[Bioc-sig-seq] Comparing two chipseq position sets

[Ivan Gregoretti]

Hello Bioc-sig-seq,

Say you run your ChIP-seq and find binding positions like this

chr1  3660781  3662707
chr1  4481742  4482656
chr1  4482813  4484003
chr1  4561320  4562262
chr1  4774887  4776304
chr1  4797291  4798822
chr1	 4847807  4848846
chr1  5008093  5009386
chr1  5009514  5010046
chr1  5010095  5010583
...[many more loci and chromosomes]...

Then you want to compare it to published data like this

chr1  3659579  3662079
chr1  4773791  4776291
chr1  4797473  4799973
chr1  4847394  4849894
chr1  5007460  5009960
chr1  5072753  5075253
chr1  6204242  6206742
chr1  7078730  7081230
chr1  9282452  9284952
chr1  9683423  9685923
...[many more loci and chromosomes]...

What method would you use to test whether these two lists are
significantly different?

Any pointer would be appreciated.

Ivan

Ivan Gregoretti, PhD
National Institute of Diabetes and Digestive and Kidney Diseases
National Institutes of Health
5 Memorial Dr, Building 5, Room 205.
Bethesda, MD 20892. USA.
Phone: 1-301-496-1592
Fax: 1-301-496-9878