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Open Access Highly Accessed Methodology article

HPeak: an HMM-based algorithm for defining read-enriched regions in ChIP-Seq data

Zhaohui S Qin*, Jianjun Yu, Jincheng Shen, Christopher A Maher, Ming Hu, Shanker Kalyana-Sundaram, Jindan Yu and Arul M Chinnaiyan

BMC Bioinformatics 2010, 11:369  doi:10.1186/1471-2105-11-369

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Important Omission

Dario Strbenac   (2013-03-10 13:19)  University of Sydney email

The authors state that "Currently, HPeak is capable of analyzing ChIP-Seq data collected from human and mouse and can easily be extended to other species.", which is not true. Reading through the function 'realignfileread' in summary.pl, it is evident that the human chromosome names are hard-coded. For users who don't have Perl programming experience, it would be difficult to use for other species. It would be nice if reviewers could verify such broad statements before accepting articles for publication.

Competing interests

None.

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