Abstract
Hi-C data are commonly normalized using single sample processing methods, with focus on comparisons between regions within a given contact map. Here, we aim to compare contact maps across different samples. We demonstrate that unwanted variation, of likely technical origin, is present in Hi-C data with replicates from different individuals, and that properties of this unwanted variation change across the contact map. We present band-wise normalization and batch correction, a method for normalization and batch correction of Hi-C data and show that it substantially improves comparisons across samples, including in a quantitative trait loci analysis as well as differential enrichment across cell types.
Original language | English (US) |
---|---|
Article number | bbae217 |
Journal | Briefings in bioinformatics |
Volume | 25 |
Issue number | 3 |
DOIs | |
State | Published - May 1 2024 |
Keywords
- bioinformatics
- Hi-C
ASJC Scopus subject areas
- Information Systems
- Molecular Biology