I have Ensembl IDs that I am mapping to gene names. The way I've been doing it is going to biomart, selecting Ensembl Genes 101, and then human genes (GRCh38.p13.) I go attributes and select GENE STABLE ID and GENE NAME and download the resulting file (with ~67000 ensembl -> gene mappings.) Using R, I then map gene names back to my ensembl IDs, filter so each gene name only is listed once, ect.
However, just for fun, I decided to take my ensembl IDs and submit them to Biomart so they can do the mapping for me. To my surprise, the mapping is LESS (I cannot map around ~2,000 ensembl Ids.) I tested this was the Biomart R package, and it's the same. Why is it when you download the database, there are more mappings, but less when you submit your ids? Any help would be appreciated.