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NTAP: for NimbleGen tiling array ChIP-chip data analysis.

Kun He1, Xueyong Li, Junli Zhou

  • 1College of Life Sciences, Center for Bioinformatics, National Laboratory of Protein Engineering and Plant Genetic Engineering, Peking University, Beijing 100871, China. hekun78@gmail.com

Bioinformatics (Oxford, England)
|May 27, 2009
PubMed
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NimbleGen Tiling Array analysis Pipeline (NTAP) offers customizable ChIP-chip data analysis for epigenetic studies. This tool supports full data processing or post-processing modules, with outputs compatible with standard visualization tools.

Area of Science:

  • Bioinformatics
  • Genomics
  • Epigenetics

Background:

  • ChIP-chip assays generate large datasets requiring specialized analysis tools.
  • NimbleGen tiling arrays are a common platform for such experiments.
  • Epigenetic studies benefit from accurate and efficient data processing.

Purpose of the Study:

  • To introduce NTAP, a novel software tool for analyzing ChIP-chip data from NimbleGen tiling arrays.
  • To provide a customizable platform for pattern recognition in epigenetic studies.
  • To facilitate the analysis of both raw and pre-processed epigenetic data.

Main Methods:

  • NTAP is implemented in Perl and R, offering a modular design.
  • The software supports full data processing pipelines for NimbleGen arrays.

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  • Users can select specific post-processing modules for pre-processed data.

    • Main Results:

    • NTAP enables comprehensive analysis of ChIP-chip data.
    • The modularity allows for high customization of data processing workflows.
    • Outputs are compatible with standard formats like GFF for visualization in GBrowse.

    Conclusions:

    • NTAP is a versatile and customizable tool for ChIP-chip data analysis, particularly valuable for epigenetic research.
    • Its modular design enhances flexibility, accommodating various analysis needs.
    • The software supports integration with existing visualization platforms for enhanced data interpretation.