Peak length after annotation

Question

[oldtownroald]

Hi, I am annotating my CLIP-seq peaks after using PEAKachu peak caller program. I tried used bedtools windowbed and bedtools intersect to annotate the peaks using the the drosophila melanogaster gtf annotation file. However, the annotated peaks always come up 1000X longer than the original peak size (so originally it was 50bp and now its 12kbp)

Why is this happening and how do I avoid this problem?

I also used RCAS to annotate the peaks and the peak lengths are also increased after annotation.