Software for Estimation of Human Transcriptome Isoform Expression Using RNA-Seq Data

<p>The goal of this thesis research was to develop software to be used with RNA-Seq data for transcriptome quantification that was capable of handling multireads and quantifying isoforms on a more global level. Current software available for these purposes uses various forms of parameter alteration in order to work with multireads. Many still analyze isoforms per gene or per researcher determined clusters as well. By doing so, the effects of multireads are diminished or possibly wrongly represented. To address this issue, two programs, GWIE and ChromIE, were developed based on a simple iterative EM-like algorithm with no parameter manipulation. These programs are used to produce accurate isoform expression levels.</p>

Name thesis:degree_name

M.S.

Level thesis:degree_level

Thesis

Discipline thesis:degree_discipline

Computer Science

Year

2012

Author dc:creator

• Johnson, Kristen

Contributors dc:contributor

• Dongxiao Zhu
• Jaime Nino
• Christopher Taylor

• RNA-Seq
• Transcriptome Quantification
• Isoform Expression
• Multireads
• Expectation-Maximization (EM) Algorithm
• Numerical Analysis and Scientific Computing
• Other Computer Sciences

Repository record dc:identifier

https://scholarworks.uno.edu/td/1448

OAI identifier oai:identifier

oai:scholarworks.uno.edu:td-2463