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.