FourCSeq: analysis of 4C sequencing data.

ABSTRACT:

Motivation

Circularized Chromosome Conformation Capture (4C) is a powerful technique for studying the spatial interactions of a specific genomic region called the 'viewpoint' with the rest of the genome, both in a single condition or comparing different experimental conditions or cell types. Observed ligation frequencies typically show a strong, regular dependence on genomic distance from the viewpoint, on top of which specific interaction peaks are superimposed. Here, we address the computational task to find these specific peaks and to detect changes between different biological conditions.

Results

We model the overall trend of decreasing interaction frequency with genomic distance by fitting a smooth monotonically decreasing function to suitably transformed count data. Ba

SUBMITTER: Klein FA 

PROVIDER: S-EPMC4576695 | biostudies-literature | 2015 Oct

REPOSITORIES: biostudies-literature