Hi Peng, One of our engineers has this to say: "-multiple really only means use multiple best chains, but here we only have one chain, and one bed4 block, and it just expands the interval until it is large enough." We have noted your request.
Please contact us again at [email protected] if you have any further questions. --- Luvina Guruvadoo UCSC Genome Bioinformatics Group On 6/7/2012 8:38 PM, Peng Yu wrote: > 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! > _______________________________________________ Genome maillist - [email protected] https://lists.soe.ucsc.edu/mailman/listinfo/genome
