Isoform prefiltering improves performance of count-based methods for analysis of differential transcript usage.

ABSTRACT:

Background

RNA-seq has been a boon to the quantitative analysis of transcriptomes. A notable application is the detection of changes in transcript usage between experimental conditions. For example, discovery of pathological alternative splicing may allow the development of new treatments or better management of patients. From an analysis perspective, there are several ways to approach RNA-seq data to unravel differential transcript usage, such as annotation-based exon-level counting, differential analysis of the percentage spliced in, or quantitative analysis of assembled transcripts. The goal of this research is to compare and contrast current state-of-the-art methods, and to suggest improvements to commonly used work flows.

Results

We assess the performance of representat

SUBMITTER: Soneson C 

PROVIDER: S-EPMC4729156 | biostudies-literature | 2016 Jan

REPOSITORIES: biostudies-literature