Hi Harry, I think I see another problem. The regions you have specified are of length zero. For instance, chr20:25320-25320 makes sense when using position format, but in BED format, chr20 25320 25320 is the same thing as specifying position chr20:25321-25320. You need to subtract one from all of the chromStart coordinates to specify a region of one base in BED format.
Also see this FAQ: http://genome.ucsc.edu/FAQ/FAQtracks#tracks1 -- Brooke Rhead UCSC Genome Bioinformatics Group On 01/19/10 10:01, Galt Barber wrote: > Try "chr20" instead of "20". > > -Galt > > Ar 1/19/2010 8:57 AM, scríobh Harry Noyes: >> Dear UCSC >> I am struggling with liftover on a local installation to convert from >> cow UMD3 to cow Bta4. >> I have downloaded the program and the over chain files. >> I have an input file with 11 million lines in tab separated format >> (chr, start, end id) called boranMD3.bed: >> 20 25320 25320 0 >> 20 38034 38034 1 >> 20 46945 46945 2 >> 20 60000 60000 3 >> 20 67502 67502 4 >> 20 67848 67848 5 >> 20 73108 73108 6 >> 20 76763 76763 7 >> 20 76768 76768 8 >> >> I run the command >> ./liftOver boranMD3.bed bosTauMd3ToBosTau4.over.chain boranBt4.bed >> boranUnmapped.bed >> >> On completion boranBt4.bed is empty and boranUnmapped.bed has all 11 >> million lines with the comment "Deleted in New". >> I have tried on the website (original assembly: Aug 2009 (UMD3); new >> assembly: Oct 2007) with the first 12 lines of data and that gives the >> same result. Also on the website I have tried adding a "chr" prefix to >> the chromosome name ie chr20 but that did not work and I have tried >> reducing the ratio of bases that must remap to 0.1. All these fail >> with the same error for each line: "Deleted in New". I also tried >> using a single space as a delimiter but it complained that it was not >> in BED format. >> >> Any idea what I might be doing wrong? >> >> Thanks >> >> Harry >> >> >> Harry Noyes >> Room 231 BioSciences Building >> University of Liverpool >> Crown Street >> Liverpool >> L69 7ZB >> 0151 795 4512 >> www.genomics.liv.ac.uk/tryps >> >> >> _______________________________________________ >> 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
