Good Morning August: UCSC does not have a copy of the "gorGor3" version of the genome. Our current browser is displaying the "gorGor3.1" version of the assembly. However, there is an easy route to confusion here because UCSC has named its database "gorGor3" We use the sequence from NCBI: ftp://ftp.ncbi.nlm.nih.gov/genbank/genomes/Eukaryotes/vertebrates_mammals/Gorilla_gorilla/gorGor3.1/
I believe the so-called original "gorGor3" assembly is actually identical to this "gorGor3.1" genome with only a change in some of the gap annotations in the assemblies. Unfortunately the change in the gap annotations would change the positions of features on assembled chromosomes. --Hiram Woerner, August E - (augustw) wrote: > Hi! > I am interested in relating information mapped to gorGor3 to gorGor3.1. What > is the best way to go about this? I realize that liftOver would be a great > solution to this problem, but I doubt that many other people would have need > of this particular conversion. What would you suggest I do? I would be more > than happy to generate the liftover files myself, if someone could give me a > protocol for doing so. > Much thanks! > -August > > PS > On a completely unrelated note, the sex-averaged recombination rate data for > the human X chromosome is a little... wrong, on this site. I tried alerting > UCSC to this fact many years ago, and nothing ever happened. It's not your > fault, mind you-- it's the table itself that has the wrong information. The > short of it is that the population sex-averaged recombination rate of the X > is 2/3 of the female rate (ignoring the parts of the X that recombine w/ the > Y), and, if memory serves, the rate that shows up as the "sex-averaged" value > is the female value (sometimes... I think in some of the maps it's 1/2 the > female rate). Regardless, correcting these tables might help those of us that > study the X! > Thanks again! And I love your site! _______________________________________________ Genome maillist - [email protected] https://lists.soe.ucsc.edu/mailman/listinfo/genome
