How to subtract a coverage track of mock IP from a set of ChIP tracks?

[DerIch]

I have a set of ChIP data, most of them with a transcription factor, but also control data, which was not the raw input chromatin, but instead they performed a "mock" ChIP, i.e. pulled out chromatin with a bead on which no antibodies were attached.

This mock track shows a strong co-movement with the actual ChIP tracks, which made me wonder if there is a way to correct this bias in the actual ChIP tracks. My first naive idea would be to just subtract the mock track from the ChIP tracks. This is of course not smart, but hopefully clarifies what I'm looking for.

Does anyone know of literature that addresses this problem?

[crazyhottommy]

you can use MACS2 for this object
if you have bedgraph file

https://github.com/taoliu/MACS/wiki/Build-Signal-Track#wiki-Run_MACS2_bdgcmp_to_generate_foldenrichment_and_logLR_track

if you have wig file

http://palpant.us/java-genomics-toolkit/

use wigmath subtract