Hello, The wording is confusing, but it has to do with the way that the data is processed. For practical purposes, use the command line like this:
liftOver hg18_oldFile hg18ToRn4.over.chain rn4_newFile unMapped where the over.chain file is the liftOver file from Downloads hg18_oldFile are the coordinates from hg18 that are known and that you want to map rn4_newFile are the coordinates from rn4 that are unknown and that you want to find out, based on the files above. Note that you are supplying a file name here - no data or actual file should exist at the time the command is first run. unMapped are the coordinates from hg18_oldFile that were unable to be mapped using the over.chain file and the parameters supplied to the program. For cross-species liftOver, we general lower -minmatch=0.1 and add in -multiple, to maximise the number of locations mapped, however this can produce a large number of spurious hits. Try also adding in a -minChain or -minSize length for either the query (hg18) or the target (rn4) - 300, 500, or 1000 - test and see which work best for you to reduce the unwanted noise from short or non-specific matches. Or, run a few cycles, starting out strict, then making the parameters more permissive with the unMapped set based on the failure reason. We hope this helps. Jennifer Jackson ------------------------------------------------ Jennifer Jackson UCSC Genome Bioinformatics Group ----- "Zhi-Qiang Ye" <[email protected]> wrote: > From: "Zhi-Qiang Ye" <[email protected]> > To: [email protected] > Sent: Sunday, November 8, 2009 5:53:39 AM GMT -08:00 US/Canada Pacific > Subject: [Genome] confused by the help of liftover > > Dear sir, > > I am confused by the help of liftover concerning the map.chain: > > usage: > liftOver oldFile map.chain newFile unMapped > "The map.chain file has the old genome as the __target__ and the new > genome > as the __query__" > > If I want to map from hg18 to rn4, does this mean that I should > download > "rn4ToHg18.over.chain" ? > > Regards, > -- > Zhi-Qiang Ye > Ph.D in Bioinformatics > _______________________________________________ > Genome maillist - [email protected] > https://lists.soe.ucsc.edu/mailman/listinfo/genome _______________________________________________ Genome maillist - [email protected] https://lists.soe.ucsc.edu/mailman/listinfo/genome
