Effect of diversity and missing data on genetic assignment with RAD-Seq markers

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 b...

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Autores principales: Chattopadhyay, Balaji, Garg, Kritika M, Ramakrishnan, Uma
Formato: Online Artículo Texto
Lenguaje:English
Publicado: BioMed Central 2014
Materias:
Correspondence
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4256836/
https://www.ncbi.nlm.nih.gov/pubmed/25424532
http://dx.doi.org/10.1186/1756-0500-7-841
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author Chattopadhyay, Balaji
Garg, Kritika M
Ramakrishnan, Uma
author_facet Chattopadhyay, Balaji
Garg, Kritika M
Ramakrishnan, Uma
author_sort Chattopadhyay, Balaji
collection PubMed
description 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. ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (doi:10.1186/1756-0500-7-841) contains supplementary material, which is available to authorized users.
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spelling pubmed-42568362014-12-05 Effect of diversity and missing data on genetic assignment with RAD-Seq markers Chattopadhyay, Balaji Garg, Kritika M Ramakrishnan, Uma BMC Res Notes Correspondence 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. ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (doi:10.1186/1756-0500-7-841) contains supplementary material, which is available to authorized users. BioMed Central 2014-11-25 /pmc/articles/PMC4256836/ /pubmed/25424532 http://dx.doi.org/10.1186/1756-0500-7-841 Text en © Chattopadhyay et al.; licensee BioMed Central Ltd. 2014 This article is published under license to BioMed Central Ltd. This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/4.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly credited. The Creative Commons Public Domain Dedication waiver (http://creativecommons.org/publicdomain/zero/1.0/) applies to the data made available in this article, unless otherwise stated.
spellingShingle Correspondence
Chattopadhyay, Balaji
Garg, Kritika M
Ramakrishnan, Uma
Effect of diversity and missing data on genetic assignment with RAD-Seq markers
title Effect of diversity and missing data on genetic assignment with RAD-Seq markers
title_full Effect of diversity and missing data on genetic assignment with RAD-Seq markers
title_fullStr Effect of diversity and missing data on genetic assignment with RAD-Seq markers
title_full_unstemmed Effect of diversity and missing data on genetic assignment with RAD-Seq markers
title_short Effect of diversity and missing data on genetic assignment with RAD-Seq markers
title_sort effect of diversity and missing data on genetic assignment with rad-seq markers
topic Correspondence
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4256836/
https://www.ncbi.nlm.nih.gov/pubmed/25424532
http://dx.doi.org/10.1186/1756-0500-7-841
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