Genes & Genomics

, Volume 37, Issue 3, pp 305–311 | Cite as

An automated analysis pipeline for a large set of ChIP-seq data: AutoChIP

  • Taemook Kim
  • Wooseok Lee
  • Kyudong Han
  • Keunsoo Kang
Research Article


Although there are many applications available for the analysis of chromatin immunoprecipitation with massively parallel DNA sequencing (ChIP-seq), users need some knowledge about the installation, alignment, and peak calling procedures prior to the analysis. Here, we present an easy-to-use application for ChIP-seq analysis called AutoChIP. With AutoChIP, installation of necessary programs, alignment of unmapped reads to a reference genome, and identification of genome-wide binding sites can be done in a single step with a large set of ChIP-seq data. Evaluation of the cocktail algorithm implemented in AutoChIP showed that it outperformed a single ChIP-seq tool in terms of the ratio of motif occurrences and the average height of normalized read density over the identified peaks. In addition, annotation of the identified peaks with the known gene and repeat elements information provides a comprehensive picture of the genome-wide binding sites of given proteins. Overall, AutoChIP provides a comprehensive platform to analyze a large set of ChIP-seq data in one step.


AutoChIP ChIP-seq STAT5 GATA3 Next-generation sequencing NGS 



We thank members of the Kang laboratory for valuable comments.

Conflict of interest

The authors state that there are no conflicts of interest.

Supplementary material

13258_2014_260_MOESM1_ESM.xlsx (10 kb)
Supplementary material 1 (XLSX 9 kb)
13258_2014_260_MOESM2_ESM.xlsx (9 kb)
Supplementary material 2 (XLSX 9 kb)


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Copyright information

© The Genetics Society of Korea and Springer-Science and Media 2014

Authors and Affiliations

  1. 1.Department of MicrobiologyDankook UniversityCheonanRepublic of Korea
  2. 2.Department of Nanobiomedical Science & BK21 PLUS NBM Global Research Center for Regenerative MedicineDankook UniversityCheonanRepublic of Korea
  3. 3.DKU-Theragen Institute for NGS Analysis (DTiNa)CheonanRepublic of Korea

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