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https://doi.org/10.1186/1756-0500-7-841
Title: | Effect of diversity and missing data on genetic assignment with RAD-Seq markers | Authors: | Chattopadhyay, B Garg, K.M Ramakrishnan, U |
Keywords: | genetic marker algorithm animal bat classification data mining gene flow gene library gene locus genetic marker genetics phylogeny population genetics single nucleotide polymorphism software Algorithms Animals Chiroptera Data Mining Gene Flow Gene Library Genetic Loci Genetic Markers Genetics, Population Phylogeny Polymorphism, Single Nucleotide Software |
Issue Date: | 2014 | Citation: | Chattopadhyay, B, Garg, K.M, Ramakrishnan, U (2014). Effect of diversity and missing data on genetic assignment with RAD-Seq markers. BMC Research Notes 7 (1) : 841. ScholarBank@NUS Repository. https://doi.org/10.1186/1756-0500-7-841 | Rights: | Attribution 4.0 International | Abstract: | Reduced representation libraries are being used as a preferred source of markers to address population genetic questions. However, libraries of RAD-Seq variants often suffer from significant percentage of missing data. In addition, algorithms used to mine SNPs from the raw data may also underscore biological variation. We investigate the effect of biological diversity in mining SNPs from the program STACKS and the effect of missing data on individual assignment implemented in STRUCTURE. We observed that changing diversity parameters in STACKS significantly alters the number of SNPs discovered and allowing for higher percentage of missing data retrieves more loci and possibly more power for individual assignment. © 2014 Chattopadhyay et al. | Source Title: | BMC Research Notes | URI: | https://scholarbank.nus.edu.sg/handle/10635/181764 | ISSN: | 17560500 | DOI: | 10.1186/1756-0500-7-841 | Rights: | Attribution 4.0 International |
Appears in Collections: | Staff Publications Elements |
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