PeakRanger: A cloud-enabled peak caller for ChIP-seq data |
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| Authors: | Xin Feng Robert Grossman Lincoln Stein |
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| Affiliation: | (1) Department of Biomedical Engineering, Stony Brook University, Stony Brook, NY 11794, USA;(2) Cold Spring Harbor Laboratory, One Bungtown Road, Cold Spring Harbor, NY 11724, USA;(3) Ontario Institute for Cancer Research, MaRS Centre, South Tower, 101 College Street, Suite 800, Toronto, ON, M5G 0A3, Canada;(4) Institute for Genomics & Systems Biology, The University of Chicago, Cummings Life Sciences Center 431A, 920 East 58th Street, Chicago, IL 60637, USA |
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| 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. |
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