使用免费的R CRAN库RawGeno v 2.0对扩增片段长度多态性（AFLPs）进行自动评分。
Automated scoring of AFLPs using RawGeno v 2.0, a free R CRAN library.
作者信息
Arrigo Nils, Holderegger Rolf, Alvarez Nadir
机构信息
Laboratory of Evolutionary Botany, Institute of Biology, University of Neuchâtel, Neuchâtel, Switzerland.
出版信息
Methods Mol Biol. 2012;888:155-75. doi: 10.1007/978-1-61779-870-2_10.
Amplified Fragment Length Polymorphisms (AFLPs) are a cheap and efficient protocol for generating large sets of genetic markers. This technique has become increasingly used during the last decade in various fields of biology, including population genomics, phylogeography, and genome mapping. Here, we present RawGeno, an R library dedicated to the automated scoring of AFLPs (i.e., the coding of electropherogram signals into ready-to-use datasets). Our program includes a complete suite of tools for binning, editing, visualizing, and exporting results obtained from AFLP experiments. RawGeno can either be used with command lines and program analysis routines or through a user-friendly graphical user interface. We describe the whole RawGeno pipeline along with recommendations for (a) setting the analysis of electropherograms in combination with PeakScanner, a program freely distributed by Applied Biosystems; (b) performing quality checks; (c) defining bins and proceeding to scoring; (d) filtering nonoptimal bins; and (e) exporting results in different formats.
扩增片段长度多态性（AFLP）是一种用于生成大量遗传标记的廉价且高效的方法。在过去十年中，这项技术在生物学的各个领域，包括群体基因组学、系统地理学和基因组作图中得到了越来越广泛的应用。在此，我们展示了RawGeno，一个专门用于AFLP自动评分（即将电泳图谱信号编码为可用数据集）的R库。我们的程序包括一套完整的工具，用于对AFLP实验获得的结果进行分箱、编辑、可视化和导出。RawGeno既可以与命令行和程序分析例程一起使用，也可以通过用户友好的图形用户界面使用。我们描述了整个RawGeno流程，并给出了以下方面的建议：（a）结合PeakScanner（由应用生物系统公司免费分发的一个程序）设置电泳图谱分析；（b）进行质量检查；（c）定义箱并进行评分；（d）过滤非最优箱；（e）以不同格式导出结果。
Zotero 插件