You should now examine your items carefully to confirm that they actually begin at the base you think they should and they are as long as you expect them to be. You probably have off-by-one errors now in either your start position or your stop position. 1-relative doesn't mean add one to both start and stop.
See also: http://genomewiki.ucsc.edu/index.php/Coordinate_Transforms --Hiram Lakshmanan, Abirami wrote: > Thank you Greg, > > I added start+1 and stop+1 to all my gtf entries and now I don’t get that > error. > > Abi > > > On 1/25/12 3:10 PM, "Greg Roe" <[email protected]> wrote: > > Hi Abi, > > Negative one is an illegal value for a chromStart. GTF files are 1-relative > coordinates where the first base of a chromosome is 1, the equivalent > chromStart value is 0. See also: > http://genome.ucsc.edu/FAQ/FAQformat.html#format4 > > Please let us know if you have any additional questions: [email protected] > > - > Greg Roe > UCSC Genome Bioinformatics Group > > On 1/23/12 12:58 PM, Lakshmanan, Abirami wrote: > > Hi, > > I am trying to upload a gtf file (output from cufflinks/cuffmerge of ucsc > refseq zv9 and ucsc ensembl gene zv9) as a custom track to the UCSC site and > I keep getting this following error. > > Error track load error (track name='ct_UserTrack_3545'): > start -1, end 3618 out of range in findBin (max is 512M) > > I tried removing the entries which start at 1, 0 and are on the negative > strand and still I get the same error. > Has anyone encountered this before? > Thanks for the help. > > Abi > > _______________________________________________ > Genome maillist - [email protected] > https://lists.soe.ucsc.edu/mailman/listinfo/genome > > > _______________________________________________ > Genome maillist - [email protected] > https://lists.soe.ucsc.edu/mailman/listinfo/genome > _______________________________________________ Genome maillist - [email protected] https://lists.soe.ucsc.edu/mailman/listinfo/genome
