I am trying to predict enhancer regions in the ChIP-Seq data derived from Glioma Stem Cells (human). I already have aligned the data to hg19 and called the peaks. I understand ChromHMM and Encode annotations for histone marks may do the trick but I am lost on the step by step procedure since this cell line is not covered in any of the state models.
Any help will be much appreciated on either using ChromHMM or annotation packages. Thanks.