Hi everyone,
I am in need of a practice SNP dataset because I would like to play around in the R package adegenet before I generate my dataset.
The holy grail would be one that will be in similar format as to mine, which would be in format generated from STRUCTURE (.str/.stru), include a couple hundred individuals of several populations and generated by RAD-seq.
The package does come with mock datasets, however they aren't really what I will be generating and I figured I would ask around before I use them.
Thank you!
Brenna
You can simulate raw RAD data using the simRRL package (http://dereneaton.com/radseq/simulating_raw_radseq_data/) or there are plenty of published datasets available. Most studies using RAD-type methods likely have some form of data available on Data Dryad.
For example, I googled "population structure RADseq" and investigated one of the first hits, Catchen et al (2013). In the "data accessibility" footnote they link to a dryad reposity (http://datadryad.org/resource/doi:10.5061/dryad.c7c8f) which contains aomng several other files, a "batch_2.structure.tsv" which is an input for Structure created by the RAD processing pipeline Stacks. This file is an input for Structure and looks like its in the '2-fow' format (2 rows per individual) with 591 individuals and 114,879 SNPs.
Hope that helps- good luck figuring out your analyses!
https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3712868/
Hi Tyler,
Thank you so much! I ended up getting dataset from a lab mate, which was an adventure to load but worked!
All the best,
Brenna
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