HiChIP-Peaks: a HiChIP peak calling algorithm.

ABSTRACT:

Motivation

HiChIP is a powerful tool to interrogate 3D chromatin organization. Current tools to analyse chromatin looping mechanisms using HiChIP data require the identification of loop anchors to work properly. However, current approaches to discover these anchors from HiChIP data are not satisfactory, having either a very high false discovery rate or strong dependence on sequencing depth. Moreover, these tools do not allow quantitative comparison of peaks across different samples, failing to fully exploit the information available from HiChIP datasets.

Results

We develop a new tool based on a representation of HiChIP data centred on the re-ligation sites to identify peaks from HiChIP datasets, which can subsequently be used in other tools for loop discovery. This increases

SUBMITTER: Shi C 

PROVIDER: S-EPMC7320601 | biostudies-literature | 2020 Jun

REPOSITORIES: biostudies-literature