Hi Zhen-Xia, This previously answered question should provide you with all the details for creating your own liftOver files: https://lists.soe.ucsc.edu/pipermail/genome/2010-January/020985.html
Please contact us again at [email protected] if you have any further questions. --- Luvina Guruvadoo UCSC Genome Bioinformatics Group On 6/28/2012 3:39 PM, Chen, Zhen-Xia (NIH/NIDDK) [F] wrote: > To whom it may concerned, > I'm Zhenxia Chen, a postdoc in National Institutes of Health. I'm doing > validation of D.melanogaster annotation with RNA-seq data from 19 other fly > species, including 8 new fly species. > Therefore, I want to liftover chain files to liftover dm3 annotation to all > other 19 fly species. > However, the genomes and liftover chain files of the eight new species are > not available on UCSC yet. > I have made chain files myself with the instruction: > http://hgwdev.cse.ucsc.edu/~kent/src/unzipped/hg/doc/liftOver.txt. > However, I found the chain files made by myself is quite different from those > downloaded from UCSC. > For example, I can can get 10475 annotation from dm3 lifted over to droAna3 > with dm3ToDroAna3.over.chain downloaded from UCSC while only 527 with the > chain file I made myself. And only nine are of the same coordinates. > > I'm not sure what might be the problem. It's likely that I need to do blastz > rather than blat, since it was not liftover between same species. > > I'm looking forward to getting liftover chain files for the eight new > species. Is it possible for you to show me the script for making chain files, > so that I can do it myself? Thanks. > > Zhenxia > > > _______________________________________________ > Genome maillist - [email protected] > https://lists.soe.ucsc.edu/mailman/listinfo/genome _______________________________________________ Genome maillist - [email protected] https://lists.soe.ucsc.edu/mailman/listinfo/genome
