Hi Martin, One of our engineers pointed out that my advice of changing the -minMatch would be good advice for most situations, but since your examples are all simple SNPs of just 1 base, they will either map or they won't. It's not a case of 10% or 95%.
So, we tried using liftOver with your sample bed here and weren't able to reproduce your errors. On the command line, like the web version, the first item doesn't map but the others do. Please make sure you're using this over.chain file: http://hgdownload.cse.ucsc.edu/goldenPath/mm9/liftOver/mm9ToHg19.over.chain.gz. If you are still having problems, please email our mailing list ([email protected]) again and let us know where you downloaded the over.chain.gz file and provide the exact command you are using. Thank you, Katrina Learned UCSC Genome Bioinformatics Group On 9/12/11 11:33 AM, Katrina Learned wrote: > Hi Martin, > > At its default settings, the program is quite conservative -- any > conversions that are even slightly questionable will be written to a > separate file that can be reviewed manually. > > Since you are lifting between species, try changing the parameters on > the liftOver tool to be less stringent by lowering the minimum ratio of > bases that must map. The default in the line command tool is 0.95 > (strict, intended for lifts from one version of the same genome to > another version of the same genome). In the Browser tool, the default > automatically changes for cross-species conversions to 0.1 to allow for > cross-species lifts to have a better chance of success. To do this with > the command line tool, specify -minMatch 0.1 when you run the command > (when you do not specify -minMatch you will be using the default of 0.95). > > You can see all liftOver options at the command line by just typing > "liftOver". > > I hope this information is helpful. Please don't hesitate to contact the > mail list again if you have any further questions. > > Please contact the mail list ([email protected]) again if you have any > further questions. > > Katrina Learned > UCSC Genome Bioinformatics Group > > > On 9/9/11 10:51 AM, Martin Hemberg wrote: >> Dear Sir or Madam, >> >> I am trying to use the liftOver tool to convert from mm9 to Hg19. For >> illustration purposes, consider the .bed file below: >> >> chr1 21606900 21606901 >> chr1 12107460 12107461 >> chr1 26838080 26838081 >> chr1 33258730 33258731 >> chr1 33258771 33258772 >> >> when running it locally with the default settings, it fails to map three >> of the entries: >> >> #Deleted in new >> chr1 26838080 26838081 >> #Duplicated in new >> chr1 33258730 33258731 >> #Duplicated in new >> chr1 33258771 33258772 >> >> However, when I run it on your website, it only fails with the first of >> the entries (which I believe is the correct behavior). I downloaded the >> chain file earlier is this week, so I don't believe that should be the >> issue. Do you have any idea what the problem is? >> >> Best Regards >> >> Martin Hemberg >> > _______________________________________________ > Genome maillist - [email protected] > https://lists.soe.ucsc.edu/mailman/listinfo/genome _______________________________________________ Genome maillist - [email protected] https://lists.soe.ucsc.edu/mailman/listinfo/genome
