Assessment of transcript reconstruction methods for RNA-seq
Tamara Steijger,Josep F. Abril,Pär G. Engström,Pär G. Engström,Felix Kokocinski,Tim Hubbard,Roderic Guigó,Jennifer Harrow,Paul Bertone +8 more
TLDR
The results show that most algorithms are able to identify discrete transcript components with high success rates but that assembly of complete isoform structures poses a major challenge even when all constituent elements are identified.Abstract:
We evaluated 25 protocol variants of 14 independent computational methods for exon identification, transcript reconstruction and expression-level quantification from RNA-seq data. Our results show that most algorithms are able to identify discrete transcript components with high success rates but that assembly of complete isoform structures poses a major challenge even when all constituent elements are identified. Expression-level estimates also varied widely across methods, even when based on similar transcript models. Consequently, the complexity of higher eukaryotic genomes imposes severe limitations on transcript recall and splice product discrimination that are likely to remain limiting factors for the analysis of current-generation RNA-seq data.read more
Citations
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StringTie enables improved reconstruction of a transcriptome from RNA-seq reads
Mihaela Pertea,Geo Pertea,Corina Antonescu,Tsung Cheng Chang,Joshua T. Mendell,Steven L. Salzberg +5 more
TL;DR: StringTie, a computational method that applies a network flow algorithm originally developed in optimization theory, together with optional de novo assembly, to assemble these complex data sets into transcripts produces more complete and accurate reconstructions of genes and better estimates of expression levels.
Journal ArticleDOI
The landscape of long noncoding RNAs in the human transcriptome
Matthew K. Iyer,Yashar S. Niknafs,Rohit Malik,Udit Singhal,Anirban Sahu,Yasuyuki Hosono,Terrence R. Barrette,John R. Prensner,Joseph R. Evans,Shuang G. Zhao,Anton Poliakov,Xuhong Cao,Saravana M. Dhanasekaran,Yi-Mi Wu,Dan R. Robinson,David G. Beer,Felix Y. Feng,Hariharan K. Iyer,Arul M. Chinnaiyan +18 more
TL;DR: The lncRNA landscape characterized here may shed light on normal biology and cancer pathogenesis and may be valuable for future biomarker development.
Journal ArticleDOI
GENCODE reference annotation for the human and mouse genomes.
Adam Frankish,Mark Diekhans,Anne-Maud Ferreira,Rory Johnson,Irwin Jungreis,Irwin Jungreis,Jane E. Loveland,Jonathan M. Mudge,Cristina Sisu,Cristina Sisu,James C. Wright,Joel Armstrong,If Barnes,Andrew Berry,Alexandra Bignell,Silvia Carbonell Sala,Jacqueline Chrast,Fiona Cunningham,Tomás Di Domenico,Sarah Donaldson,Ian T. Fiddes,Carlos García Girón,Jose Manuel Gonzalez,Tiago Grego,Matthew P. Hardy,Thibaut Hourlier,Toby Hunt,Osagie G. Izuogu,Julien Lagarde,Fergal J. Martin,Laura Martinez,Shamika Mohanan,Paul R. Muir,Fabio C. P. Navarro,Anne Parker,Baikang Pei,Fernando Pozo,Magali Ruffier,Bianca M. Schmitt,Eloise Stapleton,Marie-Marthe Suner,Irina Sycheva,Barbara Uszczynska-Ratajczak,Jinuri Xu,Andrew D. Yates,Daniel R. Zerbino,Yan Zhang,Yan Zhang,Bronwen Aken,Jyoti S. Choudhary,Mark Gerstein,Roderic Guigó,Tim Hubbard,Manolis Kellis,Manolis Kellis,Benedict Paten,Alexandre Reymond,Michael L. Tress,Paul Flicek +58 more
TL;DR: This work generates primary data, creates bioinformatics tools and provides analysis to support the work of expert manual gene annotators and automated gene annotation pipelines to identify and characterise gene loci to the highest standard.
Journal ArticleDOI
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.
Journal ArticleDOI
PacBio Sequencing and Its Applications.
Anthony Rhoads,Kin Fai Au +1 more
TL;DR: Single-molecule, real-time sequencing developed by Pacific BioSciences offers longer read lengths than the second-generation sequencing technologies, making it well-suited for unsolved problems in genome, transcriptome, and epigenetics research.
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