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BMCBI
2011

PeakRanger: A cloud-enabled peak caller for ChIP-seq data

10 years 3 months ago
PeakRanger: A cloud-enabled peak caller for ChIP-seq data
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 parallel cloud computing environment to obtain extremely high performance on very large data sets. We present a series of benchmarks to evaluate PeakRanger against 10 other peak callers, and demonstrate the performance...
Xin Feng, Robert Grossman, Lincoln Stein
Added 24 Aug 2011
Updated 24 Aug 2011
Type Journal
Year 2011
Where BMCBI
Authors Xin Feng, Robert Grossman, Lincoln Stein
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