Currently, within CUT-RUN_PE MACS2 callpeak includes the --broad parameter while ChIPseq_PE does not. The user should be able to select the appropriate peak calling mode based on the protein target (e.g. TF vs histone mark). Perhaps, it would be best to call peaks with both modes by default. To make these changes the snakefiles and FRP.py script would need to be edited.
Currently, within CUT-RUN_PE MACS2 callpeak includes the --broad parameter while ChIPseq_PE does not. The user should be able to select the appropriate peak calling mode based on the protein target (e.g. TF vs histone mark). Perhaps, it would be best to call peaks with both modes by default. To make these changes the snakefiles and FRP.py script would need to be edited.