Hi Valeriya, We recommend lifting from mm5 (may 2004) to mm8 and then from mm8 to mm9. Our liftOver tool (http://genome.ucsc.edu/cgi-bin/hgLiftOver) should be the easiest way to convert your coordinates.
I hope this information is helpful. Please feel free to contact the mail list again if you require further assistance. Best, Mary ------------------ Mary Goldman UCSC Bioinformatics Group On 7/2/10 7:17 AM, Valeriya Gaysinskaya wrote: > Hi, I would like to use Liftover tool to compare mouse mm5 to mouse mm9 > assembly. However, it seems like there is no conversion available for these > two assemblies. I very much need to compare specific, 100 kilobasepair > regions between these two assemblies, for which i don't think the other > conversion tool will be useful. Could you please let me know if mm5 to mm9 > conversion is possible, and, how do I specifically compare a region, say, > from assembly mm5 to the same region in mm9: The problem is that the regions > I am interested in comparing are different, both, in coordinates and, to a > lesser degree, the genomic context. But I need find the equivalent of these > specific regions in both, mm5 and mm9 assemblies. Please let me know how to > proceed. > Thank you very much, > Valeriya Gaysinskaya > _______________________________________________ > Genome maillist - [email protected] > https://lists.soe.ucsc.edu/mailman/listinfo/genome > _______________________________________________ Genome maillist - [email protected] https://lists.soe.ucsc.edu/mailman/listinfo/genome
