Sorry, I am a software engineer, not a biologist. Even though I did take some biology and genetics courses at university, it is so many years ago that I forgot most of it and, even if I did remember, what I learned at the time is most probably completely outdated (I don't think that anyone ever dreamed at the time of, one day, sequencing the human genome). In brief, I just don't understand your questions. I don't even know what a BED file is, and if I remember to a certain extent what RNA is about, I do not not have a clue on what smallRNAs and microRNAs are.

I sincerely hope that some monk here might be able to help you, and it might happen, but i would really suggest that you explain your problem in CS terms, show some code that is failing to do what you want, explain what result you are looking for and how what you get is different, etc. If you do that, then you have a real chance of getting help. With the way you presented your problem, it would really be big luck.

Or, maybe, as already suggested, you should go to a Bioperl forum, where you are much more likely to find people understanding you and your language.