A survey of best practices for RNA-seq data analysis
Ana Conesa,Pedro Madrigal,Pedro Madrigal,Sonia Tarazona,David Gomez-Cabrero,Alejandra Cervera,Andrew McPherson,Michał Wojciech Szcześniak,Daniel J. Gaffney,Laura L. Elo,Xuegong Zhang,Ali Mortazavi +11 more
TL;DR: All of the major steps in RNA-seq data analysis are reviewed, 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.
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Abstract: 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.
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References
Chimeric transcript discovery by paired-end transcriptome sequencing
Christopher G. Maher,Nallasivam Palanisamy,J.C. Brenner,Xuhong Cao,Shanker Kalyana-Sundaram,Shujun Luo,Irina Khrebtukova,Terrence R. Barrette,Catherine S. Grasso,Jindan Yu,Robert J. Lonigro,Gary P. Schroth,Chandan Kumar-Sinha,Arul M. Chinnaiyan +13 more
TL;DR: A sensitive, high-throughput methodology to comprehensively catalog functional gene fusions in cancer by evaluating a paired-end transcriptome sequencing strategy is established and is successfully used to detect previously undescribed ETS gene fusion in prostate tumors.
Commonality but Diversity in Cancer Gene Fusions
TL;DR: A recurring feature of carcinoma gene fusions, in contrast to those in hematopoietic and mesenchymal malignancies, is that they result in aberrant cell signaling, which may reflect differences in the differentiation programs of these tissues.
Efficient experimental design and analysis strategies for the detection of differential expression using RNA-Sequencing
José A Robles,Sumaira E. Qureshi,Stuart Stephen,Sue Wilson,Sue Wilson,Conrad J. Burden,Jennifer M. Taylor +6 more
TL;DR: Analysis of the power to detect differential expression in a range of scenarios including simulated null and differential expression distributions with varying numbers of biological or technical replicates, sequencing depths and analysis methods suggests that greater power is gained through the use of biological replicates relative to library (technical) replicates and sequencing depth.
Genome-Wide Associations of Gene Expression Variation in Humans
Barbara E. Stranger,Matthew S. Forrest,Andrew G. Clark,Andrew G. Clark,Mark J Minichiello,Samuel Deutsch,Samuel Deutsch,Robert Lyle,Robert Lyle,Sarah E. Hunt,Brenda Kahl,Brenda Kahl,Stylianos E. Antonarakis,Stylianos E. Antonarakis,Simon Tavaré,Simon Tavaré,Simon Tavaré,Panagiotis Deloukas,Emmanouil T. Dermitzakis +18 more
TL;DR: The results suggest that regulatory polymorphism is widespread in the human genome and show that the 5-kb (phase I) HapMap has sufficient density to enable linkage disequilibrium mapping in humans.
Finding consistent patterns: A nonparametric approach for identifying differential expression in RNA-Seq data
Jun Li,Robert Tibshirani +1 more
TL;DR: A simple, non-parametric method with resampling to account for the different sequencing depths is introduced, and it is found that the method discovers more consistent patterns than competing methods.