Computer Engineering Commons^™

Accurate Estimation Of Isoform And Gene Expression Levels From Next Generation Sequencing Data, Marius Nicolae

Master's Theses

Massively parallel transcriptome sequencing is quickly replacing microarrays as the technology of choice for performing gene expression profiling due to its wider dynamic range and digital quantitation capabilities. However, accurate estimation of expression levels from sequencing data remains challenging due to the short read length delivered by current sequencing technologies and still poorly understood protocol- and technology-specific biases.

To date, two main transcriptome sequencing protocols have been proposed in the literature. The most commonly used one, referred to as RNA-Seq, generates short (single or paired) sequencing tags from the ends of randomly generated cDNA fragments. An alternative protocol, referred to …