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2015 ; 9
(Suppl 1
): 29-46
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Advanced Applications of RNA Sequencing and Challenges
#MMPMID26609224
Han Y
; Gao S
; Muegge K
; Zhang W
; Zhou B
Bioinform Biol Insights
2015[]; 9
(Suppl 1
): 29-46
PMID26609224
show ga
Next-generation sequencing technologies have revolutionarily advanced
sequence-based research with the advantages of high-throughput, high-sensitivity,
and high-speed. RNA-seq is now being used widely for uncovering multiple facets
of transcriptome to facilitate the biological applications. However, the
large-scale data analyses associated with RNA-seq harbors challenges. In this
study, we present a detailed overview of the applications of this technology and
the challenges that need to be addressed, including data preprocessing,
differential gene expression analysis, alternative splicing analysis, variants
detection and allele-specific expression, pathway analysis, co-expression network
analysis, and applications combining various experimental procedures beyond the
achievements that have been made. Specifically, we discuss essential principles
of computational methods that are required to meet the key challenges of the
RNA-seq data analyses, development of various bioinformatics tools, challenges
associated with the RNA-seq applications, and examples that represent the
advances made so far in the characterization of the transcriptome.