FreePSI: an alignment-free approach to estimating exon-inclusion ratios without a reference transcriptome.

ABSTRACT: Alternative splicing plays an important role in many cellular processes of eukaryotic organisms. The exon-inclusion ratio, also known as percent spliced in, is often regarded as one of the most effective measures of alternative splicing events. The existing methods for estimating exon-inclusion ratios at the genome scale all require the existence of a reference transcriptome. In this paper, we propose an alignment-free method, FreePSI, to perform genome-wide estimation of exon-inclusion ratios from RNA-Seq data without relying on the guidance of a reference transcriptome. It uses a novel probabilistic generative model based on k-mer profiles to quantify the exon-inclusion ratios at the genome scale and an efficient expectation-maximization algorithm based on a divide-and-conquer strategy a

SUBMITTER: Zhou J 

PROVIDER: S-EPMC5778508 | biostudies-literature | 2018 Jan

REPOSITORIES: biostudies-literature