Data from: Detection of individual ploidy levels with genotyping-by-sequencing (GBS) analysis

Gompert Z, Mock KE

Date Published: January 30, 2017

DOI: http://dx.doi.org/10.5061/dryad.5vs40

 

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Title R script to run gbs2ploidy on the aspen data
Downloaded 19 times
Description This script formats and summarizes the aspen data and then runs gbs2ploidy on the data set. The files needed for analysis are included in this Dryad submission.
Download aspenAnalysis.R (686 bytes)
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Title Aspen ID file
Downloaded 11 times
Description This csv text file contains population and individual IDs for the aspen samples, as well as ploidy levels inferred from microsatellites or flow cytometry.
Download DT_aspen_1Jul16.csv (5.352 Kb)
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Title Simulation code
Downloaded 6 times
Description R script to generate the simulated data used to test gbs2ploidy.
Download ploidySims.R (8.132 Kb)
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Title Simulation data
Downloaded 8 times
Description This is a R workspace object. It contains the simulation output from the allo- and autotetraploid simulations. It was generated with the ploidySims.R code also included with this Dryad submission.
Download simsAlloTet.Rdata (21.78 Mb)
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Title Allele sepecific read counts
Downloaded 15 times
Description This file contains the allele specific read counts for the aspen data. Each row contains the data for one SNP and each pair of columns has the data for an individual. These two columns contain the number of reads of each allele (one allele per column) if the individual was heterozygous at that SNP. Otherwise there is a NA for each column.
Download hetAlleleDepth.txt (60.66 Mb)
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Title Variant file for the aspen data
Downloaded 93 times
Description This vcf (variant call format) contains the filtered variant data for the aspen samples.
Download filtered2x_aspenvariants.vcf (235.7 Mb)
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When using this data, please cite the original publication:

Gompert Z, Mock KE (2017) Detection of individual ploidy levels with genotyping-by-sequencing (GBS) analysis. Molecular Ecology Resources, online in advance of print. http://dx.doi.org/10.1111/1755-0998.12657

Additionally, please cite the Dryad data package:

Gompert Z, Mock KE (2017) Data from: Detection of individual ploidy levels with genotyping-by-sequencing (GBS) analysis. Dryad Digital Repository. http://dx.doi.org/10.5061/dryad.5vs40
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