From raw AFLP chromatograms to ready-to-use binary matrices using RawGeno 2.0, an user-friendly interface for automatized and semi-automatized bining and scoring of genotypes in the R environment
| Autor: | Arrigo N Holderegger R Alvarez N |
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| Rok vydání: | 2012 |
| DOI: | 10.1007/978-1-61779-870-2_10 |
| Popis: | 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. |
| Databáze: | OpenAIRE |
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