Hi fellow bioinformaticians,
I am trying to use multiIntersectBed to find intersections of genomic regions (copy number variations) in ~1400 samples. For each sample, I have a sorted bed file.
When I used multiIntersectBed on 5 bed files as a test, it worked perfectly. But when I used it on all ~1400 samples, I received the following error: "Error: The requested bed file (file1.bed) could not be opened. Exiting!"
However, this bed file runs fine if I only input a few bed files instead of 1400 . Therefore it seems to me like a problem regarding the number of files I can open at a time.
Does anyone know if there is a limit in the number of bed files that multiIntersectBed accepts? If so, is there a way to work around it?
Thank you very much for your help!