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
