I ran a CUT&RUN experiment targeting a transcription factor in a normal control cell line and its shRNA-knockdown. I would like to prove that the antibody for the transcription factor I used worked. I used MACS2 to peak call this data and have generated 2 narrowPeak files respectively. I would like to order the peaks and select the highest peaks in the normal control dataset and see if correlational peaks are lower in the knockdown, perhaps even by generating a heatmap for qualitative confirmation.
I am attempting to use computeMatrix from deeptools. Does anybody have experience attempting a similar experiment?