how to annotate mapping peaks within a defined genomic region？
I have some small RNA seq data that I have mapped to the genome. Using a software, I annotated some big genomic loci (~1kb) where 25-32bp small piRNA reads are produced, in bed format. So within these loci there are multiple 25-32bp mapping peaks. Is there a tool I can use to get all the genomic coordinates of these peaks, in bed format?
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