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
