Hi Li, We recommend that you take a look at the Hg18 Diff track (located in Mapping and Sequencing Tracks Section) in the hg19 browser or if you are using the hg18 browser you can use the Hg19 Diff track.
The hg18 assembly and the hg19 assembly aren't the same which means that not everything will map. It is also quite possible that a particular SNP could be missing due to our SNP filtering. We hope that this clarifies things for you. If you have further questions, please contact the mailing list: [email protected]. Vanessa Kirkup Swing UCSC Genome Bioinformatics Group ---------- Forwarded message ---------- From: yuanf li <[email protected]> Date: Wed, Sep 7, 2011 at 8:21 PM Subject: [Genome] about liftover To: [email protected] Dear export: Sorry to interupt you again. I have solved the problem which I send you before. But I have another problem. I download hg18tohg19 chain, but when I use liftover, I found that 6000 snps can not convert to hg19, I think it is because of unintegrity of chain. I search the NCBI for failure snps, for example, rs230525, it displays that it has position of hg18 and hg19. I wonder your advice. Thanks. Li _______________________________________________ Genome maillist - [email protected] https://lists.soe.ucsc.edu/mailman/listinfo/genome _______________________________________________ Genome maillist - [email protected] https://lists.soe.ucsc.edu/mailman/listinfo/genome
