The evolution of DNA sequencing technology has brought more attention to how the readout from functional genomic assays, such as those for gene expression and DNA binding, differ between individuals. Moreover, 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. Our pipeline first takes as input genomic sequence variants including SNPs, indels and structural variants derived from an individual and constructs a diploid personal genome sequence. By mapping functional genomic data onto this personal genome, we can identify locations where differences in number of mapped reads between maternally- and paternally-derived sequences constitute evidence for allele-specific events.
Rozowsky J. et al. AlleleSeq: analysis of allele-specific expression and binding in a network framework. Mol Syst Biol. 2011.