MACS: output of MACS as an control file?

[jaaker]

I have three sets of data: immature wild-type cells, mature wild-type cells and mature knockout cells. We ran the knockout cells to control for any off target binding of our antibody for ChIP-seq. I have ran MACS to subtract out my mature knockout cells from my mature wild-type cells. Using any of those output files, can I subtract out those peaks/summits/areas/sequences from the immature wild-type cells? We think there is more important information in the immature wild-type cells but want to remove off-target binding (mature knockout cells) and changes during development (mature wild-type cells).

I would like to run this in MACS:
Treatment: Immature wild-type cells
Input: (Mature wild-type cells minus mature Knockout cells)
e.g. (Immature - (Mature WT - mature KO))

Or do I need to perform some other option once I have the BED files from the MACS output?

Thanks!
-Josh

Popko Lab
University of Chicago