Towards reliable isoform quantification using RNA-SEQ data.

ABSTRACT:

Background

In eukaryotes, alternative splicing often generates multiple splice variants from a single gene. Here we explore the use of RNA sequencing (RNA-Seq) datasets to address the isoform quantification problem. Given a set of known splice variants, the goal is to estimate the relative abundance of the individual variants.

Methods

Our method employs a linear models framework to estimate the ratios of known isoforms in a sample. A key feature of our method is that it takes into account the non-uniformity of RNA-Seq read positions along the targeted transcripts.

Results

Preliminary tests indicate that the model performs well on both simulated and real data. In two publicly available RNA-Seq datasets, we identified several alternatively-spliced genes with switch-like

SUBMITTER: Howard BE 

PROVIDER: S-EPMC2863065 | biostudies-literature | 2010 Apr

REPOSITORIES: biostudies-literature