[Genome] Request - WIG files can have overlapped regions

[Keith Lamont]

We have the same issue, so I am interested in solutions to this.

Keith Lamont


On Mar 6, 2008, at 2:36 PM, Ann Zweig wrote:

> 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
>>
>> _______________________________________________
>> Genome maillist  -  Genome at soe.ucsc.edu
>> http://www.soe.ucsc.edu/mailman/listinfo/genome
> _______________________________________________
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