I have a table for chromosomal positioning fro the human genome of the following structure:
chromosome start end chrY 3447096 6114264 chrY 6114264 6733959 chrY 6733959 7142013 chrY 7142013 9175071 ...
I would like to find for each of these regions the genes which overlaps these region, independent of completely or only a partial overlap.
Can someone please recommend a way to it. Is it possible to do such analysis using R or a direct query of the UCSC genome broswer. The problem with UCSC is that there are no genome coordinates table to download, only CDS or transcripts. I tried to run biomart, but I keep getting an error message.
I will appreciate any help and ideas