Hello Alex, Any file that has the extension .wig is 1-based. Derivative files such as bedGraph or those contained in the browser's mySQL database in a modified BED format (example: gc5Base), are 0-based.
File format specifications can be reviewed here: http://genome.ucsc.edu/FAQ/FAQformat.html Not all file formats are directly linked from this page, some are linked from related/source file types. For example, bedGraph is linked from the wiggle page to here: http://genome.ucsc.edu/goldenPath/help/bedgraph.html Hopefully this helps, but if you have a specific file in mind that you have a question about, bringing up a test line of coordinates in the browser can usually help resolve the question. Or, you can always write the mailing list and we can clarify. Warm regards, Jen UCSC Genome Browser Support On 9/13/10 3:55 PM, Alex Reynolds wrote: > Is there a way to determine if coordinates in a wiggle (.wig) file should be > 1-based or 0-based? > > The UCSC specification says that wiggle files are one-based, as for custom > tracks. However, UCSC's hgWiggle tool writes 0-based files. > > Is it reasonable to guess the source from the file headers? > > For example: > > -- 1-based custom track in wiggle format has a "track" header line. > -- 0-based hgWiggle output has a comment: > # This data has been compressed with a minor loss in resolution. > > Are the other real-world cases that wiggle file users might encounter that > would change the source's coordinate type? > > Thanks, > Alex > _______________________________________________ > Genome maillist - [email protected] > https://lists.soe.ucsc.edu/mailman/listinfo/genome _______________________________________________ Genome maillist - [email protected] https://lists.soe.ucsc.edu/mailman/listinfo/genome
