R Microsatellite Binning
Description
Functions to process scored microsatellite track data exported from Geneious.
Individual steps after preparing the samples in Geneious (check ladder peaks and score alleles in Geneious/microsatellite plugin; export all files from Geneious to one file for each multiplex; extract the individual multiplex files):
- read scored Geneious-XML-files and transform to data frame
- read processed geneious data frame and determine fragment lengths
- read raw fragment lengths and separate into individual microsatellite loci
- reformat alleles in two alleles per loci
- add additional information (original individual TreeID and SiteID)
- binning fragment length into integers
- import the binned data and convert to genind-object and run first example analyses Expample data is provided and further details on each step can be found in the R-script.
Currently supported:
- size ladder LIZ600
- microsatellite assay consisting of three multiplexes
- bcLK241, bcLK066, bcLK253, bcLK211, Ld101 (N=5)
- bcLK260, bcLK056, bcLK224, Ld45, bcLK263, bcLK228 (N=6)
- bcLK225, bcLK235, bcLK189, Ld56, Ld42 (N=5)
The multiplexes were developed and applied, and accordingly, these functions compiled/developed during the analyses of microsatellite data for the manuscript: "High gene flow and complex treeline dynamics of Larix Mill. stands on the Taymyr Peninsula (north-central Siberia) revealed by nuclear microsatellites" by Kruse, S., Epp, L. S., Wieczorek, M., Pestryakova, L. A., Stoof-Leichsenring, K. R., Herzschuh, U., accepted for publication in Tree Genetics & Genomes, doi:10.1007/s11295-018-1235-3
Files
StefanKruse/R_MicrosatelliteBinning-v1.0.zip
Files
(4.0 MB)
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Additional details
Related works
- Is supplement to
- https://github.com/StefanKruse/R_MicrosatelliteBinning/tree/v1.0 (URL)