Introgressed mitochondrial fragments from archaic hominins alter nuclear genome function in modern humans

This repository contains the custom scripts in the study: "Introgressed mitochondrial fragments from archaic hominins alter nuclear genome function in modern humans" Included-------------- 1. mapping_pe.sh Shell script used to map paired-end reads from high-coverage archaic hominin genomes to the human reference genome. 2. mapping_se.sh Shell script used to map single-end reads from high-coverage archaic hominin genomes to the human reference genome. 3. nearby-gene-expression.R R script for analyzing the effect of NUMTs on the expression of nearby genes. 4. plot_permutation.R R script to visualize the results of permutation tests. 5. Table_s1_to_s13.xlsx Summary data corresponding to Supplementary Tables S1–S13. Notes: The original raw datasets (archaic hominin genomes, modern human genomes, RNA-seq data, and other resources) used in this study are publicly available from the repositories cited in the main text and in the Supplementary Materials.