ALEA: A toolbox for allele-specific epigenomics analysis

Hamid Younesy, Torsten Möller, Alireza Heravi-Moussavi, Jeffrey B. Cheng, Joseph F. Costello, Matthew C. Lorincz, Mohammad M. Karimi, Steven J M Jones

Research output: Contribution to journalArticle

12 Citations (Scopus)


The assessment of expression and epigenomic status using sequencing based methods provides an unprecedented opportunity to identify and correlate allelic differences with epigenomic status. We present ALEA, a computational toolbox for allele-specific epigenomics analysis, which incorporates allelic variation data within existing resources, allowing for the identification of significant associations between epigenetic modifications and specific allelic variants in human and mouse cells. ALEA provides a customizable pipeline of command line tools for allele-specific analysis of next-generation sequencing data (ChIP-seq, RNA-seq, etc.) that takes the raw sequencing data and produces separate allelic tracks ready to be viewed on genome browsers. The pipeline has been validated using human and hybrid mouse ChIP-seq and RNA-seq data.

Original languageEnglish
Pages (from-to)1172-1174
Number of pages3
Issue number8
Publication statusPublished - 2014
Externally publishedYes


ASJC Scopus subject areas

  • Biochemistry
  • Molecular Biology
  • Computational Theory and Mathematics
  • Computer Science Applications
  • Computational Mathematics
  • Statistics and Probability

Cite this

Younesy, H., Möller, T., Heravi-Moussavi, A., Cheng, J. B., Costello, J. F., Lorincz, M. C., Karimi, M. M., & Jones, S. J. M. (2014). ALEA: A toolbox for allele-specific epigenomics analysis. Bioinformatics, 30(8), 1172-1174.