I need to align a dataset mapped to GRCh38.p2 (ensembl 79) and a dataset mapped to GRCh38.p13 (ensembl 98).
The first dataset (ensembl 79) has gene names and entrez IDs. The second dataset (ensembl 98) has gene names and ENSG IDs. I want to convert ensembl 79 entrez IDs to ENSG IDs. When I query on biomaRt, almost half of the genes are not found. I have tried using both "external_gene_name" and "enterezgene" as filters. I have tried using both the most recent mart and archived marts (ensembl 77-80).
FYI: approximately 25000 genes were not found, and of these genes about 10000 of them are pseudogenes.
I need to align a dataset mapped to GRCh38.p2 (ensembl 79) and a dataset mapped to GRCh38.p13 (ensembl 98).
The first dataset (ensembl 79) has gene names and entrez IDs. The second dataset (ensembl 98) has gene names and ENSG IDs. I want to convert ensembl 79 entrez IDs to ENSG IDs. When I query on biomaRt, almost half of the genes are not found. I have tried using both "external_gene_name" and "enterezgene" as filters. I have tried using both the most recent mart and archived marts (ensembl 77-80).
FYI: approximately 25000 genes were not found, and of these genes about 10000 of them are pseudogenes.
Code below: