Hi, I have 2 fasta files (one of precursor novel microRNAs and one of mature novel microRNAs), and a bed file of the precursors. What I want to do is find where the 2 fasta files overlap and get the coordinates, relative to the precursor bed. I can't find any tool that would let me do this... the closest is bedtools getfasta, but I guess I want to do the opposite, rather than get a fasta sequence of overlapping regions I want to get the coordinates.
I considered converting the bed to gtf, indexing precursor gtf, and then mapping to this. But I realised the coordinates won't match that of where it actually is in the genome. Any suggestions would be really helpful!