Thanks Brooke. I will use the command line tool. I cannot use the online tool as the option to liftover to mm9 and 10 are not available.
Best, Suganthi On Fri, Apr 27, 2012 at 4:43 PM, Brooke Rhead <[email protected]> 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
