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
