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
Citations
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Journal ArticleDOI
Diversity within diversity: Parasite species richness in poison frogs assessed by transcriptomics.
TL;DR: It is proposed that endoparasites may escape poison frogs' chemical defenses by colonizing tissues with fewer alkaloids than the frog's skin, where most toxins are stored.
Journal ArticleDOI
Differential gene expression during placentation in pregnancies conceived with different fertility treatments compared with spontaneous pregnancies.
Bora Lee,Alexander F. Koeppel,Erica T. Wang,Erica T. Wang,Tania L Gonzalez,Tianyanxin Sun,Lindsay Kroener,Yayu Lin,N. Joshi,N. Joshi,Tejal Ghadiali,Stephen D. Turner,Stephen S. Rich,Charles R. Farber,Jerome I. Rotter,Yii-Der Ida Chen,Mark O. Goodarzi,Seth Guller,Bryna Harwood,Tania Basu Serna,John W Williams,John W Williams,Margareta D. Pisarska,Margareta D. Pisarska +23 more
TL;DR: Gene expression differences found to be highest in the NIFT group suggest that the underlying infertility, in addition to treatment-related factors, may contribute to the observed gene expression profiles.
Posted ContentDOI
Extensive Copy Number Variation in Fermentation-Related Genes among Saccharomyces cerevisiae Wine Strains
Jacob L. Steenwyk,Antonis Rokas +1 more
TL;DR: The results suggest that CN variation is a substantial contributor to the genomic diversity of wine yeast strains and identify several candidate loci whose levels of CN variation may affect the adaptation and performance ofwine yeast strains during fermentation.
Book ChapterDOI
Targeted DNA Region Re-sequencing
TL;DR: This chapter describes various re-sequencing methods with a focus on target enrichment, and lays out experimental design considerations, bioinformatics pipelines, and proper reporting of results for target enrichment.
Journal ArticleDOI
Helping decision making for reliable and cost‐effective 2b‐RAD sequencing and genotyping analyses in non‐model species
Anna Barbanti,Héctor Torrado,Héctor Torrado,Enrique Macpherson,Luca Bargelloni,Rafaella Franch,Carlos Carreras,Marta Pascual +7 more
TL;DR: It is demonstrated that selective‐base ligation does not affect genomic differentiation between individuals, indicating that this technique can be used in species with large genome sizes to adjust the number of loci to the study scope and to maintain suitable sequencing depth for a reliable genotyping without compromising the results.
References
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Journal ArticleDOI
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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.