Hello, I need to display genome-scale profiles in mm9. The profiles will consist of long sections with constant heights that are separated by shorter sections in which heights vary.
Because the files are large, I'd prefer to use the compact fixedStep format. A year ago I did such work with files that combined fixedStep sections and BED-format lines, but the WIG format description has changed since then. Now, your help page (genome.ucsc.edu/goldenPath/help/wiggle.html) says: "Note that for both variableStep and fixedStep formats, the same span must be used throughout the dataset. If no span is specified, the default span of one is used." The span restriction seems to require me to use either: a) fixedStep inefficiently (e.g. span=1, even through kb-long constant-height sections), or b) bedGraph, which would give large files for which a bigBedGraph format is unavailable (or does bigBed also handle bedGraph?). For this application, it will probably be practical to use a fixedStep WIG after converting the file to bigWig. But do I understand the span restriction correctly? I ask because the WIG format design is generally very simple and effective, and it's less obvious why span values would be restricted. Could you clarify two other points that are not stated explicitly on your WIG help page? 1. Can a single WIG file contain only fixedStep or variableStep sections, but not both types? 2. Do the current fixedStep and variableStep formats permit WIG 'blocks' to overlap? Overlapped blocks could be generated by values assigned to start, step and span. Thanks for your help with these points. G -- Gordon Robertson Gene Regulation Informatics Canada's Michael Smith Genome Sciences Centre Vancouver BC Canada www.bcgsc.ca _______________________________________________ Genome maillist - [email protected] https://lists.soe.ucsc.edu/mailman/listinfo/genome
