or_stickleback.tar

The contents of or_sticleback.tar.gz relate to the study, "The population structure and recent colonization history of Oregon threespine stickleback determined using RAD-seq" by Catchen, Julian, Bassham, Susan, Wilson, Taylor, Currey, Mark, O'Brien, Conor, Yeates, Quick, and Cresko, William. The raw data used to create these files are available from the Sequence Read Archive (SRA), accession SRA070979. The Stickleback used for this study were collected from both marine and freshwater sites along the Oregon coast, and from freshwater habitats in the Willamette Basin and central Oregon. Extracted genomic DNA was processed into RAD libraries using the restriction enzyme SbfI-HF to digest the genome. After sequencing, reads were aligned to the stickleback reference genome using GSnap and processed with the Stacks pipeline. File Contents ------------- build_samples.sh - this file contains the commands run to clean and demultiplex the data. This transforms the raw data files into cleaned sample files, one per individual stickleback fish, named according to population. build_tags.sh - this file contains the commands run to align demultiplexed reads to the stickleback reference genome and to execute the Stacks pipeline. batch_2.fst_summary.tsv - a summary of the Fst values for each population. batch_2.structure_1000.tsv - 1000, randomly selected loci take from the batch_2.structure.tsv file for analysis in Structure. batch_2.structure.tsv - all variant sites in the Oregon dataset formatted for analysis in Structure. batch_2.sumstats_summary.tsv - summaries of the summary statistics, Pi, observed/expected heterozygosity, Fis, etc. batch_2.sumstats.tsv - summary statistics for each variable site in the set, Pi, observed/expected heterozygosity, Fis, etc. batch_2.vcf - variant sites in the Oregon dataset formatted in VCF (http://www.1000genomes.org/node/101). popmap - the population map file fed to the populations program. Describes which samples belong to which populations. Here is the population key: Crooked River 1 Cushman Slough 2 Pony Creek Reservoir 3 Paulina Lake 4 South Jetty 5 South Twin Lake 6 Winchester Creek 7 Riverbend 8 Millport Slough 9