Using the Ingest Tools,

  1. Go to Manage Jena Models and add a new, temporary model.
  2. Use the "load RDF data" button below it to add to this temporary model the RDF you ultimately want to delete.
  3. Go to back to the Ingest Tools menu, select Subtract One Model from Another.
  4. Set "model to be subtracted from" and "model in which difference should be saved" to the graph you wanted to delete from in the first place. Set "model to subtract" to the temporary graph you just created.
  5. Run the subtraction.
  6. Go back to Manage Jena Models and remove the temporary model.