[Genome] Request - WIG files can have overlapped regions

[Ann Zweig]

Gordon and Hiram are discussion possible solutions to this off-list.  If you are 
particularly interested in the solutions they come up with, please don't 
hesitate to write back to the list for details.

Regards,

----------
Ann Zweig
UCSC Genome Bioinformatics Group
http://genome.ucsc.edu




Gordon Robertson wrote:
> I discussed this a few months ago, perhaps with Hriam, and understand that
> your current WIG functionality does not allow BED-format records to overlap.
> 
> But such overlap occurs in many published datasets. The case I face today is
> a set of ~24k promoter regions in mouse (Barrera et al. 2008), which I
> lifted from mm5 to mm8 through your web interface. If I select out the
> scored BED records for a tissue from these data, and format the records as a
> BED-format WIG file, I cannot load the file, because at least one pair of
> records overlaps. 
> 
> I anticipate that changing the functionality of your code to permit overlap
> in all three WIG file types is nontrivial, but could I ask that you consider
> addressing this? 
> 
> Barrera LO, Li Z, Smith AD, Arden KC, Cavenee WK, Zhang MQ, Green RD, Ren B.
> 2008. Genome-wide mapping and analysis of active promoters in mouse
> embryonic stem cells and adult organs. Genome Res. 18(1):46-59.
> 
> G
> ---
> Gordon Robertson
> Gene Regulation Informatics
> Canada's Michael Smith Genome Sciences Centre
> Vancouver BC Canada
> www.bcgsc.ca
> grobertson at bcgsc.ca
> 
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