The bed file consists of called peaks done separately? Is there any
peak calling done with ChIP vs Input?
Or are the bed files location of reads. If the number of lines more
than 100000 then its not peak locations but reads.
It is very important to do peak calling against an input.
You can do this in galaxy if the bed files are reads: NGS: Peak
Calling => MACS
Otherwise, if you have no other option, you can try subtracting the
input peaks from the ip peaks.
Operate on Genomic Intervals => Subtract
has also a lot of analysis tools