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.

Yixing Han

Shouguo Gao

Kathrin Muegge

Wei Zhang

Bing Zhou

Bioinformatics and Biology Insights

An open access, peer reviewed electronic journal that covers computational biology, particularly computational methods used in the analysis and annotation of structures.

Bioinformatics and Biology Insights is an open access, peer-reviewed electronic journal that focuses on computational biology, particularly the computational methods used for the analysis and annotation of biological structures.

《Bioinformatics and Biology Insights》是一本开放获取、经过同行评审的电子期刊，专注于计算生物学，尤其是用于结构分析和注释的计算方法。

Advanced Applications of RNA Sequencing and Challenges

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Journal Info

Category	Quartile
BIOCHEMICAL RESEARCH METHODS	3