ASElux: an ultra-fast and accurate allelic reads counter.

ABSTRACT:

Motivation

Mapping bias causes preferential alignment to the reference allele, forming a major obstacle in allele-specific expression (ASE) analysis. The existing methods, such as simulation and SNP-aware alignment, are either inaccurate or relatively slow. To fast and accurately count allelic reads for ASE analysis, we developed a novel approach, ASElux, which utilizes the personal SNP information and counts allelic reads directly from unmapped RNA-sequence (RNA-seq) data. ASElux significantly reduces runtime by disregarding reads outside single nucleotide polymorphisms (SNPs) during the alignment.

Results

When compared to other tools on simulated and experimental data, ASElux achieves a higher accuracy on ASE estimation than non-SNP-aware aligners and requires a much short

SUBMITTER: Miao Z 

PROVIDER: S-EPMC5905663 | biostudies-literature | 2018 Apr

REPOSITORIES: biostudies-literature