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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Journal ArticleDOI
Quasispecies evolution of the prototypical genotype 1 porcine reproductive and respiratory syndrome virus early during in vivo infection is rapid and tissue specific
Zen H. Lu,Zen H. Lu,Xinglong Wang,Xinglong Wang,Alison D. Wilson,Daniel Dorey-Robinson,Alan Archibald,Tahar Ait-Ali,Jean-Pierre Frossard +8 more
TL;DR: Microevolutionary events taking place within the viral quasispecies population in lung and lymph node 3 days post infection following experimental in vivo infection with the prototypical Lelystad PRRSV (LV) suggest that microevolution of these variants is rapid and some may be tissue-specific.
Posted ContentDOI
Deep sampling and pooled amplicon sequencing reveals hidden genic variation in heterogeneous rye accessions
Anna Hawliczek,Leszek Bolibok,Katarzyna Tofil,Ewa Borzęcka,Joanna Jankowicz-Cieślak,Piotr Gawroński,Adam Kral,Bradley J. Till,Hanna Bolibok-Brągoszewska +8 more
TL;DR: A pooled amplicon sequencing approach is developed and applied to out-crossing cereal rye, concluding that this approach provides a rapid and flexible method for evaluating stock heterogeneity, probing allele diversity, and recovering previously hidden variation.
Dissertation
Epigenetic Modification of mitochondrial genes in Alzheimer's disease (AD)
TL;DR: In this article, the authors present a Table of Table 1.2 Acknowledgements 4 Table 2.1 Table 3.4 Table 4.2 Table 5.3 Table 6.
Journal ArticleDOI
Bayesian hierarchical negative binomial models for multivariable analyses with applications to human microbiome count data.
TL;DR: A Bayesian hierarchical negative binomial model is presented as an efficient technique capable of compensating for multivariable sets including tens or hundreds of host characteristics as covariates further expanding analyses of human microbiome count data.
Journal ArticleDOI
Comment on ‘SARS-CoV-2 suppresses anticoagulant and fibrinolytic gene expression in the lung’
TL;DR: Mast et al. as mentioned in this paper analyzed transcriptome data derived from RNA-sequencing (RNA-seq) of COVID-19 patient bronchoalveolar lavage fluid (BALF) samples, as compared to BALF RNA-seq samples from a study investigating microbiome and inflammatory interactions in obese and asthmatic adults.
References
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edgeR: a Bioconductor package for differential expression analysis of digital gene expression data.
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Journal ArticleDOI
Initial sequencing and analysis of the human genome.
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TL;DR: The results of an international collaboration to produce and make freely available a draft sequence of the human genome are reported and an initial analysis is presented, describing some of the insights that can be gleaned from the sequence.
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
RNA-Seq: a revolutionary tool for transcriptomics
TL;DR: The RNA-Seq approach to transcriptome profiling that uses deep-sequencing technologies provides a far more precise measurement of levels of transcripts and their isoforms than other methods.
Journal ArticleDOI
TopHat: discovering splice junctions with RNA-Seq
TL;DR: The TopHat pipeline is much faster than previous systems, mapping nearly 2.2 million reads per CPU hour, which is sufficient to process an entire RNA-Seq experiment in less than a day on a standard desktop computer.