6.4 years ago by
I think HOMER may be able to do what you are asking.
HOMER manual for annotatePeaks.pl
If you carry out the detailed annotation, the output should contain information about the distance of peaks to many known genomic features, including CpG islands. I think you could parse the information you want from this file.
I provided a link to the manual for the command that may give you what you need so you can try to ascertain whether or not HOMER can provide the functionality you desire. I would suggest reading the preceding parts of the manual in its entirety, as HOMER will do some things like normalization that you may or may not want, and there are preceding steps you will need to carry out before using annotatePeaks.pl including downloaded the version of your genome of interest via HOMER, making tag directories, etc.
I wish I could provide more detailed and expert advice, but I am new to this analysis myself.
Someone suggested SeqMiner. My concern with SeqMiner is the poor documentation. It can generate heatmaps from data VERY quickly, which is attractive, but seems to be more of a black box than HOMER. I think SeqMiner give you less control over the analysis, and/or the control you do have is less intuitive, at least to me.