Hi Daniel, Our internal database representations of coordinates always have a zero-based start and a one-based end. We add 1 to the start before displaying coordinates in the Genome Browser. Therefore, they appear as one-based start, one-based end in the graphical display. Please see this FAQ for more information: http://genome.ucsc.edu/FAQ/FAQtracks#tracks1. Since your position is a single base, in BED format you will have to subtract 1 from the start coordinate to get the correct conversion (chr12 541582 541583). The coordinates you had (chr12 541583 541583) translated into a region of size 0 in BED format.
I hope this helps. Please contact us again at [email protected] if you have any further questions. --- Luvina Guruvadoo UCSC Genome Bioinformatics Group Daniel E. Weeks wrote: > I am trying to do a liftover for Human data from NCBI36/hg18 to GRCh37/ > hg19 > > If my input is in position format: > > chr12:541583-541583 > > the web-based Liftover tool happily converts it to: > > chr12:671322-671322 > > > But if my input is in BED format: > > chr12 541583 541583 > > Liftover fails with this output: > > #Deleted in new > chr12 541583 541583 > > Why this work when the input is in 'position' format but fails when > the same information is in 'BED' format? > > This is mystifying to me, as BED-format data from the example BED file > like this: > chr7 127471196 127472363 > is happily converted by the liftover tool. > > Thank you, > -- Dan -- > > > _______________________________________________ > Genome maillist - [email protected] > https://lists.soe.ucsc.edu/mailman/listinfo/genome > _______________________________________________ Genome maillist - [email protected] https://lists.soe.ucsc.edu/mailman/listinfo/genome
