I am trying for the first time to run SICER for calling broad peaks in my ChIP-seq dataset. Many people suggested me to use this tool rather than MACS2 (with --broad option).
When running SICER, I am calling it with
recognicer command, since it seems to be the correct one for broad peak calling.
However, the default window size is only 200bp and I think it is a bit too short for broad peaks?
I am working on gH2Ax, which is a very broad histone mark. How would you suggest to adjust the window size?
So far, I decided to use 2kb as window size, which is the same value I was trying to use as bin size when running bamCompare/bamCoverage for generating .bigWig files.
Any opinion and suggestion is very appreciated!
Thanks in advance :)