With the evolution of DNA sequencing technology, it is now possible to study expression and DNA binding differences between pairs of sequence alleles on the maternally- and paternally-derived chromosomes within an individual, phenomena known as allele-specific expression (ASE) and allele specific binding (ASB).
To study these allele-specific events, we have developed a computational pipeline, AlleleSeq, which
(1) first constructs a diploid personal genome from genomic sequence variants of a family trio, including SNPs, indels and structural variants;
(2) then maps functional genomic data (e.g. RNA-seq expression or ChIP-seq binding data) onto this personal genome.
Rozowsky J. et al. AlleleSeq: analysis of allele-specific expression and binding in a network framework. Mol Syst Biol. 2011.