I am working with some chip-seq data for a broad epigenetic mark and want to perform some peak calling analysis. From some initial qc analysis based on deeptools fingerprint plots, it seems my chip efficiency was not very good and there is a lot of background (but I have also read that this may be normal for broad marks?).
My initial peak calling with macs2 and homer using pretty liberal parameters yielded much fewer peaks than expected (~5000 compared to ~20000 in literature). My first question is if it would be ok for me to proceed with the analysis of these peaks? In other words, is it normal to see such big differences between my data and published results for the same mark? Are there any other things I can try to get more peaks or reduce background?
Alternatively, if this is because of low chip efficiency, would it make sense if I don’t do a peak calling analysis but still use the data by quantifying the signal at specific regions such as promoters and maybe do some clustering (both deeptools and homer have some good tools for this)? I am comparing the occupancy of this mark between two different conditions so I am assuming both conditions would be equally affected by the low efficiency.
Any tips would be appreciated.