Hi, I am trying to answer your question. I guess you use the bed format as the input. For bed format, the start and end number can not be the same because the start position is 0-base and the end position is 1-base.
Mingfeng On Tue, Aug 30, 2011 at 7:40 AM, Linda Koster <[email protected]> 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 > -- ********************************************* Mingfeng Li, Ph.D. Postdoctoral Associate Department of Neurobiology Yale University School of Medicine 333 Cedar Street, SHM C-327C New Haven, CT 06510 E-mail: [email protected] Lab: (203) 785-5941 Lab website: www.sestanlab.org ********************************************* _______________________________________________ Genome maillist - [email protected] https://lists.soe.ucsc.edu/mailman/listinfo/genome
