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has been cited by the following article:

• TITLE: Evaluation of RNA-Seq software in gene expression quantification

  AUTHORS: Yan Ji, Ziliang Qian, Jia Wei

  KEYWORDS: RNA-Seq; Next Generation Sequencing

  JOURNAL NAME: Journal of Biomedical Science and Engineering, Vol.6 No.4, April 29, 2013

  ABSTRACT: High-throughput RNA sequencing (RNA-Seq) promises a complete annotation and quantification of all genes and their isoforms across samples. Because sequencing reads from this new technology are shorter than transcripts from which they are derived, expression estimation with RNA-Seq requires increasingly complex computational methods. In recent years, a number of expression quantification methods have been published from both public and commercial sources. Here we presented an overview of these attempts on quantifying gene expression. We then defined a set of criteria and compared the performance of several programs based on these criteria, and we further provided advices on selecting suitable tools for different biological applications.