Hello Zheng, You can convert one of them using liftOver on the line command. Download the tool and mapping file, convert, then load back in and use the Table browser for the intersection, or just use the flat files with unix and your own tools/methods.
LiftOver has three parts - the input file of coordinates, the "mapping" file, and the utility itself. You might get better results mapping mm8->mm9, although trying the comparison both ways might be a good sanity check. Link to liftOver utility source (includes precompiled versions): http://hgdownload.cse.ucsc.edu/downloads.html#source_downloads And also on the Downloads page, find liftOver mapping files in [each] assembly's "LiftOver files" directory. For mouse assemblies, look under here: http://hgdownload.cse.ucsc.edu/downloads.html#mouse If you do not have unix access, liftOver is also incorporated into Galaxy. The key is to label the custom tracks with the proper database (use the "edit" function). To do this, send your custom tracks over there, do the lift, compare there with an Interval tool or send back to UCSC to use the Table browser tools. Hopefully one of these options work for you. Please feel free to contact the mailing list again for more assistance, Best, Jen UCSC Genome Support On 8/31/10 8:07 AM, Zheng Sun wrote: > I'd like to compare two custom annotation tracks. But they are based > on different genome assembly (mouse mm8 VS mm9). What should I do? > _______________________________________________ > Genome maillist - [email protected] > https://lists.soe.ucsc.edu/mailman/listinfo/genome _______________________________________________ Genome maillist - [email protected] https://lists.soe.ucsc.edu/mailman/listinfo/genome
