Submitting batch jobs to UCSC Genome Browser

Question

[gve96622]

I am using the UCSC Table Browser to get gene names from a list of regions. The browser has a limit of 1,000 regions at a time, whereas I have closer to 100,000 regions. I wrote a script to split my regions into groups of 1,000, but is there a way to submit these files to the browser as a batch job? It's very tedious to manually upload each file containing 1,000 regions.

Thanks!

Answer 1

[Pierre Lindenbaum]

download the flat files from UCSC and get your results using a combination of bedtools intersect and join

[gve96622]

Could you please elaborate? I'm not familiar with the UCSC flat files