RNA SEQ Data read counts from known and unknown regions

[deveci]

I am doing RNA SEQ analysis, and I simply need to get the number of the reads from known regions and unknown regions. I was using Partek, and I am sure it has to have that information, but I couldn't find how to get that. Can you help me if you know how to retrieve that information on Partek, or on any other publicly available tool?
Thank you.