Read counts from bam file without available annotation file

Question

[E]

Hi,

I have small RNA data from gonadal tissue. A high amount of these sRNAs should therefore be piRNAs mapping to tranposable elements. I would like to quantify how many piRNAs correspond to a specific TE.

I already mapped my library to TE consensus sequences I got from RepBase. Now I would like to extract read counts but the only software I can find doing this needs an annotation file.

Does anybody know software which requires only the mapping file to extract read counts?

Thanks in advance