Hi Alexander, Can you send me the first few lines of the file you are using?
The BED format FAQ may be helpful: http://genome.ucsc.edu/FAQ/FAQformat.html#format1 - Greg Roe UCSC Genome Bioinformatics Group On 6/3/12 8:25 AM, Navarini, Alexander wrote: > Dear Kayla, > > I get an error message with the liftOver tool that I cannot understand. > > ./liftOver all_03_qc.gen hg18ToHg19.over.chain.gz all_03_qc_hg19.gen unMapped > Reading liftover chains > Mapping coordinates > invalid unsigned integer: "rs9755941" > > I can transform my .BED files on your website just fine, so I'm puzzled. > > Could you please give me advice there? > > Thanks, Alexander > > I downloaded the liftOver executable just now and gave it permissions. > wget http://hgdownload.cse.ucsc.edu/admin/exe/linux.x86_64/liftOver > wget > http://hgdownload.cse.ucsc.edu/goldenPath/hg18/liftOver/hg18ToHg19.over.chain.gz > > > --------------------------------------------------------------------------------------------------------- > Alexander Navarini > > Dr.med. Dr.sc.nat., Dermatologist& Venereologist FMH UEMS EBDV > Division of Genetics and Molecular Medicine, King's College London > St John's Institute of Dermatology, Guy's Hospital, Great Maze Pond > SE1 9RT London, United Kingdom > [email protected]<mailto:[email protected]> > > _______________________________________________ > Genome maillist - [email protected] > https://lists.soe.ucsc.edu/mailman/listinfo/genome _______________________________________________ Genome maillist - [email protected] https://lists.soe.ucsc.edu/mailman/listinfo/genome
