ALEA: a toolbox for allele-specific epigenomics analysis

Bioinformatics. 2014 Apr 15;30(8):1172-1174. doi: 10.1093/bioinformatics/btt744. Epub 2013 Dec 26.


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.

Availability: The package, test data and usage instructions are available online at CONTACT: : or Supplementary information: Supplementary data are available at Bioinformatics online.

MeSH terms

  • Alleles
  • Animals
  • Chromatin Immunoprecipitation
  • Computational Biology / methods*
  • Epigenomics / methods*
  • High-Throughput Nucleotide Sequencing / methods
  • Humans
  • Mice
  • RNA / genetics
  • Sequence Analysis, RNA / methods
  • Software*


  • RNA

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