Determining differential expression of Splice Variants in RNA-seq

Abstract

To determine differential expression between different genes, different samples and different experiments quantified data should be normalized using a uniform method. Many protocols and algorithms have been developed over the last years to analyze RNA-seq data, although the field is still in its early days of standardization. A complicating factor in RNA-seq analysis is the existence of genes with multiple splice variants. These variants complicate the task of assigning reads to unique transcripts. In this thesis we will give an overview of the tools and methods available in the literature for analyzing RNA-seq data including differential expression of splice variants for organisms that have a reference genome. In recent years great advances have been made in analyzing the differential expression of alternatively spliced transcripts. For all four steps of the analysis path there are suitable tools available to address the problems alternative splicing causes.