HiChIP-Peaks: a HiChIP peak calling algorithm | Zendy

Chenfu Shi | Zendy; Magnus Rattray | Zendy; Gisela Orozco | Zendy

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HiChIP-Peaks: a HiChIP peak calling algorithm

Author(s) -

Chenfu Shi,

Magnus Rattray,

Gisela Orozco

Publication year - 2020

Publication title -

bioinformatics

Language(s) - Uncategorized

Resource type - Journals

SCImago Journal Rank - 3.599

H-Index - 390

eISSN - 1367-4811

pISSN - 1367-4803

DOI - 10.1093/bioinformatics/btaa202

Subject(s) - computer science , exploit , data mining , identification (biology) , reliability (semiconductor) , representation (politics) , algorithm , false discovery rate , loop (graph theory) , software , biology , mathematics , power (physics) , biochemistry , botany , physics , computer security , quantum mechanics , combinatorics , politics , political science , gene , law , programming language

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.

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