ArticleMolecular ecology2013
Special features of RAD Sequencing data: implications for genotyping.
Article in Molecular ecology, 2013. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 140 papers.
What it found
Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.
The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
The trial behind it
Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.
Who cites it
140 citing papers in PubMed.
- Deciphering genetic diversity and selection footprints in Rathi cattle through ddRAD-based genome-wide analysis.Mammalian genome : official journal of the International Mammalian Genome Society · 2026Article
- SLAF-seq efficiently identifies SNP markers for wheat (Triticum aestivum L.) improvement.BMC genomics · 2026Article
- Sequencing Ultraconserved Elements (UCEs) for Marine Population Genomics: A Proof-of-Concept Using a Deep-Sea Mussel Species.Evolutionary applications · 2026Article
- Polymorphic microsatellite loci from ddRAD sequencing data in different Indian yak populations adapted to diverse climatic conditions.BMC genomics · 2025Article
- Biodiversity Genomics Research Practices Require Harmonising to Meet Stakeholder Needs in Conservation.Molecular ecology · 2025Review
- Genome-Wide SNP Analysis Reveals Population Structure and Genetic Diversity inPlants (Basel, Switzerland) · 2025Article
- Optimization and Evaluation of the bestRAD Sequencing Approach: Towards Ascertainment of the Invasion Routes of the Oriental Fruit Fly, Bactrocera dorsalis.Molecular ecology resources · 2025Article
- NewtCap: An Efficient Target Capture Approach to Boost Genomic Studies in Salamandridae (True Salamanders and Newts).Ecology and evolution · 2025Article
- Scaling-up RADseq methods for large datasets of non-invasive samples: Lessons for library construction and data preprocessing.Molecular ecology resources · 2025Article
- Genomic Signals of Local Adaptation Associated With Environmental Variables inEcology and evolution · 2025Article
- First Complete Mitochondrial Genome Analysis of Tree Frog,International journal of molecular sciences · 2025Article
- Fine-tuning GBS data with comparison of reference and mock genome approaches for advancing genomic selection in less studied farmed species.BMC genomics · 2025Article
- Development of genomic markers for monitoring and research on plethodontid salamanders.PloS one · 2025Article
- Genetic evolution of parental populations and construction of core germplasm populations in qinghai spruce seed orchard based on SLAF-seq technology.Frontiers in genetics · 2025Article
- Polygenic response to selection by transgenic Bt-expressing crops in wild Helicoverpa zea and characterization of a major effect locus.BMC genomics · 2024Article
- Article
- Genotyping-by-sequencing informs conservation of Andean palms sources of non-timber forest products.Evolutionary applications · 2024Article
- Analysis of genetic diversity by the SLAF-seq among the farmed Onychostoma macrolepis populations.BMC research notes · 2024Article
- Reference Genome Choice and Filtering Thresholds Jointly Influence Phylogenomic Analyses.Systematic biology · 2024Article
- Readsynth: short-read simulation for consideration of composition-biases in reduced metagenome sequencing approaches.BMC bioinformatics · 2024Article
80 more citing papers are in PubMed but not listed here.
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
6 authors.
Funding
Abstract
Restriction site-associated DNA Sequencing (RAD-Seq) is an economical and efficient method for SNP discovery and genotyping. As with other sequencing-by-synthesis methods, RAD-Seq produces stochastic count data and requires sensitive analysis to develop or genotype markers accurately. We show that there are several sources of bias specific to RAD-Seq that are not explicitly addressed by current genotyping tools, namely restriction fragment bias, restriction site heterozygosity and PCR GC content bias. We explore the performance of existing analysis tools given these biases and discuss approaches to limiting or handling biases in RAD-Seq data. While these biases need to be taken seriously, we believe RAD loci affected by them can be excluded or processed with relative ease in most cases and that most RAD loci will be accurately genotyped by existing tools.
Indexed as
Identifiers
What OpenQuestion holds
Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.