Hi @lillybiology
I tried Intersect the intervals of two datasets (Galaxy Version 1.0.0) on Galaxy Australia and cannot reproduce the issue, e.g. the score value from 1st BED file is present in the output file. It is hard to say why it does not work. Do you see BED header on preview? Here is my history if you want to check the files
https://usegalaxy.org.au/u/igor/h/bedintersect
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