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
