I also want to know where to download the chain file to covert mm9 to mm10.
best, Mingfeng On Fri, Apr 27, 2012 at 12:56 PM, Brooke Rhead <[email protected]> wrote: > Hi Suganthi, > > I'm confused (or maybe I said something confusing!). You will need to > do these sequential lifts whether you use the online tool or the command > line tool: > > mm6 -> mm8 > mm8 -> mm9 > mm9 -> mm10 > > I see those options on the online tool. Are you using our official site > (http://genome.ucsc.edu/cgi-bin/hgLiftOver), or are you possibly looking > at a mirror site? > > -- > Brooke Rhead > UCSC Genome Bioinformatics Group > > > On 4/27/12 1:47 PM, Suganthi Bala wrote: > > 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] > > <mailto:[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] <mailto:[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 > -- ********************************************* Mingfeng Li, Ph.D. Postdoctoral Associate Department of Neurobiology Yale University School of Medicine 333 Cedar Street, SHM C-327C New Haven, CT 06510 E-mail: [email protected] Lab: (203) 785-5941 Lab website: www.sestanlab.org ********************************************* _______________________________________________ Genome maillist - [email protected] https://lists.soe.ucsc.edu/mailman/listinfo/genome
