Fine mapping chromatin contacts in capture Hi-C data.

ABSTRACT:

Background

Hi-C and capture Hi-C (CHi-C) are used to map physical contacts between chromatin regions in cell nuclei using high-throughput sequencing. Analysis typically proceeds considering the evidence for contacts between each possible pair of fragments independent from other pairs. This can produce long runs of fragments which appear to all make contact with the same baited fragment of interest.

Results

We hypothesised that these long runs could result from a smaller subset of direct contacts and propose a new method, based on a Bayesian sparse variable selection approach, which attempts to fine map these direct contacts. Our model is conceptually novel, exploiting the spatial pattern of counts in CHi-C data. Although we use only the CHi-C count data in fitting the model,

SUBMITTER: Eijsbouts CQ 

PROVIDER: S-EPMC6343296 | biostudies-literature | 2019 Jan

REPOSITORIES: biostudies-literature