PeakRanger: a cloud-enabled peak caller for ChIP-seq data.

ABSTRACT:

Background

Chromatin immunoprecipitation (ChIP), coupled with massively parallel short-read sequencing (seq) is used to probe chromatin dynamics. Although there are many algorithms to call peaks from ChIP-seq datasets, most are tuned either to handle punctate sites, such as transcriptional factor binding sites, or broad regions, such as histone modification marks; few can do both. Other algorithms are limited in their configurability, performance on large data sets, and ability to distinguish closely-spaced peaks.

Results

In this paper, we introduce PeakRanger, a peak caller software package that works equally well on punctate and broad sites, can resolve closely-spaced peaks, has excellent performance, and is easily customized. In addition, PeakRanger can be run in a parall

SUBMITTER: Feng X 

PROVIDER: S-EPMC3103446 | biostudies-literature | 2011 May

REPOSITORIES: biostudies-literature