Overview of available methods for diverse RNA-Seq data analyses
- PMID: 22227904
- DOI: 10.1007/s11427-011-4255-x
Overview of available methods for diverse RNA-Seq data analyses
Abstract
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.
Similar articles
-
How to analyze gene expression using RNA-sequencing data.Methods Mol Biol. 2012;802:259-74. doi: 10.1007/978-1-61779-400-1_17. Methods Mol Biol. 2012. PMID: 22130886
-
Characterizing short read sequencing for gene discovery and RNA-Seq analysis in Crassostrea gigas.Comp Biochem Physiol Part D Genomics Proteomics. 2012 Jun;7(2):94-9. doi: 10.1016/j.cbd.2011.12.003. Epub 2011 Dec 29. Comp Biochem Physiol Part D Genomics Proteomics. 2012. PMID: 22244882
-
Designing a transcriptome next-generation sequencing project for a nonmodel plant species.Am J Bot. 2012 Feb;99(2):257-66. doi: 10.3732/ajb.1100292. Epub 2012 Jan 19. Am J Bot. 2012. PMID: 22268224 Review.
-
Deep surveying of alternative splicing complexity in the human transcriptome by high-throughput sequencing.Nat Genet. 2008 Dec;40(12):1413-5. doi: 10.1038/ng.259. Epub 2008 Nov 2. Nat Genet. 2008. PMID: 18978789
-
Small RNA transcriptome investigation based on next-generation sequencing technology.J Genet Genomics. 2011 Nov 20;38(11):505-13. doi: 10.1016/j.jgg.2011.08.006. Epub 2011 Aug 31. J Genet Genomics. 2011. PMID: 22133681 Review.
Cited by
-
Systems biology of chromium-plant interaction: insights from omics approaches.Front Plant Sci. 2024 Jan 8;14:1305179. doi: 10.3389/fpls.2023.1305179. eCollection 2023. Front Plant Sci. 2024. PMID: 38259926 Free PMC article. Review.
-
Transcriptomic profiling reveals candidate allelopathic genes in rice responsible for interactions with barnyardgrass.Front Plant Sci. 2023 Feb 17;14:1104951. doi: 10.3389/fpls.2023.1104951. eCollection 2023. Front Plant Sci. 2023. PMID: 36875579 Free PMC article.
-
Single-Cell Transcriptomics: Current Methods and Challenges in Data Acquisition and Analysis.Front Neurosci. 2021 Apr 22;15:591122. doi: 10.3389/fnins.2021.591122. eCollection 2021. Front Neurosci. 2021. PMID: 33967674 Free PMC article. Review.
-
Single-Cell RNA-Seq Technologies and Related Computational Data Analysis.Front Genet. 2019 Apr 5;10:317. doi: 10.3389/fgene.2019.00317. eCollection 2019. Front Genet. 2019. PMID: 31024627 Free PMC article. Review.
-
Identification and quantification of domestic feline cytochrome P450 transcriptome across multiple tissues.J Vet Pharmacol Ther. 2019 Jan;42(1):7-15. doi: 10.1111/jvp.12708. Epub 2018 Aug 31. J Vet Pharmacol Ther. 2019. PMID: 30171610 Free PMC article.
Publication types
MeSH terms
LinkOut - more resources
Full Text Sources