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Peter T. Euclide Garrett J. McKinney Matthew Bootsma Charlene Tarsa Mariah H. Meek Wesley A. Larson 《Molecular ecology resources》2020,20(1):66-78
Interpretation of high‐throughput sequence data requires an understanding of how decisions made during bioinformatic data processing can influence results. One source of bias that is often cited is PCR clones (or PCR duplicates). PCR clones are common in restriction site‐associated sequencing (RAD‐seq) data sets, which are increasingly being used for molecular ecology. To determine the influence PCR clones and the bioinformatic handling of clones have on genotyping, we evaluate four RAD‐seq data sets. Data sets were compared before and after clones were removed to estimate the number of clones present in RAD‐seq data, quantify how often the presence of clones in a data set causes genotype calls to change compared to when clones were removed, investigate the mechanisms that lead to genotype call changes and test whether clones bias heterozygosity estimates. Our RAD‐seq data sets contained 30%–60% PCR clones, but 95% of RAD‐tags had five or fewer clones. Relatively few genotypes changed once clones were removed (5%–10%), and the vast majority of these changes (98%) were associated with genotypes switching from a called to no‐call state or vice versa. PCR clones had a larger influence on genotype calls in individuals with low read depth but appeared to influence genotype calls at all loci similarly. Removal of PCR clones reduced the number of called genotypes by 2% but had almost no influence on estimates of heterozygosity. As such, while steps should be taken to limit PCR clones during library preparation, PCR clones are likely not a substantial source of bias for most RAD‐seq studies. 相似文献
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dos Santos Fernanda Marcelia Pflüger Pricila Fernandes Lazzarotto Leticia Uczay Mariana de Aguida Wesley Roberto da Silva Lisiane Santos Boaretto Fernanda Brião Menezes de Sousa Jayne Torres Picada Jaqueline Nascimento da Silva Torres Iraci Lucena Pereira Patrícia 《Neurochemical research》2021,46(8):2066-2078
Neurochemical Research - Gamma-decanolactone (GD) has been shown to reduce epileptic behavior in different models, inflammatory decreasing, oxidative stress, and genotoxic parameters. This study... 相似文献
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Kuczenski Brandon Mutel Chris Srocka Michael Scanlon Kelly Ingwersen Wesley 《The International Journal of Life Cycle Assessment》2021,26(3):483-496
The International Journal of Life Cycle Assessment - The flexibility of life cycle inventory (LCI) background data selection is increasing with the increasing availability of data, but this comes... 相似文献
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Manfred Schartl Susanne Kneitz Jenny Ormanns Cornelia Schmidt Jennifer L. Anderson Angel Amores Julian Catchen Catherine Wilson Dietmar Geiger Kang Du Mateo Garcia-Olazábal Sudha Sudaram Christoph Winkler Rainer Hedrich Wesley C. Warren Ronald Walter Axel Meyer John H. Postlethwait 《Current biology : CB》2021,31(5):911-922.e4
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