Hello Sabrina, The over.chain file you have identified is the correct one to use. It is based on the same process used to generate the "Chain" tracks in the browser. Going into the bosTau4 assembly and clicking on one these tracks in the Comparative Genomics group will explain the baseline methods.
There is no guarantee that all positions will map, but the comparison is done between the entire contents of the reference genomes. The % of coverage can be determined from the over.chain file itself. A quick BLAT of any missing regions could help elucidate why a particular region was not included (no hit, poor hit, etc.). Hopefully this is helpful. Please feel free to contact the mailing list support team again if you would like more assistance. Warm regards, Jen UCSC Genome Browser Support On 9/7/10 1:02 AM, srodriguez wrote: > Dear Sir, Madam, > > I am a bioinformatician working at INRA (french national institute for > agriculture) in the animal genetics department for bovine genomes. > > I am interested in finding some corresponding positions between UMD3 > cow genome assembly and btau4 cow genome assembly. > > I have seen that a liftover file was available for that purpose: > http://hgdownload.cse.ucsc.edu/goldenPath/bosTauMd3/liftOver/bosTauMd3ToBosTau4.over.chain.gz > > Could you please tell me if all positions can be matched between UMD3 > and btau4? > In other words, is it possible for me to match any positions from UMD3 > to Btau4 using this file (inluding positions from UMD3 that are > situated on unknown contigs to btau4)? > > Could you please also tell me how the liftover files were generated? > > Thank you very much in advance. > > Best regards, > > Sabrina. > > > ******************************************* > Sabrina Rodriguez > Département de Génétique animale > Unité GABI > Domaine de Vilvert > 78532 Jouy en josas > > +33 (0) 1 34 65 29 53 > > _______________________________________________ > Genome maillist - [email protected] > https://lists.soe.ucsc.edu/mailman/listinfo/genome _______________________________________________ Genome maillist - [email protected] https://lists.soe.ucsc.edu/mailman/listinfo/genome
