High-throughput sequencing data, codes and scripts used for statistical analyses, associated with the article entitled "Gene copy number variations at the within-host population level modulate gene expression in a multipartite virus" by Gallet et al. (2022)

Résumé 0

The compressed archive contains three subdirectories: The subdirectory data/ contains the final datasets, which consist in sequencing data of twenty parallel lineages of faba bean necrotic stunt virus (FBNSV), passaged from faba bean (Vicia faba) plants to alfalfa (Medicago truncatula) plants. All files are text files with tab separators. The subdirectory data/ also contains the R script parse_data.R, which purpose is to parse the sequencing data for subsequent analyses. The subdirectory abc/ contains the source files of the TmprlDiffABC software package, which purpose is to perform stochastic simulations mimicking the passage from faba bean (Vicia faba) plants to alfalfa (Medicago truncatula) plants. The subdirectory abc/ also contains the R script abc_inference.R which purpose is to perform ABC inference, using both the observed and the simulated statistics. The subdirectory test/ contains the source files of the TmprlDiffSEL software package, which purpose is to test the null hypothesis that the locus-specific differentiation measured at each SNP between the faba bean and the alfalfa samples is only due to genetic drift. The subdirectory test/ also contains the R script neutrality_test.R which purpose is to parse the outputs of the TmprlDiffSEL analyses.