How To Map Data From Ncbi To The Encode Database

Question

[dror.hilman]

I have a scan data I made, that found specific sites of interest on the genome sequences of various organisms. Now I want to cross this data with the ENCODE data. The data I have is in terms of NCBI refseq genomic positions, and the ENCODE data have a different mapping format. Can I cross these databases?, for example how to I move from refseq ID 224589808 ['Homo sapiens chromosome 17, GRCh37.p5 Primary Assembly'] with position 7571719 - 7590862 to the relevant ENCODE data ? How can I tell, for thousands of sequences, whether they are inside DnaseI HS areas for example?

[friveroll]

may be this post could help you http://www.biostars.org/post/show/8207/hg19-promoters-bed-file/

Answer 1

[Sean Davis]

The GRCh37 genome coordinates are the same as the hg19 build at UCSC. Therefore, you can compare ENCODE data at UCSC to those directly.

You mention other organisms, also. If those organisms are available at UCSC, you can try using their liftover tool to get your data into UCSC hg19 coordinates.