RNA-Sequencing technologies are being used to determine the single nucleotide polymorphisms, insertions, deletions and gene expression. The purpose of this study was to analyze the effect of myostatin in the triceps muscles of mice using 65 bases single-end RNA-Sequencing data from the Illumina platform. Another aim was to analyze alternative splicing events for differentially expressed genes in the above data. Finally, commercially available and open source software packages were compared for their splice junction detection abilities. CASAVA was used for determining the exon, gene and splice junction counts. Partek Genomic Suite was used to perform a two-way analysis of variance followed by the identification of differentially expressed genes. The splicing events were identified using the software packages CASAVA, TopHat, MapSplice and SpliceMap. The results of splice junction detection were viewed in the UCSC genome browser. The performance and features of the above software were compared. The results revealed that myostatin deficiency significantly alters gene expression. This study provides an unbiased view towards commercial and open source RNA-Sequencing software using a very significant dataset. The results show that a preliminary inspection for alternative splicing can be performed; however, currently no software alone can fully analyze the RNA-Seq data and needs complementary software to assist in the complete analysis. The results of this study would benefit researchers in choosing the right software for their purposes considering the resources like time, man-power and money available.

Library of Congress Subject Headings

Nucleotide sequence; RNA splicing; Mice--Genetics

Publication Date


Document Type


Department, Program, or Center

Thomas H. Gosnell School of Life Sciences (COS)


Skuse, Gary

Advisor/Committee Member

Welle, Stephen

Advisor/Committee Member

Reyes, Vicente


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