I found some questions similiar to this, but the answers do not apply as the species I work with is not readily available. I basically have a bed file with coordinates:
Chr1 0 500 Chr1 501 551 Chr1 552 601
In another file, I have annotations for specific featrues
chr1 0 600 gene1 chr1 601 799 gene2
I want to annoate the first bed file, using information from the second file. I tried using Bedtools Intersect (and some Bedops), but it didn't end up working like I wanted. All help would be much appreciated.