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Transcriptome assembly and isoform expression level estimation from biased RNA-Seq reads

Wei Li, Tao Jiang
2012 Computer applications in the biosciences : CABIOS  
Results: Here, we propose a statistical framework for both transcriptome assembly and isoform expression level estimation from biased RNA-Seq data.  ...  However, RNA-Seq reads are usually not uniformly distributed and biases in RNA-Seq data post great challenges in many applications including transcriptome assembly and the expression level estimation of  ...  and real RNA-Seq experiments and analyze the effects of RNA-Seq biases on both transcriptome assembly and isoform abundance level estimation.  ... 
doi:10.1093/bioinformatics/bts559 pmid:23060617 pmcid:PMC3496342 fatcat:lv6v3rk2rrelzp6jtqbenansui

Analysis of Whole Transcriptome Sequencing Data: Workflow and Software

In Seok Yang, Sangwoo Kim
2015 Genomics & Informatics  
In this review, we introduce routine RNA-seq workflow together with related software, focusing particularly on transcriptome reconstruction and expression quantification.  ...  RNA-seq is a powerful technique for characterizing and quantifying the transcriptome and accelerates the development of bioinformatics software.  ...  Acknowledgments This work was supported by the Bio-Synergy Research Project (NRF-2014M3A9C4066449) of the Ministry of Science, ICT and Future Planning through the National Research Foundation.  ... 
doi:10.5808/gi.2015.13.4.119 pmid:26865842 pmcid:PMC4742321 fatcat:y4q3sgeckbbpdmcgnpmakhlvku

Bioinformatics Tools for RNA-seq Gene and Isoform Quantification

Chi Zhang, Baohong Zhang, Michael S Vincent, Shanrong Zhao
2016 Journal of Next Generation Sequencing & Applications  
In recent years, RNA-seq has emerged as a powerful technology in estimation of gene or transcript expression. 'Union-exon' and transcript based approaches are widely used in gene quantification.  ...  Recently, a number of tools have been developed for RNA-seq isoform quantification.  ...  This is because identification of isoforms from RNA-seq data is far from being solved and is still challenging, due in particular to the incomplete nature of RNA-seq reads and the fact that the number  ... 
doi:10.4172/2469-9853.1000140 fatcat:5ov3cuwjrngfnjicxofzlw6rd4

A comprehensive comparison between reference-based and 'de novo' isoform assembly approaches

Oscar Rodriguez, Juan Carlos Triviño, Rebeca Miñambres, Sheila Zuñiga, Sonia Santillán, Mayte Gil, Reyes Claramunt, Celia Buades
2013 EMBnet journal  
Gene expression levels were estimated using FPKM values as given by Cufflinks (Trapnell et al., 2010) and DESeq (Anders and Huber, 2010) .  ...  In the present studio we provide a comprehensive comparison between these two transcriptome analysis methodologies for isoforms reconstruction based on genome annotation and isoform expression levels using  ... 
doi:10.14806/ej.19.a.621 fatcat:rzhmzxfsijgcxobspoemkbuhmi

Overview of available methods for diverse RNA-Seq data analyses

Geng Chen, Charles Wang, TieLiu Shi
2011 Science China Life Sciences  
or isoform expression quantification, differential expression analysis and transcriptome reconstruction. next generation sequencing, transcriptome, RNA-Seq data analysis, transcriptomics  ...  RNA-Seq technology is becoming widely used in various transcriptomics studies; however, analyzing and interpreting the RNA-Seq data face serious challenges.  ...  However, when quantifying the expression of genes, microarrays are limited to the gene level. By contrast, RNA-Seq can estimate gene expression at both the gene and the isoform levels.  ... 
doi:10.1007/s11427-011-4255-x pmid:22227904 fatcat:lxmiyizomrfxzhm6l5kmswraga

Letting the data speak for themselves: a fully Bayesian approach to transcriptome assembly

Marcel H Schulz
2014 Genome Biology  
A novel method for transcriptome assembly, Bayesembler, provides greater accuracy without sacrifice of computational speed, and particular advantages for alternative transcripts expressed at low levels  ...  Acknowledgements The author acknowledges Hugues Richard for proofreading and discussion.  ...  Third, in RNA-seq experiments, the number of reads for each transcript correlates with the expression level of the transcripts.  ... 
doi:10.1186/s13059-014-0498-8 pmid:25830215 pmcid:PMC4318165 fatcat:5vhj7imkdbc75g66lumhvce5pe

Impact of RNA-seq attributes on false positive rates in differential expression analysis of de novo assembled transcriptomes

Emmanuel González, Simon Joly
2013 BMC Research Notes  
Results: We tested how using different types of reads from the ones used to assemble a de novo transcriptome (both differing in length and pairing attributes) could potentially affect differential expression  ...  High-throughput RNA sequencing studies are becoming increasingly popular and differential expression studies represent an important downstream analysis that often follow de novo transcriptome assembly.  ...  Acknowledgements The authors to thank Julie Marleau and Hermine Alexandre for laboratory work, Werther Guidi for providing willow plant material, and Adriana Almeida-Rodriguez, Frederic Pitre and Michel  ... 
doi:10.1186/1756-0500-6-503 pmid:24298906 pmcid:PMC4222115 fatcat:lwgoa5ndwjeyve7ohnh3i3u6bm

Modeling and analysis of RNA-seq data: a review from a statistical perspective

Wei Vivian Li, Jingyi Jessica Li
2018 Quantitative Biology  
We review RNA-seq analysis tools at the sample, gene, transcript, and exon levels from a statistical perspective.  ...  The analysis of RNA-seq data at four different levels (samples, genes, transcripts, and exons) involve multiple statistical and computational questions, some of which remain challenging up to date.  ...  from short RNA-seq reads.  ... 
doi:10.1007/s40484-018-0144-7 pmid:31456901 pmcid:PMC6711375 fatcat:qd2ssgwzgrdw5gm5gkueayvf3i

Computational methods for transcriptome annotation and quantification using RNA-seq

Manuel Garber, Manfred G Grabherr, Mitchell Guttman, Cole Trapnell
2011 Nature Methods  
RNA-Seq promises a comprehensive picture of the transcriptome allowing for the complete annotation and quantification of all genes and their isoforms in any given sample.  ...  We break these methods into three categories: (i) read alignment, (ii) transcriptome reconstruction, and (iii) expression quantification.  ...  Acknowledgments We would like to thank Leslie Gaffney for help with figures, Brian Haas, Yarden Katz, Andrea Pauli, and Mike Zody for helpful discussions and comments on the manuscript and to Jessica Alfoldi  ... 
doi:10.1038/nmeth.1613 pmid:21623353 fatcat:3wddb7ubkfbhdcfxytfdzwj7hu

RNA Sequencing and Analysis

Kimberly R. Kukurba, Stephen B. Montgomery
2015 Cold Spring Harbor Protocols  
K.R.K. is supported by the National Defense Science and Engineering Graduate (NDSEG) Fellowship from the U.S. Department of Defense, and S.B.M. is funded by the Edward Mallinckrodt, Jr. Foundation.  ...  ACKNOWLEDGMENTS The authors gratefully acknowledge their colleagues, Tuuli Lappalainen and Jin Billy Li, as well as fellow laboratory members, including Zach Zappala, Kevin Smith, Marianne DeGorter and  ...  Beyond surveying gene expression levels, RNA-Seq can also be applied to discover novel gene structures, alternatively spliced isoforms, and allele-specific expression (ASE).  ... 
doi:10.1101/pdb.top084970 pmid:25870306 pmcid:PMC4863231 fatcat:iqwyhy37jrh5bmrfw4wjukraja

A survey of best practices for RNA-seq data analysis

Ana Conesa, Pedro Madrigal, Sonia Tarazona, David Gomez-Cabrero, Alejandra Cervera, Andrew McPherson, Michał Wojciech Szcześniak, Daniel J. Gaffney, Laura L. Elo, Xuegong Zhang, Ali Mortazavi
2016 Genome Biology  
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  ...  We discuss the analysis of small RNAs and the integration of RNA-seq with other functional genomics techniques.  ...  Research in PM's laboratory is supported by ERC starting grant Relieve-IMDs and by a core support grant from the Wellcome Trust and MRC to the Wellcome Trust-Medical Research Council Cambridge Stem Cell  ... 
doi:10.1186/s13059-016-0881-8 pmid:26813401 pmcid:PMC4728800 fatcat:pidog3wat5fgzirqpjxfd5nnta

RNA-seq data science: From raw data to effective interpretation [article]

Dhrithi Deshpande, Karishma Chhugani, Yutong Chang, Aaron Karlsberg, Caitlin Loeffler, Jinyang Zhang, Agata Muszynska, Jeremy Rotman, Laura Tao, Brunilda Balliu, Elizabeth Tseng, Eleazar Eskin (+4 others)
2021 arXiv   pre-print
It generates enormous amounts of transcriptomic data in the form of nucleotide sequences, known as reads.  ...  Our review provides a systemic overview of RNA-seq technology and 235 available RNA-seq tools across various domains published from 2008 to 2020, discussing the interdisciplinary nature of bioinformatics  ...  Patro for his valuable comments and suggestions on the manuscript. Competing Interests The authors declare no competing interests. References  ... 
arXiv:2010.02391v3 fatcat:krgm7uzmibdlfh2ylgqxmnh2qu

Transcriptome Analysis for Non-Model Organism: Current Status and Best-Practices [chapter]

Vahap Eldem, Gokmen Zararsiz, Tunahan Taşçi, Izzet Parug Duru, Yakup Bakir, Melike Erkan
2017 Applications of RNA-Seq and Omics Strategies - From Microorganisms to Human Health  
In spite of immense potential of RNA-Seq-based methods, particularly in recovering full-length transcripts and spliced isoforms from short-reads, the accurate results can be only obtained by the procedures  ...  Since transcriptome analysis provides genome-wide sequence and gene expression information, transcript reconstruction using RNA-Seq sequence reads has become popular during recent years.  ...  This work was partly supported by the Istanbul University Scientific Research Project (Project No. 46473 and 29506) and also partly supported by Marmara University Research Fund (Grant Number: FEN-A-100616  ... 
doi:10.5772/intechopen.68983 fatcat:vatg4hbanrchxhuxbf3meb3hye

Transcriptome assembly and quantification from Ion Torrent RNA-Seq data

Serghei Mangul, Adrian Caciula, Sahar Al Seesi, Dumitru Brinza, Ion Mӑndoiu, Alex Zelikovsky
2014 BMC Genomics  
A new version of the IsoEM algorithm suitable for Ion Torrent RNA-Seq reads is used to accurately estimate transcript expression levels.  ...  Results: We present MaLTA, a method for simultaneous transcriptome assembly and quantification from Ion Torrent RNA-Seq data.  ...  .: Transcriptome assembly and quantification from Ion Torrent RNA-Seq data.  ... 
doi:10.1186/1471-2164-15-s5-s7 pmid:25082147 pmcid:PMC4120146 fatcat:2pqjoiiqafgylft7tskibudnjy

Sparse linear modeling of next-generation mRNA sequencing (RNA-Seq) data for isoform discovery and abundance estimation

J. J. Li, C.-R. Jiang, J. B. Brown, H. Huang, P. J. Bickel
2011 Proceedings of the National Academy of Sciences of the United States of America  
There are also efforts on formulating the abundance estimation problem as a linear model (15) , where the independent and dependent variables are isoform expression levels and categorized RNA-Seq read  ...  Unlike microarrays, RNA-Seq data have novel splice junction information in addition to gene expression, thus facilitating whole-transcriptome assembly and mRNA isoform quantification.  ...  This work is supported in part by Grants HG004695, HG005639, and EY019094 from the National Institutes of Health.  ... 
doi:10.1073/pnas.1113972108 pmid:22135461 pmcid:PMC3250192 fatcat:o5jqwd7q5be33daplc4zyikkya
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