Journal
SCIENCE CHINA-LIFE SCIENCES
Volume 54, Issue 12, Pages 1121-1128Publisher
SCIENCE PRESS
DOI: 10.1007/s11427-011-4255-x
Keywords
next generation sequencing; transcriptome; RNA-Seq data analysis; transcriptomics
Categories
Funding
- National Basic Research Program of China [2010CB945401, 2007CB108800]
- National Natural Science Foundation of China [30870575, 31071162, 31000590]
- Science and Technology Commission of Shanghai Municipality [11DZ2260300]
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RNA-Seq technology is becoming widely used in various transcriptomics studies; however, analyzing and interpreting the RNA-Seq data face serious challenges. With the development of high-throughput sequencing technologies, the sequencing cost is dropping dramatically with the sequencing output increasing sharply. However, the sequencing reads are still short in length and contain various sequencing errors. Moreover, the intricate transcriptome is always more complicated than we expect. These challenges proffer the urgent need of efficient bioinformatics algorithms to effectively handle the large amount of transcriptome sequencing data and carry out diverse related studies. This review summarizes a number of frequently-used applications of transcriptome sequencing and their related analyzing strategies, including short read mapping, exon-exon splice junction detection, gene or isoform expression quantification, differential expression analysis and transcriptome reconstruction.
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