Effect of read-mapping biases on detecting allele-specific expression from RNA-sequencing data.

ABSTRACT: Next-generation sequencing has become an important tool for genome-wide quantification of DNA and RNA. However, a major technical hurdle lies in the need to map short sequence reads back to their correct locations in a reference genome. Here we investigate the impact of SNP variation on the reliability of read-mapping in the context of detecting allele-specific expression (ASE).We generated sixteen million 35 bp reads from mRNA of each of two HapMap Yoruba individuals. When we mapped these reads to the human genome we found that, at heterozygous SNPs, there was a significant bias towards higher mapping rates of the allele in the reference sequence, compared to the alternative allele. Masking known SNP positions in the genome sequence eliminated the reference bias but, surprisingly, did

ORGANISM(S): Homo sapiens

SUBMITTER: Jacob Degner 

PROVIDER: E-GEOD-18156 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress