In a fit of pique: Analyzing microbial ChIP-Seq data with Pique

, , ,
1 Genome Center, University of California, Davis, Davis, CA, USA
2 Microbiology Graduate Group, University of California, Davis, Davis, CA, USA
3 Department of Biomedical Engineering, University of California, Davis, Davis, CA, USA
DOI
10.7287/peerj.preprints.290v2
Published
Accepted
Subject Areas
Bioinformatics, Genomics
Keywords
ChIP-seq, genomics, bacteria, bioinformatics, archaea
Copyright
© 2014 Neches et al.
Licence
This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, reproduction and adaptation in any medium and for any purpose provided that it is properly attributed. For attribution, the original author(s), title, publication source (PeerJ PrePrints) and either DOI or URL of the article must be cited.
Cite this article
Neches RY, Seitzer PM, Wilbanks EG, Facciotti MT. 2014. In a fit of pique: Analyzing microbial ChIP-Seq data with Pique. PeerJ PrePrints 2:e290v2

Abstract

While numerous effective peak finders have been developed for eukaryotic systems, we have found that the approaches used can be error prone when run on high coverage bacterial and archaeal ChIP-Seq datasets. We have developed Pique, an easy to use ChIP-Seq peak finding application for bacterial and archaeal ChIP-Seq experiments. The software is cross-platform and Open Source, and based on only freely licensed dependencies. Output is provided in standardized file formats, and may be easily imported by the Gaggle Genome Browser (Bare et al. 2010) for manual curation and data exploration, or into statistical and graphics software such as R (R Core Team 2013) for further analysis. The software is available under the BSD-3 license, and tutorial and test data are included with the documentation.

http://github.com/ryneches/pique.

Author Comment

This manuscript is intended for review at PeerJ. Comments regarding developments since 2012 would be appreciated. The Acknowledgements and Funding Statement have been updated to include an additional grant.