Journal ArticleDOI
Sequencing depth and coverage: key considerations in genomic analyses
TLDR
The issue of sequencing depth in the design of next-generation sequencing experiments is discussed and current guidelines and precedents on the issue of coverage are reviewed for four major study designs, including de novo genome sequencing, genome resequencing, transcriptome sequencing and genomic location analyses.Abstract:
Sequencing technologies have placed a wide range of genomic analyses within the capabilities of many laboratories. However, sequencing costs often set limits to the amount of sequences that can be generated and, consequently, the biological outcomes that can be achieved from an experimental design. In this Review, we discuss the issue of sequencing depth in the design of next-generation sequencing experiments. We review current guidelines and precedents on the issue of coverage, as well as their underlying considerations, for four major study designs, which include de novo genome sequencing, genome resequencing, transcriptome sequencing and genomic location analyses (for example, chromatin immunoprecipitation followed by sequencing (ChIP-seq) and chromosome conformation capture (3C)).read more
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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
Estimating the population abundance of tissue-infiltrating immune and stromal cell populations using gene expression
Etienne Becht,Nicolas A. Giraldo,Nicolas A. Giraldo,Nicolas A. Giraldo,Laetitia Lacroix,Laetitia Lacroix,Laetitia Lacroix,Bénédicte Buttard,Bénédicte Buttard,Bénédicte Buttard,Nabila Elarouci,Florent Petitprez,Janick Selves,Pierre Laurent-Puig,Catherine Sautès-Fridman,Catherine Sautès-Fridman,Catherine Sautès-Fridman,Wolf H. Fridman,Wolf H. Fridman,Wolf H. Fridman,Aurélien de Reyniès +20 more
TL;DR: The Microenvironment Cell Populations-counter method is introduced, which allows the robust quantification of the absolute abundance of eight immune and two stromal cell populations in heterogeneous tissues from transcriptomic data and demonstrates that MCP-counter overcomes several limitations or weaknesses of previously proposed computational approaches.
Journal ArticleDOI
Recovery of nearly 8,000 metagenome-assembled genomes substantially expands the tree of life
Donovan H. Parks,Christian Rinke,Maria Chuvochina,Pierre-Alain Chaumeil,Ben J. Woodcroft,Paul N. Evans,Philip Hugenholtz,Gene W. Tyson +7 more
TL;DR: The recovery of 7,903 bacterial and archaeal metagenome-assembled genomes increases the phylogenetic diversity represented by public genome repositories and provides the first representatives from 20 candidate phyla.
Journal ArticleDOI
Qualimap 2: advanced multi-sample quality control for high-throughput sequencing data
TL;DR: Qualimap 2 represents a next step in the QC analysis of HTS data, along with comprehensive single-sample analysis of alignment data, and includes new modes that allow simultaneous processing and comparison of multiple samples.
Journal ArticleDOI
UMI-tools: modeling sequencing errors in Unique Molecular Identifiers to improve quantification accuracy
TL;DR: It is shown that errors in the UMI sequence are common and network-based methods to account for these errors when identifying PCR duplicates are introduced, demonstrating the value of properly accounting for errors in UMIs.
References
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Eva Gottwein,David L. Corcoran,Neelanjan Mukherjee,Rebecca L. Skalsky,Markus Hafner,Markus Hafner,Jeffrey Nusbaum,Jeffrey Nusbaum,Priscilla Shamulailatpam,Cassandra Love,Sandeep S. Dave,Thomas Tuschl,Thomas Tuschl,Uwe Ohler,Bryan R. Cullen +14 more
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Widespread binding of FUS along nascent RNA regulates alternative splicing in the brain
Boris Rogelj,Laura E. Easton,Gireesh K. Bogu,Lawrence W. Stanton,Gregor Rot,Tomaž Curk,Blaž Zupan,Yoichiro Sugimoto,Miha Modic,Nejc Haberman,James R. Tollervey,James R. Tollervey,Ritsuko Fujii,Toru Takumi,Christopher Shaw,Jernej Ule +15 more
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Journal ArticleDOI
Methylome analysis using MeDIP-seq with low DNA concentrations
Oluwatosin Taiwo,Gareth A. Wilson,Tiffany Morris,Stefanie Seisenberger,Wolf Reik,Wolf Reik,Daniel J. Pearce,Stephan Beck,Lee M. Butcher +8 more
TL;DR: MeDIP-seq as mentioned in this paper combines MeDIP with massively parallel DNA sequencing and achieves comparable results for specificity and enrichment over a wide range of DNA concentrations (5,000-50 ng) and demonstrates the utility of the protocol for the generation of methylomes from rare bone marrow cells using 160-300 ng of starting DNA.
Journal ArticleDOI
Comparison of solution-based exome capture methods for next generation sequencing.
Anna-Maija Kristiina Sulonen,Pekka Ellonen,Henrikki Almusa,Maija Lepistö,Samuli Eldfors,Sari Hannula,Timo Miettinen,Henna Tyynismaa,Perttu Salo,Perttu Salo,Caroline A. Heckman,Heikki Joensuu,Taneli Raivio,Taneli Raivio,Anu Suomalainen,Janna Saarela +15 more
TL;DR: A systematic comparison of the solution-based exome capture kits provided by Agilent and Roche NimbleGen and a bioinformatics pipeline for quality control, short read alignment, variant identification and annotation of the sequence data are developed.
Journal ArticleDOI
The genome sequence of the colonial chordate, Botryllus schlosseri
Ayelet Voskoboynik,Norma F. Neff,Debashis Sahoo,Aaron M. Newman,Dmitry Pushkarev,Winston Koh,Benedetto Passarelli,H. Christina Fan,Gary L. Mantalas,Karla J. Palmeri,Katherine J. Ishizuka,Carmela Gissi,Francesca Griggio,Rachel Ben-Shlomo,Daniel M. Corey,Lolita Penland,Richard A. White,Irving L. Weissman,Stephen R. Quake +18 more
TL;DR: Using a novel method for high-throughput sequencing of eukaryotic genomes, the B. schlosseri genome is sequenced and assembled and revealed genomic events underlying the evolution of vertebrates and lymphoid-mediated immunity.