Date of Award
Spring 5-2012
Degree Type
Thesis
Degree Name
M.S.
Degree Program
Computer Science
Department
Computer Science
Major Professor
Dongxiao Zhu
Second Advisor
Jaime Nino
Third Advisor
Christopher Taylor
Abstract
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.
Creative Commons License
This work is licensed under a Creative Commons Attribution 3.0 License.
Recommended Citation
Johnson, Kristen, "Software for Estimation of Human Transcriptome Isoform Expression Using RNA-Seq Data" (2012). University of New Orleans Theses and Dissertations. 1448.
https://scholarworks.uno.edu/td/1448
Rights
The University of New Orleans and its agents retain the non-exclusive license to archive and make accessible this dissertation or thesis in whole or in part in all forms of media, now or hereafter known. The author retains all other ownership rights to the copyright of the thesis or dissertation.