Hi, ~/linux/test/ucsc/bin/liftOver$ cat map.chain chain 18119282189 chr1 100000 + 0 4000 chr1 100000 + 0 4000 1 1000 0 1000 1000 1000 0 1000
I have the above chain file with represents the following mapping between intervals in old and new sequence. old (reference): [0,1000), [1000,2000), [3000,4000) new (query): [0,1000), [2000,3000), [3000,4000) I have the following old file. ~/linux/test/ucsc/bin/liftOver$ cat oldFile.txt chr1 0 100 chr1:0:100 chr1 900 1100 chr1:900:1100 chr1 2000 2100 chr1:2000:2100 chr1 2900 3100 chr1:2900:3100 After running the following command, liftOver oldFile.txt map.chain newFile.txt unMapped.txt the new file is the following. Note that chr1:900:1100 in the old sequence is expanded to chr1:900:2100, i.e., the size has been increased from 200 to 1200. This seems to be unreasonable to me. Does anybody know what is the rational for designing liftOver this way? ~/linux/test/ucsc/bin/liftOver$ cat newFile.txt chr1 0 100 chr1:0:100 chr1 900 2100 chr1:900:1100 Is there a way to tell liftOver to get the following results instead for chr1 900 1100? chr1 900 1000 chr1:900:1100 chr1 2000 2100 chr1:900:1100 Thanks! -- Regards, Peng _______________________________________________ Genome maillist - [email protected] https://lists.soe.ucsc.edu/mailman/listinfo/genome
