Is there a way to compare peaks from two different conditions of a ribosomal profiling experiment similar to a ChiP-Seq analysis? Can one use for example the MACS2 tools used there as well. Where I see the difficulty is that MACS2 looks for double peaks as are exists in the ChiP-Seq results due to the way the samples are made.

Is there a better way to statistically compare distinct peaks between conditions?

thanks