Hi Ivan,
The package genomeIntervals (Bioconductor) is a good a starting point
to compare two list of loci: i.e. use the interval_overlap function to
find those binding positions in the first list that overlap with some
in the second list. An important point here, is to make sure that the
coordinate from your ChIP-seq and the one from the published data are
based on the same genome assembly (same genome version).
Hope this helps,
---------------------------------------------------------------
Nicolas Delhomme
High Throughput Functional Genomics Center
European Molecular Biology Laboratory
Tel: +49 6221 387 8426
Email: [email protected]
Meyerhofstrasse 1 - Postfach 10.2209
69102 Heidelberg, Germany
---------------------------------------------------------------
On 6 May 2009, at 21:40, Ivan Gregoretti wrote:
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
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