstract Background Hi-C is currently the most widely used assay to investigate the 3D organization of the genome and to study its role in gene regulation, DNA replication, and disease. However, Hi-C experiments are costly to perform and involve multiple complex experimental steps; thus, accurate methods for measuring the quality and reproducibility of Hi-C data are essential to determine whether the output should be used further in a study. Results Using real and simulated data, we profile the performance of several recently proposed methods for assessing reproducibility of population Hi-C data, including HiCRep, GenomeDISCO, HiC-Spector, and QuASAR-Rep. By explicitly controlling noise and sparsity through simulations, we demonstrate the deficiencies of performing simple correlation analysis on pairs of matrices, and we show that methods developed specifically for Hi-C data produce better measures of reproducibility. We also show how to use established measures, such as the ratio of intra- to interchromosomal interactions, and novel ones, such as QuASAR-QC, to identify low-quality experiments. Conclusions In this work, we assess reproducibility and quality measures by varying sequencing depth, resolution and noise levels in Hi-C data from 13 cell lines, with two biological replicates each, as well as 176 simulated matrices. Through this extensive validation and benchmarking of Hi-C data, we describe best practices for reproducibility and quality assessment of Hi-C experiments. We make all software publicly available at http://github.com/kundajelab/3DChromatin_ReplicateQC to facilitate adoption in the community.
- Subjects :
- Biology (General)
QH301-705.5
Genetics
QH426-470
Subjects
Details
- Language :
- English
- ISSN :
- 1474760X
- Volume :
- 20
- Issue :
- 1
- Database :
- Directory of Open Access Journals
- Journal :
- Genome Biology
- Publication Type :
- Academic Journal
- Accession number :
- edsdoj.5c3304bc21c457993be8f6384642f01
- Document Type :
- article
- Full Text :
- https://doi.org/10.1186/s13059-019-1658-7