Hi,
I am trying to use a shrunken centroid model that someone built that relies on CNV data. The issue is that the they report CNV segments in the form of BAC clones (e.g. RP11-338N10). I have other CNV data that I'm trying to apply this model to, but it is from either arrayCGH or a SNPChip that has gone through segmentation and has CNVs with genomic locations in coordinate formation (e.g., chr1:7658861-7860915). I am trying to convert the genomic locations and see which BACs they fall under so that I can classify patients based on this model. As they use 3277 BACs I would really prefer not to do this by hand. Does anybody know of any resources (a conversion table for instance or BAC end sequence locations) or have any tips of how I might be able to switch between BAC and genomic locations without looking up each BAC they use individually.
The original arrayCGH platform data (GPL4560) has a table of BAC clones and genomic positions -- but they only provide a single coordinate, not a range, and I'm not sure how to interpret that.
Any assistance or comments would be great!
The arrayCGH record that you mention above has clone ID's and for some sequence appears to be available: http://www.ncbi.nlm.nih.gov/clone/554254/ and http://www.ncbi.nlm.nih.gov/clone/577597/ Look at clone placement/associated sequence tabs.Not all clones appear to be in the clone database.