Inference of allele specific expression levels from RNA-Seq data
نویسنده
چکیده
Accurate allele specific expression estimation requires the availability of a diploid transcriptome, which makes it a challenging problem. Most existing methods rely on simple counting of alleles coverage at heterozygous Single Nucleotide Polymorphic sites. In this work, we present RNA-PhASE, a pipeline for Allele Specific gene and isoform Expression estimation from RNA-Seq Reads. The pipeline integrates methods for SNV detection and phasing with a new diploid version of an Expectation Maximization algorithm for gene/isoform estimation. Within this pipeline, we couple an existing phasing algorithm with a novel method for coverage based phasing.
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