Hi Guys, I am new to the field.I have a question about processing the chip-seq data using the bigwig file. In general, I wonder what is the standard way to plot chip-seq profile for a specific TF or histone modifications. Here is how I did it: I downloaded the bigwig data and transfer into bedgraph, which contains the number of reads in each uniform intervals and plot it in a profile. Basically I have the following two questions:
How to plot the continuous chip-seq profile like the ones in some published paper? As I am having all the concrete number of reads for each interval, e.g. 10bp or 25bp. Do I need to coarse grain the signal, like combine into a larger interval, like 10kb? Or do any kind of smooth?
How can I deal with the control file in this manner? I also have the bigwig file for the control but do I need to somehow subtract control from the target data? If so, what types of treatment does it need, like direct subtraction, or Poisson process to determine the significance? Or if someone can know if the bigwig for the target is simply ready to use.
Thanks in advance for any help. If there would be any idea I would be really appreciate!