ChIP-seq peak calling with MACS2 - some large peaks for transcription factor
I have been using MACS2 to call peaks for ChIP-seq data on a phosphorylated human transcription factor. After probing through the data, I noticed I was getting a few abnormally large peaks, ranging from 5kb-16kb. This is what the track from the UCSC genome browser looks like when we performed ChIP-seq for this transcription factor using an antibody that was not specific to the phosphorylation site we're studying:
And here is the track for this region for the phosphorylated TF:
It seems in this particular region the antibody against the phosphorylation site may have picked up some non-specific background (it is thankfully not like this genome-wide). Are there any parameters in MACS2 I can adjust to narrow the peak calling for regions like this? I have already tried making the FDR more stringent (from 5% down to 0.1%) but this peak still ended up being called as about 14kb long vs the original 16kb. Is this just a situation where the antibody was "dirty" in this region and it won't be possible to bring out the "true" peak?
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