Hi, I'm using the LiftOver utility to update a list of gene and exon locations from mm8 to mm9, using the 'mm8ToMm9.over.chain' file. My problem is with the BED format and liftOver. I have a text file with 42000 rows that looks like so:
chr8 68547513 69399414 March1 0 = 68896145 69397519 0 8 239,77,209,51,80,181,148,2194, 68547513,68808318,68896035,69205650,69315428,69347804,69385041,69397220 chr17 33292398 33325385 March2 0 = 33294782 33316635 0 6 2531,135,210,196,228,125, 33292398,33298704,33302721,33309785,33316459,33325260 chr18 56887084 57050917 March3 0 = 56887883 56937388 0 5 853,210,205,244,242, 56887084,56908387,56933032,56937200,57050675 chr1 72360320 72469772 March4 0 = 0 0 0 0 0, 0, chr19 37272964 37287281 March5 0 = 37273013 37286650 0 6 84,203,131,184,167,748, 37272964,37275814,37282326,37285446,37285782,37286533, Using all 12 of the parameters allowed in the BED file format (it's ordered properly; http://genome.ucsc.edu/FAQ/FAQformat#format1). The problem lies in the blockCounts. If I have zero known exons, as is the case in the gene March4, the program throws me a Catch-22. I am required to put "0" in the blockCount when there are no exons; the program breaks if I leave it as null. However, if I put "0 0, 0," the program throws (as expected) a segmentation fault at me (since I told it to expect 0 elements, but it got 1). e.g. if I run a file using only the first 3 lines: "$ ./liftOver GeneListmm8_LiftOverThis.txt mm8ToMm9.over.chain GeneListmm9.txt unMapped.txt Reading liftover chains Mapping coordinates" but if I include line 4 I either get (with blockCount = 0) "$ ./liftOver GeneListmm8_LiftOverThis.txt mm8ToMm9.over.chain GeneListmm9.txt unMapped.txt Reading liftover chains Mapping coordinates Segmentation fault" or (removing blockCount; if I say 0 blockCount and remove blockSizes and blockStarts I also get an error, just "got 10" instead of "got 9") "$ ./liftOver GeneListmm8_LiftOverThis.txt mm8ToMm9.over.chain GeneListmm9.txt unMapped.txt Reading liftover chains Mapping coordinates Expecting 12 words line 4 of GeneListmm8_LiftOverThis.txt got 9" I suppose I could do this by splitting it into two files; one with genes with exons, the other with genes without, but that seems clumsy. Am I missing something or doing something wrong, or is this a bug in liftOver? Thank you. Evan Williams _______________________________________________ Genome maillist - [email protected] https://lists.soe.ucsc.edu/mailman/listinfo/genome
