Hi mgamar. How are your readers here to know what a BED file is? When asking questions don't depart from your own position but try to imagine that of the person you're talking to.

Especially on a site like PerlMonks. Many people here are happy to help but please provide appropriate links to the context of your question; in the case of BED files, that is the UCSC site.

Explain what a BED file normally is for (I'll assume you know), and its format. Perhaps include the first 5 lines of one of your BED files. It'd only be polite to include wikipedia links to 'jargon' words like smallRNA, microRNA.

( I remembered they (UCSC) explain the format quite clearly; look what I found in the FAQ. )