Dear CY, While we do not provide advice on research direction, one of our engineers had these comments about your questions:
You may want to use liftOver, at least to get an idea where your regions map. As you know, the liftOver chains are built from the cross-species alignments, so that's the best mapping we can provide, but you will certainly need to do some validation that the resulting mapped regions make sense, perhaps most importantly, using BLAT to make sure that your region is unique in the rhesus and human genomes. Duplications play havoc with establishing homology. Hopefully this information was helpful and answers your question. If you have further questions or require clarification feel free to contact the mailing list at [email protected]. Best regards, Pauline Fujita UCSC Genome Bioinformatics Group http://genome.ucsc.edu On 10/26/10 11:23 PM, Li Chuan_Yun wrote: > Dear UCSC scientists, > > I want to transform some Rhesus genome coordinates to human using the > liftOver tool; however, I found a warning message as follows: > > WARNING: liftOver was only designed to work between different assemblies > of the same organism; it may not do what you want if you are lifting > between different organisms. > > It seems UCSC has already performed genome-wide alignment between > different genomes. Does it make sense to perform the transformation > between Rhesus and human using LiftOver (some other groups reported this > protocol before (in the section ‘HTR definition and analysis’): > > http://www.ploscompbiol.org/article/info%3Adoi%2F10.1371%2Fjournal.pcbi.1000843 > > Or are there any other tools to transform the coordinates between species? > I look forward to your response. Thank you. > > Best regards, > > CY > > > _______________________________________________ > Genome maillist - [email protected] > https://lists.soe.ucsc.edu/mailman/listinfo/genome > _______________________________________________ Genome maillist - [email protected] https://lists.soe.ucsc.edu/mailman/listinfo/genome
