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Bioinformatics. 2019 Mar 28. pii: btz232. doi: 10.1093/bioinformatics/btz232. [Epub ahead of print]

epic2 efficiently finds diffuse domains in ChIP-seq data.

Stovner EB1,2,3,4, Sætrom P1,2,3,4.

Author information

1
Department of Computer Science, Norwegian University of Science and Technology, Trondheim, Norway.
2
Department of Clinical and Molecular Medicine, Norwegian University of Science and Technology, Trondheim, Norway.
3
Bioinformatics Core Facility, Norwegian University of Science and Technology, Trondheim, Norway.
4
K.G. Jebsen Center for Genetic Epidemiology, Department of Public Health and Nursing, Norwegian University of Science and Technology, Trondheim, Norway.

Abstract

SUMMARY:

Data from chromatin immunoprecipitation (ChIP) followed by high throughput sequencing (ChIP-seq) generally contain either narrow peaks or broad and diffusely enriched domains. The SICER ChIP-seq caller has proven adept at finding diffuse domains in ChIP-seq data, but it is slow, requires much memory, needs manual installation steps and is hard to use. epic2 is a complete rewrite of SICER that is focused on speed, low memory overhead and ease-of-use.

AVAILABILITY:

The MIT-licensed code is available at https://github.com/biocore-ntnu/epic2.

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