I have a list of ~1500 (over a few samples) chromosome:peakstart:peakend from my recent CLIP-seq experiment. I want to know: 1) What genes each peak maps to 2) What sequences are included in those peaks. Is there a quick way to do this? I only could figure out how to the full CDS, not just the peak.
I was able to find all the genes by inputting my peaks as a csv into UCSC Table Browser, but when I get an output it puts every transcript possible on different lines (ex if my peak mapped to gene X, I would get gene X transcript 1, gene X transcript 2, etc). I would like to copy back this list to my original data in excel, but now the lines don't match up. Does anyone have a recommendation?