A survey of best practices for RNA-seq data analysis
Обзор лучших практик анализа данных RNA-seq
2016-01-26
SCID: 54.1/rgweufs3
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RNA-seq data analysisalternative splicingdifferential gene expressioneQTL mappingread alignment
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Abstract (AI)
RNA-sequencing (RNA-seq) has a wide variety of applications, but no single analysis pipeline can be used in all cases. We review all of the major steps in 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 the 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.
Key Findings
1
Analysis of small RNAs and integration of RNA-seq with other functional genomics techniques are important complementary approaches.
2
Downstream analyses such as visualization, differential expression, alternative splicing, functional analysis, gene fusion detection, and eQTL mapping each present distinct challenges.
3
Emerging novel technologies are changing transcriptomics and will affect future RNA-seq analysis practices.
4
Major steps requiring careful attention include experimental design, quality control, read alignment, and quantification of gene/transcript levels.
5
No single RNA-seq analysis pipeline fits all applications; analysis must be tailored to specific study goals.
Research Object
RNA-sequencing (RNA-seq) data analysis workflow
Research Subject
Best practices and methodological considerations across major RNA-seq analysis steps (experimental design, QC, read alignment, quantification, visualization, differential expression, alternative splicing, functional analysis, fusion detection, eQTL mapping, small RNA analysis, and integration with other functional genomics)
Publication Details
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2016-01-26
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