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Bioinformatics Advance Access originally published online on May 25, 2009
Bioinformatics 2009 25(14):1838-1840; doi:10.1093/bioinformatics/btp320
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© 2009 The Author(s)
This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (http://creativecommons.org/licenses/by-nc/2.0/uk/) which permits unrestricted non-commercial use, distribution, and reproduction in any medium, provided the original work is properly cited.

NTAP: for NimbleGen tiling array ChIP-chip data analysis

Kun He 1,2,*, Xueyong Li 3,4, Junli Zhou 3,5, Xing-Wang Deng 3, Hongyu Zhao 6 and Jingchu Luo 1,*

1 College of Life Sciences, Center for Bioinformatics, National Laboratory of Protein Engineering and Plant Genetic Engineering, Peking University, Beijing 100871, China, 2 Department of Plant Biology, Carnegie Institution, Stanford, CA 94305, 3 Department of Molecular, Cellular, and Developmental Biology, Yale University, New Haven, CT 06520, USA, 4 Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing 100081, 5 Beijing Kaituo DNA Biotech Research Center CO., Ltd., 39 West Shangdi Rd, Haidian District, Beijing 100085, China and 6 Department of Epidemiology and Public Health, Yale University School of Medicine, New Haven, CT 06520, USA

* To whom correspondence should be addressed.


  Abstract

Summary:NTAP is designed to analyze ChIP-chip data generated by the NimbleGen tiling array platform and to accomplish various pattern recognition tasks that are useful especially for epigenetic studies. The modular design of NTAP makes the data processing highly customizable. Users can either use NTAP to perform the full process of NimbleGen tiling array data analysis, or choose post-processing modules in NTAP to analyze pre-processed epigenetic data generated by other platforms. The output of NTAP can be saved in standard GFF format files and visualized in GBrowse.

Availability and Implementation:The source code of NTAP is freely available at http://ntap.cbi.pku.edu.cn/. It is implemented in Perl and R and can be used on Linux, Mac and Windows platforms.

Contact: ntap{at}mail.cbi.pku.edu.cn; luojc{at}pku.edu.cn; hekun78{at}gmail.com

Associate Editor: John Quackenbush

Received on January 24, 2009; revised on May 10, 2009; accepted on May 12, 2009

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