I have an extended list of gene locations (chr#, start and end site) with respect to hg19 as extracted from not very specific alignments. I would like to find which genes fall in each of the regions (which consists of >20,000). For instance:
I would like to see what genes fall between each.. indeed, if i had just a handful, I could go to genome.browser and just look there and jot down the genes. However, i need this automated as i have > 20,000 of those and not all of them fall perfectly within the exact start to end of a gene. So if it was in the middle of a gene, i still need to account for that. I think if I have a file of the following columns: GeneID (NOT Transcript), Gene Name, chromosome, Start and End (i.e. bed file) but with respect to hg19 and with the GENE id (not transcript ID) as identifier then i could use that and write a python code. But i couldnt find such a file with GENE ID at beginning. If anyone has any suggestions, please let me know.