How To Use Hmmseg Program Before Running Segmentation

Question

[Maria]

Hi All, Does anybody know how to use HMMseg program (http://noble.gs.washington.edu/proj/hmmseg/)? before running segmentation, we need to pre-process bed file (make equally-spaced coordinates). There is two script, bed.R and interp.R which I think get the data (hg17) from UCSC(ENCODE) and ... How about local data? and mm9?

Thank you very much in advance