Correction in my last paragraph: For usage of the parameters (Q/T), considering file hg18ToRn4.over.chain
the query is (rn4) and the target is (hg18) Very easy to mix up - Jenn ------------------------------------------------ Jennifer Jackson UCSC Genome Bioinformatics Group ----- "Jennifer Jackson" <[email protected]> wrote: > From: "Jennifer Jackson" <[email protected]> > To: "Zhi-Qiang Ye" <[email protected]> > Cc: [email protected] > Sent: Monday, November 9, 2009 9:04:12 AM GMT -08:00 US/Canada Pacific > Subject: Re: [Genome] confused by the help of liftover > > 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
