Hi,
Thanks for reaching out!
We are currently using indices generated with Gencode v38 for STAR and RSEM, and the Nov2020 version of Biomart to map Ensembl IDs to gene names. They are not the most up-to-date at the moment, and that should be why there are unmatched novel proteins and retired IDs in our data sets. We hope to update them in the future to minimize the number of mismatches.
Best,
Simone
