Hello Ariel, You are correct, the Custom track feature no longer supports contigs position. Your file will need to be converted to chromosome position using your own tools and our mapping file.
Mapping file: ctgPos table/file in Table browser or on Downloads page. #contig size chrom chromStart chromEnd NT_166307.1 175968 chr7_random 0 175968 NT_166308.1 136522 chr7_random 225968 362490 Other options: There is a utility that does this type of lift, but it is in the kent source tree and would require considerable set-up to use. If you are already a kent source user, then the utility is called "liftUp" (not the same of liftOver). Perhaps also review the Galaxy web tool set: http://galaxy.psu.edu/ Going forward: The team is discussing options concerning this functionality but nothing has been decided. If/when an implementation is made in the next week or so, we'll send you an email. After that, please feel free to check back later for an update. Thanks, Jennifer Jackson Paulson, Ariel wrote: > Hi, > > I have a bed file in which the coordinates for random chromosomes are given > by the contig instead, such as NT_166307 or NT_166038 instead of chr7_random. > For instance: > > NT_166307 162 1062 > NT_166307 685 1608 > NT_166307 1253 2173 > > The help files for BED format claim that this is possible, and I know these > contig-based coordinates exist because I can paste them directly into the > genome browser and they work. But trying to load the bed file gives me the > "NT_166307 not a chromosome (note: chrom names are case sensitive)" error. > > I see that this problem has come up before in the mailing list archives > (April 8 2002) and supposedly it was fixed... So what am I doing wrong? > > Thanks, > Ariel > > _______________________________________________ > Genome maillist - [email protected] > https://lists.soe.ucsc.edu/mailman/listinfo/genome > _______________________________________________ Genome maillist - [email protected] https://lists.soe.ucsc.edu/mailman/listinfo/genome
