@@ -4,8 +4,8 @@ This project contains the codes and datasets used in the paper 'Genetic dietary
...
@@ -4,8 +4,8 @@ This project contains the codes and datasets used in the paper 'Genetic dietary
Codes:
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.
- 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.
- 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.
- genes_with_CNV_at_pop_lvl_extracter.R: this R-executable script extract genes presenting CNV at population level in at least one species (either Neandertals or Sapiens) and adds two columns indicating gains and losses.
- 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.
- 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:
Datasets:
- CNV_in_Ancient_Genomes.tsv: copy number estimates for selected diet related genes in all analysed ancient genomes.
- 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.
- CNV_in_Modern_Genomes.tsv: copy number estimates for selected diet related genes in all analysed modern genomes.
