Hi Linda, In BED format, if the start and end positions are the same, this indicates a region of size zero; a liftover can't be performed on a region of size zero. Please see this previously answered questions for clarification: https://lists.soe.ucsc.edu/pipermail/genome/2011-May/025941.html https://lists.soe.ucsc.edu/pipermail/genome-mirror/2011-July/002691.html
I hope this helps. Please contact us again at [email protected] if you have any further questions. --- Luvina Guruvadoo UCSC Genome Bioinformatics Group On 8/30/2011 5:40 AM, Linda Koster wrote: > Dear sir/madam, > > I have a question about the liftOver conversion tool. I'm trying to use > the linux command line version of liftOver to convert my data from hg18 > to hg19, seeing that my data is quite large. However, when the begin > position is the same as the end position (insertions for example have > the same start as end position) than the program says that this is > "deleted in new". If I use the online version of liftOver, there's no > problem and I get the position in the newer build. > Am I doing something wrong? Is there a special command that I have to > give to prevent this? > > Thank you in advance. > > Kind regards, > Linda Koster > > _______________________________________________ > Genome maillist - [email protected] > https://lists.soe.ucsc.edu/mailman/listinfo/genome > _______________________________________________ Genome maillist - [email protected] https://lists.soe.ucsc.edu/mailman/listinfo/genome
