A comprehensive evaluation of normalization methods for Illumina high-throughput RNA sequencing data analysis
Marie-Agnès Dillies,Andrea Rau,Julie Aubert,Christelle Hennequet-Antier,Marine Jeanmougin,Nicolas Servant,Céline Keime,Guillemette Marot,David Castel,Jordi Estellé,Gregory Guernec,Bernd Jagla,Luc Jouneau,Denis Laloë,Caroline Le Gall,Brigitte Schaeffer,Stéphane Le Crom,Mickaël Guedj,Florence Jaffrézic +18 more
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TLDR
This work focuses on a comprehensive comparison of seven recently proposed normalization methods for the differential analysis of RNA-seq data, with an emphasis on the use of varied real and simulated datasets involving different species and experimental designs to represent data characteristics commonly observed in practice.Abstract:
During the last 3 years, a number of approaches for the normalization of RNA sequencing data have emerged in the literature, differing both in the type of bias adjustment and in the statistical strategy adopted. However, as data continue to accumulate, there has been no clear consensus on the appropriate normalization method to be used or the impact of a chosen method on the downstream analysis. In this work, we focus on a comprehensive comparison of seven recently proposed normalization methods for the differential analysis of RNA-seq data, with an emphasis on the use of varied real and simulated datasets involving different species and experimental designs to represent data characteristics commonly observed in practice. Based on this comparison study, we propose practical recommendations on the appropriate normalization method to be used and its impact on the differential analysis of RNA-seq data.read more
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De novo transcript sequence reconstruction from RNA-seq using the Trinity platform for reference generation and analysis
Brian J. Haas,Alexie Papanicolaou,Moran Yassour,Moran Yassour,Manfred Grabherr,Philip D. Blood,Joshua C. Bowden,M. B. Couger,David Eccles,Bo Li,Matthias Lieber,Matthew D. MacManes,Michael Ott,Joshua Orvis,Nathalie Pochet,Nathalie Pochet,Francesco Strozzi,Nathan T. Weeks,Rick Westerman,Thomas William,Colin N. Dewey,Robert Henschel,Richard D. LeDuc,Nir Friedman,Aviv Regev +24 more
TL;DR: This protocol provides a workflow for genome-independent transcriptome analysis leveraging the Trinity platform and presents Trinity-supported companion utilities for downstream applications, including RSEM for transcript abundance estimation, R/Bioconductor packages for identifying differentially expressed transcripts across samples and approaches to identify protein-coding genes.
Journal ArticleDOI
Early allopolyploid evolution in the post-Neolithic Brassica napus oilseed genome
Boulos Chalhoub,Shengyi Liu,Isobel A. P. Parkin,Haibao Tang,Haibao Tang,Xiyin Wang,Julien Chiquet,Harry Belcram,Chaobo Tong,Birgit Samans,Margot Correa,Corinne Da Silva,Jérémy Just,Cyril Falentin,Chu Shin Koh,Isabelle Le Clainche,Maria Bernard,Pascal Bento,Benjamin Noel,Karine Labadie,Adriana Alberti,Mathieu Charles,Dominique Arnaud,Hui Guo,Christian Daviaud,Salman Alamery,Kamel Jabbari,Kamel Jabbari,Meixia Zhao,Patrick P. Edger,Houda Chelaifa,David C. Tack,Gilles Lassalle,Imen Mestiri,Nicolas Schnel,Marie-Christine Le Paslier,Guangyi Fan,Victor Renault,Philippe E. Bayer,Agnieszka A. Golicz,Sahana Manoli,Tae-Ho Lee,Vinh Ha Dinh Thi,Smahane Chalabi,Qiong Hu,Chuchuan Fan,Reece Tollenaere,Yunhai Lu,Christophe Battail,Jinxiong Shen,Christine Sidebottom,Xinfa Wang,Aurélie Canaguier,Aurélie Chauveau,Aurélie Bérard,G. Deniot,Mei Guan,Zhongsong Liu,Fengming Sun,Yong Pyo Lim,Eric Lyons,Christopher D. Town,Ian Bancroft,Xiaowu Wang,Jinling Meng,Jianxin Ma,J. Chris Pires,Graham J.W. King,Dominique Brunel,Régine Delourme,Michel Renard,Jean-Marc Aury,Keith L. Adams,Jacqueline Batley,Jacqueline Batley,Rod J. Snowdon,Jörg Tost,David Edwards,David Edwards,Yongming Zhou,Wei Hua,Andrew G. Sharpe,Andrew H. Paterson,Chunyun Guan,Patrick Wincker,Patrick Wincker,Patrick Wincker +86 more
TL;DR: The polyploid genome of Brassica napus, which originated from a recent combination of two distinct genomes approximately 7500 years ago and gave rise to the crops of rape oilseed, is sequenced.
Journal ArticleDOI
Normalization of RNA-seq data using factor analysis of control genes or samples
TL;DR: This work proposes a normalization strategy, called remove unwanted variation (RUV), that adjusts for nuisance technical effects by performing factor analysis on suitable sets of control genes or samples and leads to more accurate estimates of expression fold-changes and tests of differential expression compared to state-of-the-art normalization methods.
Journal ArticleDOI
Normalization and microbial differential abundance strategies depend upon data characteristics
Sophie Weiss,Zhenjiang Zech Xu,Shyamal D. Peddada,Amnon Amir,Kyle Bittinger,Antonio Gonzalez,Catherine A. Lozupone,Jesse R. Zaneveld,Yoshiki Vázquez-Baeza,Amanda Birmingham,Embriette R. Hyde,Rob Knight +11 more
TL;DR: These findings guide which normalization and differential abundance techniques to use based on the data characteristics of a given study.
Journal ArticleDOI
jvenn: an interactive Venn diagram viewer.
TL;DR: jvenn is a new JavaScript library that processes lists and produces Venn diagrams and handles up to six input lists and presents results using classical or Edwards-Venn layouts.
References
More filters
Journal ArticleDOI
Controlling the false discovery rate: a practical and powerful approach to multiple testing
Yoav Benjamini,Yosef Hochberg +1 more
TL;DR: In this paper, a different approach to problems of multiple significance testing is presented, which calls for controlling the expected proportion of falsely rejected hypotheses -the false discovery rate, which is equivalent to the FWER when all hypotheses are true but is smaller otherwise.
Journal ArticleDOI
Full-length transcriptome assembly from RNA-Seq data without a reference genome.
Manfred Grabherr,Brian J. Haas,Moran Yassour,Moran Yassour,Joshua Z. Levin,Dawn Thompson,Ido Amit,Xian Adiconis,Lin Fan,Raktima Raychowdhury,Qiandong Zeng,Zehua Chen,Evan Mauceli,Nir Hacohen,Andreas Gnirke,Nicholas Rhind,Federica Di Palma,Bruce W. Birren,Chad Nusbaum,Kerstin Lindblad-Toh,Kerstin Lindblad-Toh,Nir Friedman,Aviv Regev +22 more
TL;DR: The Trinity method for de novo assembly of full-length transcripts and evaluate it on samples from fission yeast, mouse and whitefly, whose reference genome is not yet available, providing a unified solution for transcriptome reconstruction in any sample.
Journal ArticleDOI
RSEM: accurate transcript quantification from RNA-Seq data with or without a reference genome
Bo Li,Colin N. Dewey +1 more
TL;DR: It is shown that accurate gene-level abundance estimates are best obtained with large numbers of short single-end reads, and estimates of the relative frequencies of isoforms within single genes may be improved through the use of paired- end reads, depending on the number of possible splice forms for each gene.
Journal ArticleDOI
Differential expression analysis for sequence count data.
Simon Anders,Wolfgang Huber +1 more
TL;DR: A method based on the negative binomial distribution, with variance and mean linked by local regression, is proposed and an implementation, DESeq, as an R/Bioconductor package is presented.
Journal ArticleDOI
Transcript assembly and quantification by RNA-Seq reveals unannotated transcripts and isoform switching during cell differentiation
Cole Trapnell,Cole Trapnell,Brian A. Williams,Geo Pertea,Ali Mortazavi,Gordon Kwan,Marijke J. van Baren,Steven L. Salzberg,Barbara J. Wold,Lior Pachter +9 more
TL;DR: The results suggest that Cufflinks can illuminate the substantial regulatory flexibility and complexity in even this well-studied model of muscle development and that it can improve transcriptome-based genome annotation.
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