AlleleSeq: analysis of allele-specific expression and binding in a network framework.

ABSTRACT: To study allele-specific expression (ASE) and binding (ASB), that is, differences between the maternally and paternally derived alleles, we have developed a computational pipeline (AlleleSeq). Our pipeline initially constructs a diploid personal genome sequence (and corresponding personalized gene annotation) using genomic sequence variants (SNPs, indels, and structural variants), and then identifies allele-specific events with significant differences in the number of mapped reads between maternal and paternal alleles. There are many technical challenges in the construction and alignment of reads to a personal diploid genome sequence that we address, for example, bias of reads mapping to the reference allele. We have applied AlleleSeq to variation data for NA12878 from the 1000 Genomes Pro

SUBMITTER: Rozowsky J 

PROVIDER: S-EPMC3208341 | biostudies-literature | 2011 Aug

REPOSITORIES: biostudies-literature