Hello Brent, Your result would be expected.
>From a scientific perspective, any dataset not based on the exact genome the >custom data is loaded into would be non-useable. >From a technical perspective, a dataset might actual load across several >genomes - if you got lucky and the chromosome names matched up and the >annotation coordinates did not exceed the length of that genome's chromosomes >(for certain data types this matters). But it is still non-useable for >analysis. For your case, the exact technical reason the data did not load is because the chromosome names are in a different format between the two genomes, causing the format error. The data would be invalid even if it did load into any other genomes except GRCh37, if it is based on GRCh37. The custom track tool uses certain data keys to incorporate the new annotation - it doesn't know where the data came from - only what the data is and where you are trying to put it. If there is a conflict between a required match key (such as chromosome name), a format error will result. So, knowing the data source would be a good thing to keep track of for custom tracks - one simple way to do this is to put the source somewhere in the track line "description" variable's contents. That way it always stays with the data and it is easy to see if a mix up occurred when using the custom track (if it happened to load across genomes). Some help links for custom tracks that you may find useful to review are: How to: http://genome.ucsc.edu/goldenPath/help/hgTracksHelp.html#CustomTracks More examples: http://genome.ucsc.edu/goldenPath/customTracks/custTracks.html If you have any other questions, please let us know, Jennifer ------------------------------------------------ Jennifer Jackson UCSC Genome Bioinformatics Group ----- "Brent Shepherd" <[email protected]> wrote: > From: "Brent Shepherd" <[email protected]> > To: [email protected] > Sent: Thursday, January 21, 2010 5:52:06 PM GMT -08:00 US/Canada Pacific > Subject: [Genome] format error with C. elegans custom tracks > > To whom it may concern, > > I am trying to read in custom tracks for the May 2008 assembly of C. > elegans. I have the data in .BED format, and it reads in just fine > with the > human GRCh37 assembly. This exact same data, when I paste it to the > aforementioned C. elegans assembly, however, returns a formatting > error > message. Do you have any ideas of what the problem may be? Thank you > for > your time. > > Brent > _______________________________________________ > Genome maillist - [email protected] > https://lists.soe.ucsc.edu/mailman/listinfo/genome _______________________________________________ Genome maillist - [email protected] https://lists.soe.ucsc.edu/mailman/listinfo/genome
