https://github.com/pdimens/c.acronotus-data-2019

SNP dataset associated with Dimens et al. 2019 "A genomic assessment of movement and gene flow around the South Florida vicariance zone in the migratory coastal blacknose shark, Carcharhinus acronotus"
https://github.com/pdimens/c.acronotus-data-2019

Last synced: 9 months ago
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SNP dataset associated with Dimens et al. 2019 "A genomic assessment of movement and gene flow around the South Florida vicariance zone in the migratory coastal blacknose shark, Carcharhinus acronotus"

• Host: GitHub
• URL: https://github.com/pdimens/c.acronotus-data-2019
• Owner: pdimens
• Created: 2019-05-14T01:12:48.000Z (about 7 years ago)
• Default Branch: master
• Last Pushed: 2019-05-14T15:02:40.000Z (about 7 years ago)
• Last Synced: 2024-12-08T22:17:42.925Z (over 1 year ago)
• Language: R
• Size: 2.41 MB
• Stars: 1
• Watchers: 1
• Forks: 1
• Open Issues: 0
• Metadata Files:
  • Readme: README.md

Awesome Lists containing this project

README

          
## SNP dataset associated with Dimens et al. 2019 "A genomic assessment of movement and gene flow around the South Florida vicariance zone in the migratory coastal blacknose shark, Carcharhinus acronotus"

#### acro_assignment_allloci_stru_input

Input used for Structure analysis

#### acronotus_manuscript.gen

The final SNP dataset used in subsequent analyses

#### acronotus_manuscript_nokey.gen

Same as above, but omitting the individuals from the Florida Keys

#### geneplot plotting.R

R code used to generate Supplemental Figure 2

#### geneplot results assignment.csv

Data used with the R code above to generate Supplemental Figure 2

#### interactive_bokeh_figures.py

Python code used to generate the interactive variant to Figure 2 (Structure plot)

#### K means and DAPC.R

R code used for K-means clustering and DAPC

#### acronotus all metadata.txt

Catch data associated with the individuals used in the study

#### reference.individuals

List of individuals used for reference assembly creation

#### structure assignment results.txt

Final Structure results discussed in the manuscript

#### TotalRawSNPs.vcf

Available by request Please contact the Marine Genomics Lab PI David Portnoy at david.portnoy@tamucc.edu

#### VCFfiltering_MASTER.xlsx

Excel file describing VCF filtering schema