queen-quality

GS and GWAS on queen size and fertility traits

Dylan Ryals, Bradley Metz, Luiz Brito, David Tarpy, Brock Harpur

Sample and sequence data are currently available on NCBI under BioProject accession PRJNA1469566

• The script 1_data_prep.sh is designed for SLURM protocol on an HPC. It filters raw data and performs initial analyses:
  • The pheno directory contains raw phenotypes for queens.
  • The scripts directory contains scripts for cleaning, filtering, and adjusting data.
  • Processed data are output to the data directory.
• The R markdown file 2_analysis.Rmd runs analyses and generates figures, with 2_analysis.html displaying all outputs.
  • Publication figures are output to the fig directory.
• Cleaned phenotypic data are temporarily available as cleaned_pheno.csv until permanent archiving upon publication.