A Survey of Best Practices for RNA-seq Data Analysis
Wojciech Szcześniak, Michał
Elo, Laura L.
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Conesa, A., Madrigal, P., Tarazona, S., Gomez-Cabrero, D., Cervera, A., McPherson, A., Wojciech Szcześniak, M., et al. (2016). A Survey of Best Practices for RNA-seq Data Analysis. 17 (13)https://doi.org/10.1186/s13059-016-0881-8
This is the final published version. It first appeared at http://genomebiology.biomedcentral.com/articles/10.1186/s13059-016-0881-8.
RNA sequencing (RNA-seq) has a wide variety of applications, but no single analysis pipeline can be used in all cases. We review all major steps of RNA-seq data analysis including experimental design, quality control, read alignment, quantification of gene and transcript levels, visualization, differential gene expression, alternative splicing, functional analysis, gene fusion detection and eQTL mapping. We highlight challenges associated with each step. We discuss the analysis of small RNAs and the integration of RNA-seq with other functional genomics techniques. Finally, we discuss the outlook for novel technologies that are changing the state of the art in transcriptomics.
RNA-seq, Next-generation sequencing, transcriptomics, differential gene expression, guidelines, standards
External DOI: https://doi.org/10.1186/s13059-016-0881-8
This record's URL: https://www.repository.cam.ac.uk/handle/1810/253244
Attribution 2.0 UK: England & Wales, Creative Commons Attribution License 2.0 UK
Licence URL: http://creativecommons.org/licenses/by/2.0/uk/