This project contains the codes and datasets used in the paper 'Genetic dietary adaptation in Neandertals, Denisovans and Sapiens revealed by gene copy number variation'.\\
Codes:\\
- read2CNV.slurm: slurm file that takes as input the reads of a single ancient genome, maps it to the reference GRCh38/hg38 and, after due filtering described in detail in the supplementary materials and methods of the paper, returns the copy number estimate of each gene.
- CNV_Analyses.slum: slurm file that takes the estimates of each single ancient genome as input and combines them into a single dataset in which clusters of recent paralogues are grouped into single lines (one per gene/cluster of genes) and in which each column corresponds to an ancient genome.
- HPA_Info_Extracter.R: this R-executable script extracts information from the two downloadable Human Protein Atlas expression datasets at https://www.proteinatlas.org/about/download, for rna (https://www.proteinatlas.org/download/rna_tissue_consensus.tsv.zip) and protein (https://www.proteinatlas.org/download/normal_tissue.tsv.zip) respectively. For each gene, the 3 organs (or tissue groups) with the highest expression in the rna dataset and the protein dataset are identified. In the case of ties, a frequent occurrence in the discrete categories of the protein dataset, more than 3 organs are taken. These data can then be cross-referenced with a list of genes of interest, in our case with the list of genes with CNVs at population level. Before running the script, change to your own reference paths.\\
Datasets:\\
- CNV_in_Ancient_Genomes.tsv: copy number estimates for selected diet related genes in all analysed ancient genomes.
- CNV_in_Modern_Genomes.tsv: copy number estimates for selected diet related genes in all analysed modern genomes.
- HPA_in_Digestive_related_Tissues.tsv: digestion-related tissue with highest expression in selected diet related genes.
- GO_Terms_with_Trends.tsv: genes grouped by GO-terms, in turn grouped by similar functions.
