Optimizing a Massive Parallel Sequencing Workflow for Quantitative miRNA Expression Analysis

Next Generation Sequencing methods (MPS) can extend and improve the knowledge obtained by conventional microarray technology, both for mRNAs and short non-coding RNAs, e.g. microRNAs. The processing methods used to extract and interpret the information are an important aspect of dealing with the vast amounts of data generated from short read sequencing. The mapping, counting and characterization of the short sequence reads produced by Illumina GA (Genome Analyzer) and Applied Biosystems SOLiD technologies results in a bottle neck in data analysis. Although the number of computational tools for MPS data analysis is constantly growing, their strengths and weaknesses as part of a complex analytical pipe-line have not yet been well investigated.