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
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/) and the various over.chain > files (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 _______________________________________________ Genome maillist - [email protected] https://lists.soe.ucsc.edu/mailman/listinfo/genome
