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Protocols

RawGeno specifications

Information


Unique identifier OMICS_13872
Name RawGeno
Software type Package/Module
Interface Graphical user interface
Restrictions to use None
Input data A PeakScanner file
Input format TXTAll platforms
Operating system Unix/Linux
Programming languages R
License GNU General Public License version 2.0
Computer skills Medium
Version 2.0.1
Stability Alpha
Requirements
PeekScanner
Maintained Yes

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Publication for RawGeno

RawGeno citations

 (18)
library_books

Epigenetic and genetic variation among three separate introductions of the house sparrow (Passer domesticus) into Australia

2018
R Soc Open Sci
PMCID: 5936936
PMID: 29765671
DOI: 10.1098/rsos.172185

[…] Georgia Genomics Facility (University of Georgia) for fragment analysis on an ABI 3130XL. We used Peakscanner v. 1.0 (Applied Biosystems) to analyse resultant gel files and define fragment sizes and Rawgeno [] to define particular bands. We duplicated the entire protocol for at least two individuals from each location to identify bands that consistently occurred and we eliminated bands that incon […]

library_books

Living in two worlds: Evolutionary mechanisms act differently in the native and introduced ranges of an invasive plant

2018
Ecol Evol
PMCID: 5838077
PMID: 29531666
DOI: 10.1002/ece3.3869

[…] units (rfu) were not scored due to the possibility of instrument error (Arrigo, Tuszynski, Ehrich, Gerdes, & Alvarez, ; Herrmann et al., ). The un‐normalized peak height data were then imported into RawGeno v. 2.0.1 (Arrigo et al., ), an R package (R Core Team, ) for binning and scoring AFLP fragments. The maximum bin size was set to 2 bp, the minimum bin size to 1.5 bp, the scoring range was set […]

library_books

Small ocean temperature increases elicit stage dependent changes in DNA methylation and gene expression in a fish, the European sea bass

2017
Sci Rep
PMCID: 5622125
PMID: 28963513
DOI: 10.1038/s41598-017-10861-6

[…] of amplicon size categories and how the genotyping error per primer was calculated can be found in Additional Supporting Information. The scoring of electropherograms was performed using the package RawGeno (v. 2.0.2) in R (v. 3.2.5) and Rstudio (v. 1.0.136),. Further MSAP analyses were performed using the R package msap (v. 1.1.9) following a band-based strategy. The bands were scored as unmethy […]

library_books

Dealing with AFLP genotyping errors to reveal genetic structure in Plukenetia volubilis (Euphorbiaceae) in the Peruvian Amazon

2017
PLoS One
PMCID: 5598967
PMID: 28910307
DOI: 10.1371/journal.pone.0184259

[…] In RawGeno datasets, 25 AFLP markers were obtained per combination for the all-100 dataset, 18 markers for the all-150 dataset, 14 markers for the rep-100 dataset and 11 markers for the rep-150 dataset. […]

library_books

A genomic assessment of species boundaries and hybridization in a group of highly polymorphic anoles (distichus species complex)

2017
Ecol Evol
PMCID: 5468153
PMID: 28616163
DOI: 10.1002/ece3.2751

[…] lyzed AFLP electropherograms using PeakScanner v1.0 (Applied Biosystems) with light peak smoothing and default settings. We analyzed results from PeakScanner using a modified version of the R package RawGeno (Arrigo, Tuszynski, Ehrich, Gerdes & Alvarez, ). For analyses of individual sets, we set the maximum bin width to two base pairs (bp), minimum bin width to one bp, minimum fragment size to 50  […]

library_books

Patterns of rapid diversification in heteroploid Knautia sect. Trichera (Caprifoliaceae, Dipsacoideae), one of the most intricate taxa of the European flora

2016
BMC Evol Biol
PMCID: 5057222
PMID: 27724874
DOI: 10.1186/s12862-016-0773-2

[…] as well as the scoring approach followed Rešetnik et al. []; electropherograms were analysed with Peak Scanner version 1.0 (Applied Biosystems), and automated binning and scoring was performed using RawGeno version 2.0 [], a package for the software R [].The error rate [] was calculated as the ratio of mismatches (scoring of 0 vs. 1) over phenotypic comparisons in AFLP profiles of 43 replicated i […]

Citations

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RawGeno institution(s)
Laboratory of Evolutionary Botany, Institute of Biology, University of Neuchâtel, Neuchâtel, Switzerland; Science Applications International Corporation (SAIC), McLean, VA, USA; Department of Biology, University of Tromsø, Tromsø, Norway; Chromosome Laboratory, Department of Clinical Genetics, Rigshospitalet, Copenhagen, Denmark; Laboratory of Evolutionary Entomology, Institute of Biology, University of Neuchâtel, Neuchâtel, Switzerland
RawGeno funding source(s)
This study was funded by the National Centre of Competence in Research (NCCR) Plant Survival and the Swiss National Science Foundation (project No. 3100A0-116778/1).

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