[Genome] problem loading a BED-formatted WIG file

[Hiram Clawson]

Good Morning Gordon:

I think you have figured this out.  The reason why is because bed items are simply locations and
they can overlap in any manner.  WIG items are definite values at locations, and thus you can
have only one value at one location.  The wiggle graph can only display one value at one location.
If you were to give a single location more than one value, which one would you expect to be
graphed ?  That's the difficulty, and hence the error so you can have the opportunity to decide
which value you would like to see in that location.

--Hiram

Gordon Robertson wrote:
> Hello
> 
> I have a ~300k-row data file that loads without problems into hg18 if it is formatted as a BED-track. I'd like to display it as a WIG track as well, and when I try to load it as a BED-formatted WIG track, the genome browser refuses to process the file, apparently because some 'end' coords overlap subsequent 'start' coords:
>     "Error File 'h6.wig' - chrom positions not in numerical order at line 86. previous: 869786 > 869479 <-current"
> ...
> chr1	869409	869437	7.02055
> chr1	869479	869787	6.35444  <<<
> chr1	869479	869794	9.46824  <<<
> chr1	869838	869989	7.57466
> ...
>  Do I understand the browser rules for BED and WIG files correctly -- that BED-formatted BED-track features can overlap, but BED-formatted WIG-track features cannot overlap? Because the width of the features varies, the 'variableStep' format is inappropriate.  
> 
> Thanks for your help -
> 
> ---
> Gordon Robertson
> Gene Regulation Informatics
> Canada's Michael Smith Genome Sciences Centre
> Vancouver BC Canada
> www.bcgsc.ca
> grobertson at bcgsc.ca