Thanks Brooke. I don't need it now, but it will be useful for future. On Wed, May 2, 2012 at 5:03 PM, Brooke Rhead <[email protected]> wrote:
> Hi again Suganthi, > > There is now an over.chain file from mm6 -> mm10 available: > http://hgdownload.cse.ucsc.**edu/goldenPath/mm6/liftOver/** > mm6ToMm10.over.chain.gz<http://hgdownload.cse.ucsc.edu/goldenPath/mm6/liftOver/mm6ToMm10.over.chain.gz> > > This lift is now available for the online tool, as well. > > (We were in the process of making some other mm10 lift files and included > this one.) > > Not sure if you need it at this point, but it is available! > > > -- > Brooke Rhead > UCSC Genome Bioinformatics Group > > > On 4/27/12 1:43 PM, Brooke Rhead wrote: > >> Hello Suganthi, >> >> That is exactly right: you should do sequential lifts from mm6 -> mm8 -> >> mm9 -> mm10. You can do it with the online tool, or you could use the >> command-line tool (executables available here: >> http://hgdownload.cse.ucsc.**edu/admin/exe/<http://hgdownload.cse.ucsc.edu/admin/exe/>) >> and the various over.chain >> files >> (http://hgdownload.cse.ucsc.**edu/downloads.html#mouse<http://hgdownload.cse.ucsc.edu/downloads.html#mouse>) >> and do the >> lifts locally. >> >> If you have further questions, please contact us again at >> [email protected]. >> >> -- >> Brooke Rhead >> UCSC Genome Bioinformatics Group >> >> >> >> On 4/27/12 12:58 PM, Suganthi Bala wrote: >> >>> Hi, >>> >>> I have to liftover mm6 coordinates to mm10. bu the online utility only >>> allows mm6 to mm8. Would it be easy to update the online tool? >>> If not, what is the easiest way to do the liftover. The way I see it , I >>> will have to liftover to mm8b and then serially lift to mm9 and then mm10 >>> using the chain file. Is this correct? Thanks. >>> >>> Best, >>> Suganthi >>> Associate Research Scientist >>> Yale University >>> >> ______________________________**_________________ >> Genome maillist - [email protected] >> https://lists.soe.ucsc.edu/**mailman/listinfo/genome<https://lists.soe.ucsc.edu/mailman/listinfo/genome> >> > _______________________________________________ Genome maillist - [email protected] https://lists.soe.ucsc.edu/mailman/listinfo/genome
