Hello Jamie, There are two possibilities to consider first for the graphical display differences:
1) If loading as a custom track, perhaps the configuration options for the loads were different? Specifically, the track line attributes that control graphing behavior such as windowingFunction and smoothingWindow? Correcting this seems like the most likely remedy. For both track type=bedGraph and type=wiggle_0, windowingFunction is a required parameter and smoothingWindow=off is default. Checking that they are the same is a good place to start. 2) Perhaps the files are not actually identical in content? Fixed/variable steps and fixed/variable spans are both possibilities with these data types. If the data really are the same, it is probably the case that one of the formats would be optimal: http://genome.ucsc.edu/goldenPath/help/bedgraph.html http://genome.ucsc.edu/goldenPath/help/wiggle.html Quote from the WIG file FAQ: The wiggle (WIG) format is for display of dense, continuous data such as GC percent, probability scores, and transcriptome data. Wiggle data elements must be equally sized. If you need to display continuous data that is sparse or contains elements of varying size, use the BedGraph format instead. If you have a very large data set and you would like to keep it on your own server, you should use the bigWig data format. http://genomewiki.ucsc.edu/index.php/Selecting_a_graphing_track_data_format If this does not help to resolve the issue, please send me a *small* sample of each dataset in the original format (representing the same region, perhaps just the region you sent earlier?). Also send the exact command-line you used to convert each to bigWig format. Then, include the complete browser/track lines used for each bigWig and the target assembly (hg18? A mirror or UCSC?) you loaded into using the Custom track submission form. You can send the data directly to me and I can provide feedback with our developer's input. Thanks! Jennifer --------------------------------- Jennifer Jackson UCSC Genome Informatics Group http://genome.ucsc.edu/ ------------------------------------------------------------------------ Subject: bigwig discrepancy From: Jamie Rosner <[email protected]> Date: Tue, 18 May 2010 16:37:15 -0700 To: "[email protected]" <[email protected]> To: "[email protected]" <[email protected]> Hi there, I’m having an issue when converting bedgraph files into bigwig (using /bedGraphTobigWig/). The image below shows a section of 2 bigwig tracks, one converted from bedgraph and another converted from wiggle. I’ve double checked the source files (wiggle and bedGraph) to make sure that they contain the same information (albeit in a different format). I’ve also tried using “-unc” when running bedGraphTobigWig, but to no avail. Any ideas why this might be happening? Thanks, Jamie _ _ _ __________________________________________ Jamie Rosner, BMath, BA Senior Microarray Production Specialist Vancouver Prostate Centre 2660 Oak Street, Vancouver BC, Canada V6H 3Z6 (604) 875-4111 ext. 66074 [email protected] <mailto:[email protected]> _______________________________________________ Genome maillist - [email protected] https://lists.soe.ucsc.edu/mailman/listinfo/genome
